#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_AAChange	i_ACHILLES_Lineage_Results_Top_Genes	i_Algorithm	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Confidence	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_NTotCov	i_NVarCov	i_NVarRat	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov	i_TVarCov	i_TVarRat	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNP_AF	i_dbSNP_PopFreq	i_dbSNP_Strength	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification
TBP	6908	hgsc.bcm.edu	37	6	170871013	170871014	+	In_Frame_Ins	INS	-	-	CAG	rs201732168|rs113202486|rs574714675|rs71010672	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:170871013_170871014insCAG	ENST00000392092.2	+	3	468_469	c.189_190insCAG	c.(190-192)cag>CAGcag	p.64_64Q>QQ	TBP_ENST00000230354.6_In_Frame_Ins_p.64_64Q>QQ|TBP_ENST00000540980.1_In_Frame_Ins_p.44_44Q>QQ	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	64	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|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 from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q63_Q64insQ(1)|p.Q63Q(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcaacaacaacagcagcagca	0.55																																					p.Q63delinsQQ		Atlas-Indel	.											TBP,NS,carcinoma,0,5	TBP	58	5	2	Insertion - In frame(1)|Substitution - coding silent(1)	prostate(1)|breast(1)	c.189_190insCAG						PASS	.																																			SO:0001652	inframe_insertion	6908	exon3			.	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.211_213dupCAG	6.37:g.170871020_170871022dupCAG	ENSP00000375942:p.Gln95dup	Somatic	50	0	0		WXS	Illumina HiSeq	Phase_I	64	30	0.46875	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	In_Frame_Ins	INS	ENST00000392092.2	37	CCDS5315.1																																																																																			-|0.138;CAG|0.862	0.862	strong		0.550	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
CA9	768	hgsc.bcm.edu	37	9	35674191	35674208	+	In_Frame_Del	DEL	GGAGAGGAGGATCTACCT	GGAGAGGAGGATCTACCT	-	rs113042654|rs201260414|rs137897809|rs146966274	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	GGAGAGGAGGATCTACCT	GGAGAGGAGGATCTACCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:35674191_35674208delGGAGAGGAGGATCTACCT	ENST00000378357.4	+	1	339_356	c.235_252delGGAGAGGAGGATCTACCT	c.(235-252)ggagaggaggatctacctdel	p.GEEDLP91del	RN7SL22P_ENST00000471800.2_RNA	NM_001216.2	NP_001207.2	Q16790	CAH9_HUMAN	carbonic anhydrase IX	91	Proteoglycan-like (PG).				bicarbonate transport (GO:0015701)|cellular response to hypoxia (GO:0071456)|morphogenesis of an epithelium (GO:0002009)|one-carbon metabolic process (GO:0006730)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|response to drug (GO:0042493)|response to testosterone (GO:0033574)|secretion (GO:0046903)|small molecule metabolic process (GO:0044281)	basolateral plasma membrane (GO:0016323)|cell projection (GO:0042995)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	carbonate dehydratase activity (GO:0004089)|zinc ion binding (GO:0008270)	p.P84P(1)|p.G79_P84delGEEDLP(1)		kidney(1)|large_intestine(3)|lung(5)|ovary(4)|prostate(1)|skin(2)|urinary_tract(1)	17	all_epithelial(49;0.217)		Lung(28;0.00276)|LUSC - Lung squamous cell carcinoma(32;0.00418)|STAD - Stomach adenocarcinoma(86;0.194)		Benzthiazide(DB00562)|Hydrochlorothiazide(DB00999)|Hydroflumethiazide(DB00774)|Zonisamide(DB00909)	GGATCCACCCGGAGAGGAGGATCTACCTGGAGAGGAGG	0.55														354	0.0706869	0.0991	0.0202	5008	,	,		22837	0.127		0.0408	False		,,,				2504	0.0409				p.78_84del		Atlas-Indel	.											.	CA9	48	.	2	Substitution - coding silent(1)|Deletion - In frame(1)	urinary_tract(1)|skin(1)	c.234_251del						PASS	.			326,3938		23,280,1829						-6.7	0.0			54	243,8011		14,215,3898	no	coding	CA9	NM_001216.2		37,495,5727	A1A1,A1R,RR		2.944,7.6454,4.5455				569,11949				SO:0001651	inframe_deletion	768	exon1			.	X66839	CCDS6585.1	9p13.3	2012-08-21			ENSG00000107159	ENSG00000107159		"""Carbonic anhydrases"""	1383	protein-coding gene	gene with protein product	"""carbonic dehydratase"", ""RCC-associated protein G250"""	603179				8661007, 9787087	Standard	NM_001216		Approved	MN, CAIX	uc003zxo.4	Q16790	OTTHUMG00000021029	ENST00000378357.4:c.235_252delGGAGAGGAGGATCTACCT	9.37:g.35674191_35674208delGGAGAGGAGGATCTACCT	ENSP00000367608:p.Gly91_Pro96del	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	98	28	0.285714	NM_001216	Q5T4R1	In_Frame_Del	DEL	ENST00000378357.4	37	CCDS6585.1																																																																																			GGAGAGGAGGATCTACCT|0.933;-|0.067	0.067	strong		0.550	CA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055479.1	NM_001216	
SUPT20HL1	100130302	hgsc.bcm.edu	37	X	24382373	24382374	+	IGR	INS	-	-	TGCTGC	rs371342199|rs35206911|rs201827126		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:24382373_24382374insTGCTGC								AC004552.1 (15350 upstream) : PDK3 (100963 downstream)																							gctgctgctattgctgctgctg	0.574																																					p.I499delinsIAA		Atlas-Indel	.											.	.	.	.	0			c.1496_1497insTGCTGC						PASS	.																																			SO:0001628	intergenic_variant	100130302	exon1			.																													X.37:g.24382374_24382379dupTGCTGC		Somatic	261	0	0		WXS	Illumina HiSeq	Phase_I	206	37	0.179612	NM_001136234		In_Frame_Ins	INS		37																																																																																				.	.	alt	0	0.574								
SETD1B	23067	hgsc.bcm.edu	37	12	122248312	122248312	+	Frame_Shift_Del	DEL	G	G	-			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:122248312delG	ENST00000604567.1	+	6	1529	c.1461delG	c.(1459-1461)tcgfs	p.S488fs	SETD1B_ENST00000267197.5_Frame_Shift_Del_p.S488fs|SETD1B_ENST00000542440.1_Frame_Shift_Del_p.S488fs			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	488	Pro-rich.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						CGCTGGAGTCGTCCCCTGCAG	0.692																																					p.S487fs		Atlas-Indel	.											.	SETD1B	105	.	0			c.1460delC						PASS	.						22.0	27.0	25.0					12																	122248312		692	1591	2283	SO:0001589	frameshift_variant	23067	exon5			.	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.1461delG	12.37:g.122248312delG	ENSP00000474253:p.Ser488fs	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	80	35	0.4375	NM_015048	F6MFW1	Frame_Shift_Del	DEL	ENST00000604567.1	37																																																																																				.	.	none		0.692	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
WDR13	64743	hgsc.bcm.edu	37	X	48462764	48462765	+	Frame_Shift_Ins	INS	-	-	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:48462764_48462765insG	ENST00000218056.5	+	8	1764_1765	c.1259_1260insG	c.(1258-1263)caggggfs	p.QG420fs	WDR13_ENST00000376729.5_Frame_Shift_Ins_p.QG420fs	NM_001166426.1|NM_017883.4	NP_001159898.1|NP_060353	Q9H1Z4	WDR13_HUMAN	WD repeat domain 13	420						cytoplasm (GO:0005737)|nucleus (GO:0005634)				endometrium(1)|large_intestine(4)|lung(4)|ovary(2)	11						TCCTTCCGCCAGGGGGCCTGCG	0.629																																					p.Q420fs		Pindel,Atlas-Indel	.											.	WDR13	96	.	0			c.1259_1260insG						PASS	.																																			SO:0001589	frameshift_variant	64743	exon8			.	AF329819	CCDS14302.1	Xp11.23	2013-01-09			ENSG00000101940	ENSG00000101940		"""WD repeat domain containing"""	14352	protein-coding gene	gene with protein product		300512					Standard	NM_017883		Approved		uc004dkj.2	Q9H1Z4	OTTHUMG00000024119	ENST00000218056.5:c.1264dupG	X.37:g.48462769_48462769dupG	ENSP00000218056:p.Gln420fs	Somatic	121	.	.		WXS	Illumina HiSeq	Phase_I	45	25	0.556	NM_017883	Q06DW8|Q06DX0|Q06DX1|Q9BUL7|Q9NWW4	Frame_Shift_Ins	INS	ENST00000218056.5	37	CCDS14302.1																																																																																			.	.	none		0.629	WDR13-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060743.2		
KIF1A	547	hgsc.bcm.edu	37	2	241696841	241696843	+	Intron	DEL	TCC	TCC	-	rs537608637|rs10594016|rs533559120		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	TCC	TCC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:241696841_241696843delTCC	ENST00000320389.7	-	25	2714				KIF1A_ENST00000498729.2_In_Frame_Del_p.E917del	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A						anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		ctcctcctcatcctcctcctcct	0.675																																					p.918_918del		Pindel	.											.	KIF1A	152	.	0			c.2752_2754del						PASS	.																																			SO:0001627	intron_variant	547	exon27			.	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.2555+933GGA>-	2.37:g.241696850_241696852delTCC		Somatic	59	.	.		WXS	Illumina HiSeq	Phase_I	68	13	0.191	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	In_Frame_Del	DEL	ENST00000320389.7	37	CCDS46561.1																																																																																			.	.	strong		0.675	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	
SLC35F5	80255	hgsc.bcm.edu	37	2	114500277	114500277	+	Frame_Shift_Del	DEL	A	A	-			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:114500277delA	ENST00000245680.2	-	7	1155	c.742delT	c.(742-744)tgcfs	p.C248fs	SLC35F5_ENST00000409342.1_Frame_Shift_Del_p.C242fs	NM_025181.2	NP_079457.2	Q8WV83	S35F5_HUMAN	solute carrier family 35, member F5	248					transport (GO:0006810)	integral component of membrane (GO:0016021)		p.C248fs*22(2)|p.?(1)		endometrium(1)|kidney(4)|large_intestine(2)|lung(7)|ovary(2)|prostate(3)|skin(1)	20						ACCACAAAGCAAAAAAAAAAG	0.343																																					p.C248fs		Pindel	.											SLC35F5,colon,carcinoma,+1,1	SLC35F5	60	1	3	Deletion - Frameshift(2)|Unknown(1)	ovary(2)|skin(1)	c.743delG						PASS	.						105.0	103.0	104.0					2																	114500277		2203	4300	6503	SO:0001589	frameshift_variant	80255	exon7			.	AF529364	CCDS2119.1	2q14.1	2013-05-22			ENSG00000115084	ENSG00000115084		"""Solute carriers"""	23617	protein-coding gene	gene with protein product							Standard	XM_005263799		Approved	FLJ22004	uc002tku.1	Q8WV83	OTTHUMG00000131361	ENST00000245680.2:c.742delT	2.37:g.114500277delA	ENSP00000245680:p.Cys248fs	Somatic	54	.	.		WXS	Illumina HiSeq	Phase_I	59	11	0.186	NM_025181	Q9H6P8|Q9H7D8	Frame_Shift_Del	DEL	ENST00000245680.2	37	CCDS2119.1																																																																																			.	.	none		0.343	SLC35F5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254150.1	NM_025181	
TMPRSS13	84000	hgsc.bcm.edu	37	11	117789313	117789327	+	In_Frame_Del	DEL	GGGCTGGAGATGCCT	GGGCTGGAGATGCCT	-	rs577467360|rs201746372|rs200205086|rs61900346|rs371814093|rs58754377|rs201983451|rs368164118|rs201369736	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	GGGCTGGAGATGCCT	GGGCTGGAGATGCCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:117789313_117789327delGGGCTGGAGATGCCT	ENST00000430170.2	-	2	335_349	c.248_262delAGGCATCTCCAGCCC	c.(247-264)caggcatctccagcccgg>cgg	p.QASPA83del	TMPRSS13_ENST00000526090.1_In_Frame_Del_p.QASPA83del|TMPRSS13_ENST00000524993.1_In_Frame_Del_p.QASPA83del|TMPRSS13_ENST00000528626.1_In_Frame_Del_p.QASPA83del|TMPRSS13_ENST00000445164.2_In_Frame_Del_p.QASPA83del	NM_001244995.1	NP_001231924.1	Q9BYE2	TMPSD_HUMAN	transmembrane protease, serine 13	83	13 X 5 AA repeats of A-S-P-A-[GLQR].|Ala-rich.					blood microparticle (GO:0072562)|integral component of membrane (GO:0016021)	scavenger receptor activity (GO:0005044)|serine-type endopeptidase activity (GO:0004252)	p.Q83_A87delQASPA(1)		endometrium(1)|kidney(3)|large_intestine(6)|lung(7)|pancreas(1)|prostate(1)|urinary_tract(1)	20	all_hematologic(175;0.0487)	Medulloblastoma(222;0.0425)|all_hematologic(192;0.196)|all_neural(223;0.234)		BRCA - Breast invasive adenocarcinoma(274;1.78e-05)|Epithelial(105;0.00106)		GGAGATGCCCGGGCTGGAGATGCCTGGGCTGGAGA	0.66																																					p.83_88del		Pindel	.											TMPRSS13_ENST00000445164,NS,NS,0,3	TMPRSS13	75	3	1	Deletion - In frame(1)	urinary_tract(1)	c.249_263del						PASS	.		,,	2974,624		1262,450,87					,,	0.0	0.0		dbSNP_126	58	5904,1944		2214,1476,234	no	coding,coding,coding	TMPRSS13	NM_001206790.1,NM_001206789.1,NM_001077263.2	,,	3476,1926,321	A1A1,A1R,RR		24.7706,17.343,22.4358	,,	,,		8878,2568				SO:0001651	inframe_deletion	84000	exon2			.	AB048796	CCDS41721.1, CCDS55788.1, CCDS55789.1, CCDS58185.1	11q23	2010-04-13	2005-03-11	2005-03-12	ENSG00000137747	ENSG00000137747		"""Serine peptidases / Transmembrane"""	29808	protein-coding gene	gene with protein product		610050	"""transmembrane protease, serine 11"""	TMPRSS11		11267681	Standard	NM_001077263		Approved	MSPL	uc001prs.2	Q9BYE2	OTTHUMG00000166992	ENST00000430170.2:c.248_262delAGGCATCTCCAGCCC	11.37:g.117789313_117789327delGGGCTGGAGATGCCT	ENSP00000387702:p.Gln83_Ala87del	Somatic	97	.	.		WXS	Illumina HiSeq	Phase_I	115	27	0.235	NM_001206789	B4DTM9|E9PIJ5|F8WAJ3|Q86YM4|Q96JY8|Q9BYE1	In_Frame_Del	DEL	ENST00000430170.2	37	CCDS58185.1																																																																																			GGGCTGGAGATGCCT|0.257;-|0.743	0.743	strong		0.660	TMPRSS13-006	PUTATIVE	basic|appris_candidate|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000392318.1	NM_032046	
OR2T2	401992	hgsc.bcm.edu	37	1	248616705	248616711	+	Frame_Shift_Del	DEL	TGCTGCG	TGCTGCG	-	rs199823862|rs372931983		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	TGCTGCG	TGCTGCG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:248616705_248616711delTGCTGCG	ENST00000342927.3	+	1	629_635	c.607_613delTGCTGCG	c.(607-615)tgctgcgtgfs	p.CCV203fs		NM_001004136.1	NP_001004136.1	Q6IF00	OR2T2_HUMAN	olfactory receptor, family 2, subfamily T, member 2	203						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(5)|kidney(1)|large_intestine(2)|lung(21)|ovary(1)|skin(5)|upper_aerodigestive_tract(1)	37	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)			GATGTATGCCTGCTGCGTGCTGATGCT	0.527																																					p.202_204del		Pindel	.											.	OR2T2	73	.	0			c.606_612del						PASS	.			51,3755		2,47,1854						-2.5	0.6			76	261,7371		12,237,3567	no	frameshift	OR2T2	NM_001004136.1		14,284,5421	A1A1,A1R,RR		3.4198,1.34,2.7277				312,11126				SO:0001589	frameshift_variant	401992	exon1			.	BK004462	CCDS31116.1	1q44	2012-08-09	2002-11-13	2002-11-15	ENSG00000196240	ENSG00000196240		"""GPCR / Class A : Olfactory receptors"""	14725	protein-coding gene	gene with protein product			"""olfactory receptor, family 2, subfamily T, member 2 pseudogene"""	OR2T2P		14983052	Standard	NM_001004136		Approved		uc001iek.1	Q6IF00	OTTHUMG00000040480	ENST00000342927.3:c.607_613delTGCTGCG	1.37:g.248616705_248616711delTGCTGCG	ENSP00000343062:p.Cys203fs	Somatic	399	.	.		WXS	Illumina HiSeq	Phase_I	258	48	0.186	NM_001004136	B2RNM1|B9EH01	Frame_Shift_Del	DEL	ENST00000342927.3	37	CCDS31116.1																																																																																			.	.	weak		0.527	OR2T2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097421.1	NM_001004136	
SETD1B	23067	hgsc.bcm.edu	37	12	122248314	122248314	+	Frame_Shift_Del	DEL	C	C	-			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:122248314delC	ENST00000604567.1	+	6	1531	c.1463delC	c.(1462-1464)tccfs	p.S488fs	SETD1B_ENST00000267197.5_Frame_Shift_Del_p.S488fs|SETD1B_ENST00000542440.1_Frame_Shift_Del_p.S488fs			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	488	Pro-rich.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						CTGGAGTCGTCCCCTGCAGGG	0.687																																					p.S488fs		Pindel	.											.	SETD1B	105	.	0			c.1462delT						PASS	.						22.0	27.0	25.0					12																	122248314		692	1591	2283	SO:0001589	frameshift_variant	23067	exon5			.	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.1463delC	12.37:g.122248314delC	ENSP00000474253:p.Ser488fs	Somatic	59	.	.		WXS	Illumina HiSeq	Phase_I	83	26	0.313	NM_015048	F6MFW1	Frame_Shift_Del	DEL	ENST00000604567.1	37																																																																																				.	.	none		0.687	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
ZNF384	171017	hgsc.bcm.edu	37	12	6777070	6777072	+	In_Frame_Del	DEL	TGC	TGC	-	rs78573212|rs72393318|rs544124628|rs3835029	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	TGC	TGC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:6777070_6777072delTGC	ENST00000396801.3	-	11	1749_1751	c.1542_1544delGCA	c.(1540-1545)cagcaa>caa	p.514_515QQ>Q	ZNF384_ENST00000355772.4_In_Frame_Del_p.398_399QQ>Q|RP4-761J14.8_ENST00000586338.1_RNA|RP4-761J14.8_ENST00000589924.1_RNA|ZNF384_ENST00000396799.2_In_Frame_Del_p.453_454QQ>Q|ZNF384_ENST00000361959.3_In_Frame_Del_p.514_515QQ>Q|ZNF384_ENST00000396795.1_In_Frame_Del_p.453_454QQ>Q|ZNF384_ENST00000319770.3_In_Frame_Del_p.437_438QQ>Q	NM_001135734.2	NP_001129206.1	Q8TF68	ZN384_HUMAN	zinc finger protein 384	514	Gln-rich.				nucleocytoplasmic transport (GO:0006913)|positive regulation of protein secretion (GO:0050714)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	focal adhesion (GO:0005925)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)	p.L139delL(6)|p.Q455delQ(3)|p.Q516delQ(3)	EWSR1/ZNF384(4)	breast(3)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(6)|prostate(1)|urinary_tract(1)	18						TGGTGgctgttgctgctgctgct	0.665			T	"""EWSR1, TAF15 """	ALL									4006	0.79992	0.8253	0.8501	5008	,	,		14338	0.8125		0.7753	False		,,,				2504	0.7423				p.515_515del		Pindel	.		Dom	yes		12	12p13	171017	zinc finger protein 384 (CIZ/NMP4)		L	ZNF384_ENST00000361959,caecum,carcinoma,0,4	ZNF384	102	4	12	Deletion - In frame(12)	breast(12)	c.1543_1545del						PASS	.																																			SO:0001651	inframe_deletion	171017	exon11			.	U80738	CCDS8557.1, CCDS31732.1, CCDS44817.1	12p12	2013-01-08	2002-05-23	2002-05-24		ENSG00000126746		"""Zinc fingers, C2H2-type"""	11955	protein-coding gene	gene with protein product		609951	"""trinucleotide repeat containing 1"""	TNRC1		9225980, 11149472	Standard	NM_001135734		Approved	CAGH1A, CIZ, NMP4, NP	uc010sfh.2	Q8TF68		ENST00000396801.3:c.1542_1544delGCA	12.37:g.6777079_6777081delTGC	ENSP00000380019:p.Gln516del	Somatic	55	.	.		WXS	Illumina HiSeq	Phase_I	50	14	0.280	NM_001135734	O15407|Q7Z722|Q8N938	In_Frame_Del	DEL	ENST00000396801.3	37	CCDS44817.1																																																																																			.	.	strong		0.665	ZNF384-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400712.1		
SMARCA2	6595	hgsc.bcm.edu	37	9	2039777	2039779	+	In_Frame_Del	DEL	CAG	CAG	-	rs376509101|rs62639301	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	CAG	CAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:2039777_2039779delCAG	ENST00000382203.1	+	4	876_878	c.667_669delCAG	c.(667-669)cagdel	p.Q238del	SMARCA2_ENST00000357248.2_In_Frame_Del_p.Q238del|SMARCA2_ENST00000382194.1_In_Frame_Del_p.Q238del|RP11-264I13.2_ENST00000426860.1_RNA|SMARCA2_ENST00000491574.1_3'UTR|SMARCA2_ENST00000349721.2_In_Frame_Del_p.Q238del			P51531	SMCA2_HUMAN	SWI/SNF related, matrix associated, actin dependent regulator of chromatin, subfamily a, member 2	238	Poly-Gln.			Missing (in Ref. 1; CAA51407). {ECO:0000305}.	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)		gcagcagcaacagcagcagcagc	0.635																																					p.222_223del		Pindel	.											SMARCA2_ENST00000349721,NS,carcinoma,0,2	SMARCA2	313	2	0			c.666_668del						PASS	.																																			SO:0001651	inframe_deletion	6595	exon4			.	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.667_669delCAG	9.37:g.2039786_2039788delCAG	ENSP00000371638:p.Gln238del	Somatic	75	.	.		WXS	Illumina HiSeq	Phase_I	71	13	0.183	NM_139045	B1ALG3|B1ALG4|D3DRH4|D3DRH5	In_Frame_Del	DEL	ENST00000382203.1	37	CCDS34977.1																																																																																			.	.	weak		0.635	SMARCA2-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000051505.1	NM_003070	
C3orf52	79669	hgsc.bcm.edu	37	3	111831724	111831724	+	Intron	DEL	A	A	-	rs76778672		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:111831724delA	ENST00000264848.5	+	5	526				C3orf52_ENST00000430855.1_Intron|MIR567_ENST00000385205.1_RNA|C3orf52_ENST00000467942.2_Intron|C3orf52_ENST00000431717.2_Intron	NM_024616.2	NP_078892	Q5BVD1	TTMP_HUMAN	chromosome 3 open reading frame 52							endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)				endometrium(1)|large_intestine(1)|lung(1)|urinary_tract(1)	4						ATGCAAAACTAAAAAAAAAAA	0.323																																					.		Pindel	.											.	.	.	.	0			.						PASS	.						45.0	42.0	43.0					3																	111831724		1560	3556	5116	SO:0001627	intron_variant	693152	.			.	AY830714	CCDS46887.1, CCDS54620.1	3q13.2	2006-01-30			ENSG00000114529	ENSG00000114529			26255	protein-coding gene	gene with protein product	"""TPA induced trans-membrane protein"""	611956				15737651	Standard	NM_024616		Approved	FLJ23186, TTMP	uc011bhs.2	Q5BVD1	OTTHUMG00000159230	ENST00000264848.5:c.468-87A>-	3.37:g.111831724delA		Somatic	48	.	.		WXS	Illumina HiSeq	Phase_I	120	21	0.175	.	B4DNV2|B4E0Z2|Q96AJ4|Q9H5Q1	RNA	DEL	ENST00000264848.5	37	CCDS46887.1																																																																																			.	.	none		0.323	C3orf52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353961.1	NM_024616	
LNPEP	4012	hgsc.bcm.edu	37	5	96315248	96315249	+	Frame_Shift_Ins	INS	-	-	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:96315248_96315249insA	ENST00000231368.5	+	2	1118_1119	c.426_427insA	c.(427-429)aaafs	p.K143fs	LNPEP_ENST00000395770.3_Frame_Shift_Ins_p.K129fs	NM_005575.2	NP_005566.2	Q9UIQ6	LCAP_HUMAN	leucyl/cystinyl aminopeptidase	143					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-independent (GO:0002480)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell-cell signaling (GO:0007267)|female pregnancy (GO:0007565)|membrane organization (GO:0061024)|protein catabolic process (GO:0030163)|protein polyubiquitination (GO:0000209)|proteolysis (GO:0006508)	cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|early endosome lumen (GO:0031905)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|intracellular (GO:0005622)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|skin(1)|urinary_tract(1)	34		all_cancers(142;7e-07)|all_epithelial(76;9.52e-10)|all_lung(232;0.00101)|Lung NSC(167;0.00137)|Ovarian(225;0.024)|Colorectal(57;0.0269)|Breast(839;0.244)		COAD - Colon adenocarcinoma(37;0.072)		AAGGCTGCCATAAAAAAAACCA	0.45																																					p.H142fs		Pindel	.											.	LNPEP	80	.	0			c.426_427insA						PASS	.																																			SO:0001589	frameshift_variant	4012	exon2			.	D50810	CCDS4087.1, CCDS43346.1	5q15	2011-07-25			ENSG00000113441	ENSG00000113441	3.4.11.3		6656	protein-coding gene	gene with protein product	"""cystinyl aminopeptidase"", ""placental leucine aminopeptidase"""	151300				8550619	Standard	NM_175920		Approved	CAP, PLAP, P-LAP	uc003kmw.1	Q9UIQ6	OTTHUMG00000128719	ENST00000231368.5:c.434dupA	5.37:g.96315256_96315256dupA	ENSP00000231368:p.Lys143fs	Somatic	141	.	.		WXS	Illumina HiSeq	Phase_I	174	42	0.241	NM_005575	O00769|Q15145|Q59H76|Q9TNQ2|Q9TNQ3|Q9UIQ7	Frame_Shift_Ins	INS	ENST00000231368.5	37	CCDS4087.1																																																																																			.	.	none		0.450	LNPEP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250624.1	NM_005575	
ST8SIA6	338596	hgsc.bcm.edu	37	10	17363043	17363043	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:17363043C>T	ENST00000377602.4	-	8	1105	c.1031G>A	c.(1030-1032)tGg>tAg	p.W344*		NM_001004470.1	NP_001004470.1	P61647	SIA8F_HUMAN	ST8 alpha-N-acetyl-neuraminide alpha-2,8-sialyltransferase 6	344					carbohydrate biosynthetic process (GO:0016051)|cellular protein metabolic process (GO:0044267)|ganglioside biosynthetic process (GO:0001574)|glycolipid biosynthetic process (GO:0009247)|glycoprotein metabolic process (GO:0009100)|oligosaccharide metabolic process (GO:0009311)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|protein O-linked glycosylation (GO:0006493)|sialylation (GO:0097503)	Golgi membrane (GO:0000139)|integral component of Golgi membrane (GO:0030173)	sialyltransferase activity (GO:0008373)			endometrium(3)|kidney(3)|large_intestine(4)|liver(1)|lung(24)|ovary(1)|skin(1)	37						AGAGAAGGGCCAGAATCCATA	0.438																																					p.W344X		Atlas-SNP	.											ST8SIA6,NS,carcinoma,-1,1	ST8SIA6	85	1	0			c.G1031A						scavenged	.						201.0	191.0	194.0					10																	17363043		2203	4300	6503	SO:0001587	stop_gained	338596	exon8			AAGGGCCAGAATC		CCDS31158.1	10p13	2013-03-01	2005-02-07	2005-02-07	ENSG00000148488	ENSG00000148488		"""Sialyltransferases"""	23317	protein-coding gene	gene with protein product	"""ST8Sia VI"""	610139	"""sialyltransferase 8F (alpha-2, 8-sialyltransferase)"""	SIAT8F		11980897	Standard	XR_242697		Approved		uc001ipd.3	P61647	OTTHUMG00000017748	ENST00000377602.4:c.1031G>A	10.37:g.17363043C>T	ENSP00000366827:p.Trp344*	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	159	2	0.0125786	NM_001004470	B0YJ97|B9EH72|Q5VZH4	Nonsense_Mutation	SNP	ENST00000377602.4	37	CCDS31158.1	.	.	.	.	.	.	.	.	.	.	C	37	6.490326	0.97607	.	.	ENSG00000148488	ENST00000377602	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-4.0972	19.5559	0.95347	0.0:1.0:0.0:0.0	.	.	.	.	X	344	.	ENSP00000366827:W344X	W	-	2	0	ST8SIA6	17403049	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.651000	0.83577	2.861000	0.98227	0.650000	0.86243	TGG	.	.	none		0.438	ST8SIA6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047036.1	NM_001004470	
OVCH1	341350	hgsc.bcm.edu	37	12	29617550	29617550	+	Missense_Mutation	SNP	G	G	A	rs11050243	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:29617550G>A	ENST00000318184.5	-	18	2014	c.2015C>T	c.(2014-2016)tCt>tTt	p.S672F	OVCH1-AS1_ENST00000549411.1_Intron|OVCH1-AS1_ENST00000551108.1_Intron	NM_183378.2	NP_899234.2	Q7RTY7	OVCH1_HUMAN	ovochymase 1	672	Peptidase S1 2. {ECO:0000255|PROSITE- ProRule:PRU00274}.		S -> F (in dbSNP:rs11050243).			extracellular region (GO:0005576)	metal ion binding (GO:0046872)|serine-type endopeptidase activity (GO:0004252)	p.S672F(1)		NS(2)|breast(4)|central_nervous_system(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(43)|ovary(5)|pancreas(3)|prostate(2)|skin(1)|soft_tissue(1)|stomach(3)	92	Lung NSC(12;1.84e-09)|Acute lymphoblastic leukemia(23;0.00885)|all_hematologic(23;0.0155)					CTCCAGAGGAGAGCTTAGTTG	0.493													G|||	912	0.182109	0.3585	0.1023	5008	,	,		18329	0.0853		0.1352	False		,,,				2504	0.1483				p.S672F		Atlas-SNP	.											OVCH1,NS,carcinoma,0,1	OVCH1	195	1	1	Substitution - Missense(1)	stomach(1)	c.C2015T						scavenged	.	G	PHE/SER	1315,2565		217,881,842	125.0	125.0	125.0		2015	2.7	0.6	12	dbSNP_120	125	1174,7148		90,994,3077	yes	missense	OVCH1	NM_183378.2	155	307,1875,3919	AA,AG,GG		14.1072,33.8918,20.3983	probably-damaging	672/1135	29617550	2489,9713	1940	4161	6101	SO:0001583	missense	341350	exon18			AGAGGAGAGCTTA	BN000128		12p11.23	2012-11-08			ENSG00000187950	ENSG00000187950			23080	protein-coding gene	gene with protein product						12838346	Standard	NM_183378		Approved	OVCH	uc001rix.1	Q7RTY7	OTTHUMG00000167741	ENST00000318184.5:c.2015C>T	12.37:g.29617550G>A	ENSP00000326708:p.Ser672Phe	Somatic	190	0	0		WXS	Illumina HiSeq	Phase_I	171	2	0.0116959	NM_183378		Missense_Mutation	SNP	ENST00000318184.5	37		355	0.16254578754578755	164	0.3333333333333333	29	0.08011049723756906	59	0.10314685314685315	103	0.1358839050131926	G	16.70	3.194855	0.58017	0.338918	0.141072	ENSG00000187950	ENST00000318184	T	0.61859	0.07	2.73	2.73	0.32206	Peptidase cysteine/serine, trypsin-like (1);Peptidase S1/S6, chymotrypsin/Hap (3);	.	.	.	.	T	0.00012	0.0000	M	0.71920	2.185	0.41092	P	0.014395999999999964	D	0.89917	1.0	D	0.81914	0.995	T	0.13818	-1.0495	8	0.45353	T	0.12	.	7.0766	0.25207	0.0:0.0:0.7311:0.2689	rs11050243;rs60892337;rs11050243	672	Q7RTY7	OVCH1_HUMAN	F	672	ENSP00000326708:S672F	ENSP00000326708:S672F	S	-	2	0	OVCH1	29508817	0.587000	0.26791	0.559000	0.28332	0.394000	0.30568	1.776000	0.38594	1.836000	0.53414	0.655000	0.94253	TCT	G|0.825;A|0.175	0.175	strong		0.493	OVCH1-001	KNOWN	non_canonical_TEC|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395997.2	NM_183378	
SPAG17	200162	hgsc.bcm.edu	37	1	118567949	118567949	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:118567949G>A	ENST00000336338.5	-	27	3886	c.3821C>T	c.(3820-3822)aCg>aTg	p.T1274M		NM_206996.2	NP_996879.1	Q6Q759	SPG17_HUMAN	sperm associated antigen 17	1274						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)		TGGCATCACCGTTTTATAGAA	0.463																																					p.T1274M		Atlas-SNP	.											.	SPAG17	263	.	0			c.C3821T						PASS	.						96.0	93.0	94.0					1																	118567949		2203	4300	6503	SO:0001583	missense	200162	exon27			ATCACCGTTTTAT		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.3821C>T	1.37:g.118567949G>A	ENSP00000337804:p.Thr1274Met	Somatic	56	0	0		WXS	Illumina HiSeq	Phase_I	90	44	0.488889	NM_206996	Q8NAZ1|Q9NT21	Missense_Mutation	SNP	ENST00000336338.5	37	CCDS899.1	.	.	.	.	.	.	.	.	.	.	G	15.63	2.889137	0.52014	.	.	ENSG00000155761	ENST00000336338	T	0.19532	2.14	5.58	4.67	0.58626	.	0.573492	0.19744	N	0.107042	T	0.20700	0.0498	L	0.51422	1.61	0.09310	N	1	D	0.71674	0.998	P	0.58130	0.833	T	0.04178	-1.0971	10	0.59425	D	0.04	.	12.3516	0.55151	0.0788:0.0:0.9212:0.0	.	1274	Q6Q759	SPG17_HUMAN	M	1274	ENSP00000337804:T1274M	ENSP00000337804:T1274M	T	-	2	0	SPAG17	118369472	0.008000	0.16893	0.013000	0.15412	0.441000	0.31987	1.697000	0.37784	1.350000	0.45770	0.655000	0.94253	ACG	.	.	none		0.463	SPAG17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033723.1	NM_206996	
TCHH	7062	hgsc.bcm.edu	37	1	152081138	152081138	+	Missense_Mutation	SNP	C	C	T	rs189687085	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:152081138C>T	ENST00000368804.1	-	2	4554	c.4555G>A	c.(4555-4557)Gag>Aag	p.E1519K		NM_007113.2	NP_009044.2	Q07283	TRHY_HUMAN	trichohyalin	1519	23 X 26 AA approximate tandem repeats.				keratinization (GO:0031424)	cytoskeleton (GO:0005856)	calcium ion binding (GO:0005509)	p.E1519Q(1)		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)			TGTTCCTCCTCGAGGAATTTT	0.587													-|||	4	0.000798722	0.003	0.0	5008	,	,		18571	0.0		0.0	False		,,,				2504	0.0				p.E1519K		Atlas-SNP	.											TCHH,NS,carcinoma,0,1	TCHH	275	1	1	Substitution - Missense(1)	lung(1)	c.G4555A						scavenged	.	C	LYS/GLU	4,3766		0,4,1881	53.0	55.0	54.0		4555	0.1	0.0	1		54	0,8228		0,0,4114	yes	missense	TCHH	NM_007113.2	56	0,4,5995	TT,TC,CC		0.0,0.1061,0.0333	possibly-damaging	1519/1944	152081138	4,11994	1885	4114	5999	SO:0001583	missense	7062	exon3			CCTCCTCGAGGAA	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.4555G>A	1.37:g.152081138C>T	ENSP00000357794:p.Glu1519Lys	Somatic	155	2	0.0129032		WXS	Illumina HiSeq	Phase_I	255	4	0.0156863	NM_007113	Q5VUI3	Missense_Mutation	SNP	ENST00000368804.1	37	CCDS41396.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	-	4.431	0.079727	0.08533	0.001061	0.0	ENSG00000159450	ENST00000368804	T	0.04603	3.59	0.113	0.113	0.14631	.	.	.	.	.	T	0.01905	0.0060	M	0.66939	2.045	0.09310	N	1	P	0.44090	0.826	B	0.39617	0.305	T	0.44832	-0.9302	8	0.27082	T	0.32	.	.	.	.	.	1519	Q07283	TRHY_HUMAN	K	1519	ENSP00000357794:E1519K	ENSP00000357794:E1519K	E	-	1	0	TCHH	150347762	0.000000	0.05858	0.001000	0.08648	0.038000	0.13279	-0.405000	0.07196	0.183000	0.20059	0.186000	0.17326	GAG	C|1.000;T|0.000	0.000	strong		0.587	TCHH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000036671.2	NM_007113	
KAT6B	23522	hgsc.bcm.edu	37	10	76789942	76789942	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:76789942C>T	ENST00000287239.4	+	18	5849	c.5360C>T	c.(5359-5361)aCg>aTg	p.T1787M	KAT6B_ENST00000372724.1_Missense_Mutation_p.T1495M|KAT6B_ENST00000372725.1_Missense_Mutation_p.T1495M|KAT6B_ENST00000372714.1_Missense_Mutation_p.T1495M|KAT6B_ENST00000372711.1_Missense_Mutation_p.T1604M	NM_001256468.1|NM_012330.3	NP_001243397.1|NP_036462.2	Q8WYB5	KAT6B_HUMAN	K(lysine) acetyltransferase 6B	1787	Interaction with RUNX1 and RUNX2.				chromatin organization (GO:0006325)|histone acetylation (GO:0016573)|histone H3 acetylation (GO:0043966)|negative regulation of transcription, DNA-templated (GO:0045892)|nucleosome assembly (GO:0006334)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	MOZ/MORF histone acetyltransferase complex (GO:0070776)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	acetyltransferase activity (GO:0016407)|DNA binding (GO:0003677)|histone acetyltransferase activity (GO:0004402)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)										ATCCCCGAGACGAGCAACGCC	0.592																																					p.T1787M		Atlas-SNP	.											MYST4,colon,carcinoma,0,1	.	.	1	0			c.C5360T						scavenged	.						55.0	54.0	54.0					10																	76789942		2203	4300	6503	SO:0001583	missense	23522	exon18			CCGAGACGAGCAA	AF113514	CCDS7345.1, CCDS58084.1, CCDS58085.1	10q22.2	2013-01-28	2011-07-21	2011-07-21	ENSG00000156650	ENSG00000156650		"""Chromatin-modifying enzymes / K-acetyltransferases"", ""Zinc fingers, C2HC-type containing"", ""Zinc fingers, PHD-type"""	17582	protein-coding gene	gene with protein product	"""MOZ-related factor"""	605880	"""MYST histone acetyltransferase (monocytic leukemia) 4"""	MYST4		9205841, 10497217	Standard	NM_012330		Approved	querkopf, qkf, Morf, MOZ2, ZC2HC6B	uc001jwn.2	Q8WYB5	OTTHUMG00000018509	ENST00000287239.4:c.5360C>T	10.37:g.76789942C>T	ENSP00000287239:p.Thr1787Met	Somatic	87	0	0		WXS	Illumina HiSeq	Phase_I	140	2	0.0142857	NM_012330	O15087|Q86Y05|Q8WU81|Q9UKW2|Q9UKW3|Q9UKX0	Missense_Mutation	SNP	ENST00000287239.4	37	CCDS7345.1	.	.	.	.	.	.	.	.	.	.	C	13.15	2.150922	0.37923	.	.	ENSG00000156650	ENST00000372725;ENST00000372724;ENST00000287239;ENST00000372714;ENST00000372711	T;T;T;T;T	0.78595	-1.18;-1.18;-1.19;-1.18;-1.18	5.54	5.54	0.83059	.	0.251265	0.27876	N	0.017490	T	0.76962	0.4061	N	0.14661	0.345	0.34048	D	0.65577	D;P;P	0.76494	0.999;0.872;0.635	P;B;B	0.62014	0.897;0.337;0.294	D	0.84038	0.0363	10	0.72032	D	0.01	-0.0174	14.3331	0.66572	0.1483:0.8517:0.0:0.0	.	1604;1495;1787	Q8WYB5-2;Q8WYB5-3;Q8WYB5	.;.;KAT6B_HUMAN	M	1495;1495;1787;1495;1604	ENSP00000361810:T1495M;ENSP00000361809:T1495M;ENSP00000287239:T1787M;ENSP00000361799:T1495M;ENSP00000361796:T1604M	ENSP00000287239:T1787M	T	+	2	0	KAT6B	76459948	0.667000	0.27484	0.520000	0.27837	0.830000	0.47004	2.928000	0.48908	2.592000	0.87571	0.563000	0.77884	ACG	.	.	none		0.592	KAT6B-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048771.1	NM_012330	
UBB	7314	hgsc.bcm.edu	37	17	16285542	16285542	+	Silent	SNP	G	G	A	rs17052364	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:16285542G>A	ENST00000395837.1	+	2	502	c.321G>A	c.(319-321)caG>caA	p.Q107Q	UBB_ENST00000578649.1_Intron|UBB_ENST00000535788.1_Intron|UBB_ENST00000302182.3_Silent_p.Q107Q|UBB_ENST00000395839.1_Silent_p.Q107Q|RP11-138I1.4_ENST00000583934.1_RNA	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	107	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)		p.Q107Q(1)		breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		CCAAGATCCAGGATAAAGAAG	0.537																																					p.Q107Q	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											UBB,NS,carcinoma,0,1	UBB	30	1	1	Substitution - coding silent(1)	lung(1)	c.G321A						scavenged	.						114.0	110.0	112.0					17																	16285542		2203	4300	6503	SO:0001819	synonymous_variant	7314	exon2			GATCCAGGATAAA		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.321G>A	17.37:g.16285542G>A		Somatic	161	1	0.00621118		WXS	Illumina HiSeq	Phase_I	174	5	0.0287356	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			G|0.540;A|0.460	0.460	strong		0.537	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
PDE4DIP	9659	hgsc.bcm.edu	37	1	144857010	144857010	+	Missense_Mutation	SNP	T	T	C	rs3853916		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:144857010T>C	ENST00000369354.3	-	40	6664	c.6475A>G	c.(6475-6477)Acc>Gcc	p.T2159A	PDE4DIP_ENST00000369356.4_Missense_Mutation_p.T2159A|PDE4DIP_ENST00000313382.9_Missense_Mutation_p.T2053A|PDE4DIP_ENST00000369359.4_Missense_Mutation_p.T2295A|PDE4DIP_ENST00000524974.1_5'UTR|RP4-791M13.4_ENST00000532137.1_RNA|PDE4DIP_ENST00000530740.1_Missense_Mutation_p.T2244A			Q5VU43	MYOME_HUMAN	phosphodiesterase 4D interacting protein	2159					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)	p.T2159A(1)		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)		TTGGGAGGGGTCTTCATTACT	0.443			T	PDGFRB	MPD																																p.T2159A		Atlas-SNP	.		Dom	yes		1	1q12	9659	phosphodiesterase 4D interacting protein (myomegalin)		L	PDE4DIP,NS,carcinoma,0,1	PDE4DIP	817	1	1	Substitution - Missense(1)	prostate(1)	c.A6475G						scavenged	.						76.0	72.0	74.0					1																	144857010		2203	4296	6499	SO:0001583	missense	9659	exon40			GAGGGGTCTTCAT	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.6475A>G	1.37:g.144857010T>C	ENSP00000358360:p.Thr2159Ala	Somatic	825	11	0.0133333		WXS	Illumina HiSeq	Phase_I	1080	35	0.0324074	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	.	.	.	.	.	.	.	.	.	.	.	12.27	1.889088	0.33348	.	.	ENSG00000178104	ENST00000313382;ENST00000369354;ENST00000369356;ENST00000530740;ENST00000369359	T;T;T;T;T	0.01613	4.73;4.83;4.84;4.84;4.84	4.16	-0.82	0.10826	.	.	.	.	.	T	0.00637	0.0021	L	0.40543	1.245	0.09310	N	1	B;B	0.18461	0.015;0.028	B;B	0.12837	0.006;0.008	T	0.41893	-0.9483	9	0.49607	T	0.09	.	7.8317	0.29347	0.0:0.3889:0.0:0.6111	rs3853916;rs4067557	2053;2159	Q5VU43-3;Q5VU43	.;MYOME_HUMAN	A	2053;2159;2159;2244;2295	ENSP00000327209:T2053A;ENSP00000358360:T2159A;ENSP00000358363:T2159A;ENSP00000435654:T2244A;ENSP00000358366:T2295A	ENSP00000327209:T2053A	T	-	1	0	PDE4DIP	143568367	0.002000	0.14202	0.005000	0.12908	0.631000	0.37964	-0.164000	0.09983	-0.097000	0.12307	0.369000	0.22263	ACC	.	.	weak		0.443	PDE4DIP-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000038858.2	NM_022359	
DRD5	1816	hgsc.bcm.edu	37	4	9783905	9783905	+	Silent	SNP	C	C	T	rs2227848	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:9783905C>T	ENST00000304374.2	+	1	648	c.252C>T	c.(250-252)gcC>gcT	p.A84A		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	84					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	TGTCTCTGGCCGTGTCAGACC	0.642																																					p.A84A		Atlas-SNP	.											DRD5,colon,carcinoma,+1,1	DRD5	119	1	0			c.C252T						scavenged	.						54.0	47.0	49.0					4																	9783905		2203	4300	6503	SO:0001819	synonymous_variant	1816	exon1			TCTGGCCGTGTCA	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"""GPCR / Class A : Dopamine receptors"""	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.252C>T	4.37:g.9783905C>T		Somatic	139	6	0.0431655		WXS	Illumina HiSeq	Phase_I	138	12	0.0869565	NM_000798	B2R9S3|Q8NEQ8	Silent	SNP	ENST00000304374.2	37	CCDS3405.1																																																																																			C|0.963;T|0.037	0.037	strong		0.642	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1		
CD19	930	hgsc.bcm.edu	37	16	28944721	28944721	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:28944721G>A	ENST00000324662.3	+	4	770	c.726G>A	c.(724-726)atG>atA	p.M242I	CD19_ENST00000567541.1_Missense_Mutation_p.M242I|CD19_ENST00000538922.1_Missense_Mutation_p.M242I			P15391	CD19_HUMAN	CD19 molecule	242	Ig-like C2-type 2.				B cell receptor signaling pathway (GO:0050853)|cell surface receptor signaling pathway (GO:0007166)|cellular defense response (GO:0006968)|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)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of immune response (GO:0050776)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor signaling protein activity (GO:0005057)	p.M242I(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(4)|urinary_tract(1)	29						TGTGGGTAATGGAGACGGGTC	0.582																																					p.M242I		Atlas-SNP	.											CD19,trunk,malignant_melanoma,0,1	CD19	65	1	1	Substitution - Missense(1)	skin(1)	c.G726A						scavenged	.						68.0	64.0	66.0					16																	28944721		2197	4300	6497	SO:0001583	missense	930	exon4			GGTAATGGAGACG		CCDS10644.1, CCDS53998.1	16p11.2	2014-09-17	2006-03-28		ENSG00000177455	ENSG00000177455		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1633	protein-coding gene	gene with protein product		107265	"""CD19 antigen"""				Standard	NM_001770		Approved		uc010byo.2	P15391	OTTHUMG00000097049	ENST00000324662.3:c.726G>A	16.37:g.28944721G>A	ENSP00000313419:p.Met242Ile	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	83	2	0.0240964	NM_001178098	A0N0P9|F5H635|Q96S68|Q9BRD6	Missense_Mutation	SNP	ENST00000324662.3	37	CCDS10644.1	.	.	.	.	.	.	.	.	.	.	G	6.453	0.451715	0.12223	.	.	ENSG00000177455	ENST00000538922;ENST00000324662;ENST00000537306	T;T	0.35048	1.33;1.33	4.26	-0.124	0.13523	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	4.873430	0.00644	N	0.000525	T	0.28433	0.0703	L	0.34521	1.04	0.09310	N	1	B;B	0.06786	0.001;0.0	B;B	0.04013	0.001;0.0	T	0.12630	-1.0540	10	0.24483	T	0.36	3.7036	7.3046	0.26440	0.4285:0.0:0.5715:0.0	.	242;242	F5H635;P15391	.;CD19_HUMAN	I	242;242;91	ENSP00000437940:M242I;ENSP00000313419:M242I	ENSP00000313419:M242I	M	+	3	0	CD19	28852222	0.381000	0.25140	0.006000	0.13384	0.019000	0.09904	0.705000	0.25675	0.053000	0.16036	0.313000	0.20887	ATG	.	.	none		0.582	CD19-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000214152.2		
SRCAP	10847	hgsc.bcm.edu	37	16	30731498	30731498	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:30731498C>T	ENST00000262518.4	+	19	3218	c.2833C>T	c.(2833-2835)Cga>Tga	p.R945*	SRCAP_ENST00000344771.4_Nonsense_Mutation_p.R945*|SRCAP_ENST00000395059.2_Nonsense_Mutation_p.R945*	NM_006662.2	NP_006653.2	Q6ZRS2	SRCAP_HUMAN	Snf2-related CREBBP activator protein	945					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)	p.R945*(1)		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)			AGACATGGGTCGATTTGACCT	0.502																																					p.R945X		Atlas-SNP	.											SRCAP,NS,carcinoma,0,1	SRCAP	298	1	1	Substitution - Nonsense(1)	ovary(1)	c.C2833T						scavenged	.						218.0	215.0	216.0					16																	30731498		2197	4300	6497	SO:0001587	stop_gained	10847	exon19			ATGGGTCGATTTG	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.2833C>T	16.37:g.30731498C>T	ENSP00000262518:p.Arg945*	Somatic	249	2	0.00803213		WXS	Illumina HiSeq	Phase_I	253	3	0.0118577	NM_006662	B0JZA6|O15026|Q7Z744|Q9Y5L9	Nonsense_Mutation	SNP	ENST00000262518.4	37	CCDS10689.2	.	.	.	.	.	.	.	.	.	.	C	40	8.230233	0.98717	.	.	ENSG00000080603	ENST00000262518;ENST00000395059;ENST00000344771	.	.	.	5.69	5.69	0.88448	.	0.270493	0.26680	N	0.023058	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.22706	T	0.39	-2.8432	12.1209	0.53891	0.2744:0.7256:0.0:0.0	.	.	.	.	X	945	.	ENSP00000262518:R945X	R	+	1	2	SRCAP	30638999	1.000000	0.71417	0.987000	0.45799	0.982000	0.71751	3.679000	0.54634	2.685000	0.91497	0.484000	0.47621	CGA	.	.	none		0.502	SRCAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255523.1	NM_006662	
BCL3	602	hgsc.bcm.edu	37	19	45261657	45261657	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:45261657C>T	ENST00000164227.5	+	7	1290	c.1046C>T	c.(1045-1047)gCg>gTg	p.A349V		NM_005178.4	NP_005169.2	P20749	BCL3_HUMAN	B-cell CLL/lymphoma 3	349					antimicrobial humoral response (GO:0019730)|cellular response to DNA damage stimulus (GO:0006974)|defense response to bacterium (GO:0042742)|defense response to protozoan (GO:0042832)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|extracellular matrix organization (GO:0030198)|follicular dendritic cell differentiation (GO:0002268)|germinal center formation (GO:0002467)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|maintenance of protein location in nucleus (GO:0051457)|marginal zone B cell differentiation (GO:0002315)|negative regulation of apoptotic process (GO:0043066)|negative regulation of interleukin-8 biosynthetic process (GO:0045415)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of tumor necrosis factor biosynthetic process (GO:0042536)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-10 biosynthetic process (GO:0045082)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of translation (GO:0045727)|protein import into nucleus, translocation (GO:0000060)|regulation of apoptotic process (GO:0042981)|regulation of DNA binding (GO:0051101)|regulation of NF-kappaB import into nucleus (GO:0042345)|response to UV-C (GO:0010225)|response to virus (GO:0009615)|spleen development (GO:0048536)|T-helper 1 type immune response (GO:0042088)|T-helper 2 cell differentiation (GO:0045064)|transcription, DNA-templated (GO:0006351)	Bcl3-Bcl10 complex (GO:0032996)|Bcl3/NF-kappaB2 complex (GO:0033257)|cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|protein binding, bridging (GO:0030674)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	10	Lung NSC(12;0.000698)|all_lung(12;0.002)	Ovarian(192;0.0728)				CTCATGGTGGCGCGCAGCCGC	0.711			T	IGH@	CLL																																p.A349V		Atlas-SNP	.		Dom	yes		19	19q13	602	B-cell CLL/lymphoma 3		L	.	BCL3	28	.	0			c.C1046T						PASS	.						6.0	5.0	6.0					19																	45261657		1987	3872	5859	SO:0001583	missense	602	exon7			TGGTGGCGCGCAG	M31732	CCDS12642.2	19q13.1-q13.2	2013-01-10			ENSG00000069399	ENSG00000069399		"""Ankyrin repeat domain containing"""	998	protein-coding gene	gene with protein product	"""B-cell lymphoma 3-encoded protein"", ""B-cell leukemia/lymphoma 3"", ""chronic lymphatic leukemia protein"""	109560		D19S37, BCL4		1501714, 2180580	Standard	NM_005178		Approved		uc010xxe.2	P20749	OTTHUMG00000151517	ENST00000164227.5:c.1046C>T	19.37:g.45261657C>T	ENSP00000164227:p.Ala349Val	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	82	41	0.5	NM_005178		Missense_Mutation	SNP	ENST00000164227.5	37	CCDS12642.2	.	.	.	.	.	.	.	.	.	.	C	33	5.265975	0.95399	.	.	ENSG00000069399	ENST00000403534;ENST00000164227	T	0.62364	0.03	4.88	4.88	0.63580	Ankyrin repeat-containing domain (3);	0.409242	0.20420	N	0.092683	T	0.67711	0.2922	M	0.62209	1.925	0.45648	D	0.998571	D	0.89917	1.0	P	0.49332	0.607	T	0.73065	-0.4100	10	0.72032	D	0.01	-29.5782	15.5034	0.75719	0.0:1.0:0.0:0.0	.	349	P20749	BCL3_HUMAN	V	309;349	ENSP00000164227:A349V	ENSP00000164227:A349V	A	+	2	0	BCL3	49953497	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	3.532000	0.53553	2.257000	0.74773	0.491000	0.48974	GCG	.	.	none		0.711	BCL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322976.1	NM_005178	
KRT4	3851	hgsc.bcm.edu	37	12	53207583	53207583	+	Missense_Mutation	SNP	C	C	G	rs76773498|rs11267392	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:53207583C>G	ENST00000551956.1	-	1	752	c.260G>C	c.(259-261)gGt>gCt	p.G87A	KRT4_ENST00000458244.2_Missense_Mutation_p.G67A|KRT4_ENST00000293774.4_Missense_Mutation_p.G161A			P19013	K2C4_HUMAN	keratin 4	87	Gly-rich.|Head.		Missing (in allele K4B). {ECO:0000269|PubMed:16541075, ECO:0000269|PubMed:7684424}.		cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CCCAAATCCACCACCAAAGCC	0.602																																					p.G87A	Pancreas(190;284 2995 41444 45903)	Atlas-SNP	.											KRT4,rectum,carcinoma,+1,2	KRT4	110	2	0			c.G260C						scavenged	.						43.0	59.0	54.0					12																	53207583		2120	4256	6376	SO:0001583	missense	3851	exon1			AATCCACCACCAA		CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6441	protein-coding gene	gene with protein product	"""cytokeratin 4"", ""keratin, type II cytoskeletal 4"""	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.260G>C	12.37:g.53207583C>G	ENSP00000448220:p.Gly87Ala	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	62	6	0.0967742	NM_002272	F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Missense_Mutation	SNP	ENST00000551956.1	37	CCDS41787.2	.	.	.	.	.	.	.	.	.	.	C	11.36	1.614915	0.28712	.	.	ENSG00000170477	ENST00000551956;ENST00000293774;ENST00000458244	D;T;D	0.98717	-3.14;0.68;-5.09	5.14	4.25	0.50352	.	0.974741	0.08394	N	0.952444	D	0.97123	0.9060	L	0.45581	1.43	0.29836	N	0.829633	B	0.21071	0.051	B	0.17979	0.02	D	0.93594	0.6924	10	0.31617	T	0.26	.	14.3364	0.66592	0.1484:0.8516:0.0:0.0	.	101	P19013	K2C4_HUMAN	A	87;161;67	ENSP00000448220:G87A;ENSP00000293774:G161A;ENSP00000387904:G67A	ENSP00000293774:G161A	G	-	2	0	KRT4	51493850	0.011000	0.17503	0.856000	0.33681	0.125000	0.20455	0.972000	0.29409	1.483000	0.48342	0.585000	0.79938	GGT	.	.	weak		0.602	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1	NM_002272	
OR2H1	26716	hgsc.bcm.edu	37	6	29429915	29429915	+	Silent	SNP	T	T	C	rs538200065	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:29429915T>C	ENST00000377136.1	+	4	834	c.369T>C	c.(367-369)gcT>gcC	p.A123A	OR2H1_ENST00000377132.1_Silent_p.A123A|OR2H1_ENST00000377133.1_Silent_p.A123A|OR2H1_ENST00000473369.1_3'UTR|OR2H1_ENST00000442615.1_Silent_p.A123A|OR2H1_ENST00000396792.2_Silent_p.A123A			Q9GZK4	OR2H1_HUMAN	olfactory receptor, family 2, subfamily H, member 1	123						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			large_intestine(5)|lung(12)	17						GATACGTGGCTGTCTGCCAGC	0.582																																					p.A123A		Atlas-SNP	.											.	OR2H1	38	.	0			c.T369C						PASS	.						163.0	167.0	165.0					6																	29429915		1510	2709	4219	SO:0001819	synonymous_variant	26716	exon3			CGTGGCTGTCTGC	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.369T>C	6.37:g.29429915T>C		Somatic	88	0	0		WXS	Illumina HiSeq	Phase_I	111	6	0.0540541	NM_030883	B0S7T4|O43629|O43661|O43662|Q5SUN6|Q9GZK9	Silent	SNP	ENST00000377136.1	37	CCDS4660.1																																																																																			.	.	none		0.582	OR2H1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194014.3		
PLXNB2	23654	hgsc.bcm.edu	37	22	50714348	50714348	+	Silent	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr22:50714348G>A	ENST00000449103.1	-	36	5522	c.5382C>T	c.(5380-5382)ctC>ctT	p.L1794L	PLXNB2_ENST00000359337.4_Silent_p.L1794L|AL022328.1_ENST00000595015.1_Missense_Mutation_p.E56K			O15031	PLXB2_HUMAN	plexin B2	1794					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)		TGTATTGGTAGAGCTGGTGGA	0.672											OREG0026679	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.L1794L		Atlas-SNP	.											.	PLXNB2	172	.	0			c.C5382T						PASS	.						51.0	62.0	58.0					22																	50714348		2082	4203	6285	SO:0001819	synonymous_variant	23654	exon36			TTGGTAGAGCTGG		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.5382C>T	22.37:g.50714348G>A		Somatic	138	0	0	971	WXS	Illumina HiSeq	Phase_I	126	38	0.301587	NM_012401	A6QRH0|Q7KZU3|Q9BSU7	Silent	SNP	ENST00000449103.1	37	CCDS43035.1																																																																																			.	.	none		0.672	PLXNB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316874.3	NM_012401	
MUC4	4585	hgsc.bcm.edu	37	3	195506974	195506974	+	Missense_Mutation	SNP	G	G	A	rs142066159	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:195506974G>A	ENST00000463781.3	-	2	11936	c.11477C>T	c.(11476-11478)cCt>cTt	p.P3826L	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P3826L	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.P3826L(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)		GTCGGTGACAGGAAGAGGGGT	0.582													.|||	246	0.0491214	0.1225	0.0144	5008	,	,		9155	0.003		0.0258	False		,,,				2504	0.046				p.P3826L		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	2	Substitution - Missense(2)	endometrium(2)	c.C11477T						scavenged	.						5.0	5.0	5.0					3																	195506974		403	1208	1611	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.11477C>T	3.37:g.195506974G>A	ENSP00000417498:p.Pro3826Leu	Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	133	12	0.0902256	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	5.523	0.281411	0.10458	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.56941	1.22;0.43	.	.	.	.	.	.	.	.	T	0.48205	0.1487	N	0.19112	0.55	0.20307	N	0.999915	D	0.64830	0.994	P	0.62885	0.908	T	0.36261	-0.9755	7	.	.	.	.	5.844	0.18652	9.0E-4:0.0:0.9991:0.0	.	3698	E7ESK3	.	L	3826	ENSP00000417498:P3826L;ENSP00000420243:P3826L	.	P	-	2	0	MUC4	196991753	0.014000	0.17966	0.086000	0.20670	0.086000	0.17979	1.838000	0.39211	0.064000	0.16427	0.064000	0.15345	CCT	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
LPIN1	23175	hgsc.bcm.edu	37	2	11944623	11944623	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:11944623C>T	ENST00000256720.2	+	15	2073	c.1980C>T	c.(1978-1980)cgC>cgT	p.R660R	LPIN1_ENST00000396097.1_Silent_p.R390R|LPIN1_ENST00000404113.2_Silent_p.R161R|LPIN1_ENST00000449576.2_Silent_p.R745R|LPIN1_ENST00000396099.1_Silent_p.R702R|LPIN1_ENST00000425416.2_Silent_p.R666R	NM_145693.2	NP_663731.1	Q14693	LPIN1_HUMAN	lipin 1	660	C-LIP.				cellular lipid metabolic process (GO:0044255)|fatty acid catabolic process (GO:0009062)|glycerophospholipid biosynthetic process (GO:0046474)|phosphatidylcholine biosynthetic process (GO:0006656)|phosphatidylethanolamine biosynthetic process (GO:0006646)|phospholipid metabolic process (GO:0006644)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|triglyceride biosynthetic process (GO:0019432)|triglyceride mobilization (GO:0006642)	cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	phosphatidate phosphatase activity (GO:0008195)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(2)|kidney(5)|large_intestine(15)|liver(1)|lung(10)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	45	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.11)|OV - Ovarian serous cystadenocarcinoma(76;0.173)		GCACGTGCCGCTGTGAGGGCA	0.468																																					p.R745R		Atlas-SNP	.											LPIN1,caecum,carcinoma,+2,1	LPIN1	99	1	0			c.C2235T						scavenged	.						120.0	105.0	110.0					2																	11944623		2203	4300	6503	SO:0001819	synonymous_variant	23175	exon17			GTGCCGCTGTGAG	D80010	CCDS1682.1, CCDS58699.1, CCDS58700.1, CCDS58701.1	2p25.1	2008-05-23			ENSG00000134324	ENSG00000134324			13345	protein-coding gene	gene with protein product		605518				11138012, 8724849, 16950137	Standard	NM_145693		Approved	KIAA0188	uc010yjm.3	Q14693	OTTHUMG00000119082	ENST00000256720.2:c.1980C>T	2.37:g.11944623C>T		Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	119	3	0.0252101	NM_001261428	A8MU38|B4DET9|B4DGS4|B4DGZ6|B5MC18|B7Z858|D6W506|E7ESE7|F5GY24|Q53T25	Silent	SNP	ENST00000256720.2	37	CCDS1682.1																																																																																			.	.	none		0.468	LPIN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000239296.3	NM_145693	
ZNF717	100131827	hgsc.bcm.edu	37	3	75790797	75790797	+	De_novo_Start_InFrame	SNP	C	C	T	rs147946451	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:75790797C>T	ENST00000478296.1	-	0	274				ZNF717_ENST00000400845.3_Missense_Mutation_p.V43M|ZNF717_ENST00000477374.1_Missense_Mutation_p.V50M|ZNF717_ENST00000491507.1_5'UTR|ZNF717_ENST00000422325.1_Missense_Mutation_p.V50M			Q9BY31	ZN717_HUMAN	zinc finger protein 717						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(6)|endometrium(3)|lung(2)|ovary(1)|stomach(7)	19						TCCAGCATCACGTCCCTGTAC	0.502																																					p.V50M		Atlas-SNP	.											ZNF717,NS,malignant_melanoma,0,1	ZNF717	160	1	0			c.G148A						scavenged	.						16.0	13.0	14.0					3																	75790797		444	1237	1681			100131827	exon3			GCATCACGTCCCT	AF226994		3p12.3	2013-01-08			ENSG00000227124	ENSG00000227124		"""Zinc fingers, C2H2-type"", ""-"""	29448	protein-coding gene	gene with protein product			"""zinc finger protein 838"""	ZNF838			Standard	NM_001128223		Approved	X17	uc011bgi.2	Q9BY31	OTTHUMG00000158965		3.37:g.75790797C>T		Somatic	7	0	0		WXS	Illumina HiSeq	Phase_I	13	4	0.307692	NM_001128223		Missense_Mutation	SNP	ENST00000478296.1	37		562	0.2573260073260073	83	0.16869918699186992	111	0.30662983425414364	134	0.23426573426573427	234	0.3087071240105541	.	14.80	2.645039	0.47258	.	.	ENSG00000227124	ENST00000477374;ENST00000422325;ENST00000400845;ENST00000468296	T;T;T;T	0.04015	3.73;3.73;3.73;3.73	1.97	1.97	0.26223	.	.	.	.	.	T	0.00012	0.0000	M	0.92833	3.35	0.36926	P	0.10836100000000004	D	0.89917	1.0	D	0.64776	0.929	T	0.22417	-1.0217	8	0.72032	D	0.01	.	9.6897	0.40120	0.0:1.0:0.0:0.0	.	50	C9JSV9	.	M	50;50;43;50	ENSP00000417902:V50M;ENSP00000409514:V50M;ENSP00000383643:V43M;ENSP00000418187:V50M	ENSP00000383643:V43M	V	-	1	0	ZNF717	75873487	0.243000	0.23878	0.981000	0.43875	0.552000	0.35366	1.184000	0.32053	1.127000	0.42034	0.545000	0.68477	GTG	C|0.753;T|0.247	0.247	strong		0.502	ZNF717-002	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000352764.2	NM_001128223	
TWISTNB	221830	hgsc.bcm.edu	37	7	19738329	19738329	+	Silent	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:19738329T>C	ENST00000222567.5	-	4	697	c.627A>G	c.(625-627)gaA>gaG	p.E209E		NM_001002926.1	NP_001002926.1	Q3B726	RPA43_HUMAN	TWIST neighbor	209					transcription from RNA polymerase I promoter (GO:0006360)	DNA-directed RNA polymerase I complex (GO:0005736)|microtubule cytoskeleton (GO:0015630)|nucleolus (GO:0005730)|nucleus (GO:0005634)	DNA-directed RNA polymerase activity (GO:0003899)			kidney(1)|large_intestine(3)|lung(13)|ovary(1)|prostate(2)	20						CTTCAGAAACTTCAGAGCGCT	0.323																																					p.E209E		Atlas-SNP	.											.	TWISTNB	63	.	0			c.A627G						PASS	.						53.0	61.0	59.0					7																	19738329		2199	4289	6488	SO:0001819	synonymous_variant	221830	exon4			AGAAACTTCAGAG	AK090846	CCDS34606.1	7p21.1	2010-08-05			ENSG00000105849	ENSG00000105849			18027	protein-coding gene	gene with protein product		608312				12438708	Standard	NM_001002926		Approved		uc003sup.1	Q3B726	OTTHUMG00000152497	ENST00000222567.5:c.627A>G	7.37:g.19738329T>C		Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	49	24	0.489796	NM_001002926	A0PJ45|B7Z724	Silent	SNP	ENST00000222567.5	37	CCDS34606.1																																																																																			.	.	none		0.323	TWISTNB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000326463.1		
LIPM	340654	hgsc.bcm.edu	37	10	90574359	90574359	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:90574359G>T	ENST00000404743.4	+	4	704	c.537G>T	c.(535-537)aaG>aaT	p.K179N	LIPM_ENST00000539337.1_Missense_Mutation_p.K139N	NM_001128215.1	NP_001121687.1	Q5VYY2	LIPM_HUMAN	lipase, family member M	179					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						GCCAGGAAAAGATCTATTATG	0.413																																					p.K179N		Atlas-SNP	.											.	LIPM	17	.	0			c.G537T						PASS	.						155.0	126.0	135.0					10																	90574359		692	1591	2283	SO:0001583	missense	340654	exon4			GGAAAAGATCTAT		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.537G>T	10.37:g.90574359G>T	ENSP00000383901:p.Lys179Asn	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	62	18	0.290323	NM_001128215	A6PVS3|B2RXK7|B5MCR3	Missense_Mutation	SNP	ENST00000404743.4	37	CCDS44457.1	.	.	.	.	.	.	.	.	.	.	G	14.99	2.699396	0.48307	.	.	ENSG00000173239	ENST00000404743;ENST00000539337	T;T	0.73681	-0.77;-0.77	6.03	1.54	0.23209	Alpha/beta hydrolase fold-1 (1);	0.189236	0.38111	N	0.001803	T	0.66066	0.2752	L	0.60904	1.88	0.31588	N	0.654267	B;B	0.33288	0.23;0.406	B;B	0.34590	0.11;0.186	T	0.66842	-0.5821	10	0.59425	D	0.04	-19.6872	5.9596	0.19293	0.1926:0.0:0.5454:0.262	.	139;179	B2RXK7;Q5VYY2	.;LIPM_HUMAN	N	179;139	ENSP00000383901:K179N;ENSP00000440375:K139N	ENSP00000383901:K179N	K	+	3	2	LIPM	90564339	0.058000	0.20735	1.000000	0.80357	0.996000	0.88848	0.209000	0.17435	0.417000	0.25871	0.555000	0.69702	AAG	.	.	none		0.413	LIPM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049261.3	XM_291663	
ERBB2IP	55914	hgsc.bcm.edu	37	5	65349497	65349497	+	Nonsense_Mutation	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:65349497C>A	ENST00000284037.5	+	21	2740	c.2351C>A	c.(2350-2352)tCa>tAa	p.S784*	ERBB2IP_ENST00000380939.2_Nonsense_Mutation_p.S784*|ERBB2IP_ENST00000416865.2_Intron|ERBB2IP_ENST00000511297.1_Nonsense_Mutation_p.S780*|ERBB2IP_ENST00000506030.1_Nonsense_Mutation_p.S784*|ERBB2IP_ENST00000380936.1_Nonsense_Mutation_p.S784*|ERBB2IP_ENST00000380943.2_Nonsense_Mutation_p.S784*|ERBB2IP_ENST00000380935.1_Nonsense_Mutation_p.S784*|ERBB2IP_ENST00000380938.2_Nonsense_Mutation_p.S784*|ERBB2IP_ENST00000508515.1_Nonsense_Mutation_p.S784*	NM_001253697.1	NP_001240626.1	Q96RT1	LAP2_HUMAN	erbb2 interacting protein	784					basal protein localization (GO:0045175)|cell adhesion (GO:0007155)|cell cycle (GO:0007049)|cell growth (GO:0016049)|epidermal growth factor receptor signaling pathway (GO:0007173)|establishment or maintenance of epithelial cell apical/basal polarity (GO:0045197)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|signal transduction (GO:0007165)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|hemidesmosome (GO:0030056)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ErbB-2 class receptor binding (GO:0005176)|integrin binding (GO:0005178)|structural constituent of cytoskeleton (GO:0005200)	p.S784*(1)		breast(2)|central_nervous_system(2)|endometrium(3)|kidney(5)|large_intestine(8)|lung(11)|ovary(3)|skin(2)	36		Lung NSC(167;9.45e-06)|Prostate(74;0.0139)|Ovarian(174;0.0547)|Breast(144;0.093)|Colorectal(97;0.234)		UCEC - Uterine corpus endometrioid carcinoma (4;0.0767)|Lung(70;0.00191)		ATGGAAAGATCAAAAACACAG	0.323																																					p.S784X		Atlas-SNP	.											ERBB2IP,medulla,primitive_neuroectodermal_tumour-medulloblastoma,0,1	ERBB2IP	120	1	1	Substitution - Nonsense(1)	central_nervous_system(1)	c.C2351A						PASS	.						48.0	50.0	49.0					5																	65349497		2203	4299	6502	SO:0001587	stop_gained	55914	exon21			AAAGATCAAAAAC		CCDS3990.1, CCDS34172.1, CCDS58951.1, CCDS58952.1, CCDS58953.1, CCDS58954.1	5p14.3-q12.3	2008-07-18	2001-11-29		ENSG00000112851	ENSG00000112851			15842	protein-coding gene	gene with protein product	"""densin-180-like protein"", ""ERBB2-interacting protein"""	606944	"""erbb2-interacting protein"""			10574462, 10878805	Standard	NM_001253697		Approved	ERBIN, LAP2	uc011cqx.2	Q96RT1	OTTHUMG00000097808	ENST00000284037.5:c.2351C>A	5.37:g.65349497C>A	ENSP00000284037:p.Ser784*	Somatic	48	0	0		WXS	Illumina HiSeq	Phase_I	59	32	0.542373	NM_001253699	A0AVR1|B4E3F1|B7ZLV9|E7EQW9|E9PCR8|Q1RMD0|Q86W38|Q9NR18|Q9NW48|Q9ULJ5	Nonsense_Mutation	SNP	ENST00000284037.5	37	CCDS58953.1	.	.	.	.	.	.	.	.	.	.	C	38	6.691405	0.97768	.	.	ENSG00000112851	ENST00000284037;ENST00000380943;ENST00000380939;ENST00000380936;ENST00000380935;ENST00000380938;ENST00000511297;ENST00000506030;ENST00000508515	.	.	.	5.56	4.69	0.59074	.	0.350015	0.29653	N	0.011556	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	.	9.0238	0.36215	0.0:0.7891:0.0:0.2109	.	.	.	.	X	784;784;784;784;784;784;780;784;784	.	ENSP00000284037:S784X	S	+	2	0	ERBB2IP	65385253	1.000000	0.71417	1.000000	0.80357	0.516000	0.34256	2.844000	0.48246	1.347000	0.45714	0.467000	0.42956	TCA	.	.	none		0.323	ERBB2IP-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000215070.1	NM_018695	
HRNR	388697	hgsc.bcm.edu	37	1	152188847	152188847	+	Missense_Mutation	SNP	A	A	G	rs145667921		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:152188847A>G	ENST00000368801.2	-	3	5333	c.5258T>C	c.(5257-5259)gTc>gCc	p.V1753A	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	1753					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)			TTGACCAAAGACAGAAGAGTG	0.562																																					p.V1753A		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	0			c.T5258C						scavenged	.						1.0	1.0	1.0					1																	152188847		388	960	1348	SO:0001583	missense	388697	exon3			CCAAAGACAGAAG	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.5258T>C	1.37:g.152188847A>G	ENSP00000357791:p.Val1753Ala	Somatic	518	47	0.0907336		WXS	Illumina HiSeq	Phase_I	726	52	0.0716253	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	.	.	.	.	.	.	.	.	.	.	C	13.29	2.191978	0.38707	.	.	ENSG00000197915	ENST00000368801	T	0.01548	4.78	3.15	2.19	0.27852	.	.	.	.	.	T	0.00412	0.0013	L	0.40543	1.245	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.48103	-0.9064	9	0.07482	T	0.82	.	1.9459	0.03356	0.2121:0.4632:0.2061:0.1186	.	1753	Q86YZ3	HORN_HUMAN	A	1753	ENSP00000357791:V1753A	ENSP00000357791:V1753A	V	-	2	0	HRNR	150455471	0.000000	0.05858	0.001000	0.08648	0.003000	0.03518	-0.214000	0.09292	0.170000	0.19704	-0.294000	0.09567	GTC	.	.	weak		0.562	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
GRM8	2918	hgsc.bcm.edu	37	7	126544620	126544620	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:126544620G>A	ENST00000339582.2	-	4	1653	c.845C>T	c.(844-846)gCc>gTc	p.A282V	GRM8_ENST00000444921.2_Missense_Mutation_p.A282V|GRM8_ENST00000405249.1_Missense_Mutation_p.A282V|GRM8_ENST00000480995.1_5'UTR|GRM8_ENST00000358373.3_Missense_Mutation_p.A282V			O00222	GRM8_HUMAN	glutamate receptor, metabotropic 8	282					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)	p.A282D(1)		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)				ATCCTCATTGGCAAACATAAT	0.388										HNSCC(24;0.065)																											p.A282V		Atlas-SNP	.											GRM8,NS,carcinoma,0,1	GRM8	377	1	1	Substitution - Missense(1)	lung(1)	c.C845T						scavenged	.						115.0	109.0	111.0					7																	126544620		2203	4298	6501	SO:0001583	missense	2918	exon3			TCATTGGCAAACA		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.845C>T	7.37:g.126544620G>A	ENSP00000344173:p.Ala282Val	Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	180	4	0.0222222	NM_000845	A4D0Y3|B0FZ74|B0M0L0|O15493|O95945|O95946|Q3MIV9|Q52M02|Q6J165	Missense_Mutation	SNP	ENST00000339582.2	37	CCDS5794.1	.	.	.	.	.	.	.	.	.	.	G	24.4	4.524524	0.85600	.	.	ENSG00000179603	ENST00000339582;ENST00000444921;ENST00000358373;ENST00000405249;ENST00000457830	D;D;D;D;D	0.83419	-1.72;-1.72;-1.72;-1.72;-1.72	5.24	5.24	0.73138	Extracellular ligand-binding receptor (1);	0.000000	0.85682	D	0.000000	D	0.87410	0.6170	L	0.53780	1.695	0.80722	D	1	P;D;P	0.58268	0.678;0.982;0.592	B;P;B	0.58013	0.421;0.831;0.348	D	0.87157	0.2212	10	0.45353	T	0.12	.	17.8349	0.88693	0.0:0.0:1.0:0.0	.	282;282;282	O00222-3;O00222-2;O00222	.;.;GRM8_HUMAN	V	282	ENSP00000344173:A282V;ENSP00000409790:A282V;ENSP00000351142:A282V;ENSP00000385731:A282V;ENSP00000415522:A282V	ENSP00000344173:A282V	A	-	2	0	GRM8	126331856	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.779000	0.99018	2.445000	0.82738	0.557000	0.71058	GCC	.	.	none		0.388	GRM8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000059209.4		
PRKD2	25865	hgsc.bcm.edu	37	19	47207494	47207494	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:47207494C>T	ENST00000291281.4	-	5	1046	c.821G>A	c.(820-822)cGg>cAg	p.R274Q	PRKD2_ENST00000601806.1_Missense_Mutation_p.R117Q|PRKD2_ENST00000600194.1_Missense_Mutation_p.R117Q|PRKD2_ENST00000433867.1_Missense_Mutation_p.R274Q|PRKD2_ENST00000595515.1_Missense_Mutation_p.R274Q			Q9BZL6	KPCD2_HUMAN	protein kinase D2	274					angiogenesis (GO:0001525)|cell adhesion (GO:0007155)|cell death (GO:0008219)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|endothelial tube morphogenesis (GO:0061154)|intracellular signal transduction (GO:0035556)|peptidyl-serine phosphorylation (GO:0018105)|positive regulation of angiogenesis (GO:0045766)|positive regulation of blood vessel endothelial cell migration (GO:0043536)|positive regulation of cell adhesion (GO:0045785)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell chemotaxis by VEGF-activated vascular endothelial growth factor receptor signaling pathway (GO:0038033)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast growth factor receptor signaling pathway (GO:0045743)|positive regulation of histone deacetylase activity (GO:1901727)|positive regulation of interleukin-2 production (GO:0032743)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of intracellular signal transduction (GO:1902533)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of T cell receptor signaling pathway (GO:0050862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|T cell receptor signaling pathway (GO:0050852)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein kinase C activity (GO:0004697)|protein serine/threonine kinase activity (GO:0004674)	p.R274Q(1)		central_nervous_system(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(13)|ovary(2)|prostate(2)|skin(1)|stomach(2)|urinary_tract(1)	41		Ovarian(192;0.0129)|all_neural(266;0.0459)|Breast(70;0.212)		OV - Ovarian serous cystadenocarcinoma(262;0.000189)|all cancers(93;0.000545)|Epithelial(262;0.0219)|GBM - Glioblastoma multiforme(486;0.0353)		AACGGTGGGCCGTGTATAGCT	0.592											OREG0025578	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.R274Q		Atlas-SNP	.											PRKD2,NS,carcinoma,0,1	PRKD2	94	1	1	Substitution - Missense(1)	lung(1)	c.G821A						scavenged	.						149.0	135.0	140.0					19																	47207494		2203	4300	6503	SO:0001583	missense	25865	exon5			GTGGGCCGTGTAT	AF151021	CCDS12689.1, CCDS59401.1	19q13.2	2013-01-10				ENSG00000105287		"""Pleckstrin homology (PH) domain containing"""	17293	protein-coding gene	gene with protein product		607074				11042152, 11062248	Standard	NM_001079880		Approved	PKD2, HSPC187, DKFZP586E0820	uc002pfj.3	Q9BZL6		ENST00000291281.4:c.821G>A	19.37:g.47207494C>T	ENSP00000291281:p.Arg274Gln	Somatic	240	2	0.00833333	945	WXS	Illumina HiSeq	Phase_I	240	3	0.0125	NM_016457	Q8TB08|Q9P0T6|Q9Y3X8	Missense_Mutation	SNP	ENST00000291281.4	37	CCDS12689.1	.	.	.	.	.	.	.	.	.	.	C	34	5.405082	0.96051	.	.	ENSG00000105287	ENST00000291281;ENST00000433867	D;D	0.92249	-3.0;-3.0	5.18	5.18	0.71444	Protein kinase C-like, phorbol ester/diacylglycerol binding (4);	0.178892	0.35936	N	0.002885	D	0.93226	0.7842	L	0.37897	1.145	0.52099	D	0.99994	D;D	0.65815	0.991;0.995	P;P	0.62491	0.861;0.903	D	0.93113	0.6518	10	0.46703	T	0.11	-45.0909	17.8348	0.88693	0.0:1.0:0.0:0.0	.	274;274	E7ER94;Q9BZL6	.;KPCD2_HUMAN	Q	274	ENSP00000291281:R274Q;ENSP00000393978:R274Q	ENSP00000291281:R274Q	R	-	2	0	PRKD2	51899334	1.000000	0.71417	0.999000	0.59377	0.873000	0.50193	7.426000	0.80270	2.579000	0.87056	0.448000	0.29417	CGG	.	.	none		0.592	PRKD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466591.1	NM_016457	
EXOC3L1	283849	hgsc.bcm.edu	37	16	67220777	67220777	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:67220777G>A	ENST00000314586.6	-	7	1409	c.1169C>T	c.(1168-1170)tCt>tTt	p.S390F	KIAA0895L_ENST00000290881.7_5'Flank|KIAA0895L_ENST00000561621.1_5'Flank|EXOC3L1_ENST00000562887.1_5'Flank|KIAA0895L_ENST00000563902.1_5'Flank	NM_178516.3	NP_848611.2	Q86VI1	EX3L1_HUMAN	exocyst complex component 3-like 1	390					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						CAGCCACTGAGACACACTTGC	0.592																																					p.S390F		Atlas-SNP	.											.	EXOC3L1	52	.	0			c.C1169T						PASS	.						55.0	60.0	58.0					16																	67220777		2198	4300	6498	SO:0001583	missense	283849	exon7			CACTGAGACACAC	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.1169C>T	16.37:g.67220777G>A	ENSP00000325674:p.Ser390Phe	Somatic	35	0	0		WXS	Illumina HiSeq	Phase_I	28	25	0.892857	NM_178516	A8K7I9|Q8NAD2|Q8TEN2	Missense_Mutation	SNP	ENST00000314586.6	37	CCDS10832.1	.	.	.	.	.	.	.	.	.	.	G	7.721	0.697108	0.15106	.	.	ENSG00000179044	ENST00000314586	T	0.07114	3.22	5.19	3.21	0.36854	.	0.413929	0.26723	N	0.022835	T	0.05318	0.0141	N	0.14661	0.345	0.22754	N	0.998779	B	0.02656	0.0	B	0.01281	0.0	T	0.33599	-0.9862	10	0.56958	D	0.05	-0.2662	9.1371	0.36881	0.2452:0.0:0.7548:0.0	.	390	Q86VI1	EX3L1_HUMAN	F	390	ENSP00000325674:S390F	ENSP00000325674:S390F	S	-	2	0	EXOC3L1	65778278	0.101000	0.21875	0.823000	0.32752	0.108000	0.19459	2.780000	0.47742	0.576000	0.29452	0.455000	0.32223	TCT	.	.	none		0.592	EXOC3L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000268827.2	NM_178516	
KIRREL	55243	hgsc.bcm.edu	37	1	158064854	158064854	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:158064854T>C	ENST00000359209.6	+	15	2285	c.2218T>C	c.(2218-2220)Tcc>Ccc	p.S740P	KIRREL_ENST00000360089.4_Missense_Mutation_p.S576P|KIRREL_ENST00000416935.2_Missense_Mutation_p.S640P|KIRREL_ENST00000392272.2_Missense_Mutation_p.S637P|KIRREL_ENST00000368172.1_Missense_Mutation_p.S554P|KIRREL_ENST00000368173.3_Missense_Mutation_p.S756P			Q96J84	KIRR1_HUMAN	kin of IRRE like (Drosophila)	740					excretion (GO:0007588)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of actin filament polymerization (GO:0030838)|single organismal cell-cell adhesion (GO:0016337)	cell-cell junction (GO:0005911)|dendritic shaft (GO:0043198)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	myosin binding (GO:0017022)			NS(1)|autonomic_ganglia(1)|breast(2)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|prostate(5)|skin(3)|stomach(1)	38	all_hematologic(112;0.0378)					CTCCTACACCTCCCAGCACTC	0.647																																					p.S740P		Atlas-SNP	.											KIRREL_ENST00000368173,NS,carcinoma,-2,3	KIRREL	346	3	0			c.T2218C						scavenged	.						45.0	40.0	42.0					1																	158064854		2203	4300	6503	SO:0001583	missense	55243	exon15			TACACCTCCCAGC	AK001707	CCDS1172.2, CCDS72952.1	1q21-q25	2013-01-29			ENSG00000183853	ENSG00000183853		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	15734	protein-coding gene	gene with protein product	"""nephrin-like protein 1"""	607428				12424224	Standard	NM_001286349		Approved	NEPH1	uc001frn.4	Q96J84	OTTHUMG00000022438	ENST00000359209.6:c.2218T>C	1.37:g.158064854T>C	ENSP00000352138:p.Ser740Pro	Somatic	81	3	0.037037		WXS	Illumina HiSeq	Phase_I	100	6	0.06	NM_018240	Q5W0F8|Q5XKC6|Q7Z696|Q7Z7N8|Q8TB15|Q9H9N1|Q9NVA5	Missense_Mutation	SNP	ENST00000359209.6	37	CCDS1172.2	.	.	.	.	.	.	.	.	.	.	T	21.7	4.186867	0.78789	.	.	ENSG00000183853	ENST00000360089;ENST00000368173;ENST00000392272;ENST00000359209;ENST00000416935;ENST00000368172	T;T;T;T;T;T	0.81163	-0.47;-1.46;-0.85;-1.08;-1.01;-0.66	5.0	3.88	0.44766	.	0.000000	0.42682	D	0.000663	T	0.73830	0.3637	L	0.27053	0.805	0.54753	D	0.999989	D;D;D;D	0.76494	0.999;0.999;0.994;0.998	D;D;P;P	0.63488	0.915;0.915;0.796;0.796	T	0.78463	-0.2194	10	0.87932	D	0	-30.8918	8.1799	0.31305	0.0:0.095:0.0:0.905	.	640;576;554;740	B4DN67;Q5W0F9;Q5W0G0;Q96J84	.;.;.;KIRR1_HUMAN	P	576;756;637;740;640;554	ENSP00000353202:S576P;ENSP00000357155:S756P;ENSP00000376098:S637P;ENSP00000352138:S740P;ENSP00000389674:S640P;ENSP00000357154:S554P	ENSP00000352138:S740P	S	+	1	0	KIRREL	156331478	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.229000	0.78088	1.881000	0.54492	0.459000	0.35465	TCC	.	.	none		0.647	KIRREL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058342.3	NM_018240	
ZNF665	79788	hgsc.bcm.edu	37	19	53668754	53668754	+	Missense_Mutation	SNP	C	C	T	rs374379778		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:53668754C>T	ENST00000600412.1	-	2	909	c.794G>A	c.(793-795)cGc>cAc	p.R265H	ZNF665_ENST00000396424.3_Missense_Mutation_p.R330H|CTD-2245F17.2_ENST00000600257.1_RNA			Q9H7R5	ZN665_HUMAN	zinc finger protein 665	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)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.R330L(1)|p.R265L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(10)|lung(16)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	35				GBM - Glioblastoma multiforme(134;0.0196)		CAGGCTTGAGCGAACACTAAA	0.428																																					p.R330H		Atlas-SNP	.											ZNF665,rectum,carcinoma,-1,2	ZNF665	136	2	2	Substitution - Missense(2)	lung(2)	c.G989A						scavenged	.	C	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	119.0	124.0	122.0		989	-4.5	0.0	19		122	0,8598		0,0,4299	no	missense	ZNF665	NM_024733.3	29	0,1,6501	TT,TC,CC		0.0,0.0227,0.0077	benign	330/679	53668754	1,13003	2203	4299	6502	SO:0001583	missense	79788	exon4			CTTGAGCGAACAC		CCDS46169.1	19q13.42	2013-01-08				ENSG00000197497		"""Zinc fingers, C2H2-type"", ""-"""	25885	protein-coding gene	gene with protein product							Standard	NM_024733		Approved	FLJ14345	uc010eqm.1	Q9H7R5		ENST00000600412.1:c.794G>A	19.37:g.53668754C>T	ENSP00000469154:p.Arg265His	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	84	2	0.0238095	NM_024733	A8K5T8	Missense_Mutation	SNP	ENST00000600412.1	37		.	.	.	.	.	.	.	.	.	.	C	3.735	-0.054780	0.07362	2.27E-4	0.0	ENSG00000197497	ENST00000396424	T	0.01015	5.44	2.26	-4.52	0.03472	.	.	.	.	.	T	0.00552	0.0018	N	0.12527	0.23	0.09310	N	1	B	0.23990	0.095	B	0.16722	0.016	T	0.45220	-0.9276	9	0.14252	T	0.57	.	5.1546	0.15029	0.1381:0.3683:0.0:0.4936	.	330	Q9H7R5-2	.	H	330	ENSP00000379702:R330H	ENSP00000379702:R330H	R	-	2	0	ZNF665	58360566	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-4.991000	0.00162	-1.719000	0.01382	-0.436000	0.05848	CGC	.	.	weak		0.428	ZNF665-002	PUTATIVE	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000464179.1	NM_024733	
MUC6	4588	hgsc.bcm.edu	37	11	1016770	1016770	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:1016770G>A	ENST00000421673.2	-	31	6081	c.6031C>T	c.(6031-6033)Cct>Tct	p.P2011S		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	2011	Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.P2011S(1)		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)		GTGGAGAAAGGTGGAACGTGA	0.532																																					p.P2011S		Atlas-SNP	.											MUC6_ENST00000421673,extremity,malignant_melanoma,0,1	MUC6	408	1	1	Substitution - Missense(1)	skin(1)	c.C6031T						scavenged	.																																			SO:0001583	missense	4588	exon31			AGAAAGGTGGAAC	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.6031C>T	11.37:g.1016770G>A	ENSP00000406861:p.Pro2011Ser	Somatic	1132	16	0.0141343		WXS	Illumina HiSeq	Phase_I	1279	24	0.0187647	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	G	0.013	-1.638370	0.00799	.	.	ENSG00000184956	ENST00000421673	T	0.17370	2.28	2.4	-4.79	0.03200	.	.	.	.	.	T	0.06735	0.0172	N	0.21194	0.64	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.39014	-0.9634	9	0.07990	T	0.79	.	1.1636	0.01810	0.3722:0.1007:0.2914:0.2356	.	2011	Q6W4X9	MUC6_HUMAN	S	2011	ENSP00000406861:P2011S	ENSP00000406861:P2011S	P	-	1	0	MUC6	1006770	0.000000	0.05858	0.000000	0.03702	0.006000	0.05464	-2.781000	0.00773	-2.945000	0.00295	-0.671000	0.03813	CCT	.	.	none		0.532	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
LRP5	4041	hgsc.bcm.edu	37	11	68171003	68171003	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:68171003C>T	ENST00000294304.7	+	8	1743	c.1637C>T	c.(1636-1638)cCg>cTg	p.P546L		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	546	Beta-propeller 2.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)			autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						GACAAGCTCCCGCACATTTTT	0.602																																					p.P546L		Atlas-SNP	.											LRP5,NS,carcinoma,-1,1	LRP5	136	1	0			c.C1637T						scavenged	.						100.0	82.0	88.0					11																	68171003		2200	4294	6494	SO:0001583	missense	4041	exon8			AGCTCCCGCACAT	AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.1637C>T	11.37:g.68171003C>T	ENSP00000294304:p.Pro546Leu	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	192	2	0.0104167	NM_002335	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	37	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.611938	0.87258	.	.	ENSG00000162337	ENST00000294304	D	0.95622	-3.76	4.13	4.13	0.48395	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.48767	U	0.000174	D	0.96926	0.8996	M	0.67569	2.06	0.80722	D	1	D	0.63880	0.993	D	0.63703	0.917	D	0.97633	1.0143	10	0.87932	D	0	.	16.9721	0.86303	0.0:1.0:0.0:0.0	.	546	O75197	LRP5_HUMAN	L	546	ENSP00000294304:P546L	ENSP00000294304:P546L	P	+	2	0	LRP5	67927579	1.000000	0.71417	0.980000	0.43619	0.995000	0.86356	7.514000	0.81750	2.321000	0.78463	0.650000	0.86243	CCG	.	.	none		0.602	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1	NM_002335	
MUC4	4585	hgsc.bcm.edu	37	3	195508902	195508902	+	Silent	SNP	C	C	G	rs144571919		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:195508902C>G	ENST00000463781.3	-	2	10008	c.9549G>C	c.(9547-9549)acG>acC	p.T3183T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T3183T	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)		CAGGAAGAGGCGTGGTGTCAC	0.597																																					p.T3183T		Atlas-SNP	.											MUC4_ENST00000463781,NS,malignant_melanoma,-1,2	MUC4	1505	2	0			c.G9549C						scavenged	.																																			SO:0001819	synonymous_variant	4585	exon2			AAGAGGCGTGGTG	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.9549G>C	3.37:g.195508902C>G		Somatic	89	8	0.0898876		WXS	Illumina HiSeq	Phase_I	108	11	0.101852	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			C|0.500;G|0.500	0.500	weak		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DSCAML1	57453	hgsc.bcm.edu	37	11	117374656	117374656	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:117374656G>A	ENST00000321322.6	-	11	2444	c.2443C>T	c.(2443-2445)Cgc>Tgc	p.R815C	DSCAML1_ENST00000527706.1_Missense_Mutation_p.R545C	NM_020693.2	NP_065744.2	Q8TD84	DSCL1_HUMAN	Down syndrome cell adhesion molecule like 1	755	Ig-like C2-type 9.				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)		AGGACGTGGCGGATCAGCAGC	0.607																																					p.R815C		Atlas-SNP	.											DSCAML1,NS,carcinoma,+1,1	DSCAML1	286	1	0			c.C2443T						PASS	.						110.0	91.0	97.0					11																	117374656		2201	4296	6497	SO:0001583	missense	57453	exon11			CGTGGCGGATCAG		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.2443C>T	11.37:g.117374656G>A	ENSP00000315465:p.Arg815Cys	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_020693	Q76MU9|Q8IZY3|Q8IZY4|Q8WXU7|Q9ULT7	Missense_Mutation	SNP	ENST00000321322.6	37	CCDS8384.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.192049	0.78902	.	.	ENSG00000177103	ENST00000527706;ENST00000321322;ENST00000446508	T;T	0.68479	-0.33;-0.33	4.29	4.29	0.51040	Immunoglobulin I-set (1);Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	.	.	.	.	D	0.82944	0.5147	M	0.84433	2.695	0.80722	D	1	D	0.89917	1.0	D	0.70487	0.969	D	0.86461	0.1779	9	0.66056	D	0.02	.	16.9369	0.86205	0.0:0.0:1.0:0.0	.	755	Q8TD84	DSCL1_HUMAN	C	545;815;522	ENSP00000434335:R545C;ENSP00000315465:R815C	ENSP00000315465:R815C	R	-	1	0	DSCAML1	116879866	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.560000	0.53763	2.237000	0.73441	0.462000	0.41574	CGC	.	.	none		0.607	DSCAML1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000392907.2	NM_020693	
TBP	6908	hgsc.bcm.edu	37	6	170871040	170871040	+	Silent	SNP	A	A	G	rs71815788|rs55736770	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:170871040A>G	ENST00000392092.2	+	3	495	c.216A>G	c.(214-216)caA>caG	p.Q72Q	TBP_ENST00000230354.6_Silent_p.Q72Q|TBP_ENST00000540980.1_Silent_p.Q52Q	NM_003194.4	NP_003185.1	P20226	TBP_HUMAN	TATA box binding protein	72	Poly-Gln.				cell death (GO:0008219)|gene expression (GO:0010467)|positive regulation of transcription, DNA-templated (GO:0045893)|spermatogenesis (GO:0007283)|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 from RNA polymerase III promoter (GO:0006383)|transcription initiation from RNA polymerase I promoter (GO:0006361)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	cytoplasm (GO:0005737)|female pronucleus (GO:0001939)|male pronucleus (GO:0001940)|nuclear euchromatin (GO:0005719)|nucleoplasm (GO:0005654)|transcription factor TFIIA complex (GO:0005672)|transcription factor TFIID complex (GO:0005669)	repressing transcription factor binding (GO:0070491)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.Q72del(3)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(2)|lung(9)|ovary(1)|prostate(4)|urinary_tract(1)	26		Breast(66;5.08e-05)|Ovarian(120;0.125)|Esophageal squamous(34;0.246)		OV - Ovarian serous cystadenocarcinoma(33;1.07e-22)|BRCA - Breast invasive adenocarcinoma(81;5.01e-06)|GBM - Glioblastoma multiforme(31;0.00591)		agcagcagcaacagcaacagc	0.567																																					p.Q72Q		Atlas-SNP	.											.	TBP	58	.	3	Deletion - In frame(3)	ovary(1)|prostate(1)|breast(1)	c.A216G						PASS	.						12.0	14.0	13.0					6																	170871040		1995	3894	5889	SO:0001819	synonymous_variant	6908	exon3			GCAGCAACAGCAA	M55654	CCDS5315.1, CCDS55077.1	6q27	2014-04-02			ENSG00000112592	ENSG00000112592		"""General transcription factors"""	11588	protein-coding gene	gene with protein product		600075		GTF2D1, SCA17		2194289, 11448935	Standard	NM_003194		Approved	TFIID	uc003qxu.3	P20226	OTTHUMG00000016084	ENST00000392092.2:c.216A>G	6.37:g.170871040A>G		Somatic	6	0	0		WXS	Illumina HiSeq	Phase_I	52	16	0.307692	NM_003194	B4E3B3|F5H869|Q16845|Q6IBM6|Q9UC02	Silent	SNP	ENST00000392092.2	37	CCDS5315.1																																																																																			A|0.357;G|0.643	0.643	strong		0.567	TBP-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043271.2	NM_003194	
KRTAP5-4	387267	hgsc.bcm.edu	37	11	1643255	1643255	+	Silent	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:1643255G>A	ENST00000399682.1	-	1	113	c.69C>T	c.(67-69)ggC>ggT	p.G23G		NM_001012709.1	NP_001012727	Q6L8H1	KRA54_HUMAN	keratin associated protein 5-4	0						keratin filament (GO:0045095)		p.G23G(1)		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)		cagagccacagcccccacagc	0.687																																					p.G23G		Atlas-SNP	.											KRTAP5-4,NS,carcinoma,0,1	KRTAP5-4	78	1	1	Substitution - coding silent(1)	kidney(1)	c.C69T						scavenged	.						4.0	8.0	7.0					11																	1643255		646	1526	2172	SO:0001819	synonymous_variant	387267	exon1			GCCACAGCCCCCA	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.69C>T	11.37:g.1643255G>A		Somatic	124	2	0.016129		WXS	Illumina HiSeq	Phase_I	165	8	0.0484848	NM_001012709		Silent	SNP	ENST00000399682.1	37																																																																																				.	.	none		0.687	KRTAP5-4-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000127918.1	NM_001012709	
RALGPS1	9649	hgsc.bcm.edu	37	9	129958862	129958862	+	Missense_Mutation	SNP	G	G	T	rs57728614	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:129958862G>T	ENST00000259351.5	+	13	1414	c.1147G>T	c.(1147-1149)Ggc>Tgc	p.G383C	RALGPS1_ENST00000373434.1_Intron|RALGPS1_ENST00000424082.2_Intron	NM_014636.2	NP_055451.1	Q5JS13	RGPS1_HUMAN	Ral GEF with PH domain and SH3 binding motif 1	383					intracellular signal transduction (GO:0035556)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ral GTPase activity (GO:0032852)|regulation of Ral protein signal transduction (GO:0032485)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ral guanyl-nucleotide exchange factor activity (GO:0008321)	p.G383C(1)		kidney(2)|large_intestine(6)|lung(7)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	19						CCCCCGAAGGGGCCTGGCTCT	0.582													G|||	157	0.0313498	0.0	0.0014	5008	,	,		19483	0.0893		0.0	False		,,,				2504	0.0675				p.G383C		Atlas-SNP	.											RALGPS1_ENST00000259351,NS,carcinoma,0,1	RALGPS1	86	1	1	Substitution - Missense(1)	stomach(1)	c.G1147T						scavenged	.	G	,,CYS/GLY	2,4404	4.2+/-10.8	0,2,2201	117.0	113.0	114.0		,,1147	4.6	1.0	9	dbSNP_129	114	3,8597	3.0+/-9.4	0,3,4297	yes	intron,intron,missense	RALGPS1	NM_001190728.1,NM_001190729.1,NM_014636.2	,,159	0,5,6498	TT,TG,GG		0.0349,0.0454,0.0384	,,benign	,,383/558	129958862	5,13001	2203	4300	6503	SO:0001583	missense	9649	exon13			CGAAGGGGCCTGG	AB002349	CCDS35143.1, CCDS55344.1, CCDS55345.1, CCDS55346.1	9q33.3	2013-01-10			ENSG00000136828	ENSG00000136828		"""Pleckstrin homology (PH) domain containing"""	16851	protein-coding gene	gene with protein product		614444				9205841, 10747847	Standard	NM_001190728		Approved	RALGPS1A, RALGEF2, KIAA0351	uc004bqo.2	Q5JS13	OTTHUMG00000020696	ENST00000259351.5:c.1147G>T	9.37:g.129958862G>T	ENSP00000259351:p.Gly383Cys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	134	4	0.0298507	NM_014636	B4DR86|E9PBQ5|O15059|Q5JT60|Q5JT65|Q5JUG5|Q8N4S6|Q8N5H4|Q8WUV7|Q9NZ16	Missense_Mutation	SNP	ENST00000259351.5	37	CCDS35143.1	60	0.027472527472527472	0	0.0	1	0.0027624309392265192	59	0.10314685314685315	0	0.0	G	15.14	2.744675	0.49151	4.54E-4	3.49E-4	ENSG00000136828	ENST00000259351	T	0.26660	1.72	5.48	4.57	0.56435	.	1.540210	0.03169	N	0.170414	T	0.00524	0.0017	N	0.19112	0.55	0.09310	P	1.0	B	0.06786	0.001	B	0.15484	0.013	T	0.04579	-1.0941	9	0.72032	D	0.01	.	6.3292	0.21260	0.2426:0.0:0.7574:0.0	rs57728614	383	Q5JS13	RGPS1_HUMAN	C	383	ENSP00000259351:G383C	ENSP00000259351:G383C	G	+	1	0	RALGPS1	128998683	1.000000	0.71417	1.000000	0.80357	0.809000	0.45718	4.607000	0.61133	2.572000	0.86782	0.491000	0.48974	GGC	G|0.992;T|0.008	0.008	strong		0.582	RALGPS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054133.1	NM_014636	
PLD6	201164	hgsc.bcm.edu	37	17	17106253	17106253	+	Missense_Mutation	SNP	C	C	T	rs201208806		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:17106253C>T	ENST00000321560.3	-	2	615	c.587G>A	c.(586-588)cGg>cAg	p.R196Q	RP11-45M22.4_ENST00000427497.3_3'UTR	NM_178836.3	NP_849158.2	Q8N2A8	PLD6_HUMAN	phospholipase D family, member 6	196					DNA methylation involved in gamete generation (GO:0043046)|glycerophospholipid biosynthetic process (GO:0046474)|lipid catabolic process (GO:0016042)|meiotic nuclear division (GO:0007126)|mitochondrial fusion (GO:0008053)|P granule organization (GO:0030719)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|piRNA metabolic process (GO:0034587)|small molecule metabolic process (GO:0044281)|spermatid development (GO:0007286)	integral component of membrane (GO:0016021)|mitochondrial outer membrane (GO:0005741)	cardiolipin hydrolase activity (GO:0035755)|endonuclease activity (GO:0004519)|metal ion binding (GO:0046872)|protein homodimerization activity (GO:0042803)			endometrium(1)|lung(1)	2						CAGAAAAAGCCGCACGTACTC	0.507													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20543	0.0		0.0	False		,,,				2504	0.0				p.R196Q		Atlas-SNP	.											PLD6,right_upper_lobe,carcinoma,+1,1	PLD6	9	1	0			c.G587A						scavenged	.	C	GLN/ARG	1,4405	2.1+/-5.4	0,1,2202	135.0	132.0	133.0		587	-0.3	0.4	17		133	1,8599	1.2+/-3.3	0,1,4299	yes	missense	PLD6	NM_178836.3	43	0,2,6501	TT,TC,CC		0.0116,0.0227,0.0154	benign	196/253	17106253	2,13004	2203	4300	6503	SO:0001583	missense	201164	exon2			AAAAGCCGCACGT	AK090899	CCDS11182.1	17p11.2	2008-08-14			ENSG00000179598	ENSG00000179598			30447	protein-coding gene	gene with protein product		614960				12477932	Standard	NM_178836		Approved		uc002gqz.3	Q8N2A8	OTTHUMG00000059278	ENST00000321560.3:c.587G>A	17.37:g.17106253C>T	ENSP00000317177:p.Arg196Gln	Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	192	3	0.015625	NM_178836	Q8N5Y1	Missense_Mutation	SNP	ENST00000321560.3	37	CCDS11182.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	13.08	2.130140	0.37630	2.27E-4	1.16E-4	ENSG00000179598	ENST00000321560	T	0.20463	2.07	5.6	-0.318	0.12728	.	0.352194	0.27936	N	0.017256	T	0.11665	0.0284	N	0.20574	0.59	0.30815	N	0.738383	B	0.22080	0.064	B	0.20955	0.032	T	0.18745	-1.0327	10	0.26408	T	0.33	-16.8066	10.8068	0.46522	0.0:0.3963:0.0:0.6037	.	196	Q8N2A8	PLD6_HUMAN	Q	196	ENSP00000317177:R196Q	ENSP00000317177:R196Q	R	-	2	0	PLD6	17046978	0.199000	0.23386	0.431000	0.26735	0.822000	0.46500	-0.405000	0.07196	-0.035000	0.13691	0.655000	0.94253	CGG	C|1.000;T|0.000	0.000	strong		0.507	PLD6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131600.2	NM_178836	
OTOP2	92736	hgsc.bcm.edu	37	17	72923357	72923357	+	Missense_Mutation	SNP	G	G	A	rs374632139		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:72923357G>A	ENST00000580223.1	+	3	520	c.490G>A	c.(490-492)Gtc>Atc	p.V164I	OTOP2_ENST00000331427.4_Missense_Mutation_p.V164I			Q7RTS6	OTOP2_HUMAN	otopetrin 2	164						integral component of membrane (GO:0016021)		p.V164I(1)		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)					CTGCGTTCACGTCCACCTGGA	0.532																																					p.V164I		Atlas-SNP	.											OTOP2,NS,carcinoma,0,1	OTOP2	81	1	1	Substitution - Missense(1)	prostate(1)	c.G490A						PASS	.	G	ILE/VAL	0,4406		0,0,2203	169.0	136.0	147.0		490	-4.9	0.0	17		147	1,8599	1.2+/-3.3	0,1,4299	no	missense	OTOP2	NM_178160.2	29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	benign	164/563	72923357	1,13005	2203	4300	6503	SO:0001583	missense	92736	exon4			GTTCACGTCCACC	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.490G>A	17.37:g.72923357G>A	ENSP00000463837:p.Val164Ile	Somatic	186	0	0		WXS	Illumina HiSeq	Phase_I	185	89	0.481081	NM_178160		Missense_Mutation	SNP	ENST00000580223.1	37	CCDS11708.1	.	.	.	.	.	.	.	.	.	.	G	8.144	0.785922	0.16189	0.0	1.16E-4	ENSG00000183034	ENST00000331427	T	0.21734	1.99	4.96	-4.9	0.03094	.	1.057470	0.07294	N	0.873019	T	0.15003	0.0362	L	0.33753	1.03	0.09310	N	1	B	0.10296	0.003	B	0.13407	0.009	T	0.36456	-0.9747	10	0.21540	T	0.41	-6.2717	13.0707	0.59059	0.6472:0.0:0.3528:0.0	.	164	Q7RTS6	OTOP2_HUMAN	I	164	ENSP00000332528:V164I	ENSP00000332528:V164I	V	+	1	0	OTOP2	70434952	0.000000	0.05858	0.021000	0.16686	0.635000	0.38103	-0.132000	0.10467	-0.832000	0.04251	-1.020000	0.02445	GTC	.	.	weak		0.532	OTOP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000445306.1	NM_178160	
GSTA2	2939	hgsc.bcm.edu	37	6	52616491	52616491	+	Missense_Mutation	SNP	C	C	T	rs377008730		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:52616491C>T	ENST00000493422.1	-	6	585	c.430G>A	c.(430-432)Gga>Aga	p.G144R		NM_000846.4	NP_000837.3	P09210	GSTA2_HUMAN	glutathione S-transferase alpha 2	144	GST C-terminal.				epithelial cell differentiation (GO:0030855)|glutathione derivative biosynthetic process (GO:1901687)|glutathione metabolic process (GO:0006749)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	glutathione transferase activity (GO:0004364)	p.G144R(2)		breast(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	16	Lung NSC(77;0.118)				Azathioprine(DB00993)|Busulfan(DB01008)|Chloroquine(DB00608)|Clofibrate(DB00636)|Ethacrynic acid(DB00903)|Glutathione(DB00143)|Vitamin E(DB00163)	TAGTCTTGTCCGTGGCTCTTT	0.532																																					p.G144R		Atlas-SNP	.											GSTA2,trunk,malignant_melanoma,0,2	GSTA2	33	2	2	Substitution - Missense(2)	skin(2)	c.G430A						scavenged	.						137.0	122.0	127.0					6																	52616491		2203	4300	6503	SO:0001583	missense	2939	exon6			CTTGTCCGTGGCT	AL109918	CCDS4944.1	6p12.2	2012-06-21	2008-11-26		ENSG00000244067	ENSG00000244067	2.5.1.18	"""Glutathione S-transferases / Soluble"""	4627	protein-coding gene	gene with protein product		138360	"""glutathione S-transferase A2"""	GST2			Standard	NM_000846		Approved		uc003pay.3	P09210	OTTHUMG00000016263	ENST00000493422.1:c.430G>A	6.37:g.52616491C>T	ENSP00000420168:p.Gly144Arg	Somatic	129	1	0.00775194		WXS	Illumina HiSeq	Phase_I	139	3	0.0215827	NM_000846	Q12759|Q16491|Q9NTY6	Missense_Mutation	SNP	ENST00000493422.1	37	CCDS4944.1	.	.	.	.	.	.	.	.	.	.	c	11.35	1.612815	0.28712	.	.	ENSG00000244067	ENST00000493422	T	0.14640	2.49	2.88	1.97	0.26223	Glutathione S-transferase, C-terminal-like (2);Glutathione S-transferase/chloride channel, C-terminal (1);Glutathione S-transferase, C-terminal (1);	0.146928	0.44097	D	0.000493	T	0.08447	0.0210	M	0.78801	2.425	0.30500	N	0.77048	B	0.32283	0.362	B	0.36885	0.235	T	0.06092	-1.0846	10	0.59425	D	0.04	.	8.0615	0.30635	0.0:0.8677:0.0:0.1323	.	144	P09210	GSTA2_HUMAN	R	144	ENSP00000420168:G144R	ENSP00000420168:G144R	G	-	1	0	GSTA2	52724450	0.783000	0.28701	0.913000	0.36048	0.615000	0.37417	2.533000	0.45667	0.524000	0.28502	0.485000	0.47835	GGA	.	.	weak		0.532	GSTA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043589.1	NM_000846	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230371	23230371	+	Missense_Mutation	SNP	A	A	T	rs554492007	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr22:23230371A>T	ENST00000526893.1	+	1	412	c.138A>T	c.(136-138)caA>caT	p.Q46H	IGLL5_ENST00000531372.1_Missense_Mutation_p.Q46H|IGLL5_ENST00000532223.2_Missense_Mutation_p.Q46H|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	46						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						TTGCACCGCAAAGCGGGGACC	0.682																																					p.Q46H		Atlas-SNP	.											.	IGLL5	26	.	0			c.A138T						PASS	.																																			SO:0001583	missense	100423062	exon1			ACCGCAAAGCGGG	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.138A>T	22.37:g.23230371A>T	ENSP00000431254:p.Gln46His	Somatic	131	0	0		WXS	Illumina HiSeq	Phase_I	63	49	0.777778	NM_001178126		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1	.	.	.	.	.	.	.	.	.	.	A	13.60	2.284481	0.40394	.	.	ENSG00000254709	ENST00000532223;ENST00000526893;ENST00000531372	T;T	0.00597	6.31;6.41	3.55	-2.34	0.06704	.	.	.	.	.	T	0.00496	0.0016	N	0.24115	0.695	0.09310	N	1	P	0.52316	0.952	B	0.42692	0.395	T	0.53556	-0.8422	9	0.59425	D	0.04	.	7.4227	0.27081	0.5576:0.0:0.4424:0.0	.	46	B9A064	IGLL5_HUMAN	H	46	ENSP00000436353:Q46H;ENSP00000431254:Q46H	ENSP00000431254:Q46H	Q	+	3	2	IGLL5	21560371	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.209000	0.09358	-0.338000	0.08413	-1.039000	0.02377	CAA	.	.	none		0.682	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
CSK	1445	hgsc.bcm.edu	37	15	75090639	75090639	+	Start_Codon_SNP	SNP	A	A	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:75090639A>T	ENST00000220003.9	+	2	730	c.1A>T	c.(1-3)Atg>Ttg	p.M1L	CSK_ENST00000567571.1_Start_Codon_SNP_p.M1L|CSK_ENST00000309470.9_Start_Codon_SNP_p.M1L|CSK_ENST00000439220.2_Start_Codon_SNP_p.M1L	NM_004383.2	NP_004374.1	P41240	CSK_HUMAN	c-src tyrosine kinase	1					adherens junction organization (GO:0034332)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cellular response to peptide hormone stimulus (GO:0071375)|epidermal growth factor receptor signaling pathway (GO:0007173)|negative regulation of bone resorption (GO:0045779)|negative regulation of cell proliferation (GO:0008285)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of Golgi to plasma membrane protein transport (GO:0042997)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of kinase activity (GO:0033673)|negative regulation of low-density lipoprotein particle clearance (GO:0010989)|negative regulation of phagocytosis (GO:0050765)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet activation (GO:0030168)|positive regulation of MAP kinase activity (GO:0043406)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of Fc receptor mediated stimulatory signaling pathway (GO:0060368)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein C-terminus binding (GO:0008022)|protein tyrosine kinase activity (GO:0004713)			central_nervous_system(1)|lung(2)	3						TCCTGAGAAGATGTCAGCAAT	0.562																																					p.M1L		Atlas-SNP	.											.	CSK	43	.	0			c.A1T						PASS	.						69.0	60.0	63.0					15																	75090639		2197	4296	6493	SO:0001582	initiator_codon_variant	1445	exon3			GAGAAGATGTCAG		CCDS10269.1	15q24.1	2013-02-14			ENSG00000103653	ENSG00000103653	2.7.10.1	"""SH2 domain containing"""	2444	protein-coding gene	gene with protein product		124095				1377109	Standard	NM_004383		Approved		uc010bka.3	P41240	OTTHUMG00000142814	ENST00000220003.9:c.1A>T	15.37:g.75090639A>T	ENSP00000220003:p.Met1Leu	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	78	35	0.448718	NM_001127190	Q2M3N2|Q6FGZ6	Missense_Mutation	SNP	ENST00000220003.9	37	CCDS10269.1	.	.	.	.	.	.	.	.	.	.	A	17.66	3.445454	0.63178	.	.	ENSG00000103653	ENST00000220003;ENST00000439220;ENST00000451345;ENST00000309470	T;T;T	0.73681	-0.77;-0.77;-0.77	5.29	5.29	0.74685	Src homology-3 domain (1);	0.200615	0.49305	D	0.000152	T	0.78654	0.4317	.	.	.	0.80722	D	1	P	0.39940	0.696	P	0.51170	0.661	T	0.76929	-0.2777	9	0.34782	T	0.22	-17.2848	12.9023	0.58133	1.0:0.0:0.0:0.0	.	1	P41240	CSK_HUMAN	L	1	ENSP00000220003:M1L;ENSP00000414764:M1L;ENSP00000438808:M1L	ENSP00000220003:M1L	M	+	1	0	CSK	72877692	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.640000	0.67875	2.142000	0.66516	0.459000	0.35465	ATG	.	.	none		0.562	CSK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286398.2	NM_004383	Missense_Mutation
CACNA1B	774	hgsc.bcm.edu	37	9	140773504	140773504	+	Splice_Site	SNP	A	A	C	rs140008467|rs77221813		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:140773504A>C	ENST00000371372.1	+	2	429		c.e2-1		CACNA1B_ENST00000277549.5_Splice_Site|CACNA1B_ENST00000277551.2_Splice_Site|RP11-188C12.3_ENST00000371390.1_RNA|CACNA1B_ENST00000371355.4_Intron|CACNA1B_ENST00000371363.1_Splice_Site|CACNA1B_ENST00000371357.1_Splice_Site	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit						calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	TAACTCACGCACTCCATTCGA	0.632																																					.		Atlas-SNP	.											CACNA1B,colon,carcinoma,0,1	CACNA1B	266	1	0			c.285-2A>C						scavenged	.						34.0	38.0	37.0					9																	140773504		2144	4242	6386	SO:0001630	splice_region_variant	774	exon2			TCACGCACTCCAT	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.285-1A>C	9.37:g.140773504A>C		Somatic	51	5	0.0980392		WXS	Illumina HiSeq	Phase_I	77	4	0.0519481	NM_001243812	B1AQK5	Splice_Site	SNP	ENST00000371372.1	37	CCDS59522.1	.	.	.	.	.	.	.	.	.	.	A	9.642	1.139206	0.21205	.	.	ENSG00000148408	ENST00000371372;ENST00000277551;ENST00000371363;ENST00000371357	.	.	.	4.52	3.37	0.38596	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	9.8471	0.41034	0.9182:0.0:0.0818:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	CACNA1B	139893325	1.000000	0.71417	1.000000	0.80357	0.072000	0.16883	8.392000	0.90180	0.597000	0.29811	-0.379000	0.06801	.	.	.	weak		0.632	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718	Intron
C16orf58	64755	hgsc.bcm.edu	37	16	31510677	31510677	+	Silent	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:31510677A>G	ENST00000327237.2	-	5	585	c.546T>C	c.(544-546)gcT>gcC	p.A182A	C16orf58_ENST00000570164.1_Silent_p.A182A|C16orf58_ENST00000430477.2_Silent_p.A40A|C16orf58_ENST00000567994.1_Silent_p.A137A			Q96GQ5	RUS1_HUMAN	chromosome 16 open reading frame 58	182						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						GGTATACAGGAGCCATAATCT	0.517																																					p.S182S		Atlas-SNP	.											.	C16orf58	28	.	0			c.T546C						PASS	.						94.0	87.0	89.0					16																	31510677		2197	4300	6497	SO:0001819	synonymous_variant	64755	exon5			TACAGGAGCCATA	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.546T>C	16.37:g.31510677A>G		Somatic	156	0	0		WXS	Illumina HiSeq	Phase_I	175	9	0.0514286	NM_022744	Q53GL8|Q8NAJ4|Q9BVY3|Q9H887	Silent	SNP	ENST00000327237.2	37	CCDS10715.1																																																																																			.	.	none		0.517	C16orf58-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255629.2	NM_022744	
DYNC1H1	1778	hgsc.bcm.edu	37	14	102476412	102476412	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr14:102476412C>T	ENST00000360184.4	+	30	6374	c.6210C>T	c.(6208-6210)gtC>gtT	p.V2070V		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	2070	AAA 1. {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						ACAAAATCGTCCCGTTTTTTA	0.418																																					p.V2070V		Atlas-SNP	.											.	DYNC1H1	395	.	0			c.C6210T						PASS	.						61.0	65.0	64.0					14																	102476412		2203	4299	6502	SO:0001819	synonymous_variant	1778	exon30			AATCGTCCCGTTT	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.6210C>T	14.37:g.102476412C>T		Somatic	38	0	0		WXS	Illumina HiSeq	Phase_I	53	4	0.0754717	NM_001376	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																			.	.	none		0.418	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414574.1	NM_001376	
ADGB	79747	hgsc.bcm.edu	37	6	147103217	147103217	+	Silent	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:147103217T>C	ENST00000397944.3	+	30	4000	c.3924T>C	c.(3922-3924)agT>agC	p.S1308S	ADGB_ENST00000367488.1_Silent_p.S31S|ADGB_ENST00000367493.3_Silent_p.S623S|ADGB_ENST00000523560.1_3'UTR	NM_024694.3	NP_078970.3	Q8N7X0	ADGB_HUMAN	androglobin	1308					oxygen transport (GO:0015671)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)	calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)			breast(1)|endometrium(2)|kidney(2)	5						ACACTATTAGTGAGGGACAAA	0.373																																					p.S1308S		Atlas-SNP	.											.	ADGB	93	.	0			c.T3924C						PASS	.						76.0	68.0	70.0					6																	147103217		692	1591	2283	SO:0001819	synonymous_variant	79747	exon30			TATTAGTGAGGGA	AK026774		6q24.2	2012-02-03	2012-02-03	2012-02-03	ENSG00000118492	ENSG00000118492			21212	protein-coding gene	gene with protein product		614630	"""chromosome 6 open reading frame 103"""	C6orf103		22115833	Standard	NM_024694		Approved	FLJ23121, dJ408K24.1	uc010khx.3	Q8N7X0	OTTHUMG00000015758	ENST00000397944.3:c.3924T>C	6.37:g.147103217T>C		Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	93	4	0.0430108	NM_024694	Q5T402|Q5T904|Q5T905	Silent	SNP	ENST00000397944.3	37																																																																																				.	.	none		0.373	ADGB-009	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000376350.2	NM_024694	
LURAP1L	286343	hgsc.bcm.edu	37	9	12775861	12775861	+	Silent	SNP	T	T	C	rs3833707|rs139315731		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:12775861T>C	ENST00000319264.3	+	1	842	c.147T>C	c.(145-147)ggT>ggC	p.G49G	LURAP1L_ENST00000489107.1_3'UTR|RP11-3L8.3_ENST00000417638.1_RNA	NM_203403.1	NP_981948.1	Q8IV03	LUR1L_HUMAN	leucine rich adaptor protein 1-like	52	Gly-rich.		Missing.					p.G49_G50insGGG(2)									gcggtggtggtggcggcggcg	0.687																																					p.G49G		Atlas-SNP	.											C9orf150,NS,carcinoma,0,1	.	.	1	2	Insertion - In frame(2)	prostate(1)|central_nervous_system(1)	c.T147C						scavenged	.						4.0	5.0	5.0					9																	12775861		2038	3961	5999	SO:0001819	synonymous_variant	286343	exon1			TGGTGGTGGCGGC	AK095824	CCDS6473.1	9p22.3	2012-02-01	2012-02-01	2012-02-01	ENSG00000153714	ENSG00000153714			31452	protein-coding gene	gene with protein product	"""similar to DNA segment, Chr 4, Brigham & Womens Genetics 0951 expressed"""		"""chromosome 9 open reading frame 150"""	C9orf150		12766061	Standard	NM_203403		Approved	MGC46502, FLJ38505, bA3L8.2	uc003zkw.3	Q8IV03	OTTHUMG00000019557	ENST00000319264.3:c.147T>C	9.37:g.12775861T>C		Somatic	12	2	0.166667		WXS	Illumina HiSeq	Phase_I	15	5	0.333333	NM_203403	Q5VZX7|Q8N923|Q8NCG2	Silent	SNP	ENST00000319264.3	37	CCDS6473.1																																																																																			.	.	none		0.687	LURAP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051730.1	NM_203403	
FAM47A	158724	hgsc.bcm.edu	37	X	34148961	34148961	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:34148961G>A	ENST00000346193.3	-	1	1486	c.1435C>T	c.(1435-1437)Cac>Tac	p.H479Y		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	479										NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						TGTTCCGGGTGGGGATGGGAC	0.622																																					p.H479Y		Atlas-SNP	.											.	FAM47A	249	.	0			c.C1435T						PASS	.						48.0	54.0	52.0					X																	34148961		2170	4263	6433	SO:0001583	missense	158724	exon1			CCGGGTGGGGATG	BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"""similar to hypothetical protein FLJ35782"""					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.1435C>T	X.37:g.34148961G>A	ENSP00000345029:p.His479Tyr	Somatic	92	0	0		WXS	Illumina HiSeq	Phase_I	84	67	0.797619	NM_203408	A8K8I9|Q8TAA0	Missense_Mutation	SNP	ENST00000346193.3	37	CCDS43926.1	.	.	.	.	.	.	.	.	.	.	g	1.827	-0.470858	0.04445	.	.	ENSG00000185448	ENST00000346193	T	0.13657	2.57	0.48	-0.96	0.10340	.	.	.	.	.	T	0.06234	0.0161	N	0.03608	-0.345	0.20873	N	0.999838	D	0.54772	0.968	P	0.46758	0.526	T	0.22243	-1.0222	8	0.40728	T	0.16	.	.	.	.	.	479	Q5JRC9	FA47A_HUMAN	Y	479	ENSP00000345029:H479Y	ENSP00000345029:H479Y	H	-	1	0	FAM47A	34058882	0.002000	0.14202	0.009000	0.14445	0.040000	0.13550	-0.289000	0.08365	-0.679000	0.05217	0.183000	0.17082	CAC	.	.	none		0.622	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1	NM_203408	
ZNF518B	85460	hgsc.bcm.edu	37	4	10446230	10446230	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:10446230T>C	ENST00000326756.3	-	3	2161	c.1723A>G	c.(1723-1725)Aac>Gac	p.N575D		NM_053042.2	NP_444270.2	Q9C0D4	Z518B_HUMAN	zinc finger protein 518B	575					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(2)|cervix(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(16)|ovary(3)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)	42						TCTGTCTGGTTATCTTCCTGC	0.373																																					p.N575D		Atlas-SNP	.											ZNF518B,NS,carcinoma,+1,1	ZNF518B	116	1	0			c.A1723G						scavenged	.						93.0	87.0	89.0					4																	10446230		2203	4300	6503	SO:0001583	missense	85460	exon3			TCTGGTTATCTTC	AB051516	CCDS33960.1	4p16.1	2007-12-07				ENSG00000178163		"""Zinc fingers, C2H2-type"""	29365	protein-coding gene	gene with protein product						11214970	Standard	XM_005248193		Approved	KIAA1729	uc003gmn.3	Q9C0D4		ENST00000326756.3:c.1723A>G	4.37:g.10446230T>C	ENSP00000317614:p.Asn575Asp	Somatic	179	0	0		WXS	Illumina HiSeq	Phase_I	194	3	0.0154639	NM_053042	Q96LN8	Missense_Mutation	SNP	ENST00000326756.3	37	CCDS33960.1	.	.	.	.	.	.	.	.	.	.	T	12.80	2.046658	0.36085	.	.	ENSG00000178163	ENST00000326756	T	0.01527	4.8	5.15	0.0537	0.14308	.	1.471350	0.03957	N	0.289469	T	0.01287	0.0042	N	0.14661	0.345	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.47222	-0.9134	10	0.12430	T	0.62	-1.4755	4.6115	0.12404	0.0:0.3292:0.3434:0.3275	.	575	Q9C0D4	Z518B_HUMAN	D	575	ENSP00000317614:N575D	ENSP00000317614:N575D	N	-	1	0	ZNF518B	10055328	0.000000	0.05858	0.000000	0.03702	0.222000	0.24845	0.313000	0.19415	0.106000	0.17784	0.533000	0.62120	AAC	.	.	none		0.373	ZNF518B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359040.1	NM_053042	
MUC4	4585	hgsc.bcm.edu	37	3	195505742	195505742	+	Missense_Mutation	SNP	G	G	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:195505742G>C	ENST00000463781.3	-	2	13168	c.12709C>G	c.(12709-12711)Cac>Gac	p.H4237D	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H4237D	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	994					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.H4237D(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)		GGGGTGGCGTGACCTGTGGAT	0.587																																					p.H4237D		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	1	Substitution - Missense(1)	lung(1)	c.C12709G						scavenged	.						49.0	50.0	49.0					3																	195505742		2110	4203	6313	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.12709C>G	3.37:g.195505742G>C	ENSP00000417498:p.His4237Asp	Somatic	133	8	0.0601504		WXS	Illumina HiSeq	Phase_I	130	8	0.0615385	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	2.170	-0.390211	0.04932	.	.	ENSG00000145113	ENST00000463781;ENST00000475231;ENST00000392409	T;T	0.30448	1.55;1.53	2.31	-0.661	0.11417	.	.	.	.	.	T	0.21841	0.0526	L	0.38175	1.15	0.09310	N	1	P;P	0.47604	0.797;0.898	B;B	0.43623	0.343;0.425	T	0.13019	-1.0525	8	.	.	.	.	4.9563	0.14041	0.5176:0.0:0.4824:0.0	.	4109;994	E7ESK3;Q99102	.;MUC4_HUMAN	D	4237;4237;963	ENSP00000417498:H4237D;ENSP00000420243:H4237D	.	H	-	1	0	MUC4	196990521	0.025000	0.19082	0.033000	0.17914	0.009000	0.06853	1.101000	0.31037	-0.196000	0.10366	-0.213000	0.12676	CAC	.	.	none		0.587	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NBPF10	100132406	hgsc.bcm.edu	37	1	145296403	145296403	+	Silent	SNP	C	C	T	rs4996269	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:145296403C>T	ENST00000342960.5	+	3	360	c.325C>T	c.(325-327)Cta>Tta	p.L109L	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000369338.1_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	109						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)			NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GCTGACCCAGCTAAGGGAGAA	0.517																																					p.L109L		Atlas-SNP	.											NBPF10,NS,carcinoma,0,1	NBPF10	221	1	0			c.C325T						scavenged	.																																			SO:0001819	synonymous_variant	100132406	exon3			ACCCAGCTAAGGG	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.325C>T	1.37:g.145296403C>T		Somatic	130	1	0.00769231		WXS	Illumina HiSeq	Phase_I	237	5	0.021097	NM_001039703	Q5RHC0|Q9NWN6	Silent	SNP	ENST00000342960.5	37	CCDS53355.1																																																																																			T|0.001;G|0.956	0.001	strong		0.517	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
GALNT16	57452	hgsc.bcm.edu	37	14	69727023	69727023	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr14:69727023G>A	ENST00000337827.4	+	1	343	c.16G>A	c.(16-18)Gcc>Acc	p.A6T	GALNT16_ENST00000448469.3_Missense_Mutation_p.A6T|RP11-363J20.2_ENST00000556316.1_lincRNA|GALNT16_ENST00000553669.1_Missense_Mutation_p.A6T|GALNT16_ENST00000554858.1_3'UTR	NM_001168368.1|NM_020692.2	NP_001161840.1|NP_065743.2	Q8N428	GLT16_HUMAN	polypeptide N-acetylgalactosaminyltransferase 16	6					protein glycosylation (GO:0006486)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)										GAAGATCCGCGCCAATGCCAT	0.697																																					p.A6T		Atlas-SNP	.											.	GALNT16	8	.	0			c.G16A						PASS	.						84.0	65.0	72.0					14																	69727023		2202	4300	6502	SO:0001583	missense	57452	exon1			ATCCGCGCCAATG	AB032956	CCDS32107.1	14q24.1	2014-03-13	2014-03-13	2013-01-25	ENSG00000100626	ENSG00000100626	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	23233	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 16"""	615132	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase-like 1"", ""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 16"""	GALNTL1		10574461, 22186971	Standard	NM_020692		Approved	KIAA1130, GalNAc-T16	uc010aqu.2	Q8N428	OTTHUMG00000171231	ENST00000337827.4:c.16G>A	14.37:g.69727023G>A	ENSP00000336729:p.Ala6Thr	Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	72	4	0.0555556	NM_001168368	Q4KMG3|Q58A55|Q9ULT9	Missense_Mutation	SNP	ENST00000337827.4	37	CCDS32107.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.722824	0.89298	.	.	ENSG00000100626	ENST00000337827;ENST00000448469;ENST00000553669	T;T;T	0.56941	0.56;0.56;0.43	4.35	2.45	0.29901	.	0.240329	0.32736	N	0.005718	T	0.37919	0.1021	L	0.43152	1.355	0.51012	D	0.999904	B;B	0.18166	0.014;0.026	B;B	0.06405	0.002;0.002	T	0.10870	-1.0611	10	0.13470	T	0.59	.	8.5824	0.33637	0.0828:0.0:0.7656:0.1517	.	6;6	Q8N428;Q58A55	GLTL1_HUMAN;.	T	6	ENSP00000336729:A6T;ENSP00000402970:A6T;ENSP00000451200:A6T	ENSP00000336729:A6T	A	+	1	0	GALNTL1	68796776	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	5.332000	0.65911	0.360000	0.24265	0.455000	0.32223	GCC	.	.	none		0.697	GALNT16-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412434.1	NM_001168368	
KIAA1377	57562	hgsc.bcm.edu	37	11	101834522	101834522	+	Missense_Mutation	SNP	C	C	T	rs370774279		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:101834522C>T	ENST00000263468.8	+	6	3026	c.2756C>T	c.(2755-2757)cCg>cTg	p.P919L	KIAA1377_ENST00000537689.1_Missense_Mutation_p.P720L	NM_020802.2	NP_065853.2	Q9P2H0	K1377_HUMAN	KIAA1377	919										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)		GAAAGTTATCCGTCTGTGACT	0.403																																					p.P919L		Atlas-SNP	.											KIAA1377,NS,carcinoma,-1,2	KIAA1377	111	2	0			c.C2756T						PASS	.	C	LEU/PRO	0,4406		0,0,2203	88.0	94.0	92.0		2756	0.1	0.0	11		92	1,8597	1.2+/-3.3	0,1,4298	no	missense	KIAA1377	NM_020802.2	98	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	benign	919/1118	101834522	1,13003	2203	4299	6502	SO:0001583	missense	57562	exon6			GTTATCCGTCTGT	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.2756C>T	11.37:g.101834522C>T	ENSP00000263468:p.Pro919Leu	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	134	65	0.485075	NM_020802	Q4G0U6	Missense_Mutation	SNP	ENST00000263468.8	37	CCDS31658.1	.	.	.	.	.	.	.	.	.	.	C	4.369	0.067932	0.08436	0.0	1.16E-4	ENSG00000110318	ENST00000263468;ENST00000537689	T;T	0.06068	3.35;3.35	5.51	0.134	0.14771	.	0.796339	0.11112	N	0.598499	T	0.05868	0.0153	L	0.47716	1.5	0.09310	N	1	B	0.32425	0.371	B	0.19148	0.024	T	0.33879	-0.9851	10	0.08599	T	0.76	3.4773	16.234	0.82361	0.3611:0.6389:0.0:0.0	.	919	Q9P2H0	K1377_HUMAN	L	919;720	ENSP00000263468:P919L;ENSP00000443184:P720L	ENSP00000263468:P919L	P	+	2	0	KIAA1377	101339732	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	0.508000	0.22692	0.123000	0.18342	-0.266000	0.10368	CCG	.	.	weak		0.403	KIAA1377-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394140.1	NM_020802	
MUC4	4585	hgsc.bcm.edu	37	3	195506746	195506746	+	Missense_Mutation	SNP	G	G	A	rs192522651		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:195506746G>A	ENST00000463781.3	-	2	12164	c.11705C>T	c.(11704-11706)gCc>gTc	p.A3902V	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A3902V	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.A3902V(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)		AAGAGGGGTGGCGTGACGTGT	0.597																																					p.A3902V		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,-1,4	MUC4	1505	4	2	Substitution - Missense(2)	kidney(2)	c.C11705T						scavenged	.						10.0	9.0	9.0					3																	195506746		528	1056	1584	SO:0001583	missense	4585	exon2			GGGGTGGCGTGAC	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.11705C>T	3.37:g.195506746G>A	ENSP00000417498:p.Ala3902Val	Somatic	61	3	0.0491803		WXS	Illumina HiSeq	Phase_I	64	7	0.109375	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	108	0.04945054945054945	8	0.016260162601626018	19	0.052486187845303865	56	0.0979020979020979	25	0.032981530343007916	g	7.407	0.633932	0.14322	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.33216	1.45;1.42	.	.	.	.	.	.	.	.	T	0.00384	0.0012	N	0.19112	0.55	0.09310	N	1	B	0.22909	0.077	B	0.09377	0.004	T	0.24048	-1.0171	7	.	.	.	.	2.8356	0.05513	3.0E-4:2.0E-4:0.5012:0.4983	.	3774	E7ESK3	.	V	3902	ENSP00000417498:A3902V;ENSP00000420243:A3902V	.	A	-	2	0	MUC4	196991525	0.001000	0.12720	0.003000	0.11579	0.003000	0.03518	0.241000	0.18065	0.064000	0.16427	0.064000	0.15345	GCC	G|0.951;A|0.049	0.049	strong		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
NAT10	55226	hgsc.bcm.edu	37	11	34144051	34144051	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:34144051C>T	ENST00000257829.3	+	9	1032	c.826C>T	c.(826-828)Ctg>Ttg	p.L276L	NAT10_ENST00000531159.2_Silent_p.L204L|NAT10_ENST00000527971.1_Intron	NM_024662.2	NP_078938	Q9H0A0	NAT10_HUMAN	N-acetyltransferase 10 (GCN5-related)	276						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)				TGAAAAGACCCTGAGGAGTAC	0.507																																					p.L276L		Atlas-SNP	.											NAT10,right_lower_lobe,carcinoma,-2,1	NAT10	78	1	0			c.C826T						scavenged	.						87.0	87.0	87.0					11																	34144051		2202	4298	6500	SO:0001819	synonymous_variant	55226	exon9			AAGACCCTGAGGA	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.826C>T	11.37:g.34144051C>T		Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	152	4	0.0263158	NM_024662	B4DFD5|E7ESU4|E9PMN9|Q86WK5|Q9C0F4|Q9HA61|Q9NVF2	Silent	SNP	ENST00000257829.3	37	CCDS7889.1																																																																																			.	.	none		0.507	NAT10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388693.1	NM_024662	
NHSL1	57224	hgsc.bcm.edu	37	6	138745866	138745866	+	Silent	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:138745866G>A	ENST00000427025.2	-	7	4813	c.4185C>T	c.(4183-4185)ggC>ggT	p.G1395G	NHSL1_ENST00000343505.5_Silent_p.G1391G	NM_020464.1	NP_065197.1	Q5SYE7	NHSL1_HUMAN	NHS-like 1	1395										breast(2)|endometrium(4)|kidney(1)	7						TTGGGGCAGCGCCGGTGGGTG	0.547																																					p.G1395G		Atlas-SNP	.											.	NHSL1	99	.	0			c.C4185T						PASS	.						32.0	33.0	33.0					6																	138745866		692	1591	2283	SO:0001819	synonymous_variant	57224	exon7			GGCAGCGCCGGTG	AB037778	CCDS47487.1, CCDS55063.1	6q23.3	2009-02-18	2004-10-07	2004-10-07	ENSG00000135540	ENSG00000135540			21021	protein-coding gene	gene with protein product			"""chromosome 6 open reading frame 63"""	C6orf63			Standard	NM_001144060		Approved	bA43P8.1, KIAA1357	uc011edp.2	Q5SYE7	OTTHUMG00000016321	ENST00000427025.2:c.4185C>T	6.37:g.138745866G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	85	37	0.435294	NM_020464	Q3ZCS5|Q5SYE8|Q9P2J0	Silent	SNP	ENST00000427025.2	37	CCDS55063.1																																																																																			.	.	none		0.547	NHSL1-001	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043700.2	XM_050421	
PCLO	27445	hgsc.bcm.edu	37	7	82784833	82784833	+	Missense_Mutation	SNP	T	T	G	rs71074627		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:82784833T>G	ENST00000333891.9	-	2	1461	c.1124A>C	c.(1123-1125)cAg>cCg	p.Q375P	PCLO_ENST00000423517.2_Missense_Mutation_p.Q375P	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						TGACCCAGTCTGCTGAGCTGG	0.587																																					p.Q375P		Atlas-SNP	.											Q9Y6V0-3,NS,carcinoma,+1,2	PCLO	1506	2	0			c.A1124C						scavenged	.						51.0	52.0	52.0					7																	82784833		1971	4166	6137	SO:0001583	missense	27445	exon2			CCAGTCTGCTGAG	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.1124A>C	7.37:g.82784833T>G	ENSP00000334319:p.Gln375Pro	Somatic	149	5	0.033557		WXS	Illumina HiSeq	Phase_I	167	9	0.0538922	NM_014510		Missense_Mutation	SNP	ENST00000333891.9	37	CCDS47630.1	.	.	.	.	.	.	.	.	.	.	T	3.271	-0.149197	0.06585	.	.	ENSG00000186472	ENST00000431819;ENST00000333891;ENST00000423517	T;T	0.18338	2.23;2.22	5.28	-1.91	0.07641	.	.	.	.	.	T	0.13243	0.0321	L	0.39898	1.24	0.22001	N	0.999425	B;B	0.02656	0.0;0.0	B;B	0.08055	0.003;0.003	T	0.32929	-0.9888	9	0.87932	D	0	.	8.2544	0.31746	0.2246:0.0:0.4622:0.3132	.	375;375	Q9Y6V0-5;Q9Y6V0-6	.;.	P	375	ENSP00000334319:Q375P;ENSP00000388393:Q375P	ENSP00000334319:Q375P	Q	-	2	0	PCLO	82622769	0.976000	0.34144	0.001000	0.08648	0.658000	0.38924	1.551000	0.36233	-0.136000	0.11475	-0.264000	0.10439	CAG	.	.	none		0.587	PCLO-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337368.5	NM_014510	
ADAR	103	hgsc.bcm.edu	37	1	154574477	154574477	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:154574477T>C	ENST00000368474.4	-	2	840	c.641A>G	c.(640-642)gAc>gGc	p.D214G	ADAR_ENST00000471068.1_5'Flank|ADAR_ENST00000292205.5_Missense_Mutation_p.D257G|ADAR_ENST00000368471.3_5'UTR	NM_001111.4|NM_015840.3|NM_015841.3	NP_001102|NP_056655.2|NP_056656.2	P55265	DSRAD_HUMAN	adenosine deaminase, RNA-specific	214					adenosine to inosine editing (GO:0006382)|base conversion or substitution editing (GO:0016553)|cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|miRNA loading onto RISC involved in gene silencing by miRNA (GO:0035280)|mRNA modification (GO:0016556)|mRNA processing (GO:0006397)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|negative regulation of viral genome replication (GO:0045071)|positive regulation of viral genome replication (GO:0045070)|pre-miRNA processing (GO:0031054)|protein export from nucleus (GO:0006611)|protein import into nucleus (GO:0006606)|response to interferon-alpha (GO:0035455)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|supraspliceosomal complex (GO:0044530)	DNA binding (GO:0003677)|double-stranded RNA adenosine deaminase activity (GO:0003726)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(9)|lung(20)|ovary(4)|prostate(2)|skin(2)	51	all_lung(78;2.22e-29)|Lung NSC(65;3.66e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.0997)		LUSC - Lung squamous cell carcinoma(543;0.185)	Colorectal(1306;0.115)		GCTATGACCGTCTGGTCTTAC	0.517																																					p.D214G		Atlas-SNP	.											ADAR,colon,carcinoma,-1,1	ADAR	113	1	0			c.A641G						scavenged	.						94.0	99.0	97.0					1																	154574477		2203	4300	6503	SO:0001583	missense	103	exon2			TGACCGTCTGGTC	BC038227	CCDS1071.1, CCDS30879.1	1q21.3	2012-03-22			ENSG00000160710	ENSG00000160710	3.5.4.-		225	protein-coding gene	gene with protein product		146920	"""interferon-induced protein 4"""	IFI4, G1P1		7972084	Standard	NM_001111		Approved	ADAR1	uc001ffh.3	P55265	OTTHUMG00000037261	ENST00000368474.4:c.641A>G	1.37:g.154574477T>C	ENSP00000357459:p.Asp214Gly	Somatic	150	0	0		WXS	Illumina HiSeq	Phase_I	282	5	0.0177305	NM_015840	B1AQQ9|B1AQR0|D3DV76|O15223|O43859|O43860|Q9BYM3|Q9BYM4	Missense_Mutation	SNP	ENST00000368474.4	37	CCDS1071.1	.	.	.	.	.	.	.	.	.	.	T	8.950	0.968007	0.18659	.	.	ENSG00000160710	ENST00000292205;ENST00000368474;ENST00000529168	T;T;T	0.13901	2.55;2.56;2.58	2.54	1.37	0.22104	.	1.816150	0.03411	N	0.204721	T	0.03178	0.0093	L	0.43923	1.385	0.09310	N	1	B;B;B	0.26672	0.001;0.001;0.156	B;B;B	0.26770	0.004;0.004;0.073	T	0.37220	-0.9715	10	0.11182	T	0.66	-6.1474	4.3941	0.11355	0.0:0.1664:0.0:0.8336	.	214;214;214	P55265-3;P55265-2;P55265	.;.;DSRAD_HUMAN	G	257;214;209	ENSP00000292205:D257G;ENSP00000357459:D214G;ENSP00000431794:D209G	ENSP00000292205:D257G	D	-	2	0	ADAR	152841101	0.000000	0.05858	0.002000	0.10522	0.028000	0.11728	-0.114000	0.10757	0.376000	0.24707	0.260000	0.18958	GAC	.	.	none		0.517	ADAR-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000090691.2	NM_001111	
SEC24C	9632	hgsc.bcm.edu	37	10	75528653	75528653	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:75528653G>A	ENST00000339365.2	+	17	2429	c.2267G>A	c.(2266-2268)cGg>cAg	p.R756Q	SEC24C_ENST00000496827.1_3'UTR|SEC24C_ENST00000345254.4_Missense_Mutation_p.R756Q|SEC24C_ENST00000540668.1_Missense_Mutation_p.R4Q|SEC24C_ENST00000535742.1_Missense_Mutation_p.R4Q|SEC24C_ENST00000411652.2_Missense_Mutation_p.R637Q	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	756					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)|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(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					ATGCGGGTCCGGACAAGCACT	0.567																																					p.R756Q		Atlas-SNP	.											SEC24C,colon,carcinoma,+1,1	SEC24C	86	1	0			c.G2267A						scavenged	.						163.0	130.0	141.0					10																	75528653		2203	4300	6503	SO:0001583	missense	9632	exon16			GGGTCCGGACAAG	D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"""SEC24 (S. cerevisiae) related gene family, member C"", ""SEC24 family, member C (S. cerevisiae)"""			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.2267G>A	10.37:g.75528653G>A	ENSP00000343405:p.Arg756Gln	Somatic	211	1	0.00473934		WXS	Illumina HiSeq	Phase_I	231	3	0.012987	NM_198597	B4DZT4|Q8WV25	Missense_Mutation	SNP	ENST00000339365.2	37	CCDS7332.1	.	.	.	.	.	.	.	.	.	.	G	36	5.645599	0.96704	.	.	ENSG00000176986	ENST00000535742;ENST00000345254;ENST00000540668;ENST00000339365;ENST00000411652	T;T;T;T;T	0.54479	0.57;0.57;0.57;0.57;0.57	5.72	5.72	0.89469	Sec23/Sec24 beta-sandwich (1);	0.000000	0.85682	D	0.000000	D	0.83138	0.5189	H	0.97103	3.94	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.985;0.996;0.999	D	0.88326	0.2965	10	0.87932	D	0	-18.0683	19.8791	0.96888	0.0:0.0:1.0:0.0	.	637;756;756	E7EP00;G5EA31;P53992	.;.;SC24C_HUMAN	Q	4;756;4;756;637	ENSP00000446174:R4Q;ENSP00000321845:R756Q;ENSP00000445023:R4Q;ENSP00000343405:R756Q;ENSP00000402913:R637Q	ENSP00000343405:R756Q	R	+	2	0	SEC24C	75198659	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	9.869000	0.99810	2.706000	0.92434	0.467000	0.42956	CGG	.	.	none		0.567	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1		
MUC4	4585	hgsc.bcm.edu	37	3	195509374	195509374	+	Missense_Mutation	SNP	T	T	G	rs573840119	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:195509374T>G	ENST00000463781.3	-	2	9536	c.9077A>C	c.(9076-9078)cAt>cCt	p.H3026P	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.H3026P	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.H3026P(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)		GCTGGTGACATGAAGAGGGGT	0.582													.|||	717	0.143171	0.1808	0.1023	5008	,	,		10228	0.0486		0.2137	False		,,,				2504	0.1462				p.H3026P		Atlas-SNP	.											MUC4_ENST00000463781,extremity,malignant_melanoma,0,1	MUC4	1505	1	1	Substitution - Missense(1)	skin(1)	c.A9077C						scavenged	.						25.0	18.0	20.0					3																	195509374		655	1532	2187	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.9077A>C	3.37:g.195509374T>G	ENSP00000417498:p.His3026Pro	Somatic	115	19	0.165217		WXS	Illumina HiSeq	Phase_I	121	23	0.190083	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	7.939	0.742287	0.15642	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.28454	1.61;1.61	.	.	.	.	.	.	.	.	T	0.13030	0.0316	N	0.19112	0.55	0.26070	N	0.981239	P	0.42993	0.797	B	0.31337	0.128	T	0.12967	-1.0527	7	.	.	.	.	4.198	0.10452	0.0:0.0:0.0:1.0	.	2898	E7ESK3	.	P	3026	ENSP00000417498:H3026P;ENSP00000420243:H3026P	.	H	-	2	0	MUC4	196994153	0.006000	0.16342	0.030000	0.17652	0.000000	0.00434	-0.139000	0.10358	0.402000	0.25451	0.000000	0.15137	CAT	.	.	weak		0.582	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
MUC17	140453	hgsc.bcm.edu	37	7	100678932	100678932	+	Missense_Mutation	SNP	A	A	G	rs114941002		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:100678932A>G	ENST00000306151.4	+	3	4299	c.4235A>G	c.(4234-4236)gAg>gGg	p.E1412G		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1412	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)					GTCAGTTCTGAGGCTAGCACC	0.502																																					p.E1412G		Atlas-SNP	.											MUC17,NS,carcinoma,+1,1	MUC17	804	1	0			c.A4235G						scavenged	.						272.0	277.0	275.0					7																	100678932		2203	4300	6503	SO:0001583	missense	140453	exon3			GTTCTGAGGCTAG	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.4235A>G	7.37:g.100678932A>G	ENSP00000302716:p.Glu1412Gly	Somatic	80	1	0.0125		WXS	Illumina HiSeq	Phase_I	95	7	0.0736842	NM_001040105	O14761|Q685J2|Q8TDH7	Missense_Mutation	SNP	ENST00000306151.4	37	CCDS34711.1	.	.	.	.	.	.	.	.	.	.	a	1.916	-0.449416	0.04572	.	.	ENSG00000169876	ENST00000306151	T	0.02737	4.18	0.838	-0.578	0.11724	.	.	.	.	.	T	0.01592	0.0051	N	0.17082	0.46	0.09310	N	1	B	0.27765	0.188	B	0.19946	0.027	T	0.48502	-0.9030	9	0.23891	T	0.37	.	3.0434	0.06146	0.6909:0.0:0.3091:0.0	.	1412	Q685J3	MUC17_HUMAN	G	1412	ENSP00000302716:E1412G	ENSP00000302716:E1412G	E	+	2	0	MUC17	100465652	0.000000	0.05858	0.000000	0.03702	0.021000	0.10359	-0.362000	0.07602	-0.153000	0.11137	0.113000	0.15668	GAG	.	.	weak		0.502	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
PRKG2	5593	hgsc.bcm.edu	37	4	82092909	82092909	+	Silent	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:82092909A>G	ENST00000395578.1	-	4	794	c.678T>C	c.(676-678)ccT>ccC	p.P226P	PRKG2_ENST00000264399.1_Silent_p.P226P|RP11-100N20.1_ENST00000505175.1_RNA|RP11-100N20.1_ENST00000512502.1_RNA|PRKG2_ENST00000418486.2_Silent_p.P226P			Q13237	KGP2_HUMAN	protein kinase, cGMP-dependent, type II	226					blood coagulation (GO:0007596)|circadian regulation of gene expression (GO:0032922)|nitric oxide metabolic process (GO:0046209)|protein phosphorylation (GO:0006468)|regulation of nitric-oxide synthase activity (GO:0050999)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|cGMP binding (GO:0030553)|cGMP-dependent protein kinase activity (GO:0004692)|protein kinase activity (GO:0004672)			NS(1)|breast(4)|central_nervous_system(2)|endometrium(3)|kidney(3)|large_intestine(7)|lung(14)|ovary(1)|skin(2)	37						TGGTCCACATAGGGATGGAGG	0.408																																					p.P226P		Atlas-SNP	.											.	PRKG2	195	.	0			c.T678C						PASS	.						97.0	99.0	98.0					4																	82092909		2203	4300	6503	SO:0001819	synonymous_variant	5593	exon3			CCACATAGGGATG	X94612	CCDS3589.1, CCDS75150.1	4q13.1-q21.1	2009-07-10			ENSG00000138669	ENSG00000138669	2.7.11.1		9416	protein-coding gene	gene with protein product		601591				7498513	Standard	XM_005263126		Approved	cGKII, PRKGR2	uc003hmh.2	Q13237	OTTHUMG00000130296	ENST00000395578.1:c.678T>C	4.37:g.82092909A>G		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	77	5	0.0649351	NM_006259	B4DMX3|E7EPE6|O00125|O60916	Silent	SNP	ENST00000395578.1	37	CCDS3589.1																																																																																			.	.	none		0.408	PRKG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252639.1	NM_006259	
EML5	161436	hgsc.bcm.edu	37	14	89206866	89206866	+	Silent	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr14:89206866A>G	ENST00000380664.5	-	5	575	c.576T>C	c.(574-576)ggT>ggC	p.G192G	EML5_ENST00000352093.5_Silent_p.G192G|EML5_ENST00000554922.1_Silent_p.G192G			Q05BV3	EMAL5_HUMAN	echinoderm microtubule associated protein like 5	192						cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|microtubule (GO:0005874)	catalytic activity (GO:0003824)			breast(1)|endometrium(3)|kidney(4)|large_intestine(17)|lung(14)|ovary(3)|pancreas(1)|prostate(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	50						CACCCGTCTTACCAAAGACAC	0.373																																					p.G192G		Atlas-SNP	.											EML5,NS,carcinoma,-2,1	EML5	141	1	0			c.T576C						scavenged	.						153.0	143.0	146.0					14																	89206866		1872	4115	5987	SO:0001819	synonymous_variant	161436	exon5			CGTCTTACCAAAG	AY357725	CCDS45148.1	14q31.3	2013-01-10				ENSG00000165521		"""WD repeat domain containing"""	18197	protein-coding gene	gene with protein product							Standard	NM_183387		Approved	HuEMAP-2, EMAP-2	uc021ryf.1	Q05BV3		ENST00000380664.5:c.576T>C	14.37:g.89206866A>G		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	189	4	0.021164	NM_183387	B9EK59|Q5H9N6|Q6UYC9|Q6ZRP3|Q6ZT03	Silent	SNP	ENST00000380664.5	37	CCDS45148.1																																																																																			.	.	none		0.373	EML5-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000410491.1		
ABLIM2	84448	hgsc.bcm.edu	37	4	8089920	8089920	+	Missense_Mutation	SNP	C	C	T	rs371815593		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:8089920C>T	ENST00000341937.5	-	4	494	c.430G>A	c.(430-432)Gcg>Acg	p.A144T	ABLIM2_ENST00000296372.8_Missense_Mutation_p.A144T|ABLIM2_ENST00000447017.2_Missense_Mutation_p.A144T|ABLIM2_ENST00000318888.4_5'UTR|ABLIM2_ENST00000545242.1_Missense_Mutation_p.A144T|ABLIM2_ENST00000361581.5_Missense_Mutation_p.A144T|ABLIM2_ENST00000407564.3_Missense_Mutation_p.A144T|ABLIM2_ENST00000361737.5_Missense_Mutation_p.A144T|ABLIM2_ENST00000505872.1_Missense_Mutation_p.A144T|ABLIM2_ENST00000546334.1_Missense_Mutation_p.A144T|ABLIM2_ENST00000428004.2_Missense_Mutation_p.A144T	NM_001130084.1	NP_001123556.1	Q6H8Q1	ABLM2_HUMAN	actin binding LIM protein family, member 2	144					actin cytoskeleton organization (GO:0030036)|axon guidance (GO:0007411)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|myofibril (GO:0030016)	zinc ion binding (GO:0008270)			NS(2)|central_nervous_system(1)|endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|pancreas(3)|prostate(2)|urinary_tract(1)	25						GACAGGTGCGCGCTGCTGCCC	0.627																																					p.A144T		Atlas-SNP	.											.	ABLIM2	59	.	0			c.G430A						PASS	.	C	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4108		0,0,2054	34.0	40.0	38.0		430,430,430,430,430,430,430	-1.5	0.0	4		38	2,8350		0,2,4174	no	missense,missense,missense,missense,missense,missense,missense	ABLIM2	NM_001130083.1,NM_001130084.1,NM_001130085.1,NM_001130086.1,NM_001130087.1,NM_001130088.1,NM_032432.4	58,58,58,58,58,58,58	0,2,6228	TT,TC,CC		0.0239,0.0,0.0161	benign,benign,benign,benign,benign,benign,benign	144/646,144/612,144/573,144/560,144/532,144/471,144/522	8089920	2,12458	2054	4176	6230	SO:0001583	missense	84448	exon4			GGTGCGCGCTGCT	AB058711	CCDS47011.1, CCDS47012.1, CCDS47013.1, CCDS47014.1, CCDS47015.1, CCDS47016.1, CCDS54719.1, CCDS68669.1	4p16.1	2012-05-16			ENSG00000163995	ENSG00000163995			19195	protein-coding gene	gene with protein product		612544	"""actin binding LIM protein 2"""				Standard	NM_001130083		Approved	KIAA1808	uc003gkj.4	Q6H8Q1	OTTHUMG00000057427	ENST00000341937.5:c.430G>A	4.37:g.8089920C>T	ENSP00000342813:p.Ala144Thr	Somatic	399	0	0		WXS	Illumina HiSeq	Phase_I	394	190	0.482233	NM_001130083	E9PF39|Q08E71|Q19VH0|Q6H8Q0|Q6NX73|Q8N3C5|Q8N9E9|Q8N9G2|Q96JL7	Missense_Mutation	SNP	ENST00000341937.5	37	CCDS47013.1	.	.	.	.	.	.	.	.	.	.	C	4.648	0.120390	0.08881	0.0	2.39E-4	ENSG00000163995	ENST00000361737;ENST00000400045;ENST00000296372;ENST00000545242;ENST00000546334;ENST00000447017;ENST00000341937;ENST00000361581;ENST00000407564;ENST00000505872;ENST00000428004	T;T;T;T;T;T;T;T;T;T	0.43294	0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95;0.95	4.02	-1.51	0.08664	.	0.721192	0.12976	U	0.423720	T	0.23289	0.0563	L	0.37850	1.14	0.09310	N	0.999998	B;B;B;B;B;B;B;B	0.15141	0.012;0.001;0.007;0.0;0.001;0.0;0.001;0.0	B;B;B;B;B;B;B;B	0.09377	0.003;0.002;0.004;0.002;0.002;0.0;0.0;0.0	T	0.16689	-1.0394	10	0.30078	T	0.28	.	0.3069	0.00282	0.2364:0.3013:0.2088:0.2534	.	149;144;144;144;144;144;144;144	B7Z6W4;Q6H8Q1-6;Q08E71;Q6H8Q1-2;Q6H8Q1-3;Q6H8Q1;Q19VH0;E9PF39	.;.;.;.;.;ABLM2_HUMAN;.;.	T	144	ENSP00000354887:A144T;ENSP00000296372:A144T;ENSP00000441255:A144T;ENSP00000444365:A144T;ENSP00000393511:A144T;ENSP00000342813:A144T;ENSP00000355003:A144T;ENSP00000384658:A144T;ENSP00000421283:A144T;ENSP00000389410:A144T	ENSP00000296372:A144T	A	-	1	0	ABLIM2	8140820	0.000000	0.05858	0.000000	0.03702	0.067000	0.16453	-0.120000	0.10660	-0.226000	0.09899	-0.263000	0.10527	GCG	.	.	weak		0.627	ABLIM2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000358862.2	NM_001130083	
USP6	9098	hgsc.bcm.edu	37	17	5049419	5049419	+	Missense_Mutation	SNP	C	C	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:5049419C>G	ENST00000574788.1	+	28	4499	c.2269C>G	c.(2269-2271)Ctt>Gtt	p.L757V	USP6_ENST00000332776.4_Missense_Mutation_p.L757V|USP6_ENST00000250066.6_Missense_Mutation_p.L757V|USP6_ENST00000304328.5_Missense_Mutation_p.L440V			P35125	UBP6_HUMAN	ubiquitin specific peptidase 6	757	USP.				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						TCTCTGTGGACTTAATTCAGA	0.358			T	"""COL1A1, CDH11, ZNF9, OMD"""	aneurysmal bone cysts																																p.L757V		Atlas-SNP	.		Dom	yes		17	17p13	9098	ubiquitin specific peptidase 6 (Tre-2 oncogene)		M	.	USP6	213	.	0			c.C2269G						PASS	.						149.0	147.0	148.0					17																	5049419		2203	4300	6503	SO:0001583	missense	9098	exon20			TGTGGACTTAATT	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.2269C>G	17.37:g.5049419C>G	ENSP00000460380:p.Leu757Val	Somatic	425	0	0		WXS	Illumina HiSeq	Phase_I	457	172	0.376368	NM_004505	Q15634|Q86WP6|Q8IWT4	Missense_Mutation	SNP	ENST00000574788.1	37	CCDS11069.2	.	.	.	.	.	.	.	.	.	.	C	8.818	0.936782	0.18206	.	.	ENSG00000129204	ENST00000332776;ENST00000250066;ENST00000304328	T;T;T	0.14144	2.53;2.94;2.55	2.55	2.55	0.30701	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.14614	0.0353	N	0.16833	0.445	0.50813	D	0.999894	D;D	0.71674	0.998;0.966	D;P	0.77557	0.99;0.908	T	0.23655	-1.0182	10	0.15499	T	0.54	.	5.4016	0.16299	0.0:0.8349:0.0:0.1651	.	440;757	P35125-2;P35125	.;UBP6_HUMAN	V	757;757;440	ENSP00000328010:L757V;ENSP00000250066:L757V;ENSP00000305473:L440V	ENSP00000250066:L757V	L	+	1	0	USP6	4990143	1.000000	0.71417	0.999000	0.59377	0.133000	0.20885	3.846000	0.55888	1.433000	0.47394	0.194000	0.17425	CTT	.	.	none		0.358	USP6-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438990.1	NM_004505	
FYB	2533	hgsc.bcm.edu	37	5	39135063	39135063	+	Silent	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:39135063T>C	ENST00000351578.6	-	8	1759	c.1569A>G	c.(1567-1569)aaA>aaG	p.K523K	FYB_ENST00000540520.1_Silent_p.K533K|FYB_ENST00000515010.1_Silent_p.K523K|FYB_ENST00000512982.1_Silent_p.K523K|FYB_ENST00000505428.1_Silent_p.K523K	NM_199335.3	NP_955367.1	O15117	FYB_HUMAN	FYN binding protein	523	SH3.				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)			TCTTTCCTCCTTTGACATCAC	0.403																																					p.K533K		Atlas-SNP	.											FYB_ENST00000540520,NS,carcinoma,-1,4	FYB	354	4	0			c.A1599G						scavenged	.						182.0	165.0	170.0					5																	39135063		1860	4117	5977	SO:0001819	synonymous_variant	2533	exon8			TCCTCCTTTGACA	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.1569A>G	5.37:g.39135063T>C		Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	296	3	0.0101351	NM_001243093	A8K2Y8|B4DLN2|E9PBV9|O00359|Q9NZI9	Silent	SNP	ENST00000351578.6	37	CCDS47200.1																																																																																			.	.	none		0.403	FYB-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000367098.1	NM_001465	
NBPF10	100132406	hgsc.bcm.edu	37	1	145299808	145299808	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:145299808T>C	ENST00000369338.1	+	2	234	c.44T>C	c.(43-45)aTg>aCg	p.M15T	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000342960.5_Missense_Mutation_p.M286T			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	286						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.M286T(1)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		AAGGCAGAGATGAACATTCTA	0.498																																					p.M286T		Atlas-SNP	.											NBPF10_ENST00000369338,extremity,malignant_melanoma,-1,3	NBPF10	221	3	1	Substitution - Missense(1)	skin(1)	c.T857C						scavenged	.						11.0	9.0	9.0					1																	145299808		690	1573	2263	SO:0001583	missense	100132406	exon6			CAGAGATGAACAT	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369338.1:c.44T>C	1.37:g.145299808T>C	ENSP00000358344:p.Met15Thr	Somatic	106	1	0.00943396		WXS	Illumina HiSeq	Phase_I	186	13	0.0698925	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369338.1	37		.	.	.	.	.	.	.	.	.	.	.	9.355	1.066495	0.20067	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960	T;T	0.03004	4.08;4.09	1.05	1.05	0.20165	.	.	.	.	.	T	0.01800	0.0057	M	0.61703	1.905	0.09310	N	1	B	0.18863	0.031	B	0.28638	0.092	T	0.42649	-0.9439	9	0.62326	D	0.03	.	4.3442	0.11124	0.0:0.0:0.0:1.0	.	15	Q86T75-2	.	T	211;15;15;286	ENSP00000358344:M15T;ENSP00000345684:M286T	ENSP00000345684:M286T	M	+	2	0	NBPF10	144011165	0.000000	0.05858	0.004000	0.12327	0.031000	0.12232	-1.183000	0.03079	0.731000	0.32448	0.234000	0.17832	ATG	.	.	none		0.498	NBPF10-003	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038552.1	NM_001039703	
ENPP3	5169	hgsc.bcm.edu	37	6	132043370	132043370	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:132043370T>C	ENST00000414305.1	+	19	1899	c.1571T>C	c.(1570-1572)cTt>cCt	p.L524P	ENPP3_ENST00000357639.3_Missense_Mutation_p.L524P|ENPP3_ENST00000358229.5_Missense_Mutation_p.L524P			O14638	ENPP3_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 3	524					immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|nucleoside triphosphate catabolic process (GO:0009143)|phosphate-containing compound metabolic process (GO:0006796)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)	metal ion binding (GO:0046872)|NADH pyrophosphatase activity (GO:0035529)|nucleic acid binding (GO:0003676)|nucleoside-triphosphate diphosphatase activity (GO:0047429)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)			NS(1)|breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(24)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	53	Breast(56;0.0753)			GBM - Glioblastoma multiforme(226;0.0252)|OV - Ovarian serous cystadenocarcinoma(155;0.0511)		AAAACAGATCTTCTACGCATT	0.418																																					p.L524P		Atlas-SNP	.											ENPP3,NS,carcinoma,+1,1	ENPP3	117	1	0			c.T1571C						scavenged	.						105.0	96.0	99.0					6																	132043370		2203	4300	6503	SO:0001583	missense	5169	exon18			CAGATCTTCTACG	AF005632	CCDS5148.1	6q22	2010-06-23			ENSG00000154269	ENSG00000154269	3.1.4.1, 3.6.1.9	"""CD molecules"""	3358	protein-coding gene	gene with protein product		602182		PDNP3		9344668	Standard	NM_005021		Approved	PD-IBETA, gp130RB13-6, B10, CD203c	uc003qcv.3	O14638	OTTHUMG00000016292	ENST00000414305.1:c.1571T>C	6.37:g.132043370T>C	ENSP00000406261:p.Leu524Pro	Somatic	75	0	0		WXS	Illumina HiSeq	Phase_I	112	3	0.0267857	NM_005021	Q5JTL3	Missense_Mutation	SNP	ENST00000414305.1	37	CCDS5148.1	.	.	.	.	.	.	.	.	.	.	T	20.7	4.027371	0.75390	.	.	ENSG00000154269	ENST00000414305;ENST00000357639;ENST00000358229	T;T;T	0.80566	-1.39;-1.39;-1.39	5.64	5.64	0.86602	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.095606	0.43919	D	0.000501	D	0.91382	0.7281	H	0.94847	3.59	0.80722	D	1	D	0.89917	1.0	D	0.72338	0.977	D	0.93673	0.6992	10	0.87932	D	0	-24.1597	15.8281	0.78730	0.0:0.0:0.0:1.0	.	524	O14638	ENPP3_HUMAN	P	524	ENSP00000406261:L524P;ENSP00000350265:L524P;ENSP00000350964:L524P	ENSP00000350265:L524P	L	+	2	0	ENPP3	132085063	1.000000	0.71417	1.000000	0.80357	0.940000	0.58332	6.441000	0.73439	2.279000	0.76181	0.528000	0.53228	CTT	.	.	none		0.418	ENPP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043627.2		
STXBP5	134957	hgsc.bcm.edu	37	6	147612247	147612247	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:147612247G>T	ENST00000321680.6	+	9	856	c.856G>T	c.(856-858)Ggg>Tgg	p.G286W	STXBP5_ENST00000546097.1_Missense_Mutation_p.G286W|STXBP5_ENST00000367481.3_Missense_Mutation_p.G286W|STXBP5_ENST00000367480.3_Missense_Mutation_p.G286W|STXBP5_ENST00000179882.6_5'UTR	NM_001127715.2	NP_001121187.1	Q5T5C0	STXB5_HUMAN	syntaxin binding protein 5 (tomosyn)	286					exocytosis (GO:0006887)|negative regulation of exocytosis (GO:0045920)|positive regulation of exocytosis (GO:0045921)|protein transport (GO:0015031)|regulation of blood coagulation (GO:0030193)|regulation of gene expression (GO:0010468)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|synapse (GO:0045202)	syntaxin-1 binding (GO:0017075)			breast(2)|endometrium(4)|kidney(3)|large_intestine(6)|lung(21)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	42		Ovarian(120;0.0164)		OV - Ovarian serous cystadenocarcinoma(155;1.77e-09)|GBM - Glioblastoma multiforme(68;0.0694)		GTTAAAGGATGGGAAGAAGCC	0.308																																					p.G286W		Atlas-SNP	.											.	STXBP5	163	.	0			c.G856T						PASS	.						93.0	89.0	90.0					6																	147612247		2203	4300	6503	SO:0001583	missense	134957	exon9			AAGGATGGGAAGA	AK055484	CCDS5211.1, CCDS47499.1	6q24.3	2013-01-10			ENSG00000164506	ENSG00000164506		"""WD repeat domain containing"""	19665	protein-coding gene	gene with protein product		604586				9620695, 14767561	Standard	NM_139244		Approved	tomosyn, LLGL3	uc010khz.2	Q5T5C0	OTTHUMG00000015766	ENST00000321680.6:c.856G>T	6.37:g.147612247G>T	ENSP00000321826:p.Gly286Trp	Somatic	114	0	0		WXS	Illumina HiSeq	Phase_I	97	45	0.463918	NM_139244	Q14DF3|Q5T5C1|Q5T5C2|Q8NBG8|Q96NG9	Missense_Mutation	SNP	ENST00000321680.6	37	CCDS47499.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.511125	0.85389	.	.	ENSG00000164506	ENST00000367481;ENST00000546097;ENST00000321680;ENST00000367480	T;D;T;T	0.86366	2.45;-2.11;2.44;2.56	5.35	5.35	0.76521	WD40 repeat-like-containing domain (1);Lethal giant larvae homologue 2 (1);	0.000000	0.85682	D	0.000000	D	0.92172	0.7518	M	0.65975	2.015	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.92395	0.5924	10	0.72032	D	0.01	.	19.0338	0.92969	0.0:0.0:1.0:0.0	.	286;286	Q5T5C0-2;Q5T5C0	.;STXB5_HUMAN	W	286	ENSP00000356451:G286W;ENSP00000441479:G286W;ENSP00000321826:G286W;ENSP00000356450:G286W	ENSP00000321826:G286W	G	+	1	0	STXBP5	147653940	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.580000	0.90784	2.656000	0.90262	0.650000	0.86243	GGG	.	.	none		0.308	STXBP5-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000042606.1		
AKR1C4	1109	hgsc.bcm.edu	37	10	5238850	5238850	+	Missense_Mutation	SNP	G	G	A	rs373855442		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:5238850G>A	ENST00000380448.1	+	3	273	c.20G>A	c.(19-21)cGt>cAt	p.R7H	AKR1CL1_ENST00000445191.1_Intron|U8_ENST00000516100.1_RNA|AKR1C4_ENST00000263126.1_Missense_Mutation_p.R7H			P17516	AK1C4_HUMAN	aldo-keto reductase family 1, member C4	7					androgen metabolic process (GO:0008209)|bile acid and bile salt transport (GO:0015721)|bile acid biosynthetic process (GO:0006699)|bile acid metabolic process (GO:0008206)|cellular response to jasmonic acid stimulus (GO:0071395)|daunorubicin metabolic process (GO:0044597)|doxorubicin metabolic process (GO:0044598)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	aldo-keto reductase (NADP) activity (GO:0004033)|androsterone dehydrogenase activity (GO:0047023)|bile acid transmembrane transporter activity (GO:0015125)|chlordecone reductase activity (GO:0047743)|electron carrier activity (GO:0009055)|oxidoreductase activity, acting on NAD(P)H, quinone or similar compound as acceptor (GO:0016655)|retinal dehydrogenase activity (GO:0001758)			NS(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|skin(2)|stomach(2)|urinary_tract(1)	18						AAATATCAGCGTGTAGAGCTA	0.408																																					p.R7H		Atlas-SNP	.											AKR1C4,NS,carcinoma,+1,3	AKR1C4	57	3	0			c.G20A						scavenged	.	G	HIS/ARG	1,4405	2.1+/-5.4	0,1,2202	253.0	205.0	221.0		20	-3.6	0.0	10		221	0,8600		0,0,4300	no	missense	AKR1C4	NM_001818.3	29	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	benign	7/324	5238850	1,13005	2203	4300	6503	SO:0001583	missense	1109	exon1			ATCAGCGTGTAGA	M33375	CCDS7064.1	10p15.1	2012-12-04	2012-12-04		ENSG00000198610	ENSG00000198610	1.1.1.225	"""Aldo-keto reductases"""	387	protein-coding gene	gene with protein product	"""chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4"""	600451	"""aldo-keto reductase family 1, member C4 (chlordecone reductase; 3-alpha hydroxysteroid dehydrogenase, type I; dihydrodiol dehydrogenase 4)"""	CHDR		7789999	Standard	NM_001818		Approved	DD4, HAKRA, C11, 3-alpha-HSD, CDR, MGC22581	uc001ihw.2	P17516	OTTHUMG00000017591	ENST00000380448.1:c.20G>A	10.37:g.5238850G>A	ENSP00000369814:p.Arg7His	Somatic	171	0	0		WXS	Illumina HiSeq	Phase_I	176	4	0.0227273	NM_001818	Q5T6A3|Q8WW84|Q9NS54	Missense_Mutation	SNP	ENST00000380448.1	37	CCDS7064.1	.	.	.	.	.	.	.	.	.	.	G	5.139	0.211236	0.09757	2.27E-4	0.0	ENSG00000198610	ENST00000380448;ENST00000263126;ENST00000397357	T;T	0.55930	0.49;0.49	2.92	-3.61	0.04556	NADP-dependent oxidoreductase domain (2);	1.662580	0.03590	N	0.231684	T	0.31327	0.0793	N	0.25485	0.75	0.09310	N	1	B	0.10296	0.003	B	0.06405	0.002	T	0.05784	-1.0864	10	0.14656	T	0.56	.	1.2306	0.01943	0.3178:0.15:0.3804:0.1518	.	7	P17516	AK1C4_HUMAN	H	7	ENSP00000369814:R7H;ENSP00000263126:R7H	ENSP00000263126:R7H	R	+	2	0	AKR1C4	5228850	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.805000	0.04530	-0.745000	0.04772	0.591000	0.81541	CGT	.	.	none		0.408	AKR1C4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046543.2	NM_001818	
PAPSS2	9060	hgsc.bcm.edu	37	10	89503202	89503202	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:89503202G>A	ENST00000361175.4	+	10	1649	c.1280G>A	c.(1279-1281)cGc>cAc	p.R427H	PAPSS2_ENST00000427144.2_Missense_Mutation_p.R431H|PAPSS2_ENST00000456849.1_Missense_Mutation_p.R432H	NM_004670.3	NP_004661.2	O95340	PAPS2_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 2	427					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|blood coagulation (GO:0007596)|bone development (GO:0060348)|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)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	20		Melanoma(5;0.019)|Colorectal(252;0.123)		UCEC - Uterine corpus endometrioid carcinoma (6;0.00164)|Colorectal(12;0.000323)|COAD - Colon adenocarcinoma(12;0.00124)		GACACTCGCCGCAGGCTCCTA	0.582																																					p.R432H		Atlas-SNP	.											PAPSS2,NS,carcinoma,0,1	PAPSS2	46	1	0			c.G1295A						scavenged	.						108.0	104.0	106.0					10																	89503202		2203	4300	6503	SO:0001583	missense	9060	exon11			CTCGCCGCAGGCT	AF091242	CCDS7385.1, CCDS44453.1	10q24	2008-02-07			ENSG00000198682	ENSG00000198682	2.7.7.4, 2.7.1.25		8604	protein-coding gene	gene with protein product		603005				9771708	Standard	NM_004670		Approved	ATPSK2	uc001kex.3	O95340	OTTHUMG00000018683	ENST00000361175.4:c.1280G>A	10.37:g.89503202G>A	ENSP00000354436:p.Arg427His	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	144	3	0.0208333	NM_001015880	Q9BZL2|Q9P0G6|Q9UHM1|Q9UKD3|Q9UP30	Missense_Mutation	SNP	ENST00000361175.4	37	CCDS7385.1	.	.	.	.	.	.	.	.	.	.	G	22.8	4.333777	0.81801	.	.	ENSG00000198682	ENST00000361175;ENST00000456849;ENST00000427144;ENST00000371981	T;T;T	0.31247	1.5;1.5;1.5	5.33	3.49	0.39957	Sulphate adenylyltransferase (2);Rossmann-like alpha/beta/alpha sandwich fold (1);	0.094954	0.85682	D	0.000000	T	0.52517	0.1739	M	0.76328	2.33	0.58432	D	0.999998	D;D	0.89917	0.998;1.0	D;D	0.79784	0.938;0.993	T	0.53194	-0.8473	10	0.52906	T	0.07	-19.4179	11.5618	0.50780	0.1428:0.0:0.8572:0.0	.	427;432	O95340;O95340-2	PAPS2_HUMAN;.	H	427;432;431;431	ENSP00000354436:R427H;ENSP00000406157:R432H;ENSP00000397123:R431H	ENSP00000354436:R427H	R	+	2	0	PAPSS2	89493182	1.000000	0.71417	0.027000	0.17364	0.993000	0.82548	9.257000	0.95545	0.826000	0.34661	0.561000	0.74099	CGC	.	.	none		0.582	PAPSS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049229.1		
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39253949	39253949	+	Missense_Mutation	SNP	T	T	A	rs200040006	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:39253949T>A	ENST00000333822.4	-	1	444	c.388A>T	c.(388-390)Agc>Tgc	p.S130C		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	130	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						ctggagatgctgcagctgggg	0.677													T|||	312	0.0623003	0.0787	0.0865	5008	,	,		15319	0.0278		0.0616	False		,,,				2504	0.0593				p.S130C		Atlas-SNP	.											KRTAP4-8,NS,carcinoma,0,4	KRTAP4-8	57	4	0			c.A388T						scavenged	.						4.0	6.0	5.0					17																	39253949		641	1513	2154	SO:0001583	missense	728224	exon1			AGATGCTGCAGCT	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.388A>T	17.37:g.39253949T>A	ENSP00000328444:p.Ser130Cys	Somatic	49	2	0.0408163		WXS	Illumina HiSeq	Phase_I	75	7	0.0933333	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	5.252	0.232015	0.09969	.	.	ENSG00000204880	ENST00000333822	T	0.00593	6.34	3.73	2.64	0.31445	.	.	.	.	.	T	0.00144	0.0004	N	0.00027	-2.645	0.24205	N	0.995495	B	0.02656	0.0	B	0.01281	0.0	T	0.37709	-0.9694	9	0.02654	T	1	.	7.9032	0.29746	0.8151:0.0:0.0:0.1849	.	130	Q9BYQ9	KRA48_HUMAN	C	130	ENSP00000328444:S130C	ENSP00000328444:S130C	S	-	1	0	KRTAP4-8	36507475	0.993000	0.37304	0.954000	0.39281	0.491000	0.33493	4.109000	0.57824	0.430000	0.26230	-0.595000	0.04109	AGC	.	.	weak		0.677	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
SSX2IP	117178	hgsc.bcm.edu	37	1	85116180	85116180	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:85116180G>A	ENST00000342203.3	-	13	1798	c.1535C>T	c.(1534-1536)tCg>tTg	p.S512L	SSX2IP_ENST00000605755.1_Missense_Mutation_p.S485L|SSX2IP_ENST00000370612.4_Missense_Mutation_p.S512L|SSX2IP_ENST00000437941.2_Missense_Mutation_p.S485L|SSX2IP_ENST00000603677.1_Missense_Mutation_p.S31L	NM_001166293.1|NM_001166294.1|NM_014021.3	NP_001159765.1|NP_001159766.1|NP_054740.3	Q9Y2D8	ADIP_HUMAN	synovial sarcoma, X breakpoint 2 interacting protein	512					cell adhesion (GO:0007155)|centrosome organization (GO:0051297)|regulation of cell motility (GO:2000145)|regulation of Rac protein signal transduction (GO:0035020)	cell leading edge (GO:0031252)|cell-cell adherens junction (GO:0005913)|centriolar satellite (GO:0034451)|nucleus (GO:0005634)|protein complex (GO:0043234)				endometrium(5)|kidney(1)|large_intestine(4)|lung(6)|ovary(2)|urinary_tract(1)	19				all cancers(265;0.0053)|Epithelial(280;0.0214)|OV - Ovarian serous cystadenocarcinoma(397;0.173)		CGGCTGCCTCGAGTGCACTAT	0.413																																					p.S512L		Atlas-SNP	.											SSX2IP,NS,carcinoma,+1,1	SSX2IP	53	1	0			c.C1535T						scavenged	.						164.0	179.0	174.0					1																	85116180		2203	4300	6503	SO:0001583	missense	117178	exon14			TGCCTCGAGTGCA		CCDS699.1, CCDS53337.1	1p22.3	2008-02-05			ENSG00000117155	ENSG00000117155			16509	protein-coding gene	gene with protein product		608690					Standard	NM_014021		Approved		uc001dkj.3	Q9Y2D8	OTTHUMG00000009926	ENST00000342203.3:c.1535C>T	1.37:g.85116180G>A	ENSP00000340279:p.Ser512Leu	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	103	2	0.0194175	NM_001166417	A8K8W0|B4DFE3|D3DT13|J3KR02|Q6P2P8|Q6ULS1|Q7L168|Q9UIX0	Missense_Mutation	SNP	ENST00000342203.3	37	CCDS699.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.687571	0.29962	.	.	ENSG00000117155	ENST00000342203;ENST00000437941;ENST00000370612	T;T	0.46819	0.86;0.86	5.25	4.27	0.50696	.	0.449637	0.23826	N	0.044191	T	0.26629	0.0651	L	0.54323	1.7	0.28729	N	0.902588	B;B;B	0.26975	0.165;0.051;0.041	B;B;B	0.22152	0.038;0.004;0.003	T	0.09840	-1.0656	10	0.45353	T	0.12	-1.2358	12.7402	0.57249	0.0:0.1653:0.8347:0.0	.	512;512;485	Q9Y2D8-2;Q9Y2D8;B4DFE3	.;ADIP_HUMAN;.	L	512;485;512	ENSP00000340279:S512L;ENSP00000412781:S485L	ENSP00000340279:S512L	S	-	2	0	SSX2IP	84888768	0.988000	0.35896	0.925000	0.36789	0.097000	0.18754	2.150000	0.42254	2.619000	0.88677	0.655000	0.94253	TCG	.	.	none		0.413	SSX2IP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027469.1	NM_014021	
ADAM21	8747	hgsc.bcm.edu	37	14	70924294	70924294	+	Silent	SNP	C	C	T	rs112060847		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr14:70924294C>T	ENST00000603540.1	+	2	336	c.78C>T	c.(76-78)tcC>tcT	p.S26S	RP11-486O13.4_ENST00000556646.1_lincRNA|ADAM21_ENST00000267499.3_Silent_p.S26S	NM_003813.3	NP_003804.2	Q9UKJ8	ADA21_HUMAN	ADAM metallopeptidase domain 21	26					binding of sperm to zona pellucida (GO:0007339)|multicellular organism reproduction (GO:0032504)|single fertilization (GO:0007338)	axon (GO:0030424)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(10)|lung(10)|pancreas(1)|prostate(1)|skin(2)|stomach(1)	31				all cancers(60;0.00326)|BRCA - Breast invasive adenocarcinoma(234;0.00646)|OV - Ovarian serous cystadenocarcinoma(108;0.0401)		TGTCTATTTCCGGCTACTGTC	0.542																																					p.S26S		Atlas-SNP	.											ADAM21_ENST00000267499,NS,malignant_melanoma,+1,4	ADAM21	181	4	0			c.C78T						scavenged	.						101.0	110.0	107.0					14																	70924294		2203	4300	6503	SO:0001819	synonymous_variant	8747	exon2			TATTTCCGGCTAC	AF029900	CCDS9804.1	14q24.1	2008-09-05	2005-08-18		ENSG00000139985	ENSG00000139985		"""ADAM metallopeptidase domain containing"""	200	protein-coding gene	gene with protein product		603713	"""a disintegrin and metalloproteinase domain 21"""			9469942	Standard	NM_003813		Approved	ADAM31	uc001xmd.3	Q9UKJ8		ENST00000603540.1:c.78C>T	14.37:g.70924294C>T		Somatic	210	4	0.0190476		WXS	Illumina HiSeq	Phase_I	243	7	0.0288066	NM_003813	O43507|Q2VPC6|Q32MR0	Silent	SNP	ENST00000603540.1	37	CCDS9804.1																																																																																			C|0.779;T|0.221	0.221	strong		0.542	ADAM21-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413008.3		
HCAR3	8843	hgsc.bcm.edu	37	12	123200477	123200477	+	Missense_Mutation	SNP	G	G	A	rs562598836		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:123200477G>A	ENST00000528880.2	-	1	962	c.808C>T	c.(808-810)Cgc>Tgc	p.R270C	HCAR1_ENST00000356987.2_Intron|RP11-324E6.6_ENST00000543611.1_lincRNA	NM_006018.2	NP_006009.2	P49019	HCAR3_HUMAN	hydroxycarboxylic acid receptor 3	270					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)			endometrium(1)|large_intestine(1)|lung(5)|ovary(1)|skin(1)	9					Niacin(DB00627)	TCCACCGAGCGGTACACTTCA	0.547													g|||	1	0.000199681	0.0	0.0014	5008	,	,		17943	0.0		0.0	False		,,,				2504	0.0				p.R270C		Atlas-SNP	.											.	HCAR3	49	.	0			c.C808T						PASS	.						14.0	17.0	16.0					12																	123200477		2072	4240	6312	SO:0001583	missense	8843	exon1			CCGAGCGGTACAC	D10923	CCDS53842.1	12q24.31	2012-08-08	2011-05-30	2011-05-30		ENSG00000255398		"""GPCR / Class A : Hydroxy-carboxylic acid receptors"""	16824	protein-coding gene	gene with protein product		606039	"""G protein-coupled receptor 109B"""	GPR109B		7505609, 9205127, 18983141, 21454438	Standard	NM_006018		Approved	HCA3, HM74	uc001ucy.4	P49019		ENST00000528880.2:c.808C>T	12.37:g.123200477G>A	ENSP00000436714:p.Arg270Cys	Somatic	118	0	0		WXS	Illumina HiSeq	Phase_I	148	20	0.135135	NM_006018	A8K4G5|B2R830|E9PI97|Q8NGE4	Missense_Mutation	SNP	ENST00000528880.2	37	CCDS53842.1	.	.	.	.	.	.	.	.	.	.	g	12.25	1.881324	0.33255	.	.	ENSG00000255398	ENST00000528880	T	0.37584	1.19	3.26	2.01	0.26516	.	.	.	.	.	T	0.47097	0.1427	L	0.60067	1.865	0.09310	N	1	D	0.57899	0.981	P	0.59595	0.86	T	0.27938	-1.0059	9	0.66056	D	0.02	.	6.4754	0.22033	0.2217:0.0:0.7783:0.0	.	270	E9PI97	.	C	270	ENSP00000436714:R270C	ENSP00000436714:R270C	R	-	1	0	HCAR3	121766430	0.000000	0.05858	0.023000	0.16930	0.275000	0.26752	-0.123000	0.10611	0.206000	0.20587	0.184000	0.17185	CGC	.	.	weak		0.547	HCAR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387549.2	NM_006018	
RAPGEF6	51735	hgsc.bcm.edu	37	5	130764633	130764633	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:130764633T>C	ENST00000509018.1	-	27	4947	c.4742A>G	c.(4741-4743)aAa>aGa	p.K1581R	CTC-432M15.3_ENST00000514667.1_Missense_Mutation_p.K1631R|RAPGEF6_ENST00000296859.6_Missense_Mutation_p.K1589R|RAPGEF6_ENST00000507093.1_Intron|RAPGEF6_ENST00000307984.5_Intron	NM_001164386.1|NM_016340.5	NP_001157858.1|NP_057424.3	Q8TEU7	RPGF6_HUMAN	Rap guanine nucleotide exchange factor (GEF) 6	1581					positive regulation of GTPase activity (GO:0043547)|Ras protein signal transduction (GO:0007265)|regulation of GTPase activity (GO:0043087)|regulation of small GTPase mediated signal transduction (GO:0051056)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTP-dependent protein binding (GO:0030742)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)			breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(7)|lung(10)|ovary(3)|skin(1)|stomach(1)	31			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	Lung(113;0.0721)		ATCTCCTAGTTTAGGATGGAA	0.443																																					p.K1589R	Melanoma(168;435 1955 13113 13877 23213)	Atlas-SNP	.											RAPGEF6_ENST00000509018,NS,carcinoma,-1,1	RAPGEF6	361	1	0			c.A4766G						scavenged	.						125.0	118.0	120.0					5																	130764633		2203	4300	6503	SO:0001583	missense	51735	exon28			CCTAGTTTAGGAT	AF117947	CCDS34225.1, CCDS54897.1, CCDS54898.1, CCDS54899.1, CCDS54900.1	5q31.1	2008-02-05	2004-03-01	2004-03-02	ENSG00000158987	ENSG00000158987			20655	protein-coding gene	gene with protein product		610499	"""PDZ domain containing guanine nucleotide exchange factor (GEF) 2"""	PDZGEF2		11524421, 12095257	Standard	NM_016340		Approved	RA-GEF-2, PDZ-GEF2	uc010jdi.2	Q8TEU7	OTTHUMG00000162683	ENST00000509018.1:c.4742A>G	5.37:g.130764633T>C	ENSP00000421684:p.Lys1581Arg	Somatic	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	168	2	0.0119048	NM_001164386	A3KN82|A5PLL6|B7ZML2|E9PDV7|Q8NI21|Q8TEU6|Q96PC1	Missense_Mutation	SNP	ENST00000509018.1	37	CCDS34225.1	.	.	.	.	.	.	.	.	.	.	T	2.691	-0.273241	0.05716	.	.	ENSG00000158987;ENSG00000158987;ENSG00000217128	ENST00000509018;ENST00000296859;ENST00000514667	T;T;T	0.20881	2.04;2.04;2.12	4.8	2.34	0.29019	.	0.340605	0.28803	N	0.014094	T	0.10165	0.0249	L	0.27053	0.805	0.44181	D	0.996998	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.24657	-1.0154	10	0.02654	T	1	.	6.1666	0.20394	0.0:0.149:0.1364:0.7146	.	1589;1631;1581	B7ZML2;E9PCH4;Q8TEU7	.;.;RPGF6_HUMAN	R	1581;1589;1631	ENSP00000421684:K1581R;ENSP00000296859:K1589R;ENSP00000426948:K1631R	ENSP00000426948:K1631R	K	-	2	0	RAPGEF6;FNIP1	130792532	0.979000	0.34478	0.804000	0.32291	0.534000	0.34807	1.341000	0.33907	0.329000	0.23460	0.533000	0.62120	AAA	.	.	none		0.443	RAPGEF6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000370059.1	NM_016340	
LOXHD1	125336	hgsc.bcm.edu	37	18	44140108	44140108	+	Missense_Mutation	SNP	C	C	T	rs374290761		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr18:44140108C>T	ENST00000398722.4	-	12	2164	c.2165G>A	c.(2164-2166)cGg>cAg	p.R722Q	LOXHD1_ENST00000536736.1_Missense_Mutation_p.R1000Q|LOXHD1_ENST00000582408.1_5'Flank|LOXHD1_ENST00000300591.6_5'Flank|LOXHD1_ENST00000441893.2_5'Flank|LOXHD1_ENST00000441551.2_Intron			Q8IVV2	LOXH1_HUMAN	lipoxygenase homology domains 1	722	Glu-rich.				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						CTCCTTGCCCCGGGCCAGCCA	0.637													C|||	1	0.000199681	0.0	0.0	5008	,	,		13228	0.001		0.0	False		,,,				2504	0.0				p.R1000Q		Atlas-SNP	.											LOXHD1_ENST00000398722,colon,carcinoma,-1,2	LOXHD1	367	2	0			c.G2999A						scavenged	.						41.0	44.0	43.0					18																	44140108		692	1591	2283	SO:0001583	missense	125336	exon19			TTGCCCCGGGCCA	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.2165G>A	18.37:g.44140108C>T	ENSP00000381707:p.Arg722Gln	Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	153	4	0.0261438	NM_144612	B7WNN3|B7WNT1|B7WPI9|Q6ZRY7|Q86WW9|Q96DL7	Missense_Mutation	SNP	ENST00000398722.4	37		.	.	.	.	.	.	.	.	.	.	C	14.14	2.447163	0.43429	.	.	ENSG00000167210	ENST00000398722;ENST00000536736;ENST00000335730	T;T	0.06449	3.35;3.3	5.24	3.32	0.38043	.	0.213034	0.45126	N	0.000391	T	0.05227	0.0139	L	0.42245	1.32	0.80722	D	1	B;P	0.41265	0.417;0.744	B;B	0.30401	0.074;0.115	T	0.40553	-0.9557	10	0.54805	T	0.06	.	9.5071	0.39053	0.0:0.7037:0.1333:0.163	.	1000;722	F5GZB4;Q8IVV2-2	.;.	Q	722;1000;722	ENSP00000381707:R722Q;ENSP00000444586:R1000Q	ENSP00000338222:R722Q	R	-	2	0	LOXHD1	42394106	0.069000	0.21087	1.000000	0.80357	0.977000	0.68977	0.353000	0.20130	1.212000	0.43366	0.448000	0.29417	CGG	.	.	alt		0.637	LOXHD1-201	KNOWN	basic	protein_coding	protein_coding		NM_144612	
GPR56	9289	hgsc.bcm.edu	37	16	57691387	57691387	+	Missense_Mutation	SNP	G	G	A	rs147479620	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:57691387G>A	ENST00000388812.4	+	10	1710	c.1270G>A	c.(1270-1272)Gcc>Acc	p.A424T	GPR56_ENST00000568909.1_Missense_Mutation_p.A424T|GPR56_ENST00000538815.1_Missense_Mutation_p.A424T|GPR56_ENST00000456916.1_Missense_Mutation_p.A424T|GPR56_ENST00000562631.1_Missense_Mutation_p.A424T|GPR56_ENST00000388813.5_Missense_Mutation_p.A424T|GPR56_ENST00000540164.2_Missense_Mutation_p.A424T|GPR56_ENST00000379696.3_Missense_Mutation_p.A424T|GPR56_ENST00000544297.1_Missense_Mutation_p.A249T|GPR56_ENST00000568908.1_Missense_Mutation_p.A424T|GPR56_ENST00000379694.4_Missense_Mutation_p.A254T|GPR56_ENST00000567835.1_Missense_Mutation_p.A424T|GPR56_ENST00000562558.1_Missense_Mutation_p.A424T			Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56	424					angiogenesis (GO:0001525)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cerebral cortex radial glia guided migration (GO:0021801)|G-protein coupled receptor signaling pathway (GO:0007186)|layer formation in cerebral cortex (GO:0021819)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell adhesion (GO:0045785)|positive regulation of Rho protein signal transduction (GO:0035025)|protein kinase C signaling (GO:0070528)|Rho protein signal transduction (GO:0007266)|vascular endothelial growth factor production (GO:0010573)	extracellular vesicular exosome (GO:0070062)|glial limiting end-foot (GO:0097451)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	15						CACCATTGCCGCCTACCTCTG	0.647													G|||	2	0.000399361	0.0	0.0	5008	,	,		13233	0.0		0.002	False		,,,				2504	0.0				p.A429T		Atlas-SNP	.											.	GPR56	44	.	0			c.G1285A						PASS	.	G	THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA,THR/ALA	0,4396		0,0,2198	153.0	137.0	142.0		1270,1270,1270,1285,1270,1270,1270,1270	1.7	1.0	16	dbSNP_134	142	9,8591	7.1+/-27.0	0,9,4291	yes	missense,missense,missense,missense,missense,missense,missense,missense	GPR56	NM_001145770.1,NM_001145771.1,NM_001145772.1,NM_001145773.1,NM_001145774.1,NM_005682.5,NM_201524.2,NM_201525.2	58,58,58,58,58,58,58,58	0,9,6489	AA,AG,GG		0.1047,0.0,0.0693	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	424/688,424/694,424/688,429/693,424/688,424/694,424/688,424/688	57691387	9,12987	2198	4300	6498	SO:0001583	missense	9289	exon10			ATTGCCGCCTACC	AJ011001	CCDS32460.1, CCDS32461.1, CCDS73893.1	16q13	2014-08-08				ENSG00000205336		"""-"", ""GPCR / Class B : Orphans"""	4512	protein-coding gene	gene with protein product		604110				10049584, 10100861	Standard	XM_005256237		Approved	TM7LN4, TM7XN1	uc002emb.2	Q9Y653		ENST00000388812.4:c.1270G>A	16.37:g.57691387G>A	ENSP00000373464:p.Ala424Thr	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	24	20	0.833333	NM_001145773	A6NIT7|A6NJV9|B0M0K4|B4DR54|O95966|Q6ZMP1|Q8NGB3|Q96HB4	Missense_Mutation	SNP	ENST00000388812.4	37	CCDS32460.1	1	4.578754578754579E-4	0	0.0	0	0.0	0	0.0	1	0.0013192612137203166	G	14.17	2.455466	0.43634	0.0	0.001047	ENSG00000205336	ENST00000388813;ENST00000388812;ENST00000538815;ENST00000456916;ENST00000540164;ENST00000544297;ENST00000379694;ENST00000379696	T;T;T;T;T;T;T;T	0.47177	1.13;0.85;1.13;0.85;1.13;0.85;0.85;0.85	5.11	1.66	0.24008	GPCR, family 2-like (1);	0.474781	0.19007	N	0.125183	T	0.15522	0.0374	N	0.02391	-0.57	0.29960	N	0.819489	P;P;B;P;P	0.49783	0.911;0.928;0.37;0.91;0.928	B;B;B;B;B	0.40534	0.224;0.332;0.04;0.264;0.332	T	0.07385	-1.0775	10	0.13470	T	0.59	.	3.5997	0.08020	0.2112:0.0:0.4261:0.3628	.	249;429;424;424;254	F5H144;B4DR54;Q9Y653-2;Q9Y653;E7ENB2	.;.;.;GPR56_HUMAN;.	T	424;424;424;424;424;249;254;424	ENSP00000373465:A424T;ENSP00000373464:A424T;ENSP00000444415:A424T;ENSP00000398034:A424T;ENSP00000444911:A424T;ENSP00000438006:A249T;ENSP00000369016:A254T;ENSP00000369018:A424T	ENSP00000369016:A254T	A	+	1	0	GPR56	56248888	0.879000	0.30193	0.974000	0.42286	0.663000	0.39108	1.354000	0.34056	1.142000	0.42291	0.491000	0.48974	GCC	G|0.999;A|0.001	0.001	strong		0.647	GPR56-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433436.3		
MAGEL2	54551	hgsc.bcm.edu	37	15	23890645	23890645	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:23890645G>A	ENST00000532292.1	-	1	530	c.436C>T	c.(436-438)Cgc>Tgc	p.R146C		NM_019066.4	NP_061939.3	Q9UJ55	MAGL2_HUMAN	MAGE-like 2	29					Arp2/3 complex-mediated actin nucleation (GO:0034314)|protein K63-linked ubiquitination (GO:0070534)|retrograde transport, endosome to Golgi (GO:0042147)	endosome (GO:0005768)	ubiquitin-protein transferase activity (GO:0004842)			breast(1)|endometrium(1)|large_intestine(2)|lung(2)|upper_aerodigestive_tract(1)	7		all_cancers(20;1.78e-24)|all_epithelial(15;7.75e-22)|Lung NSC(15;2.96e-18)|all_lung(15;2.8e-17)|Breast(32;0.000625)|Colorectal(260;0.14)		all cancers(64;1.84e-06)|Epithelial(43;1.2e-05)|BRCA - Breast invasive adenocarcinoma(123;0.00177)		AAGATCATGCGGTCTTTTGAA	0.602																																					p.R749C		Atlas-SNP	.											MAGEL2_ENST00000532292,colon,carcinoma,0,2	MAGEL2	108	2	0			c.C2245T						PASS	.						33.0	37.0	35.0					15																	23890645		1971	4150	6121	SO:0001583	missense	54551	exon1			TCATGCGGTCTTT	AJ243531	CCDS73700.1	15q11-q12	2008-07-18				ENSG00000254585			6814	protein-coding gene	gene with protein product		605283		NDNL1		10556298	Standard	NM_019066		Approved	nM15	uc001ywj.4	Q9UJ55		ENST00000532292.1:c.436C>T	15.37:g.23890645G>A	ENSP00000433433:p.Arg146Cys	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	88	34	0.386364	NM_019066		Missense_Mutation	SNP	ENST00000532292.1	37																																																																																				.	.	none		0.602	MAGEL2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000395182.2	NM_019066	
BAZ1B	9031	hgsc.bcm.edu	37	7	72873950	72873950	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:72873950C>T	ENST00000339594.4	-	13	3686	c.3348G>A	c.(3346-3348)aaG>aaA	p.K1116K	BAZ1B_ENST00000404251.1_Silent_p.K1116K	NM_032408.3	NP_115784.1	Q9UIG0	BAZ1B_HUMAN	bromodomain adjacent to zinc finger domain, 1B	1116					cellular response to DNA damage stimulus (GO:0006974)|chromatin assembly or disassembly (GO:0006333)|chromatin-mediated maintenance of transcription (GO:0048096)|double-strand break repair (GO:0006302)|heart morphogenesis (GO:0003007)|histone phosphorylation (GO:0016572)|peptidyl-tyrosine phosphorylation (GO:0018108)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)|pericentric heterochromatin (GO:0005721)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|histone kinase activity (GO:0035173)|lysine-acetylated histone binding (GO:0070577)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein tyrosine kinase activity (GO:0004713)|vitamin D receptor activator activity (GO:0071884)|zinc ion binding (GO:0008270)			NS(1)|breast(5)|cervix(1)|endometrium(5)|kidney(5)|large_intestine(12)|lung(20)|ovary(5)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	61		Lung NSC(55;0.0659)|all_lung(88;0.152)				TTCTCTTTTGCTTGGGAGCCA	0.388																																					p.K1116K	Esophageal Squamous(112;1167 1561 21085 43672 48228)	Atlas-SNP	.											BAZ1B,NS,carcinoma,0,1	BAZ1B	147	1	0			c.G3348A						scavenged	.						156.0	150.0	152.0					7																	72873950		2203	4300	6503	SO:0001819	synonymous_variant	9031	exon13			CTTTTGCTTGGGA	AF084479	CCDS5549.1	7q11.23	2013-01-28			ENSG00000009954	ENSG00000009954		"""Zinc fingers, PHD-type"""	961	protein-coding gene	gene with protein product	"""Williams-Beuren syndrome chromosome region 9"", ""Williams-Beuren syndrome chromosome region 10"", ""transcription factor WSTF"""	605681		WBSCR9, WBSCR10		9858827, 9828126	Standard	NM_032408		Approved	WSTF	uc003tyc.3	Q9UIG0	OTTHUMG00000023847	ENST00000339594.4:c.3348G>A	7.37:g.72873950C>T		Somatic	176	1	0.00568182		WXS	Illumina HiSeq	Phase_I	149	3	0.0201342	NM_032408	B9EGK3|D3DXE9|O95039|O95247|O95277|Q6P1K4|Q86UJ6	Silent	SNP	ENST00000339594.4	37	CCDS5549.1																																																																																			.	.	none		0.388	BAZ1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252123.4	NM_032408	
GORAB	92344	hgsc.bcm.edu	37	1	170508593	170508593	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:170508593G>A	ENST00000367763.3	+	2	399	c.379G>A	c.(379-381)Ggc>Agc	p.G127S	GORAB_ENST00000367762.1_Missense_Mutation_p.G127S|GORAB_ENST00000465717.1_3'UTR	NM_152281.2	NP_689494.2	Q5T7V8	GORAB_HUMAN	golgin, RAB6-interacting	127						cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|nucleolus (GO:0005730)|nucleus (GO:0005634)				endometrium(2)|large_intestine(3)|liver(2)|lung(8)|prostate(1)|upper_aerodigestive_tract(1)	17						ACAACCACAGGGCATTGAAAG	0.453																																					p.G127S		Atlas-SNP	.											GORAB,NS,carcinoma,0,1	GORAB	41	1	0			c.G379A						scavenged	.						94.0	93.0	93.0					1																	170508593		2203	4300	6503	SO:0001583	missense	92344	exon2			CCACAGGGCATTG	AK021814	CCDS1289.1, CCDS53428.1	1q24.2	2009-02-13	2009-02-13	2009-02-13	ENSG00000120370	ENSG00000120370			25676	protein-coding gene	gene with protein product	"""gerodermia osteodysplastica"""	607983	"""SCY1-like 1 binding protein 1"""	SCYL1BP1		12783284, 15781263, 18997784	Standard	NM_152281		Approved	FLJ11752, NTKL-BP1, GO	uc001gha.2	Q5T7V8	OTTHUMG00000035228	ENST00000367763.3:c.379G>A	1.37:g.170508593G>A	ENSP00000356737:p.Gly127Ser	Somatic	108	1	0.00925926		WXS	Illumina HiSeq	Phase_I	217	3	0.0138249	NM_152281	Q49A22|Q6P1P9|Q9HAE6|Q9Y350	Missense_Mutation	SNP	ENST00000367763.3	37	CCDS1289.1	.	.	.	.	.	.	.	.	.	.	G	4.148	0.025892	0.08054	.	.	ENSG00000120370	ENST00000367763;ENST00000367762	T;T	0.62639	0.01;0.01	5.21	-0.74	0.11115	.	1.308880	0.04522	N	0.384690	T	0.29093	0.0723	L	0.50333	1.59	0.09310	N	1	B	0.16802	0.019	B	0.13407	0.009	T	0.07290	-1.0780	10	0.30078	T	0.28	-14.3446	3.1647	0.06531	0.2658:0.1187:0.4949:0.1206	.	127	Q5T7V8	GORAB_HUMAN	S	127	ENSP00000356737:G127S;ENSP00000356736:G127S	ENSP00000356736:G127S	G	+	1	0	GORAB	168775217	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.450000	0.21762	-0.028000	0.13850	-0.237000	0.12165	GGC	.	.	none		0.453	GORAB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000085226.1	NM_152281	
SYNE1	23345	hgsc.bcm.edu	37	6	152651974	152651974	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:152651974C>T	ENST00000367255.5	-	78	14447	c.13846G>A	c.(13846-13848)Gaa>Aaa	p.E4616K	SYNE1_ENST00000341594.5_Missense_Mutation_p.E4363K|SYNE1_ENST00000448038.1_Missense_Mutation_p.E4545K|SYNE1_ENST00000423061.1_Missense_Mutation_p.E4545K|SYNE1_ENST00000265368.4_Missense_Mutation_p.E4616K	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	4616					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)			NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		AGAAGATTTTCATATTCTGGA	0.383										HNSCC(10;0.0054)																											p.E4616K		Atlas-SNP	.											.	SYNE1	3227	.	0			c.G13846A						PASS	.						164.0	166.0	165.0					6																	152651974		2203	4300	6503	SO:0001583	missense	23345	exon78			GATTTTCATATTC	AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.13846G>A	6.37:g.152651974C>T	ENSP00000356224:p.Glu4616Lys	Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	74	34	0.459459	NM_182961	E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	C	19.37	3.815534	0.70912	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.53857	1.33;1.33;1.33;1.33;0.6	5.93	5.93	0.95920	.	0.000000	0.64402	D	0.000004	T	0.64832	0.2634	L	0.54323	1.7	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;0.997;0.997;0.999	T	0.59434	-0.7455	10	0.41790	T	0.15	.	20.3368	0.98748	0.0:1.0:0.0:0.0	.	4616;4616;4616;4545	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	K	4616;4545;4616;4545;4363	ENSP00000356224:E4616K;ENSP00000396024:E4545K;ENSP00000265368:E4616K;ENSP00000390975:E4545K;ENSP00000341887:E4363K	ENSP00000265368:E4616K	E	-	1	0	SYNE1	152693667	1.000000	0.71417	0.951000	0.38953	0.909000	0.53808	7.818000	0.86416	2.805000	0.96524	0.655000	0.94253	GAA	.	.	none		0.383	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2	NM_182961	
SPPL2C	162540	hgsc.bcm.edu	37	17	43923211	43923211	+	Silent	SNP	G	G	A	rs150961436		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:43923211G>A	ENST00000329196.5	+	1	956	c.939G>A	c.(937-939)ccG>ccA	p.P313P	MAPT-AS1_ENST00000579244.1_RNA|MAPT-AS1_ENST00000581125.1_RNA|MAPT-AS1_ENST00000579599.1_RNA	NM_175882.2	NP_787078.2	Q8IUH8	SPP2C_HUMAN	signal peptide peptidase like 2C	313						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)										AGAGGCCTCCGCACAGCCTCT	0.642													G|||	1	0.000199681	0.0008	0.0	5008	,	,		17815	0.0		0.0	False		,,,				2504	0.0				p.P313P		Atlas-SNP	.											IMP5,colon,carcinoma,+1,1	.	.	1	0			c.G939A						PASS	.	G		1,4405	2.1+/-5.4	0,1,2202	47.0	51.0	50.0		939	1.1	0.0	17	dbSNP_134	50	0,8600		0,0,4300	no	coding-synonymous	IMP5	NM_175882.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		313/685	43923211	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	162540	exon1			GCCTCCGCACAGC		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.939G>A	17.37:g.43923211G>A		Somatic	33	0	0		WXS	Illumina HiSeq	Phase_I	47	19	0.404255	NM_175882	Q8TC67|Q8WVZ6	Silent	SNP	ENST00000329196.5	37	CCDS32673.1																																																																																			G|1.000;A|0.000	0.000	weak		0.642	SPPL2C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441156.1	NM_175882	
KRTAP10-6	386674	hgsc.bcm.edu	37	21	46012354	46012354	+	Silent	SNP	G	G	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr21:46012354G>T	ENST00000400368.1	-	1	32	c.12C>A	c.(10-12)tcC>tcA	p.S4S	TSPEAR_ENST00000323084.4_Intron	NM_198688.2	NP_941961.2	P60371	KR106_HUMAN	keratin associated protein 10-6	4						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						CGGACATGGTGGACGCGGCCA	0.632																																					p.S4S		Atlas-SNP	.											KRTAP10-6,NS,carcinoma,-1,2	KRTAP10-6	57	2	0			c.C12A						scavenged	.						71.0	75.0	74.0					21																	46012354		2182	4282	6464	SO:0001819	synonymous_variant	386674	exon1			CATGGTGGACGCG	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.12C>A	21.37:g.46012354G>T		Somatic	169	0	0		WXS	Illumina HiSeq	Phase_I	241	3	0.0124481	NM_198688		Silent	SNP	ENST00000400368.1	37	CCDS42959.1																																																																																			.	.	none		0.632	KRTAP10-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128037.1	NM_198688	
LIMD2	80774	hgsc.bcm.edu	37	17	61775957	61775957	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:61775957C>T	ENST00000259006.3	-	5	497	c.339G>A	c.(337-339)gaG>gaA	p.E113E	LIMD2_ENST00000578061.1_Silent_p.E113E|LIMD2_ENST00000582055.1_Silent_p.E64E|LIMD2_ENST00000583211.1_Silent_p.E64E|LIMD2_ENST00000578993.1_Silent_p.E73E|LIMD2_ENST00000578402.1_Silent_p.E113E	NM_030576.3	NP_085053.1	Q9BT23	LIMD2_HUMAN	LIM domain containing 2	113							zinc ion binding (GO:0008270)			kidney(1)|lung(2)	3						GGGCCCAGAGCTCCTTGTGCT	0.637																																					p.E113E		Atlas-SNP	.											.	LIMD2	6	.	0			c.G339A						PASS	.						67.0	53.0	58.0					17																	61775957		2203	4300	6503	SO:0001819	synonymous_variant	80774	exon5			CCAGAGCTCCTTG	AK092301	CCDS11641.1	17q23.3	2006-02-03				ENSG00000136490			28142	protein-coding gene	gene with protein product						12477932	Standard	NM_030576		Approved	MGC10986	uc002jbj.4	Q9BT23		ENST00000259006.3:c.339G>A	17.37:g.61775957C>T		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	55	23	0.418182	NM_030576	D3DU16|Q96S91	Silent	SNP	ENST00000259006.3	37	CCDS11641.1																																																																																			.	.	none		0.637	LIMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443877.1	NM_030576	
ARMC9	80210	hgsc.bcm.edu	37	2	232099952	232099952	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:232099952T>C	ENST00000349938.4	+	8	832	c.638T>C	c.(637-639)cTc>cCc	p.L213P	ARMC9_ENST00000483477.1_3'UTR	NM_001271466.1|NM_025139.4	NP_001258395.1|NP_079415	Q7Z3E5	ARMC9_HUMAN	armadillo repeat containing 9	213						extracellular vesicular exosome (GO:0070062)				endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|lung(5)|ovary(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	22		Renal(207;0.0112)|all_lung(227;0.0744)|all_hematologic(139;0.0749)|Acute lymphoblastic leukemia(138;0.167)|Medulloblastoma(418;0.184)|Lung NSC(271;0.205)		Epithelial(121;1.43e-10)|LUSC - Lung squamous cell carcinoma(224;0.017)|Lung(119;0.0189)		TTGCAGCAGCTCCACCAGCAG	0.398																																					p.L213P		Atlas-SNP	.											.	ARMC9	129	.	0			c.T638C						PASS	.						57.0	57.0	57.0					2																	232099952		2203	4300	6503	SO:0001583	missense	80210	exon8			AGCAGCTCCACCA	BC004514	CCDS2484.1, CCDS74666.1	2q37.1	2013-02-14			ENSG00000135931	ENSG00000135931		"""Armadillo repeat containing"""	20730	protein-coding gene	gene with protein product						11347906	Standard	NM_025139		Approved	FLJ12584, KIAA1868, ARM, KU-MEL-1	uc031rrs.1	Q7Z3E5	OTTHUMG00000133229	ENST00000349938.4:c.638T>C	2.37:g.232099952T>C	ENSP00000258417:p.Leu213Pro	Somatic	61	0	0		WXS	Illumina HiSeq	Phase_I	88	4	0.0454545	NM_025139	Q53TI3|Q6P162|Q7L594|Q86WG2|Q96JF9|Q9H9R8	Missense_Mutation	SNP	ENST00000349938.4	37	CCDS2484.1	.	.	.	.	.	.	.	.	.	.	T	19.54	3.846960	0.71603	.	.	ENSG00000135931	ENST00000349938;ENST00000359743	T	0.19669	2.13	5.61	5.61	0.85477	.	0.000000	0.64402	D	0.000001	T	0.46814	0.1412	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.46665	-0.9175	10	0.66056	D	0.02	-21.8479	15.7937	0.78388	0.0:0.0:0.0:1.0	.	213	Q7Z3E5	ARMC9_HUMAN	P	213	ENSP00000258417:L213P	ENSP00000258417:L213P	L	+	2	0	ARMC9	231808196	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	5.588000	0.67517	2.126000	0.65437	0.533000	0.62120	CTC	.	.	none		0.398	ARMC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256966.3	NM_025139	
SNRPE	6635	hgsc.bcm.edu	37	1	203831348	203831348	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:203831348A>G	ENST00000414487.2	+	2	124	c.79A>G	c.(79-81)Aat>Gat	p.N27D	SNRPE_ENST00000483099.1_3'UTR|SNRPE_ENST00000367208.1_5'Flank	NM_003094.2	NP_003085.1	P62304	RUXE_HUMAN	small nuclear ribonucleoprotein polypeptide E	27					gene expression (GO:0010467)|hair cycle (GO:0042633)|histone mRNA metabolic process (GO:0008334)|mRNA 3'-end processing (GO:0031124)|mRNA splicing, via spliceosome (GO:0000398)|ncRNA metabolic process (GO:0034660)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|spliceosomal complex assembly (GO:0000245)|spliceosomal snRNP assembly (GO:0000387)|termination of RNA polymerase II transcription (GO:0006369)|transcription from RNA polymerase II promoter (GO:0006366)	catalytic step 2 spliceosome (GO:0071013)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|methylosome (GO:0034709)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|pICln-Sm protein complex (GO:0034715)|small nuclear ribonucleoprotein complex (GO:0030532)|SMN-Sm protein complex (GO:0034719)|spliceosomal complex (GO:0005681)|U1 snRNP (GO:0005685)|U12-type spliceosomal complex (GO:0005689)|U4 snRNP (GO:0005687)|U7 snRNP (GO:0005683)	RNA binding (GO:0003723)			breast(1)|large_intestine(2)|lung(1)|skin(1)	5	all_cancers(21;0.103)		BRCA - Breast invasive adenocarcinoma(75;0.109)			ATACTTACAAAATGTACGTAA	0.378																																					p.N27D	Ovarian(83;324 1318 17952 32395 39614)	Atlas-SNP	.											SNRPE,NS,carcinoma,0,2	SNRPE	8	2	0			c.A79G						scavenged	.						138.0	126.0	130.0					1																	203831348		2203	4300	6503	SO:0001583	missense	6635	exon2			TTACAAAATGTAC	M37716	CCDS30979.1	1q32	2011-10-11			ENSG00000182004	ENSG00000182004			11161	protein-coding gene	gene with protein product		128260				1835977, 2143747	Standard	NM_003094		Approved	Sm-E	uc001hai.3	P62304	OTTHUMG00000035985	ENST00000414487.2:c.79A>G	1.37:g.203831348A>G	ENSP00000400591:p.Asn27Asp	Somatic	155	0	0		WXS	Illumina HiSeq	Phase_I	214	3	0.0140187	NM_003094	B2R5B9|P08578|Q15498|Q5BKT2	Missense_Mutation	SNP	ENST00000414487.2	37	CCDS30979.1	.	.	.	.	.	.	.	.	.	.	A	25.6	4.654891	0.88056	.	.	ENSG00000182004	ENST00000414487	T	0.39406	1.08	5.25	5.25	0.73442	Like-Sm ribonucleoprotein (LSM) domain, eukaryotic/archaea-type (1);Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.000000	0.85682	D	0.000000	T	0.46795	0.1411	.	.	.	0.80722	D	1	P	0.45634	0.863	P	0.46685	0.524	T	0.45469	-0.9259	9	0.46703	T	0.11	.	15.103	0.72296	1.0:0.0:0.0:0.0	.	27	P62304	RUXE_HUMAN	D	27	ENSP00000400591:N27D	ENSP00000400591:N27D	N	+	1	0	SNRPE	202097971	1.000000	0.71417	1.000000	0.80357	0.969000	0.65631	7.260000	0.78391	2.109000	0.64355	0.402000	0.26972	AAT	.	.	none		0.378	SNRPE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087703.1	NM_003094	
SLC35G3	146861	hgsc.bcm.edu	37	17	33520358	33520358	+	Silent	SNP	A	A	G	rs74740601		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:33520358A>G	ENST00000297307.5	-	1	1054	c.969T>C	c.(967-969)atT>atC	p.I323I	RP11-799D4.2_ENST00000590144.1_RNA	NM_152462.2	NP_689675.1	Q8N808	S35G3_HUMAN	solute carrier family 35, member G3	323	EamA 2.					integral component of membrane (GO:0016021)		p.I323I(1)									TCTGGGCTGTAATGATGGCAA	0.547																																					p.I323I		Atlas-SNP	.											AMAC1,NS,carcinoma,0,1	.	.	1	1	Substitution - coding silent(1)	lung(1)	c.T969C						scavenged	.																																			SO:0001819	synonymous_variant	146861	exon1			GGCTGTAATGATG	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.969T>C	17.37:g.33520358A>G		Somatic	158	3	0.0189873		WXS	Illumina HiSeq	Phase_I	159	2	0.0125786	NM_152462	B9EGE9	Silent	SNP	ENST00000297307.5	37	CCDS11293.1																																																																																			.	.	weak		0.547	SLC35G3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256445.2	NM_152462	
RGPD3	653489	hgsc.bcm.edu	37	2	107049631	107049631	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:107049631C>T	ENST00000409886.3	-	16	2403	c.2316G>A	c.(2314-2316)gcG>gcA	p.A772A	RGPD3_ENST00000304514.7_Silent_p.A772A	NM_001144013.1	NP_001137485.1	A6NKT7	RGPD3_HUMAN	RANBP2-like and GRIP domain containing 3	772					protein targeting to Golgi (GO:0000042)			p.A772A(4)		breast(2)|central_nervous_system(1)|endometrium(50)|kidney(4)|lung(11)|ovary(1)|urinary_tract(2)	71						TTTCTGAATCCGCATTTCGCA	0.373																																					p.A772A		Atlas-SNP	.											RGPD3_ENST00000304514,bladder,carcinoma,0,6	RGPD3	316	6	4	Substitution - coding silent(4)	kidney(2)|endometrium(2)	c.G2316A						scavenged	.						81.0	68.0	72.0					2																	107049631		692	1590	2282	SO:0001819	synonymous_variant	653489	exon16			TGAATCCGCATTT		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.2316G>A	2.37:g.107049631C>T		Somatic	383	0	0		WXS	Illumina HiSeq	Phase_I	444	10	0.0225225	NM_001144013	B8ZZM4	Silent	SNP	ENST00000409886.3	37	CCDS46379.1																																																																																			.	.	weak		0.373	RGPD3-002	KNOWN	not_best_in_genome_evidence|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000329975.1	XM_929931	
TREML2	79865	hgsc.bcm.edu	37	6	41166095	41166095	+	Missense_Mutation	SNP	T	T	C	rs141238140		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:41166095T>C	ENST00000483722.1	-	2	313	c.128A>G	c.(127-129)tAt>tGt	p.Y43C		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	43	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					GTAGCCCTTATAGGAGCACTG	0.522																																					p.Y43C		Atlas-SNP	.											.	TREML2	41	.	0			c.A128G						PASS	.						158.0	166.0	163.0					6																	41166095		2203	4300	6503	SO:0001583	missense	79865	exon2			CCCTTATAGGAGC	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.128A>G	6.37:g.41166095T>C	ENSP00000418767:p.Tyr43Cys	Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	94	6	0.0638298	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	37	CCDS4853.2	.	.	.	.	.	.	.	.	.	.	.	14.49	2.551853	0.45487	.	.	ENSG00000112195	ENST00000483722	T	0.68624	-0.34	4.75	4.75	0.60458	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.49305	D	0.000157	T	0.81307	0.4795	M	0.93106	3.38	0.38602	D	0.95069	D	0.89917	1.0	D	0.97110	1.0	D	0.85899	0.1433	10	0.87932	D	0	-20.157	10.9548	0.47351	0.0:0.0:0.0:1.0	.	43	Q5T2D2	TRML2_HUMAN	C	43	ENSP00000418767:Y43C	ENSP00000418767:Y43C	Y	-	2	0	TREML2	41274073	1.000000	0.71417	1.000000	0.80357	0.352000	0.29268	1.308000	0.33528	1.901000	0.55032	0.460000	0.39030	TAT	.	.	weak		0.522	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807	
PAK2	5062	hgsc.bcm.edu	37	3	196529902	196529902	+	Missense_Mutation	SNP	G	G	C	rs201465227	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:196529902G>C	ENST00000327134.3	+	4	625	c.303G>C	c.(301-303)caG>caC	p.Q101H		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	101	Autoregulatory region. {ECO:0000250}.|GTPase-binding. {ECO:0000250}.				apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		TGCCAGAACAGTGGGCTCGAT	0.373																																					p.Q101H		Atlas-SNP	.											PAK2_ENST00000327134,colon,carcinoma,0,4	PAK2	113	4	0			c.G303C						scavenged	.						82.0	72.0	76.0					3																	196529902		2203	4300	6503	SO:0001583	missense	5062	exon4			AGAACAGTGGGCT	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"""S6/H4 kinase"""	605022	"""p21 (CDKN1A)-activated kinase 2"""			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.303G>C	3.37:g.196529902G>C	ENSP00000314067:p.Gln101His	Somatic	136	3	0.0220588		WXS	Illumina HiSeq	Phase_I	107	4	0.0373832	NM_002577	Q13154|Q6ISC3	Missense_Mutation	SNP	ENST00000327134.3	37	CCDS3321.1	.	.	.	.	.	.	.	.	.	.	G	17.81	3.480973	0.63849	.	.	ENSG00000180370	ENST00000327134	D	0.86366	-2.11	5.51	1.7	0.24286	PAK-box/P21-Rho-binding (2);	0.000000	0.85682	D	0.000000	D	0.92283	0.7552	M	0.91090	3.175	0.52099	D	0.999949	D	0.60160	0.987	P	0.61275	0.886	D	0.90843	0.4725	10	0.72032	D	0.01	.	6.8738	0.24135	0.4882:0.0:0.5118:0.0	.	101	Q13177	PAK2_HUMAN	H	101	ENSP00000314067:Q101H	ENSP00000314067:Q101H	Q	+	3	2	PAK2	198014299	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	0.826000	0.27407	0.705000	0.31890	-0.253000	0.11424	CAG	G|0.914;C|0.086	0.086	strong		0.373	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
FBN1	2200	hgsc.bcm.edu	37	15	48779516	48779516	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:48779516C>T	ENST00000316623.5	-	28	3911	c.3456G>A	c.(3454-3456)gcG>gcA	p.A1152A		NM_000138.4	NP_000129	P35555	FBN1_HUMAN	fibrillin 1	1152	EGF-like 17; 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)		TACCGATACACGCGGAGATGT	0.488																																					p.A1152A		Atlas-SNP	.											FBN1,colon,carcinoma,-1,1	FBN1	310	1	0			c.G3456A						scavenged	.						98.0	98.0	98.0					15																	48779516		2198	4296	6494	SO:0001819	synonymous_variant	2200	exon28			GATACACGCGGAG	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.3456G>A	15.37:g.48779516C>T		Somatic	96	1	0.0104167		WXS	Illumina HiSeq	Phase_I	71	38	0.535211	NM_000138	B2RUU0|D2JYH6|Q15972|Q75N87	Silent	SNP	ENST00000316623.5	37	CCDS32232.1																																																																																			.	.	none		0.488	FBN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417355.1		
RP1L1	94137	hgsc.bcm.edu	37	8	10469677	10469677	+	Missense_Mutation	SNP	C	C	T	rs374296911		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr8:10469677C>T	ENST00000382483.3	-	4	2154	c.1931G>A	c.(1930-1932)cGg>cAg	p.R644Q		NM_178857.5	NP_849188.4	Q8IWN7	RP1L1_HUMAN	retinitis pigmentosa 1-like 1	644					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)		TGCACTGGCCCGGCTTCTGTG	0.642																																					p.R644Q		Atlas-SNP	.											RP1L1,NS,carcinoma,-1,1	RP1L1	453	1	0			c.G1931A						scavenged	.	C	GLN/ARG	0,4186		0,0,2093	42.0	51.0	48.0		1931	-2.8	0.0	8		48	2,8424		0,2,4211	no	missense	RP1L1	NM_178857.5	43	0,2,6304	TT,TC,CC		0.0237,0.0,0.0159	probably-damaging	644/2401	10469677	2,12610	2093	4213	6306	SO:0001583	missense	94137	exon4			CTGGCCCGGCTTC	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.1931G>A	8.37:g.10469677C>T	ENSP00000371923:p.Arg644Gln	Somatic	150	1	0.00666667		WXS	Illumina HiSeq	Phase_I	73	2	0.0273973	NM_178857	Q86SQ1|Q8IWN8|Q8IWN9|Q8IWP0|Q8IWP1|Q8IWP2	Missense_Mutation	SNP	ENST00000382483.3	37	CCDS43708.1	.	.	.	.	.	.	.	.	.	.	C	8.317	0.823379	0.16678	0.0	2.37E-4	ENSG00000183638	ENST00000382483	T	0.04502	3.61	4.55	-2.77	0.05877	.	0.694155	0.10974	N	0.613478	T	0.02380	0.0073	L	0.29908	0.895	0.09310	N	1	P	0.35011	0.48	B	0.21151	0.033	T	0.41161	-0.9524	10	0.56958	D	0.05	-2.7183	0.9228	0.01318	0.2228:0.2855:0.2932:0.1986	.	644	A6NKC6	.	Q	644	ENSP00000371923:R644Q	ENSP00000371923:R644Q	R	-	2	0	RP1L1	10507087	0.000000	0.05858	0.001000	0.08648	0.043000	0.13939	-0.139000	0.10358	-0.211000	0.10124	0.455000	0.32223	CGG	.	.	weak		0.642	RP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375673.1		
CACTIN	58509	hgsc.bcm.edu	37	19	3612193	3612193	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:3612193G>A	ENST00000429344.2	-	10	2057	c.2005C>T	c.(2005-2007)Ccg>Tcg	p.P669S	CACTIN_ENST00000248420.5_Missense_Mutation_p.P669S|CACTIN-AS1_ENST00000592274.1_RNA|CACTIN_ENST00000221899.3_Missense_Mutation_p.P601S	NM_001080543.1	NP_001074012.1	Q8WUQ7	CATIN_HUMAN	cactin, spliceosome C complex subunit	669					cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|innate immune response (GO:0045087)|mRNA splicing, via spliceosome (GO:0000398)|multicellular organismal development (GO:0007275)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-8 production (GO:0032717)|negative regulation of lipopolysaccharide-mediated signaling pathway (GO:0031665)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of toll-like receptor signaling pathway (GO:0034122)|negative regulation of tumor necrosis factor production (GO:0032720)|negative regulation of type I interferon-mediated signaling pathway (GO:0060339)	catalytic step 2 spliceosome (GO:0071013)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)										ATCTTGGGCGGTGGGTTGTCA	0.587																																					p.P669S		Atlas-SNP	.											.	.	.	.	0			c.C2005T						PASS	.						139.0	156.0	150.0					19																	3612193		2166	4255	6421	SO:0001583	missense	58509	exon10			TGGGCGGTGGGTT	BC019848	CCDS45920.1	19p13.3	2012-06-08	2012-06-08	2012-06-08	ENSG00000105298	ENSG00000105298			29938	protein-coding gene	gene with protein product	"""NY REN 24 antigen"", ""functional spliceosome-associated protein c"", ""cactin homolog (Drosophila)"""		"""chromosome 19 open reading frame 29"""	C19orf29		8619474, 9110174, 21429463, 20829348	Standard	NM_001080543		Approved	NY-REN-24, fSAPc, cactin	uc002lyh.3	Q8WUQ7		ENST00000429344.2:c.2005C>T	19.37:g.3612193G>A	ENSP00000415078:p.Pro669Ser	Somatic	201	0	0		WXS	Illumina HiSeq	Phase_I	222	107	0.481982	NM_021231	A6NNA9|A9UL12|O75229|Q7LE08|Q9BTA6|Q9Y5A4	Missense_Mutation	SNP	ENST00000429344.2	37	CCDS45920.1	.	.	.	.	.	.	.	.	.	.	G	13.96	2.393353	0.42410	.	.	ENSG00000105298	ENST00000429344;ENST00000248420;ENST00000221899	.	.	.	4.2	2.06	0.26882	Cactin protein, cactus-binding domain, C-terminal (1);	0.120124	0.56097	D	0.000023	T	0.80226	0.4584	M	0.91300	3.195	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.998	T	0.80841	-0.1202	9	0.87932	D	0	.	9.1523	0.36971	0.1829:0.0:0.8171:0.0	.	669;669	Q8WUQ7-2;Q8WUQ7	.;CS029_HUMAN	S	669;669;601	.	ENSP00000221899:P601S	P	-	1	0	C19orf29	3563193	1.000000	0.71417	0.029000	0.17559	0.001000	0.01503	9.150000	0.94667	0.539000	0.28788	-0.148000	0.13756	CCG	.	.	none		0.587	CACTIN-007	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000457370.2		
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274172	39274172	+	Silent	SNP	G	G	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:39274172G>T	ENST00000391413.2	-	1	434	c.396C>A	c.(394-396)ccC>ccA	p.P132P		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	132	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)				endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			ggcagcaggtgggctggcagc	0.672																																					p.P132P		Atlas-SNP	.											KRTAP4-11,NS,carcinoma,-2,2	KRTAP4-11	94	2	0			c.C396A						scavenged	.						7.0	12.0	11.0					17																	39274172		675	1578	2253	SO:0001819	synonymous_variant	653240	exon1			GCAGGTGGGCTGG	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.396C>A	17.37:g.39274172G>T		Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	93	4	0.0430108	NM_033059	A0AUY2	Silent	SNP	ENST00000391413.2	37	CCDS45675.1																																																																																			.	.	none		0.672	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
PTN	5764	hgsc.bcm.edu	37	7	136936058	136936058	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:136936058G>A	ENST00000348225.2	-	4	797	c.370C>T	c.(370-372)Cga>Tga	p.R124*	PTN_ENST00000393083.2_Nonsense_Mutation_p.R124*	NM_002825.5	NP_002816.1	P21246	PTN_HUMAN	pleiotrophin	124					bone mineralization (GO:0030282)|learning (GO:0007612)|negative regulation of catalytic activity (GO:0043086)|nervous system development (GO:0007399)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|transmembrane receptor protein tyrosine phosphatase signaling pathway (GO:0007185)	endoplasmic reticulum (GO:0005783)|extracellular space (GO:0005615)	heparin binding (GO:0008201)|protein phosphatase inhibitor activity (GO:0004864)			NS(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(10)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	23						TGCAGGGCTCGCTTCAGACTT	0.527																																					p.R124X		Atlas-SNP	.											.	PTN	38	.	0			c.C370T						PASS	.						292.0	266.0	275.0					7																	136936058		2203	4300	6503	SO:0001587	stop_gained	5764	exon4			GGGCTCGCTTCAG	M57399	CCDS5844.1	7q33	2014-01-30	2008-07-31		ENSG00000105894	ENSG00000105894		"""Endogenous ligands"""	9630	protein-coding gene	gene with protein product	"""heparin binding growth factor 8"""	162095	"""neurite growth-promoting factor 1"""	NEGF1		1457401, 1768439	Standard	NM_002825		Approved	HBNF, HBGF8	uc003vtq.2	P21246	OTTHUMG00000155709	ENST00000348225.2:c.370C>T	7.37:g.136936058G>A	ENSP00000341170:p.Arg124*	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	274	131	0.478102	NM_002825	Q5U0B0|Q6ICQ5|Q9UCC6	Nonsense_Mutation	SNP	ENST00000348225.2	37	CCDS5844.1	.	.	.	.	.	.	.	.	.	.	G	39	7.527019	0.98339	.	.	ENSG00000105894	ENST00000348225;ENST00000393083	.	.	.	6.02	4.05	0.47172	.	0.115288	0.64402	D	0.000017	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06625	T	0.88	-9.3356	14.1566	0.65422	0.0:0.0:0.5946:0.4054	.	.	.	.	X	124	.	ENSP00000341170:R124X	R	-	1	2	PTN	136586598	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.741000	0.47426	1.528000	0.49103	0.650000	0.86243	CGA	.	.	none		0.527	PTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341339.1	NM_002825	
RBM42	79171	hgsc.bcm.edu	37	19	36124108	36124108	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:36124108C>T	ENST00000262633.4	+	6	743	c.638C>T	c.(637-639)gCt>gTt	p.A213V	RBM42_ENST00000588161.1_Missense_Mutation_p.A183V|RBM42_ENST00000589559.1_Missense_Mutation_p.A184V|RBM42_ENST00000360475.4_Missense_Mutation_p.A184V|RBM42_ENST00000592202.1_Missense_Mutation_p.A159V|RBM42_ENST00000586618.1_Intron|RBM42_ENST00000589871.1_Missense_Mutation_p.A191V	NM_024321.3	NP_077297.2	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	213	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)			ATGGCTCGGGCTCCAGGGCCC	0.697																																					p.A213V		Atlas-SNP	.											.	RBM42	40	.	0			c.C638T						PASS	.						38.0	49.0	45.0					19																	36124108		2196	4291	6487	SO:0001583	missense	79171	exon6			CTCGGGCTCCAGG	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.638C>T	19.37:g.36124108C>T	ENSP00000262633:p.Ala213Val	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	32	4	0.125	NM_024321	O00320|Q8N5R7|Q9BU66	Missense_Mutation	SNP	ENST00000262633.4	37	CCDS12468.1	.	.	.	.	.	.	.	.	.	.	C	18.22	3.576124	0.65878	.	.	ENSG00000126254	ENST00000262633;ENST00000360475	T;T	0.06449	3.3;3.34	5.05	5.05	0.67936	.	0.180852	0.47455	D	0.000236	T	0.11537	0.0281	N	0.14661	0.345	0.29843	N	0.829062	D;D;D;D	0.60575	0.988;0.988;0.988;0.98	D;D;D;D	0.70935	0.971;0.971;0.971;0.935	T	0.03555	-1.1025	10	0.48119	T	0.1	-7.1616	13.7681	0.63008	0.0:1.0:0.0:0.0	.	179;184;183;213	Q9BTD8-4;Q9BTD8-3;Q9BTD8-2;Q9BTD8	.;.;.;RBM42_HUMAN	V	213;184	ENSP00000262633:A213V;ENSP00000353663:A184V	ENSP00000262633:A213V	A	+	2	0	RBM42	40815948	0.988000	0.35896	1.000000	0.80357	0.968000	0.65278	2.033000	0.41136	2.628000	0.89032	0.561000	0.74099	GCT	.	.	none		0.697	RBM42-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459057.2	NM_024321	
PRR21	643905	hgsc.bcm.edu	37	2	240981668	240981668	+	Silent	SNP	C	C	A	rs199598022	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:240981668C>A	ENST00000408934.1	-	1	731	c.732G>T	c.(730-732)acG>acT	p.T244T		NM_001080835.1	NP_001074304.1	Q8WXC7	PRR21_HUMAN	proline rich 21	244	Pro-rich.							p.T244T(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						GACGAAGGGCCGTGGGTGAAG	0.642													c|||	752	0.15016	0.1861	0.1138	5008	,	,		9753	0.1012		0.1431	False		,,,				2504	0.1851				p.T244T		Atlas-SNP	.											PRR21,caecum,carcinoma,0,2	PRR21	53	2	2	Substitution - coding silent(2)	large_intestine(2)	c.G732T						scavenged	.						1.0	1.0	1.0					2																	240981668		446	864	1310	SO:0001819	synonymous_variant	643905	exon1			AAGGGCCGTGGGT	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.732G>T	2.37:g.240981668C>A		Somatic	5	1	0.2		WXS	Illumina HiSeq	Phase_I	3	2	0.666667	NM_001080835		Silent	SNP	ENST00000408934.1	37	CCDS33417.1																																																																																			C|0.678;A|0.322	0.322	strong		0.642	PRR21-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001080835	
SORL1	6653	hgsc.bcm.edu	37	11	121429298	121429298	+	Splice_Site	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:121429298A>G	ENST00000260197.7	+	20	2792		c.e20-1			NM_003105.5	NP_003096	Q92673	SORL_HUMAN	sortilin-related receptor, L(DLR class) A repeats containing						cell death (GO:0008219)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipid transport (GO:0006869)|negative regulation of aspartic-type endopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902960)|negative regulation of beta-amyloid formation (GO:1902430)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of metalloendopeptidase activity involved in amyloid precursor protein catabolic process (GO:1902963)|negative regulation of neurofibrillary tangle assembly (GO:1902997)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron death (GO:1901215)|negative regulation of protein binding (GO:0032091)|negative regulation of protein oligomerization (GO:0032460)|negative regulation of tau-protein kinase activity (GO:1902948)|positive regulation of choline O-acetyltransferase activity (GO:1902771)|positive regulation of early endosome to recycling endosome transport (GO:1902955)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of ER to Golgi vesicle-mediated transport (GO:1902953)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of protein exit from endoplasmic reticulum (GO:0070863)|positive regulation of protein localization to early endosome (GO:1902966)|post-Golgi vesicle-mediated transport (GO:0006892)|protein maturation (GO:0051604)|protein retention in Golgi apparatus (GO:0045053)|protein targeting (GO:0006605)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|receptor-mediated endocytosis (GO:0006898)|regulation of smooth muscle cell migration (GO:0014910)|signal transduction (GO:0007165)	early endosome (GO:0005769)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi cisterna (GO:0031985)|integral component of plasma membrane (GO:0005887)|low-density lipoprotein particle (GO:0034362)|membrane (GO:0016020)|multivesicular body (GO:0005771)|neuronal cell body (GO:0043025)|nuclear envelope lumen (GO:0005641)|recycling endosome (GO:0055037)|trans-Golgi network (GO:0005802)	ADP-ribosylation factor binding (GO:0030306)|beta-amyloid binding (GO:0001540)|low-density lipoprotein particle binding (GO:0030169)|transmembrane signaling receptor activity (GO:0004888)			NS(1)|breast(5)|central_nervous_system(1)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(14)|liver(2)|lung(34)|ovary(5)|pancreas(1)|skin(12)|stomach(2)|upper_aerodigestive_tract(2)	91		Breast(109;0.00119)|Medulloblastoma(222;0.0429)|all_neural(223;0.113)		BRCA - Breast invasive adenocarcinoma(274;3.34e-05)|OV - Ovarian serous cystadenocarcinoma(223;0.108)		CATTTTCGCTAGGGTGATGTT	0.473																																					.		Atlas-SNP	.											.	SORL1	218	.	0			c.2664-2A>G						PASS	.						168.0	163.0	164.0					11																	121429298		2203	4299	6502	SO:0001630	splice_region_variant	6653	exon20			TTCGCTAGGGTGA	Y08110	CCDS8436.1	11q23.2-q24.4	2014-06-05	2011-01-25		ENSG00000137642	ENSG00000137642		"""Fibronectin type III domain containing"""	11185	protein-coding gene	gene with protein product	"""LDLR relative with 11 ligand-binding repeats"""	602005	"""chromosome 11 open reading frame 32"", ""sortilin-related receptor, L(DLR class) A repeats-containing"""	C11orf32		9157966, 8940146	Standard	NM_003105		Approved	gp250, LR11, LRP9, SorLA, SorLA-1	uc001pxx.3	Q92673	OTTHUMG00000166057	ENST00000260197.7:c.2664-1A>G	11.37:g.121429298A>G		Somatic	90	0	0		WXS	Illumina HiSeq	Phase_I	101	37	0.366337	NM_003105	B2RNX7|Q92856	Splice_Site	SNP	ENST00000260197.7	37	CCDS8436.1	.	.	.	.	.	.	.	.	.	.	A	16.57	3.160296	0.57368	.	.	ENSG00000137642	ENST00000260197	.	.	.	5.53	5.53	0.82687	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.6637	0.77209	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	SORL1	120934508	1.000000	0.71417	0.337000	0.25536	0.644000	0.38419	9.087000	0.94110	2.105000	0.64084	0.533000	0.62120	.	.	.	none		0.473	SORL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387626.2	NM_003105	Intron
KRT24	192666	hgsc.bcm.edu	37	17	38859553	38859553	+	Silent	SNP	G	G	T	rs367736597		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:38859553G>T	ENST00000264651.2	-	1	449	c.393C>A	c.(391-393)ggC>ggA	p.G131G		NM_019016.2	NP_061889.2	Q2M2I5	K1C24_HUMAN	keratin 24	131	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)				GCCCCCCATCGCCAACACCAC	0.537																																					p.G131G	GBM(61;380 1051 14702 23642 31441)	Atlas-SNP	.											.	KRT24	60	.	0			c.C393A						PASS	.						176.0	194.0	188.0					17																	38859553		2203	4300	6503	SO:0001819	synonymous_variant	192666	exon1			CCCATCGCCAACA		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.393C>A	17.37:g.38859553G>T		Somatic	77	0	0		WXS	Illumina HiSeq	Phase_I	69	34	0.492754	NM_019016	Q9NXG7	Silent	SNP	ENST00000264651.2	37	CCDS11372.1																																																																																			.	.	alt		0.537	KRT24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257217.1	NM_019016	
ABCA3	21	hgsc.bcm.edu	37	16	2326687	2326687	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:2326687C>A	ENST00000301732.5	-	33	5803	c.5103G>T	c.(5101-5103)gaG>gaT	p.E1701D	ABCA3_ENST00000382381.3_Missense_Mutation_p.E1643D|MIR4717_ENST00000584656.1_RNA	NM_001089.2	NP_001080.2	Q99758	ABCA3_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 3	1701					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)	ATCGCCCCTCCTCTGCGGTGG	0.612																																					p.E1701D		Atlas-SNP	.											ABCA3,NS,carcinoma,-2,1	ABCA3	176	1	0			c.G5103T						PASS	.						47.0	45.0	46.0					16																	2326687		2198	4300	6498	SO:0001583	missense	21	exon33			CCCCTCCTCTGCG	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.5103G>T	16.37:g.2326687C>A	ENSP00000301732:p.Glu1701Asp	Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	56	24	0.428571	NM_001089	B2RU09|Q54A95|Q6P5P9|Q92473	Missense_Mutation	SNP	ENST00000301732.5	37	CCDS10466.1	.	.	.	.	.	.	.	.	.	.	C	10.36	1.328649	0.24167	.	.	ENSG00000167972	ENST00000301732;ENST00000382381	D	0.83673	-1.75	5.44	-7.48	0.01360	.	0.438733	0.26503	N	0.024012	T	0.52773	0.1755	N	0.12422	0.21	0.26390	N	0.97659	B;B	0.06786	0.001;0.0	B;B	0.06405	0.002;0.001	T	0.50092	-0.8868	10	0.19590	T	0.45	.	0.6966	0.00900	0.3859:0.1226:0.1741:0.3175	.	1705;1701	Q4LE27;Q99758	.;ABCA3_HUMAN	D	1701;1705	ENSP00000301732:E1701D	ENSP00000301732:E1701D	E	-	3	2	ABCA3	2266688	0.000000	0.05858	0.198000	0.23420	0.008000	0.06430	-0.742000	0.04850	-1.113000	0.02981	-0.895000	0.02911	GAG	.	.	none		0.612	ABCA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250784.2	NM_001089	
B4GALNT3	283358	hgsc.bcm.edu	37	12	661327	661327	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:661327C>T	ENST00000266383.5	+	12	1219	c.1206C>T	c.(1204-1206)gaC>gaT	p.D402D		NM_173593.3	NP_775864.3	Q6L9W6	B4GN3_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 3	402					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)			breast(1)|central_nervous_system(1)|endometrium(6)|kidney(3)|large_intestine(1)|lung(10)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(10;0.0158)|all_epithelial(11;0.0274)|Ovarian(42;0.0512)|all_lung(10;0.154)|Lung NSC(10;0.215)		OV - Ovarian serous cystadenocarcinoma(31;0.00018)|BRCA - Breast invasive adenocarcinoma(9;0.0262)			ACTACCAAGACCGGTGAGAGA	0.562																																					p.D402D		Atlas-SNP	.											B4GALNT3,NS,carcinoma,+1,1	B4GALNT3	64	1	0			c.C1206T						scavenged	.						85.0	80.0	82.0					12																	661327		2203	4300	6503	SO:0001819	synonymous_variant	283358	exon12			CCAAGACCGGTGA	AB089940	CCDS8504.1	12p13.33	2013-02-19			ENSG00000139044	ENSG00000139044	2.4.1.-	"""Beta 4-glycosyltransferases"""	24137	protein-coding gene	gene with protein product		612220				12966086	Standard	NM_173593		Approved	B4GalNac-T3, FLJ16224, FLJ40362	uc001qii.1	Q6L9W6	OTTHUMG00000129283	ENST00000266383.5:c.1206C>T	12.37:g.661327C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	171	2	0.0116959	NM_173593	Q6ZNC1|Q8N7T6	Silent	SNP	ENST00000266383.5	37	CCDS8504.1																																																																																			.	.	none		0.562	B4GALNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251406.2	NM_173593	
KCNC1	3746	hgsc.bcm.edu	37	11	17793670	17793670	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:17793670C>T	ENST00000379472.3	+	2	1059	c.1029C>T	c.(1027-1029)aaC>aaT	p.N343N	KCNC1_ENST00000265969.6_Silent_p.N343N	NM_004976.4	NP_004967.1	P48547	KCNC1_HUMAN	potassium voltage-gated channel, Shaw-related subfamily, member 1	343					potassium ion transport (GO:0006813)|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)|voltage-gated potassium channel activity (GO:0005249)			breast(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(9)|lung(7)|pancreas(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	33					Dalfampridine(DB06637)	CCAGCACCAACGAGTTCCTGC	0.617																																					p.N343N		Atlas-SNP	.											.	KCNC1	149	.	0			c.C1029T						PASS	.						37.0	35.0	36.0					11																	17793670		2200	4293	6493	SO:0001819	synonymous_variant	3746	exon2			CACCAACGAGTTC	M96747	CCDS7827.1, CCDS44547.1	11p15	2012-07-05			ENSG00000129159	ENSG00000129159		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6233	protein-coding gene	gene with protein product		176258				8449507, 16382104	Standard	NM_004976		Approved	Kv3.1	uc009yhc.1	P48547	OTTHUMG00000166359	ENST00000379472.3:c.1029C>T	11.37:g.17793670C>T		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_I	64	31	0.484375	NM_004976	K4DI87	Silent	SNP	ENST00000379472.3	37	CCDS7827.1																																																																																			.	.	none		0.617	KCNC1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389389.1	NM_004976	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240805	39240805	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:39240805G>T	ENST00000391417.4	+	1	347	c.347G>T	c.(346-348)cGc>cTc	p.R116L		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	141	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		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						agctgctgccgcccctgctgc	0.672																																					p.R116L		Atlas-SNP	.											KRTAP4-7,caecum,carcinoma,+1,1	KRTAP4-7	49	1	0			c.G347T						scavenged	.						18.0	18.0	18.0					17																	39240805		692	1587	2279	SO:0001583	missense	100132476	exon1			GCTGCCGCCCCTG	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.347G>T	17.37:g.39240805G>T	ENSP00000375236:p.Arg116Leu	Somatic	64	1	0.015625		WXS	Illumina HiSeq	Phase_I	55	5	0.0909091	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	6.805	0.517638	0.13005	.	.	ENSG00000240871	ENST00000391417	T	0.00606	6.26	3.15	2.13	0.27403	.	0.163808	0.19966	U	0.102091	T	0.00496	0.0016	.	.	.	0.09310	N	1	B	0.18461	0.028	B	0.15052	0.012	T	0.45804	-0.9236	9	0.28530	T	0.3	.	9.2621	0.37619	0.0:0.0:0.7821:0.2179	.	171	Q9BYR0	KRA47_HUMAN	L	116	ENSP00000375236:R116L	ENSP00000375236:R116L	R	+	2	0	KRTAP4-7	36494331	0.000000	0.05858	0.028000	0.17463	0.502000	0.33828	-0.081000	0.11321	0.603000	0.29913	0.289000	0.19496	CGC	.	.	none		0.672	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
ZNF746	155061	hgsc.bcm.edu	37	7	149191527	149191527	+	Missense_Mutation	SNP	C	C	T	rs397832784		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:149191527C>T	ENST00000340622.3	-	2	372	c.92G>A	c.(91-93)cGc>cAc	p.R31H	ZNF746_ENST00000461958.2_Missense_Mutation_p.R31H|ZNF746_ENST00000458143.2_Missense_Mutation_p.R31H			Q6NUN9	ZN746_HUMAN	zinc finger protein 746	31					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)			GGAAAGCAGGCGAGCAGCCTG	0.552																																					p.R31H		Atlas-SNP	.											ZNF746,colon,carcinoma,+1,2	ZNF746	68	2	0			c.G92A						scavenged	.						93.0	95.0	94.0					7																	149191527		2203	4300	6503	SO:0001583	missense	155061	exon2			AGCAGGCGAGCAG	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.92G>A	7.37:g.149191527C>T	ENSP00000345140:p.Arg31His	Somatic	206	4	0.0194175		WXS	Illumina HiSeq	Phase_I	244	4	0.0163934	NM_001163474	A8K6Z9|Q6ZRF9	Missense_Mutation	SNP	ENST00000340622.3	37	CCDS5897.1	.	.	.	.	.	.	.	.	.	.	.	15.88	2.962584	0.53400	.	.	ENSG00000181220	ENST00000340622;ENST00000458143;ENST00000461958	T;T	0.25085	1.82;1.82	4.64	4.64	0.57946	.	0.000000	0.43747	D	0.000521	T	0.27798	0.0684	.	.	.	0.34184	D	0.671235	P;P	0.43094	0.758;0.799	B;B	0.42214	0.329;0.38	T	0.49485	-0.8935	9	0.87932	D	0	-24.5085	13.0146	0.58749	0.0:1.0:0.0:0.0	.	31;31	Q6NUN9-2;Q6NUN9	.;ZN746_HUMAN	H	31;31;18	ENSP00000345140:R31H;ENSP00000395007:R31H	ENSP00000345140:R31H	R	-	2	0	ZNF746	148822460	0.972000	0.33761	0.999000	0.59377	0.893000	0.52053	2.208000	0.42797	2.119000	0.64992	0.514000	0.50259	CGC	.	.	none		0.552	ZNF746-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000352730.1	NM_152557	
STAG2	10735	hgsc.bcm.edu	37	X	123182892	123182892	+	Missense_Mutation	SNP	A	A	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:123182892A>T	ENST00000371160.1	+	10	1147	c.857A>T	c.(856-858)aAt>aTt	p.N286I	STAG2_ENST00000218089.9_Missense_Mutation_p.N286I|STAG2_ENST00000371145.3_Missense_Mutation_p.N286I|STAG2_ENST00000371157.3_Missense_Mutation_p.N286I|STAG2_ENST00000371144.3_Missense_Mutation_p.N286I|STAG2_ENST00000354548.5_Missense_Mutation_p.N217I|STAG2_ENST00000469481.1_Intron	NM_001282418.1	NP_001269347.1	Q8N3U4	STAG2_HUMAN	stromal antigen 2	286					meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|negative regulation of DNA endoreduplication (GO:0032876)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	actin cytoskeleton (GO:0015629)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	chromatin binding (GO:0003682)			breast(5)|central_nervous_system(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(5)|kidney(8)|large_intestine(9)|lung(21)|ovary(5)|prostate(2)|skin(5)|urinary_tract(4)	78						AATATGATGAATGCAATATTT	0.294																																					p.N286I		Atlas-SNP	.											.	STAG2	309	.	0			c.A857T						PASS	.						100.0	93.0	96.0					X																	123182892		2203	4297	6500	SO:0001583	missense	10735	exon10			TGATGAATGCAAT	Z75331	CCDS14607.1, CCDS43990.1	Xq25	2014-09-17			ENSG00000101972	ENSG00000101972			11355	protein-coding gene	gene with protein product		300826				9305759	Standard	NM_001042750		Approved	SA-2, SCC3B	uc004eua.3	Q8N3U4	OTTHUMG00000022725	ENST00000371160.1:c.857A>T	X.37:g.123182892A>T	ENSP00000360202:p.Asn286Ile	Somatic	341	0	0		WXS	Illumina HiSeq	Phase_I	256	21	0.0820312	NM_001042749	B1AMT5|D3DTF5|O00540|Q5JTI6|Q68DE9|Q9H1N8	Missense_Mutation	SNP	ENST00000371160.1	37	CCDS14607.1	.	.	.	.	.	.	.	.	.	.	A	23.5	4.419454	0.83559	.	.	ENSG00000101972	ENST00000218089;ENST00000455404;ENST00000354548;ENST00000371160;ENST00000371157;ENST00000371145;ENST00000371144	T;T;T;T;T;T;T	0.33438	1.41;1.41;1.41;1.41;1.41;1.41;1.41	5.47	5.47	0.80525	Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.58192	0.2105	M	0.85041	2.73	0.80722	D	1	D;D	0.63046	0.987;0.992	D;D	0.65684	0.937;0.933	T	0.65059	-0.6260	10	0.62326	D	0.03	-0.079	14.1713	0.65512	1.0:0.0:0.0:0.0	.	286;286	Q8N3U4-2;Q8N3U4	.;STAG2_HUMAN	I	286;286;217;286;286;286;286	ENSP00000218089:N286I;ENSP00000397265:N286I;ENSP00000346555:N217I;ENSP00000360202:N286I;ENSP00000360199:N286I;ENSP00000360187:N286I;ENSP00000360186:N286I	ENSP00000218089:N286I	N	+	2	0	STAG2	123010573	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.228000	0.95250	1.809000	0.52856	0.486000	0.48141	AAT	.	.	none		0.294	STAG2-018	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000156159.2	NM_006603	
PSME3	10197	hgsc.bcm.edu	37	17	40985663	40985663	+	Silent	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:40985663G>A	ENST00000590720.1	+	1	248	c.15G>A	c.(13-15)ctG>ctA	p.L5L	PSME3_ENST00000592169.1_Silent_p.L5L|PSME3_ENST00000541124.1_Silent_p.L5L|PSME3_ENST00000592578.1_3'UTR|PSME3_ENST00000545225.1_Intron|PSME3_ENST00000441946.2_5'UTR|PSME3_ENST00000293362.3_Silent_p.L5L			P61289	PSME3_HUMAN	proteasome (prosome, macropain) activator subunit 3 (PA28 gamma; Ki)	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 extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of endopeptidase activity (GO:0010950)|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 proteasomal protein catabolic process (GO:0061136)|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)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome activator complex (GO:0008537)|proteasome complex (GO:0000502)	endopeptidase activator activity (GO:0061133)|MDM2/MDM4 family protein binding (GO:0097371)|p53 binding (GO:0002039)			NS(1)|cervix(1)|large_intestine(3)|lung(1)	6		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		CCTCGTTGCTGAAGGTGGATC	0.652																																					p.L5L		Atlas-SNP	.											.	PSME3	11	.	0			c.G15A						PASS	.						69.0	58.0	62.0					17																	40985663		2203	4300	6503	SO:0001819	synonymous_variant	10197	exon1			GTTGCTGAAGGTG	U11292	CCDS11442.1, CCDS45689.1, CCDS59290.1	17q12-q21	2004-02-17				ENSG00000131467		"""Proteasome (prosome, macropain) subunits"""	9570	protein-coding gene	gene with protein product		605129				7951316	Standard	NM_005789		Approved	Ki, PA28-gamma, REG-GAMMA, PA28G	uc002ibq.4	P61289		ENST00000590720.1:c.15G>A	17.37:g.40985663G>A		Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	160	70	0.4375	NM_176863	A8K9A3|O35563|P97373|Q12920|Q13172|Q9BQD9	Silent	SNP	ENST00000590720.1	37	CCDS45689.1																																																																																			.	.	none		0.652	PSME3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452430.1	NM_176863	
LILRA6	79168	hgsc.bcm.edu	37	19	54744722	54744722	+	Missense_Mutation	SNP	T	T	C	rs56257556	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:54744722T>C	ENST00000396365.2	-	5	979	c.940A>G	c.(940-942)Aac>Gac	p.N314D	LILRA6_ENST00000245621.5_Missense_Mutation_p.N314D|LILRA6_ENST00000419410.2_Missense_Mutation_p.N314D|LILRA6_ENST00000270464.5_Intron|LILRA6_ENST00000440558.2_Missense_Mutation_p.N314D|LILRA6_ENST00000391735.3_3'UTR|LILRB3_ENST00000407860.2_Intron	NM_024318.2	NP_077294	Q6PI73	LIRA6_HUMAN	leukocyte immunoglobulin-like receptor, subfamily A (with TM domain), member 6	314	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)		ATCAGGATGTTCAGGGGGTCG	0.682																																					p.N314D		Atlas-SNP	.											LILRA6,NS,carcinoma,+2,1	LILRA6	75	1	0			c.A940G						scavenged	.						22.0	32.0	29.0					19																	54744722		2100	4147	6247	SO:0001583	missense	79168	exon5			GGATGTTCAGGGG	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.940A>G	19.37:g.54744722T>C	ENSP00000379651:p.Asn314Asp	Somatic	213	1	0.00469484		WXS	Illumina HiSeq	Phase_I	289	8	0.0276817	NM_024318		Missense_Mutation	SNP	ENST00000396365.2	37	CCDS42610.1	207	0.09478021978021978	73	0.1483739837398374	41	0.1132596685082873	19	0.033216783216783216	74	0.09762532981530343	T	0	-2.690915	0.00100	.	.	ENSG00000244482	ENST00000440558;ENST00000419410;ENST00000421123;ENST00000396365;ENST00000245621	T;T;T;T	0.13778	2.56;2.56;2.56;2.56	2.16	1.1	0.20463	Immunoglobulin subtype (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.389073	0.18849	N	0.129445	T	0.00012	0.0000	N	0.00022	-2.725	0.80722	D	1	B;B;B;B	0.17852	0.002;0.024;0.0;0.0	B;B;B;B	0.28385	0.002;0.089;0.0;0.001	T	0.46020	-0.9221	10	0.02654	T	1	.	5.0417	0.14462	0.0:0.8181:0.0:0.1819	rs56257556	314;314;314;314	C9JFH3;Q6PI73;F8WCY4;D3YTC4	.;LIRA6_HUMAN;.;.	D	314	ENSP00000390120:N314D;ENSP00000411227:N314D;ENSP00000379651:N314D;ENSP00000245621:N314D	ENSP00000245621:N314D	N	-	1	0	LILRA6	59436534	0.686000	0.27661	0.905000	0.35620	0.042000	0.13812	1.191000	0.32138	0.467000	0.27218	-1.232000	0.01568	AAC	CATCAGGATGTT|0.500;GATCAGGATGTC|0.500	.	alt		0.682	LILRA6-003	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000313725.1	NM_024318	
LCE1E	353135	hgsc.bcm.edu	37	1	152759850	152759850	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:152759850C>T	ENST00000368770.3	+	2	128	c.75C>T	c.(73-75)ccC>ccT	p.P25P	LCE1E_ENST00000368771.1_Silent_p.P25P	NM_178353.1	NP_848130.1	Q5T753	LCE1E_HUMAN	late cornified envelope 1E	25	Cys-rich.				keratinization (GO:0031424)					lung(5)|stomach(1)	6	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;0.206)			ccaagtgTCCCACCCCCAAAT	0.627																																					p.P25P		Atlas-SNP	.											LCE1E,NS,carcinoma,+2,1	LCE1E	26	1	0			c.C75T						scavenged	.						96.0	99.0	98.0					1																	152759850		2203	4300	6503	SO:0001819	synonymous_variant	353135	exon2			GTGTCCCACCCCC	BC038391	CCDS1024.1	1q21.3	2008-02-05			ENSG00000186226	ENSG00000186226		"""Late cornified envelopes"""	29466	protein-coding gene	gene with protein product		612607				11698679	Standard	NM_178353		Approved	LEP5	uc001fan.3	Q5T753	OTTHUMG00000012405	ENST00000368770.3:c.75C>T	1.37:g.152759850C>T		Somatic	215	0	0		WXS	Illumina HiSeq	Phase_I	253	3	0.0118577	NM_178353	D3DV30	Silent	SNP	ENST00000368770.3	37	CCDS1024.1																																																																																			.	.	none		0.627	LCE1E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034525.1	NM_178353	
IL31RA	133396	hgsc.bcm.edu	37	5	55178961	55178961	+	Missense_Mutation	SNP	G	G	A	rs77015584		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:55178961G>A	ENST00000447346.2	+	5	609	c.544G>A	c.(544-546)Gcg>Acg	p.A182T	IL31RA_ENST00000354961.4_Missense_Mutation_p.A163T|IL31RA_ENST00000490985.1_Missense_Mutation_p.A40T|IL31RA_ENST00000297015.3_Missense_Mutation_p.A40T|IL31RA_ENST00000396836.2_Missense_Mutation_p.A182T|IL31RA_ENST00000396834.1_Missense_Mutation_p.A163T|IL31RA_ENST00000359040.5_Missense_Mutation_p.A182T	NM_001242636.1|NM_139017.5	NP_001229565.1|NP_620586.3	Q8NI17	IL31R_HUMAN	interleukin 31 receptor A	150	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|homeostatic process (GO:0042592)|JAK-STAT cascade (GO:0007259)|macrophage differentiation (GO:0030225)|MAPK cascade (GO:0000165)|monocyte differentiation (GO:0030224)|negative regulation of apoptotic process (GO:0043066)|negative regulation of macrophage activation (GO:0043031)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|positive regulation of tyrosine phosphorylation of Stat5 protein (GO:0042523)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cytokine binding (GO:0019955)|cytokine receptor activity (GO:0004896)|protein kinase binding (GO:0019901)|transcription coactivator activity (GO:0003713)			endometrium(2)|kidney(2)|large_intestine(7)|lung(8)|ovary(1)|stomach(1)	21		Lung NSC(810;6.93e-05)|Prostate(74;0.00741)|Breast(144;0.0544)|Ovarian(174;0.223)				GCCTGAGTTGGCGCCTGTTTC	0.378																																					p.A182T		Atlas-SNP	.											IL31RA,NS,carcinoma,-1,1	IL31RA	84	1	0			c.G544A						scavenged	.						98.0	94.0	95.0					5																	55178961		2203	4300	6503	SO:0001583	missense	133396	exon5			GAGTTGGCGCCTG	AY499339	CCDS3970.2, CCDS56365.1, CCDS56366.1, CCDS56367.1, CCDS75244.1, CCDS75245.1	5q11.2	2013-02-11			ENSG00000164509	ENSG00000164509		"""Interleukins and interleukin receptors"", ""Fibronectin type III domain containing"""	18969	protein-coding gene	gene with protein product		609510				15184896, 11877449	Standard	NM_139017		Approved	CRL3, GLM-R, CRL, Glmr, IL-31RA	uc003jql.3	Q8NI17	OTTHUMG00000097045	ENST00000447346.2:c.544G>A	5.37:g.55178961G>A	ENSP00000415900:p.Ala182Thr	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	105	2	0.0190476	NM_001242637	A6NIF8|Q2TBA1|Q6EBC3|Q6EBC4|Q6EBC5|Q6EBC6|Q6UWL8|Q8WYJ0	Missense_Mutation	SNP	ENST00000447346.2	37	CCDS3970.2	.	.	.	.	.	.	.	.	.	.	G	10.73	1.431152	0.25726	.	.	ENSG00000164509	ENST00000396836;ENST00000396834;ENST00000447346;ENST00000359040;ENST00000297015;ENST00000490985;ENST00000354961	T;T;T;T;T;T;T	0.55588	0.51;0.51;0.51;0.51;0.51;0.51;0.51	6.0	-2.62	0.06152	Fibronectin, type III (4);Immunoglobulin-like fold (1);	5.676280	0.01574	U	0.020707	T	0.36717	0.0977	L	0.42245	1.32	0.09310	N	1	B;B;B;B;B	0.33637	0.136;0.138;0.063;0.264;0.42	B;B;B;B;B	0.32928	0.055;0.037;0.032;0.055;0.155	T	0.06303	-1.0834	10	0.13108	T	0.6	-12.1995	0.5175	0.00606	0.3567:0.1256:0.2612:0.2565	.	150;182;163;182;182	Q8NI17;Q8NI17-5;Q8NI17-3;Q8NI17-2;Q8NI17-8	IL31R_HUMAN;.;.;.;.	T	182;163;182;182;40;40;163	ENSP00000380048:A182T;ENSP00000380046:A163T;ENSP00000415900:A182T;ENSP00000351935:A182T;ENSP00000297015:A40T;ENSP00000427533:A40T;ENSP00000347047:A163T	ENSP00000297015:A40T	A	+	1	0	IL31RA	55214718	0.001000	0.12720	0.000000	0.03702	0.016000	0.09150	-0.048000	0.11944	-0.224000	0.09928	0.650000	0.86243	GCG	.	.	alt		0.378	IL31RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000214148.1	NM_139017	
ABCA7	10347	hgsc.bcm.edu	37	19	1049321	1049321	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:1049321G>A	ENST00000263094.6	+	18	2668	c.2437G>A	c.(2437-2439)Gag>Aag	p.E813K	ABCA7_ENST00000435683.2_Missense_Mutation_p.E675K|ABCA7_ENST00000433129.1_Missense_Mutation_p.E813K	NM_019112.3	NP_061985.2	Q8IZY2	ABCA7_HUMAN	ATP-binding cassette, sub-family A (ABC1), member 7	813	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)		TCGCAGCCTGGAGAAGCGCTT	0.677																																					p.E813K		Atlas-SNP	.											.	ABCA7	174	.	0			c.G2437A						PASS	.						49.0	57.0	55.0					19																	1049321		2202	4296	6498	SO:0001583	missense	10347	exon18			AGCCTGGAGAAGC	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.2437G>A	19.37:g.1049321G>A	ENSP00000263094:p.Glu813Lys	Somatic	132	0	0		WXS	Illumina HiSeq	Phase_I	133	6	0.0451128	NM_019112	Q96S58|Q9BZC4|Q9NR73|Q9UKP8	Missense_Mutation	SNP	ENST00000263094.6	37	CCDS12055.1	.	.	.	.	.	.	.	.	.	.	G	9.960	1.222447	0.22457	.	.	ENSG00000064687	ENST00000263094;ENST00000433129	T;T	0.79554	-1.28;-1.28	4.0	2.94	0.34122	ABC transporter-like (1);	.	.	.	.	T	0.56001	0.1956	N	0.03209	-0.39	0.26432	N	0.975921	B;B	0.13145	0.007;0.004	B;B	0.14578	0.011;0.003	T	0.38351	-0.9665	9	0.07813	T	0.8	.	9.7753	0.40614	0.109:0.0:0.891:0.0	.	675;813	Q8IZY2-2;Q8IZY2	.;ABCA7_HUMAN	K	813	ENSP00000263094:E813K;ENSP00000414062:E813K	ENSP00000263094:E813K	E	+	1	0	ABCA7	1000321	1.000000	0.71417	0.995000	0.50966	0.197000	0.23852	5.512000	0.67030	0.777000	0.33496	0.462000	0.41574	GAG	.	.	none		0.677	ABCA7-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000394993.1	NM_019112	
TNFRSF11B	4982	hgsc.bcm.edu	37	8	119938922	119938922	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr8:119938922C>A	ENST00000297350.4	-	4	1006	c.628G>T	c.(628-630)Gct>Tct	p.A210S		NM_002546.3	NP_002537.3	O00300	TR11B_HUMAN	tumor necrosis factor receptor superfamily, member 11b	210	Death 1.				apoptotic process (GO:0006915)|extracellular matrix organization (GO:0030198)|negative regulation of bone resorption (GO:0045779)|negative regulation of odontogenesis of dentin-containing tooth (GO:0042489)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to estrogen (GO:0043627)|response to magnesium ion (GO:0032026)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	cytokine activity (GO:0005125)|receptor activity (GO:0004872)			breast(1)|central_nervous_system(3)|endometrium(4)|large_intestine(6)|lung(7)|prostate(3)|skin(1)	25	all_cancers(13;3.71e-26)|Lung NSC(37;1.69e-07)|Ovarian(258;0.018)|all_neural(195;0.0592)|Hepatocellular(40;0.234)		STAD - Stomach adenocarcinoma(47;0.00193)			GTAGGAACAGCAAACCTGAAG	0.413																																					p.A210S		Atlas-SNP	.											.	TNFRSF11B	87	.	0			c.G628T						PASS	.						102.0	91.0	95.0					8																	119938922		2203	4300	6503	SO:0001583	missense	4982	exon4			GAACAGCAAACCT	U94332	CCDS6326.1	8q24	2008-07-31	2008-07-31		ENSG00000164761	ENSG00000164761		"""Tumor necrosis factor receptor superfamily"""	11909	protein-coding gene	gene with protein product		602643	"""osteoprotegerin"""	OPG		9108485	Standard	NM_002546		Approved	OCIF, TR1	uc003yon.4	O00300	OTTHUMG00000164969	ENST00000297350.4:c.628G>T	8.37:g.119938922C>A	ENSP00000297350:p.Ala210Ser	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	106	5	0.0471698	NM_002546	B2R9A8|O60236|Q53FX6|Q9UHP4	Missense_Mutation	SNP	ENST00000297350.4	37	CCDS6326.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.599564	0.87055	.	.	ENSG00000164761	ENST00000297350	T	0.62639	0.01	5.6	5.6	0.85130	DEATH-like (1);	0.151580	0.44097	D	0.000494	T	0.71517	0.3349	L	0.44542	1.39	0.40998	D	0.984908	D	0.76494	0.999	D	0.63793	0.918	T	0.69499	-0.5129	9	.	.	.	-6.7848	17.8092	0.88610	0.0:1.0:0.0:0.0	.	210	O00300	TR11B_HUMAN	S	210	ENSP00000297350:A210S	.	A	-	1	0	TNFRSF11B	120008103	1.000000	0.71417	1.000000	0.80357	0.967000	0.64934	2.309000	0.43699	2.652000	0.90054	0.563000	0.77884	GCT	.	.	none		0.413	TNFRSF11B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381220.1		
MUC2	4583	hgsc.bcm.edu	37	11	1092885	1092885	+	Silent	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:1092885G>A	ENST00000441003.2	+	30	4731	c.4704G>A	c.(4702-4704)acG>acA	p.T1568T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1569T|MUC2_ENST00000333592.6_5'Flank	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)	CCACCACCACGGTGaccccaa	0.637																																					p.T1568T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,+1,8	MUC2	614	8	0			c.G4704A						scavenged	.						124.0	160.0	148.0					11																	1092885		1964	3666	5630	SO:0001819	synonymous_variant	4583	exon30			CACCACGGTGACC	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.4704G>A	11.37:g.1092885G>A		Somatic	70	2	0.0285714		WXS	Illumina HiSeq	Phase_I	91	9	0.0989011	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				.	.	none		0.637	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
STAB1	23166	hgsc.bcm.edu	37	3	52549477	52549477	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:52549477C>T	ENST00000321725.6	+	37	3979	c.3903C>T	c.(3901-3903)ttC>ttT	p.F1301F		NM_015136.2	NP_055951.2	Q9NY15	STAB1_HUMAN	stabilin 1	1301					cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|defense response to bacterium (GO:0042742)|inflammatory response (GO:0006954)|negative regulation of angiogenesis (GO:0016525)|oxidation-reduction process (GO:0055114)|receptor-mediated endocytosis (GO:0006898)	endocytic vesicle membrane (GO:0030666)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	hyaluronic acid binding (GO:0005540)|low-density lipoprotein particle binding (GO:0030169)|low-density lipoprotein receptor activity (GO:0005041)|protein disulfide oxidoreductase activity (GO:0015035)|scavenger receptor activity (GO:0005044)			breast(4)|central_nervous_system(3)|endometrium(7)|kidney(2)|large_intestine(13)|liver(1)|lung(27)|ovary(1)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(3)	76				BRCA - Breast invasive adenocarcinoma(193;1.73e-05)|Kidney(197;0.00182)|KIRC - Kidney renal clear cell carcinoma(197;0.00205)|OV - Ovarian serous cystadenocarcinoma(275;0.0482)		GATCTGGCTTCTCCTTCTCCC	0.612																																					p.F1301F		Atlas-SNP	.											.	STAB1	178	.	0			c.C3903T						PASS	.						82.0	76.0	78.0					3																	52549477		2202	4300	6502	SO:0001819	synonymous_variant	23166	exon37			TGGCTTCTCCTTC	AJ275213	CCDS33768.1	3p21.31	2008-07-18			ENSG00000010327	ENSG00000010327			18628	protein-coding gene	gene with protein product	"""MS-1 antigen"", ""fasciclin egf-like, laminin-type egf-like, and link domain-containing scavenger receptor-1"", ""common lymphatic endothelial and vascular endothelial receptor-1"""	608560				11829752, 12077138	Standard	XM_005264973		Approved	KIAA0246, STAB-1, FEEL-1, CLEVER-1, FELE-1, FEX1	uc003dej.3	Q9NY15	OTTHUMG00000158574	ENST00000321725.6:c.3903C>T	3.37:g.52549477C>T		Somatic	108	0	0		WXS	Illumina HiSeq	Phase_I	95	4	0.0421053	NM_015136	A7E297|Q8IUH0|Q8IUH1|Q93072	Silent	SNP	ENST00000321725.6	37	CCDS33768.1																																																																																			.	.	none		0.612	STAB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351380.2	NM_015136	
NRP1	8829	hgsc.bcm.edu	37	10	33510716	33510716	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:33510716G>A	ENST00000265371.4	-	9	1738	c.1213C>T	c.(1213-1215)Cga>Tga	p.R405*	NRP1_ENST00000395995.1_Nonsense_Mutation_p.R405*|NRP1_ENST00000374867.2_Nonsense_Mutation_p.R405*|NRP1_ENST00000374816.3_Nonsense_Mutation_p.R405*|NRP1_ENST00000374823.5_Nonsense_Mutation_p.R405*|NRP1_ENST00000374822.4_Nonsense_Mutation_p.R405*|NRP1_ENST00000374875.1_Nonsense_Mutation_p.R224*|NRP1_ENST00000432372.2_Nonsense_Mutation_p.R405*|NRP1_ENST00000374821.5_Nonsense_Mutation_p.R405*			O14786	NRP1_HUMAN	neuropilin 1	405	F5/8 type C 1. {ECO:0000255|PROSITE- ProRule:PRU00081}.				angiogenesis (GO:0001525)|angiogenesis involved in coronary vascular morphogenesis (GO:0060978)|artery morphogenesis (GO:0048844)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|axonogenesis involved in innervation (GO:0060385)|branchiomotor neuron axon guidance (GO:0021785)|cell adhesion (GO:0007155)|cell migration involved in sprouting angiogenesis (GO:0002042)|cell-cell signaling (GO:0007267)|cellular response to hepatocyte growth factor stimulus (GO:0035729)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|commissural neuron axon guidance (GO:0071679)|coronary artery morphogenesis (GO:0060982)|dendrite development (GO:0016358)|dichotomous subdivision of terminal units involved in salivary gland branching (GO:0060666)|endothelial cell chemotaxis (GO:0035767)|endothelial tip cell fate specification (GO:0097102)|facial nerve structural organization (GO:0021612)|gonadotrophin-releasing hormone neuronal migration to the hypothalamus (GO:0021828)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of neuron apoptotic process (GO:0043524)|nerve development (GO:0021675)|neural crest cell migration involved in autonomic nervous system development (GO:1901166)|neuron migration (GO:0001764)|organ morphogenesis (GO:0009887)|patterning of blood vessels (GO:0001569)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of cytokine activity (GO:0060301)|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 peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of retinal ganglion cell axon guidance (GO:1902336)|positive regulation of smooth muscle cell migration (GO:0014911)|protein localization to early endosome (GO:1902946)|regulation of retinal ganglion cell axon guidance (GO:0090259)|regulation of vesicle-mediated transport (GO:0060627)|renal artery morphogenesis (GO:0061441)|response to wounding (GO:0009611)|retina vasculature morphogenesis in camera-type eye (GO:0061299)|retinal ganglion cell axon guidance (GO:0031290)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|semaphorin-plexin signaling pathway involved in neuron projection guidance (GO:1902285)|signal transduction (GO:0007165)|sprouting angiogenesis (GO:0002040)|sympathetic ganglion development (GO:0061549)|sympathetic neuron projection extension (GO:0097490)|sympathetic neuron projection guidance (GO:0097491)|trigeminal nerve structural organization (GO:0021637)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|VEGF-activated neuropilin signaling pathway (GO:0038190)|VEGF-activated neuropilin signaling pathway involved in axon guidance (GO:1902378)	axon (GO:0030424)|cell surface (GO:0009986)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|growth cone (GO:0030426)|integral component of membrane (GO:0016021)|neurofilament (GO:0005883)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|semaphorin receptor complex (GO:0002116)|sorting endosome (GO:0097443)	coreceptor activity (GO:0015026)|cytokine binding (GO:0019955)|growth factor binding (GO:0019838)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)|semaphorin receptor activity (GO:0017154)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(2)|breast(6)|central_nervous_system(4)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(16)|ovary(1)|pancreas(1)|prostate(1)|skin(3)|stomach(2)	48					Palifermin(DB00039)|Pegaptanib(DB04895)	GGCTTGATTCGGACAAATCGA	0.428																																					p.R405X	Melanoma(104;886 1489 44640 45944 51153)	Atlas-SNP	.											NRP1,right_upper_lobe,carcinoma,0,1	NRP1	126	1	0			c.C1213T						scavenged	.						172.0	162.0	165.0					10																	33510716		2203	4300	6503	SO:0001587	stop_gained	8829	exon8			TGATTCGGACAAA	AF016050	CCDS7177.1, CCDS31179.1, CCDS31180.1	10p12	2006-02-23			ENSG00000099250	ENSG00000099250		"""CD molecules"""	8004	protein-coding gene	gene with protein product		602069				9529250, 9331348	Standard	NM_003873		Approved	NRP, VEGF165R, CD304	uc001iwx.4	O14786	OTTHUMG00000019343	ENST00000265371.4:c.1213C>T	10.37:g.33510716G>A	ENSP00000265371:p.Arg405*	Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	143	3	0.020979	NM_001244973	B0LPG9|O60461|Q5T7F1|Q5T7F2|Q5T7F3|Q86T59|Q96I90|Q96IH5	Nonsense_Mutation	SNP	ENST00000265371.4	37	CCDS7177.1	.	.	.	.	.	.	.	.	.	.	G	37	6.612153	0.97705	.	.	ENSG00000099250	ENST00000265371;ENST00000374875;ENST00000374867;ENST00000395995;ENST00000374822;ENST00000374821;ENST00000374823;ENST00000374816;ENST00000432372	.	.	.	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-11.1889	14.4851	0.67611	0.0:0.0:0.7419:0.2581	.	.	.	.	X	405;224;405;405;405;405;405;405;78	.	ENSP00000265371:R405X	R	-	1	2	NRP1	33550722	1.000000	0.71417	1.000000	0.80357	0.890000	0.51754	5.119000	0.64679	2.941000	0.99782	0.655000	0.94253	CGA	.	.	none		0.428	NRP1-001	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051203.2		
PCDHA11	56138	hgsc.bcm.edu	37	5	140250132	140250132	+	Missense_Mutation	SNP	G	G	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:140250132G>C	ENST00000398640.2	+	1	1444	c.1444G>C	c.(1444-1446)Gac>Cac	p.D482H	PCDHA3_ENST00000522353.2_Intron|PCDHA6_ENST00000527624.1_Intron|PCDHA9_ENST00000532602.1_Intron|PCDHA5_ENST00000529859.1_Intron|PCDHA1_ENST00000394633.3_Intron|PCDHA5_ENST00000529619.1_Intron|PCDHA4_ENST00000512229.2_Intron|PCDHA4_ENST00000530339.1_Intron|PCDHA10_ENST00000506939.2_Intron|PCDHA2_ENST00000526136.1_Intron|PCDHA6_ENST00000529310.1_Intron|PCDHA7_ENST00000525929.1_Intron|PCDHA10_ENST00000307360.5_Intron|PCDHA1_ENST00000504120.2_Intron|PCDHA8_ENST00000531613.1_Intron	NM_018902.3	NP_061725.1	Q9Y5I1	PCDAB_HUMAN	protocadherin alpha 11	482	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(1)|lung(1)	2			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCGGGACGCGGACGCGCAGGA	0.667																																					p.D482H		Atlas-SNP	.											PCDHA11_ENST00000398640,NS,carcinoma,-2,1	PCDHA11	209	1	0			c.G1444C						scavenged	.						89.0	93.0	92.0					5																	140250132		2203	4300	6503	SO:0001583	missense	56138	exon1			GACGCGGACGCGC	AF152476	CCDS47284.1, CCDS75326.1	5q31	2010-11-26			ENSG00000249158	ENSG00000249158		"""Cadherins / Protocadherins : Clustered"""	8665	other	complex locus constituent	"""KIAA0345-like 3"", ""ortholog of mouse CNR7"""	606317		CNRS7		10380929, 10662547	Standard	NM_018902		Approved	CNR7, CRNR7, CNRN7, PCDH-ALPHA11		Q9Y5I1	OTTHUMG00000163369	ENST00000398640.2:c.1444G>C	5.37:g.140250132G>C	ENSP00000381636:p.Asp482His	Somatic	153	0	0		WXS	Illumina HiSeq	Phase_I	122	2	0.0163934	NM_018902	B2RN58|O75279	Missense_Mutation	SNP	ENST00000398640.2	37	CCDS47284.1	.	.	.	.	.	.	.	.	.	.	G	15.27	2.784938	0.49997	.	.	ENSG00000249158	ENST00000398640	T	0.74632	-0.86	5.55	5.55	0.83447	Cadherin (4);Cadherin-like (1);	.	.	.	.	D	0.93449	0.7910	H	0.99800	4.79	0.48632	D	0.999687	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.96457	0.9338	9	0.87932	D	0	.	19.1659	0.93557	0.0:0.0:1.0:0.0	.	482;482	Q9Y5I1-2;Q9Y5I1	.;PCDAB_HUMAN	H	482	ENSP00000381636:D482H	ENSP00000381636:D482H	D	+	1	0	PCDHA11	140230316	1.000000	0.71417	1.000000	0.80357	0.046000	0.14306	9.333000	0.96459	2.618000	0.88619	0.556000	0.70494	GAC	.	.	none		0.667	PCDHA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372885.2	NM_018902	
SUPT5H	6829	hgsc.bcm.edu	37	19	39964876	39964876	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:39964876A>G	ENST00000599117.1	+	28	3021	c.2654A>G	c.(2653-2655)tAc>tGc	p.Y885C	SUPT5H_ENST00000598725.1_Missense_Mutation_p.Y885C|SUPT5H_ENST00000432763.2_Missense_Mutation_p.Y885C|SUPT5H_ENST00000359191.6_Missense_Mutation_p.Y881C|SUPT5H_ENST00000402194.2_Missense_Mutation_p.Y881C			O00267	SPT5H_HUMAN	suppressor of Ty 5 homolog (S. cerevisiae)	885	10 X 8 AA approximate tandem repeats of P-[TS]-P-S-P-[QA]-[SG]-Y, motif CTR2.|Pro-rich.				7-methylguanosine mRNA capping (GO:0006370)|cell cycle (GO:0007049)|chromatin remodeling (GO:0006338)|DNA-templated transcription, elongation (GO:0006354)|gene expression (GO:0010467)|negative regulation of DNA-templated transcription, elongation (GO:0032785)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of viral transcription (GO:0050434)|response to organic substance (GO:0010033)|single stranded viral RNA replication via double stranded DNA intermediate (GO:0039692)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|viral process (GO:0016032)	DSIF complex (GO:0032044)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|enzyme binding (GO:0019899)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			breast(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(13)|lung(12)|ovary(3)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)	51	all_cancers(60;6.69e-07)|all_lung(34;2.66e-08)|Lung NSC(34;3e-08)|all_epithelial(25;1.57e-06)|Ovarian(47;0.159)		Epithelial(26;3.9e-26)|all cancers(26;1.35e-23)|LUSC - Lung squamous cell carcinoma(53;0.000657)			CTCTGCAGGTACAACACAGAC	0.627											OREG0025462	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.Y885C		Atlas-SNP	.											SUPT5H,NS,carcinoma,+1,1	SUPT5H	119	1	0			c.A2654G						scavenged	.						140.0	140.0	140.0					19																	39964876		2203	4300	6503	SO:0001583	missense	6829	exon26			GCAGGTACAACAC	U56402	CCDS12536.1, CCDS46072.1	19q13	2008-07-22	2001-11-28			ENSG00000196235			11469	protein-coding gene	gene with protein product		602102	"""suppressor of Ty (S.cerevisiae) 5 homolog"""			8975720	Standard	NM_003169		Approved	SPT5H, SPT5, FLJ34157	uc002olp.4	O00267		ENST00000599117.1:c.2654A>G	19.37:g.39964876A>G	ENSP00000470252:p.Tyr885Cys	Somatic	181	0	0	889	WXS	Illumina HiSeq	Phase_I	202	3	0.0148515	NM_003169	O43279|Q59G52|Q99639	Missense_Mutation	SNP	ENST00000599117.1	37	CCDS12536.1	.	.	.	.	.	.	.	.	.	.	A	18.81	3.703162	0.68501	.	.	ENSG00000196235	ENST00000432763;ENST00000402194;ENST00000378524;ENST00000359191	.	.	.	4.83	4.83	0.62350	.	0.000000	0.85682	D	0.000000	T	0.61464	0.2349	L	0.36672	1.1	0.80722	D	1	D;D;P	0.71674	0.998;0.964;0.939	P;P;P	0.59288	0.855;0.819;0.664	T	0.59815	-0.7383	8	.	.	.	-16.7403	13.5134	0.61526	1.0:0.0:0.0:0.0	.	677;881;885	B4DJK4;O00267-2;O00267	.;.;SPT5H_HUMAN	C	885;881;863;885	.	.	Y	+	2	0	SUPT5H	44656716	1.000000	0.71417	1.000000	0.80357	0.853000	0.48598	8.865000	0.92300	2.034000	0.60081	0.379000	0.24179	TAC	.	.	none		0.627	SUPT5H-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464918.1	NM_003169	
RGAG1	57529	hgsc.bcm.edu	37	X	109697658	109697658	+	Silent	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:109697658G>A	ENST00000465301.2	+	3	4059	c.3813G>A	c.(3811-3813)cgG>cgA	p.R1271R	RGAG1_ENST00000540313.1_Silent_p.R1271R	NM_020769.2	NP_065820.1	Q8NET4	RGAG1_HUMAN	retrotransposon gag domain containing 1	1271										NS(1)|autonomic_ganglia(1)|breast(2)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(15)|liver(1)|lung(29)|ovary(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	73						CCATTCTACGGACCAGGTTTC	0.522																																					p.R1271R		Atlas-SNP	.											.	RGAG1	168	.	0			c.G3813A						PASS	.						126.0	122.0	123.0					X																	109697658		2203	4300	6503	SO:0001819	synonymous_variant	57529	exon3			TCTACGGACCAGG	AY121804	CCDS14552.1	Xq23	2008-02-05			ENSG00000243978	ENSG00000243978			29245	protein-coding gene	gene with protein product						10718198, 15716091, 16093683	Standard	NM_020769		Approved	KIAA1318, Mart9, Mar9	uc004eor.2	Q8NET4	OTTHUMG00000022196	ENST00000465301.2:c.3813G>A	X.37:g.109697658G>A		Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	107	8	0.0747664	NM_020769	Q9P2M8	Silent	SNP	ENST00000465301.2	37	CCDS14552.1																																																																																			.	.	none		0.522	RGAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057906.2	NM_020769	
MST1L	11223	hgsc.bcm.edu	37	1	17085373	17085373	+	RNA	SNP	C	C	T	rs2092130		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:17085373C>T	ENST00000455405.2	-	0	0							Q2TV78	MST1L_HUMAN	macrophage stimulating 1-like							extracellular region (GO:0005576)	serine-type endopeptidase activity (GO:0004252)	p.G440R(1)|p.G397R(1)									TGGCTATCCCCATCTGGGTCT	0.602																																					p.G440R		Atlas-SNP	.											Q13209_HUMAN,NS,carcinoma,0,6	.	.	6	2	Substitution - Missense(2)	kidney(2)	c.G1318A						scavenged	.																																					11223	exon10			TATCCCCATCTGG	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.17085373C>T		Somatic	600	24	0.04		WXS	Illumina HiSeq	Phase_I	630	44	0.0698413	NM_001271733	B7WPB1|Q13209	Missense_Mutation	SNP	ENST00000455405.2	37		.	.	.	.	.	.	.	.	.	.	.	3.164	-0.171433	0.06421	.	.	ENSG00000186715	ENST00000389184;ENST00000334998;ENST00000442552	.	.	.	.	.	.	.	0.699669	0.12362	N	0.475555	T	0.21761	0.0524	.	.	.	.	.	.	B	0.16166	0.016	B	0.17979	0.02	T	0.23940	-1.0174	5	.	.	.	.	3.5811	0.07954	2.0E-4:0.4998:0.4998:2.0E-4	rs2092130;rs2095110;rs4567270;rs9701105	440	Q2TV78-2	.	R	397;440;440	.	.	G	-	1	0	MST1P9	16957960	1.000000	0.71417	0.000000	0.03702	0.000000	0.00434	1.482000	0.35486	-0.000000	0.14550	0.000000	0.15137	GGG	C|1.000;|0.000	.	weak		0.602	MST1L-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000400328.1	NM_001271733	
MUC2	4583	hgsc.bcm.edu	37	11	1093365	1093365	+	Silent	SNP	T	T	C	rs56021606	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:1093365T>C	ENST00000441003.2	+	30	5211	c.5184T>C	c.(5182-5184)acT>acC	p.T1728T	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Silent_p.T1695T|MUC2_ENST00000333592.6_Silent_p.T16T	NM_002457.2	NP_002448.2	Q02817	MUC2_HUMAN	mucin 2, oligomeric mucus/gel-forming	0	Approximate repeats.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	Golgi lumen (GO:0005796)|inner mucus layer (GO:0070702)|outer mucus layer (GO:0070703)				NS(3)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(5)|lung(22)|ovary(2)|prostate(16)|skin(5)|stomach(1)|upper_aerodigestive_tract(2)	102		all_cancers(49;1.08e-07)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.191)		BRCA - Breast invasive adenocarcinoma(625;0.000207)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)	Pranlukast(DB01411)	ccaccaccactacggtgaccc	0.652																																					p.T1728T		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,+1,6	MUC2	614	6	0			c.T5184C						scavenged	.																																			SO:0001819	synonymous_variant	4583	exon30			CACCACTACGGTG	L21998		11p15.5	2011-01-28	2006-03-14		ENSG00000198788	ENSG00000198788		"""Mucins"""	7512	protein-coding gene	gene with protein product		158370	"""mucin 2, intestinal/tracheal"""			15081123	Standard	NM_002457		Approved		uc001lsx.1	Q02817	OTTHUMG00000156800	ENST00000441003.2:c.5184T>C	11.37:g.1093365T>C		Somatic	81	14	0.17284		WXS	Illumina HiSeq	Phase_I	92	9	0.0978261	NM_002457	Q14878	Silent	SNP	ENST00000441003.2	37																																																																																				T|0.500;C|0.500	0.500	strong		0.652	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
TNXB	7148	hgsc.bcm.edu	37	6	32021402	32021402	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:32021402C>T	ENST00000375244.3	-	25	8755	c.8554G>A	c.(8554-8556)Gtg>Atg	p.V2852M	TNXB_ENST00000375247.2_Missense_Mutation_p.V2850M			P22105	TENX_HUMAN	tenascin XB	2899	Fibronectin type-III 20. {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)	p.V2852M(1)|p.V2928M(1)		endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GCATCTGTCACGGTCAGCTCC	0.632																																					p.V2850M		Atlas-SNP	.											TNXB_ENST00000375247,NS,carcinoma,0,2	TNXB	553	2	2	Substitution - Missense(2)	lung(2)	c.G8548A						scavenged	.						76.0	87.0	83.0					6																	32021402		1327	2582	3909	SO:0001583	missense	7148	exon25			CTGTCACGGTCAG	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.8554G>A	6.37:g.32021402C>T	ENSP00000364393:p.Val2852Met	Somatic	184	0	0		WXS	Illumina HiSeq	Phase_I	193	2	0.0103627	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Missense_Mutation	SNP	ENST00000375244.3	37		.	.	.	.	.	.	.	.	.	.	c	13.97	2.397061	0.42512	.	.	ENSG00000168477	ENST00000375244;ENST00000375247	T;T	0.61158	0.13;0.13	4.38	4.38	0.52667	.	.	.	.	.	T	0.78547	0.4300	H	0.95982	3.75	0.28037	N	0.933906	D	0.89917	1.0	D	0.91635	0.999	T	0.75013	-0.3467	9	0.66056	D	0.02	.	13.8698	0.63612	0.0:1.0:0.0:0.0	.	2850	P22105-3	.	M	2852;2850	ENSP00000364393:V2852M;ENSP00000364396:V2850M	ENSP00000364393:V2852M	V	-	1	0	TNXB	32129380	0.227000	0.23707	0.514000	0.27761	0.139000	0.21198	1.178000	0.31981	1.985000	0.57927	0.536000	0.68110	GTG	.	.	none		0.632	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
VIT	5212	hgsc.bcm.edu	37	2	36970315	36970315	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:36970315C>A	ENST00000389975.3	+	4	493	c.191C>A	c.(190-192)gCa>gAa	p.A64E	VIT_ENST00000401530.1_Missense_Mutation_p.A64E|VIT_ENST00000404084.1_Missense_Mutation_p.A42E|VIT_ENST00000497382.1_5'UTR|VIT_ENST00000379241.3_Missense_Mutation_p.A64E|VIT_ENST00000457137.2_Missense_Mutation_p.A64E|VIT_ENST00000379242.3_Missense_Mutation_p.A64E	NM_001177969.1|NM_001177970.1	NP_001171440.1|NP_001171441.1	Q6UXI7	VITRN_HUMAN	vitrin	64	LCCL. {ECO:0000255|PROSITE- ProRule:PRU00123}.				extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	interstitial matrix (GO:0005614)	glycosaminoglycan binding (GO:0005539)			autonomic_ganglia(1)|breast(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(15)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	57		all_hematologic(82;0.248)				AAATGTCCAGCAGGATGCCAA	0.483																																					p.A64E		Atlas-SNP	.											.	VIT	138	.	0			c.C191A						PASS	.						173.0	142.0	152.0					2																	36970315		2203	4300	6503	SO:0001583	missense	5212	exon4			GTCCAGCAGGATG	AF063833	CCDS33180.1, CCDS54347.1, CCDS54348.1, CCDS54349.1, CCDS54350.1	2p22.2	2008-05-15			ENSG00000205221	ENSG00000205221			12697	protein-coding gene	gene with protein product							Standard	NM_001177969		Approved		uc002rpl.3	Q6UXI7	OTTHUMG00000152149	ENST00000389975.3:c.191C>A	2.37:g.36970315C>A	ENSP00000374625:p.Ala64Glu	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	101	48	0.475248	NM_001177969	A1A526|A6NKI9|A8K7Y4|E9PF47|Q6P7T3|Q96DM8|Q96DT1|Q9UDN0	Missense_Mutation	SNP	ENST00000389975.3	37	CCDS54347.1	.	.	.	.	.	.	.	.	.	.	C	26.3	4.721566	0.89298	.	.	ENSG00000205221	ENST00000379242;ENST00000389975;ENST00000402257;ENST00000457137;ENST00000404084;ENST00000379241;ENST00000401530	D;D;D;D;D;D	0.89681	-2.55;-2.55;-2.55;-2.55;-2.55;-2.55	4.77	4.77	0.60923	LCCL (5);	0.124941	0.52532	D	0.000062	D	0.93598	0.7956	M	0.75777	2.31	0.47584	D	0.999461	D;D;D;D;D;D	0.71674	0.998;0.998;0.994;0.996;0.995;0.997	D;P;P;D;P;P	0.65773	0.932;0.903;0.897;0.938;0.888;0.888	D	0.94337	0.7567	10	0.72032	D	0.01	-8.2082	16.3687	0.83346	0.0:1.0:0.0:0.0	.	64;64;64;64;64;64	B4DRU4;E9PF47;Q6UXI7-2;Q6UXI7;Q6UXI7-4;Q6UXI7-3	.;.;.;VITRN_HUMAN;.;.	E	64;64;64;64;42;64;64	ENSP00000368544:A64E;ENSP00000374625:A64E;ENSP00000393561:A64E;ENSP00000384154:A42E;ENSP00000368543:A64E;ENSP00000385658:A64E	ENSP00000368543:A64E	A	+	2	0	VIT	36823819	1.000000	0.71417	0.995000	0.50966	0.912000	0.54170	5.496000	0.66918	2.358000	0.79984	0.650000	0.86243	GCA	.	.	none		0.483	VIT-201	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding			
PHEX	5251	hgsc.bcm.edu	37	X	22117216	22117216	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:22117216C>T	ENST00000379374.4	+	9	1591	c.1026C>T	c.(1024-1026)cgC>cgT	p.R342R	PHEX_ENST00000475778.1_3'UTR|PHEX_ENST00000537599.1_Silent_p.R342R|PHEX_ENST00000418858.3_Silent_p.R45R|PHEX_ENST00000535894.1_Silent_p.R245R	NM_000444.4	NP_000435.3	P78562	PHEX_HUMAN	phosphate regulating endopeptidase homolog, X-linked	342					bone mineralization (GO:0030282)|cell-cell signaling (GO:0007267)|cellular protein modification process (GO:0006464)|organophosphate metabolic process (GO:0019637)|proteolysis (GO:0006508)|skeletal system development (GO:0001501)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	aminopeptidase activity (GO:0004177)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			breast(1)|cervix(2)|endometrium(2)|large_intestine(12)|liver(1)|lung(19)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	42						TGGTGGTCCGCGTCCCGCAGT	0.448																																					p.R342R		Atlas-SNP	.											.	PHEX	95	.	0			c.C1026T						PASS	.						117.0	106.0	110.0					X																	22117216		2203	4300	6503	SO:0001819	synonymous_variant	5251	exon9			GGTCCGCGTCCCG	U82970	CCDS14204.1	Xp22.2-p22.1	2008-07-31	2008-07-31		ENSG00000102174	ENSG00000102174			8918	protein-coding gene	gene with protein product		300550	"""phosphate regulating gene with homologies to endopeptidases on the X chromosome (hypophosphatemia, vitamin D resistant rickets)"""	HYP, HPDR		7550339, 9070861	Standard	NM_000444		Approved	PEX, HPDR1, HYP1, XLH	uc004dah.3	P78562	OTTHUMG00000021241	ENST00000379374.4:c.1026C>T	X.37:g.22117216C>T		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	64	6	0.09375	NM_000444	O00678|Q13646|Q2M325|Q93032|Q99827	Silent	SNP	ENST00000379374.4	37	CCDS14204.1																																																																																			.	.	none		0.448	PHEX-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056035.1	NM_000444	
HLA-DQB1	3119	hgsc.bcm.edu	37	6	32634341	32634341	+	Missense_Mutation	SNP	A	A	G	rs3189152	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:32634341A>G	ENST00000399082.3	-	1	88	c.44T>C	c.(43-45)gTa>gCa	p.V15A	HLA-DQB1_ENST00000399079.3_Missense_Mutation_p.V15A|HLA-DQB1_ENST00000399084.1_Missense_Mutation_p.V15A|HLA-DQB1_ENST00000374943.4_Missense_Mutation_p.V15A|HLA-DQB1_ENST00000434651.2_Missense_Mutation_p.V15A			P01920	DQB1_HUMAN	major histocompatibility complex, class II, DQ beta 1	15			A -> V (in allele DQB1*03:02, allele DQB1*03:03, allele DQB1*04:01, allele DQB1*05:01, allele DQB1*05:02, allele DQB1*06:02 and allele DQB1*06:12; dbSNP:rs3189152). {ECO:0000269|PubMed:3584986}.		antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cytokine-mediated signaling pathway (GO:0019221)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|immune response (GO:0006955)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|interferon-gamma-mediated signaling pathway (GO:0060333)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)	clathrin-coated endocytic vesicle membrane (GO:0030669)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)|integral component of lumenal side of endoplasmic reticulum membrane (GO:0071556)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|MHC class II protein complex (GO:0042613)|plasma membrane (GO:0005886)|trans-Golgi network membrane (GO:0032588)|transport vesicle membrane (GO:0030658)	MHC class II receptor activity (GO:0032395)|peptide antigen binding (GO:0042605)			breast(1)|large_intestine(1)|lung(1)|pancreas(1)	4					"""""""Insulin(DB00071)"""	GACAGTTGCTACCCGAAGGTC	0.577									T-cell Lymphoma, (Cutaneous) , Familial Clustering of;Sjgren syndrome;Melanoma, Familial Clustering of;ACTH-independent macronodular adrenal hyperplasia				a|||	1916	0.382588	0.3646	0.3487	5008	,	,		10661	0.3661		0.3549	False		,,,				2504	0.4765				p.V15A	Esophageal Squamous(151;720 1825 15000 40336 43415)	Atlas-SNP	.											HLA-DQB1,NS,carcinoma,0,1	HLA-DQB1	15	1	0			c.T44C						scavenged	.	G	ALA/VAL	1086,2800		255,576,1112	53.0	51.0	52.0		44	-0.2	0.0	6	dbSNP_105	52	2480,5732		644,1192,2270	yes	missense	HLA-DQB1	NM_002123.4	64	899,1768,3382	GG,GA,AA		30.1997,27.9465,29.4759	benign	15/262	32634341	3566,8532	1943	4106	6049	SO:0001583	missense	3119	exon1	Familial Cancer Database	incl.: Mycosis Fungoides, Sezary syndrome, Adult T-cell Lymphoma;Sjogren syndrome; ;AIMAH, Cushing disease, Adrenal, Familial	GTTGCTACCCGAA		CCDS43451.1, CCDS59006.1	6p21.3	2013-01-11			ENSG00000179344	ENSG00000179344		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4944	protein-coding gene	gene with protein product		604305		HLA-DQB			Standard	NM_001243962		Approved	IDDM1, CELIAC1	uc031snw.1	P01920	OTTHUMG00000031124	ENST00000399082.3:c.44T>C	6.37:g.32634341A>G	ENSP00000382032:p.Val15Ala	Somatic	6	6	1		WXS	Illumina HiSeq	Phase_I	20	20	1	NM_002123	A1KR27|A2RPH3|A4Q9R4|A4USG2|A4USG5|A6N8I7|A9YQA0|B0S7Y7|B1A0K6|B1GXI3|B3VLT3|B5BLN7|B7VU69|C0MQ34|C0MQ35|C8ZL52|C8ZLJ8|C8ZLJ9|C9DRQ3|O19708|O19713|O19724|O62861|O78046|O78221|O78223|O98034|O98201|P01917|P01918|P01919|P03992|P05537|P79482|P79526|P79544|P79551|Q08GC8|Q09035|Q0E4V9|Q1M312|Q29731|Q29877|Q29884|Q29915|Q29966|Q2P9N3|Q2QK85|Q30061|Q30075|Q30076|Q30080|Q30081|Q30082|Q30083|Q30084|Q30089|Q30095|Q31633|Q38I47|Q45UE3|Q4QZB5|Q53I44|Q564J6|Q5G841|Q5ISH1|Q5ISH3|Q5W1E1|Q5Y7G8|Q643R4|Q6B9X1|Q70VH8|Q7YP69|Q8HWH0|Q8MH58|Q8SNB4|Q8SND1|Q8SP70|Q8WMA3|Q9BD17|Q9MYH2|Q9TPA9|Q9XRY6|Q9XRY7|Q9XRZ2	Missense_Mutation	SNP	ENST00000399082.3	37		634	0.2902930402930403	133	0.2703252032520325	113	0.31215469613259667	187	0.3269230769230769	201	0.26517150395778366	.	0.440	-0.899235	0.02472	0.279465	0.301997	ENSG00000179344	ENST00000399082;ENST00000399079;ENST00000374943;ENST00000434651;ENST00000399084;ENST00000447884	T;T;T;T;T	0.03496	3.91;8.45;8.45;8.45;8.45	4.07	-0.196	0.13232	.	536.546000	0.00447	N	0.000082	T	0.00906	0.0030	.	.	.	0.80722	P	0.0	B;B;B;B	0.14438	0.01;0.0;0.0;0.0	B;B;B;B	0.11329	0.006;0.0;0.0;0.0	T	0.47394	-0.9121	8	0.45353	T	0.12	.	2.9773	0.05942	0.1685:0.2496:0.4568:0.125	rs3189152;rs9274520	25;15;15;15	Q59F80;A2AAZ0;Q5Y7D6;Q5Y7A9	.;.;.;.	A	15	ENSP00000382032:V15A;ENSP00000382029:V15A;ENSP00000364080:V15A;ENSP00000407332:V15A;ENSP00000382034:V15A	ENSP00000364080:V15A	V	-	2	0	HLA-DQB1	32742319	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.331000	0.07914	-0.498000	0.06632	-3.953000	0.00015	GTA	A|0.710;G|0.290	0.290	strong		0.577	HLA-DQB1-007	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000276131.1	NM_002123	
MUC4	4585	hgsc.bcm.edu	37	3	195508722	195508722	+	Silent	SNP	G	G	T	rs201248411	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:195508722G>T	ENST00000463781.3	-	2	10188	c.9729C>A	c.(9727-9729)acC>acA	p.T3243T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T3243T	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	992					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.T3243T(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)		TGGCATGACCGGTGGATGCTG	0.577													.|||	14	0.00279553	0.0083	0.0014	5008	,	,		10446	0.001		0.001	False		,,,				2504	0.0				p.T3243T		Atlas-SNP	.											MUC4_ENST00000463781,brain,primitive_neuroectodermal_tumour-medulloblastoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	central_nervous_system(1)	c.C9729A						scavenged	.						2.0	2.0	2.0					3																	195508722		481	1089	1570	SO:0001819	synonymous_variant	4585	exon2			ATGACCGGTGGAT	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.9729C>A	3.37:g.195508722G>T		Somatic	93	1	0.0107527		WXS	Illumina HiSeq	Phase_I	114	2	0.0175439	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Silent	SNP	ENST00000463781.3	37	CCDS54700.1																																																																																			.	.	weak		0.577	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
SHPRH	257218	hgsc.bcm.edu	37	6	146215303	146215303	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:146215303G>A	ENST00000367505.2	-	27	4942	c.4678C>T	c.(4678-4680)Cgt>Tgt	p.R1560C	SHPRH_ENST00000438092.2_Missense_Mutation_p.R1564C|SHPRH_ENST00000367503.3_Missense_Mutation_p.R1564C|SHPRH_ENST00000275233.7_Missense_Mutation_p.R1560C			Q149N8	SHPRH_HUMAN	SNF2 histone linker PHD RING helicase, E3 ubiquitin protein ligase	1560	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				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)		GTCTTAACACGACTGATTTGT	0.308																																					p.R1564C		Atlas-SNP	.											SHPRH_ENST00000367505,NS,carcinoma,+1,3	SHPRH	169	3	0			c.C4690T						scavenged	.						116.0	108.0	111.0					6																	146215303		1835	4097	5932	SO:0001583	missense	257218	exon27			TAACACGACTGAT	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.4678C>T	6.37:g.146215303G>A	ENSP00000356475:p.Arg1560Cys	Somatic	62	0	0		WXS	Illumina HiSeq	Phase_I	81	2	0.0246914	NM_173082	Q149N9|Q5VV79|Q68DS5|Q7Z5J5|Q8IVE8|Q8IWQ9|Q8N1S8|Q8NBR7	Missense_Mutation	SNP	ENST00000367505.2	37	CCDS43513.2	.	.	.	.	.	.	.	.	.	.	G	19.09	3.759830	0.69763	.	.	ENSG00000146414	ENST00000367507;ENST00000367505;ENST00000367503;ENST00000438092;ENST00000275233	T;T;T;T	0.75477	-0.94;-0.94;-0.94;-0.94	5.46	4.54	0.55810	Helicase, C-terminal (2);	0.073245	0.53938	D	0.000048	T	0.64216	0.2578	N	0.14661	0.345	0.58432	D	0.999993	D;D	0.76494	0.999;0.999	P;P	0.60682	0.878;0.72	T	0.70037	-0.4982	10	0.56958	D	0.05	-17.4466	11.7616	0.51908	0.0:0.2721:0.7279:0.0	.	1560;1564	Q149N8;Q149N8-4	SHPRH_HUMAN;.	C	8;1560;1564;1564;1560	ENSP00000356475:R1560C;ENSP00000356473:R1564C;ENSP00000412797:R1564C;ENSP00000275233:R1560C	ENSP00000275233:R1560C	R	-	1	0	SHPRH	146256996	1.000000	0.71417	1.000000	0.80357	0.881000	0.50899	6.241000	0.72369	2.710000	0.92621	0.585000	0.79938	CGT	.	.	none		0.308	SHPRH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000042571.2	NM_173082	
MUC2	4583	hgsc.bcm.edu	37	11	1093411	1093411	+	Missense_Mutation	SNP	A	A	C	rs55824838		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:1093411A>C	ENST00000441003.2	+	30	5257	c.5230A>C	c.(5230-5232)Acg>Ccg	p.T1744P	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.T1711P|MUC2_ENST00000333592.6_Missense_Mutation_p.T32P	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)	gaccccaaccacgacacccat	0.642																																					p.T1744P		Atlas-SNP	.											MUC2_ENST00000441003,NS,lymphoid_neoplasm,-1,4	MUC2	614	4	0			c.A5230C						scavenged	.						210.0	243.0	232.0					11																	1093411		2024	3933	5957	SO:0001583	missense	4583	exon30			CCAACCACGACAC	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.5230A>C	11.37:g.1093411A>C	ENSP00000415183:p.Thr1744Pro	Somatic	76	2	0.0263158		WXS	Illumina HiSeq	Phase_I	89	13	0.146067	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	a	1.604	-0.525698	0.04141	.	.	ENSG00000198788	ENST00000441003;ENST00000359061;ENST00000333592	T;T;T	0.11604	2.8;2.76;2.79	1.64	-3.28	0.05033	.	2.578920	0.03359	U	0.197396	T	0.06508	0.0167	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27938	-1.0059	9	0.34782	T	0.22	.	0.093	0.00041	0.343:0.2052:0.1661:0.2856	rs55824838	1744	E7EUV1	.	P	1744;1711;32	ENSP00000415183:T1744P;ENSP00000351956:T1711P;ENSP00000331373:T32P	ENSP00000331373:T32P	T	+	1	0	MUC2	1083411	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-1.917000	0.01575	-3.171000	0.00225	-3.140000	0.00059	ACG	.	.	weak		0.642	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
SNED1	25992	hgsc.bcm.edu	37	2	241992639	241992639	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:241992639C>T	ENST00000310397.8	+	16	2153	c.2153C>T	c.(2152-2154)gCg>gTg	p.A718V	AC005237.4_ENST00000458377.1_RNA|SNED1_ENST00000405547.3_Missense_Mutation_p.A718V|SNED1_ENST00000469006.1_3'UTR|SNED1_ENST00000342631.6_Missense_Mutation_p.A718V|SNED1_ENST00000401884.1_Missense_Mutation_p.A718V	NM_001080437.1	NP_001073906.1	Q8TER0	SNED1_HUMAN	sushi, nidogen and EGF-like domains 1	718	Sushi. {ECO:0000255|PROSITE- ProRule:PRU00302}.				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)		CGGCTGGGCGCGGTGGCCCTG	0.697																																					p.A718V		Atlas-SNP	.											.	SNED1	76	.	0			c.C2153T						PASS	.						19.0	25.0	23.0					2																	241992639		2042	4152	6194	SO:0001583	missense	25992	exon16			TGGGCGCGGTGGC	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.2153C>T	2.37:g.241992639C>T	ENSP00000308893:p.Ala718Val	Somatic	63	0	0		WXS	Illumina HiSeq	Phase_I	46	29	0.630435	NM_001080437	B5MDC3|B7WNK6|B7WPM0|Q336F4|Q336F5|Q8N369|Q8TEP7	Missense_Mutation	SNP	ENST00000310397.8	37	CCDS46562.1	.	.	.	.	.	.	.	.	.	.	C	9.411	1.080605	0.20309	.	.	ENSG00000162804	ENST00000401884;ENST00000405547;ENST00000310397;ENST00000342631	T;T;T;T	0.25414	1.8;1.8;1.8;1.8	4.28	4.28	0.50868	Complement control module (1);Sushi/SCR/CCP (2);	0.437637	0.19414	N	0.114867	T	0.16514	0.0397	L	0.39326	1.205	0.24368	N	0.994843	P	0.42993	0.797	B	0.27500	0.08	T	0.14643	-1.0465	10	0.33141	T	0.24	.	12.5961	0.56470	0.0:0.8327:0.1673:0.0	.	718	Q8TER0	SNED1_HUMAN	V	718	ENSP00000384871:A718V;ENSP00000386007:A718V;ENSP00000308893:A718V;ENSP00000342992:A718V	ENSP00000308893:A718V	A	+	2	0	SNED1	241641312	0.996000	0.38824	0.010000	0.14722	0.007000	0.05969	4.403000	0.59729	1.927000	0.55829	0.561000	0.74099	GCG	.	.	none		0.697	SNED1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323935.2	XM_059482	
MBD3L2	125997	hgsc.bcm.edu	37	19	7051376	7051376	+	Missense_Mutation	SNP	G	G	A	rs200081225	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:7051376G>A	ENST00000381393.3	+	2	423	c.370G>A	c.(370-372)Ggt>Agt	p.G124S		NM_144614.3	NP_653215.2	Q8NHZ7	MB3L2_HUMAN	methyl-CpG binding domain protein 3-like 2	124				G -> S (in Ref. 1; AAM28154 and 3; BE502398). {ECO:0000305}.						endometrium(1)	1	all_hematologic(4;0.166)			Lung(535;0.179)		GGGGACGGCCGGTGAATCTCT	0.637													-|||	3194	0.63778	0.562	0.6931	5008	,	,		28287	0.6002		0.659	False		,,,				2504	0.7178				p.G124S		Atlas-SNP	.											MBD3L2,cerebellum,glioma,0,1	MBD3L2	2	1	0			c.G370A						scavenged	.						1.0	1.0	1.0					19																	7051376		536	1374	1910	SO:0001583	missense	125997	exon2			ACGGCCGGTGAAT	AF503919	CCDS42483.1	19p13.3	2011-01-31			ENSG00000230522	ENSG00000230522			18532	protein-coding gene	gene with protein product		607964					Standard	NM_144614		Approved		uc010dvf.1	Q8NHZ7		ENST00000381393.3:c.370G>A	19.37:g.7051376G>A	ENSP00000370800:p.Gly124Ser	Somatic	156	152	0.974359		WXS	Illumina HiSeq	Phase_I	196	191	0.97449	NM_144614		Missense_Mutation	SNP	ENST00000381393.3	37	CCDS42483.1	.	.	.	.	.	.	.	.	.	.	.	5.414	0.261475	0.10239	.	.	ENSG00000230522	ENST00000412046;ENST00000381393	.	.	.	0.791	-0.446	0.12238	.	.	.	.	.	T	0.23611	0.0571	L	0.54323	1.7	0.80722	P	0.0	P	0.51537	0.946	B	0.41088	0.347	T	0.33007	-0.9885	7	0.08837	T	0.75	-14.6112	3.2492	0.06808	0.3319:0.0:0.6681:0.0	.	124	Q8NHZ7	MB3L2_HUMAN	S	124	.	ENSP00000370800:G124S	G	+	1	0	MBD3L2	7002376	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	0.103000	0.15292	-0.088000	0.12506	0.448000	0.29417	GGT	.	.	weak		0.637	MBD3L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000458499.1	NM_144614	
MTMR10	54893	hgsc.bcm.edu	37	15	31266590	31266590	+	Nonsense_Mutation	SNP	A	A	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:31266590A>C	ENST00000435680.1	-	5	498	c.401T>G	c.(400-402)tTa>tGa	p.L134*	MTMR10_ENST00000425768.1_Nonsense_Mutation_p.L134*|MTMR10_ENST00000314404.8_5'UTR|MTMR10_ENST00000563714.1_Nonsense_Mutation_p.L52*	NM_017762.2	NP_060232.2	Q9NXD2	MTMRA_HUMAN	myotubularin related protein 10	134							phosphatase activity (GO:0016791)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(2)|large_intestine(2)|ovary(1)|upper_aerodigestive_tract(1)	9		all_lung(180;2.81e-11)		all cancers(64;7.26e-15)|Epithelial(43;7.2e-11)|GBM - Glioblastoma multiforme(186;0.000158)|BRCA - Breast invasive adenocarcinoma(123;0.00426)|Lung(196;0.174)		ATAAATAATTAACTCTGTTGG	0.323																																					p.L134X		Atlas-SNP	.											.	MTMR10	74	.	0			c.T401G						PASS	.						52.0	52.0	52.0					15																	31266590		1797	4057	5854	SO:0001587	stop_gained	54893	exon5			ATAATTAACTCTG	AK000320	CCDS45204.1	15q13.3	2011-06-09				ENSG00000166912		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	25999	protein-coding gene	gene with protein product						12495846	Standard	NM_017762		Approved	FLJ20313	uc001zfh.1	Q9NXD2		ENST00000435680.1:c.401T>G	15.37:g.31266590A>C	ENSP00000402537:p.Leu134*	Somatic	104	0	0		WXS	Illumina HiSeq	Phase_I	127	70	0.551181	NM_017762	Q6P4Q6	Nonsense_Mutation	SNP	ENST00000435680.1	37	CCDS45204.1	.	.	.	.	.	.	.	.	.	.	A	37	6.370397	0.97511	.	.	ENSG00000166912	ENST00000435680;ENST00000425768;ENST00000340566	.	.	.	5.49	3.15	0.36227	.	0.065888	0.64402	D	0.000011	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	7.7074	0.28659	0.8072:0.0:0.068:0.1248	.	.	.	.	X	134;134;52	.	ENSP00000340637:L52X	L	-	2	0	MTMR10	29053882	1.000000	0.71417	0.998000	0.56505	0.997000	0.91878	8.910000	0.92685	0.446000	0.26666	0.533000	0.62120	TTA	.	.	none		0.323	MTMR10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000430747.1	NM_017762	
DGKH	160851	hgsc.bcm.edu	37	13	42772647	42772647	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr13:42772647G>T	ENST00000337343.4	+	18	2222	c.2201G>T	c.(2200-2202)gGg>gTg	p.G734V	DGKH_ENST00000536612.1_Missense_Mutation_p.G598V|DGKH_ENST00000379274.2_Missense_Mutation_p.G598V|DGKH_ENST00000540693.1_Missense_Mutation_p.G734V|DGKH_ENST00000498255.2_3'UTR|DGKH_ENST00000538674.1_Missense_Mutation_p.G489V|DGKH_ENST00000261491.5_Missense_Mutation_p.G734V	NM_178009.3	NP_821077.1	Q86XP1	DGKH_HUMAN	diacylglycerol kinase, eta	734					blood coagulation (GO:0007596)|intracellular signal transduction (GO:0035556)|platelet activation (GO:0030168)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|protein oligomerization (GO:0051259)	cytoplasm (GO:0005737)|endosome (GO:0005768)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|diacylglycerol kinase activity (GO:0004143)|metal ion binding (GO:0046872)|NAD+ kinase activity (GO:0003951)	p.G734A(1)		breast(2)|endometrium(3)|kidney(5)|large_intestine(11)|lung(9)|ovary(4)|pancreas(1)|prostate(1)|skin(2)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	43		Lung NSC(96;1.02e-05)|Prostate(109;0.0168)|Lung SC(185;0.0262)|Breast(139;0.0709)|Hepatocellular(98;0.114)		OV - Ovarian serous cystadenocarcinoma(117;5.88e-05)|GBM - Glioblastoma multiforme(144;0.000935)|BRCA - Breast invasive adenocarcinoma(63;0.109)		TCAATTGCTGGGAGTTCGATT	0.418																																					p.G734V		Atlas-SNP	.											DGKH,colon,carcinoma,+1,2	DGKH	106	2	1	Substitution - Missense(1)	ovary(1)	c.G2201T						scavenged	.						136.0	127.0	130.0					13																	42772647		2203	4300	6503	SO:0001583	missense	160851	exon19			TTGCTGGGAGTTC	AB078967	CCDS9381.1, CCDS9382.1, CCDS55898.1	13q13.3	2013-01-10			ENSG00000102780	ENSG00000102780		"""Sterile alpha motif (SAM) domain containing"", ""Pleckstrin homology (PH) domain containing"""	2854	protein-coding gene	gene with protein product		604071				8702685	Standard	XM_005266271		Approved	DGKeta	uc001uyl.2	Q86XP1	OTTHUMG00000016804	ENST00000337343.4:c.2201G>T	13.37:g.42772647G>T	ENSP00000337572:p.Gly734Val	Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	169	2	0.0118343	NM_001204504	A2A2W7|A6NFX7|B4DZ34|Q5VZW0|Q6PI56|Q86XP2|Q8N3N0|Q8N7J9	Missense_Mutation	SNP	ENST00000337343.4	37	CCDS9381.1	.	.	.	.	.	.	.	.	.	.	G	21.5	4.155511	0.78114	.	.	ENSG00000102780	ENST00000540693;ENST00000337343;ENST00000261491;ENST00000379274;ENST00000536612;ENST00000538674	D;D;D;D;D;T	0.83075	-1.67;-1.54;-1.67;-1.68;-1.68;1.55	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.90971	0.7161	M	0.71581	2.175	0.80722	D	1	D;D;D;B	0.89917	0.998;0.99;1.0;0.435	D;P;D;B	0.91635	0.966;0.905;0.999;0.097	D	0.90533	0.4497	10	0.54805	T	0.06	.	19.8372	0.96661	0.0:0.0:1.0:0.0	.	489;598;734;734	F5GYP2;Q86XP1-3;Q86XP1-2;Q86XP1	.;.;.;DGKH_HUMAN	V	734;734;734;598;598;489	ENSP00000440823:G734V;ENSP00000337572:G734V;ENSP00000261491:G734V;ENSP00000368576:G598V;ENSP00000445114:G598V;ENSP00000441308:G489V	ENSP00000261491:G734V	G	+	2	0	DGKH	41670647	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	8.825000	0.92029	2.770000	0.95276	0.655000	0.94253	GGG	.	.	none		0.418	DGKH-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044699.2	NM_178009	
ATP11A	23250	hgsc.bcm.edu	37	13	113512594	113512594	+	Missense_Mutation	SNP	T	T	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr13:113512594T>A	ENST00000487903.1	+	22	2745	c.2657T>A	c.(2656-2658)tTc>tAc	p.F886Y	ATP11A_ENST00000283558.8_Missense_Mutation_p.F886Y|ATP11A_ENST00000375645.3_Missense_Mutation_p.F886Y|ATP11A_ENST00000375630.2_Missense_Mutation_p.F886Y			P98196	AT11A_HUMAN	ATPase, class VI, type 11A	886					phospholipid translocation (GO:0045332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)|recycling endosome (GO:0055037)	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(6)|kidney(4)|large_intestine(12)|lung(17)|ovary(4)|skin(1)|stomach(1)|urinary_tract(1)	51	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_lung(25;0.134)|all_epithelial(44;0.141)				GTGCAGTACTTCTTCTATAAG	0.498																																					p.F886Y		Atlas-SNP	.											ATP11A_ENST00000375630,NS,carcinoma,-1,4	ATP11A	225	4	0			c.T2657A						scavenged	.						75.0	75.0	75.0					13																	113512594		2203	4300	6503	SO:0001583	missense	23250	exon22			AGTACTTCTTCTA	AB028944	CCDS32011.1	13q34	2010-04-20	2007-09-19		ENSG00000068650	ENSG00000068650	3.6.3.1	"""ATPases / P-type"""	13552	protein-coding gene	gene with protein product	"""potential phospholipid-transporting ATPase IH"", ""phospholipid-translocating ATPase"""	605868	"""ATPase, Class VI, type 11A"""			11015572	Standard	NM_032189		Approved	ATPIH, ATPIS, KIAA1021	uc001vsj.4	P98196	OTTHUMG00000017371	ENST00000487903.1:c.2657T>A	13.37:g.113512594T>A	ENSP00000420387:p.Phe886Tyr	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	96	2	0.0208333	NM_032189	Q5VXT2	Missense_Mutation	SNP	ENST00000487903.1	37	CCDS32011.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	20.5|20.5	4.007441|4.007441	0.75046|0.75046	.|.	.|.	ENSG00000068650|ENSG00000068650	ENST00000487903;ENST00000375630;ENST00000375645;ENST00000283558;ENST00000432166|ENST00000418678	T;T;T;T|.	0.57107|.	0.42;0.42;0.42;0.42|.	5.62|5.62	5.62|5.62	0.85841|0.85841	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.80788|0.80788	0.4690|0.4690	M|M	0.88181|0.88181	2.935|2.935	0.80722|0.80722	D|D	1|1	D;P;B|.	0.65815|.	0.995;0.756;0.162|.	P;B;B|.	0.62435|.	0.902;0.391;0.285|.	D|D	0.84135|0.84135	0.0414|0.0414	10|5	0.39692|.	T|.	0.17|.	.|.	15.827|15.827	0.78718|0.78718	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	886;886;886|.	E9PCW5;E9PEJ6;P98196|.	.;.;AT11A_HUMAN|.	Y|T	886;886;886;886;327|861	ENSP00000420387:F886Y;ENSP00000364781:F886Y;ENSP00000364796:F886Y;ENSP00000283558:F886Y|.	ENSP00000283558:F886Y|.	F|S	+|+	2|1	0|0	ATP11A|ATP11A	112560595|112560595	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.778000|0.778000	0.44026|0.44026	7.223000|7.223000	0.78033|0.78033	2.129000|2.129000	0.65627|0.65627	0.533000|0.533000	0.62120|0.62120	TTC|TCT	.	.	none		0.498	ATP11A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045834.3	NM_015205	
PIKFYVE	200576	hgsc.bcm.edu	37	2	209215527	209215527	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:209215527C>T	ENST00000264380.4	+	37	5625	c.5467C>T	c.(5467-5469)Cgg>Tgg	p.R1823W		NM_015040.3	NP_055855.2	Q9Y2I7	FYV1_HUMAN	phosphoinositide kinase, FYVE finger containing	1823	PIPK. {ECO:0000255|PROSITE- ProRule:PRU00781}.				cellular protein metabolic process (GO:0044267)|intracellular signal transduction (GO:0035556)|myelin assembly (GO:0032288)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phospholipid metabolic process (GO:0006644)|protein localization to nucleus (GO:0034504)|retrograde transport, endosome to Golgi (GO:0042147)|small molecule metabolic process (GO:0044281)	cell-cell junction (GO:0005911)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome membrane (GO:0031901)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|late endosome membrane (GO:0031902)|membrane raft (GO:0045121)|perinuclear region of cytoplasm (GO:0048471)|vesicle membrane (GO:0012506)	1-phosphatidylinositol-3-phosphate 5-kinase activity (GO:0000285)|1-phosphatidylinositol-4-phosphate 5-kinase activity (GO:0016308)|ATP binding (GO:0005524)|phosphatidylinositol-3,5-bisphosphate 5-phosphatase activity (GO:0043813)|zinc ion binding (GO:0008270)			NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(14)|kidney(6)|large_intestine(25)|lung(40)|ovary(7)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	107						GTTTTACTGTCGGCTCTACTA	0.413																																					p.R1823W		Atlas-SNP	.											PIKFYVE,colon,carcinoma,-1,1	PIKFYVE	223	1	0			c.C5467T						scavenged	.						118.0	118.0	118.0					2																	209215527		2203	4300	6503	SO:0001583	missense	200576	exon37			TACTGTCGGCTCT	AB023198	CCDS2382.1, CCDS33368.1, CCDS54431.1	2q34	2014-01-15	2009-04-17	2009-04-17	ENSG00000115020	ENSG00000115020		"""Zinc fingers, FYVE domain containing"""	23785	protein-coding gene	gene with protein product	"""zinc finger, FYVE domain containing 29"""	609414	"""phosphatidylinositol-3-phosphate/phosphatidylinositol 5-kinase, type III"""	PIP5K3		9858586, 12270933	Standard	NM_015040		Approved	MGC40423, KIAA0981, PIKfyve, PIP5K, p235, ZFYVE29, FAB1	uc002vcz.3	Q9Y2I7	OTTHUMG00000132945	ENST00000264380.4:c.5467C>T	2.37:g.209215527C>T	ENSP00000264380:p.Arg1823Trp	Somatic	134	1	0.00746269		WXS	Illumina HiSeq	Phase_I	171	3	0.0175439	NM_015040	Q08AR7|Q08AR8|Q53ST3|Q53T36|Q8N5H0|Q8NB67	Missense_Mutation	SNP	ENST00000264380.4	37	CCDS2382.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.485260	0.84854	.	.	ENSG00000115020	ENST00000264380	T	0.30714	1.52	5.43	5.43	0.79202	Phosphatidylinositol-4-phosphate 5-kinase, core (1);Phosphatidylinositol-4-phosphate 5-kinase, core, subgroup (1);	0.000000	0.85682	D	0.000000	T	0.55257	0.1909	M	0.75777	2.31	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.58244	-0.7670	10	0.72032	D	0.01	-13.8009	13.991	0.64367	0.1506:0.8494:0.0:0.0	.	1823	Q9Y2I7	FYV1_HUMAN	W	1823	ENSP00000264380:R1823W	ENSP00000264380:R1823W	R	+	1	2	PIKFYVE	208923772	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.926000	0.70070	2.554000	0.86153	0.655000	0.94253	CGG	.	.	none		0.413	PIKFYVE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256477.2	NM_015040	
OR4C6	219432	hgsc.bcm.edu	37	11	55433434	55433434	+	Silent	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:55433434C>A	ENST00000314259.3	+	1	821	c.792C>A	c.(790-792)ccC>ccA	p.P264P		NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C, member 6	264						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.P264P(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						TCACTCACCCCATAGACAAGG	0.483																																					p.P264P		Atlas-SNP	.											OR4C6,NS,carcinoma,0,1	OR4C6	114	1	1	Substitution - coding silent(1)	lung(1)	c.C792A						PASS	.						105.0	103.0	104.0					11																	55433434		2200	4296	6496	SO:0001819	synonymous_variant	219432	exon1			TCACCCCATAGAC	CR593785	CCDS31506.1	11q11	2012-08-09			ENSG00000181903	ENSG00000181903		"""GPCR / Class A : Olfactory receptors"""	14743	protein-coding gene	gene with protein product							Standard	NM_001004704		Approved		uc010rik.2	Q8NH72	OTTHUMG00000166800	ENST00000314259.3:c.792C>A	11.37:g.55433434C>A		Somatic	106	0	0		WXS	Illumina HiSeq	Phase_I	146	64	0.438356	NM_001004704	B2RP11|Q6IFD2	Silent	SNP	ENST00000314259.3	37	CCDS31506.1																																																																																			.	.	none		0.483	OR4C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391504.1	NM_001004704	
MANEA	79694	hgsc.bcm.edu	37	6	96053987	96053987	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:96053987C>T	ENST00000358812.4	+	5	1229	c.1095C>T	c.(1093-1095)atC>atT	p.I365I		NM_024641.3	NP_078917.2	Q5SRI9	MANEA_HUMAN	mannosidase, endo-alpha	365	Catalytic. {ECO:0000305}.				cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glycoprotein endo-alpha-1,2-mannosidase activity (GO:0004569)			breast(2)|endometrium(3)|kidney(2)|liver(2)|lung(13)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)	26		all_cancers(76;1.01e-06)|Acute lymphoblastic leukemia(125;3.58e-09)|all_hematologic(75;1.22e-06)|all_epithelial(107;0.00433)|Colorectal(196;0.0341)		BRCA - Breast invasive adenocarcinoma(108;0.148)		ATACCAGCATCCGTCCATGGA	0.423																																					p.I365I		Atlas-SNP	.											.	MANEA	58	.	0			c.C1095T						PASS	.						99.0	107.0	104.0					6																	96053987		2203	4300	6503	SO:0001819	synonymous_variant	79694	exon5			CAGCATCCGTCCA	AK022900	CCDS5032.1	6q16.2	2008-02-05			ENSG00000172469	ENSG00000172469			21072	protein-coding gene	gene with protein product		612327					Standard	NM_024641		Approved	FLJ12838, mandaselin	uc003poo.2	Q5SRI9	OTTHUMG00000016296	ENST00000358812.4:c.1095C>T	6.37:g.96053987C>T		Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	50	28	0.56	NM_024641	A6H8M6|Q5SRJ0|Q6MZV0|Q70JE9|Q7Z3V7|Q8WWX5|Q9H9D2	Silent	SNP	ENST00000358812.4	37	CCDS5032.1																																																																																			.	.	none		0.423	MANEA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043644.1	NM_024641	
KLHL29	114818	hgsc.bcm.edu	37	2	23785138	23785138	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:23785138C>T	ENST00000486442.1	+	3	789	c.72C>T	c.(70-72)aaC>aaT	p.N24N		NM_052920.1	NP_443152.1	Q96CT2	KLH29_HUMAN	kelch-like family member 29	24										breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|lung(1)|ovary(3)	10						GGAGCGTCAACGGGACGCATG	0.701																																					p.N24N		Atlas-SNP	.											.	KLHL29	47	.	0			c.C72T						PASS	.						14.0	22.0	20.0					2																	23785138		692	1591	2283	SO:0001819	synonymous_variant	114818	exon3			CGTCAACGGGACG		CCDS54335.1	2p23.3	2013-09-27	2013-02-22	2007-01-09	ENSG00000119771	ENSG00000119771		"""Kelch-like"", ""BTB/POZ domain containing"""	29404	protein-coding gene	gene with protein product			"""kelch repeat and BTB (POZ) domain containing 9"", ""kelch-like 29 (Drosophila)"""	KBTBD9		11572484	Standard	NM_052920		Approved	KIAA1921	uc010ykg.2	Q96CT2	OTTHUMG00000151899	ENST00000486442.1:c.72C>T	2.37:g.23785138C>T		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	66	26	0.393939	NM_052920	Q8N388|Q96BF0|Q96PW7	Silent	SNP	ENST00000486442.1	37	CCDS54335.1																																																																																			.	.	none		0.701	KLHL29-001	KNOWN	mRNA_start_NF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324315.3	NM_052920	
MUC17	140453	hgsc.bcm.edu	37	7	100678918	100678918	+	Silent	SNP	G	G	A	rs200627718|rs71286278	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:100678918G>A	ENST00000306151.4	+	3	4285	c.4221G>A	c.(4219-4221)ccG>ccA	p.P1407P		NM_001040105.1	NP_001035194.1	Q685J3	MUC17_HUMAN	mucin 17, cell surface associated	1407	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)					GCACCACGCCGGTAGTCAGTT	0.512																																					p.P1407P		Atlas-SNP	.											MUC17,colon,carcinoma,+1,1	MUC17	804	1	0			c.G4221A						scavenged	.						272.0	277.0	276.0					7																	100678918		2203	4300	6503	SO:0001819	synonymous_variant	140453	exon3			CACGCCGGTAGTC	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.4221G>A	7.37:g.100678918G>A		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	90	3	0.0333333	NM_001040105	O14761|Q685J2|Q8TDH7	Silent	SNP	ENST00000306151.4	37	CCDS34711.1																																																																																			G|0.998;A|0.002	0.002	strong		0.512	MUC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347161.1	NM_001040105	
MAGI3	260425	hgsc.bcm.edu	37	1	114191926	114191926	+	Silent	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:114191926A>G	ENST00000307546.9	+	13	2298	c.2223A>G	c.(2221-2223)ctA>ctG	p.L741L	MAGI3_ENST00000369617.4_Silent_p.L766L|MAGI3_ENST00000369611.4_Silent_p.L741L|MAGI3_ENST00000369615.1_Silent_p.L741L	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	766					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)		TCAGGGTGCTAGGAGGAGATG	0.413																																					p.L741L		Atlas-SNP	.											.	MAGI3	181	.	0			c.A2223G						PASS	.						127.0	126.0	126.0					1																	114191926		2203	4300	6503	SO:0001819	synonymous_variant	260425	exon13			GGTGCTAGGAGGA	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.2223A>G	1.37:g.114191926A>G		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	85	4	0.0470588	NM_152900	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Silent	SNP	ENST00000307546.9	37	CCDS44196.1																																																																																			.	.	none		0.413	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900	
PLAC1	10761	hgsc.bcm.edu	37	X	133700486	133700486	+	Missense_Mutation	SNP	C	C	T	rs200146589		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:133700486C>T	ENST00000359237.4	-	3	512	c.227G>A	c.(226-228)cGt>cAt	p.R76H	PLAC1_ENST00000476971.1_5'UTR	NM_021796.3	NP_068568.1			placenta-specific 1											large_intestine(4)|lung(1)|pancreas(1)	6	Acute lymphoblastic leukemia(192;0.000127)					TTCAGTAACACGGTAGGTGAA	0.488													C|||	1	0.000264901	0.0	0.0	3775	,	,		17035	0.001		0.0	False		,,,				2504	0.0				p.R76H		Atlas-SNP	.											.	PLAC1	17	.	0			c.G227A						PASS	.						234.0	193.0	207.0					X																	133700486		2203	4300	6503	SO:0001583	missense	10761	exon3			GTAACACGGTAGG	AF234654	CCDS14642.1	Xq26.3	2013-10-14			ENSG00000170965	ENSG00000170965			9044	protein-coding gene	gene with protein product	"""cancer/testis antigen 92"""	300296				10995572	Standard	NM_021796		Approved	CT92, OOSP2L	uc004exo.1	Q9HBJ0	OTTHUMG00000022457	ENST00000359237.4:c.227G>A	X.37:g.133700486C>T	ENSP00000352173:p.Arg76His	Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	116	5	0.0431034	NM_021796		Missense_Mutation	SNP	ENST00000359237.4	37	CCDS14642.1	1	6.027727546714888E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	C	15.39	2.818858	0.50633	.	.	ENSG00000170965	ENST00000359237	D	0.82526	-1.62	4.5	3.63	0.41609	.	0.165937	0.29159	N	0.012976	D	0.88085	0.6342	M	0.72479	2.2	0.32859	D	0.507722	D	0.89917	1.0	D	0.76575	0.988	D	0.88235	0.2906	10	0.35671	T	0.21	-20.1143	8.8436	0.35157	0.2223:0.7777:0.0:0.0	.	76	Q9HBJ0	PLAC1_HUMAN	H	76	ENSP00000352173:R76H	ENSP00000352173:R76H	R	-	2	0	PLAC1	133528152	0.907000	0.30839	0.869000	0.34112	0.580000	0.36256	1.622000	0.36997	1.226000	0.43582	0.600000	0.82982	CGT	C|0.999;T|0.001	0.001	strong		0.488	PLAC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058375.1	NM_021796	
ANKRD35	148741	hgsc.bcm.edu	37	1	145561400	145561400	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:145561400G>A	ENST00000355594.4	+	10	1175	c.1088G>A	c.(1087-1089)cGg>cAg	p.R363Q		NM_144698.3	NP_653299.4	Q8N283	ANR35_HUMAN	ankyrin repeat domain 35	363										NS(1)|biliary_tract(1)|central_nervous_system(1)|endometrium(7)|kidney(2)|large_intestine(9)|lung(16)|ovary(4)|prostate(3)|skin(2)|urinary_tract(1)	47	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					TCTAGTCTCCGGCCTGGAGGG	0.567																																					p.R363Q	Melanoma(9;127 754 22988 51047)	Atlas-SNP	.											ANKRD35,NS,carcinoma,+1,1	ANKRD35	96	1	0			c.G1088A						scavenged	.						35.0	36.0	35.0					1																	145561400		2203	4300	6503	SO:0001583	missense	148741	exon10			GTCTCCGGCCTGG	AK091120	CCDS72867.1, CCDS72868.1	1q21.1	2013-01-10			ENSG00000198483	ENSG00000198483		"""Ankyrin repeat domain containing"""	26323	protein-coding gene	gene with protein product							Standard	NM_144698		Approved	FLJ25124	uc001eob.1	Q8N283	OTTHUMG00000013743	ENST00000355594.4:c.1088G>A	1.37:g.145561400G>A	ENSP00000347802:p.Arg363Gln	Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	155	2	0.0129032	NM_144698	A6NEU0|B4DL62|Q3MJ10|Q96LS3	Missense_Mutation	SNP	ENST00000355594.4	37	CCDS919.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.789105	0.49997	.	.	ENSG00000198483	ENST00000453670;ENST00000355594	T	0.78003	-1.14	6.07	5.16	0.70880	.	0.142348	0.32258	N	0.006342	T	0.55689	0.1936	M	0.70595	2.14	0.80722	D	1	B	0.30193	0.272	B	0.20955	0.032	T	0.58423	-0.7639	10	0.08381	T	0.77	-26.0565	11.2527	0.49034	0.0835:0.0:0.9165:0.0	.	363	Q8N283	ANR35_HUMAN	Q	272;363	ENSP00000347802:R363Q	ENSP00000347802:R363Q	R	+	2	0	ANKRD35	144272757	0.938000	0.31826	0.943000	0.38184	0.658000	0.38924	1.945000	0.40273	1.571000	0.49722	0.655000	0.94253	CGG	.	.	none		0.567	ANKRD35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038515.1	NM_144698	
TONSL	4796	hgsc.bcm.edu	37	8	145659566	145659566	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr8:145659566G>A	ENST00000409379.3	-	21	3211	c.3182C>T	c.(3181-3183)cCc>cTc	p.P1061L	AC084125.4_ENST00000544423.1_RNA	NM_013432.4	NP_038460.4	Q96HA7	TONSL_HUMAN	tonsoku-like, DNA repair protein	1061					cytoplasmic sequestering of transcription factor (GO:0042994)|double-strand break repair via homologous recombination (GO:0000724)|regulation of RNA biosynthetic process (GO:2001141)|replication fork processing (GO:0031297)	cytoplasm (GO:0005737)|nuclear replication fork (GO:0043596)|nucleus (GO:0005634)	histone binding (GO:0042393)|transcription corepressor activity (GO:0003714)			biliary_tract(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|lung(14)|ovary(3)|prostate(1)|skin(1)	26						CCGCAGCAGGGGTGTAAGCTG	0.697																																					p.P1061L		Atlas-SNP	.											TONSL_ENST00000409379,right_upper_lobe,carcinoma,0,2	TONSL	128	2	0			c.C3182T						scavenged	.						17.0	19.0	18.0					8																	145659566		2202	4293	6495	SO:0001583	missense	4796	exon21			AGCAGGGGTGTAA		CCDS34968.2	8q24.3	2013-01-10	2010-12-02	2010-11-30	ENSG00000160949	ENSG00000160949		"""Ankyrin repeat domain containing"""	7801	protein-coding gene	gene with protein product		604546	"""nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor-like 2"""	NFKBIL2		7738005, 11246458	Standard	NM_013432		Approved	IKBR	uc011llg.2	Q96HA7	OTTHUMG00000153122	ENST00000409379.3:c.3182C>T	8.37:g.145659566G>A	ENSP00000386239:p.Pro1061Leu	Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	129	2	0.0155039	NM_013432	B5MDP0|C9JKB1|C9JNV8|Q13006|Q9UGJ2	Missense_Mutation	SNP	ENST00000409379.3	37	CCDS34968.2	.	.	.	.	.	.	.	.	.	.	G	28.8	4.952988	0.92660	.	.	ENSG00000160949	ENST00000409379;ENST00000422691	T	0.49720	0.77	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	T	0.65365	0.2684	L	0.60455	1.87	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	T	0.68526	-0.5385	10	0.87932	D	0	-35.9592	15.9642	0.79952	0.0:0.0:1.0:0.0	.	1061	Q96HA7	TONSL_HUMAN	L	1061;1060	ENSP00000386239:P1061L	ENSP00000386239:P1061L	P	-	2	0	TONSL	145630374	1.000000	0.71417	0.925000	0.36789	0.966000	0.64601	8.797000	0.91882	2.368000	0.80403	0.462000	0.41574	CCC	.	.	none		0.697	TONSL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000329668.2	NM_013432	
PRKCSH	5589	hgsc.bcm.edu	37	19	11558370	11558370	+	Silent	SNP	G	G	A	rs77563879		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:11558370G>A	ENST00000589838.1	+	10	966	c.966G>A	c.(964-966)gaG>gaA	p.E322E	PRKCSH_ENST00000592741.1_Silent_p.E322E|PRKCSH_ENST00000412601.1_Silent_p.E322E|PRKCSH_ENST00000252455.2_Silent_p.E322E|PRKCSH_ENST00000587327.1_Silent_p.E322E|PRKCSH_ENST00000591462.1_Silent_p.E322E			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	322	Glu-rich (acidic).				cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)	p.E321_E322delEE(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						aggaggaggaggaagaagagg	0.632																																					p.E322E		Atlas-SNP	.											PRKCSH,caecum,carcinoma,0,1	PRKCSH	55	1	1	Deletion - In frame(1)	central_nervous_system(1)	c.G966A						scavenged	.						27.0	27.0	27.0					19																	11558370		2200	4298	6498	SO:0001819	synonymous_variant	5589	exon11			GGAGGAGGAAGAA		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"""EF-hand domain containing"""	9411	protein-coding gene	gene with protein product		177060	"""polycystic liver disease"""	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.966G>A	19.37:g.11558370G>A		Somatic	100	1	0.01		WXS	Illumina HiSeq	Phase_I	137	3	0.0218978	NM_001001329	A8K318|Q96BU9|Q96D06|Q9P0W9	Silent	SNP	ENST00000589838.1	37	CCDS32911.1																																																																																			.	.	weak		0.632	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1		
CUL7	9820	hgsc.bcm.edu	37	6	43007981	43007981	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:43007981A>G	ENST00000265348.3	-	22	4292	c.4207T>C	c.(4207-4209)Tca>Cca	p.S1403P	CUL7_ENST00000535468.1_Missense_Mutation_p.S1487P			Q14999	CUL7_HUMAN	cullin 7	1403					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)|epithelial to mesenchymal transition (GO:0001837)|Golgi organization (GO:0007030)|microtubule cytoskeleton organization (GO:0000226)|mitotic cytokinesis (GO:0000281)|placenta development (GO:0001890)|positive regulation of dendrite morphogenesis (GO:0050775)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of mitosis (GO:0007088)|ubiquitin-dependent protein catabolic process (GO:0006511)|vasculogenesis (GO:0001570)|viral process (GO:0016032)	3M complex (GO:1990393)|anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|Cul7-RING ubiquitin ligase complex (GO:0031467)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)				breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(8)|liver(1)|lung(11)|ovary(3)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	49			all cancers(41;0.00231)|Colorectal(64;0.00237)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0442)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			TGGCAGATTGAGGCAACAGGC	0.552																																					p.S1487P		Atlas-SNP	.											.	CUL7	133	.	0			c.T4459C						PASS	.						163.0	123.0	136.0					6																	43007981		2203	4300	6503	SO:0001583	missense	9820	exon22			AGATTGAGGCAAC	BC033647	CCDS4881.1, CCDS55003.1	6p21.1	2011-05-24	2004-03-22	2004-03-22	ENSG00000044090	ENSG00000044090			21024	protein-coding gene	gene with protein product		609577	"""KIAA0076"""	KIAA0076		12481031, 12904573	Standard	NM_014780		Approved	dJ20C7.5	uc011dvb.2	Q14999	OTTHUMG00000014718	ENST00000265348.3:c.4207T>C	6.37:g.43007981A>G	ENSP00000265348:p.Ser1403Pro	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	123	5	0.0406504	NM_001168370	B4DYZ0|F5H0L1|Q5T654	Missense_Mutation	SNP	ENST00000265348.3	37	CCDS4881.1	.	.	.	.	.	.	.	.	.	.	A	10.75	1.438588	0.25900	.	.	ENSG00000044090	ENST00000265348;ENST00000535468	T;T	0.79653	-1.29;-1.29	5.71	4.58	0.56647	Cullin, N-terminal (1);Cullin homology (2);	0.242102	0.45126	D	0.000398	T	0.45895	0.1365	N	0.25286	0.73	0.44117	D	0.996898	B;B;B;B	0.33171	0.05;0.061;0.031;0.4	B;B;B;B	0.37833	0.019;0.032;0.017;0.259	T	0.55134	-0.8188	10	0.02654	T	1	-1.3666	5.3129	0.15841	0.8032:0.0:0.1968:0.0	.	1487;1403;1487;1403	F5H0L1;A8K9U1;B4DYZ0;Q14999	.;.;.;CUL7_HUMAN	P	1403;1487	ENSP00000265348:S1403P;ENSP00000438788:S1487P	ENSP00000265348:S1403P	S	-	1	0	CUL7	43115959	0.997000	0.39634	0.953000	0.39169	0.828000	0.46876	1.426000	0.34870	2.179000	0.69175	0.459000	0.35465	TCA	.	.	none		0.552	CUL7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040575.1	NM_014780	
KCNN3	3782	hgsc.bcm.edu	37	1	154842250	154842250	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:154842250G>T	ENST00000271915.4	-	1	506	c.191C>A	c.(190-192)cCg>cAg	p.P64Q	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	64	Gln-rich.|Pro-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	ctgaagctgcggaggctgagg	0.697																																					p.P64Q		Atlas-SNP	.											KCNN3,colon,carcinoma,0,1	KCNN3	141	1	0			c.C191A						PASS	.						5.0	4.0	5.0					1																	154842250		1971	3893	5864	SO:0001583	missense	3782	exon1			AGCTGCGGAGGCT	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.191C>A	1.37:g.154842250G>T	ENSP00000271915:p.Pro64Gln	Somatic	16	0	0		WXS	Illumina HiSeq	Phase_I	26	5	0.192308	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	37	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	g	0.383	-0.927562	0.02377	.	.	ENSG00000143603	ENST00000271915;ENST00000539103	T	0.56776	0.44	4.41	3.47	0.39725	.	4.657150	0.00567	N	0.000284	T	0.17916	0.0430	N	0.03608	-0.345	0.80722	D	1	.	.	.	.	.	.	T	0.04115	-1.0976	8	0.27082	T	0.32	-7.4946	9.6132	0.39676	0.0:0.0:0.7634:0.2366	.	.	.	.	Q	64;159	ENSP00000271915:P64Q	ENSP00000271915:P64Q	P	-	2	0	KCNN3	153108874	0.000000	0.05858	0.998000	0.56505	0.997000	0.91878	0.235000	0.17948	1.372000	0.46190	0.563000	0.77884	CCG	.	.	none		0.697	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249	
HYOU1	10525	hgsc.bcm.edu	37	11	118917360	118917360	+	Missense_Mutation	SNP	C	C	T	rs143927145		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:118917360C>T	ENST00000404233.3	-	23	2874	c.2750G>A	c.(2749-2751)cGg>cAg	p.R917Q	HYOU1_ENST00000525859.1_Missense_Mutation_p.R855Q|HYOU1_ENST00000529972.1_Missense_Mutation_p.R855Q|RP11-110I1.6_ENST00000531886.1_RNA	NM_001130991.1|NM_006389.3	NP_001124463.1|NP_006380.1	Q9Y4L1	HYOU1_HUMAN	hypoxia up-regulated 1	917					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)|response to ischemia (GO:0002931)|response to stress (GO:0006950)	endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|membrane (GO:0016020)	ATP binding (GO:0005524)			NS(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(9)|lung(10)|prostate(1)|skin(2)	33	all_hematologic(175;0.0839)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)|all_hematologic(192;0.207)		BRCA - Breast invasive adenocarcinoma(274;7.78e-05)		GTCCTTAGGCCGGGGCCGGGG	0.572																																					p.R917Q		Atlas-SNP	.											HYOU1,NS,carcinoma,-1,1	HYOU1	88	1	0			c.G2750A						scavenged	.						104.0	106.0	105.0					11																	118917360		2200	4295	6495	SO:0001583	missense	10525	exon23			TTAGGCCGGGGCC	U65785	CCDS8408.1	11q23.1-q23.3	2011-09-02			ENSG00000149428	ENSG00000149428		"""Heat shock proteins / HSP70"""	16931	protein-coding gene	gene with protein product	"""glucose-regulated protein 170"""	601746				9020069, 10037731	Standard	XM_005271390		Approved	ORP150, HSP12A, Grp170	uc001pux.3	Q9Y4L1	OTTHUMG00000166354	ENST00000404233.3:c.2750G>A	11.37:g.118917360C>T	ENSP00000384144:p.Arg917Gln	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	127	2	0.015748	NM_006389	A8C1Z0|B7Z909|Q2I204|Q53H25	Missense_Mutation	SNP	ENST00000404233.3	37	CCDS8408.1	.	.	.	.	.	.	.	.	.	.	C	11.45	1.642054	0.29157	.	.	ENSG00000149428	ENST00000404233;ENST00000353883;ENST00000529972;ENST00000535579;ENST00000525859;ENST00000544701	T;T;T	0.01304	5.06;5.03;5.03	6.04	5.13	0.70059	.	0.200699	0.45867	D	0.000328	T	0.01189	0.0039	L	0.43152	1.355	0.80722	D	1	P;P;P;P	0.41710	0.663;0.76;0.663;0.663	B;B;B;B	0.25614	0.054;0.062;0.054;0.054	T	0.66248	-0.5971	10	0.46703	T	0.11	-15.1767	5.3873	0.16224	0.0:0.6236:0.1527:0.2238	.	908;899;917;917	B3KXH0;B7Z2N4;Q9Y4L1;A8C1Z0	.;.;HYOU1_HUMAN;.	Q	917;908;855;766;855;898	ENSP00000384144:R917Q;ENSP00000437313:R855Q;ENSP00000433397:R855Q	ENSP00000278752:R908Q	R	-	2	0	HYOU1	118422570	1.000000	0.71417	0.997000	0.53966	0.046000	0.14306	2.355000	0.44107	1.568000	0.49683	0.561000	0.74099	CGG	C|1.000;A|0.000	.	alt		0.572	HYOU1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389353.1	NM_006389	
EIF2AK2	5610	hgsc.bcm.edu	37	2	37353531	37353531	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:37353531A>G	ENST00000233057.4	-	11	1131	c.809T>C	c.(808-810)aTa>aCa	p.I270T	EIF2AK2_ENST00000395127.2_Missense_Mutation_p.I270T|EIF2AK2_ENST00000405334.1_Intron	NM_001135651.2	NP_001129123.1	P19525	E2AK2_HUMAN	eukaryotic translation initiation factor 2-alpha kinase 2	270	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)				AATTAATTCTATTTCTTTAAA	0.388																																					p.I270T		Atlas-SNP	.											EIF2AK2,NS,carcinoma,+1,1	EIF2AK2	54	1	0			c.T809C						scavenged	.						72.0	75.0	74.0					2																	37353531		2203	4300	6503	SO:0001583	missense	5610	exon11			AATTCTATTTCTT	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.809T>C	2.37:g.37353531A>G	ENSP00000233057:p.Ile270Thr	Somatic	137	0	0		WXS	Illumina HiSeq	Phase_I	153	2	0.0130719	NM_001135651	A8K3P0|D6W584|E9PC80|Q52M43|Q7Z6F6|Q9UIR4	Missense_Mutation	SNP	ENST00000233057.4	37	CCDS1786.1	.	.	.	.	.	.	.	.	.	.	A	16.85	3.236705	0.58886	.	.	ENSG00000055332	ENST00000233057;ENST00000395127;ENST00000379156	T;T	0.51574	0.7;0.7	4.81	4.81	0.61882	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.097380	0.44902	D	0.000403	T	0.62085	0.2399	L	0.49571	1.57	0.50171	D	0.999851	D;D;D	0.69078	0.99;0.997;0.997	D;D;D	0.75484	0.976;0.965;0.986	T	0.65594	-0.6130	10	0.87932	D	0	-21.9987	13.4084	0.60926	1.0:0.0:0.0:0.0	.	270;270;270	Q8IW76;B7ZKK7;P19525	.;.;E2AK2_HUMAN	T	270	ENSP00000233057:I270T;ENSP00000378559:I270T	ENSP00000233057:I270T	I	-	2	0	EIF2AK2	37207035	1.000000	0.71417	0.031000	0.17742	0.025000	0.11179	5.804000	0.69135	1.810000	0.52873	0.514000	0.50259	ATA	.	.	none		0.388	EIF2AK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000218571.2	NM_002759	
MEA1	4201	hgsc.bcm.edu	37	6	42981024	42981024	+	Silent	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:42981024T>C	ENST00000244711.3	-	2	286	c.132A>G	c.(130-132)gaA>gaG	p.E44E	KLHDC3_ENST00000244670.8_5'Flank|KLHDC3_ENST00000326974.4_5'Flank	NM_014623.2	NP_055438.1	Q16626	MEA1_HUMAN	male-enhanced antigen 1	44					cell differentiation (GO:0030154)|male gonad development (GO:0008584)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)				central_nervous_system(1)|large_intestine(3)|lung(1)|skin(1)	6			Colorectal(64;0.00237)|all cancers(41;0.00411)|COAD - Colon adenocarcinoma(64;0.00473)|OV - Ovarian serous cystadenocarcinoma(102;0.0664)|KIRC - Kidney renal clear cell carcinoma(15;0.133)|Kidney(15;0.188)			CCCCAGTGCCTTCTGAAGGGC	0.597																																					p.E44E		Atlas-SNP	.											MEA1,NS,carcinoma,-2,1	MEA1	11	1	0			c.A132G						scavenged	.						107.0	111.0	110.0					6																	42981024		2203	4300	6503	SO:0001819	synonymous_variant	4201	exon2			AGTGCCTTCTGAA		CCDS4879.1	6p21.3-p21.1	2008-08-15	2005-06-02	2005-06-02	ENSG00000124733	ENSG00000124733			6986	protein-coding gene	gene with protein product		143170	"""male-enhanced antigen"""	MEA		2813404, 12444059	Standard	NM_014623		Approved		uc003otk.3	Q16626	OTTHUMG00000014717	ENST00000244711.3:c.132A>G	6.37:g.42981024T>C		Somatic	104	1	0.00961538		WXS	Illumina HiSeq	Phase_I	113	3	0.0265487	NM_014623	Q5TC36|Q9BV01	Silent	SNP	ENST00000244711.3	37	CCDS4879.1																																																																																			.	.	none		0.597	MEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040574.2		
SNX13	23161	hgsc.bcm.edu	37	7	17874490	17874490	+	Splice_Site	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:17874490T>C	ENST00000409389.1	-	14	1532		c.e14-2		SNX13_ENST00000428135.3_Splice_Site			Q9Y5W8	SNX13_HUMAN	sorting nexin 13						intracellular protein transport (GO:0006886)|positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	early endosome (GO:0005769)|membrane (GO:0016020)	phosphatidylinositol binding (GO:0035091)			breast(1)|central_nervous_system(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(10)|lung(13)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	38	Lung NSC(10;0.0261)|all_lung(11;0.0521)					TGGAGATGCCTAACAGAGAAA	0.299																																					.		Atlas-SNP	.											.	SNX13	113	.	0			c.1360-2A>G						PASS	.						41.0	40.0	40.0					7																	17874490		1805	4059	5864	SO:0001630	splice_region_variant	23161	exon15			GATGCCTAACAGA	AF420470	CCDS47551.1	7p21.1	2008-03-11			ENSG00000071189	ENSG00000071189		"""Sorting nexins"""	21335	protein-coding gene	gene with protein product		606589				11485546, 11729322	Standard	NM_015132		Approved	RGS-PX1, KIAA0713	uc003stv.3	Q9Y5W8	OTTHUMG00000152730	ENST00000409389.1:c.1360-2A>G	7.37:g.17874490T>C		Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	89	4	0.0449438	NM_015132	B2RCI9|O94821|Q8WVZ2|Q8WXH8	Splice_Site	SNP	ENST00000409389.1	37		.	.	.	.	.	.	.	.	.	.	T	19.85	3.904370	0.72868	.	.	ENSG00000071189	ENST00000409389;ENST00000428135;ENST00000242044	.	.	.	4.93	4.93	0.64822	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.863	0.70394	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	-	.	.	SNX13	17841015	1.000000	0.71417	0.951000	0.38953	0.887000	0.51463	5.681000	0.68175	1.979000	0.57680	0.402000	0.26972	.	.	.	none		0.299	SNX13-002	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000327608.1	NM_015132	Intron
CYP2A6	1548	hgsc.bcm.edu	37	19	41355765	41355765	+	Nonsense_Mutation	SNP	G	G	A	rs199545200		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:41355765G>A	ENST00000301141.5	-	2	321	c.301C>T	c.(301-303)Cga>Tga	p.R101*	CTC-490E21.12_ENST00000601627.1_Intron	NM_000762.5	NP_000753	P11509	CP2A6_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 6	101					coumarin catabolic process (GO:0046226)|coumarin metabolic process (GO:0009804)|drug metabolic process (GO:0017144)|exogenous drug catabolic process (GO:0042738)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|xenobiotic metabolic process (GO:0006805)	cytoplasmic microtubule (GO:0005881)|endoplasmic reticulum membrane (GO:0005789)	coumarin 7-hydroxylase activity (GO:0008389)|enzyme binding (GO:0019899)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|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(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(3)|prostate(5)|skin(2)|upper_aerodigestive_tract(2)	37			LUSC - Lung squamous cell carcinoma(20;0.000219)|Lung(22;0.000959)		Acetaminophen(DB00316)|Amiodarone(DB01118)|Amlodipine(DB00381)|Amobarbital(DB01351)|Amphetamine(DB00182)|Antipyrine(DB01435)|Arformoterol(DB01274)|Azelastine(DB00972)|Azithromycin(DB00207)|Buprenorphine(DB00921)|Bupropion(DB01156)|Chlorzoxazone(DB00356)|Cinnarizine(DB00568)|Cisapride(DB00604)|Clofibrate(DB00636)|Clomifene(DB00882)|Clotrimazole(DB00257)|Clozapine(DB00363)|Cyclophosphamide(DB00531)|Dapagliflozin(DB06292)|Desipramine(DB01151)|Dexamethasone(DB01234)|Dexfenfluramine(DB01191)|Diethylstilbestrol(DB00255)|Dronabinol(DB00470)|Eletriptan(DB00216)|Ezogabine(DB04953)|Flunarizine(DB04841)|Flunitrazepam(DB01544)|Fluorouracil(DB00544)|Flurazepam(DB00690)|Fomepizole(DB01213)|Formoterol(DB00983)|Halothane(DB01159)|Ifosfamide(DB01181)|Isoniazid(DB00951)|Ketoconazole(DB01026)|Letrozole(DB01006)|Lidocaine(DB00281)|Lorcaserin(DB04871)|Memantine(DB01043)|Menadione(DB00170)|Methimazole(DB00763)|Methoxsalen(DB00553)|Methoxyflurane(DB01028)|Metyrapone(DB01011)|Miconazole(DB01110)|Montelukast(DB00471)|Nevirapine(DB00238)|Nicotine(DB00184)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Norfloxacin(DB01059)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Pilocarpine(DB01085)|Prednisolone(DB00860)|Progesterone(DB00396)|Propofol(DB00818)|Rifampicin(DB01045)|Rosiglitazone(DB00412)|Selegiline(DB01037)|Sevoflurane(DB01236)|Sulfaphenazole(DB06729)|Tamoxifen(DB00675)|Tranylcypromine(DB00752)|Tretinoin(DB00755)|Troleandomycin(DB01361)|Valproic Acid(DB00313)|Zidovudine(DB00495)	TGCTCGCCTCGCCCGCTGAAC	0.632													.|||	1	0.000199681	0.0	0.0	5008	,	,		18422	0.001		0.0	False		,,,				2504	0.0				p.R101X		Atlas-SNP	.											CYP2A6,brain,primitive_neuroectodermal_tumour-medulloblastoma,+1,1	CYP2A6	69	1	0			c.C301T	GRCh37	CM057912	CYP2A6	M		scavenged	.						68.0	65.0	66.0					19																	41355765		2203	4297	6500	SO:0001587	stop_gained	1548	exon2			CGCCTCGCCCGCT	AF182275	CCDS12568.1	19q13.2	2013-11-11	2003-01-14		ENSG00000255974	ENSG00000255974		"""Cytochrome P450s"""	2610	protein-coding gene	gene with protein product		122720	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 6"""	CYP2A3		7668294, 2748347	Standard	NM_000762		Approved	CPA6, CYP2A	uc002opl.4	P11509	OTTHUMG00000182713	ENST00000301141.5:c.301C>T	19.37:g.41355765G>A	ENSP00000301141:p.Arg101*	Somatic	361	7	0.0193906		WXS	Illumina HiSeq	Phase_I	388	10	0.0257732	NM_000762	A7YAE5|B2R7F6|P00190|P10890|Q16803|Q4VAT9|Q4VAU0|Q4VAU1|Q9H1Z7|Q9UCU0|Q9UK48	Nonsense_Mutation	SNP	ENST00000301141.5	37	CCDS12568.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	-	20.8	4.055138	0.75960	.	.	ENSG00000255974	ENST00000301141	.	.	.	2.72	1.61	0.23674	.	0.000000	0.64402	U	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.0179	0.30391	0.0:0.0:0.396:0.604	.	.	.	.	X	101	.	ENSP00000301141:R101X	R	-	1	2	CYP2A6	46047605	0.004000	0.15560	0.122000	0.21767	0.368000	0.29767	-0.012000	0.12699	0.289000	0.22422	0.185000	0.17295	CGA	G|1.000;A|0.000	0.000	strong		0.632	CYP2A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463259.1	NM_000762	
LDOC1	23641	hgsc.bcm.edu	37	X	140271025	140271025	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:140271025C>A	ENST00000370526.2	-	1	285	c.182G>T	c.(181-183)aGc>aTc	p.S61I	LDOC1_ENST00000460721.1_Intron	NM_012317.2	NP_036449.1	O95751	LDOC1_HUMAN	leucine zipper, down-regulated in cancer 1	61					negative regulation of cell proliferation (GO:0008285)	nucleus (GO:0005634)				endometrium(6)|large_intestine(1)|lung(6)|ovary(1)	14	Acute lymphoblastic leukemia(192;7.65e-05)					GAGCCGGGAGCTCTCGCCATT	0.617																																					p.S61I		Atlas-SNP	.											.	LDOC1	26	.	0			c.G182T						PASS	.						49.0	44.0	45.0					X																	140271025		2203	4300	6503	SO:0001583	missense	23641	exon1			CGGGAGCTCTCGC	AB019527	CCDS14672.1	Xq27	2008-02-05			ENSG00000182195	ENSG00000182195			6548	protein-coding gene	gene with protein product		300402		BCUR1		10403563, 15716091, 16093683	Standard	NM_012317		Approved	Mar7, Mart7	uc004fbj.3	O95751	OTTHUMG00000022558	ENST00000370526.2:c.182G>T	X.37:g.140271025C>A	ENSP00000359557:p.Ser61Ile	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	35	24	0.685714	NM_012317	Q6IAR6	Missense_Mutation	SNP	ENST00000370526.2	37	CCDS14672.1	.	.	.	.	.	.	.	.	.	.	.	12.62	1.991895	0.35131	.	.	ENSG00000182195	ENST00000370526	T	0.32023	1.47	3.61	1.75	0.24633	.	0.179052	0.36591	N	0.002511	T	0.22244	0.0536	L	0.46157	1.445	0.09310	N	0.999999	P	0.39665	0.682	B	0.33690	0.168	T	0.09885	-1.0654	10	0.51188	T	0.08	-8.3488	8.8927	0.35444	0.0:0.5574:0.4426:0.0	.	61	O95751	LDOC1_HUMAN	I	61	ENSP00000359557:S61I	ENSP00000359557:S61I	S	-	2	0	LDOC1	140098691	0.893000	0.30496	0.335000	0.25508	0.944000	0.59088	0.619000	0.24388	0.331000	0.23511	0.287000	0.19450	AGC	.	.	none		0.617	LDOC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058592.1	NM_012317	
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324104	39324104	+	Silent	SNP	A	A	G	rs368619075		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:39324104A>G	ENST00000391356.2	-	1	320	c.321T>C	c.(319-321)tcT>tcC	p.S107S		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	107	29 X 5 AA repeats of C-C-[GIKRQVH]-[SPT]- [STA].		Missing (in allele KAP3-v2). {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.S107S(1)		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)			TGCAGCAACTAGAAATGCAGC	0.597																																					p.S107S		Atlas-SNP	.											KRTAP4-3,colon,carcinoma,0,1	KRTAP4-3	40	1	1	Substitution - coding silent(1)	large_intestine(1)	c.T321C						scavenged	.						18.0	23.0	21.0					17																	39324104		2109	4252	6361	SO:0001819	synonymous_variant	85290	exon1			GCAACTAGAAATG	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.321T>C	17.37:g.39324104A>G		Somatic	206	6	0.0291262		WXS	Illumina HiSeq	Phase_I	314	9	0.0286624	NM_033187		Silent	SNP	ENST00000391356.2	37	CCDS42331.1																																																																																			.	.	weak		0.597	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
ANAPC1	64682	hgsc.bcm.edu	37	2	112625615	112625615	+	Missense_Mutation	SNP	C	C	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:112625615C>G	ENST00000341068.3	-	7	1442	c.670G>C	c.(670-672)Gtt>Ctt	p.V224L		NM_022662.3	NP_073153.1	Q9H1A4	APC1_HUMAN	anaphase promoting complex subunit 1	224					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)		p.V224L(1)		NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(7)|lung(16)|pancreas(1)|prostate(3)|skin(5)|stomach(1)|urinary_tract(1)	49						GATTTACAAACAAGTGGAGTT	0.323																																					p.V224L		Atlas-SNP	.											ANAPC1,NS,other,0,1	ANAPC1	116	1	1	Substitution - Missense(1)	pancreas(1)	c.G670C						scavenged	.						53.0	57.0	56.0					2																	112625615		2203	4297	6500	SO:0001583	missense	64682	exon7			TACAAACAAGTGG	AJ278357	CCDS2093.1	2q12.1	2011-06-15			ENSG00000153107	ENSG00000153107		"""Anaphase promoting complex subunits"""	19988	protein-coding gene	gene with protein product		608473				11179667	Standard	NM_022662		Approved	MCPR, TSG24, APC1	uc002ssh.3	Q9H1A4	OTTHUMG00000131277	ENST00000341068.3:c.670G>C	2.37:g.112625615C>G	ENSP00000339109:p.Val224Leu	Somatic	412	17	0.0412621		WXS	Illumina HiSeq	Phase_I	478	39	0.08159	NM_022662	Q2M3H8|Q9BSE6|Q9H8D0	Missense_Mutation	SNP	ENST00000341068.3	37	CCDS2093.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.059198	0.76074	.	.	ENSG00000153107	ENST00000341068	.	.	.	4.32	4.32	0.51571	.	0.000000	0.39274	U	0.001404	T	0.61961	0.2389	L	0.33189	0.99	0.58432	D	0.999999	D	0.63046	0.992	D	0.77004	0.989	T	0.54925	-0.8220	9	0.02654	T	1	-23.1921	17.3402	0.87293	0.0:1.0:0.0:0.0	.	224	Q9H1A4	APC1_HUMAN	L	224	.	ENSP00000339109:V224L	V	-	1	0	ANAPC1	112342086	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	3.051000	0.49885	2.381000	0.81170	0.557000	0.71058	GTT	.	.	none		0.323	ANAPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254045.2	NM_022662	
C5orf24	134553	hgsc.bcm.edu	37	5	134190831	134190831	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:134190831A>G	ENST00000394976.3	+	2	469	c.241A>G	c.(241-243)Aag>Gag	p.K81E	C5orf24_ENST00000435259.2_Missense_Mutation_p.K81E|C5orf24_ENST00000338051.4_Missense_Mutation_p.K81E|C5orf24_ENST00000504727.1_Missense_Mutation_p.K81E	NM_001135586.1	NP_001129058.1	Q7Z6I8	CE024_HUMAN	chromosome 5 open reading frame 24	81										breast(2)|endometrium(2)|lung(2)	6			KIRC - Kidney renal clear cell carcinoma(527;0.0101)|Kidney(363;0.0233)			ACTAAAGAAAAAGAAGAATCT	0.478																																					p.K81E		Atlas-SNP	.											C5orf24,NS,carcinoma,-2,1	C5orf24	9	1	0			c.A241G						scavenged	.						77.0	84.0	82.0					5																	134190831		2203	4300	6503	SO:0001583	missense	134553	exon2			AAGAAAAAGAAGA	BC053677	CCDS4179.1, CCDS75307.1	5q31.1	2008-02-05			ENSG00000181904	ENSG00000181904			26746	protein-coding gene	gene with protein product						12477932	Standard	NM_152409		Approved	FLJ37562	uc003kzz.3	Q7Z6I8	OTTHUMG00000129121	ENST00000394976.3:c.241A>G	5.37:g.134190831A>G	ENSP00000378427:p.Lys81Glu	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	125	2	0.016	NM_001135586	D3DQA7|Q86Y53|Q8N1T9	Missense_Mutation	SNP	ENST00000394976.3	37	CCDS4179.1	.	.	.	.	.	.	.	.	.	.	A	20.7	4.037715	0.75617	.	.	ENSG00000181904	ENST00000338051;ENST00000394976;ENST00000504727;ENST00000435259	.	.	.	5.98	5.98	0.97165	.	0.189750	0.56097	D	0.000032	T	0.48187	0.1486	L	0.34521	1.04	0.49051	D	0.99974	B;B	0.31817	0.341;0.341	B;B	0.25140	0.058;0.058	T	0.50996	-0.8761	9	0.87932	D	0	-7.8943	16.4622	0.84064	1.0:0.0:0.0:0.0	.	81;81	Q7Z6I8-2;Q7Z6I8	.;CE024_HUMAN	E	81	.	ENSP00000337044:K81E	K	+	1	0	C5orf24	134218730	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.946000	0.70234	2.289000	0.77006	0.533000	0.62120	AAG	.	.	none		0.478	C5orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251167.1	NM_152409	
MME	4311	hgsc.bcm.edu	37	3	154856016	154856016	+	Silent	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:154856016A>G	ENST00000460393.1	+	9	966	c.846A>G	c.(844-846)gaA>gaG	p.E282E	MME_ENST00000462745.1_Silent_p.E282E|MME_ENST00000492661.1_Silent_p.E282E|MME_ENST00000493237.1_Silent_p.E282E|MME_ENST00000360490.2_Silent_p.E282E	NM_000902.3|NM_007287.2	NP_000893.2|NP_009218.2	P08473	NEP_HUMAN	membrane metallo-endopeptidase	282					angiotensin maturation (GO:0002003)|beta-amyloid metabolic process (GO:0050435)|cellular protein metabolic process (GO:0044267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to UV-A (GO:0071492)|cellular response to UV-B (GO:0071493)|creatinine metabolic process (GO:0046449)|kidney development (GO:0001822)|peptide metabolic process (GO:0006518)|proteolysis (GO:0006508)|replicative senescence (GO:0090399)|sensory perception of pain (GO:0019233)	axon (GO:0030424)|brush border (GO:0005903)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|neuron projection terminus (GO:0044306)|plasma membrane (GO:0005886)|synapse (GO:0045202)|synaptic vesicle (GO:0008021)	endopeptidase activity (GO:0004175)|metalloendopeptidase activity (GO:0004222)|peptide binding (GO:0042277)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(31)|ovary(3)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	64		all_neural(597;0.00391)|Myeloproliferative disorder(1037;0.0122)	LUSC - Lung squamous cell carcinoma(72;0.114)|Lung(72;0.135)		Candoxatril(DB00616)|Liraglutide(DB06655)	TGGAAAAAGAAATTGCCAATG	0.343																																					p.E282E		Atlas-SNP	.											MME,colon,carcinoma,+2,1	MME	133	1	0			c.A846G						scavenged	.						88.0	91.0	90.0					3																	154856016		2203	4300	6503	SO:0001819	synonymous_variant	4311	exon9			AAAAGAAATTGCC		CCDS3172.1	3q25.2	2012-01-31	2007-02-21		ENSG00000196549	ENSG00000196549	3.4.24.11	"""CD molecules"""	7154	protein-coding gene	gene with protein product	"""neutral endopeptidase"", ""enkephalinase"", ""neprilysin"""	120520					Standard	NM_007287		Approved	CALLA, CD10, NEP	uc003fad.1	P08473	OTTHUMG00000158455	ENST00000460393.1:c.846A>G	3.37:g.154856016A>G		Somatic	79	0	0		WXS	Illumina HiSeq	Phase_I	153	2	0.0130719	NM_007287	A8K6U6|D3DNJ9|Q3MIX4	Silent	SNP	ENST00000460393.1	37	CCDS3172.1																																																																																			.	.	none		0.343	MME-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351076.1	NM_000902	
CLIP1	6249	hgsc.bcm.edu	37	12	122862149	122862149	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:122862149C>T	ENST00000540338.1	-	2	485	c.444G>A	c.(442-444)ccG>ccA	p.P148P	CLIP1_ENST00000358808.2_Silent_p.P148P|CLIP1_ENST00000361654.4_Silent_p.P148P|CLIP1_ENST00000537178.1_Silent_p.P148P|CLIP1_ENST00000302528.7_Silent_p.P148P			P30622	CLIP1_HUMAN	CAP-GLY domain containing linker protein 1	148	Ser-rich.				microtubule bundle formation (GO:0001578)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|positive regulation of microtubule polymerization (GO:0031116)|transport (GO:0006810)	cell projection (GO:0042995)|centrosome (GO:0005813)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|endosome (GO:0005768)|intermediate filament (GO:0005882)|kinetochore (GO:0000776)|membrane (GO:0016020)|microtubule (GO:0005874)|microtubule cytoskeleton (GO:0015630)	metal ion binding (GO:0046872)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)|nucleic acid binding (GO:0003676)|protein homodimerization activity (GO:0042803)|tubulin binding (GO:0015631)|zinc ion binding (GO:0008270)	p.P148P(1)		NS(1)|breast(5)|endometrium(4)|kidney(5)|large_intestine(16)|liver(1)|lung(21)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	60	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;1.81e-05)|Epithelial(86;6.85e-05)|BRCA - Breast invasive adenocarcinoma(302;0.226)		AAGTGCACAGCGGTGAAGTAG	0.537																																					p.P148P		Atlas-SNP	.											CLIP1,colon,carcinoma,0,1	CLIP1	126	1	1	Substitution - coding silent(1)	large_intestine(1)	c.G444A						scavenged	.						162.0	143.0	149.0					12																	122862149		2203	4300	6503	SO:0001819	synonymous_variant	6249	exon3			GCACAGCGGTGAA		CCDS9232.1, CCDS9233.1, CCDS58285.1	12q24.3	2013-01-17	2007-01-05	2007-01-05	ENSG00000130779	ENSG00000130779			10461	protein-coding gene	gene with protein product	"""restin"""	179838	"""restin (Reed-Steinberg cell-expressed intermediate filament-associated protein)"""	RSN		8222754	Standard	NM_001247997		Approved	CYLN1, CLIP170, CLIP, CLIP-170	uc001ucg.2	P30622	OTTHUMG00000168922	ENST00000540338.1:c.444G>A	12.37:g.122862149C>T		Somatic	97	0	0		WXS	Illumina HiSeq	Phase_I	118	2	0.0169492	NM_002956	A0AVD3|Q17RS4|Q29RG0	Silent	SNP	ENST00000540338.1	37	CCDS58285.1																																																																																			.	.	none		0.537	CLIP1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000401625.1	NM_002956	
COL3A1	1281	hgsc.bcm.edu	37	2	189864021	189864021	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:189864021G>A	ENST00000304636.3	+	30	2203	c.2033G>A	c.(2032-2034)gGt>gAt	p.G678D	COL3A1_ENST00000317840.5_Missense_Mutation_p.G678D	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	678	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)			NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	GGTGATGCTGGTGCCCCTGGT	0.498																																					p.G678D		Atlas-SNP	.											.	COL3A1	292	.	0			c.G2033A						PASS	.						40.0	40.0	40.0					2																	189864021		2202	4299	6501	SO:0001583	missense	1281	exon30			ATGCTGGTGCCCC	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.2033G>A	2.37:g.189864021G>A	ENSP00000304408:p.Gly678Asp	Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	62	35	0.564516	NM_000090	D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Missense_Mutation	SNP	ENST00000304636.3	37	CCDS2297.1	.	.	.	.	.	.	.	.	.	.	G	20.8	4.056475	0.76074	.	.	ENSG00000168542	ENST00000304636;ENST00000317840	D;D	0.99619	-6.28;-6.28	4.96	4.96	0.65561	.	0.000000	0.44688	D	0.000428	D	0.99792	0.9912	H	0.96720	3.87	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96883	0.9647	10	0.87932	D	0	.	18.6093	0.91277	0.0:0.0:1.0:0.0	.	678	P02461	CO3A1_HUMAN	D	678	ENSP00000304408:G678D;ENSP00000315243:G678D	ENSP00000304408:G678D	G	+	2	0	COL3A1	189572266	1.000000	0.71417	0.996000	0.52242	0.969000	0.65631	9.813000	0.99286	2.472000	0.83506	0.650000	0.86243	GGT	.	.	none		0.498	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
ZNF555	148254	hgsc.bcm.edu	37	19	2852470	2852470	+	Missense_Mutation	SNP	T	T	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:2852470T>A	ENST00000334241.4	+	4	545	c.407T>A	c.(406-408)aTt>aAt	p.I136N	ZNF555_ENST00000591539.1_Missense_Mutation_p.I135N|AC006130.3_ENST00000589365.1_RNA	NM_001172775.1|NM_152791.4	NP_001166246.1|NP_690004.4	Q8NEP9	ZN555_HUMAN	zinc finger protein 555	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)			breast(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(3)|ovary(1)|prostate(1)|skin(3)|urinary_tract(4)	23				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)		TACAAGAAAATTCCACCTGGA	0.428																																					p.I136N		Atlas-SNP	.											.	ZNF555	61	.	0			c.T407A						PASS	.						85.0	82.0	83.0					19																	2852470		2203	4300	6503	SO:0001583	missense	148254	exon4			AGAAAATTCCACC	AL832140	CCDS12096.1, CCDS59329.1	19p13.3	2013-09-20			ENSG00000186300	ENSG00000186300		"""Zinc fingers, C2H2-type"", ""-"""	28382	protein-coding gene	gene with protein product						12477932	Standard	NM_152791		Approved	MGC26707	uc002lwo.3	Q8NEP9	OTTHUMG00000180500	ENST00000334241.4:c.407T>A	19.37:g.2852470T>A	ENSP00000334853:p.Ile136Asn	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	74	30	0.405405	NM_152791	A8KA89|K7EQM2|Q8NA46|Q96MP1	Missense_Mutation	SNP	ENST00000334241.4	37	CCDS12096.1	.	.	.	.	.	.	.	.	.	.	T	10.26	1.302445	0.23736	.	.	ENSG00000186300	ENST00000334241;ENST00000382127	T	0.06933	3.24	3.62	-0.788	0.10939	.	.	.	.	.	T	0.08447	0.0210	M	0.64260	1.97	0.09310	N	1	B;B	0.23650	0.001;0.089	B;B	0.16289	0.001;0.015	T	0.32640	-0.9899	9	0.66056	D	0.02	.	3.7148	0.08434	0.0:0.4382:0.1968:0.3651	.	136;135	Q8NEP9;A8KA89	ZN555_HUMAN;.	N	136;135	ENSP00000334853:I136N	ENSP00000334853:I136N	I	+	2	0	ZNF555	2803470	0.000000	0.05858	0.000000	0.03702	0.035000	0.12851	-0.427000	0.06999	-0.198000	0.10333	0.459000	0.35465	ATT	.	.	none		0.428	ZNF555-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451637.3	NM_152791	
GOLGA6B	55889	hgsc.bcm.edu	37	15	72954612	72954612	+	Silent	SNP	G	G	A	rs201791007		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:72954612G>A	ENST00000421285.3	+	11	867	c.867G>A	c.(865-867)gcG>gcA	p.A289A	RN7SL853P_ENST00000477951.2_RNA	NM_018652.4	NP_061122.4	A6NDN3	GOG6B_HUMAN	golgin A6 family, member B	289						Golgi apparatus (GO:0005794)		p.A289A(1)		NS(1)|breast(1)|endometrium(1)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	16						CATCCCTGGCGCCCCCAGCAG	0.537																																					p.A289A		Atlas-SNP	.											GOLGA6B,mouth,carcinoma,0,1	GOLGA6B	30	1	1	Substitution - coding silent(1)	upper_aerodigestive_tract(1)	c.G867A						scavenged	.						32.0	31.0	32.0					15																	72954612		1846	3747	5593	SO:0001819	synonymous_variant	55889	exon11			CCTGGCGCCCCCA		CCDS10245.2	15q24.1	2011-10-25	2010-02-12		ENSG00000215186	ENSG00000215186			32205	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6B"""				Standard	XM_006720604		Approved		uc010uks.1	A6NDN3	OTTHUMG00000133511	ENST00000421285.3:c.867G>A	15.37:g.72954612G>A		Somatic	237	4	0.0168776		WXS	Illumina HiSeq	Phase_I	255	6	0.0235294	NM_018652	A8MYY7	Silent	SNP	ENST00000421285.3	37	CCDS10245.2																																																																																			G|0.500;A|0.500	0.500	weak		0.537	GOLGA6B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257474.4	NM_018652	
MUC4	4585	hgsc.bcm.edu	37	3	195513590	195513590	+	Missense_Mutation	SNP	C	C	T	rs74192533		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:195513590C>T	ENST00000463781.3	-	2	5320	c.4861G>A	c.(4861-4863)Gac>Aac	p.D1621N	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.D1621N	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	0	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				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																																					p.D1621N		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,2	MUC4	1505	2	0			c.G4861A						scavenged	.						16.0	21.0	19.0					3																	195513590		684	1562	2246	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.4861G>A	3.37:g.195513590C>T	ENSP00000417498:p.Asp1621Asn	Somatic	303	15	0.049505		WXS	Illumina HiSeq	Phase_I	285	16	0.0561404	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	.	.	.	.	.	.	.	.	.	.	-	6.630	0.484649	0.12641	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.35421	1.31;1.33	.	.	.	.	.	.	.	.	T	0.12774	0.0310	N	0.08118	0	0.09310	N	1	P	0.47545	0.897	B	0.35312	0.2	T	0.11690	-1.0577	7	.	.	.	.	3.6132	0.08067	2.0E-4:0.5026:0.4969:2.0E-4	.	1621	E7ESK3	.	N	1621	ENSP00000417498:D1621N;ENSP00000420243:D1621N	.	D	-	1	0	MUC4	196997985	0.000000	0.05858	0.018000	0.16275	0.018000	0.09664	-0.145000	0.10265	0.088000	0.17205	0.089000	0.15464	GAC	CGGTGACAG|0.500;TGGTGACAA|0.500	.	alt		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DNAH10	196385	hgsc.bcm.edu	37	12	124281312	124281312	+	Missense_Mutation	SNP	G	G	T	rs143386728	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:124281312G>T	ENST00000409039.3	+	12	1767	c.1742G>T	c.(1741-1743)cGg>cTg	p.R581L		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	581	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)		CTGTTCTTTCGGATTAAGCAT	0.423																																					p.R581L		Atlas-SNP	.											DNAH10_ENST00000409039,colon,carcinoma,0,4	DNAH10	888	4	0			c.G1742T						scavenged	.						145.0	128.0	134.0					12																	124281312		2203	4300	6503	SO:0001583	missense	196385	exon12			TCTTTCGGATTAA	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.1742G>T	12.37:g.124281312G>T	ENSP00000386770:p.Arg581Leu	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	161	3	0.0186335	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	G	16.53	3.149776	0.57151	.	.	ENSG00000197653	ENST00000409039	T	0.66099	-0.19	5.35	5.35	0.76521	Dynein heavy chain, domain-1 (1);	0.108055	0.36555	N	0.002521	D	0.83580	0.5285	M	0.89601	3.045	0.41076	D	0.98548	D;D;D	0.71674	0.974;0.995;0.998	P;D;D	0.76071	0.906;0.987;0.968	D	0.87237	0.2264	10	0.87932	D	0	.	19.0759	0.93161	0.0:0.0:1.0:0.0	.	581;456;581	Q8IVF4-2;C4IXU6;Q8IVF4	.;.;DYH10_HUMAN	L	581	ENSP00000386770:R581L	ENSP00000386770:R581L	R	+	2	0	DNAH10	122847265	1.000000	0.71417	0.644000	0.29465	0.101000	0.19017	7.701000	0.84566	2.506000	0.84524	0.650000	0.86243	CGG	G|1.000;A|0.000	.	alt		0.423	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
LRRN3	54674	hgsc.bcm.edu	37	7	110764121	110764121	+	Silent	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:110764121T>C	ENST00000422987.3	+	2	2124	c.1293T>C	c.(1291-1293)aaT>aaC	p.N431N	IMMP2L_ENST00000452895.1_Intron|IMMP2L_ENST00000447215.1_Intron|IMMP2L_ENST00000450877.1_Intron|LRRN3_ENST00000308478.5_Silent_p.N431N|IMMP2L_ENST00000489381.1_Intron|IMMP2L_ENST00000331762.3_Intron|IMMP2L_ENST00000437687.1_Intron|IMMP2L_ENST00000405709.2_Intron|IMMP2L_ENST00000415362.1_Intron|LRRN3_ENST00000451085.1_Silent_p.N431N	NM_018334.4	NP_060804.3	Q9H3W5	LRRN3_HUMAN	leucine rich repeat neuronal 3	431	Ig-like C2-type.				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)		TTCCTTCTAATCTAAATGTAG	0.438																																					p.N431N		Atlas-SNP	.											.	LRRN3	132	.	0			c.T1293C						PASS	.						111.0	117.0	115.0					7																	110764121		2203	4300	6503	SO:0001819	synonymous_variant	54674	exon2			TTCTAATCTAAAT	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.1293T>C	7.37:g.110764121T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	64	34	0.53125	NM_018334	O43377|Q6I9V8|Q8IYQ6	Silent	SNP	ENST00000422987.3	37	CCDS5754.1																																																																																			.	.	none		0.438	LRRN3-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000338171.2	NM_018334	
NOTCH1	4851	hgsc.bcm.edu	37	9	139391655	139391655	+	Missense_Mutation	SNP	C	C	T	rs587778571		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:139391655C>T	ENST00000277541.6	-	34	6611	c.6536G>A	c.(6535-6537)cGg>cAg	p.R2179Q		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	2179					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.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)		CTTCTTCCTCCGTGCCTTGAG	0.657			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																											p.R2179Q		Atlas-SNP	.		Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	NOTCH1_ENST00000277541,NS,carcinoma,0,2	NOTCH1	1980	2	1	Deletion - In frame(1)	haematopoietic_and_lymphoid_tissue(1)	c.G6536A						scavenged	.						43.0	50.0	48.0					9																	139391655		2182	4269	6451	SO:0001583	missense	4851	exon34			TTCCTCCGTGCCT	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.6536G>A	9.37:g.139391655C>T	ENSP00000277541:p.Arg2179Gln	Somatic	86	0	0		WXS	Illumina HiSeq	Phase_I	113	2	0.0176991	NM_017617	Q59ED8|Q5SXM3	Missense_Mutation	SNP	ENST00000277541.6	37	CCDS43905.1	.	.	.	.	.	.	.	.	.	.	C	16.70	3.195470	0.58126	.	.	ENSG00000148400	ENST00000277541	D	0.84370	-1.84	5.42	5.42	0.78866	.	0.055905	0.64402	D	0.000002	D	0.86260	0.5890	M	0.82630	2.6	0.48040	D	0.999571	P	0.51240	0.943	B	0.39185	0.293	D	0.88293	0.2944	10	0.49607	T	0.09	.	18.5525	0.91071	0.0:1.0:0.0:0.0	.	2179	P46531	NOTC1_HUMAN	Q	2179	ENSP00000277541:R2179Q	ENSP00000277541:R2179Q	R	-	2	0	NOTCH1	138511476	1.000000	0.71417	0.982000	0.44146	0.649000	0.38597	4.757000	0.62213	2.703000	0.92315	0.561000	0.74099	CGG	.	.	none		0.657	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1	NM_017617	
KCNH7	90134	hgsc.bcm.edu	37	2	163241253	163241253	+	Silent	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:163241253T>C	ENST00000332142.5	-	13	3006	c.2907A>G	c.(2905-2907)gaA>gaG	p.E969E		NM_033272.3	NP_150375.2	Q9NS40	KCNH7_HUMAN	potassium voltage-gated channel, subfamily H (eag-related), member 7	969					circadian rhythm (GO:0007623)|potassium ion transmembrane transport (GO:0071805)|protein heterooligomerization (GO:0051291)|regulation of membrane potential (GO:0042391)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)|signal transducer activity (GO:0004871)|voltage-gated potassium channel activity (GO:0005249)	p.E969D(1)		NS(1)|biliary_tract(1)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(22)|lung(53)|ovary(3)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(3)	108					Doxazosin(DB00590)|Ibutilide(DB00308)|Miconazole(DB01110)|Prazosin(DB00457)|Terazosin(DB01162)	TGGGCACTGTTTCTTCAAAAT	0.438																																					p.E969E	GBM(196;1492 2208 17507 24132 45496)	Atlas-SNP	.											KCNH7,NS,carcinoma,0,2	KCNH7	378	2	1	Substitution - Missense(1)	kidney(1)	c.A2907G						scavenged	.						176.0	170.0	172.0					2																	163241253		2203	4299	6502	SO:0001819	synonymous_variant	90134	exon13			CACTGTTTCTTCA	AF032897	CCDS2219.1, CCDS2220.1	2q24.3	2012-07-05			ENSG00000184611	ENSG00000184611		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	18863	protein-coding gene	gene with protein product		608169				16382104	Standard	NM_173162		Approved	Kv11.3, HERG3, erg3	uc002uch.2	Q9NS40	OTTHUMG00000132069	ENST00000332142.5:c.2907A>G	2.37:g.163241253T>C		Somatic	205	0	0		WXS	Illumina HiSeq	Phase_I	245	3	0.0122449	NM_033272	Q53QU4|Q53TB7|Q53TP9|Q8IV15	Silent	SNP	ENST00000332142.5	37	CCDS2219.1																																																																																			.	.	none		0.438	KCNH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255093.1	NM_033272	
KMT2D	8085	hgsc.bcm.edu	37	12	49421689	49421689	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:49421689C>A	ENST00000301067.7	-	47	14539	c.14540G>T	c.(14539-14541)gGc>gTc	p.G4847V		NM_003482.3	NP_003473.3	O14686	KMT2D_HUMAN	lysine (K)-specific methyltransferase 2D	4847					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)										TGGGCTCTTGCCTTCCAGACC	0.547																																					p.G4847V		Atlas-SNP	.											.	MLL2	1173	.	0			c.G14540T						PASS	.						60.0	62.0	61.0					12																	49421689		1987	4141	6128	SO:0001583	missense	8085	exon47			CTCTTGCCTTCCA	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.14540G>T	12.37:g.49421689C>A	ENSP00000301067:p.Gly4847Val	Somatic	145	0	0		WXS	Illumina HiSeq	Phase_I	182	65	0.357143	NM_003482	O14687	Missense_Mutation	SNP	ENST00000301067.7	37	CCDS44873.1	.	.	.	.	.	.	.	.	.	.	C	10.23	1.292727	0.23564	.	.	ENSG00000167548	ENST00000301067	T	0.79033	-1.23	5.01	2.11	0.27256	.	0.851336	0.09837	N	0.749407	T	0.66336	0.2779	L	0.38175	1.15	0.47621	D	0.999471	B	0.06786	0.001	B	0.06405	0.002	T	0.59300	-0.7480	10	0.87932	D	0	.	4.6868	0.12762	0.2706:0.5222:0.1314:0.0759	.	4847	O14686	MLL2_HUMAN	V	4847	ENSP00000301067:G4847V	ENSP00000301067:G4847V	G	-	2	0	MLL2	47707956	0.996000	0.38824	0.978000	0.43139	0.990000	0.78478	0.607000	0.24209	0.226000	0.20979	0.655000	0.94253	GGC	.	.	none		0.547	KMT2D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390183.2		
C11orf88	399949	hgsc.bcm.edu	37	11	111385703	111385703	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:111385703C>T	ENST00000375618.4	+	1	194	c.194C>T	c.(193-195)cCg>cTg	p.P65L	C11orf88_ENST00000529167.1_Missense_Mutation_p.P65L|MIR34C_ENST00000384831.1_RNA|RP11-794P6.6_ENST00000530283.1_RNA|MIR34B_ENST00000385076.1_RNA|C11orf88_ENST00000332814.6_Missense_Mutation_p.P65L|BTG4_ENST00000356018.2_5'Flank|BTG4_ENST00000525791.1_5'Flank	NM_001100388.1	NP_001093858.1	Q6PI97	CK088_HUMAN	chromosome 11 open reading frame 88	65										endometrium(1)|large_intestine(3)|lung(2)	6						CAGCGTCTGCCGGTGGCGCGG	0.597											OREG0021329	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.P65L		Atlas-SNP	.											.	C11orf88	37	.	0			c.C194T						PASS	.						40.0	47.0	44.0					11																	111385703		2153	4278	6431	SO:0001583	missense	399949	exon1			GTCTGCCGGTGGC	BC039505, AK128145	CCDS41712.1, CCDS41713.1	11q23.1	2012-08-10			ENSG00000183644	ENSG00000183644			25061	protein-coding gene	gene with protein product	"""hypothetical gene supported by BC039505"""					12477932	Standard	NM_001100388		Approved	FLJ46266	uc009yyd.3	Q6PI97	OTTHUMG00000166720	ENST00000375618.4:c.194C>T	11.37:g.111385703C>T	ENSP00000364768:p.Pro65Leu	Somatic	50	0	0	1434	WXS	Illumina HiSeq	Phase_I	59	28	0.474576	NM_001100388	E9PAN0|Q6ZRL3	Missense_Mutation	SNP	ENST00000375618.4	37	CCDS41713.1	.	.	.	.	.	.	.	.	.	.	C	13.79	2.342184	0.41498	.	.	ENSG00000183644	ENST00000375618;ENST00000529167;ENST00000332814	.	.	.	5.09	0.987	0.19790	.	0.159222	0.40144	N	0.001171	T	0.72598	0.3480	M	0.66939	2.045	0.44677	D	0.997668	D;D	0.76494	0.999;0.996	P;P	0.60886	0.88;0.866	T	0.74850	-0.3524	9	0.62326	D	0.03	-1.5825	14.7899	0.69833	0.0:0.4087:0.5913:0.0	.	65;65	E9PAN0;Q6PI97	.;CK088_HUMAN	L	65	.	ENSP00000333845:P65L	P	+	2	0	C11orf88	110890913	0.097000	0.21791	0.804000	0.32291	0.030000	0.12068	0.229000	0.17833	0.033000	0.15463	-0.282000	0.10007	CCG	.	.	none		0.597	C11orf88-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000391181.1	NM_001100388	
C1S	716	hgsc.bcm.edu	37	12	7170336	7170336	+	Missense_Mutation	SNP	G	G	A	rs12146727	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:7170336G>A	ENST00000406697.1	+	7	984	c.356G>A	c.(355-357)cGt>cAt	p.R119H	C1S_ENST00000328916.3_Missense_Mutation_p.R119H|C1S_ENST00000360817.5_Missense_Mutation_p.R119H|C1S_ENST00000402681.3_5'UTR			P09871	C1S_HUMAN	complement component 1, s subcomponent	119	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.		R -> H (in dbSNP:rs12146727).		complement activation (GO:0006956)|complement activation, classical pathway (GO:0006958)|innate immune response (GO:0045087)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)|identical protein binding (GO:0042802)|serine-type endopeptidase activity (GO:0004252)			breast(1)|endometrium(5)|kidney(2)|large_intestine(8)|liver(4)|lung(8)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	33					Abciximab(DB00054)|Adalimumab(DB00051)|Basiliximab(DB00074)|Cetuximab(DB00002)|Etanercept(DB00005)|Gemtuzumab ozogamicin(DB00056)|Ibritumomab(DB00078)|Muromonab(DB00075)|Rituximab(DB00073)|Trastuzumab(DB00072)	AATGAAGAGCGTTTTACGGGG	0.443													G|||	513	0.102436	0.093	0.0937	5008	,	,		-128	0.0923		0.1292	False		,,,				2504	0.1043				p.R119H	GBM(156;750 1943 12971 24779 31015)	Atlas-SNP	.											.	C1S	93	.	0			c.G356A						PASS	.	G	HIS/ARG,HIS/ARG	455,3951	215.8+/-234.7	29,397,1777	129.0	120.0	123.0		356,356	5.2	1.0	12	dbSNP_120	123	1135,7465	234.6+/-267.5	89,957,3254	yes	missense,missense	C1S	NM_001734.3,NM_201442.2	29,29	118,1354,5031	AA,AG,GG		13.1977,10.3268,12.2251	probably-damaging,probably-damaging	119/689,119/689	7170336	1590,11416	2203	4300	6503	SO:0001583	missense	716	exon4			AAGAGCGTTTTAC		CCDS31735.1	12p13	2014-09-17			ENSG00000182326	ENSG00000182326	3.4.21.42	"""Complement system"""	1247	protein-coding gene	gene with protein product		120580					Standard	NM_201442		Approved		uc001qsl.3	P09871	OTTHUMG00000150305	ENST00000406697.1:c.356G>A	12.37:g.7170336G>A	ENSP00000385035:p.Arg119His	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	127	42	0.330709	NM_201442	D3DUT4|Q9UCU7|Q9UCU8|Q9UCU9|Q9UCV0|Q9UCV1|Q9UCV2|Q9UCV3|Q9UCV4|Q9UCV5|Q9UM14	Missense_Mutation	SNP	ENST00000406697.1	37	CCDS31735.1	237	0.10851648351648352	47	0.09552845528455285	42	0.11602209944751381	47	0.08216783216783216	101	0.13324538258575197	G	26.9	4.784891	0.90282	0.103268	0.131977	ENSG00000182326	ENST00000406697;ENST00000328916;ENST00000360817;ENST00000382222;ENST00000403949	T;T;T;T	0.19669	2.13;2.13;2.13;2.13	6.04	5.15	0.70609	CUB (5);	0.172751	0.28021	N	0.016916	T	0.00384	0.0012	M	0.84082	2.675	0.09310	P	1.0	P	0.52692	0.955	P	0.45071	0.468	T	0.12116	-1.0560	9	0.72032	D	0.01	.	15.4346	0.75137	0.0663:0.0:0.9337:0.0	rs12146727;rs52805025;rs12146727	119	P09871	C1S_HUMAN	H	119;119;119;101;119	ENSP00000385035:R119H;ENSP00000328173:R119H;ENSP00000354057:R119H;ENSP00000384464:R119H	ENSP00000328173:R119H	R	+	2	0	C1S	7040597	1.000000	0.71417	0.974000	0.42286	0.991000	0.79684	3.781000	0.55394	1.571000	0.49722	0.561000	0.74099	CGT	G|0.885;A|0.115	0.115	strong		0.443	C1S-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000317481.1	NM_001734	
HMCN1	83872	hgsc.bcm.edu	37	1	186039814	186039814	+	Silent	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:186039814A>G	ENST00000271588.4	+	52	8293	c.8064A>G	c.(8062-8064)gtA>gtG	p.V2688V	HMCN1_ENST00000367492.2_Silent_p.V2688V	NM_031935.2	NP_114141.2	Q96RW7	HMCN1_HUMAN	hemicentin 1	2688	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						AGATCAAAGTAAACAACACTC	0.428																																					p.V2688V		Atlas-SNP	.											HMCN1,NS,carcinoma,+2,1	HMCN1	797	1	0			c.A8064G						scavenged	.						126.0	122.0	123.0					1																	186039814		2203	4300	6503	SO:0001819	synonymous_variant	83872	exon52			CAAAGTAAACAAC	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.8064A>G	1.37:g.186039814A>G		Somatic	98	0	0		WXS	Illumina HiSeq	Phase_I	193	2	0.0103627	NM_031935	A6NGE3|Q5TYR7|Q96DN3|Q96DN8|Q96SC3	Silent	SNP	ENST00000271588.4	37	CCDS30956.1																																																																																			.	.	none		0.428	HMCN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131848.1	NM_031935	
OR4D1	26689	hgsc.bcm.edu	37	17	56232687	56232687	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:56232687C>A	ENST00000268912.5	+	1	194	c.173C>A	c.(172-174)cCc>cAc	p.P58H		NM_012374.1	NP_036506.1	Q15615	OR4D1_HUMAN	olfactory receptor, family 4, subfamily D, member 1	58					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)			kidney(2)|large_intestine(4)|lung(4)|ovary(1)|stomach(1)|urinary_tract(1)	13						CTCCACACACCCATGTATTTT	0.473																																					p.P58H		Atlas-SNP	.											.	OR4D1	48	.	0			c.C173A						PASS	.						175.0	172.0	173.0					17																	56232687		2114	4269	6383	SO:0001583	missense	26689	exon1			ACACACCCATGTA	X89670	CCDS42365.1	17q22	2012-08-09			ENSG00000141194	ENSG00000141194		"""GPCR / Class A : Olfactory receptors"""	8293	protein-coding gene	gene with protein product				OR4D3		9119360	Standard	NM_012374		Approved	TPCR16	uc010wno.2	Q15615		ENST00000268912.5:c.173C>A	17.37:g.56232687C>A	ENSP00000365451:p.Pro58His	Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	131	64	0.48855	NM_012374	B2RN14|Q8NGB1|Q96R76	Missense_Mutation	SNP	ENST00000268912.5	37	CCDS42365.1	.	.	.	.	.	.	.	.	.	.	c	23.1	4.369670	0.82573	.	.	ENSG00000141194	ENST00000268912	T	0.02050	4.48	5.63	5.63	0.86233	GPCR, rhodopsin-like superfamily (1);	0.000000	0.40908	U	0.000991	T	0.22742	0.0549	H	0.97131	3.945	0.58432	D	0.99999	D	0.76494	0.999	D	0.72338	0.977	T	0.25433	-1.0132	10	0.87932	D	0	-29.8376	17.1781	0.86846	0.0:1.0:0.0:0.0	.	58	Q15615	OR4D1_HUMAN	H	58	ENSP00000365451:P58H	ENSP00000365451:P58H	P	+	2	0	OR4D1	53587686	1.000000	0.71417	0.986000	0.45419	0.980000	0.70556	5.971000	0.70440	2.652000	0.90054	0.543000	0.68304	CCC	.	.	none		0.473	OR4D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443364.1		
UBXN11	91544	hgsc.bcm.edu	37	1	26608843	26608843	+	Missense_Mutation	SNP	C	C	A	rs151149897|rs66614970|rs6667693		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:26608843C>A	ENST00000374222.1	-	16	1974	c.1510G>T	c.(1510-1512)Ggt>Tgt	p.G504C	UBXN11_ENST00000357089.4_Missense_Mutation_p.G471C|UBXN11_ENST00000374221.3_Missense_Mutation_p.G504C|UBXN11_ENST00000374217.2_Missense_Mutation_p.G471C|UBXN11_ENST00000374223.1_Missense_Mutation_p.G261C|UBXN11_ENST00000314675.7_Missense_Mutation_p.G384C			Q5T124	UBX11_HUMAN	UBX domain protein 11	504	3 X 8 AA tandem repeats of P-G-P-G-P-G-P- S.|Pro-rich.					cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.P503_G504insCP(1)|p.G490_P515delGPGPSPGPGPGPSPGPGPGPSPCPGP(1)		endometrium(3)|kidney(2)|large_intestine(4)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(3)	23						ggaccgggaccgggactgggg	0.731																																					p.G504C		Atlas-SNP	.											UBXN11,NS,carcinoma,0,1	UBXN11	54	1	2	Insertion - In frame(1)|Deletion - In frame(1)	upper_aerodigestive_tract(1)|ovary(1)	c.G1510T						scavenged	.						16.0	17.0	17.0					1																	26608843		1719	3939	5658	SO:0001583	missense	91544	exon16			CGGGACCGGGACT	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.1510G>T	1.37:g.26608843C>A	ENSP00000363339:p.Gly504Cys	Somatic	8	2	0.25		WXS	Illumina HiSeq	Phase_I	17	5	0.294118	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	.	.	.	.	.	.	.	.	.	.	-	8.299	0.819400	0.16607	.	.	ENSG00000158062	ENST00000314675;ENST00000374223;ENST00000357089;ENST00000374221;ENST00000374222;ENST00000374217	T;T;T;T;T;T	0.23950	1.88;1.92;2.21;2.14;2.14;2.21	.	.	.	.	.	.	.	.	T	0.24236	0.0587	N	0.08118	0	0.20638	N	0.999871	D;D;D	0.89917	1.0;1.0;0.999	D;D;D	0.79108	0.992;0.992;0.981	T	0.14172	-1.0482	8	0.72032	D	0.01	.	4.6597	0.12636	0.0:1.0:0.0:0.0	rs6667693	471;384;504	Q5T124-2;Q5T124-3;Q5T124	.;.;UBX11_HUMAN	C	384;261;471;504;504;471	ENSP00000324721:G384C;ENSP00000363340:G261C;ENSP00000349601:G471C;ENSP00000363338:G504C;ENSP00000363339:G504C;ENSP00000363334:G471C	ENSP00000324721:G384C	G	-	1	0	UBXN11	26481430	0.005000	0.15991	0.167000	0.22817	0.175000	0.22909	-0.694000	0.05115	-0.000000	0.14550	0.000000	0.15137	GGT	C|0.500;A|0.500	0.500	weak		0.731	UBXN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000009500.1	NM_145345	
PRR30	339779	hgsc.bcm.edu	37	2	27360666	27360666	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:27360666A>G	ENST00000335524.3	-	3	1057	c.532T>C	c.(532-534)Tgg>Cgg	p.W178R		NM_178553.3	NP_848648.2	Q53SZ7	PRR30_HUMAN		178										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)					TACTGATGCCAGCGCCATGTC	0.627																																					p.W178R		Atlas-SNP	.											.	C2orf53	45	.	0			c.T532C						PASS	.						53.0	55.0	54.0					2																	27360666		2203	4300	6503	SO:0001583	missense	339779	exon3			GATGCCAGCGCCA																												ENST00000335524.3:c.532T>C	2.37:g.27360666A>G	ENSP00000335017:p.Trp178Arg	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	96	7	0.0729167	NM_178553	Q86UE2	Missense_Mutation	SNP	ENST00000335524.3	37	CCDS1739.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	12.32|12.32	1.901753|1.901753	0.33535|0.33535	.|.	.|.	ENSG00000186143|ENSG00000186143	ENST00000432962|ENST00000335524	.|T	.|0.34072	.|1.38	4.56|4.56	0.778|0.778	0.18543|0.18543	.|.	.|0.231694	.|0.22575	.|N	.|0.058287	T|T	0.20700|0.20700	0.0498|0.0498	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	1|1	.|B	.|0.24368	.|0.102	.|B	.|0.23852	.|0.049	T|T	0.13548|0.13548	-1.0505|-1.0505	6|10	0.87932|0.59425	D|D	0|0.04	-2.4502|-2.4502	2.6344|2.6344	0.04954|0.04954	0.5896:0.0:0.2152:0.1952|0.5896:0.0:0.2152:0.1952	.|.	.|178	.|Q53SZ7	.|CB053_HUMAN	P|R	13|178	.|ENSP00000335017:W178R	ENSP00000393468:L13P|ENSP00000335017:W178R	L|W	-|-	2|1	0|0	C2orf53|C2orf53	27214170|27214170	0.075000|0.075000	0.21258|0.21258	0.008000|0.008000	0.14137|0.14137	0.183000|0.183000	0.23260|0.23260	1.140000|1.140000	0.31516|0.31516	0.773000|0.773000	0.33404|0.33404	0.459000|0.459000	0.35465|0.35465	CTG|TGG	.	.	none		0.627	C2orf53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250188.1		
MT-CYB	4519	hgsc.bcm.edu	37	M	15622	15622	+	Silent	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrM:15622T>C	ENST00000361789.2	+	1	876	c.876T>C	c.(874-876)ctT>ctC	p.L292L	MT-TE_ENST00000387459.1_RNA|MT-TT_ENST00000387460.2_RNA|MT-ND6_ENST00000361681.2_5'Flank|MT-TP_ENST00000387461.2_RNA			P00156	CYB_HUMAN	mitochondrially encoded cytochrome b	292					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						GGAGGCGTCCTTGCCCTATTA	0.453											OREG0007583	type=REGULATORY REGION|TFbs=ESR1|Dataset=Estrogen Receptor Alpha Binding Sites|EvidenceSubtype=Chromatin immunoprecipitation with tag sequencing (ChIP-TS)																									p.L292L		Atlas-SNP	.											.	.	.	.	0			c.T876C						PASS	.																																			SO:0001819	synonymous_variant	0	exon1			CGTCCTTGCCCTA			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.876T>C	M.37:g.15622T>C		Somatic	8	0	0	585	WXS	Illumina HiSeq	Phase_I	8	8	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		0.453	MT-CYB-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		YP_003024038	
RYR2	6262	hgsc.bcm.edu	37	1	237944873	237944873	+	Silent	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:237944873T>C	ENST00000366574.2	+	89	12206	c.11889T>C	c.(11887-11889)agT>agC	p.S3963S	RYR2_ENST00000542537.1_Silent_p.S3947S|RYR2_ENST00000360064.6_Silent_p.S3969S|RYR2_ENST00000609119.1_3'UTR	NM_001035.2	NP_001026.2	Q92736	RYR2_HUMAN	ryanodine receptor 2 (cardiac)	3963					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)			AGGATTCCAGTCAAATTGAGC	0.343																																					p.S3963S		Atlas-SNP	.											RYR2,NS,carcinoma,+1,1	RYR2	1273	1	0			c.T11889C						scavenged	.						92.0	91.0	91.0					1																	237944873		1897	4158	6055	SO:0001819	synonymous_variant	6262	exon89			TTCCAGTCAAATT	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.11889T>C	1.37:g.237944873T>C		Somatic	164	0	0		WXS	Illumina HiSeq	Phase_I	99	2	0.020202	NM_001035	Q15411|Q546N8|Q5T3P2	Silent	SNP	ENST00000366574.2	37	CCDS55691.1																																																																																			.	.	none		0.343	RYR2-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095402.2	NM_001035	
GTPBP10	85865	hgsc.bcm.edu	37	7	90007487	90007487	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:90007487T>C	ENST00000222511.6	+	8	805	c.739T>C	c.(739-741)Tac>Cac	p.Y247H	GTPBP10_ENST00000257659.8_Missense_Mutation_p.Y168H	NM_033107.3	NP_149098.2	A4D1E9	GTPBA_HUMAN	GTP-binding protein 10 (putative)	247	OBG-type G. {ECO:0000255|PROSITE- ProRule:PRU01047}.				ribosome biogenesis (GO:0042254)	chromosome (GO:0005694)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|magnesium ion binding (GO:0000287)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(2)|large_intestine(3)|lung(4)	10						TCACACTCAATACAGGACAGC	0.323																																					p.Y247H		Atlas-SNP	.											GTPBP10,NS,carcinoma,-1,2	GTPBP10	31	2	0			c.T739C						scavenged	.						180.0	162.0	168.0					7																	90007487		2202	4297	6499	SO:0001583	missense	85865	exon8			ACTCAATACAGGA		CCDS5617.1, CCDS43614.1	7q21.13	2006-08-15			ENSG00000105793	ENSG00000105793			25106	protein-coding gene	gene with protein product		610920				12477932	Standard	NM_001042717		Approved	DKFZP686A10121, FLJ38242	uc003ukm.2	A4D1E9	OTTHUMG00000023655	ENST00000222511.6:c.739T>C	7.37:g.90007487T>C	ENSP00000222511:p.Tyr247His	Somatic	204	0	0		WXS	Illumina HiSeq	Phase_I	214	5	0.0233645	NM_033107	B4DFY6|Q3B7A6|Q5H9V2|Q8IXG8|Q8N982|Q8WU16|Q9BSP1|Q9Y6T6	Missense_Mutation	SNP	ENST00000222511.6	37	CCDS5617.1	.	.	.	.	.	.	.	.	.	.	T	10.86	1.469930	0.26423	.	.	ENSG00000105793	ENST00000257659;ENST00000222511;ENST00000417207	T;T;T	0.16597	2.33;2.33;2.33	5.6	5.6	0.85130	GTP-binding domain, HSR1-related (1);	0.103338	0.64402	D	0.000002	T	0.23133	0.0559	N	0.16166	0.38	0.45634	D	0.998564	D;B	0.67145	0.996;0.016	D;B	0.63877	0.919;0.038	T	0.09596	-1.0667	9	.	.	.	0.0036	15.7735	0.78190	0.0:0.0:0.0:1.0	.	168;247	A4D1E9-2;A4D1E9	.;GTPBA_HUMAN	H	168;247;174	ENSP00000257659:Y168H;ENSP00000222511:Y247H;ENSP00000416596:Y174H	.	Y	+	1	0	GTPBP10	89845423	1.000000	0.71417	0.814000	0.32528	0.802000	0.45316	5.200000	0.65158	2.107000	0.64212	0.528000	0.53228	TAC	.	.	none		0.323	GTPBP10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059976.3	NM_033107	
NUF2	83540	hgsc.bcm.edu	37	1	163315530	163315530	+	Silent	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:163315530G>A	ENST00000271452.3	+	11	1149	c.870G>A	c.(868-870)caG>caA	p.Q290Q	NUF2_ENST00000367900.3_Silent_p.Q290Q|NUF2_ENST00000524800.1_Intron	NM_145697.2	NP_663735.2	Q9BZD4	NUF2_HUMAN	NUF2, NDC80 kinetochore complex component	290	Interaction with the N-terminus of NDC80.				chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|membrane (GO:0016020)|Ndc80 complex (GO:0031262)|nucleus (GO:0005634)				breast(1)|endometrium(2)|kidney(1)|large_intestine(10)|lung(15)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	35	all_hematologic(923;0.101)					CTTCATGTCAGTTGGAAGTGC	0.358																																					p.Q290Q		Atlas-SNP	.											NUF2_ENST00000271452,mucosal,malignant_melanoma,+2,2	NUF2	138	2	0			c.G870A						scavenged	.						102.0	101.0	102.0					1																	163315530		2203	4300	6503	SO:0001819	synonymous_variant	83540	exon11			ATGTCAGTTGGAA	BG354574	CCDS1245.1	1q23.3	2013-07-03	2013-07-03	2006-11-07	ENSG00000143228	ENSG00000143228			14621	protein-coding gene	gene with protein product	"""cancer/testis antigen 106"""	611772	"""cell division cycle associated 1"", ""NUF2, NDC80 kinetochore complex component, homolog (S. cerevisiae)"""	CDCA1		11266451, 11685532	Standard	NM_031423		Approved	NUF2R, CT106	uc001gcr.1	Q9BZD4	OTTHUMG00000034275	ENST00000271452.3:c.870G>A	1.37:g.163315530G>A		Somatic	82	0	0		WXS	Illumina HiSeq	Phase_I	140	4	0.0285714	NM_145697	Q8WU69|Q96HJ4|Q96Q78	Silent	SNP	ENST00000271452.3	37	CCDS1245.1																																																																																			.	.	none		0.358	NUF2-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000082812.1	NM_145697	
SRGAP2	23380	hgsc.bcm.edu	37	1	206566075	206566075	+	Silent	SNP	C	C	T	rs561152664		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:206566075C>T	ENST00000414007.1	+	2	96	c.96C>T	c.(94-96)gcC>gcT	p.A32A	SRGAP2_ENST00000419187.2_5'UTR			O75044	SRGP2_HUMAN	SLIT-ROBO Rho GTPase activating protein 2	172	F-BAR domain.|FCH. {ECO:0000255|PROSITE- ProRule:PRU00083}.				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)					TGTACAATGCCGACAGCATCA	0.527													C|||	1	0.000199681	0.0	0.0	5008	,	,		29744	0.0		0.0	False		,,,				2504	0.001				p.A19A		Atlas-SNP	.											SRGAP2_ENST00000414007,NS,carcinoma,0,1	.	.	1	0			c.C57T						scavenged	.						38.0	35.0	36.0					1																	206566075		2049	4196	6245	SO:0001819	synonymous_variant	100996712	exon2			CAATGCCGACAGC	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.96C>T	1.37:g.206566075C>T		Somatic	404	2	0.00495049		WXS	Illumina HiSeq	Phase_I	681	8	0.0117474	NM_001271887		Silent	SNP	ENST00000414007.1	37		.	.	.	.	.	.	.	.	.	.	C	10.62	1.401829	0.25291	.	.	ENSG00000163486	ENST00000295713	.	.	.	5.36	-3.3	0.05003	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.4693	0.27340	0.0:0.2798:0.198:0.5222	.	.	.	.	X	86	.	.	R	+	1	2	SRGAP2	204632698	0.030000	0.19436	0.994000	0.49952	0.996000	0.88848	-1.108000	0.03313	-0.241000	0.09681	0.455000	0.32223	CGA	.	.	none		0.527	SRGAP2-201	KNOWN	basic	protein_coding	protein_coding		NM_015326	
RGL3	57139	hgsc.bcm.edu	37	19	11529920	11529920	+	Splice_Site	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:11529920A>G	ENST00000380456.3	-	1	97		c.e1+1		RGL3_ENST00000393423.3_Splice_Site	NM_001035223.2|NM_001161616.1	NP_001030300.2|NP_001155088.1	Q3MIN7	RGL3_HUMAN	ral guanine nucleotide dissociation stimulator-like 3						small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	Ral guanyl-nucleotide exchange factor activity (GO:0008321)			breast(1)|endometrium(4)|large_intestine(2)|lung(9)|ovary(1)|skin(1)	18						TTGTCCCCTTACCAGGGCCAG	0.697																																					.	GBM(174;751 2067 17998 27979 33959)	Atlas-SNP	.											.	RGL3	100	.	0			c.33+2T>C						PASS	.						60.0	74.0	69.0					19																	11529920		2203	4300	6503	SO:0001630	splice_region_variant	57139	exon2			CCCCTTACCAGGG	BC014426	CCDS32910.1, CCDS54221.1	19p13.2	2008-02-05				ENSG00000205517			30282	protein-coding gene	gene with protein product						10869344	Standard	NM_001035223		Approved	FLJ32585	uc002mro.2	Q3MIN7		ENST00000380456.3:c.33+1T>C	19.37:g.11529920A>G		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	98	5	0.0510204	NM_001161616	B5ME84|B7ZL22|Q0P6G0	Splice_Site	SNP	ENST00000380456.3	37	CCDS32910.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.961190	0.53400	.	.	ENSG00000205517	ENST00000393423;ENST00000380456;ENST00000453604	.	.	.	4.22	3.11	0.35812	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	7.2496	0.26142	0.7737:0.2263:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	RGL3	11390920	1.000000	0.71417	1.000000	0.80357	0.895000	0.52256	1.747000	0.38298	1.694000	0.51137	0.254000	0.18369	.	.	.	none		0.697	RGL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000421208.3	XM_290867	Intron
OSBPL9	114883	hgsc.bcm.edu	37	1	52251499	52251499	+	Missense_Mutation	SNP	T	T	C	rs149501959	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:52251499T>C	ENST00000428468.1	+	21	1851	c.1849T>C	c.(1849-1851)Tct>Cct	p.S617P	OSBPL9_ENST00000435686.2_Missense_Mutation_p.S452P|OSBPL9_ENST00000447887.1_Missense_Mutation_p.S627P|OSBPL9_ENST00000361556.5_Missense_Mutation_p.S507P|OSBPL9_ENST00000462759.1_Missense_Mutation_p.S439P|OSBPL9_ENST00000371714.1_Missense_Mutation_p.S604P|OSBPL9_ENST00000453295.1_Missense_Mutation_p.S600P|OSBPL9_ENST00000531828.1_Missense_Mutation_p.S452P|OSBPL9_ENST00000530544.1_Missense_Mutation_p.S536P|OSBPL9_ENST00000337809.4_Missense_Mutation_p.S622P|OSBPL9_ENST00000486942.1_Missense_Mutation_p.S439P|OSBPL9_ENST00000371710.3_Missense_Mutation_p.S635P			Q96SU4	OSBL9_HUMAN	oxysterol binding protein-like 9	617					lipid transport (GO:0006869)	cytoplasm (GO:0005737)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)	lipid binding (GO:0008289)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(2)|lung(3)|pancreas(1)|prostate(3)|skin(1)	18						TGACAAGAAGTCTTTTTGCTC	0.388																																					p.S627P		Atlas-SNP	.											OSBPL9_ENST00000447887,bladder,carcinoma,-1,4	OSBPL9	192	4	0			c.T1879C						scavenged	.						128.0	119.0	122.0					1																	52251499		2203	4300	6503	SO:0001583	missense	114883	exon21			AAGAAGTCTTTTT	AF392445	CCDS558.1, CCDS41332.1, CCDS41333.1, CCDS41334.1, CCDS41332.2, CCDS41332.3, CCDS41333.2, CCDS44145.1, CCDS55598.1	1p32.3	2013-01-10			ENSG00000117859	ENSG00000117859		"""Oxysterol binding proteins"", ""Pleckstrin homology (PH) domain containing"""	16386	protein-coding gene	gene with protein product		606737					Standard	NM_148904		Approved		uc001csu.3	Q96SU4	OTTHUMG00000008234	ENST00000428468.1:c.1849T>C	1.37:g.52251499T>C	ENSP00000407168:p.Ser617Pro	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	152	2	0.0131579	NM_148909	B1AKJ8|B3KPQ4|D3DQ31|Q5TFC0|Q6IA67|Q86YQ3|Q8NB17|Q8TAS8|Q96SK4|Q9H9X2	Missense_Mutation	SNP	ENST00000428468.1	37	CCDS41332.3	.	.	.	.	.	.	.	.	.	.	T	3.419	-0.118614	0.06838	.	.	ENSG00000117859	ENST00000371714;ENST00000371710;ENST00000337809;ENST00000447887;ENST00000435686;ENST00000428468;ENST00000453295;ENST00000530544;ENST00000531828;ENST00000361556;ENST00000462759;ENST00000486942	T;T;T;T;T;T;T;T;T;T;T;T	0.29397	1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57;1.57	5.52	5.52	0.82312	.	0.100643	0.64402	D	0.000001	T	0.06005	0.0156	N	0.00358	-1.6	0.44207	D	0.997032	B;B;B;B;B	0.06786	0.0;0.0;0.001;0.0;0.001	B;B;B;B;B	0.11329	0.001;0.003;0.006;0.004;0.004	T	0.36286	-0.9754	10	0.02654	T	1	-15.7823	4.1355	0.10169	0.0:0.1526:0.1889:0.6585	.	600;507;633;617;622	Q86YQ3;Q96SU4-3;B1AKJ7;Q96SU4;B1AKJ6	.;.;.;OSBL9_HUMAN;.	P	604;635;622;627;452;617;600;536;452;507;439;439	ENSP00000360779:S604P;ENSP00000360775:S635P;ENSP00000337265:S622P;ENSP00000412733:S627P;ENSP00000402646:S452P;ENSP00000407168:S617P;ENSP00000413263:S600P;ENSP00000433675:S536P;ENSP00000433083:S452P;ENSP00000354970:S507P;ENSP00000433279:S439P;ENSP00000431980:S439P	ENSP00000337265:S622P	S	+	1	0	OSBPL9	52024087	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.185000	0.42584	2.320000	0.78422	0.528000	0.53228	TCT	T|0.998;A|0.002	.	alt		0.388	OSBPL9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000022584.4		
CTAGE1	64693	hgsc.bcm.edu	37	18	19996983	19996983	+	5'Flank	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr18:19996983T>C	ENST00000525417.1	-	0	0				CTAGE1_ENST00000391403.2_Silent_p.E264E			Q9HC47	CTGE1_HUMAN	cutaneous T-cell lymphoma-associated antigen 1							integral component of membrane (GO:0016021)				cervix(1)|endometrium(2)|kidney(3)|large_intestine(1)|lung(19)|ovary(1)	27	all_cancers(21;0.000361)|all_epithelial(16;9.61e-06)|Colorectal(14;0.0533)|Lung NSC(20;0.0605)|Ovarian(2;0.116)|all_lung(20;0.135)					CACTGTTCATTTCTAATTCCA	0.368																																					p.E264E		Atlas-SNP	.											CTAGE1_ENST00000391403,NS,carcinoma,-2,2	CTAGE1	146	2	0			c.A792G						scavenged	.						110.0	110.0	110.0					18																	19996983		2202	4300	6502	SO:0001631	upstream_gene_variant	64693	exon1			GTTCATTTCTAAT	AF177229	CCDS45837.1	18q11.2	2010-05-26			ENSG00000212710	ENSG00000212710			24346	protein-coding gene	gene with protein product	"""cutaneous T-cell lymphoma-associated antigen 1"", ""cutaneous T-cell lymphoma-associated antigen 2"", ""cancer/testis antigen family 21, member 1"", ""cancer/testis antigen family 21, member 2"""	608856				11149944, 12839582	Standard	NM_172241		Approved	cTAGE-1, cTAGE-2, CTAGE, CT21.1, CT21.2	uc002ktv.1	Q96RT6			18.37:g.19996983T>C	Exception_encountered	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	242	4	0.0165289	NM_172241	B0YIZ3	Silent	SNP	ENST00000525417.1	37																																																																																				.	.	none		0.368	CTAGE1-002	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000386767.1	NM_022663, NM_172241	
CACNA1D	776	hgsc.bcm.edu	37	3	53757546	53757546	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:53757546C>T	ENST00000350061.5	+	13	2263	c.1752C>T	c.(1750-1752)gtC>gtT	p.V584V	CACNA1D_ENST00000422281.2_Silent_p.V584V|CACNA1D_ENST00000288139.4_Silent_p.V604V	NM_001128840.1	NP_001122312.1	Q01668	CAC1D_HUMAN	calcium channel, voltage-dependent, L type, alpha 1D subunit	584					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|energy reserve metabolic process (GO:0006112)|membrane depolarization during action potential (GO:0086010)|membrane depolarization during cardiac muscle cell action potential (GO:0086012)|membrane repolarization during SA node cell action potential (GO:0086052)|positive regulation of calcium ion transport (GO:0051928)|regulation of atrial cardiac muscle cell membrane repolarization (GO:0060372)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of insulin secretion (GO:0050796)|regulation of potassium ion transmembrane transport (GO:1901379)|regulation of potassium ion transmembrane transporter activity (GO:1901016)|sensory perception of sound (GO:0007605)|small molecule metabolic process (GO:0044281)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|ankyrin binding (GO:0030506)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)|voltage-gated calcium channel activity involved in cardiac muscle cell action potential (GO:0086007)|voltage-gated calcium channel activity involved SA node cell action potential (GO:0086059)			breast(3)|central_nervous_system(9)|cervix(2)|endometrium(11)|kidney(7)|large_intestine(13)|liver(1)|lung(29)|ovary(6)|prostate(2)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(1)	90				BRCA - Breast invasive adenocarcinoma(193;0.00029)|KIRC - Kidney renal clear cell carcinoma(284;0.0145)|Kidney(284;0.0175)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Felodipine(DB01023)|Isradipine(DB00270)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	CATATTTCGTCTCTCTTTTCA	0.478																																					p.V604V		Atlas-SNP	.											CACNA1D_ENST00000350061,NS,carcinoma,+2,2	CACNA1D	324	2	0			c.C1812T						scavenged	.						284.0	259.0	267.0					3																	53757546		2203	4300	6503	SO:0001819	synonymous_variant	776	exon14			TTTCGTCTCTCTT	AB209171	CCDS2872.1, CCDS46848.1, CCDS46849.1	3p14.3	2012-03-07			ENSG00000157388	ENSG00000157388		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1391	protein-coding gene	gene with protein product		114206		CCHL1A2, CACNL1A2		1664412	Standard	NM_000720		Approved	Cav1.3, CACH3, CACN4	uc003dgu.5	Q01668	OTTHUMG00000158278	ENST00000350061.5:c.1752C>T	3.37:g.53757546C>T		Somatic	272	0	0		WXS	Illumina HiSeq	Phase_I	321	4	0.0124611	NM_000720	B0FYA3|Q13916|Q13931|Q71UT1|Q9UDC3	Silent	SNP	ENST00000350061.5	37	CCDS46848.1																																																																																			.	.	none		0.478	CACNA1D-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350557.1	NM_000720	
EPHB2	2048	hgsc.bcm.edu	37	1	23236932	23236932	+	Missense_Mutation	SNP	G	G	A	rs549199396		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:23236932G>A	ENST00000400191.3	+	14	2578	c.2560G>A	c.(2560-2562)Gcc>Acc	p.A854T	EPHB2_ENST00000374630.3_Missense_Mutation_p.A854T|EPHB2_ENST00000374632.3_Missense_Mutation_p.A855T|EPHB2_ENST00000374627.1_Missense_Mutation_p.A849T	NM_004442.6|NM_017449.3	NP_004433.2|NP_059145.2	P29323	EPHB2_HUMAN	EPH receptor B2	854	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				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)	p.A854T(1)		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)		CTGCCCGAGCGCCCTGCACCA	0.587																																					p.A855T		Atlas-SNP	.											EPHB2,colon,carcinoma,0,1	EPHB2	257	1	1	Substitution - Missense(1)	large_intestine(1)	c.G2563A						PASS	.						122.0	89.0	100.0					1																	23236932		2203	4300	6503	SO:0001583	missense	2048	exon14			CCGAGCGCCCTGC	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.2560G>A	1.37:g.23236932G>A	ENSP00000383053:p.Ala854Thr	Somatic	138	0	0		WXS	Illumina HiSeq	Phase_I	78	59	0.75641	NM_004442	O43477|Q5T0U6|Q5T0U7|Q5T0U8	Missense_Mutation	SNP	ENST00000400191.3	37		.	.	.	.	.	.	.	.	.	.	G	20.9	4.070225	0.76301	.	.	ENSG00000133216	ENST00000374625;ENST00000374630;ENST00000400191;ENST00000374632;ENST00000374627	D;D;D;D	0.82619	-1.63;-1.63;-1.63;-1.63	4.64	4.64	0.57946	Serine-threonine/tyrosine-protein kinase (2);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.73908	0.3647	L	0.28556	0.865	0.80722	D	1	B;B;B;B	0.32203	0.043;0.36;0.066;0.017	B;B;B;B	0.23150	0.006;0.044;0.018;0.019	T	0.76506	-0.2934	10	0.66056	D	0.02	.	16.6405	0.85070	0.0:0.0:1.0:0.0	.	796;854;872;855	A6NJM0;P29323;Q4LE53;P29323-3	.;EPHB2_HUMAN;.;.	T	796;854;854;855;849	ENSP00000363761:A854T;ENSP00000383053:A854T;ENSP00000363763:A855T;ENSP00000363758:A849T	ENSP00000363755:A796T	A	+	1	0	EPHB2	23109519	1.000000	0.71417	0.995000	0.50966	0.981000	0.71138	7.803000	0.85983	2.586000	0.87340	0.555000	0.69702	GCC	.	.	none		0.587	EPHB2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000008060.2	NM_017449	
MPDZ	8777	hgsc.bcm.edu	37	9	13150599	13150599	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:13150599C>T	ENST00000319217.7	-	25	3788	c.3541G>A	c.(3541-3543)Gtg>Atg	p.V1181M	MPDZ_ENST00000538841.1_Missense_Mutation_p.V73M|MPDZ_ENST00000541718.1_Missense_Mutation_p.V1181M|MPDZ_ENST00000536827.1_Missense_Mutation_p.V1181M|MPDZ_ENST00000546205.1_Missense_Mutation_p.V1195M|MPDZ_ENST00000381022.2_Missense_Mutation_p.V1181M|MPDZ_ENST00000447879.1_Missense_Mutation_p.V1181M|MPDZ_ENST00000381015.4_Missense_Mutation_p.V1181M	NM_001261406.1	NP_001248335.1	O75970	MPDZ_HUMAN	multiple PDZ domain protein	1181	PDZ 7. {ECO:0000255|PROSITE- ProRule:PRU00143}.				cell adhesion (GO:0007155)|myelination (GO:0042552)|viral process (GO:0016032)	apical plasma membrane (GO:0016324)|apicolateral plasma membrane (GO:0016327)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|neuron projection (GO:0043005)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)|tight junction (GO:0005923)	protein C-terminus binding (GO:0008022)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(14)|lung(15)|ovary(5)|prostate(7)|stomach(1)|urinary_tract(2)	61				GBM - Glioblastoma multiforme(50;2.03e-06)		CCCCTCATCACTTCTCCATTG	0.458																																					p.V1181M		Atlas-SNP	.											.	MPDZ	324	.	0			c.G3541A						PASS	.						140.0	138.0	138.0					9																	13150599		1911	4137	6048	SO:0001583	missense	8777	exon25			TCATCACTTCTCC	AF093419	CCDS47951.1, CCDS59119.1, CCDS59120.1	9p23	2008-05-15			ENSG00000107186	ENSG00000107186			7208	protein-coding gene	gene with protein product		603785					Standard	NM_003829		Approved	MUPP1	uc003zlb.4	O75970	OTTHUMG00000021031	ENST00000319217.7:c.3541G>A	9.37:g.13150599C>T	ENSP00000320006:p.Val1181Met	Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	109	42	0.385321	NM_003829	A6NLC2|B2RTS3|B7ZMI4|O43798|Q4LE30|Q5CZ80|Q5JTX3|Q5JTX6|Q5JTX7|Q5JUC3|Q5JUC4|Q5VZ62|Q8N790	Missense_Mutation	SNP	ENST00000319217.7	37		.	.	.	.	.	.	.	.	.	.	C	15.87	2.960646	0.53400	.	.	ENSG00000107186	ENST00000319217;ENST00000541718;ENST00000381022;ENST00000545857;ENST00000538841;ENST00000536827;ENST00000447879;ENST00000381015;ENST00000399902;ENST00000546205;ENST00000433359;ENST00000542239	T;T;T;T;T;T;T;T;T;T;T	0.47177	2.78;2.73;2.73;2.61;2.76;2.74;2.79;2.78;2.79;0.85;0.9	5.95	5.95	0.96441	.	0.000000	0.38272	N	0.001757	T	0.64450	0.2599	L	0.45352	1.415	0.80722	D	1	D;B;D;D;D	0.89917	0.992;0.057;0.99;1.0;0.99	D;B;P;D;P	0.91635	0.94;0.069;0.901;0.999;0.901	T	0.60596	-0.7232	10	0.48119	T	0.1	.	20.3854	0.98941	0.0:1.0:0.0:0.0	.	1181;73;1181;1131;1181	B7ZMI4;B7ZB24;O75970-3;E7EPZ1;O75970-2	.;.;.;.;.	M	1181;1181;1181;187;73;1181;1181;1181;1131;1195;73;73	ENSP00000320006:V1181M;ENSP00000439807:V1181M;ENSP00000370410:V1181M;ENSP00000444230:V187M;ENSP00000444717:V73M;ENSP00000444151:V1181M;ENSP00000415208:V1181M;ENSP00000370403:V1181M;ENSP00000446358:V1195M;ENSP00000389705:V73M;ENSP00000443672:V73M	ENSP00000320006:V1181M	V	-	1	0	MPDZ	13140599	1.000000	0.71417	1.000000	0.80357	0.004000	0.04260	2.324000	0.43831	2.825000	0.97269	0.655000	0.94253	GTG	.	.	none		0.458	MPDZ-001	KNOWN	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000055485.2	NM_003829	
SETD1B	23067	hgsc.bcm.edu	37	12	122248314	122248314	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:122248314C>T	ENST00000604567.1	+	6	1531	c.1463C>T	c.(1462-1464)tCc>tTc	p.S488F	SETD1B_ENST00000267197.5_Missense_Mutation_p.S488F|SETD1B_ENST00000542440.1_Missense_Mutation_p.S488F			Q9UPS6	SET1B_HUMAN	SET domain containing 1B	488	Pro-rich.				histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	histone-lysine N-methyltransferase activity (GO:0018024)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			NS(1)|endometrium(6)|kidney(2)|prostate(2)	11						CTGGAGTCGTCCCCTGCAGGG	0.687																																					p.S488F		Atlas-SNP	.											.	SETD1B	105	.	0			c.C1463T						PASS	.						22.0	27.0	25.0					12																	122248314		692	1591	2283	SO:0001583	missense	23067	exon5			AGTCGTCCCCTGC	AB028999	CCDS53838.1	12q24.31	2013-02-12			ENSG00000139718	ENSG00000139718		"""Chromatin-modifying enzymes / K-methyltransferases"", ""RNA binding motif (RRM) containing"""	29187	protein-coding gene	gene with protein product		611055				10470851, 17355966	Standard	NM_015048		Approved	KIAA1076, Set1B, KMT2G	uc001ubi.3	Q9UPS6	OTTHUMG00000169080	ENST00000604567.1:c.1463C>T	12.37:g.122248314C>T	ENSP00000474253:p.Ser488Phe	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	81	35	0.432099	NM_015048	F6MFW1	Missense_Mutation	SNP	ENST00000604567.1	37		.	.	.	.	.	.	.	.	.	.	C	12.24	1.880098	0.33162	.	.	ENSG00000139718	ENST00000542440;ENST00000267197	D;D	0.94758	-3.51;-3.51	4.97	4.97	0.65823	.	.	.	.	.	D	0.94781	0.8315	L	0.50333	1.59	0.09310	N	1	D	0.61697	0.99	P	0.54664	0.758	D	0.89400	0.3695	9	0.49607	T	0.09	.	13.7217	0.62732	0.0:1.0:0.0:0.0	.	488	Q9UPS6	SET1B_HUMAN	F	488	ENSP00000442924:S488F;ENSP00000267197:S488F	ENSP00000267197:S488F	S	+	2	0	SETD1B	120732697	0.439000	0.25610	0.039000	0.18376	0.790000	0.44656	3.940000	0.56599	2.304000	0.77564	0.462000	0.41574	TCC	.	.	none		0.687	SETD1B-002	PUTATIVE	non_canonical_U12|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000468264.1	XM_037523	
EPHA7	2045	hgsc.bcm.edu	37	6	94120454	94120454	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:94120454T>G	ENST00000369303.4	-	3	781	c.597A>C	c.(595-597)aaA>aaC	p.K199N	EPHA7_ENST00000369297.1_Missense_Mutation_p.K199N	NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	199	Cys-rich.|Eph LBD. {ECO:0000255|PROSITE- ProRule:PRU00883}.				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)		TGTAGTACACTTTGACAGAAA	0.428																																					p.K199N		Atlas-SNP	.											.	EPHA7	251	.	0			c.A597C						PASS	.						81.0	85.0	84.0					6																	94120454		2203	4300	6503	SO:0001583	missense	2045	exon3			GTACACTTTGACA	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.597A>C	6.37:g.94120454T>G	ENSP00000358309:p.Lys199Asn	Somatic	143	0	0		WXS	Illumina HiSeq	Phase_I	178	78	0.438202	NM_004440	A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Missense_Mutation	SNP	ENST00000369303.4	37	CCDS5031.1	.	.	.	.	.	.	.	.	.	.	T	17.72	3.458621	0.63401	.	.	ENSG00000135333	ENST00000369303;ENST00000369297	T;T	0.04317	3.65;3.65	5.66	3.26	0.37387	Tyrosine-protein kinase, receptor class V, conserved site (1);Ephrin receptor, ligand binding (2);Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.06005	0.0156	L	0.61036	1.89	0.52099	D	0.999943	P;D;D;D	0.63880	0.728;0.993;0.96;0.967	B;P;P;P	0.53224	0.277;0.596;0.6;0.721	T	0.10474	-1.0628	10	0.87932	D	0	.	10.4747	0.44657	0.0:0.1379:0.0:0.8621	.	199;199;199;199	Q15375-4;Q15375-3;Q15375-2;Q15375	.;.;.;EPHA7_HUMAN	N	199	ENSP00000358309:K199N;ENSP00000358303:K199N	ENSP00000358303:K199N	K	-	3	2	EPHA7	94177175	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	1.685000	0.37659	1.090000	0.41315	0.533000	0.62120	AAA	.	.	none		0.428	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1		
CSMD3	114788	hgsc.bcm.edu	37	8	114111175	114111175	+	Nonsense_Mutation	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr8:114111175C>A	ENST00000297405.5	-	5	971	c.727G>T	c.(727-729)Gga>Tga	p.G243*	CSMD3_ENST00000519485.1_5'UTR|CSMD3_ENST00000352409.3_Nonsense_Mutation_p.G243*|CSMD3_ENST00000455883.2_Nonsense_Mutation_p.G243*|CSMD3_ENST00000343508.3_Nonsense_Mutation_p.G203*	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	243	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						CTCATTGTTCCTCCACAAGCA	0.383										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																											p.G243X		Atlas-SNP	.											CSMD3_ENST00000343508,NS,carcinoma,+1,2	CSMD3	2325	2	0			c.G727T						PASS	.						110.0	96.0	101.0					8																	114111175		2203	4299	6502	SO:0001587	stop_gained	114788	exon5			TTGTTCCTCCACA	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.727G>T	8.37:g.114111175C>A	ENSP00000297405:p.Gly243*	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	80	40	0.5	NM_052900	Q96PZ3	Nonsense_Mutation	SNP	ENST00000297405.5	37	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	C	37	6.448676	0.97577	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000455883;ENST00000352409	.	.	.	5.1	5.1	0.69264	.	0.000000	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.33940	T	0.23	.	18.8655	0.92290	0.0:1.0:0.0:0.0	.	.	.	.	X	203;243;243;243	.	ENSP00000297405:G243X	G	-	1	0	CSMD3	114180351	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.771000	0.85420	2.542000	0.85734	0.591000	0.81541	GGA	.	.	none		0.383	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900	
AQP12B	653437	hgsc.bcm.edu	37	2	241621939	241621939	+	Missense_Mutation	SNP	C	C	G	rs150288484	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:241621939C>G	ENST00000407834.3	-	1	378	c.316G>C	c.(316-318)Gag>Cag	p.E106Q		NM_001102467.1	NP_001095937.1	A6NM10	AQ12B_HUMAN	aquaporin 12B	94						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)		GGCAGAGACTCCTCGGCCATG	0.692													N|||	6	0.00119808	0.003	0.0014	5008	,	,		18955	0.0		0.001	False		,,,				2504	0.0				p.E106Q		Atlas-SNP	.											AQP12B,NS,carcinoma,0,1	AQP12B	33	1	0			c.G316C						scavenged	.		GLN/GLU	23,4383		0,23,2180	42.0	44.0	43.0		316	2.9	0.1	2	dbSNP_134	43	3,8597		0,3,4297	no	missense	AQP12B	NM_001102467.1	29	0,26,6477	GG,GC,CC		0.0349,0.522,0.1999	benign	106/308	241621939	26,12980	2203	4300	6503	SO:0001583	missense	653437	exon1			GAGACTCCTCGGC	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.316G>C	2.37:g.241621939C>G	ENSP00000384894:p.Glu106Gln	Somatic	79	2	0.0253165		WXS	Illumina HiSeq	Phase_I	84	3	0.0357143	NM_001102467	A4QPB9	Missense_Mutation	SNP	ENST00000407834.3	37	CCDS46560.1	9	0.004120879120879121	5	0.01016260162601626	1	0.0027624309392265192	1	0.0017482517482517483	2	0.002638522427440633	.	4.584	0.108510	0.08780	0.00522	3.49E-4	ENSG00000185176	ENST00000407834	T	0.11063	2.81	2.87	2.87	0.33458	.	0.501171	0.21998	N	0.066053	T	0.03608	0.0103	.	.	.	0.18873	N	0.999984	B	0.28470	0.213	B	0.31101	0.124	T	0.41556	-0.9502	9	0.13470	T	0.59	3.0696	7.317	0.26505	0.262:0.738:0.0:0.0	.	106	A6NM10-2	.	Q	106	ENSP00000384894:E106Q	ENSP00000384894:E106Q	E	-	1	0	AQP12B	241270612	0.908000	0.30866	0.136000	0.22124	0.214000	0.24535	1.565000	0.36386	1.903000	0.55091	0.479000	0.44913	GAG	C|0.996;G|0.004	0.004	strong		0.692	AQP12B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000325625.1		
ESYT3	83850	hgsc.bcm.edu	37	3	138181019	138181019	+	Missense_Mutation	SNP	C	C	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:138181019C>G	ENST00000389567.4	+	8	1072	c.886C>G	c.(886-888)Ctg>Gtg	p.L296V	ESYT3_ENST00000289135.4_Missense_Mutation_p.L296V	NM_031913.3	NP_114119.2	A0FGR9	ESYT3_HUMAN	extended synaptotagmin-like protein 3	296	C2 1. {ECO:0000255|PROSITE- ProRule:PRU00041}.				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						GGGGCTGGATCTGACCAACCT	0.577																																					p.L296V		Atlas-SNP	.											.	ESYT3	64	.	0			c.C886G						PASS	.						186.0	137.0	154.0					3																	138181019		2203	4300	6503	SO:0001583	missense	83850	exon8			CTGGATCTGACCA	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.886C>G	3.37:g.138181019C>G	ENSP00000374218:p.Leu296Val	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	254	148	0.582677	NM_031913	A8K0G5|Q6ZV21|Q8NDZ5|Q9BQR9	Missense_Mutation	SNP	ENST00000389567.4	37	CCDS3101.2	.	.	.	.	.	.	.	.	.	.	C	0.363	-0.938291	0.02340	.	.	ENSG00000158220	ENST00000389567;ENST00000289135	T;T	0.35236	1.32;1.61	4.65	1.56	0.23342	.	0.297369	0.32459	N	0.006061	T	0.08846	0.0219	N	0.01624	-0.795	0.20821	N	0.999845	B	0.02656	0.0	B	0.01281	0.0	T	0.33929	-0.9849	10	0.02654	T	1	-8.7761	3.55	0.07843	0.3091:0.2142:0.4766:0.0	.	296	A0FGR9	ESYT3_HUMAN	V	296	ENSP00000374218:L296V;ENSP00000289135:L296V	ENSP00000289135:L296V	L	+	1	2	ESYT3	139663709	0.000000	0.05858	0.970000	0.41538	0.979000	0.70002	-0.565000	0.05929	0.556000	0.29098	-0.321000	0.08615	CTG	.	.	none		0.577	ESYT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000303993.1	NM_031913	
ITGB3	3690	hgsc.bcm.edu	37	17	45331302	45331302	+	Silent	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:45331302A>G	ENST00000559488.1	+	1	91	c.75A>G	c.(73-75)gtA>gtG	p.V25V	ITGB3_ENST00000560629.1_Missense_Mutation_p.R14G|ITGB3_ENST00000435993.2_5'UTR|ITGB3_ENST00000571680.1_Silent_p.V25V	NM_000212.2	NP_000203.2	P05106	ITB3_HUMAN	integrin, beta 3 (platelet glycoprotein IIIa, antigen CD61)	25					activation of protein kinase activity (GO:0032147)|angiogenesis involved in wound healing (GO:0060055)|apolipoprotein A-I-mediated signaling pathway (GO:0038027)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell growth (GO:0016049)|cell migration (GO:0016477)|cell-matrix adhesion (GO:0007160)|cell-substrate adhesion (GO:0031589)|cell-substrate junction assembly (GO:0007044)|extracellular matrix organization (GO:0030198)|heterotypic cell-cell adhesion (GO:0034113)|integrin-mediated signaling pathway (GO:0007229)|leukocyte migration (GO:0050900)|mesodermal cell differentiation (GO:0048333)|negative chemotaxis (GO:0050919)|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)|platelet activation (GO:0030168)|platelet aggregation (GO:0070527)|platelet degranulation (GO:0002576)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of vascular endothelial growth factor receptor signaling pathway (GO:0030949)|protein folding (GO:0006457)|regulation of bone resorption (GO:0045124)|smooth muscle cell migration (GO:0014909)|substrate adhesion-dependent cell spreading (GO:0034446)|tube development (GO:0035295)|viral entry into host cell (GO:0046718)|wound healing (GO:0042060)	alphav-beta3 integrin-vitronectin complex (GO:0071062)|cell surface (GO:0009986)|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 complex (GO:0008305)|lamellipodium membrane (GO:0031258)|melanosome (GO:0042470)|microvillus membrane (GO:0031528)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule membrane (GO:0031092)|receptor complex (GO:0043235)|ruffle membrane (GO:0032587)	cell adhesion molecule binding (GO:0050839)|extracellular matrix binding (GO:0050840)|fibronectin binding (GO:0001968)|identical protein binding (GO:0042802)|platelet-derived growth factor receptor binding (GO:0005161)|protease binding (GO:0002020)|protein disulfide isomerase activity (GO:0003756)|receptor activity (GO:0004872)|vascular endothelial growth factor receptor 2 binding (GO:0043184)			breast(3)|central_nervous_system(5)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(10)|lung(9)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	39					Abciximab(DB00054)|Antithymocyte globulin(DB00098)|Eptifibatide(DB00063)|Tirofiban(DB00775)	GCGTTGGCGTAGGAGGTGAGT	0.756																																					p.V25V		Atlas-SNP	.											.	ITGB3	157	.	0			c.A75G						PASS	.						3.0	4.0	4.0					17																	45331302		1794	3699	5493	SO:0001819	synonymous_variant	3690	exon1			TGGCGTAGGAGGT		CCDS11511.1	17q21.32	2014-09-17			ENSG00000259207	ENSG00000259207		"""CD molecules"", ""Integrins"""	6156	protein-coding gene	gene with protein product	"""platelet glycoprotein IIIa"""	173470		GP3A		2454952	Standard	NM_000212		Approved	CD61, GPIIIa	uc002ilj.3	P05106	OTTHUMG00000171956	ENST00000559488.1:c.75A>G	17.37:g.45331302A>G		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	7	5	0.714286	NM_000212	A0PJW2|D3DXJ8|O15495|Q12806|Q13413|Q14648|Q16499	Silent	SNP	ENST00000559488.1	37	CCDS11511.1																																																																																			.	.	none		0.756	ITGB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416111.3	NM_000212	
CPXM1	56265	hgsc.bcm.edu	37	20	2777704	2777704	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr20:2777704C>T	ENST00000380605.2	-	7	933	c.869G>A	c.(868-870)gGa>gAa	p.G290E		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	290					cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						GTCAGAGGATCCCGACGCAGG	0.532																																					p.G290E		Atlas-SNP	.											CPXM1,mouth,carcinoma,-1,1	CPXM1	107	1	0			c.G869A						scavenged	.						82.0	85.0	84.0					20																	2777704		2203	4300	6503	SO:0001583	missense	56265	exon7			GAGGATCCCGACG	AL035460	CCDS13033.1	20p13	2012-02-10	2006-08-24	2006-08-24	ENSG00000088882	ENSG00000088882			15771	protein-coding gene	gene with protein product	"""carboxypeptidase-like protein X1"""	609555	"""carboxypeptidase X (M14 family)"""	CPXM		14702039	Standard	NM_019609		Approved	CPX-1, CPX1	uc002wgu.3	Q96SM3	OTTHUMG00000031706	ENST00000380605.2:c.869G>A	20.37:g.2777704C>T	ENSP00000369979:p.Gly290Glu	Somatic	229	0	0		WXS	Illumina HiSeq	Phase_I	268	3	0.011194	NM_001184699	Q6P4G8|Q6UW65|Q9NUB5	Missense_Mutation	SNP	ENST00000380605.2	37	CCDS13033.1	.	.	.	.	.	.	.	.	.	.	C	11.45	1.643416	0.29246	.	.	ENSG00000088882	ENST00000380605	D	0.95205	-3.64	5.24	-0.307	0.12777	.	0.800421	0.11720	N	0.535977	D	0.84197	0.5419	N	0.22421	0.69	0.09310	N	0.999999	B;B	0.11235	0.004;0.002	B;B	0.06405	0.002;0.002	T	0.70107	-0.4963	10	0.02654	T	1	-0.0351	3.195	0.06630	0.1357:0.3163:0.3962:0.1518	.	290;290	Q8N2E1;Q96SM3	.;CPXM1_HUMAN	E	290	ENSP00000369979:G290E	ENSP00000369979:G290E	G	-	2	0	CPXM1	2725704	0.000000	0.05858	0.012000	0.15200	0.369000	0.29798	-0.610000	0.05629	-0.158000	0.11040	-0.175000	0.13238	GGA	.	.	none		0.532	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2	NM_019609	
ZCCHC8	55596	hgsc.bcm.edu	37	12	122975093	122975093	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:122975093C>T	ENST00000336229.4	-	4	469	c.339G>A	c.(337-339)gaG>gaA	p.E113E	SNORA9_ENST00000516383.1_RNA|ZCCHC8_ENST00000543897.1_5'UTR|ZCCHC8_ENST00000536306.1_5'UTR	NM_017612.3	NP_060082.2	Q6NZY4	ZCHC8_HUMAN	zinc finger, CCHC domain containing 8	113					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			endometrium(4)|kidney(2)|large_intestine(8)|lung(7)|skin(1)|upper_aerodigestive_tract(1)	23	all_neural(191;0.0837)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;5.25e-05)|Epithelial(86;0.000113)|BRCA - Breast invasive adenocarcinoma(302;0.202)		ATACAAATTCCTCTATTTCTT	0.333																																					p.E113E		Atlas-SNP	.											.	ZCCHC8	56	.	0			c.G339A						PASS	.						52.0	50.0	50.0					12																	122975093		1810	4068	5878	SO:0001819	synonymous_variant	55596	exon4			AAATTCCTCTATT	BC017704		12q24.31	2014-04-14				ENSG00000033030		"""Zinc fingers, CCHC domain containing"""	25265	protein-coding gene	gene with protein product						12477932	Standard	XM_005253581		Approved	DKFZp434E2220	uc001ucn.3	Q6NZY4		ENST00000336229.4:c.339G>A	12.37:g.122975093C>T		Somatic	37	0	0		WXS	Illumina HiSeq	Phase_I	78	4	0.0512821	NM_017612	Q7L2P6|Q8N2K5|Q96SK7|Q9NSS2|Q9NSS3	Silent	SNP	ENST00000336229.4	37																																																																																				.	.	none		0.333	ZCCHC8-201	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_017612	
DNAH5	1767	hgsc.bcm.edu	37	5	13721176	13721176	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:13721176C>T	ENST00000265104.4	-	71	12316	c.12212G>A	c.(12211-12213)cGt>cAt	p.R4071H		NM_001369.2	NP_001360.1	Q8TE73	DYH5_HUMAN	dynein, axonemal, heavy chain 5	4071	AAA 6. {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)	p.R4071H(1)		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)					GGACACATAACGGGTTTCTAT	0.512									Kartagener syndrome																												p.R4071H		Atlas-SNP	.											DNAH5,NS,adenocarcinoma,-1,2	DNAH5	868	2	1	Substitution - Missense(1)	large_intestine(1)	c.G12212A						scavenged	.						97.0	100.0	99.0					5																	13721176		2203	4300	6503	SO:0001583	missense	1767	exon71	Familial Cancer Database	Ciliary Dyskinesia, Primary (CILD1 - CILD13), Immotile Cilia Syndrome	ACATAACGGGTTT	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.12212G>A	5.37:g.13721176C>T	ENSP00000265104:p.Arg4071His	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	77	2	0.025974	NM_001369	Q92860|Q96L74|Q9H5S7|Q9HCG9	Missense_Mutation	SNP	ENST00000265104.4	37	CCDS3882.1	.	.	.	.	.	.	.	.	.	.	C	12.27	1.888028	0.33348	.	.	ENSG00000039139	ENST00000265104	T	0.07800	3.16	5.18	3.4	0.38934	Dynein heavy chain (1);	0.169666	0.53938	N	0.000056	T	0.06826	0.0174	L	0.35723	1.085	0.46356	D	0.999006	B	0.11235	0.004	B	0.18263	0.021	T	0.21965	-1.0230	10	0.10902	T	0.67	.	10.9226	0.47174	0.0:0.7886:0.0:0.2114	.	4071	Q8TE73	DYH5_HUMAN	H	4071	ENSP00000265104:R4071H	ENSP00000265104:R4071H	R	-	2	0	DNAH5	13774176	0.510000	0.26171	0.768000	0.31515	0.684000	0.39900	1.254000	0.32897	0.688000	0.31529	-0.259000	0.10710	CGT	.	.	none		0.512	DNAH5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207057.2	NM_001369	
TIMELESS	8914	hgsc.bcm.edu	37	12	56827699	56827699	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:56827699C>T	ENST00000553532.1	-	3	259	c.109G>A	c.(109-111)Gat>Aat	p.D37N	TIMELESS_ENST00000554616.1_Missense_Mutation_p.D37N|TIMELESS_ENST00000229201.4_Missense_Mutation_p.D37N					timeless circadian clock									p.D37Y(1)		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						CGGATCAGATCCTTCACGCTC	0.522																																					p.D37N		Atlas-SNP	.											TIMELESS,right_upper_lobe,carcinoma,0,2	TIMELESS	107	2	1	Substitution - Missense(1)	lung(1)	c.G109A						scavenged	.						107.0	106.0	107.0					12																	56827699		2203	4300	6503	SO:0001583	missense	8914	exon3			TCAGATCCTTCAC	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.109G>A	12.37:g.56827699C>T	ENSP00000450607:p.Asp37Asn	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	114	2	0.0175439	NM_003920		Missense_Mutation	SNP	ENST00000553532.1	37	CCDS8918.1	.	.	.	.	.	.	.	.	.	.	C	31	5.072642	0.93950	.	.	ENSG00000111602	ENST00000229201;ENST00000553532;ENST00000554616	T;T;T	0.53857	0.6;0.6;0.6	5.44	5.44	0.79542	Timeless protein (1);	0.000000	0.85682	D	0.000000	T	0.77350	0.4117	M	0.86740	2.835	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.997;0.998	T	0.80551	-0.1332	10	0.66056	D	0.02	-19.4834	18.4236	0.90600	0.0:1.0:0.0:0.0	.	37;37	Q9UNS1-2;Q9UNS1	.;TIM_HUMAN	N	37	ENSP00000229201:D37N;ENSP00000450607:D37N;ENSP00000450848:D37N	ENSP00000229201:D37N	D	-	1	0	TIMELESS	55113966	1.000000	0.71417	1.000000	0.80357	0.949000	0.60115	7.598000	0.82745	2.735000	0.93741	0.555000	0.69702	GAT	.	.	none		0.522	TIMELESS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000409771.1	NM_003920	
HIST1H4F	8361	hgsc.bcm.edu	37	6	26240696	26240696	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:26240696G>A	ENST00000377745.2	+	1	136	c.43G>A	c.(43-45)Ggc>Agc	p.G15S		NM_003540.3	NP_003531.1	P62805	H4_HUMAN	histone cluster 1, H4f	15					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)			cervix(1)|endometrium(1)|large_intestine(1)|lung(1)|upper_aerodigestive_tract(1)	5		all_hematologic(11;0.0945)|Acute lymphoblastic leukemia(11;0.167)				AGGAAAGGGAGGCGCCAAGCG	0.537																																					p.G15S		Atlas-SNP	.											.	HIST1H4F	9	.	0			c.G43A						PASS	.						46.0	47.0	46.0					6																	26240696		2203	4300	6503	SO:0001583	missense	8361	exon1			AAGGGAGGCGCCA	M60749	CCDS4598.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000198327			"""Histones / Replication-dependent"""	4783	protein-coding gene	gene with protein product		602824	"""H4 histone family, member C"", ""histone 1, H4f"""	H4FC		1916825, 9119399, 12408966	Standard	NM_003540		Approved	H4/c, H4	uc003nhe.1	P62805	OTTHUMG00000014443	ENST00000377745.2:c.43G>A	6.37:g.26240696G>A	ENSP00000366974:p.Gly15Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	80	37	0.4625	NM_003540	A2VCL0|P02304|P02305|Q6DRA9|Q6FGB8|Q6NWP7	Missense_Mutation	SNP	ENST00000377745.2	37	CCDS4598.1	.	.	.	.	.	.	.	.	.	.	.	15.20	2.761893	0.49468	.	.	ENSG00000198327	ENST00000377745	.	.	.	4.48	4.48	0.54585	.	0.000000	0.85682	D	0.000000	T	0.69637	0.3133	.	.	.	0.45899	D	0.998749	.	.	.	.	.	.	T	0.72861	-0.4164	6	0.59425	D	0.04	.	16.6943	0.85330	0.0:0.0:1.0:0.0	.	.	.	.	S	15	.	ENSP00000366974:G15S	G	+	1	0	HIST1H4F	26348675	1.000000	0.71417	0.813000	0.32504	0.016000	0.09150	9.222000	0.95196	2.503000	0.84419	0.655000	0.94253	GGC	.	.	none		0.537	HIST1H4F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040106.1	NM_003540	
DRD5	1816	hgsc.bcm.edu	37	4	9783971	9783971	+	Silent	SNP	C	C	T	rs113695344		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:9783971C>T	ENST00000304374.2	+	1	714	c.318C>T	c.(316-318)taC>taT	p.Y106Y		NM_000798.4	NP_000789.1	P21918	DRD5_HUMAN	dopamine receptor D5	106					activation of adenylate cyclase activity (GO:0007190)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|associative learning (GO:0008306)|cellular calcium ion homeostasis (GO:0006874)|cellular response to catecholamine stimulus (GO:0071870)|long term synaptic depression (GO:0060292)|negative regulation of blood pressure (GO:0045776)|negative regulation of NAD(P)H oxidase activity (GO:0033861)|norepinephrine-epinephrine vasoconstriction involved in regulation of systemic arterial blood pressure (GO:0001994)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of adenylate cyclase activity involved in G-protein coupled receptor signaling pathway (GO:0010579)|reactive oxygen species metabolic process (GO:0072593)|regulation of female receptivity (GO:0045924)|regulation of systemic arterial blood pressure by vasopressin (GO:0001992)|response to amphetamine (GO:0001975)|response to cocaine (GO:0042220)|sensitization (GO:0046960)|synaptic transmission (GO:0007268)|synaptic transmission, dopaminergic (GO:0001963)|transmission of nerve impulse (GO:0019226)|wound healing (GO:0042060)	brush border membrane (GO:0031526)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	dopamine binding (GO:0035240)|dopamine neurotransmitter receptor activity (GO:0004952)|dopamine neurotransmitter receptor activity, coupled via Gs (GO:0001588)			NS(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(22)|prostate(7)|skin(3)|stomach(2)|urinary_tract(1)	57					Apomorphine(DB00714)|Aripiprazole(DB01238)|Bromocriptine(DB01200)|Cabergoline(DB00248)|Chlorpromazine(DB00477)|Cinnarizine(DB00568)|Dopamine(DB00988)|Ergotamine(DB00696)|Fenoldopam(DB00800)|Imipramine(DB00458)|L-DOPA(DB01235)|Lisuride(DB00589)|Loxapine(DB00408)|Methotrimeprazine(DB01403)|Mianserin(DB06148)|Mirtazapine(DB00370)|Olanzapine(DB00334)|Pergolide(DB01186)|Pramipexole(DB00413)|Quetiapine(DB01224)|Ropinirole(DB00268)|Rotigotine(DB05271)|Trimipramine(DB00726)|Ziprasidone(DB00246)	TGGCCGGTTACTGGCCCTTTG	0.602																																					p.Y106Y		Atlas-SNP	.											DRD5,rectum,carcinoma,0,1	DRD5	119	1	0			c.C318T						scavenged	.						50.0	48.0	49.0					4																	9783971		2203	4300	6503	SO:0001819	synonymous_variant	1816	exon1			CGGTTACTGGCCC	X58454	CCDS3405.1	4p16.1	2012-08-08			ENSG00000169676	ENSG00000169676		"""GPCR / Class A : Dopamine receptors"""	3026	protein-coding gene	gene with protein product		126453		DRD1L2		1774076	Standard	NM_000798		Approved	DRD1B	uc003gmb.4	P21918	OTTHUMG00000128489	ENST00000304374.2:c.318C>T	4.37:g.9783971C>T		Somatic	115	3	0.026087		WXS	Illumina HiSeq	Phase_I	130	7	0.0538462	NM_000798	B2R9S3|Q8NEQ8	Silent	SNP	ENST00000304374.2	37	CCDS3405.1																																																																																			C|0.500;T|0.500	0.500	weak		0.602	DRD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250293.1		
SPINK5	11005	hgsc.bcm.edu	37	5	147470759	147470759	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:147470759G>A	ENST00000256084.7	+	8	676	c.634G>A	c.(634-636)Ggt>Agt	p.G212S	SPINK5_ENST00000398454.1_Missense_Mutation_p.G212S|SPINK5_ENST00000359874.3_Missense_Mutation_p.G212S|SPINK5_ENST00000476608.1_3'UTR	NM_006846.3	NP_006837.2	Q9NQ38	ISK5_HUMAN	serine peptidase inhibitor, Kazal type 5	212	Kazal-like 3. {ECO:0000255|PROSITE- ProRule:PRU00798}.				anagen (GO:0042640)|epidermal cell differentiation (GO:0009913)|epithelial cell differentiation (GO:0030855)|extracellular matrix organization (GO:0030198)|hair cell differentiation (GO:0035315)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endopeptidase activity (GO:0010951)|negative regulation of immune response (GO:0050777)|negative regulation of proteolysis (GO:0045861)|negative regulation of serine-type peptidase activity (GO:1902572)|regulation of cell adhesion (GO:0030155)|regulation of T cell differentiation (GO:0045580)	cell cortex (GO:0005938)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|epidermal lamellar body (GO:0097209)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(16)|ovary(4)|prostate(1)|skin(5)|stomach(8)|upper_aerodigestive_tract(2)	64			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CAAGCGAGAGGGTGAAACTAG	0.363																																					p.G212S		Atlas-SNP	.											.	SPINK5	245	.	0			c.G634A						PASS	.						90.0	86.0	87.0					5																	147470759		1866	4104	5970	SO:0001583	missense	11005	exon8			CGAGAGGGTGAAA	AJ228139	CCDS43382.1, CCDS47300.1, CCDS47301.1	5q31-q32	2014-09-17	2005-08-17		ENSG00000133710	ENSG00000133710		"""Serine peptidase inhibitors, Kazal type"""	15464	protein-coding gene	gene with protein product	"""lymphoepithelial Kazal-type-related inhibitor"""	605010	"""serine protease inhibitor, Kazal type 5"""			10419450	Standard	NM_001127698		Approved	VAKTI, LEKTI, LETKI, NETS, NS, FLJ21544, FLJ97536, FLJ97596, FLJ99794, DKFZp686K19184	uc003loy.2	Q9NQ38	OTTHUMG00000134305	ENST00000256084.7:c.634G>A	5.37:g.147470759G>A	ENSP00000256084:p.Gly212Ser	Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	26	10	0.384615	NM_001127699	A8MYE8|B7WPB7|D6REN5|O75770|Q3LX95|Q3LX96|Q3LX97|Q96PP2|Q96PP3	Missense_Mutation	SNP	ENST00000256084.7	37	CCDS43382.1	.	.	.	.	.	.	.	.	.	.	G	9.653	1.142058	0.21205	.	.	ENSG00000133710	ENST00000398454;ENST00000359874;ENST00000508733;ENST00000256084	T;T;T;T	0.39406	1.08;1.11;1.17;1.12	4.3	-0.561	0.11785	Proteinase inhibitor I1, Kazal (1);	1.472930	0.04149	N	0.321015	T	0.18841	0.0452	N	0.02539	-0.55	0.09310	N	1	B;B;B;B	0.22146	0.044;0.014;0.02;0.065	B;B;B;B	0.21360	0.034;0.013;0.034;0.02	T	0.16778	-1.0391	10	0.23302	T	0.38	-0.4099	7.2188	0.25975	0.5383:0.0:0.4617:0.0	.	193;212;212;212	B4DWS3;Q9NQ38-3;Q9NQ38;Q9NQ38-2	.;.;ISK5_HUMAN;.	S	212;212;193;212	ENSP00000381472:G212S;ENSP00000352936:G212S;ENSP00000421519:G193S;ENSP00000256084:G212S	ENSP00000256084:G212S	G	+	1	0	SPINK5	147450952	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	0.154000	0.16343	-0.127000	0.11661	0.650000	0.86243	GGT	.	.	none		0.363	SPINK5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000259215.2	NM_001127698	
MMP15	4324	hgsc.bcm.edu	37	16	58073912	58073912	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:58073912C>T	ENST00000219271.3	+	4	1359	c.574C>T	c.(574-576)Cag>Tag	p.Q192*		NM_002428.2	NP_002419.1	P51511	MMP15_HUMAN	matrix metallopeptidase 15 (membrane-inserted)	192					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)	GCTGCGGCGACAGAAGGAGGC	0.652																																					p.Q192X		Atlas-SNP	.											MMP15,NS,malignant_melanoma,0,1	MMP15	58	1	0			c.C574T						PASS	.						69.0	62.0	64.0					16																	58073912		2198	4300	6498	SO:0001587	stop_gained	4324	exon4			CGGCGACAGAAGG	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.574C>T	16.37:g.58073912C>T	ENSP00000219271:p.Gln192*	Somatic	84	0	0		WXS	Illumina HiSeq	Phase_I	48	6	0.125	NM_002428	A0A2U6|Q14111	Nonsense_Mutation	SNP	ENST00000219271.3	37	CCDS10792.1	.	.	.	.	.	.	.	.	.	.	C	44	11.154668	0.99523	.	.	ENSG00000102996	ENST00000219271	.	.	.	4.68	4.68	0.58851	.	0.189298	0.47455	D	0.000222	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.07175	T	0.84	.	6.2159	0.20656	0.1999:0.7043:0.0:0.0958	.	.	.	.	X	192	.	ENSP00000219271:Q192X	Q	+	1	0	MMP15	56631413	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	1.584000	0.36589	2.157000	0.67596	0.455000	0.32223	CAG	.	.	none		0.652	MMP15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257342.1	NM_002428	
S100A6	6277	hgsc.bcm.edu	37	1	153507187	153507187	+	Silent	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:153507187T>C	ENST00000368720.2	-	4	560	c.258A>G	c.(256-258)gaA>gaG	p.E86E	S100A6_ENST00000368719.4_Silent_p.E86E|BX470102.3_ENST00000420695.1_RNA|S100A6_ENST00000496817.1_Silent_p.E86E			P06703	S10A6_HUMAN	S100 calcium binding protein A6	86					axonogenesis (GO:0007409)|positive regulation of fibroblast proliferation (GO:0048146)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|nuclear envelope (GO:0005635)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)|calcium-dependent protein binding (GO:0048306)|ion transmembrane transporter activity (GO:0015075)|protein homodimerization activity (GO:0042803)|S100 protein binding (GO:0044548)|tropomyosin binding (GO:0005523)|zinc ion binding (GO:0008270)			ovary(1)	1	all_lung(78;1.66e-32)|Lung NSC(65;5.71e-31)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.171)			CCTTGAGGGCTTCATTGTAGA	0.478																																					p.E86E		Atlas-SNP	.											.	S100A6	8	.	0			c.A258G						PASS	.						69.0	69.0	69.0					1																	153507187		2203	4300	6503	SO:0001819	synonymous_variant	6277	exon3			GAGGGCTTCATTG	BC001431	CCDS1040.1	1q21	2013-01-10	2006-09-11		ENSG00000197956	ENSG00000197956		"""S100 calcium binding proteins"", ""EF-hand domain containing"""	10496	protein-coding gene	gene with protein product		114110	"""S100 calcium-binding protein A6 (calcyclin)"", ""S100 calcium binding protein A6 (calcyclin)"""	CACY			Standard	NM_014624		Approved	2A9, PRA, CABP	uc001fbw.1	P06703	OTTHUMG00000013549	ENST00000368720.2:c.258A>G	1.37:g.153507187T>C		Somatic	89	0	0		WXS	Illumina HiSeq	Phase_I	93	4	0.0430108	NM_014624	D3DV39|Q5RHS4	Silent	SNP	ENST00000368720.2	37	CCDS1040.1																																																																																			.	.	none		0.478	S100A6-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000037723.2	NM_014624	
ARFGAP1	55738	hgsc.bcm.edu	37	20	61907883	61907883	+	Silent	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr20:61907883G>A	ENST00000370283.4	+	4	362	c.222G>A	c.(220-222)aaG>aaA	p.K74K	ARFGAP1_ENST00000519273.2_De_novo_Start_OutOfFrame|ARFGAP1_ENST00000547204.1_De_novo_Start_InFrame|ARFGAP1_ENST00000519604.1_Silent_p.K21K|ARFGAP1_ENST00000370275.4_Silent_p.K74K|ARFGAP1_ENST00000353546.3_Silent_p.K74K	NM_018209.2	NP_060679.1	Q8N6T3	ARFG1_HUMAN	ADP-ribosylation factor GTPase activating protein 1	74	Arf-GAP. {ECO:0000255|PROSITE- ProRule:PRU00288}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|COPI coating of Golgi vesicle (GO:0048205)|endoplasmic reticulum unfolded protein response (GO:0030968)|membrane organization (GO:0061024)|positive regulation of GTPase activity (GO:0043547)|protein transport (GO:0015031)|regulation of ARF GTPase activity (GO:0032312)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)	cytosol (GO:0005829)|Golgi-associated vesicle membrane (GO:0030660)|synapse (GO:0045202)	ARF GTPase activator activity (GO:0008060)|GTPase activator activity (GO:0005096)|zinc ion binding (GO:0008270)			endometrium(2)|kidney(2)|large_intestine(1)|lung(6)|ovary(1)|pancreas(1)	13	all_cancers(38;1.59e-09)					AGCTTGAGAAGATGAAAGCTG	0.527																																					p.K74K		Atlas-SNP	.											.	ARFGAP1	38	.	0			c.G222A						PASS	.						135.0	111.0	119.0					20																	61907883		2203	4300	6503	SO:0001819	synonymous_variant	55738	exon4			TGAGAAGATGAAA	AK001629	CCDS13515.1, CCDS13516.1, CCDS63326.1, CCDS63327.1, CCDS63328.1	20q13.33	2009-11-30	2002-08-20	2002-08-23	ENSG00000101199	ENSG00000101199		"""ADP-ribosylation factor GTPase activating proteins"""	15852	protein-coding gene	gene with protein product		608377	"""ADP-ribosylation factor 1 GTPase activating protein"""	ARF1GAP		11210549	Standard	NM_018209		Approved	FLJ10767, bA261N11.3	uc002yel.3	Q8N6T3	OTTHUMG00000032965	ENST00000370283.4:c.222G>A	20.37:g.61907883G>A		Somatic	207	0	0		WXS	Illumina HiSeq	Phase_I	256	105	0.410156	NM_018209	B7Z3U0|B7Z8H8|B7ZBI3|E1P5I9|E7EV62|Q6PK71|Q96KC4|Q96T02|Q9NSU3|Q9NVF6|Q9UIL0	Silent	SNP	ENST00000370283.4	37	CCDS13515.1																																																																																			.	.	none		0.527	ARFGAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080134.3	NM_018209	
IL37	27178	hgsc.bcm.edu	37	2	113674819	113674819	+	Missense_Mutation	SNP	C	C	T	rs370690543		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:113674819C>T	ENST00000263326.3	+	3	301	c.259C>T	c.(259-261)Cgc>Tgc	p.R87C	IL37_ENST00000352179.3_Missense_Mutation_p.R66C|IL37_ENST00000311328.2_Missense_Mutation_p.R61C|IL37_ENST00000353225.3_Intron|IL37_ENST00000349806.3_Intron	NM_014439.3	NP_055254.2	Q9NZH6	IL37_HUMAN	interleukin 37	87					immune response (GO:0006955)|inflammatory response (GO:0006954)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|nucleus (GO:0005634)	interleukin-1 receptor binding (GO:0005149)			NS(1)|breast(2)|cervix(1)|endometrium(2)|large_intestine(1)|lung(7)|ovary(2)|skin(3)	19						AAACTACATACGCCCAGGTGA	0.493																																					p.R87C		Atlas-SNP	.											.	IL37	56	.	0			c.C259T						PASS	.		CYS/ARG,CYS/ARG,,,CYS/ARG	0,4406		0,0,2203	139.0	134.0	136.0		259,196,,,181	-0.0	0.0	2		136	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,intron,intron,missense	IL37	NM_014439.3,NM_173202.1,NM_173203.1,NM_173204.1,NM_173205.1	180,180,,,180	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,,,possibly-damaging	87/219,66/198,,,61/193	113674819	1,13005	2203	4300	6503	SO:0001583	missense	27178	exon3			TACATACGCCCAG	AF201832	CCDS2103.1, CCDS2104.1, CCDS2105.1, CCDS2106.1, CCDS2107.1	2q12-q14.1	2011-06-06	2011-06-06	2011-06-06	ENSG00000125571	ENSG00000125571		"""Interleukins and interleukin receptors"""	15563	protein-coding gene	gene with protein product	"""interleukin 1, zeta"", ""interleukin-1 homolog 4"", ""interleukin-1-related protein"""	605510	"""interleukin 1 family, member 7 (zeta)"""	IL1F7		10625660, 10512743, 12496389	Standard	NM_014439		Approved	FIL1, FIL1Z, FIL1(ZETA), IL-1H4, IL-1RP1, IL-1F7	uc002tij.3	Q9NZH6	OTTHUMG00000131345	ENST00000263326.3:c.259C>T	2.37:g.113674819C>T	ENSP00000263326:p.Arg87Cys	Somatic	121	0	0		WXS	Illumina HiSeq	Phase_I	127	42	0.330709	NM_014439	B5BU97|Q56AP9|Q8TD04|Q8TD05|Q9HBF2|Q9HBF3|Q9UHA6	Missense_Mutation	SNP	ENST00000263326.3	37	CCDS2103.1	.	.	.	.	.	.	.	.	.	.	c	5.381	0.255487	0.10185	0.0	1.16E-4	ENSG00000125571	ENST00000263326;ENST00000352179;ENST00000311328	T;T;T	0.58358	0.34;0.34;0.34	2.85	-0.033	0.13902	.	3.274280	0.01053	N	0.004506	T	0.32675	0.0837	N	0.11064	0.09	0.09310	N	1	B;B;B	0.13145	0.007;0.003;0.007	B;B;B	0.06405	0.002;0.001;0.001	T	0.24048	-1.0171	10	0.56958	D	0.05	0.8511	2.8893	0.05671	0.2145:0.5315:0.0:0.254	.	61;66;87	Q9NZH6-2;Q9NZH6-4;Q9NZH6	.;.;IL37_HUMAN	C	87;66;61	ENSP00000263326:R87C;ENSP00000263327:R66C;ENSP00000309883:R61C	ENSP00000263326:R87C	R	+	1	0	IL37	113391290	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-4.073000	0.00300	-0.016000	0.14127	-0.763000	0.03452	CGC	.	.	weak		0.493	IL37-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254126.1	NM_014439	
TAOK1	57551	hgsc.bcm.edu	37	17	27829683	27829683	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:27829683G>A	ENST00000261716.3	+	13	1799	c.1280G>A	c.(1279-1281)cGt>cAt	p.R427H	TAOK1_ENST00000536202.1_Missense_Mutation_p.R427H	NM_020791.2	NP_065842.1	Q7L7X3	TAOK1_HUMAN	TAO kinase 1	427					cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|execution phase of apoptosis (GO:0097194)|G2 DNA damage checkpoint (GO:0031572)|mitotic cell cycle (GO:0000278)|positive regulation of JNK cascade (GO:0046330)|positive regulation of stress-activated MAPK cascade (GO:0032874)|protein phosphorylation (GO:0006468)|regulation of cytoskeleton organization (GO:0051493)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|kinase activity (GO:0016301)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|transferase activity (GO:0016740)			NS(1)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|large_intestine(4)|lung(14)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	28			Colorectal(6;0.198)			CAAGTATCTCGTCACAAATCA	0.373																																					p.R427H		Atlas-SNP	.											.	TAOK1	151	.	0			c.G1280A						PASS	.						173.0	141.0	152.0					17																	27829683		2203	4300	6503	SO:0001583	missense	57551	exon13			TATCTCGTCACAA	AB037782	CCDS32601.1, CCDS56024.1	17q11.2	2014-01-28				ENSG00000160551			29259	protein-coding gene	gene with protein product		610266				10718198, 14517247	Standard	NM_020791		Approved	KIAA1361, MARKK, PSK2, MAP3K16, FLJ14314, TAO1	uc002hdz.2	Q7L7X3		ENST00000261716.3:c.1280G>A	17.37:g.27829683G>A	ENSP00000261716:p.Arg427His	Somatic	111	0	0		WXS	Illumina HiSeq	Phase_I	146	65	0.445205	NM_025142	A2RUT8|B7ZLV6|Q96L75|Q9H2K7|Q9H7S5|Q9P2I6	Missense_Mutation	SNP	ENST00000261716.3	37	CCDS32601.1	.	.	.	.	.	.	.	.	.	.	G	35	5.539205	0.96474	.	.	ENSG00000160551	ENST00000261716;ENST00000536202	T;T	0.43294	0.95;0.95	6.03	6.03	0.97812	Protein kinase-like domain (1);	0.050877	0.85682	D	0.000000	T	0.46889	0.1416	L	0.34521	1.04	0.80722	D	1	D;P;B	0.67145	0.996;0.853;0.004	P;P;B	0.50708	0.648;0.616;0.006	T	0.30851	-0.9964	10	0.48119	T	0.1	.	20.5666	0.99351	0.0:0.0:1.0:0.0	.	427;253;427	B7ZLV6;Q7L7X3-2;Q7L7X3	.;.;TAOK1_HUMAN	H	427	ENSP00000261716:R427H;ENSP00000438819:R427H	ENSP00000261716:R427H	R	+	2	0	TAOK1	24853809	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.701000	0.74624	2.854000	0.98071	0.655000	0.94253	CGT	.	.	none		0.373	TAOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447790.1	NM_020791	
IFITM3	10410	hgsc.bcm.edu	37	11	320606	320606	+	Missense_Mutation	SNP	G	G	T	rs199749095	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:320606G>T	ENST00000399808.4	-	1	444	c.208C>A	c.(208-210)Ccc>Acc	p.P70T	IFITM3_ENST00000526811.1_Missense_Mutation_p.P49T|RP11-326C3.11_ENST00000602429.1_RNA|RP11-326C3.11_ENST00000602756.1_RNA|IFITM3_ENST00000602735.1_Missense_Mutation_p.P49T|RP11-326C3.11_ENST00000508004.2_RNA|RP11-326C3.10_ENST00000534271.1_RNA|RP11-326C3.14_ENST00000602809.1_lincRNA	NM_021034.2	NP_066362.2	Q01628	IFM3_HUMAN	interferon induced transmembrane protein 3	70	Interaction with SPP1.				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)		p.P70T(3)		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)		AGGCAGCAGGGGTTCATGAAG	0.632																																					p.P70T		Atlas-SNP	.											IFITM3,caecum,carcinoma,0,13	IFITM3	132	13	3	Substitution - Missense(3)	endometrium(2)|central_nervous_system(1)	c.C208A						scavenged	.						89.0	95.0	93.0					11																	320606		2101	4210	6311	SO:0001583	missense	10410	exon1			AGCAGGGGTTCAT	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.208C>A	11.37:g.320606G>T	ENSP00000382707:p.Pro70Thr	Somatic	129	2	0.0155039		WXS	Illumina HiSeq	Phase_I	122	9	0.0737705	NM_021034	Q53Y76|Q96HK8|Q96J15	Missense_Mutation	SNP	ENST00000399808.4	37	CCDS41585.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|G	0.076|0.076	-1.193620|-1.193620	0.01594|0.01594	.|.	.|.	ENSG00000142089|ENSG00000142089	ENST00000270031|ENST00000399808;ENST00000526811	.|T;T	.|0.78595	.|-0.94;-1.19	4.65|4.65	-9.3|-9.3	0.00649|0.00649	.|.	.|.	.|.	.|.	.|.	.|T	.|0.54447	.|0.1859	L|L	0.29908|0.29908	0.895|0.895	0.09310|0.09310	N|N	0.999999|0.999999	.|B	.|0.02656	.|0.0	.|B	.|0.04013	.|0.001	.|T	.|0.32375	.|-0.9909	.|9	.|0.22109	.|T	.|0.4	.|.	2.5632|2.5632	0.04777|0.04777	0.1587:0.0951:0.2785:0.4676|0.1587:0.0951:0.2785:0.4676	.|.	.|70	.|Q01628	.|IFM3_HUMAN	.|T	-1|70;49	.|ENSP00000382707:P70T;ENSP00000432108:P49T	.|ENSP00000382707:P70T	.|P	-|-	.|1	.|0	IFITM3|IFITM3	310606|310606	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.022000|0.022000	0.10575|0.10575	-1.460000|-1.460000	0.02368|0.02368	-3.272000|-3.272000	0.00199|0.00199	-2.532000|-2.532000	0.00182|0.00182	.|CCC	G|0.936;T|0.064	0.064	strong		0.632	IFITM3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000384765.1	NM_021034	
MPP7	143098	hgsc.bcm.edu	37	10	28527517	28527517	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:28527517G>A	ENST00000375732.1	-	2	276	c.17C>T	c.(16-18)aCg>aTg	p.T6M	MPP7_ENST00000481244.1_5'UTR|MPP7_ENST00000445954.2_De_novo_Start_OutOfFrame|MPP7_ENST00000540098.1_Missense_Mutation_p.T6M|MPP7_ENST00000337532.5_Missense_Mutation_p.T6M|MPP7_ENST00000375719.3_Missense_Mutation_p.T6M			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	6					establishment of cell polarity (GO:0030010)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of signal transduction (GO:0009967)|protein localization to adherens junction (GO:0071896)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cell junction (GO:0030054)|mitochondrion (GO:0005739)|MPP7-DLG1-LIN7 complex (GO:0097025)|tight junction (GO:0005923)	protein complex scaffold (GO:0032947)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|signaling adaptor activity (GO:0035591)			autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	22						CCCAGATCCCGTTGACAAAGC	0.512																																					p.T6M		Atlas-SNP	.											MPP7,rectum,carcinoma,+1,2	MPP7	60	2	0			c.C17T						PASS	.						147.0	117.0	128.0					10																	28527517		2203	4300	6503	SO:0001583	missense	143098	exon4			GATCCCGTTGACA	BC038105	CCDS7158.1	10p12.1	2004-01-15			ENSG00000150054	ENSG00000150054			26542	protein-coding gene	gene with protein product		610973				14719143	Standard	NM_173496		Approved	FLJ32798	uc001iua.1	Q5T2T1	OTTHUMG00000017868	ENST00000375732.1:c.17C>T	10.37:g.28527517G>A	ENSP00000364884:p.Thr6Met	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	53	24	0.45283	NM_173496	B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Missense_Mutation	SNP	ENST00000375732.1	37	CCDS7158.1	.	.	.	.	.	.	.	.	.	.	G	14.76	2.632038	0.46944	.	.	ENSG00000150054	ENST00000375732;ENST00000337532;ENST00000540098;ENST00000375719;ENST00000441595	T;T;T;T;T	0.33216	2.7;2.7;2.7;2.7;1.42	6.07	5.16	0.70880	.	0.115089	0.64402	N	0.000016	T	0.32496	0.0831	L	0.36672	1.1	0.80722	D	1	P	0.39535	0.677	P	0.44732	0.459	T	0.08889	-1.0700	10	0.56958	D	0.05	.	13.615	0.62103	0.0713:0.0:0.9287:0.0	.	6	Q5T2T1	MPP7_HUMAN	M	6	ENSP00000364884:T6M;ENSP00000337907:T6M;ENSP00000438693:T6M;ENSP00000364871:T6M;ENSP00000398319:T6M	ENSP00000337907:T6M	T	-	2	0	MPP7	28567523	0.998000	0.40836	0.049000	0.19019	0.259000	0.26198	6.263000	0.72521	1.571000	0.49722	0.655000	0.94253	ACG	.	.	none		0.512	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496	
CC2D2A	57545	hgsc.bcm.edu	37	4	15601207	15601207	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:15601207C>T	ENST00000503292.1	+	37	4732	c.4552C>T	c.(4552-4554)Cgg>Tgg	p.R1518W	CC2D2A_ENST00000413206.1_Missense_Mutation_p.R1518W|CC2D2A_ENST00000389652.5_Missense_Mutation_p.R1410W|CC2D2A_ENST00000424120.1_Missense_Mutation_p.R1518W	NM_001080522.2	NP_001073991.2	Q9P2K1	C2D2A_HUMAN	coiled-coil and C2 domain containing 2A	1518					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|smoothened signaling pathway (GO:0007224)	ciliary transition zone (GO:0035869)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|TCTN-B9D complex (GO:0036038)				NS(1)|breast(2)|central_nervous_system(1)|endometrium(6)|kidney(1)|large_intestine(8)|lung(5)|ovary(1)|pancreas(2)|prostate(2)|skin(1)|urinary_tract(2)	32						CCATCTGACTCGGTGGAATAG	0.403																																					p.R1518W		Atlas-SNP	.											CC2D2A_ENST00000424120,NS,carcinoma,0,2	CC2D2A	158	2	0			c.C4552T						scavenged	.						68.0	63.0	65.0					4																	15601207		1921	4143	6064	SO:0001583	missense	57545	exon37			CTGACTCGGTGGA	AB037766, EU450799	CCDS47026.1, CCDS47027.1, CCDS47027.2, CCDS54744.1	4p15.33	2014-09-17	2007-10-19		ENSG00000048342	ENSG00000048342			29253	protein-coding gene	gene with protein product	"""Meckel syndrome, type 6"""	612013				10718198, 18513680	Standard	NM_001080522		Approved	KIAA1345, MKS6, JBTS9	uc010idv.2	Q9P2K1	OTTHUMG00000160255	ENST00000503292.1:c.4552C>T	4.37:g.15601207C>T	ENSP00000421809:p.Arg1518Trp	Somatic	148	2	0.0135135		WXS	Illumina HiSeq	Phase_I	182	2	0.010989	NM_001080522	A6ND97|B3FW08|D6RB72|E7EP21|E9PEV5|Q3SYP3|Q9H8A7	Missense_Mutation	SNP	ENST00000503292.1	37	CCDS47026.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.038616	0.75617	.	.	ENSG00000048342	ENST00000424120;ENST00000413206;ENST00000426932;ENST00000510333;ENST00000503292;ENST00000389652	T;T;T;T	0.72167	-0.63;-0.63;-0.63;-0.63	5.75	3.02	0.34903	.	0.058391	0.64402	D	0.000001	D	0.83096	0.5180	M	0.79475	2.455	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.80764	0.994;0.985	D	0.84022	0.0354	10	0.72032	D	0.01	.	14.3935	0.66996	0.3844:0.6156:0.0:0.0	.	1518;1410	Q9P2K1;Q9P2K1-2	C2D2A_HUMAN;.	W	1518;1518;1410;1410;1518;1410	ENSP00000403465:R1518W;ENSP00000398391:R1518W;ENSP00000421809:R1518W;ENSP00000374303:R1410W	ENSP00000374303:R1410W	R	+	1	2	CC2D2A	15210305	0.998000	0.40836	0.585000	0.28666	0.982000	0.71751	3.821000	0.55700	0.312000	0.23038	0.650000	0.86243	CGG	.	.	none		0.403	CC2D2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359906.2	NM_001080522	
T	6862	hgsc.bcm.edu	37	6	166578142	166578142	+	Silent	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:166578142T>C	ENST00000296946.2	-	6	1149	c.681A>G	c.(679-681)aaA>aaG	p.K227K	T_ENST00000366871.3_Silent_p.K227K	NM_003181.3	NP_003172.1	O15178	BRAC_HUMAN	T, brachyury homolog (mouse)	227					anterior/posterior axis specification, embryo (GO:0008595)|BMP signaling pathway (GO:0030509)|bone morphogenesis (GO:0060349)|canonical Wnt signaling pathway (GO:0060070)|determination of heart left/right asymmetry (GO:0061371)|embryonic skeletal system development (GO:0048706)|heart morphogenesis (GO:0003007)|mesoderm development (GO:0007498)|mesoderm migration involved in gastrulation (GO:0007509)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neural plate morphogenesis (GO:0001839)|neural tube closure (GO:0001843)|notochord formation (GO:0014028)|penetration of zona pellucida (GO:0007341)|positive regulation of cell proliferation (GO:0008284)|positive regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003257)|post-anal tail morphogenesis (GO:0036342)|primitive streak formation (GO:0090009)|signal transduction (GO:0007165)|signal transduction involved in regulation of gene expression (GO:0023019)|SMAD protein signal transduction (GO:0060395)|somitogenesis (GO:0001756)|transcription from RNA polymerase II promoter (GO:0006366)|vasculogenesis (GO:0001570)	cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleus (GO:0005634)	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 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 (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)			autonomic_ganglia(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(23)|ovary(1)|pancreas(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	39		Prostate(117;4.48e-07)|Ovarian(120;1.78e-06)|Breast(66;2.54e-06)|Lung SC(201;0.0225)|Esophageal squamous(34;0.0559)		OV - Ovarian serous cystadenocarcinoma(33;1.09e-113)|GBM - Glioblastoma multiforme(31;1.51e-108)|BRCA - Breast invasive adenocarcinoma(81;8.45e-09)|LUAD - Lung adenocarcinoma(999;0.0407)		CCATCATCTCTTTGTGATCAC	0.388									Chordoma, Familial Clustering of																												p.K227K		Atlas-SNP	.											.	T	77	.	0			c.A681G						PASS	.						95.0	97.0	96.0					6																	166578142		2203	4300	6503	SO:0001819	synonymous_variant	6862	exon6	Familial Cancer Database		CATCTCTTTGTGA	AJ001699	CCDS5290.1, CCDS59045.1	6q27	2011-06-13	2001-11-28		ENSG00000164458	ENSG00000164458		"""T-boxes"""	11515	protein-coding gene	gene with protein product		601397	"""T brachyury (mouse) homolog"""			8963900	Standard	NM_003181		Approved		uc003quu.2	O15178	OTTHUMG00000015991	ENST00000296946.2:c.681A>G	6.37:g.166578142T>C		Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	87	4	0.045977	NM_003181	E7ERD6|Q4KMP4	Silent	SNP	ENST00000296946.2	37	CCDS5290.1																																																																																			.	.	none		0.388	T-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043037.2	NM_003181	
KCNN3	3782	hgsc.bcm.edu	37	1	154842243	154842243	+	Silent	SNP	A	A	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:154842243A>C	ENST00000271915.4	-	1	513	c.198T>G	c.(196-198)ctT>ctG	p.L66L	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	66	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	gctgctgctgaagctgcggag	0.701																																					p.L66L		Atlas-SNP	.											KCNN3,NS,carcinoma,0,3	KCNN3	141	3	0			c.T198G						scavenged	.						6.0	4.0	5.0					1																	154842243		1926	3811	5737	SO:0001819	synonymous_variant	3782	exon1			CTGCTGAAGCTGC	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.198T>G	1.37:g.154842243A>C		Somatic	21	2	0.0952381		WXS	Illumina HiSeq	Phase_I	49	30	0.612245	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Silent	SNP	ENST00000271915.4	37	CCDS30880.1																																																																																			.	.	none		0.701	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249	
C1orf112	55732	hgsc.bcm.edu	37	1	169775212	169775212	+	Silent	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:169775212T>C	ENST00000286031.6	+	7	1246	c.546T>C	c.(544-546)acT>acC	p.T182T	C1orf112_ENST00000498289.1_3'UTR|C1orf112_ENST00000413811.2_Silent_p.T153T|C1orf112_ENST00000456684.1_Silent_p.T240T|C1orf112_ENST00000359326.4_Silent_p.T182T	NM_018186.2	NP_060656.2	Q9NSG2	CA112_HUMAN	chromosome 1 open reading frame 112	182										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)					ATGCCAATACTTGGAAGTTTA	0.279																																					p.T182T		Atlas-SNP	.											C1orf112,NS,carcinoma,+1,1	C1orf112	74	1	0			c.T546C						scavenged	.						89.0	83.0	85.0					1																	169775212		2203	4294	6497	SO:0001819	synonymous_variant	55732	exon7			CAATACTTGGAAG	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.546T>C	1.37:g.169775212T>C		Somatic	96	0	0		WXS	Illumina HiSeq	Phase_I	136	4	0.0294118	NM_018186	A6NFP1|B3KU42|Q3KNQ1|Q9H8L5|Q9NVJ0	Silent	SNP	ENST00000286031.6	37	CCDS1285.1																																																																																			.	.	none		0.279	C1orf112-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000087126.3	NM_018186	
HPS3	84343	hgsc.bcm.edu	37	3	148880088	148880088	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:148880088A>G	ENST00000296051.2	+	12	2400	c.2260A>G	c.(2260-2262)Att>Gtt	p.I754V	HPS3_ENST00000460120.1_Missense_Mutation_p.I589V	NM_032383.3	NP_115759.2	Q969F9	HPS3_HUMAN	Hermansky-Pudlak syndrome 3	754					organelle organization (GO:0006996)|pigmentation (GO:0043473)	BLOC-2 complex (GO:0031084)				breast(2)|endometrium(2)|kidney(1)|large_intestine(7)|lung(12)|ovary(5)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	34			LUSC - Lung squamous cell carcinoma(72;0.0473)|Lung(72;0.0607)			GAACAACAAAATTGGAATTGA	0.423									Hermansky-Pudlak syndrome																												p.I754V		Atlas-SNP	.											HPS3,NS,neuroblastoma,-2,1	HPS3	104	1	0			c.A2260G						scavenged	.						97.0	95.0	96.0					3																	148880088		2203	4300	6503	SO:0001583	missense	84343	exon12	Familial Cancer Database	HPS, HPS1-8	AACAAAATTGGAA	AY033141	CCDS3140.1	3q24	2014-06-18			ENSG00000163755	ENSG00000163755			15597	protein-coding gene	gene with protein product		606118				11455388	Standard	NM_032383		Approved	SUTAL	uc003ewu.1	Q969F9	OTTHUMG00000159548	ENST00000296051.2:c.2260A>G	3.37:g.148880088A>G	ENSP00000296051:p.Ile754Val	Somatic	87	1	0.0114943		WXS	Illumina HiSeq	Phase_I	166	3	0.0180723	NM_032383	A8K6G6|Q8WTV6|Q96AP1|Q96MR3|Q9H608	Missense_Mutation	SNP	ENST00000296051.2	37	CCDS3140.1	.	.	.	.	.	.	.	.	.	.	A	13.81	2.347200	0.41599	.	.	ENSG00000163755	ENST00000296051;ENST00000460120	T;T	0.67523	-0.27;-0.25	5.98	4.8	0.61643	.	0.106325	0.64402	D	0.000005	T	0.62624	0.2443	L	0.59436	1.845	0.43014	D	0.994554	B;B	0.31931	0.347;0.228	B;B	0.31337	0.128;0.078	T	0.60984	-0.7154	10	0.41790	T	0.15	-13.1167	13.2856	0.60241	0.8678:0.1322:0.0:0.0	.	589;754	G5E9V4;Q969F9	.;HPS3_HUMAN	V	754;589	ENSP00000296051:I754V;ENSP00000418230:I589V	ENSP00000296051:I754V	I	+	1	0	HPS3	150362778	1.000000	0.71417	0.997000	0.53966	0.842000	0.47809	2.379000	0.44318	1.042000	0.40150	0.460000	0.39030	ATT	.	.	none		0.423	HPS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356151.1	NM_032383	
TREML2	79865	hgsc.bcm.edu	37	6	41166123	41166123	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:41166123C>T	ENST00000483722.1	-	2	285	c.100G>A	c.(100-102)Ggg>Agg	p.G34R		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	34	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					AGAGTCTCCCCTTCAAGGAGC	0.493																																					p.G34R		Atlas-SNP	.											.	TREML2	41	.	0			c.G100A						PASS	.						127.0	130.0	129.0					6																	41166123		2203	4300	6503	SO:0001583	missense	79865	exon2			TCTCCCCTTCAAG	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.100G>A	6.37:g.41166123C>T	ENSP00000418767:p.Gly34Arg	Somatic	70	0	0		WXS	Illumina HiSeq	Phase_I	100	6	0.06	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	37	CCDS4853.2	.	.	.	.	.	.	.	.	.	.	.	14.59	2.581804	0.46006	.	.	ENSG00000112195	ENST00000483722	D	0.81499	-1.5	4.75	4.75	0.60458	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.000000	0.53938	D	0.000044	D	0.86623	0.5977	M	0.75085	2.285	0.40423	D	0.979861	D	0.89917	1.0	D	0.97110	1.0	D	0.88269	0.2928	10	0.72032	D	0.01	-23.1011	13.6225	0.62144	0.0:1.0:0.0:0.0	.	34	Q5T2D2	TRML2_HUMAN	R	34	ENSP00000418767:G34R	ENSP00000418767:G34R	G	-	1	0	TREML2	41274101	1.000000	0.71417	0.998000	0.56505	0.028000	0.11728	3.388000	0.52509	2.344000	0.79699	0.563000	0.77884	GGG	.	.	none		0.493	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807	
MUC4	4585	hgsc.bcm.edu	37	3	195505829	195505829	+	Missense_Mutation	SNP	G	G	A	rs560359693	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:195505829G>A	ENST00000463781.3	-	2	13081	c.12622C>T	c.(12622-12624)Cct>Tct	p.P4208S	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.P4208S	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)		ACAGGAAGAGGGGTGGCGTGA	0.597													.|||	13	0.00259585	0.0076	0.0	5008	,	,		14156	0.001		0.002	False		,,,				2504	0.0				p.P4208S		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,3	MUC4	1505	3	0			c.C12622T						scavenged	.						17.0	15.0	16.0					3																	195505829		688	1570	2258	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.12622C>T	3.37:g.195505829G>A	ENSP00000417498:p.Pro4208Ser	Somatic	136	14	0.102941		WXS	Illumina HiSeq	Phase_I	136	21	0.154412	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	11.50	1.657422	0.29425	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34667	1.52;1.35	.	.	.	.	.	.	.	.	T	0.17238	0.0414	N	0.19112	0.55	0.23180	N	0.998166	B	0.18741	0.03	B	0.18263	0.021	T	0.20405	-1.0276	7	.	.	.	.	4.6947	0.12797	1.0E-4:0.0:0.6432:0.3568	.	4080	E7ESK3	.	S	4208	ENSP00000417498:P4208S;ENSP00000420243:P4208S	.	P	-	1	0	MUC4	196990608	.	.	0.016000	0.15963	0.027000	0.11550	.	.	-1.915000	0.01077	-1.919000	0.00516	CCT	.	.	none		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TRIP11	9321	hgsc.bcm.edu	37	14	92472695	92472695	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr14:92472695C>T	ENST00000267622.4	-	11	1998	c.1625G>A	c.(1624-1626)aGa>aAa	p.R542K		NM_004239.3	NP_004230.2	Q15643	TRIPB_HUMAN	thyroid hormone receptor interactor 11	542					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)		TTGATGAACTCTCTTTTTTTC	0.308			T	PDGFRB	AML																																p.R542K	Ovarian(84;609 1888 9852 42686)	Atlas-SNP	.		Dom	yes		14	14q31-q32	9321	thyroid hormone receptor interactor 11		L	TRIP11,NS,carcinoma,0,1	TRIP11	184	1	0			c.G1625A						scavenged	.						76.0	72.0	74.0					14																	92472695		2202	4292	6494	SO:0001583	missense	9321	exon11			TGAACTCTCTTTT	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.1625G>A	14.37:g.92472695C>T	ENSP00000267622:p.Arg542Lys	Somatic	192	0	0		WXS	Illumina HiSeq	Phase_I	231	3	0.012987	NM_004239	B2RUT2|O14689|O15154|O95949	Missense_Mutation	SNP	ENST00000267622.4	37	CCDS9899.1	.	.	.	.	.	.	.	.	.	.	C	8.710	0.911804	0.17907	.	.	ENSG00000100815	ENST00000267622;ENST00000542257	T	0.03951	3.75	6.16	4.34	0.51931	.	0.207171	0.49916	N	0.000125	T	0.03178	0.0093	N	0.25485	0.75	0.26130	N	0.980432	B;B	0.15141	0.004;0.012	B;B	0.17979	0.009;0.02	T	0.44513	-0.9323	10	0.06757	T	0.87	.	7.7245	0.28753	0.0:0.6731:0.0:0.3269	.	278;542	F5H1Z0;Q15643	.;TRIPB_HUMAN	K	542;278	ENSP00000267622:R542K	ENSP00000267622:R542K	R	-	2	0	TRIP11	91542448	1.000000	0.71417	0.830000	0.32933	0.266000	0.26442	1.975000	0.40569	1.626000	0.50381	0.650000	0.86243	AGA	.	.	none		0.308	TRIP11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411823.1		
DST	667	hgsc.bcm.edu	37	6	56335907	56335907	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:56335907A>G	ENST00000361203.3	-	90	21365	c.21358T>C	c.(21358-21360)Tca>Cca	p.S7120P	DST_ENST00000370788.2_Missense_Mutation_p.S5034P|DST_ENST00000370769.4_Missense_Mutation_p.S7231P|DST_ENST00000312431.6_3'UTR|DST_ENST00000244364.6_Missense_Mutation_p.S4817P|DST_ENST00000370754.5_Missense_Mutation_p.S7409P|DST_ENST00000446842.2_Missense_Mutation_p.S6905P|DST_ENST00000421834.2_Missense_Mutation_p.S5116P			Q03001	DYST_HUMAN	dystonin	7229					axonogenesis (GO:0007409)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cell motility (GO:0048870)|cytoplasmic microtubule organization (GO:0031122)|cytoskeleton organization (GO:0007010)|extracellular matrix organization (GO:0030198)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|intermediate filament cytoskeleton organization (GO:0045104)|maintenance of cell polarity (GO:0030011)|microtubule cytoskeleton organization (GO:0000226)|regulation of microtubule polymerization or depolymerization (GO:0031110)|response to wounding (GO:0009611)|retrograde axon cargo transport (GO:0008090)	actin cytoskeleton (GO:0015629)|axon (GO:0030424)|basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic membrane-bounded vesicle (GO:0016023)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|hemidesmosome (GO:0030056)|integral component of membrane (GO:0016021)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|microtubule cytoskeleton (GO:0015630)|microtubule plus-end (GO:0035371)|neurofilament cytoskeleton (GO:0060053)|nucleus (GO:0005634)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|integrin binding (GO:0005178)|microtubule plus-end binding (GO:0051010)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)			NS(1)|breast(5)|central_nervous_system(8)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(22)|lung(43)|ovary(7)|prostate(1)|skin(4)|upper_aerodigestive_tract(3)	105	Lung NSC(77;0.103)		LUSC - Lung squamous cell carcinoma(124;0.0485)|Lung(124;0.0956)			AACTTACTTGAGGAAAGAATT	0.358																																					p.S4817P		Atlas-SNP	.											DST_ENST00000370769,NS,carcinoma,+1,2	DST	1427	2	0			c.T14449C						scavenged	.						60.0	57.0	58.0					6																	56335907		1829	4102	5931	SO:0001583	missense	667	exon76			TACTTGAGGAAAG	M22942, M69225	CCDS4959.1, CCDS47443.1, CCDS75474.1	6p12.1	2013-01-10	2004-06-25	2004-07-01	ENSG00000151914	ENSG00000151914		"""EF-hand domain containing"""	1090	protein-coding gene	gene with protein product		113810	"""bullous pemphigoid antigen 1, 230/240kDa"""	BPAG1		2461961, 2276744	Standard	NM_001144770		Approved	BP240, KIAA0728, FLJ21489, FLJ13425, FLJ32235, FLJ30627, CATX-15, BPA, MACF2	uc021zba.2	Q03001	OTTHUMG00000014913	ENST00000361203.3:c.21358T>C	6.37:g.56335907A>G	ENSP00000354508:p.Ser7120Pro	Somatic	73	1	0.0136986		WXS	Illumina HiSeq	Phase_I	110	3	0.0272727	NM_015548	B7Z3H1|O94833|Q12825|Q13266|Q13267|Q13775|Q5TBT0|Q5TBT2|Q5TF23|Q5TF24|Q8N1T8|Q8N8J3|Q8WXK8|Q8WXK9|Q96AK9|Q96DQ5|Q96J76|Q96QT5|Q9H555|Q9UGD7|Q9UGD8|Q9UN10	Missense_Mutation	SNP	ENST00000361203.3	37		.	.	.	.	.	.	.	.	.	.	A	21.2	4.115009	0.77210	.	.	ENSG00000151914	ENST00000244364;ENST00000370754;ENST00000370769;ENST00000421834;ENST00000446842;ENST00000370788;ENST00000361203	T;T;T;T;T;T;T	0.08458	3.09;3.09;3.09;3.09;3.09;3.09;3.09	6.02	6.02	0.97574	EF-hand-like domain (1);	0.000000	0.45867	D	0.000330	T	0.17831	0.0428	L	0.55990	1.75	0.35650	D	0.811676	D;D;D;D;D	0.89917	0.999;0.999;0.998;1.0;1.0	D;D;D;D;D	0.91635	0.996;0.999;0.995;0.999;0.996	T	0.00643	-1.1630	9	0.87932	D	0	.	16.5446	0.84426	1.0:0.0:0.0:0.0	.	5116;7231;7409;7229;4817	Q5TBT1;E7ERU2;E9PEB9;Q03001;Q03001-8	.;.;.;DYST_HUMAN;.	P	4817;7409;7231;5116;6905;5034;7120	ENSP00000244364:S4817P;ENSP00000359790:S7409P;ENSP00000359805:S7231P;ENSP00000400883:S5116P;ENSP00000393645:S6905P;ENSP00000359824:S5034P;ENSP00000354508:S7120P	ENSP00000244364:S4817P	S	-	1	0	DST	56443866	1.000000	0.71417	1.000000	0.80357	0.986000	0.74619	9.339000	0.96797	2.311000	0.77944	0.533000	0.62120	TCA	.	.	none		0.358	DST-004	NOVEL	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000041021.3	NM_001723	
PSPH	5723	hgsc.bcm.edu	37	7	56085002	56085002	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:56085002C>T	ENST00000395471.3	-	6	1151	c.346G>A	c.(346-348)Gta>Ata	p.V116I	PSPH_ENST00000275605.3_Missense_Mutation_p.V116I|PSPH_ENST00000459834.1_Intron			P78330	SERB_HUMAN	phosphoserine phosphatase	116					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|dephosphorylation (GO:0016311)|L-serine biosynthetic process (GO:0006564)|L-serine metabolic process (GO:0006563)|response to mechanical stimulus (GO:0009612)|response to nutrient levels (GO:0031667)|response to testosterone (GO:0033574)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|neuron projection (GO:0043005)	calcium ion binding (GO:0005509)|magnesium ion binding (GO:0000287)|phosphoserine phosphatase activity (GO:0004647)|protein homodimerization activity (GO:0042803)	p.V116I(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(6)|ovary(1)|skin(1)	11	Breast(14;0.214)		Lung(13;0.00024)|LUSC - Lung squamous cell carcinoma(13;0.00099)			ACATGCTCTACAATACTCCTA	0.393																																					p.V116I		Atlas-SNP	.											PSPH,NS,carcinoma,0,2	PSPH	23	2	1	Substitution - Missense(1)	lung(1)	c.G346A						scavenged	.						87.0	75.0	79.0					7																	56085002		2203	4300	6503	SO:0001583	missense	5723	exon6			GCTCTACAATACT	Y10275	CCDS5522.1	7p11.2	2012-10-02			ENSG00000146733	ENSG00000146733	3.1.3.3		9577	protein-coding gene	gene with protein product		172480		PSP		6297854, 9188776	Standard	NM_004577		Approved		uc003trh.3	P78330	OTTHUMG00000023441	ENST00000395471.3:c.346G>A	7.37:g.56085002C>T	ENSP00000378854:p.Val116Ile	Somatic	443	1	0.00225734		WXS	Illumina HiSeq	Phase_I	464	6	0.012931	NM_004577	B2RCR5|Q7Z3S5	Missense_Mutation	SNP	ENST00000395471.3	37	CCDS5522.1	.	.	.	.	.	.	.	.	.	.	C	10.73	1.432510	0.25813	.	.	ENSG00000146733	ENST00000275605;ENST00000395471;ENST00000421626	D;D;D	0.81908	-1.55;-1.55;-1.55	4.85	4.85	0.62838	Haloacid dehalogenase-like hydrolase (1);HAD-like domain (2);	0.000000	0.85682	D	0.000000	T	0.65228	0.2671	N	0.05124	-0.11	0.80722	D	1	B;B	0.06786	0.001;0.001	B;B	0.18263	0.021;0.021	T	0.62992	-0.6736	10	0.02654	T	1	-16.2549	17.1115	0.86676	0.0:1.0:0.0:0.0	.	116;116	Q53EY1;P78330	.;SERB_HUMAN	I	116	ENSP00000275605:V116I;ENSP00000378854:V116I;ENSP00000398653:V116I	ENSP00000275605:V116I	V	-	1	0	PSPH	56052496	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.551000	0.82182	2.297000	0.77311	0.579000	0.79373	GTA	.	.	none		0.393	PSPH-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343304.1	NM_004577	
THOC5	8563	hgsc.bcm.edu	37	22	29908012	29908012	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr22:29908012G>A	ENST00000490103.1	-	18	1917	c.1795C>T	c.(1795-1797)Cgg>Tgg	p.R599W	CTA-256D12.11_ENST00000411969.1_RNA|THOC5_ENST00000397871.1_Missense_Mutation_p.R599W|THOC5_ENST00000397872.1_Missense_Mutation_p.R599W|THOC5_ENST00000397873.2_Missense_Mutation_p.R599W	NM_003678.4	NP_003669.4	Q13769	THOC5_HUMAN	THO complex 5	599					blastocyst development (GO:0001824)|cell morphogenesis (GO:0000902)|monocyte differentiation (GO:0030224)|mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|negative regulation of DNA damage checkpoint (GO:2000002)|negative regulation of macrophage differentiation (GO:0045650)|positive regulation of DNA-templated transcription, elongation (GO:0032786)|primitive hemopoiesis (GO:0060215)|regulation of mRNA export from nucleus (GO:0010793)|regulation of stem cell division (GO:2000035)|RNA splicing (GO:0008380)|stem cell division (GO:0017145)|viral mRNA export from host cell nucleus (GO:0046784)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	mRNA binding (GO:0003729)			NS(1)|breast(4)|cervix(1)|endometrium(2)|large_intestine(4)|lung(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	21						GGTCTTACCCGAATGTTGTCA	0.582																																					p.R599W		Atlas-SNP	.											THOC5,rectum,carcinoma,+1,2	THOC5	58	2	0			c.C1795T						scavenged	.						121.0	87.0	99.0					22																	29908012		2203	4300	6503	SO:0001583	missense	8563	exon19			TTACCCGAATGTT	AB023200	CCDS13859.1	22q12	2013-02-11			ENSG00000100296	ENSG00000100296		"""THO complex subunits"""	19074	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 79"""	612733	"""chromosome 22 open reading frame 19"""	C22orf19		11979277, 8242058, 10231032, 19015024, 18373705	Standard	NM_003678		Approved	PK1.3, KIAA0983, Fmip, fSAP79	uc003afs.3	Q13769	OTTHUMG00000151291	ENST00000490103.1:c.1795C>T	22.37:g.29908012G>A	ENSP00000420306:p.Arg599Trp	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	173	2	0.0115607	NM_001002878	O60839|Q9UPZ5	Missense_Mutation	SNP	ENST00000490103.1	37	CCDS13859.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.003851	0.74932	.	.	ENSG00000100296	ENST00000490103;ENST00000397872;ENST00000397871;ENST00000397873	T;T;T;T	0.33654	1.4;1.4;1.4;1.4	5.76	5.76	0.90799	.	0.000000	0.85682	D	0.000000	T	0.61048	0.2316	M	0.77820	2.39	0.58432	D	0.999999	D	0.89917	1.0	D	0.75020	0.985	T	0.63413	-0.6643	10	0.87932	D	0	-17.9576	14.7349	0.69409	0.0:0.0:0.8552:0.1448	.	599	Q13769	THOC5_HUMAN	W	599	ENSP00000420306:R599W;ENSP00000380970:R599W;ENSP00000380969:R599W;ENSP00000380971:R599W	ENSP00000380969:R599W	R	-	1	2	THOC5	28238012	1.000000	0.71417	1.000000	0.80357	0.839000	0.47603	1.749000	0.38319	2.879000	0.98667	0.650000	0.86243	CGG	.	.	none		0.582	THOC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000322097.1	NM_003678	
SPRED1	161742	hgsc.bcm.edu	37	15	38643716	38643716	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:38643716A>G	ENST00000299084.4	+	7	2046	c.1186A>G	c.(1186-1188)Agc>Ggc	p.S396G		NM_152594.2	NP_689807.1	Q7Z699	SPRE1_HUMAN	sprouty-related, EVH1 domain containing 1	396	SPR. {ECO:0000255|PROSITE- ProRule:PRU00572}.				inactivation of MAPK activity (GO:0000188)|multicellular organismal development (GO:0007275)|negative regulation of peptidyl-threonine phosphorylation (GO:0010801)|negative regulation of phosphatase activity (GO:0010923)|positive regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043517)|regulation of protein deacetylation (GO:0090311)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatase binding (GO:0019902)|protein kinase binding (GO:0019901)|protein serine/threonine kinase inhibitor activity (GO:0030291)|stem cell factor receptor binding (GO:0005173)			kidney(6)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	25		all_cancers(109;4.88e-13)|all_epithelial(112;1.83e-11)|Lung NSC(122;2.21e-09)|all_lung(180;4.64e-08)|Melanoma(134;0.091)		GBM - Glioblastoma multiforme(113;2.41e-08)|BRCA - Breast invasive adenocarcinoma(123;0.0244)		GTGTGACACTAGCGACGACAA	0.458									Legius syndrome																												p.S396G	Melanoma(196;2146 2959 7698 16532)	Atlas-SNP	.											SPRED1,NS,carcinoma,-2,1	SPRED1	51	1	0			c.A1186G						scavenged	.						255.0	221.0	232.0					15																	38643716		2200	4297	6497	SO:0001583	missense	161742	exon7	Familial Cancer Database	Neurofibromatosis type 1 - like syndrome, SPRED1 disorder	GACACTAGCGACG	AK091222	CCDS32193.1	15q14	2014-06-13			ENSG00000166068	ENSG00000166068			20249	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 147"""	609291					Standard	NM_152594		Approved	FLJ33903, PPP1R147	uc001zka.4	Q7Z699		ENST00000299084.4:c.1186A>G	15.37:g.38643716A>G	ENSP00000299084:p.Ser396Gly	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	205	3	0.0146341	NM_152594	B2RPJ8|Q05D53|Q8N256	Missense_Mutation	SNP	ENST00000299084.4	37	CCDS32193.1	.	.	.	.	.	.	.	.	.	.	A	9.435	1.086442	0.20390	.	.	ENSG00000166068	ENST00000299084	D	0.85702	-2.02	5.81	4.69	0.59074	.	0.211473	0.56097	D	0.000023	T	0.73799	0.3633	L	0.28740	0.885	0.53005	D	0.999961	B	0.14805	0.011	B	0.19946	0.027	T	0.66304	-0.5957	10	0.22109	T	0.4	-22.9336	6.6434	0.22921	0.7913:0.0:0.0715:0.1372	.	396	Q7Z699	SPRE1_HUMAN	G	396	ENSP00000299084:S396G	ENSP00000299084:S396G	S	+	1	0	SPRED1	36431008	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	4.097000	0.57741	2.252000	0.74401	0.457000	0.33378	AGC	.	.	none		0.458	SPRED1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418217.1		
OR52E8	390079	hgsc.bcm.edu	37	11	5878458	5878458	+	Silent	SNP	G	G	A	rs549924845	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:5878458G>A	ENST00000537935.1	-	1	506	c.475C>T	c.(475-477)Ctg>Ttg	p.L159L	TRIM5_ENST00000380027.1_Intron	NM_001005168.1	NP_001005168.1	Q6IFG1	O52E8_HUMAN	olfactory receptor, family 52, subfamily E, member 8	159						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(10)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	20		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.114)		Epithelial(150;2.37e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		ACCATGTACAGGCTCCTCAGG	0.507													G|||	10	0.00199681	0.0068	0.0	5008	,	,		18808	0.0		0.0	False		,,,				2504	0.001				p.L159L		Atlas-SNP	.											OR52E8,NS,carcinoma,0,1	OR52E8	54	1	0			c.C475T						scavenged	.						135.0	147.0	143.0					11																	5878458		2154	4296	6450	SO:0001819	synonymous_variant	390079	exon1			TGTACAGGCTCCT	BK004301	CCDS31400.1	11p15.4	2012-08-09	2003-12-15		ENSG00000183269	ENSG00000183269		"""GPCR / Class A : Olfactory receptors"""	15217	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily E, member 8 pseudogene"""				Standard	NM_001005168		Approved		uc010qzr.2	Q6IFG1	OTTHUMG00000168803	ENST00000537935.1:c.475C>T	11.37:g.5878458G>A		Somatic	146	4	0.0273973		WXS	Illumina HiSeq	Phase_I	171	4	0.0233918	NM_001005168	B9EH38	Silent	SNP	ENST00000537935.1	37	CCDS31400.1																																																																																			.	.	none		0.507	OR52E8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401145.1	NM_001005168	
HNRNPCL1	343069	hgsc.bcm.edu	37	1	12907708	12907708	+	Silent	SNP	A	A	G	rs4026149	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:12907708A>G	ENST00000317869.6	-	2	660	c.435T>C	c.(433-435)cgT>cgC	p.R145R		NM_001013631.1|NM_001136561.2|NM_001146181.1	NP_001013653.1|NP_001130033.2|NP_001139653.1	O60812	HNRC1_HUMAN	heterogeneous nuclear ribonucleoprotein C-like 1	145						nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(15)|prostate(1)|skin(1)|stomach(2)	29						ATAGACGTTGACGTTTCGAGG	0.483																																					p.R145R		Atlas-SNP	.											HNRNPCL1,NS,carcinoma,-1,1	HNRNPCL1	68	1	0			c.T435C						scavenged	.						120.0	124.0	122.0					1																	12907708		2201	4297	6498	SO:0001819	synonymous_variant	343069	exon2			ACGTTGACGTTTC	BC002696	CCDS30591.1	1p36.21	2013-02-12		2008-04-18	ENSG00000179172	ENSG00000179172		"""RNA binding motif (RRM) containing"""	29295	protein-coding gene	gene with protein product				HNRPCL1			Standard	NM_001013631		Approved			O60812	OTTHUMG00000001931	ENST00000317869.6:c.435T>C	1.37:g.12907708A>G		Somatic	182	18	0.0989011		WXS	Illumina HiSeq	Phase_I	198	9	0.0454545	NM_001013631	B2RP44	Silent	SNP	ENST00000317869.6	37	CCDS30591.1																																																																																			A|0.667;G|0.333	0.333	strong		0.483	HNRNPCL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005462.1	NM_001013631	
ONECUT2	9480	hgsc.bcm.edu	37	18	55103350	55103350	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr18:55103350C>T	ENST00000491143.2	+	1	434	c.402C>T	c.(400-402)tcC>tcT	p.S134S	AC090340.1_ENST00000581316.1_RNA	NM_004852.2	NP_004843.2	O95948	ONEC2_HUMAN	one cut homeobox 2	134					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)		TGAGCATGTCCTGCGACTCGT	0.662																																					p.S134S		Atlas-SNP	.											.	ONECUT2	42	.	0			c.C402T						PASS	.						41.0	46.0	44.0					18																	55103350		2203	4300	6503	SO:0001819	synonymous_variant	9480	exon1			CATGTCCTGCGAC	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.402C>T	18.37:g.55103350C>T		Somatic	27	0	0		WXS	Illumina HiSeq	Phase_I	25	9	0.36	NM_004852		Silent	SNP	ENST00000491143.2	37	CCDS42440.1																																																																																			.	.	none		0.662	ONECUT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000357264.3		
FANCD2	2177	hgsc.bcm.edu	37	3	10108913	10108913	+	Missense_Mutation	SNP	G	G	T	rs80258959		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:10108913G>T	ENST00000419585.1	+	26	2567	c.2406G>T	c.(2404-2406)caG>caT	p.Q802H	FANCD2_ENST00000383807.1_Missense_Mutation_p.Q802H|FANCD2_ENST00000287647.3_Missense_Mutation_p.Q802H|FANCD2_ENST00000383806.1_Missense_Mutation_p.Q802H			Q9BXW9	FACD2_HUMAN	Fanconi anemia, complementation group D2	802					DNA repair (GO:0006281)|gamete generation (GO:0007276)|response to gamma radiation (GO:0010332)|synapsis (GO:0007129)	condensed chromosome (GO:0000793)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA polymerase binding (GO:0070182)	p.Q802H(2)		NS(1)|breast(3)|central_nervous_system(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(10)|ovary(1)|prostate(3)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(3)	51				OV - Ovarian serous cystadenocarcinoma(96;0.148)		CCTTCTGCCAGGAAACATCAC	0.378			"""D, Mis, N, F"""			"""AML, leukemia"""		Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.Q802H		Atlas-SNP	.	yes	Rec		Fanconi anaemia D2	3	3p26	2177	"""Fanconi anemia, complementation group D2"""		L	FANCD2,NS,carcinoma,0,2	FANCD2	253	2	2	Substitution - Missense(2)	prostate(2)	c.G2406T						scavenged	.						82.0	72.0	75.0					3																	10108913		2203	4300	6503	SO:0001583	missense	2177	exon26	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CTGCCAGGAAACA	AF340183	CCDS2595.1, CCDS33696.1	3p25.3	2014-09-17		2001-10-05	ENSG00000144554	ENSG00000144554		"""Fanconi anemia, complementation groups"""	3585	protein-coding gene	gene with protein product		613984		FACD, FANCD		7581463, 11239453, 18475298	Standard	XM_005264946		Approved	FAD, FA-D2	uc003buw.3	Q9BXW9	OTTHUMG00000128670	ENST00000419585.1:c.2406G>T	3.37:g.10108913G>T	ENSP00000398754:p.Gln802His	Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	79	3	0.0379747	NM_001018115	Q2LA86|Q69YP9|Q6PJN7|Q9BQ06|Q9H9T9	Missense_Mutation	SNP	ENST00000419585.1	37	CCDS33696.1	.	.	.	.	.	.	.	.	.	.	G	17.37	3.373535	0.61624	.	.	ENSG00000144554	ENST00000287647;ENST00000383807;ENST00000383806;ENST00000419585	T;T;T;T	0.52983	0.64;0.64;0.64;0.64	5.44	1.83	0.25207	.	0.551240	0.20789	N	0.085651	T	0.50240	0.1604	M	0.63428	1.95	0.30837	N	0.736052	P;P	0.50710	0.938;0.938	P;P	0.53988	0.739;0.739	T	0.53229	-0.8468	10	0.54805	T	0.06	.	3.6289	0.08124	0.3156:0.0:0.4962:0.1881	.	802;802	Q9BXW9-2;Q9BXW9	.;FACD2_HUMAN	H	802	ENSP00000287647:Q802H;ENSP00000373318:Q802H;ENSP00000373317:Q802H;ENSP00000398754:Q802H	ENSP00000287647:Q802H	Q	+	3	2	FANCD2	10083913	0.804000	0.28969	0.409000	0.26459	0.904000	0.53231	1.055000	0.30467	0.519000	0.28406	0.585000	0.79938	CAG	.	.	weak		0.378	FANCD2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339873.1		
DNAH1	25981	hgsc.bcm.edu	37	3	52400534	52400534	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:52400534C>T	ENST00000420323.2	+	35	5841	c.5580C>T	c.(5578-5580)ctC>ctT	p.L1860L		NM_015512.4	NP_056327	Q9P2D7	DYH1_HUMAN	dynein, axonemal, heavy chain 1	1860	AAA 2. {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)		GCCTCATGCTCGTCGGGCCCA	0.622																																					p.L1860L		Atlas-SNP	.											.	DNAH1	534	.	0			c.C5580T						PASS	.						31.0	32.0	32.0					3																	52400534		2091	4214	6305	SO:0001819	synonymous_variant	25981	exon35			CATGCTCGTCGGG	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.5580C>T	3.37:g.52400534C>T		Somatic	117	0	0		WXS	Illumina HiSeq	Phase_I	114	48	0.421053	NM_015512	B0I1R6|O00436|O15435|O95491|Q6ZU48|Q86YK7|Q8TEJ4|Q92863|Q9H8E6|Q9UFW6|Q9Y4Z7	Silent	SNP	ENST00000420323.2	37	CCDS46842.1																																																																																			.	.	none		0.622	DNAH1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350816.1	NM_015512	
MAS1	4142	hgsc.bcm.edu	37	6	160328730	160328730	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:160328730A>G	ENST00000252660.4	+	1	757	c.743A>G	c.(742-744)tAc>tGc	p.Y248C		NM_002377.2	NP_002368.1	P04201	MAS_HUMAN	MAS1 proto-oncogene, G protein-coupled receptor	248					activation of NF-kappaB-inducing kinase activity (GO:0007250)|anatomical structure morphogenesis (GO:0009653)|cell proliferation (GO:0008283)|cellular response to peptide hormone stimulus (GO:0071375)|G-protein coupled receptor signaling pathway (GO:0007186)|hippocampus development (GO:0021766)|male gonad development (GO:0008584)|negative regulation of protein phosphorylation (GO:0001933)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of inositol phosphate biosynthetic process (GO:0060732)|protein kinase C signaling (GO:0070528)|regulation of inflammatory response (GO:0050727)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to gonadotropin (GO:0034698)|spermatogenesis (GO:0007283)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	angiotensin receptor activity (GO:0001595)|angiotensin type II receptor activity (GO:0004945)|G-protein coupled receptor activity (GO:0004930)|peptide binding (GO:0042277)|peptide hormone binding (GO:0017046)			breast(2)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(1)	23		Breast(66;0.000776)|Ovarian(120;0.0303)		OV - Ovarian serous cystadenocarcinoma(65;2.44e-18)|BRCA - Breast invasive adenocarcinoma(81;5.6e-06)		AGACTCCTTTACCTGCTGTAC	0.463																																					p.Y248C		Atlas-SNP	.											MAS1,right_upper_lobe,carcinoma,-1,1	MAS1	42	1	0			c.A743G						scavenged	.						130.0	119.0	122.0					6																	160328730		2203	4300	6503	SO:0001583	missense	4142	exon1			TCCTTTACCTGCT	M13150	CCDS5272.1	6q24-q27	2014-06-26	2014-06-26		ENSG00000130368	ENSG00000130368		"""GPCR / Class A : Orphans"""	6899	protein-coding gene	gene with protein product		165180	"""MAS1 oncogene"""				Standard	NM_002377		Approved		uc003qsz.3	P04201	OTTHUMG00000015944	ENST00000252660.4:c.743A>G	6.37:g.160328730A>G	ENSP00000252660:p.Tyr248Cys	Somatic	157	0	0		WXS	Illumina HiSeq	Phase_I	196	3	0.0153061	NM_002377	E1P5B3|Q2TBC9|Q6FG47	Missense_Mutation	SNP	ENST00000252660.4	37	CCDS5272.1	.	.	.	.	.	.	.	.	.	.	A	15.87	2.959542	0.53400	.	.	ENSG00000130368	ENST00000252660	T	0.37915	1.17	5.28	5.28	0.74379	GPCR, rhodopsin-like superfamily (1);	0.000000	0.48767	D	0.000179	T	0.35219	0.0924	L	0.41824	1.3	0.41973	D	0.990767	D	0.62365	0.991	D	0.67382	0.951	T	0.20940	-1.0260	10	0.44086	T	0.13	.	9.7479	0.40457	0.8459:0.0:0.0:0.1541	.	248	P04201	MAS_HUMAN	C	248	ENSP00000252660:Y248C	ENSP00000252660:Y248C	Y	+	2	0	MAS1	160248720	0.979000	0.34478	0.978000	0.43139	0.946000	0.59487	2.850000	0.48294	1.986000	0.57962	0.533000	0.62120	TAC	.	.	none		0.463	MAS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042930.2	NM_002377	
PRB2	653247	hgsc.bcm.edu	37	12	11546395	11546395	+	Missense_Mutation	SNP	G	G	T	rs11054277	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:11546395G>T	ENST00000389362.4	-	3	652	c.617C>A	c.(616-618)cCa>cAa	p.P206Q	PRB2_ENST00000545829.1_5'Flank|PRB1_ENST00000546254.1_Intron	NM_006248.3	NP_006239.3	P02812	PRB2_HUMAN	proline-rich protein BstNI subfamily 2	206	15 X 20 AA approximate tandem repeats of P-P-G-K-P-Q-G-P-P-P-Q-G-[GD]-[NKS]-[KSQ]- [PRS]-[QRS] [GPS]-[PSAR]-[PSR].					extracellular region (GO:0005576)		p.P185Q(1)|p.P206Q(1)		NS(1)|breast(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(14)|pancreas(1)|prostate(5)|skin(4)|stomach(2)|urinary_tract(1)	37		all_cancers(2;0.00558)|Acute lymphoblastic leukemia(2;3.94e-11)|all_hematologic(2;3.6e-09)	OV - Ovarian serous cystadenocarcinoma(49;0.185)			GCCTCCTTGTGGGGGTGGTCC	0.602													g|||	257	0.0513179	0.0091	0.062	5008	,	,		19479	0.0804		0.1113	False		,,,				2504	0.0092				p.P206Q		Atlas-SNP	.											PRB2_ENST00000389362,NS,carcinoma,0,2	PRB2	168	2	2	Substitution - Missense(2)	lung(2)	c.C617A						scavenged	.						68.0	78.0	75.0					12																	11546395		2075	4125	6200	SO:0001583	missense	653247	exon3			CCTTGTGGGGGTG	K03208	CCDS41757.2	12p13.2	2012-10-02			ENSG00000121335	ENSG00000121335			9338	protein-coding gene	gene with protein product		168810				8554050	Standard	NM_006248		Approved	PRPPRB1, Ps, cP7	uc010shk.1	P02812	OTTHUMG00000156975	ENST00000389362.4:c.617C>A	12.37:g.11546395G>T	ENSP00000374013:p.Pro206Gln	Somatic	253	2	0.00790514		WXS	Illumina HiSeq	Phase_I	286	5	0.0174825	NM_006248	O00599|P02811|P04281	Missense_Mutation	SNP	ENST00000389362.4	37	CCDS41757.2	.	.	.	.	.	.	.	.	.	.	.	13.45	2.239350	0.39598	.	.	ENSG00000121335	ENST00000389362	T	0.04551	3.6	1.46	-2.65	0.06095	.	0.000000	0.35466	U	0.003186	T	0.04907	0.0132	L	0.33792	1.035	0.22888	N	0.998607	D	0.59357	0.985	P	0.52031	0.688	T	0.29882	-0.9997	10	0.42905	T	0.14	.	3.3379	0.07107	0.2091:0.2667:0.5243:0.0	.	206	P02812	PRB2_HUMAN	Q	206	ENSP00000374013:P206Q	ENSP00000374013:P206Q	P	-	2	0	PRB2	11437662	0.001000	0.12720	0.029000	0.17559	0.747000	0.42532	-0.415000	0.07106	-0.824000	0.04295	0.291000	0.19559	CCA	.	.	weak		0.602	PRB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346925.2	NM_006248	
HCAR2	338442	hgsc.bcm.edu	37	12	123187023	123187023	+	Missense_Mutation	SNP	G	G	A	rs201423596		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:123187023G>A	ENST00000328880.5	-	1	867	c.808C>T	c.(808-810)Cgc>Tgc	p.R270C	HCAR1_ENST00000356987.2_Intron|RP11-324E6.6_ENST00000543611.1_lincRNA	NM_177551.3	NP_808219.1	Q8TDS4	HCAR2_HUMAN	hydroxycarboxylic acid receptor 2	270					negative regulation of lipid catabolic process (GO:0050995)|neutrophil apoptotic process (GO:0001781)|positive regulation of adiponectin secretion (GO:0070165)|positive regulation of neutrophil apoptotic process (GO:0033031)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	nicotinic acid receptor activity (GO:0070553)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(5)|large_intestine(2)|lung(2)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	15					Niacin(DB00627)	TCCACCGAGCGGTACACTTCA	0.552																																					p.R270C		Atlas-SNP	.											.	HCAR2	36	.	0			c.C808T						PASS	.						50.0	46.0	47.0					12																	123187023		2203	4294	6497	SO:0001583	missense	338442	exon1			CCGAGCGGTACAC	AY148884	CCDS9235.1	12q24.31	2012-08-08	2011-05-30	2011-05-30	ENSG00000182782	ENSG00000182782		"""GPCR / Class A : Hydroxy-carboxylic acid receptors"""	24827	protein-coding gene	gene with protein product	"""niacin receptor 1"""	609163	"""G protein-coupled receptor 109A"""	GPR109A		21167710, 12522134, 12646212, 19141678, 18983141, 21454438	Standard	NM_177551		Approved	HCA2, HM74A, PUMAG, Puma-g, NIACR1	uc001ucx.1	Q8TDS4	OTTHUMG00000162722	ENST00000328880.5:c.808C>T	12.37:g.123187023G>A	ENSP00000375066:p.Arg270Cys	Somatic	238	0	0		WXS	Illumina HiSeq	Phase_I	285	67	0.235088	NM_177551	A0PJL5|A7LGG3	Missense_Mutation	SNP	ENST00000328880.5	37	CCDS9235.1	.	.	.	.	.	.	.	.	.	.	G	10.23	1.292018	0.23564	.	.	ENSG00000182782	ENST00000328880;ENST00000536970	T	0.37584	1.19	4.83	-1.66	0.08265	GPCR, rhodopsin-like superfamily (1);	0.524402	0.18457	N	0.140657	T	0.41465	0.1160	M	0.62088	1.915	0.09310	N	1	D	0.54207	0.965	P	0.56788	0.806	T	0.26538	-1.0100	10	0.62326	D	0.03	-6.7453	3.923	0.09251	0.3275:0.0:0.4073:0.2652	.	270	Q8TDS4	HCAR2_HUMAN	C	270	ENSP00000375066:R270C	ENSP00000375066:R270C	R	-	1	0	HCAR2	121752976	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.110000	0.10824	-0.192000	0.10432	0.563000	0.77884	CGC	.	.	weak		0.552	HCAR2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000370202.1	NM_177551	
TTC17	55761	hgsc.bcm.edu	37	11	43425620	43425620	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:43425620A>G	ENST00000039989.4	+	11	1419	c.1405A>G	c.(1405-1407)Aat>Gat	p.N469D	TTC17_ENST00000299240.6_Missense_Mutation_p.N469D|TTC17_ENST00000526774.1_3'UTR	NM_018259.5	NP_060729.2	Q96AE7	TTC17_HUMAN	tetratricopeptide repeat domain 17	469					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						GAGTGATATCAATGATTCGGT	0.398																																					p.N469D		Atlas-SNP	.											TTC17,NS,carcinoma,-1,1	TTC17	112	1	0			c.A1405G						scavenged	.						163.0	148.0	153.0					11																	43425620		2203	4300	6503	SO:0001583	missense	55761	exon11			GATATCAATGATT	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.1405A>G	11.37:g.43425620A>G	ENSP00000039989:p.Asn469Asp	Somatic	164	1	0.00609756		WXS	Illumina HiSeq	Phase_I	211	3	0.014218	NM_018259	G3XAB3|Q8NEC0	Missense_Mutation	SNP	ENST00000039989.4	37	CCDS31466.1	.	.	.	.	.	.	.	.	.	.	A	11.88	1.770495	0.31320	.	.	ENSG00000052841	ENST00000299240;ENST00000039989	T;T	0.29397	1.57;1.57	5.83	5.83	0.93111	.	0.270136	0.47093	D	0.000242	T	0.21921	0.0528	N	0.22421	0.69	0.23056	N	0.998365	B;B;B	0.18741	0.003;0.03;0.012	B;B;B	0.21151	0.009;0.011;0.033	T	0.14504	-1.0470	10	0.15952	T	0.53	-1.6142	14.7708	0.69675	1.0:0.0:0.0:0.0	.	469;469;469	Q8NEC0;Q96AE7;G3XAB3	.;TTC17_HUMAN;.	D	469	ENSP00000299240:N469D;ENSP00000039989:N469D	ENSP00000039989:N469D	N	+	1	0	TTC17	43382196	1.000000	0.71417	0.765000	0.31456	0.526000	0.34562	3.388000	0.52509	2.240000	0.73641	0.528000	0.53228	AAT	.	.	none		0.398	TTC17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389577.2	NM_018259	
DCHS2	54798	hgsc.bcm.edu	37	4	155411418	155411418	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:155411418C>T	ENST00000339452.1	-	1	1450	c.1090G>A	c.(1090-1092)Gtg>Atg	p.V364M	DCHS2_ENST00000443500.1_Missense_Mutation_p.V364M|DCHS2_ENST00000456341.2_Missense_Mutation_p.V357M	NM_001142552.1	NP_001136024.1	Q6V1P9	PCD23_HUMAN	dachsous cadherin-related 2	1533	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			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)		ACTCGCACCACGCCGCTCAGC	0.731																																					p.V364M		Atlas-SNP	.											.	DCHS2	594	.	0			c.G1090A						PASS	.						8.0	11.0	10.0					4																	155411418		688	1580	2268	SO:0001583	missense	54798	exon1			GCACCACGCCGCT	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		ENST00000339452.1:c.1090G>A	4.37:g.155411418C>T	ENSP00000345062:p.Val364Met	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	10	7	0.7	NM_001142552	B2RU14|E9PC11|Q4W5P9|Q6ZS61|Q9NXU8	Missense_Mutation	SNP	ENST00000339452.1	37	CCDS47150.1	.	.	.	.	.	.	.	.	.	.	C	11.98	1.800606	0.31869	.	.	ENSG00000197410	ENST00000339452;ENST00000544161;ENST00000456341;ENST00000443500	T;T;T	0.53423	0.62;0.62;0.62	4.7	2.9	0.33743	.	.	.	.	.	T	0.62429	0.2427	M	0.64260	1.97	0.19300	N	0.999978	P;D	0.89917	0.955;1.0	P;D	0.73380	0.523;0.98	T	0.51164	-0.8740	9	0.48119	T	0.1	.	10.3423	0.43887	0.1419:0.5835:0.2746:0.0	.	364;364	E9PG03;E9PC11	.;.	M	364;364;357;364	ENSP00000345062:V364M;ENSP00000408543:V357M;ENSP00000395539:V364M	ENSP00000345062:V364M	V	-	1	0	DCHS2	155630868	0.091000	0.21658	0.990000	0.47175	0.214000	0.24535	0.793000	0.26944	0.468000	0.27243	0.561000	0.74099	GTG	.	.	none		0.731	DCHS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000365282.1	NM_001142552	
CLASP1	23332	hgsc.bcm.edu	37	2	122135079	122135079	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:122135079T>C	ENST00000263710.4	-	34	4027	c.3638A>G	c.(3637-3639)gAt>gGt	p.D1213G	CLASP1_ENST00000541859.1_Missense_Mutation_p.D930G|CLASP1_ENST00000541377.1_Missense_Mutation_p.D1152G|CLASP1_ENST00000455322.2_Missense_Mutation_p.D1169G|CLASP1_ENST00000409078.3_Missense_Mutation_p.D1146G|CLASP1_ENST00000545861.1_Missense_Mutation_p.D920G|CLASP1_ENST00000397587.3_Missense_Mutation_p.D1153G	NM_015282.2	NP_056097.1	Q7Z460	CLAP1_HUMAN	cytoplasmic linker associated protein 1	1213					axon guidance (GO:0007411)|cell division (GO:0051301)|establishment of spindle orientation (GO:0051294)|establishment or maintenance of cell polarity (GO:0007163)|exit from mitosis (GO:0010458)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule anchoring (GO:0034453)|microtubule bundle formation (GO:0001578)|microtubule cytoskeleton organization (GO:0000226)|microtubule nucleation (GO:0007020)|microtubule organizing center organization (GO:0031023)|mitotic cell cycle (GO:0000278)|negative regulation of microtubule depolymerization (GO:0007026)|negative regulation of microtubule polymerization or depolymerization (GO:0031111)	cell cortex (GO:0005938)|centrosomal corona (GO:0031592)|centrosome (GO:0005813)|cortical microtubule cytoskeleton (GO:0030981)|cytoplasmic microtubule (GO:0005881)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|kinetochore (GO:0000776)|kinetochore microtubule (GO:0005828)|membrane (GO:0016020)|spindle microtubule (GO:0005876)	kinetochore binding (GO:0043515)|microtubule binding (GO:0008017)|microtubule plus-end binding (GO:0051010)			NS(2)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(19)|ovary(1)|prostate(1)	47	Renal(3;0.0496)					ACTTACAATATCACACTCCTT	0.378																																					p.D1213G		Atlas-SNP	.											.	CLASP1	135	.	0			c.A3638G						PASS	.						165.0	140.0	148.0					2																	122135079		1863	4104	5967	SO:0001583	missense	23332	exon33			ACAATATCACACT	AB014522		2q14.2-q14.3	2013-01-18			ENSG00000074054	ENSG00000074054			17088	protein-coding gene	gene with protein product	"""multiple asters 1"""	605852				9734811, 10899121, 16914514	Standard	NM_015282		Approved	KIAA0622, MAST1	uc002tnc.3	Q7Z460	OTTHUMG00000153331	ENST00000263710.4:c.3638A>G	2.37:g.122135079T>C	ENSP00000263710:p.Asp1213Gly	Somatic	165	0	0		WXS	Illumina HiSeq	Phase_I	157	70	0.44586	NM_015282	B7ZLX3|O75118|Q2KHQ9|Q5H9P0|Q8N5B8|Q9BQT5	Missense_Mutation	SNP	ENST00000263710.4	37		.	.	.	.	.	.	.	.	.	.	T	17.18	3.323437	0.60634	.	.	ENSG00000074054	ENST00000263710;ENST00000455322;ENST00000397587;ENST00000541377;ENST00000541859;ENST00000409078;ENST00000545861	T;T;T;T;T;T	0.47869	2.17;2.15;2.15;2.14;0.83;2.15	5.74	5.74	0.90152	Armadillo-type fold (1);	0.226336	0.44285	N	0.000463	T	0.41994	0.1183	L	0.39020	1.185	0.80722	D	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	0.28073	-1.0055	10	0.87932	D	0	-13.4635	16.0335	0.80603	0.0:0.0:0.0:1.0	.	1146;1153;1154;1213	E7EUA5;F5GWS0;A2RU21;Q7Z460	.;.;.;CLAP1_HUMAN	G	1213;1169;1153;1152;930;1146;920	ENSP00000263710:D1213G;ENSP00000389372:D1169G;ENSP00000380717:D1153G;ENSP00000441625:D1152G;ENSP00000441770:D930G;ENSP00000386442:D1146G	ENSP00000263710:D1213G	D	-	2	0	CLASP1	121851549	1.000000	0.71417	0.986000	0.45419	0.816000	0.46133	7.578000	0.82498	2.195000	0.70347	0.533000	0.62120	GAT	.	.	none		0.378	CLASP1-201	KNOWN	basic	protein_coding	protein_coding		NM_015282	
NEB	4703	hgsc.bcm.edu	37	2	152536281	152536281	+	Missense_Mutation	SNP	G	G	A	rs371710158		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:152536281G>A	ENST00000172853.10	-	32	3356	c.3209C>T	c.(3208-3210)gCg>gTg	p.A1070V	NEB_ENST00000397345.3_Missense_Mutation_p.A1070V|NEB_ENST00000427231.2_Missense_Mutation_p.A1070V|NEB_ENST00000409198.1_Missense_Mutation_p.A1070V|NEB_ENST00000604864.1_Missense_Mutation_p.A1070V|NEB_ENST00000603639.1_Missense_Mutation_p.A1070V			P20929	NEBU_HUMAN	nebulin	1070					muscle filament sliding (GO:0030049)|muscle organ development (GO:0007517)|regulation of actin filament length (GO:0030832)|somatic muscle development (GO:0007525)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Z disc (GO:0030018)	structural constituent of muscle (GO:0008307)	p.A1070V(2)		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)		GATGGGAATCGCATCAGTTCT	0.468																																					p.A1070V		Atlas-SNP	.											NEB,NS,carcinoma,0,1	NEB	1697	1	2	Substitution - Missense(2)	endometrium(2)	c.C3209T						scavenged	.						102.0	100.0	100.0					2																	152536281		1954	4153	6107	SO:0001583	missense	4703	exon32			GGAATCGCATCAG	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.3209C>T	2.37:g.152536281G>A	ENSP00000172853:p.Ala1070Val	Somatic	132	1	0.00757576		WXS	Illumina HiSeq	Phase_I	149	60	0.402685	NM_004543	F8WCL5|F8WCP0|Q15346|Q53QQ2|Q53TG8	Missense_Mutation	SNP	ENST00000172853.10	37		.	.	.	.	.	.	.	.	.	.	G	35	5.526780	0.96431	.	.	ENSG00000183091	ENST00000409198;ENST00000397345;ENST00000427231;ENST00000172853	T;T;T;T	0.49139	0.79;0.79;0.79;0.79	5.74	5.74	0.90152	.	0.000000	0.85682	D	0.000000	T	0.65554	0.2702	M	0.91406	3.205	0.80722	D	1	P	0.51147	0.942	P	0.46362	0.514	T	0.75566	-0.3273	10	0.87932	D	0	.	18.7041	0.91631	0.0:0.0:1.0:0.0	.	1070	P20929	NEBU_HUMAN	V	1070	ENSP00000386259:A1070V;ENSP00000380505:A1070V;ENSP00000416578:A1070V;ENSP00000172853:A1070V	ENSP00000172853:A1070V	A	-	2	0	NEB	152244527	1.000000	0.71417	0.687000	0.30102	0.982000	0.71751	9.705000	0.98719	2.720000	0.93068	0.650000	0.86243	GCG	.	.	alt		0.468	NEB-201	KNOWN	basic	protein_coding	protein_coding		NM_004543	
DSG3	1830	hgsc.bcm.edu	37	18	29045363	29045363	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr18:29045363C>T	ENST00000257189.4	+	10	1437	c.1354C>T	c.(1354-1356)Cga>Tga	p.R452*		NM_001944.2	NP_001935.2	P32926	DSG3_HUMAN	desmoglein 3	452	Cadherin 4. {ECO:0000255|PROSITE- ProRule:PRU00043}.				apoptotic process (GO:0006915)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|homophilic cell adhesion (GO:0007156)	cell junction (GO:0030054)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|central_nervous_system(2)|cervix(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(28)|ovary(4)|prostate(1)|skin(8)|upper_aerodigestive_tract(1)	62			OV - Ovarian serous cystadenocarcinoma(10;0.00504)			AAATATGAACCGAGATTCTAC	0.318																																					p.R452X		Atlas-SNP	.											DSG3,NS,carcinoma,-1,1	DSG3	172	1	0			c.C1354T						scavenged	.						71.0	77.0	75.0					18																	29045363		2203	4300	6503	SO:0001587	stop_gained	1830	exon10			ATGAACCGAGATT	M76482	CCDS11898.1	18q12.1	2010-06-24	2010-06-24		ENSG00000134757	ENSG00000134757		"""Cadherins / Major cadherins"""	3050	protein-coding gene	gene with protein product	"""pemphigus vulgaris antigen"""	169615	"""desmoglein 3 (pemphigus vulgaris antigen)"""			1601426	Standard	NM_001944		Approved	CDHF6	uc002kws.3	P32926	OTTHUMG00000131985	ENST00000257189.4:c.1354C>T	18.37:g.29045363C>T	ENSP00000257189:p.Arg452*	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	124	2	0.016129	NM_001944	A8K2V2	Nonsense_Mutation	SNP	ENST00000257189.4	37	CCDS11898.1	.	.	.	.	.	.	.	.	.	.	C	36	5.689264	0.96784	.	.	ENSG00000134757	ENST00000257189	.	.	.	5.82	3.94	0.45596	.	0.160258	0.27956	N	0.017164	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	5.9596	0.19293	0.1491:0.6608:0.0:0.1901	.	.	.	.	X	452	.	ENSP00000257189:R452X	R	+	1	2	DSG3	27299361	0.001000	0.12720	0.554000	0.28268	0.661000	0.39034	0.183000	0.16919	1.465000	0.48006	0.467000	0.42956	CGA	.	.	none		0.318	DSG3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254949.1	NM_001944	
KLHL6	89857	hgsc.bcm.edu	37	3	183273170	183273170	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:183273170G>A	ENST00000341319.3	-	1	307	c.272C>T	c.(271-273)gCc>gTc	p.A91V		NM_130446.2	NP_569713.2	Q8WZ60	KLHL6_HUMAN	kelch-like family member 6	91	BTB. {ECO:0000255|PROSITE- ProRule:PRU00037}.				B cell receptor signaling pathway (GO:0050853)|germinal center formation (GO:0002467)					breast(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(7)|kidney(1)|large_intestine(6)|liver(1)|lung(16)|ovary(2)|prostate(1)|skin(2)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	44	all_cancers(143;9.2e-12)|Ovarian(172;0.0172)		all cancers(12;1.29e-44)|Epithelial(37;1.24e-38)|LUSC - Lung squamous cell carcinoma(7;2.58e-24)|Lung(8;1.79e-22)|OV - Ovarian serous cystadenocarcinoma(80;2.32e-22)			GCTGGCTGCGGCAAGCACCAC	0.512																																					p.A91V		Atlas-SNP	.											.	KLHL6	100	.	0			c.C272T						PASS	.						94.0	85.0	88.0					3																	183273170		2203	4300	6503	SO:0001583	missense	89857	exon1			GCTGCGGCAAGCA	AF441792	CCDS3245.2	3q27.3	2013-01-30	2013-01-30		ENSG00000172578	ENSG00000172578		"""Kelch-like"", ""BTB/POZ domain containing"""	18653	protein-coding gene	gene with protein product	"""kelch-like protein KLHL6"""	614214	"""kelch-like 6 (Drosophila)"""			11214971, 12617994	Standard	NM_130446		Approved	FLJ00029	uc003flr.3	Q8WZ60	OTTHUMG00000148673	ENST00000341319.3:c.272C>T	3.37:g.183273170G>A	ENSP00000341342:p.Ala91Val	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	282	99	0.351064	NM_130446	B2RB31|D3DNS8|Q8N5I1|Q8N892	Missense_Mutation	SNP	ENST00000341319.3	37	CCDS3245.2	.	.	.	.	.	.	.	.	.	.	G	27.7	4.851144	0.91277	.	.	ENSG00000172578	ENST00000341319	T	0.72725	-0.68	5.56	5.56	0.83823	BTB/POZ-like (2);BTB/POZ (1);BTB/POZ fold (2);	0.000000	0.85682	D	0.000000	D	0.83059	0.5172	M	0.88570	2.965	0.80722	D	1	P	0.37370	0.592	P	0.46885	0.53	D	0.84866	0.0822	10	0.62326	D	0.03	.	19.5245	0.95199	0.0:0.0:1.0:0.0	.	91	Q8WZ60	KLHL6_HUMAN	V	91	ENSP00000341342:A91V	ENSP00000341342:A91V	A	-	2	0	KLHL6	184755864	1.000000	0.71417	0.999000	0.59377	0.985000	0.73830	7.900000	0.87376	2.608000	0.88229	0.655000	0.94253	GCC	.	.	none		0.512	KLHL6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000309024.1	NM_130446	
RANBP2	5903	hgsc.bcm.edu	37	2	109371659	109371659	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:109371659G>A	ENST00000283195.6	+	17	2536	c.2410G>A	c.(2410-2412)Gca>Aca	p.A804T		NM_006267.4	NP_006258.3	P49792	RBP2_HUMAN	RAN binding protein 2	804					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						ACCTCGATGGGCAGAAGATCA	0.308																																					p.A804T		Atlas-SNP	.											RANBP2_ENST00000283195,NS,carcinoma,0,2	RANBP2	488	2	0			c.G2410A						scavenged	.						140.0	163.0	155.0					2																	109371659		2199	4297	6496	SO:0001583	missense	5903	exon17			CGATGGGCAGAAG	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.2410G>A	2.37:g.109371659G>A	ENSP00000283195:p.Ala804Thr	Somatic	675	2	0.00296296		WXS	Illumina HiSeq	Phase_I	752	9	0.0119681	NM_006267	Q13074|Q15280|Q53TE2|Q59FH7	Missense_Mutation	SNP	ENST00000283195.6	37	CCDS2079.1	.	.	.	.	.	.	.	.	.	.	g	28.4	4.919938	0.92249	.	.	ENSG00000153201	ENST00000409491;ENST00000283195	T	0.19105	2.17	5.8	5.8	0.92144	.	.	.	.	.	T	0.34337	0.0894	L	0.34521	1.04	0.49130	D	0.999754	D	0.67145	0.996	P	0.58331	0.837	T	0.01532	-1.1331	9	0.54805	T	0.06	-13.8517	20.0609	0.97674	0.0:0.0:1.0:0.0	.	804	P49792	RBP2_HUMAN	T	804	ENSP00000283195:A804T	ENSP00000283195:A804T	A	+	1	0	RANBP2	108738091	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.714000	0.74692	2.737000	0.93849	0.542000	0.68232	GCA	.	.	none		0.308	RANBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253594.1	NM_006267	
MUC4	4585	hgsc.bcm.edu	37	3	195512263	195512263	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:195512263G>A	ENST00000463781.3	-	2	6647	c.6188C>T	c.(6187-6189)aCg>aTg	p.T2063M	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.T2063M	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)		AGGAAGAGGCGTGGTGTCACC	0.572																																					p.T2063M		Atlas-SNP	.											MUC4_ENST00000463781,rectum,carcinoma,+1,1	MUC4	1505	1	0			c.C6188T						scavenged	.						17.0	18.0	18.0					3																	195512263		682	1560	2242	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.6188C>T	3.37:g.195512263G>A	ENSP00000417498:p.Thr2063Met	Somatic	144	1	0.00694444		WXS	Illumina HiSeq	Phase_I	186	3	0.016129	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	0.701	-0.790905	0.02884	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37915	1.17;1.29	.	.	.	.	.	.	.	.	T	0.23611	0.0571	N	0.19112	0.55	0.09310	N	1	D	0.64830	0.994	P	0.47744	0.556	T	0.15549	-1.0433	7	.	.	.	.	5.4633	0.16630	1.0E-4:0.3513:0.6486:0.0	.	2063	E7ESK3	.	M	2063	ENSP00000417498:T2063M;ENSP00000420243:T2063M	.	T	-	2	0	MUC4	196996658	0.001000	0.12720	0.001000	0.08648	0.010000	0.07245	0.266000	0.18534	-0.812000	0.04363	0.064000	0.15345	ACG	.	.	none		0.572	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
GCC2	9648	hgsc.bcm.edu	37	2	109088188	109088188	+	Silent	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:109088188T>C	ENST00000309863.6	+	6	3117	c.2403T>C	c.(2401-2403)gcT>gcC	p.A801A		NM_181453.3	NP_852118	Q8IWJ2	GCC2_HUMAN	GRIP and coiled-coil domain containing 2	801					Golgi ribbon formation (GO:0090161)|late endosome to Golgi transport (GO:0034499)|microtubule anchoring (GO:0034453)|microtubule organizing center organization (GO:0031023)|protein localization to Golgi apparatus (GO:0034067)|protein targeting to Golgi (GO:0000042)|protein targeting to lysosome (GO:0006622)|recycling endosome to Golgi transport (GO:0071955)|regulation of protein exit from endoplasmic reticulum (GO:0070861)|retrograde transport, endosome to Golgi (GO:0042147)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)|trans-Golgi network (GO:0005802)	identical protein binding (GO:0042802)			breast(8)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(19)|ovary(2)|pancreas(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	54						GCAACCTGGCTTTTCAGCGTG	0.373																																					p.A801A		Atlas-SNP	.											GCC2,NS,carcinoma,+1,1	GCC2	129	1	0			c.T2403C						scavenged	.						63.0	66.0	65.0					2																	109088188		2203	4298	6501	SO:0001819	synonymous_variant	9648	exon6			CCTGGCTTTTCAG	BC020645	CCDS33268.1	2q12.3	2008-02-05	2004-03-05		ENSG00000135968	ENSG00000135968			23218	protein-coding gene	gene with protein product		612711	"""GRIP and coiled-coil domain-containing 2"""			12446665	Standard	NM_181453		Approved	GCC185, KIAA0336	uc002tec.3	Q8IWJ2	OTTHUMG00000153214	ENST00000309863.6:c.2403T>C	2.37:g.109088188T>C		Somatic	308	2	0.00649351		WXS	Illumina HiSeq	Phase_I	380	4	0.0105263	NM_181453	A6H8X8|O15045|Q4ZG46|Q8TDH3|Q9H2G8	Silent	SNP	ENST00000309863.6	37	CCDS33268.1																																																																																			.	.	none		0.373	GCC2-014	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358516.3	NM_014635	
CUX2	23316	hgsc.bcm.edu	37	12	111779831	111779831	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:111779831C>T	ENST00000261726.6	+	21	3787	c.3633C>T	c.(3631-3633)acC>acT	p.T1211T	RNA5SP373_ENST00000517271.1_RNA	NM_015267.3	NP_056082.2	O14529	CUX2_HUMAN	cut-like homeobox 2	1211					cellular response to organic substance (GO:0071310)|cognition (GO:0050890)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of dendrite morphogenesis (GO:0050775)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of gene expression (GO:0010628)|positive regulation of synapse assembly (GO:0051965)|short-term memory (GO:0007614)|transcription, DNA-templated (GO:0006351)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding (GO:0043565)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(9)|lung(24)|ovary(5)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(2)	55						AGACCAACACCGTCATCAACT	0.612																																					p.T1211T		Atlas-SNP	.											CUX2,caecum,carcinoma,0,1	CUX2	145	1	0			c.C3633T						scavenged	.						66.0	76.0	73.0					12																	111779831		2195	4300	6495	SO:0001819	synonymous_variant	23316	exon21			CAACACCGTCATC	AB006631	CCDS41837.1	12q24.12	2011-06-20	2007-11-07	2007-11-07	ENSG00000111249	ENSG00000111249		"""Homeoboxes / CUT class"""	19347	protein-coding gene	gene with protein product		610648	"""cut-like 2 (Drosophila)"""	CUTL2			Standard	NM_015267		Approved	KIAA0293, CDP2	uc001tsa.2	O14529	OTTHUMG00000169546	ENST00000261726.6:c.3633C>T	12.37:g.111779831C>T		Somatic	166	0	0		WXS	Illumina HiSeq	Phase_I	163	2	0.0122699	NM_015267	A7E2Y4	Silent	SNP	ENST00000261726.6	37	CCDS41837.1																																																																																			.	.	none		0.612	CUX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404765.1	NM_015267	
TNXB	7148	hgsc.bcm.edu	37	6	32010286	32010286	+	Silent	SNP	G	G	C	rs199762902	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:32010286G>C	ENST00000375244.3	-	40	12357	c.12156C>G	c.(12154-12156)cgC>cgG	p.R4052R	TNXB_ENST00000375247.2_Silent_p.R4050R|TNXB_ENST00000451343.1_Silent_p.R481R			P22105	TENX_HUMAN	tenascin XB	4097	Fibronectin type-III 32. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton organization (GO:0030036)|cell adhesion (GO:0007155)|cell-matrix adhesion (GO:0007160)|collagen fibril organization (GO:0030199)|collagen metabolic process (GO:0032963)|elastic fiber assembly (GO:0048251)|extracellular fibril organization (GO:0043206)|fatty acid metabolic process (GO:0006631)|regulation of JUN kinase activity (GO:0043506)|single organismal cell-cell adhesion (GO:0016337)|triglyceride metabolic process (GO:0006641)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intracellular (GO:0005622)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|integrin binding (GO:0005178)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|prostate(1)	8						GGGGCCGCTCGCGGTTGCCGT	0.667																																					p.R4050R		Atlas-SNP	.											TNXB_ENST00000375247,NS,carcinoma,-2,3	TNXB	553	3	0			c.C12150G						scavenged	.						48.0	40.0	43.0					6																	32010286		1511	2709	4220	SO:0001819	synonymous_variant	7148	exon40			CCGCTCGCGGTTG	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.12156C>G	6.37:g.32010286G>C		Somatic	326	108	0.331288		WXS	Illumina HiSeq	Phase_I	343	120	0.349854	NM_019105	P78530|P78531|Q08424|Q08AM0|Q08AM1|Q59GU7|Q5SQD3|Q5ST74|Q7L8Q4|Q8N4R1|Q9NPK9|Q9UC10|Q9UC11|Q9UC12|Q9UC13|Q9UMG7	Silent	SNP	ENST00000375244.3	37																																																																																				G|0.980;C|0.020	0.020	strong		0.667	TNXB-001	PUTATIVE	not_organism_supported|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000268927.2	NM_019105	
GRM7	2917	hgsc.bcm.edu	37	3	7721909	7721909	+	Silent	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:7721909G>A	ENST00000357716.4	+	9	2899	c.2625G>A	c.(2623-2625)agG>agA	p.R875R	GRM7_ENST00000403881.1_Silent_p.R875R|GRM7_ENST00000486284.1_Silent_p.R875R|GRM7_ENST00000389336.4_Silent_p.R875R|GRM7_ENST00000402647.2_Silent_p.R875R	NM_000844.3	NP_000835.1	Q14831	GRM7_HUMAN	glutamate receptor, metabotropic 7	875					adenylate cyclase-inhibiting G-protein coupled glutamate receptor signaling pathway (GO:0007196)|adult behavior (GO:0030534)|conditioned taste aversion (GO:0001661)|multicellular organismal response to stress (GO:0033555)|negative regulation of adenylate cyclase activity (GO:0007194)|negative regulation of cAMP biosynthetic process (GO:0030818)|negative regulation of glutamate secretion (GO:0014050)|regulation of cyclase activity (GO:0031279)|regulation of synaptic transmission, glutamatergic (GO:0051966)|sensory perception of smell (GO:0007608)|sensory perception of sound (GO:0007605)|short-term memory (GO:0007614)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)	asymmetric synapse (GO:0032279)|axon (GO:0030424)|cell cortex (GO:0005938)|dendrite (GO:0030425)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|presynaptic active zone (GO:0048786)|presynaptic membrane (GO:0042734)|receptor complex (GO:0043235)	adenylate cyclase inhibitor activity (GO:0010855)|calcium channel regulator activity (GO:0005246)|calcium ion binding (GO:0005509)|glutamate binding (GO:0016595)|glutamate receptor activity (GO:0008066)|group III metabotropic glutamate receptor activity (GO:0001642)|PDZ domain binding (GO:0030165)|serine binding (GO:0070905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(14)|lung(35)|ovary(4)|prostate(2)|skin(6)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	76						TGTCATCGAGGCTGTCACACA	0.493																																					p.R875R		Atlas-SNP	.											GRM7,NS,carcinoma,+2,1	GRM7	223	1	0			c.G2625A						scavenged	.						107.0	78.0	88.0					3																	7721909		2203	4300	6503	SO:0001819	synonymous_variant	2917	exon9			ATCGAGGCTGTCA	U92458	CCDS43042.1	3p26-p25	2014-06-12			ENSG00000196277	ENSG00000196277		"""GPCR / Class C : Glutamate receptors, metabotropic"", ""Glutamate receptors"""	4599	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 87"""	604101				8288585, 8840028	Standard	NM_000844		Approved	GLUR7, GPRC1G, mGlu7, MGLUR7, PPP1R87	uc003bql.2	Q14831	OTTHUMG00000125549	ENST00000357716.4:c.2625G>A	3.37:g.7721909G>A		Somatic	135	0	0		WXS	Illumina HiSeq	Phase_I	154	2	0.012987	NM_000844	Q8NFS2|Q8NFS3|Q8NFS4	Silent	SNP	ENST00000357716.4	37	CCDS43042.1																																																																																			.	.	none		0.493	GRM7-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000246895.3	NM_000844	
KIF1A	547	hgsc.bcm.edu	37	2	241696843	241696843	+	Intron	SNP	C	C	A	rs537608637|rs10594016|rs533559120		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:241696843C>A	ENST00000320389.7	-	25	2714				KIF1A_ENST00000498729.2_Missense_Mutation_p.E917D	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A						anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)			NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		cctcctcatcctcctcctcct	0.682													C|||	1	0.000199681	0.0	0.0014	5008	,	,		8551	0.0		0.0	False		,,,				2504	0.0				p.E917D		Atlas-SNP	.											.	KIF1A	152	.	0			c.G2751T						PASS	.																																			SO:0001627	intron_variant	547	exon27			CTCATCCTCCTCC	AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.2555+933G>T	2.37:g.241696843C>A		Somatic	42	0	0		WXS	Illumina HiSeq	Phase_I	49	4	0.0816327	NM_001244008	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	C	8.327	0.825706	0.16749	.	.	ENSG00000130294	ENST00000498729;ENST00000373308;ENST00000404283	T;T	0.73047	-0.63;-0.71	4.04	3.16	0.36331	.	.	.	.	.	T	0.50429	0.1615	.	.	.	0.27599	N	0.949023	B;B	0.02656	0.0;0.0	B;B	0.04013	0.0;0.001	T	0.21690	-1.0238	8	0.08381	T	0.77	.	12.6857	0.56946	0.1669:0.833:0.0:0.0	.	917;917	F5H045;Q12756-2	.;.	D	917	ENSP00000438388:E917D;ENSP00000384231:E917D	ENSP00000362405:E917D	E	-	3	2	KIF1A	241345516	0.997000	0.39634	0.999000	0.59377	0.888000	0.51559	0.203000	0.17315	0.685000	0.31468	-0.372000	0.07161	GAG	.	.	none		0.682	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3	NM_138483	
MUC6	4588	hgsc.bcm.edu	37	11	1017974	1017974	+	Missense_Mutation	SNP	C	C	G	rs200353019		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:1017974C>G	ENST00000421673.2	-	31	4877	c.4827G>C	c.(4825-4827)caG>caC	p.Q1609H		NM_005961.2	NP_005952.2	Q6W4X9	MUC6_HUMAN	mucin 6, oligomeric mucus/gel-forming	1609	Approximate repeats.|Pro-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)	extracellular matrix structural constituent (GO:0005201)	p.Q1609H(2)		breast(1)|central_nervous_system(1)|cervix(2)|endometrium(8)|kidney(10)|large_intestine(6)|lung(43)|ovary(4)|prostate(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	80		all_cancers(49;3.3e-08)|all_epithelial(84;5.08e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		all cancers(45;1.24e-24)|BRCA - Breast invasive adenocarcinoma(625;0.00031)|Lung(200;0.0576)|LUSC - Lung squamous cell carcinoma(625;0.0703)		GAAGTGTGGTCTGAGGGTGTG	0.547																																					p.Q1609H		Atlas-SNP	.											MUC6_ENST00000421673,colon,carcinoma,0,2	MUC6	408	2	2	Substitution - Missense(2)	large_intestine(2)	c.G4827C						scavenged	.						473.0	441.0	452.0					11																	1017974		2186	4282	6468	SO:0001583	missense	4588	exon31			TGTGGTCTGAGGG	U97698, AY312160	CCDS44513.1	11p15.5	2008-02-05	2006-03-14		ENSG00000184956	ENSG00000184956		"""Mucins"""	7517	protein-coding gene	gene with protein product		158374	"""mucin 6, gastric"""			7680650	Standard	NM_005961		Approved		uc001lsw.2	Q6W4X9	OTTHUMG00000165140	ENST00000421673.2:c.4827G>C	11.37:g.1017974C>G	ENSP00000406861:p.Gln1609His	Somatic	553	13	0.0235081		WXS	Illumina HiSeq	Phase_I	586	12	0.0204778	NM_005961	O15329|Q14394|Q2TUQ5|Q4L207|Q8N8I1|Q8NAK1	Missense_Mutation	SNP	ENST00000421673.2	37	CCDS44513.1	.	.	.	.	.	.	.	.	.	.	C	5.277	0.236564	0.10023	.	.	ENSG00000184956	ENST00000421673	T	0.35421	1.31	2.39	0.333	0.15943	.	.	.	.	.	T	0.26702	0.0653	L	0.52011	1.625	0.09310	N	1	B	0.25486	0.127	B	0.27715	0.082	T	0.28681	-1.0036	9	0.22109	T	0.4	.	3.4702	0.07565	0.0:0.5042:0.2173:0.2785	.	1609	Q6W4X9	MUC6_HUMAN	H	1609	ENSP00000406861:Q1609H	ENSP00000406861:Q1609H	Q	-	3	2	MUC6	1007974	0.000000	0.05858	0.003000	0.11579	0.027000	0.11550	-2.394000	0.01054	-0.057000	0.13199	-0.710000	0.03640	CAG	.	.	weak		0.547	MUC6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382120.2	XM_290540	
HLA-DRB5	3127	hgsc.bcm.edu	37	6	32497975	32497975	+	Silent	SNP	A	A	G	rs114195860	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:32497975A>G	ENST00000374975.3	-	1	89	c.27T>C	c.(25-27)ggT>ggC	p.G9G		NM_002125.3	NP_002116.2			major histocompatibility complex, class II, DR beta 5											NS(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(3)|pancreas(1)|prostate(1)|stomach(2)	10						CCATGTAGGAACCTCCAGGGA	0.582																																					p.G9G		Atlas-SNP	.											HLA-DRB5,NS,carcinoma,0,1	HLA-DRB5	31	1	0			c.T27C						scavenged	.						58.0	65.0	63.0					6																	32497975		2198	4282	6480	SO:0001819	synonymous_variant	3127	exon1			GTAGGAACCTCCA		CCDS4751.1	6p21.3	2013-01-11			ENSG00000198502	ENSG00000198502		"""Histocompatibility complex"", ""Immunoglobulin superfamily / C1-set domain containing"""	4953	protein-coding gene	gene with protein product		604776					Standard	NM_002125		Approved		uc003obj.3	Q30154	OTTHUMG00000031027	ENST00000374975.3:c.27T>C	6.37:g.32497975A>G		Somatic	37	36	0.972973		WXS	Illumina HiSeq	Phase_I	67	65	0.970149	NM_002125		Silent	SNP	ENST00000374975.3	37	CCDS4751.1																																																																																			A|0.546;G|0.454	0.454	strong		0.582	HLA-DRB5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076022.2	NM_002125	
CCDC130	81576	hgsc.bcm.edu	37	19	13873535	13873535	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:13873535G>A	ENST00000586600.1	+	11	1347	c.844G>A	c.(844-846)Gcg>Acg	p.A282T	CCDC130_ENST00000587019.1_3'UTR|MRI1_ENST00000040663.6_5'Flank|CCDC130_ENST00000221554.8_Missense_Mutation_p.A282T|MRI1_ENST00000319545.8_5'Flank			P13994	CC130_HUMAN	coiled-coil domain containing 130	282					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)			CCGCAGAACCGCGCTTGCCAC	0.697																																					p.A282T		Atlas-SNP	.											CCDC130,NS,carcinoma,-1,1	CCDC130	25	1	0			c.G844A						PASS	.						21.0	21.0	21.0					19																	13873535		2202	4300	6502	SO:0001583	missense	81576	exon10			AGAACCGCGCTTG	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.844G>A	19.37:g.13873535G>A	ENSP00000465776:p.Ala282Thr	Somatic	36	0	0		WXS	Illumina HiSeq	Phase_I	38	14	0.368421	NM_030818	Q9BQ72	Missense_Mutation	SNP	ENST00000586600.1	37	CCDS12296.1	.	.	.	.	.	.	.	.	.	.	G	12.72	2.023846	0.35701	.	.	ENSG00000104957	ENST00000221554	T	0.31510	1.49	5.23	-3.93	0.04143	.	0.706623	0.13770	N	0.363927	T	0.14743	0.0356	L	0.31926	0.97	0.09310	N	1	B;B	0.15141	0.012;0.012	B;B	0.09377	0.004;0.004	T	0.18967	-1.0320	10	0.24483	T	0.36	-24.402	2.0876	0.03650	0.4101:0.1249:0.3384:0.1265	.	282;282	B3KUZ1;P13994	.;CC130_HUMAN	T	282	ENSP00000221554:A282T	ENSP00000221554:A282T	A	+	1	0	CCDC130	13734535	0.000000	0.05858	0.000000	0.03702	0.015000	0.08874	-0.701000	0.05075	-0.174000	0.10743	0.561000	0.74099	GCG	.	.	none		0.697	CCDC130-001	KNOWN	alternative_5_UTR|upstream_uORF|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453216.2	NM_030818	
UBR5	51366	hgsc.bcm.edu	37	8	103269903	103269903	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr8:103269903C>T	ENST00000520539.1	-	58	8750	c.8144G>A	c.(8143-8145)tGg>tAg	p.W2715*	KB-431C1.5_ENST00000606361.1_RNA|UBR5_ENST00000518205.1_Nonsense_Mutation_p.W443*|UBR5_ENST00000220959.4_Nonsense_Mutation_p.W2714*|UBR5_ENST00000521922.1_Nonsense_Mutation_p.W2708*	NM_001282873.1|NM_015902.5	NP_001269802.1|NP_056986.2	O95071	UBR5_HUMAN	ubiquitin protein ligase E3 component n-recognin 5	2715	HECT. {ECO:0000255|PROSITE- ProRule:PRU00104}.				cell proliferation (GO:0008283)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|negative regulation of double-strand break repair (GO:2000780)|negative regulation of histone H2A K63-linked ubiquitination (GO:1901315)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of protein import into nucleus, translocation (GO:0033160)|progesterone receptor signaling pathway (GO:0050847)|protein polyubiquitination (GO:0000209)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	ligase activity (GO:0016874)|RNA binding (GO:0003723)|ubiquitin-protein transferase activity (GO:0004842)|ubiquitin-ubiquitin ligase activity (GO:0034450)|zinc ion binding (GO:0008270)			NS(1)|breast(13)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(8)|large_intestine(19)|liver(1)|lung(51)|ovary(6)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(2)|urinary_tract(2)	124	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;0.000442)			TACTATTGACCAGAACCAACG	0.323																																					p.W2715X	Ovarian(131;96 1741 5634 7352 27489)	Atlas-SNP	.											.	UBR5	285	.	0			c.G8144A						PASS	.						89.0	84.0	85.0					8																	103269903		2202	4300	6502	SO:0001587	stop_gained	51366	exon58			ATTGACCAGAACC	AF006010	CCDS34933.1, CCDS64946.1	8q22	2008-06-23	2007-06-19	2007-06-19	ENSG00000104517	ENSG00000104517		"""Ubiquitin protein ligase E3 component n-recognins"""	16806	protein-coding gene	gene with protein product		608413	"""E3 ubiquitin protein ligase, HECT domain containing, 1"""	EDD1		10030672, 16055722	Standard	NM_015902		Approved	DD5, HYD, EDD, KIAA0896	uc003ykr.2	O95071	OTTHUMG00000164755	ENST00000520539.1:c.8144G>A	8.37:g.103269903C>T	ENSP00000429084:p.Trp2715*	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	76	40	0.526316	NM_015902	B2RP24|J3KMW7|O94970|Q9NPL3	Nonsense_Mutation	SNP	ENST00000520539.1	37	CCDS34933.1	.	.	.	.	.	.	.	.	.	.	C	53	20.275754	0.99929	.	.	ENSG00000104517	ENST00000520539;ENST00000220959;ENST00000518205;ENST00000521922	.	.	.	5.47	5.47	0.80525	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	19.3216	0.94243	0.0:1.0:0.0:0.0	.	.	.	.	X	2715;2714;443;2708	.	ENSP00000220959:W2714X	W	-	2	0	UBR5	103339079	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.487000	0.81328	2.578000	0.87016	0.585000	0.79938	TGG	.	.	none		0.323	UBR5-001	KNOWN	NAGNAG_splice_site|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000380075.2	NM_015902	
POTEC	388468	hgsc.bcm.edu	37	18	14513764	14513764	+	Missense_Mutation	SNP	C	C	T	rs201788045		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr18:14513764C>T	ENST00000358970.5	-	10	1429	c.1430G>A	c.(1429-1431)cGg>cAg	p.R477Q		NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	477								p.R477Q(12)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						AAGTTGTTTCCGGGTATCATT	0.358																																					p.R477Q		Atlas-SNP	.											POTEC,NS,carcinoma,0,17	POTEC	129	17	12	Substitution - Missense(12)	endometrium(4)|kidney(3)|urinary_tract(2)|prostate(2)|soft_tissue(1)	c.G1430A						scavenged	.						13.0	9.0	10.0					18																	14513764		683	1543	2226	SO:0001583	missense	388468	exon10			TGTTTCCGGGTAT	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.1430G>A	18.37:g.14513764C>T	ENSP00000351856:p.Arg477Gln	Somatic	332	3	0.00903614		WXS	Illumina HiSeq	Phase_I	427	10	0.0234192	NM_001137671		Missense_Mutation	SNP	ENST00000358970.5	37	CCDS45835.1	492	0.22527472527472528	61	0.12398373983739837	82	0.2265193370165746	187	0.3269230769230769	162	0.21372031662269128	c	0.001	-3.539655	0.00009	.	.	ENSG00000183206	ENST00000358970	T	0.20881	2.04	1.34	0.0657	0.14358	.	.	.	.	.	T	0.00012	0.0000	N	0.00116	-2.08	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.42430	-0.9452	9	0.06757	T	0.87	.	3.4153	0.07373	0.0:0.2473:0.0:0.7527	.	477	B2RU33	POTEC_HUMAN	Q	477	ENSP00000351856:R477Q	ENSP00000351856:R477Q	R	-	2	0	POTEC	14503764	0.885000	0.30320	0.063000	0.19743	0.005000	0.04900	1.581000	0.36558	0.005000	0.14708	-1.615000	0.00797	CGG	.	.	weak		0.358	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
FOXP4	116113	hgsc.bcm.edu	37	6	41557528	41557528	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:41557528G>A	ENST00000307972.4	+	9	1097	c.1085G>A	c.(1084-1086)cGg>cAg	p.R362Q	FOXP4_ENST00000373057.3_Missense_Mutation_p.R360Q|FOXP4_ENST00000409208.1_Missense_Mutation_p.R362Q|FOXP4_ENST00000373060.1_Missense_Mutation_p.R362Q|FOXP4_ENST00000373063.3_Missense_Mutation_p.R361Q			Q8IVH2	FOXP4_HUMAN	forkhead box P4	362	Leucine-zipper.				embryonic foregut morphogenesis (GO:0048617)|heart development (GO:0007507)|lung secretory cell differentiation (GO:0061140)|negative regulation of lung goblet cell differentiation (GO:1901250)	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)			autonomic_ganglia(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|upper_aerodigestive_tract(1)	16	Ovarian(28;0.0327)|Colorectal(47;0.196)					GAGAGCGAGCGGCTGCAGGCC	0.692											OREG0004066	type=REGULATORY REGION|Gene=FOXP4|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																									p.R362Q		Atlas-SNP	.											.	FOXP4	83	.	0			c.G1085A						PASS	.						34.0	37.0	36.0					6																	41557528		2202	4298	6500	SO:0001583	missense	116113	exon10			GCGAGCGGCTGCA	AB080747	CCDS4856.1, CCDS34447.1, CCDS34448.1	6p21.1	2008-02-05			ENSG00000137166	ENSG00000137166		"""Forkhead boxes"""	20842	protein-coding gene	gene with protein product		608924					Standard	XM_006714991		Approved	FLJ40908	uc003oql.3	Q8IVH2	OTTHUMG00000014679	ENST00000307972.4:c.1085G>A	6.37:g.41557528G>A	ENSP00000309823:p.Arg362Gln	Somatic	70	0	0	902	WXS	Illumina HiSeq	Phase_I	107	35	0.327103	NM_001012426	Q5W098|Q7Z7F8|Q8IW55|Q96E19	Missense_Mutation	SNP	ENST00000307972.4	37	CCDS34447.1	.	.	.	.	.	.	.	.	.	.	G	25.2	4.615982	0.87359	.	.	ENSG00000137166	ENST00000373060;ENST00000373063;ENST00000409208;ENST00000373057;ENST00000307972	T;T;T;T;T	0.19806	2.12;2.12;2.12;2.12;2.12	4.5	4.5	0.54988	.	0.000000	0.64402	D	0.000001	T	0.32734	0.0839	M	0.74258	2.255	0.80722	D	1	D;D;D	0.67145	0.996;0.993;0.987	P;P;P	0.56563	0.801;0.801;0.701	T	0.32052	-0.9921	10	0.87932	D	0	.	17.2142	0.86938	0.0:0.0:1.0:0.0	.	361;360;362	Q8IW55;Q7Z7F8;Q8IVH2	.;.;FOXP4_HUMAN	Q	362;361;362;360;362	ENSP00000362151:R362Q;ENSP00000362154:R361Q;ENSP00000386958:R362Q;ENSP00000362148:R360Q;ENSP00000309823:R362Q	ENSP00000309823:R362Q	R	+	2	0	FOXP4	41665506	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	4.688000	0.61715	2.072000	0.62099	0.305000	0.20034	CGG	.	.	none		0.692	FOXP4-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000106767.1	NM_138457	
BPNT1	10380	hgsc.bcm.edu	37	1	220232323	220232323	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:220232323C>A	ENST00000469520.2	-	10	1239	c.790G>T	c.(790-792)Gat>Tat	p.D264Y	BPNT1_ENST00000354807.3_Missense_Mutation_p.D279Y|BPNT1_ENST00000322067.7_Missense_Mutation_p.D264Y|BPNT1_ENST00000544404.1_Missense_Mutation_p.D209Y|BPNT1_ENST00000414869.2_Missense_Mutation_p.D228Y			O95861	BPNT1_HUMAN	3'(2'), 5'-bisphosphate nucleotidase 1	264					3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|dephosphorylation (GO:0016311)|nervous system development (GO:0007399)|nucleobase-containing compound metabolic process (GO:0006139)|phosphatidylinositol phosphorylation (GO:0046854)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	3'(2'),5'-bisphosphate nucleotidase activity (GO:0008441)|inositol-1,4-bisphosphate 1-phosphatase activity (GO:0004441)|magnesium ion binding (GO:0000287)	p.D264N(1)		breast(1)|endometrium(1)|large_intestine(1)|lung(9)|ovary(1)|skin(1)	14				GBM - Glioblastoma multiforme(131;0.0558)		CCATGGATATCGGTTAACTTG	0.393																																					p.D264Y		Atlas-SNP	.											BPNT1,colon,carcinoma,0,1	BPNT1	29	1	1	Substitution - Missense(1)	large_intestine(1)	c.G790T						scavenged	.						136.0	125.0	129.0					1																	220232323		1907	4140	6047	SO:0001583	missense	10380	exon9			GGATATCGGTTAA	AF125042	CCDS41469.1, CCDS65787.1, CCDS65788.1	1q42	2008-02-05			ENSG00000162813	ENSG00000162813	3.1.3.7		1096	protein-coding gene	gene with protein product		604053				10224133	Standard	XM_005272998		Approved		uc001hma.3	O95861	OTTHUMG00000037435	ENST00000469520.2:c.790G>T	1.37:g.220232323C>A	ENSP00000446828:p.Asp264Tyr	Somatic	58	0	0		WXS	Illumina HiSeq	Phase_I	147	3	0.0204082	NM_006085	A8K7C8|B4DPS5|B4DUS9|D3DTA9|Q8WVL5|Q9UGJ3	Missense_Mutation	SNP	ENST00000469520.2	37	CCDS41469.1	.	.	.	.	.	.	.	.	.	.	C	25.1	4.600002	0.87055	.	.	ENSG00000162813	ENST00000322067;ENST00000469520;ENST00000354807;ENST00000302686;ENST00000544404;ENST00000414869	T;T;T;T;T	0.60672	0.17;0.17;0.17;0.17;0.17	5.28	5.28	0.74379	.	0.094465	0.64402	D	0.000001	D	0.84474	0.5480	H	0.95884	3.735	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	0.89300	0.3625	10	0.87932	D	0	.	19.28	0.94050	0.0:1.0:0.0:0.0	.	228;279;264	B4DUS9;A6NF51;O95861	.;.;BPNT1_HUMAN	Y	264;264;279;264;209;228	ENSP00000318852:D264Y;ENSP00000446828:D264Y;ENSP00000346862:D279Y;ENSP00000444398:D209Y;ENSP00000410348:D228Y	ENSP00000307087:D264Y	D	-	1	0	BPNT1	218298946	1.000000	0.71417	0.937000	0.37676	0.924000	0.55760	7.682000	0.84083	2.643000	0.89663	0.555000	0.69702	GAT	.	.	none		0.393	BPNT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091137.2	NM_006085	
HYDIN	54768	hgsc.bcm.edu	37	16	71025245	71025245	+	Silent	SNP	C	C	T	rs1774516	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:71025245C>T	ENST00000393567.2	-	25	3990	c.3840G>A	c.(3838-3840)acG>acA	p.T1280T		NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	1280					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)				TGGAAGCTTTCGTTTTTCTTA	0.463																																					p.T1280T		Atlas-SNP	.											LOC652153,NS,carcinoma,-1,2	HYDIN	788	2	0			c.G3840A						scavenged	.						130.0	119.0	122.0					16																	71025245		1909	4145	6054	SO:0001819	synonymous_variant	54768	exon25			AGCTTTCGTTTTT	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.3840G>A	16.37:g.71025245C>T		Somatic	147	17	0.115646		WXS	Illumina HiSeq	Phase_I	96	28	0.291667	NM_001270974	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Silent	SNP	ENST00000393567.2	37	CCDS59269.1																																																																																			C|0.977;T|0.023	0.023	strong		0.463	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3		
HORMAD1	84072	hgsc.bcm.edu	37	1	150680879	150680879	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:150680879T>C	ENST00000361824.2	-	9	505	c.400A>G	c.(400-402)Aac>Gac	p.N134D	HORMAD1_ENST00000322343.7_Missense_Mutation_p.N127D|HORMAD1_ENST00000368995.4_Missense_Mutation_p.N54D|HORMAD1_ENST00000368993.2_Missense_Mutation_p.N134D	NM_032132.4	NP_115508.2	Q86X24	HORM1_HUMAN	HORMA domain containing 1	134	HORMA. {ECO:0000255|PROSITE- ProRule:PRU00109}.				blastocyst development (GO:0001824)|meiotic DNA double-strand break formation (GO:0042138)|meiotic nuclear division (GO:0007126)|meiotic recombination checkpoint (GO:0051598)|meiotic sister chromatid cohesion (GO:0051177)|oogenesis (GO:0048477)|regulation of homologous chromosome segregation (GO:0060629)|spermatogenesis (GO:0007283)|synaptonemal complex assembly (GO:0007130)	chromosome (GO:0005694)|condensed nuclear chromosome (GO:0000794)|nucleus (GO:0005634)				breast(1)|central_nervous_system(2)|cervix(1)|endometrium(2)|large_intestine(3)|lung(4)|ovary(3)	16	all_cancers(9;3.23e-52)|all_epithelial(9;4.68e-43)|all_lung(15;5.74e-35)|Lung NSC(24;2.09e-31)|Breast(34;0.0009)|Lung SC(34;0.00471)|Ovarian(49;0.0167)|all_hematologic(923;0.0395)|Hepatocellular(266;0.108)|Melanoma(130;0.128)|Colorectal(459;0.171)		UCEC - Uterine corpus endometrioid carcinoma (35;0.0241)|Epithelial(6;2.32e-23)|all cancers(9;5.21e-23)|OV - Ovarian serous cystadenocarcinoma(6;6.72e-15)|BRCA - Breast invasive adenocarcinoma(12;0.000479)|LUSC - Lung squamous cell carcinoma(543;0.171)			TTGCTTTGGTTTTTACTAGAA	0.308																																					p.N134D		Atlas-SNP	.											HORMAD1,colon,carcinoma,+1,5	HORMAD1	59	5	0			c.A400G						scavenged	.						85.0	80.0	82.0					1																	150680879		2203	4300	6503	SO:0001583	missense	84072	exon9			TTTGGTTTTTACT	AL136755	CCDS967.1, CCDS55633.1	1q21.2	2009-03-09			ENSG00000143452	ENSG00000143452			25245	protein-coding gene	gene with protein product	"""cancer/testis antigen 46"""	609824				11230166, 15999985	Standard	NM_032132		Approved	DKFZP434A1315, CT46	uc001evk.2	Q86X24	OTTHUMG00000035005	ENST00000361824.2:c.400A>G	1.37:g.150680879T>C	ENSP00000355167:p.Asn134Asp	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	158	2	0.0126582	NM_032132	A6NMK2|B3KUK1|Q4G114|Q5T5I3|Q5T5I4|Q5T5I5|Q6FIC1|Q9H0K8	Missense_Mutation	SNP	ENST00000361824.2	37	CCDS967.1	.	.	.	.	.	.	.	.	.	.	T	16.71	3.197900	0.58126	.	.	ENSG00000143452	ENST00000368995;ENST00000368993;ENST00000368992;ENST00000540570;ENST00000322343;ENST00000361824;ENST00000368987;ENST00000442853	T;T;T;T	0.48836	0.8;1.3;1.37;1.3	5.75	4.64	0.57946	DNA-binding HORMA (4);	0.133205	0.64402	D	0.000002	T	0.26593	0.0650	L	0.41573	1.285	0.44995	D	0.998016	B;B;B	0.30870	0.298;0.193;0.287	B;B;B	0.39152	0.062;0.076;0.292	T	0.09250	-1.0683	10	0.22109	T	0.4	-15.5299	10.1818	0.42972	0.0:0.0782:0.0:0.9218	.	54;127;134	Q86X24-4;Q86X24-2;Q86X24	.;.;HORM1_HUMAN	D	54;134;63;54;127;134;63;56	ENSP00000357991:N54D;ENSP00000357989:N134D;ENSP00000326489:N127D;ENSP00000355167:N134D	ENSP00000326489:N127D	N	-	1	0	HORMAD1	148947503	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	4.143000	0.58051	2.195000	0.70347	0.533000	0.62120	AAC	.	.	none		0.308	HORMAD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000084722.1	NM_032132	
CD109	135228	hgsc.bcm.edu	37	6	74524771	74524771	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:74524771A>G	ENST00000287097.5	+	30	3948	c.3836A>G	c.(3835-3837)gAa>gGa	p.E1279G	CD109_ENST00000422508.2_Missense_Mutation_p.E1202G|CD109_ENST00000437994.2_Missense_Mutation_p.E1262G			Q6YHK3	CD109_HUMAN	CD109 molecule	1279					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						CAAAATCAAGAAGCCTTTGAT	0.333																																					p.E1279G		Atlas-SNP	.											CD109,colon,carcinoma,+1,1	CD109	170	1	0			c.A3836G						scavenged	.						104.0	103.0	103.0					6																	74524771		2203	4299	6502	SO:0001583	missense	135228	exon30			ATCAAGAAGCCTT	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.3836A>G	6.37:g.74524771A>G	ENSP00000287097:p.Glu1279Gly	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	72	2	0.0277778	NM_133493	A5YKK4|B2R948|B3KW25|Q0P6K7|Q5SYA8|Q5XUM7|Q5XUM9|Q6MZI7|Q8N3A7|Q8N915|Q8TDJ2|Q8TDJ3	Missense_Mutation	SNP	ENST00000287097.5	37	CCDS4982.1	.	.	.	.	.	.	.	.	.	.	A	13.35	2.209498	0.39003	.	.	ENSG00000156535	ENST00000437994;ENST00000422508;ENST00000287097	T;T;T	0.30714	1.52;1.52;1.52	5.45	5.45	0.79879	Alpha-macroglobulin, receptor-binding (2);	0.101090	0.64402	D	0.000002	T	0.26195	0.0639	L	0.59436	1.845	0.42587	D	0.99323	P;B;B	0.37864	0.61;0.016;0.005	B;B;B	0.42138	0.377;0.028;0.013	T	0.05550	-1.0878	10	0.52906	T	0.07	.	15.6734	0.77295	1.0:0.0:0.0:0.0	.	1202;1262;1279	Q6YHK3-2;Q6YHK3-4;Q6YHK3	.;.;CD109_HUMAN	G	1262;1202;1279	ENSP00000388062:E1262G;ENSP00000404475:E1202G;ENSP00000287097:E1279G	ENSP00000287097:E1279G	E	+	2	0	CD109	74581492	1.000000	0.71417	1.000000	0.80357	0.276000	0.26787	5.217000	0.65252	2.289000	0.77006	0.477000	0.44152	GAA	.	.	none		0.333	CD109-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000041230.3	NM_133493	
C3orf79	152118	hgsc.bcm.edu	37	3	153203809	153203809	+	Silent	SNP	C	C	T	rs57748412	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:153203809C>T	ENST00000446603.2	+	2	200	c.138C>T	c.(136-138)tcC>tcT	p.S46S	RP11-23D24.2_ENST00000493214.2_RNA	NM_001101337.1	NP_001094807.1	P0CE67	CC079_HUMAN	chromosome 3 open reading frame 79	46										endometrium(1)|large_intestine(3)	4						GACAGACTTCCGGTTGTCTAA	0.358													C|||	77	0.0153754	0.0567	0.0029	5008	,	,		16257	0.0		0.0	False		,,,				2504	0.0				p.S46S		Atlas-SNP	.											.	C3orf79	13	.	0			c.C138T						PASS	.	C		144,3480		4,136,1672	37.0	34.0	35.0		138	0.8	0.0	3	dbSNP_129	35	1,8135		0,1,4067	no	coding-synonymous	C3orf79	NM_001101337.1		4,137,5739	TT,TC,CC		0.0123,3.9735,1.233		46/101	153203809	145,11615	1812	4068	5880	SO:0001819	synonymous_variant	152118	exon2			GACTTCCGGTTGT	AF086445	CCDS46937.1	3q25.2	2009-09-30			ENSG00000237787	ENSG00000237787			37259	protein-coding gene	gene with protein product							Standard	NM_001101337		Approved		uc003ezt.3	P0CE67	OTTHUMG00000159629	ENST00000446603.2:c.138C>T	3.37:g.153203809C>T		Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	95	4	0.0421053	NM_001101337		Silent	SNP	ENST00000446603.2	37	CCDS46937.1																																																																																			C|0.985;T|0.015	0.015	strong		0.358	C3orf79-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356570.1	NM_001101337	
CHAD	1101	hgsc.bcm.edu	37	17	48543124	48543124	+	Silent	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:48543124G>A	ENST00000508540.1	-	2	1034	c.882C>T	c.(880-882)acC>acT	p.T294T	ACSF2_ENST00000300441.4_Intron|CHAD_ENST00000258969.4_Silent_p.T294T|ACSF2_ENST00000504392.1_Intron|ACSF2_ENST00000502667.1_Intron|ACSF2_ENST00000541920.1_Intron|ACSF2_ENST00000427954.2_Intron	NM_001267.2	NP_001258.2	O15335	CHAD_HUMAN	chondroadherin	294					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)			TAAGGGCGAGGGTCTCCAGGC	0.572																																					p.T294T		Atlas-SNP	.											.	CHAD	36	.	0			c.C882T						PASS	.						178.0	158.0	164.0					17																	48543124		2203	4300	6503	SO:0001819	synonymous_variant	1101	exon2			GGCGAGGGTCTCC	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.882C>T	17.37:g.48543124G>A		Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	92	40	0.434783	NM_001267	A8K812|Q6GTU0|Q96RJ5	Silent	SNP	ENST00000508540.1	37	CCDS11568.1																																																																																			.	.	none		0.572	CHAD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367447.3	NM_001267	
TNFRSF14	8764	hgsc.bcm.edu	37	1	2488105	2488105	+	Start_Codon_SNP	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:2488105T>C	ENST00000355716.4	+	1	301	c.2T>C	c.(1-3)aTg>aCg	p.M1T	RP3-395M20.8_ENST00000452793.1_RNA|TNFRSF14_ENST00000442392.2_3'UTR|RP3-395M20.8_ENST00000416860.2_RNA|TNFRSF14_ENST00000409119.1_Start_Codon_SNP_p.M1T	NM_003820.2	NP_003811.2	Q92956	TNR14_HUMAN	tumor necrosis factor receptor superfamily, member 14	1					cell surface receptor signaling pathway (GO:0007166)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|immune response (GO:0006955)|negative regulation of alpha-beta T cell proliferation (GO:0046642)|positive regulation of cytokine secretion involved in immune response (GO:0002741)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of T cell migration (GO:2000406)|T cell costimulation (GO:0031295)|tumor necrosis factor-mediated signaling pathway (GO:0033209)|viral process (GO:0016032)	external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	tumor necrosis factor-activated receptor activity (GO:0005031)|ubiquitin protein ligase binding (GO:0031625)|virus receptor activity (GO:0001618)			kidney(1)	1	all_cancers(77;0.000158)|all_epithelial(69;8.01e-05)|all_lung(157;0.0212)|Lung NSC(156;0.0376)|Ovarian(185;0.0634)	all_epithelial(116;3.18e-20)|all_lung(118;1.67e-08)|Lung NSC(185;2.69e-06)|Breast(487;0.00147)|Renal(390;0.00183)|Hepatocellular(190;0.00826)|Myeloproliferative disorder(586;0.0122)|Ovarian(437;0.0308)|Lung SC(97;0.0847)|Medulloblastoma(700;0.123)		Epithelial(90;1.1e-37)|OV - Ovarian serous cystadenocarcinoma(86;6.02e-23)|GBM - Glioblastoma multiforme(42;1.11e-08)|Colorectal(212;3.94e-05)|COAD - Colon adenocarcinoma(227;0.000193)|Kidney(185;0.000326)|BRCA - Breast invasive adenocarcinoma(365;0.00435)|KIRC - Kidney renal clear cell carcinoma(229;0.00544)|STAD - Stomach adenocarcinoma(132;0.00644)|Lung(427;0.199)		GCCTGAGGCATGGAGCCTCCT	0.642			"""Mis, N, F"""		follicular lymphoma																																p.M1T		Atlas-SNP	.		Rec	yes		1	1p36.32	8764	"""tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"""		L	.	TNFRSF14	89	.	0			c.T2C						PASS	.						36.0	39.0	38.0					1																	2488105		2199	4298	6497	SO:0001582	initiator_codon_variant	8764	exon1			GAGGCATGGAGCC	U70321	CCDS44046.1	1p36.32	2012-02-27	2011-08-11		ENSG00000157873	ENSG00000157873		"""Tumor necrosis factor receptor superfamily"", ""CD molecules"""	11912	protein-coding gene	gene with protein product	"""herpesvirus entry mediator"""	602746	"""tumor necrosis factor receptor superfamily, member 14 (herpesvirus entry mediator)"""			8898196, 9162061	Standard	XM_006711018		Approved	HVEM, ATAR, TR2, LIGHTR, HVEA, CD270	uc001ajt.1	Q92956	OTTHUMG00000000792	ENST00000355716.4:c.2T>C	1.37:g.2488105T>C	ENSP00000347948:p.Met1Thr	Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	73	69	0.945205	NM_003820	B3KW30|B9DI89|Q6IB95|Q8N634|Q8WXR1|Q96J31|Q9UM65	Missense_Mutation	SNP	ENST00000355716.4	37	CCDS44046.1	.	.	.	.	.	.	.	.	.	.	t	12.71	2.019131	0.35606	.	.	ENSG00000157873	ENST00000426449;ENST00000434817;ENST00000435221;ENST00000451778;ENST00000409119;ENST00000423768;ENST00000355716	D;D;D;D;D;D	0.88896	-2.38;-2.29;-2.29;-2.29;-2.44;-2.38	2.33	1.16	0.20824	.	.	.	.	.	D	0.90954	0.7156	.	.	.	0.80722	D	1	D;B	0.54601	0.967;0.106	P;B	0.60789	0.879;0.026	D	0.87877	0.2675	8	0.87932	D	0	-26.9813	4.2458	0.10670	0.0:0.1749:0.0:0.8251	.	1;1	B4DU65;Q92956	.;TNR14_HUMAN	T	1	ENSP00000411854:M1T;ENSP00000415254:M1T;ENSP00000399292:M1T;ENSP00000399533:M1T;ENSP00000386859:M1T;ENSP00000347948:M1T	ENSP00000347948:M1T	M	+	2	0	TNFRSF14	2486313	0.000000	0.05858	0.031000	0.17742	0.095000	0.18619	-0.986000	0.03747	0.325000	0.23359	0.155000	0.16302	ATG	.	.	none		0.642	TNFRSF14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000002088.1		Missense_Mutation
PSG2	5670	hgsc.bcm.edu	37	19	43585253	43585253	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:43585253C>T	ENST00000406487.1	-	2	308	c.210G>A	c.(208-210)ggG>ggA	p.G70G	PSG2_ENST00000491995.1_5'Flank	NM_031246.3	NP_112536.2	P11465	PSG2_HUMAN	pregnancy specific beta-1-glycoprotein 2	70	Ig-like V-type.				cell migration (GO:0016477)|female pregnancy (GO:0007565)	extracellular region (GO:0005576)		p.G70G(2)		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)				CCCTGATTTGCCCTTTGTACC	0.433																																					p.G70G		Atlas-SNP	.											PSG2,NS,carcinoma,0,2	PSG2	84	2	2	Substitution - coding silent(2)	prostate(2)	c.G210A						scavenged	.						92.0	96.0	94.0					19																	43585253		2201	4285	6486	SO:0001819	synonymous_variant	5670	exon2			GATTTGCCCTTTG		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.210G>A	19.37:g.43585253C>T		Somatic	196	7	0.0357143		WXS	Illumina HiSeq	Phase_I	201	6	0.0298507	NM_031246	Q8TCD9|Q9UEA4|Q9UQ78	Silent	SNP	ENST00000406487.1	37	CCDS12616.1																																																																																			.	.	none		0.433	PSG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323083.1	NM_031246	
MTMR1	8776	hgsc.bcm.edu	37	X	149896262	149896262	+	Splice_Site	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:149896262A>G	ENST00000370390.3	+	5	687	c.530A>G	c.(529-531)aAg>aGg	p.K177R	MTMR1_ENST00000544228.1_Splice_Site_p.K177R|MTMR1_ENST00000445323.2_Splice_Site_p.K185R|MTMR1_ENST00000451863.2_Splice_Site_p.K177R|MTMR1_ENST00000542156.1_Splice_Site_p.K177R|MTMR1_ENST00000541925.1_Splice_Site_p.K83R|MTMR1_ENST00000538506.1_Splice_Site_p.K64R	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	177					phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					ATAGTGTGCAAGGTATAATAG	0.423																																					p.K177R		Atlas-SNP	.											.	MTMR1	82	.	0			c.A530G						PASS	.						89.0	81.0	84.0					X																	149896262		2203	4300	6503	SO:0001630	splice_region_variant	8776	exon5			TGTGCAAGGTATA	U58032	CCDS14695.1	Xq28	2011-06-09			ENSG00000063601	ENSG00000063601		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7449	protein-coding gene	gene with protein product		300171				9828128	Standard	XM_005274765		Approved		uc004fei.3	Q13613	OTTHUMG00000024159	ENST00000370390.3:c.531+1A>G	X.37:g.149896262A>G		Somatic	110	0	0		WXS	Illumina HiSeq	Phase_I	67	50	0.746269	NM_003828	A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Missense_Mutation	SNP	ENST00000370390.3	37	CCDS14695.1	.	.	.	.	.	.	.	.	.	.	a	24.9	4.582513	0.86748	.	.	ENSG00000063601	ENST00000541925;ENST00000493995;ENST00000439546;ENST00000429965;ENST00000434699;ENST00000542156;ENST00000370390;ENST00000445323;ENST00000544228;ENST00000451863;ENST00000538506	D;D;D;D;D;D;D;D;D;D;D	0.88277	-2.36;-2.36;-2.36;-2.36;-2.36;-2.36;-2.36;-2.36;-2.36;-2.36;-2.36	5.08	5.08	0.68730	.	0.000000	0.85682	D	0.000000	D	0.94029	0.8087	M	0.78637	2.42	0.80722	D	1	D;D;D	0.89917	1.0;0.999;1.0	D;D;D	0.97110	1.0;0.993;0.999	D	0.94719	0.7899	10	0.87932	D	0	.	14.1476	0.65360	1.0:0.0:0.0:0.0	.	177;185;177	Q13613;F8WA39;Q8NEC6	MTMR1_HUMAN;.;.	R	83;83;83;83;83;177;177;185;177;177;64	ENSP00000441879:K83R;ENSP00000431992:K83R;ENSP00000404599:K83R;ENSP00000390736:K83R;ENSP00000405946:K83R;ENSP00000445281:K177R;ENSP00000359417:K177R;ENSP00000414178:K185R;ENSP00000440534:K177R;ENSP00000387446:K177R;ENSP00000443444:K64R	ENSP00000359417:K177R	K	+	2	0	MTMR1	149646920	1.000000	0.71417	1.000000	0.80357	0.801000	0.45260	9.026000	0.93700	1.787000	0.52448	0.441000	0.28932	AAG	.	.	none		0.423	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060863.2	NM_003828, NM_176789	Missense_Mutation
POTEC	388468	hgsc.bcm.edu	37	18	14542654	14542654	+	Silent	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr18:14542654C>A	ENST00000358970.5	-	1	491	c.492G>T	c.(490-492)acG>acT	p.T164T	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	164								p.T164T(2)		NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						TGTTCATGTCCGTGTCCCTGA	0.592																																					p.T164T		Atlas-SNP	.											POTEC,NS,carcinoma,-1,5	POTEC	129	5	2	Substitution - coding silent(2)	lung(1)|kidney(1)	c.G492T						scavenged	.						260.0	241.0	247.0					18																	14542654		692	1591	2283	SO:0001819	synonymous_variant	388468	exon1			CATGTCCGTGTCC	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.492G>T	18.37:g.14542654C>A		Somatic	567	5	0.00881834		WXS	Illumina HiSeq	Phase_I	558	9	0.016129	NM_001137671		Silent	SNP	ENST00000358970.5	37	CCDS45835.1																																																																																			.	.	none		0.592	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
JMY	133746	hgsc.bcm.edu	37	5	78587039	78587039	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:78587039T>C	ENST00000396137.4	+	4	1906	c.1444T>C	c.(1444-1446)Tat>Cat	p.Y482H		NM_152405.4	NP_689618.4	Q8N9B5	JMY_HUMAN	junction mediating and regulatory protein, p53 cofactor	482	Interaction with p300/EP300. {ECO:0000250}.				'de novo' actin filament nucleation (GO:0070060)|actin polymerization-dependent cell motility (GO:0070358)|Arp2/3 complex-mediated actin nucleation (GO:0034314)|cell cycle arrest (GO:0007050)|DNA repair (GO:0006281)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|positive regulation of apoptotic process (GO:0043065)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|regulation of transcription from RNA polymerase II promoter (GO:0006357)	cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|nucleus (GO:0005634)	transcription coactivator activity (GO:0003713)			endometrium(4)|kidney(2)|large_intestine(2)|lung(6)|skin(1)|urinary_tract(1)	16		all_lung(232;0.00051)|Lung NSC(167;0.00131)|Ovarian(174;0.0261)|Prostate(461;0.191)		OV - Ovarian serous cystadenocarcinoma(54;4.45e-45)|Epithelial(54;5.85e-40)|all cancers(79;2.89e-35)		AAAACTCCAGTATGCAGTTTC	0.403																																					p.Y482H		Atlas-SNP	.											.	JMY	82	.	0			c.T1444C						PASS	.						76.0	74.0	75.0					5																	78587039		1879	4094	5973	SO:0001583	missense	133746	exon4			CTCCAGTATGCAG	AK095189	CCDS4047.3	5q14.1	2010-03-23			ENSG00000152409	ENSG00000152409			28916	protein-coding gene	gene with protein product		604279				10518217	Standard	NM_152405		Approved	FLJ37870	uc003kfx.4	Q8N9B5	OTTHUMG00000131301	ENST00000396137.4:c.1444T>C	5.37:g.78587039T>C	ENSP00000379441:p.Tyr482His	Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	65	4	0.0615385	NM_152405	A1L4P5|B5MDS2|B5MDT0	Missense_Mutation	SNP	ENST00000396137.4	37	CCDS4047.3	.	.	.	.	.	.	.	.	.	.	T	25.6	4.659897	0.88154	.	.	ENSG00000152409	ENST00000282259;ENST00000396137	T	0.11169	2.8	5.31	5.31	0.75309	.	0.000000	0.85682	D	0.000000	T	0.33000	0.0848	M	0.72894	2.215	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.04855	-1.0922	10	0.66056	D	0.02	.	15.2486	0.73526	0.0:0.0:0.0:1.0	.	482	Q8N9B5	JMY_HUMAN	H	482	ENSP00000379441:Y482H	ENSP00000282259:Y482H	Y	+	1	0	JMY	78622795	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.223000	0.78033	1.999000	0.58509	0.454000	0.30748	TAT	.	.	none		0.403	JMY-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254070.4	NM_152405	
GLB1L3	112937	hgsc.bcm.edu	37	11	134188798	134188798	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:134188798G>A	ENST00000431683.2	+	20	1924	c.1924G>A	c.(1924-1926)Ggc>Agc	p.G642S		NM_001080407.2	NP_001073876.2	Q8NCI6	GLBL3_HUMAN	galactosidase, beta 1-like 3	642					carbohydrate metabolic process (GO:0005975)		beta-galactosidase activity (GO:0004565)			endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|pancreas(1)	13	all_hematologic(175;0.127)	all_cancers(12;5.52e-23)|all_epithelial(12;2.15e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000162)|all_neural(223;0.0182)|Medulloblastoma(222;0.0208)|Esophageal squamous(93;0.0559)		Epithelial(10;1.3e-11)|all cancers(11;2.07e-10)|BRCA - Breast invasive adenocarcinoma(10;3.09e-10)|OV - Ovarian serous cystadenocarcinoma(99;0.000873)|Lung(977;0.222)		GATGATGAGTGGCTCAGATAT	0.413																																					p.G642S		Atlas-SNP	.											.	GLB1L3	102	.	0			c.G1924A						PASS	.						116.0	106.0	109.0					11																	134188798		1871	4118	5989	SO:0001583	missense	112937	exon20			ATGAGTGGCTCAG		CCDS44780.1	11q25	2008-11-06	2008-01-29		ENSG00000166105	ENSG00000166105			25147	protein-coding gene	gene with protein product						12477932	Standard	NM_001080407		Approved	FLJ90231	uc009zdf.3	Q8NCI6	OTTHUMG00000133524	ENST00000431683.2:c.1924G>A	11.37:g.134188798G>A	ENSP00000396615:p.Gly642Ser	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	80	30	0.375	NM_001080407	A6NEM0|A6NN15|Q6P3S3|Q96FF8	Missense_Mutation	SNP	ENST00000431683.2	37	CCDS44780.1	.	.	.	.	.	.	.	.	.	.	G	18.24	3.579506	0.65878	.	.	ENSG00000166105	ENST00000431683	D	0.95588	-3.75	5.14	5.14	0.70334	Galactose-binding domain-like (1);	0.237649	0.44097	D	0.000491	D	0.88952	0.6577	N	0.11845	0.185	0.19575	N	0.999964	P	0.37824	0.609	B	0.34590	0.186	T	0.81874	-0.0732	10	0.30854	T	0.27	.	14.3466	0.66668	0.0:0.0:1.0:0.0	.	642	Q8NCI6	GLBL3_HUMAN	S	642	ENSP00000396615:G642S	ENSP00000396615:G642S	G	+	1	0	GLB1L3	133694008	0.566000	0.26618	0.093000	0.20910	0.010000	0.07245	2.785000	0.47782	2.844000	0.97970	0.650000	0.86243	GGC	.	.	none		0.413	GLB1L3-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393625.1	NM_138416	
XIRP1	165904	hgsc.bcm.edu	37	3	39228103	39228103	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:39228103C>A	ENST00000340369.3	-	2	3062	c.2834G>T	c.(2833-2835)cGg>cTg	p.R945L	XIRP1_ENST00000421646.1_Intron|XIRP1_ENST00000396251.1_Missense_Mutation_p.R945L	NM_194293.2	NP_919269.2	Q702N8	XIRP1_HUMAN	xin actin-binding repeat containing 1	945					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)	p.R945Q(1)		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)		GGGCTCCCACCGCAGACTGTG	0.647																																					p.R945L		Atlas-SNP	.											XIRP1,NS,carcinoma,0,2	XIRP1	173	2	1	Substitution - Missense(1)	endometrium(1)	c.G2834T						scavenged	.						31.0	34.0	33.0					3																	39228103		2203	4300	6503	SO:0001583	missense	165904	exon2			TCCCACCGCAGAC	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.2834G>T	3.37:g.39228103C>A	ENSP00000343140:p.Arg945Leu	Somatic	71	0	0		WXS	Illumina HiSeq	Phase_I	92	2	0.0217391	NM_001198621	A0JP25|A4QPE2|Q68DF2|Q6ZTR3|Q702N9|Q8IVN7|Q8N1N3|Q8N904|Q8TCG7	Missense_Mutation	SNP	ENST00000340369.3	37	CCDS2683.1	.	.	.	.	.	.	.	.	.	.	C	15.81	2.942450	0.53079	.	.	ENSG00000168334	ENST00000396251;ENST00000340369	T;T	0.05925	3.37;3.72	5.03	3.2	0.36748	.	0.559978	0.18073	N	0.152553	T	0.08626	0.0214	L	0.41236	1.265	0.80722	D	1	P;P	0.50272	0.933;0.891	P;B	0.48368	0.575;0.338	T	0.13072	-1.0523	10	0.72032	D	0.01	.	8.1912	0.31370	0.0:0.8027:0.0:0.1973	.	945;945	Q702N8;Q702N8-2	XIRP1_HUMAN;.	L	945	ENSP00000379550:R945L;ENSP00000343140:R945L	ENSP00000343140:R945L	R	-	2	0	XIRP1	39203107	0.911000	0.30947	0.993000	0.49108	0.970000	0.65996	1.250000	0.32850	1.278000	0.44430	0.655000	0.94253	CGG	.	.	none		0.647	XIRP1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000254065.1	XM_093522	
PAK2	5062	hgsc.bcm.edu	37	3	196530022	196530022	+	Silent	SNP	C	C	T	rs115224945	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:196530022C>T	ENST00000327134.3	+	4	745	c.423C>T	c.(421-423)agC>agT	p.S141S		NM_002577.4	NP_002568.2	Q13177	PAK2_HUMAN	p21 protein (Cdc42/Rac)-activated kinase 2	141					apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cysteine-type endopeptidase activity involved in execution phase of apoptosis (GO:2001271)|negative regulation of protein kinase activity (GO:0006469)|peptidyl-serine phosphorylation (GO:0018105)|phosphorylation (GO:0016310)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein tyrosine kinase activity (GO:0061098)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of apoptotic process (GO:0042981)|regulation of defense response to virus by virus (GO:0050690)|regulation of growth (GO:0040008)|signal transduction (GO:0007165)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|identical protein binding (GO:0042802)|protein kinase activity (GO:0004672)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activator activity (GO:0030296)			breast(1)|cervix(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(2)	12	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)|Breast(254;0.135)		Epithelial(36;1.07e-23)|all cancers(36;6.38e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.5e-18)|LUSC - Lung squamous cell carcinoma(58;1.51e-06)|Lung(62;1.95e-06)	GBM - Glioblastoma multiforme(46;0.00405)		AATATCTGAGCTTTACTCCTC	0.418																																					p.S141S		Atlas-SNP	.											PAK2_ENST00000327134,rectum,carcinoma,0,2	PAK2	113	2	0			c.C423T						scavenged	.						85.0	79.0	81.0					3																	196530022		2203	4300	6503	SO:0001819	synonymous_variant	5062	exon4			TCTGAGCTTTACT	U24153	CCDS3321.1	3q29	2008-06-17	2008-06-17			ENSG00000180370	2.7.11.1		8591	protein-coding gene	gene with protein product	"""S6/H4 kinase"""	605022	"""p21 (CDKN1A)-activated kinase 2"""			7744004, 7618083	Standard	NM_002577		Approved	PAK65, PAKgamma	uc003fwy.4	Q13177		ENST00000327134.3:c.423C>T	3.37:g.196530022C>T		Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	68	3	0.0441176	NM_002577	Q13154|Q6ISC3	Silent	SNP	ENST00000327134.3	37	CCDS3321.1																																																																																			C|0.986;T|0.015	0.015	strong		0.418	PAK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340548.1	NM_002577	
ZP3	7784	hgsc.bcm.edu	37	7	76058885	76058885	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:76058885C>T	ENST00000394857.3	+	2	424	c.366C>T	c.(364-366)ccC>ccT	p.P122P	ZP3_ENST00000336517.4_Silent_p.P71P|ZP3_ENST00000416245.1_5'UTR	NM_001110354.1	NP_001103824.1	P21754	ZP3_HUMAN	zona pellucida glycoprotein 3 (sperm receptor)	122	ZP. {ECO:0000255|PROSITE- ProRule:PRU00375}.				binding of sperm to zona pellucida (GO:0007339)|blastocyst formation (GO:0001825)|calcium ion transmembrane transport (GO:0070588)|egg coat formation (GO:0035803)|humoral immune response mediated by circulating immunoglobulin (GO:0002455)|intracellular protein transport (GO:0006886)|intracellular signal transduction (GO:0035556)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|multicellular organism reproduction (GO:0032504)|negative regulation of binding of sperm to zona pellucida (GO:2000360)|negative regulation of transcription, DNA-templated (GO:0045892)|oocyte development (GO:0048599)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of acrosomal vesicle exocytosis (GO:2000368)|positive regulation of acrosome reaction (GO:2000344)|positive regulation of antral ovarian follicle growth (GO:2000388)|positive regulation of calcium ion import (GO:0090280)|positive regulation of humoral immune response (GO:0002922)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interferon-gamma production (GO:0032729)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of leukocyte migration (GO:0002687)|positive regulation of ovarian follicle development (GO:2000386)|positive regulation of phosphatidylinositol biosynthetic process (GO:0010513)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of T cell proliferation (GO:0042102)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type IV hypersensitivity (GO:0001809)|protein kinase C signaling (GO:0070528)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|multivesicular body (GO:0005771)|outer acrosomal membrane (GO:0002081)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)|secretory granule (GO:0030141)	acrosin binding (GO:0032190)|carbohydrate binding (GO:0030246)|manganese ion transmembrane transporter activity (GO:0005384)|signal transducer activity (GO:0004871)|store-operated calcium channel activity (GO:0015279)			endometrium(1)|large_intestine(3)|lung(2)|skin(1)	7						ACCCCCGCCCCGTGGGAAACC	0.612																																					p.P122P		Atlas-SNP	.											.	ZP3	32	.	0			c.C366T						PASS	.						112.0	83.0	93.0					7																	76058885		2203	4300	6503	SO:0001819	synonymous_variant	7784	exon2			CCGCCCCGTGGGA	M60504	CCDS5586.1, CCDS47618.1	7q11.23	2014-07-04	2002-09-17	2002-09-20	ENSG00000188372	ENSG00000188372		"""Zona pellucida glycoproteins"""	13189	protein-coding gene	gene with protein product		182889	"""zona pellucida glycoprotein 3A (sperm receptor)"""	ZP3A, ZP3B		1478648	Standard	NM_007155		Approved	ZP3-424, ZP3-372, ZPC	uc003ufd.4	P21754	OTTHUMG00000130575	ENST00000394857.3:c.366C>T	7.37:g.76058885C>T		Somatic	136	0	0		WXS	Illumina HiSeq	Phase_I	127	54	0.425197	NM_001110354	Q06633|Q29RW0	Silent	SNP	ENST00000394857.3	37	CCDS47618.1																																																																																			.	.	none		0.612	ZP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253004.1		
SND1	27044	hgsc.bcm.edu	37	7	127447592	127447592	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:127447592C>T	ENST00000354725.3	+	11	1401	c.1207C>T	c.(1207-1209)Cgg>Tgg	p.R403W		NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	403	TNase-like 3. {ECO:0000255|PROSITE- ProRule:PRU00272}.				gene silencing by RNA (GO:0031047)|osteoblast differentiation (GO:0001649)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dense body (GO:0097433)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|RISC complex (GO:0016442)	nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|transcription cofactor activity (GO:0003712)			central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						GTTTGAGGCCCGGGAATTTCT	0.368																																					p.R403W		Atlas-SNP	.											.	SND1	104	.	0			c.C1207T						PASS	.						138.0	136.0	137.0					7																	127447592		2203	4300	6503	SO:0001583	missense	27044	exon11			GAGGCCCGGGAAT		CCDS34747.1	7q31.3	2014-03-24			ENSG00000197157	ENSG00000197157		"""Tudor domain containing"""	30646	protein-coding gene	gene with protein product	"""p100 EBNA2 co-activator"", ""Tudor-SN"""	602181				7651391, 9003410, 12819296	Standard	NM_014390		Approved	TDRD11, p100	uc003vmi.3	Q7KZF4	OTTHUMG00000157560	ENST00000354725.3:c.1207C>T	7.37:g.127447592C>T	ENSP00000346762:p.Arg403Trp	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	88	4	0.0454545	NM_014390	Q13122|Q96AG0	Missense_Mutation	SNP	ENST00000354725.3	37	CCDS34747.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.740470	0.89573	.	.	ENSG00000197157	ENST00000354725;ENST00000438400	T	0.34072	1.38	5.86	5.86	0.93980	Staphylococcal nuclease (SNase-like) (4);Staphylococcal nuclease (SNase-like), OB-fold (1);	0.052414	0.85682	D	0.000000	T	0.69396	0.3106	H	0.94582	3.555	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	T	0.76664	-0.2876	10	0.87932	D	0	-19.8134	12.9338	0.58303	0.1619:0.8381:0.0:0.0	.	403	Q7KZF4	SND1_HUMAN	W	403;393	ENSP00000346762:R403W	ENSP00000346762:R403W	R	+	1	2	SND1	127234828	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.304000	0.43655	2.937000	0.99478	0.650000	0.86243	CGG	.	.	none		0.368	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390	
GOLGA6L6	727832	hgsc.bcm.edu	37	15	20739874	20739874	+	Missense_Mutation	SNP	C	C	T	rs59357493		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:20739874C>T	ENST00000427390.2	-	8	1966	c.1876G>A	c.(1876-1878)Gag>Aag	p.E626K		NM_001145004.1	NP_001138476.1	A8MZA4	GG6L6_HUMAN	golgin A6 family-like 6	626	Gln-rich.|Glu-rich.									NS(3)|endometrium(4)|kidney(1)|skin(3)	11						cgtatcttctcctcctgctcc	0.547																																					p.E626K		Atlas-SNP	.											GOLGA6L6,caecum,carcinoma,0,1	GOLGA6L6	37	1	0			c.G1876A						scavenged	.						9.0	4.0	6.0					15																	20739874		615	1346	1961	SO:0001583	missense	727832	exon8			TCTTCTCCTCCTG	AK093450	CCDS45184.1	15q11.2	2014-02-12	2010-02-12		ENSG00000215405	ENSG00000277322			37225	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 6"""				Standard	NM_001145004		Approved	FLJ36131	uc001ytk.2	A8MZA4	OTTHUMG00000171663	ENST00000427390.2:c.1876G>A	15.37:g.20739874C>T	ENSP00000398615:p.Glu626Lys	Somatic	32	0	0		WXS	Illumina HiSeq	Phase_I	31	2	0.0645161	NM_001145004	D3YTC0	Missense_Mutation	SNP	ENST00000427390.2	37	CCDS45184.1	.	.	.	.	.	.	.	.	.	.	C	5.600	0.295465	0.10622	.	.	ENSG00000215405	ENST00000427390	T	0.09350	2.99	.	.	.	.	.	.	.	.	T	0.06872	0.0175	L	0.29908	0.895	0.27497	N	0.952094	B	0.23058	0.079	B	0.20384	0.029	T	0.41016	-0.9532	8	0.22109	T	0.4	.	5.9503	0.19242	0.0:0.9994:0.0:6.0E-4	rs59357493	626	A8MZA4	GG6L6_HUMAN	K	626	ENSP00000398615:E626K	ENSP00000398615:E626K	E	-	1	0	GOLGA6L6	18999888	0.240000	0.23847	0.038000	0.18304	0.038000	0.13279	-0.159000	0.10056	0.159000	0.19401	0.162000	0.16502	GAG	.	.	weak		0.547	GOLGA6L6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414660.3	NM_001145004	
NUP50	10762	hgsc.bcm.edu	37	22	45574145	45574145	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr22:45574145A>G	ENST00000347635.4	+	5	833	c.367A>G	c.(367-369)Acc>Gcc	p.T123A	NUP50_ENST00000407019.2_Missense_Mutation_p.T95A|NUP50_ENST00000396096.2_Missense_Mutation_p.T95A|NUP50_ENST00000425733.2_5'UTR|CTA-268H5.12_ENST00000610217.1_RNA|NUP50_ENST00000486184.1_3'UTR	NM_007172.3	NP_009103.2	Q9UKX7	NUP50_HUMAN	nucleoporin 50kDa	123	5 X 2 AA repeats of F-G.				carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|intracellular transport (GO:0046907)|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)	nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.T123A(1)		endometrium(1)|kidney(1)|large_intestine(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	9		Ovarian(80;0.00965)|all_neural(38;0.0244)		UCEC - Uterine corpus endometrioid carcinoma (28;0.0178)		TGGCCCTACCACCTTGGTTGA	0.403																																					p.T123A		Atlas-SNP	.											NUP50,hand,carcinoma,0,2	NUP50	24	2	1	Substitution - Missense(1)	skin(1)	c.A367G						scavenged	.						70.0	69.0	69.0					22																	45574145		2203	4300	6503	SO:0001583	missense	10762	exon5			CCTACCACCTTGG	AF107840	CCDS14062.1, CCDS14063.1	22q13.3	2007-01-22	2002-08-29		ENSG00000093000	ENSG00000093000			8065	protein-coding gene	gene with protein product		604646	"""nucleoporin 50kD"""	NPAP60L		10449902	Standard	XM_005261312		Approved		uc003bfr.3	Q9UKX7	OTTHUMG00000151265	ENST00000347635.4:c.367A>G	22.37:g.45574145A>G	ENSP00000345895:p.Thr123Ala	Somatic	240	6	0.025		WXS	Illumina HiSeq	Phase_I	249	17	0.0682731	NM_007172	B1AHA4|B2RB15|O75644|Q8N6V5|Q9NPM9|Q9NPR6|Q9P1K5	Missense_Mutation	SNP	ENST00000347635.4	37	CCDS14062.1	.	.	.	.	.	.	.	.	.	.	G	0.204	-1.042164	0.01997	.	.	ENSG00000093000	ENST00000347635;ENST00000407019;ENST00000396096	.	.	.	5.46	-6.61	0.01818	Nuclear pore complex, NUP2/50/61 (1);	1.214170	0.05550	N	0.567335	T	0.23572	0.0570	L	0.36672	1.1	0.09310	N	0.999998	B	0.02656	0.0	B	0.01281	0.0	T	0.24657	-1.0154	9	0.09338	T	0.73	-0.2565	3.9641	0.09423	0.2425:0.1011:0.4317:0.2247	.	123	Q9UKX7	NUP50_HUMAN	A	123;95;95	.	ENSP00000345895:T123A	T	+	1	0	NUP50	43952809	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-0.532000	0.06164	-1.798000	0.01250	-5.607000	0.00000	ACC	.	.	none		0.403	NUP50-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321993.2		
ASS1	445	hgsc.bcm.edu	37	9	133374905	133374905	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:133374905G>A	ENST00000372394.1	+	15	1622	c.1141G>A	c.(1141-1143)Ggt>Agt	p.G381S	ASS1_ENST00000372393.3_Missense_Mutation_p.G381S|ASS1_ENST00000352480.5_Missense_Mutation_p.G381S			P00966	ASSY_HUMAN	argininosuccinate synthase 1	381					acute-phase response (GO:0006953)|aging (GO:0007568)|arginine biosynthetic process (GO:0006526)|argininosuccinate metabolic process (GO:0000053)|aspartate metabolic process (GO:0006531)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to amine stimulus (GO:0071418)|cellular response to amino acid stimulus (GO:0071230)|cellular response to ammonium ion (GO:0071242)|cellular response to cAMP (GO:0071320)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to glucagon stimulus (GO:0071377)|cellular response to interferon-gamma (GO:0071346)|cellular response to laminar fluid shear stress (GO:0071499)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to oleic acid (GO:0071400)|cellular response to tumor necrosis factor (GO:0071356)|citrulline metabolic process (GO:0000052)|diaphragm development (GO:0060539)|kidney development (GO:0001822)|liver development (GO:0001889)|midgut development (GO:0007494)|negative regulation of leukocyte cell-cell adhesion (GO:1903038)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to growth hormone (GO:0060416)|response to mycotoxin (GO:0010046)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|small molecule metabolic process (GO:0044281)|urea cycle (GO:0000050)	cell body fiber (GO:0070852)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)|lysosome (GO:0005764)|mitochondrial outer membrane (GO:0005741)|nucleus (GO:0005634)|perikaryon (GO:0043204)	amino acid binding (GO:0016597)|argininosuccinate synthase activity (GO:0004055)|ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|toxic substance binding (GO:0015643)			breast(1)|cervix(1)|endometrium(2)|kidney(3)|large_intestine(3)|lung(4)|ovary(1)|skin(1)|urinary_tract(1)	17				OV - Ovarian serous cystadenocarcinoma(145;0.000514)	Adenosine triphosphate(DB00171)|L-Arginine(DB00125)|L-Aspartic Acid(DB00128)|L-Citrulline(DB00155)	GAACGTGCAGGGTGATTATGA	0.582																																					p.G381S		Atlas-SNP	.											ASS1,upper_leg,malignant_melanoma,0,1	ASS1	37	1	0			c.G1141A						scavenged	.						69.0	57.0	61.0					9																	133374905		2203	4300	6503	SO:0001583	missense	445	exon14			GTGCAGGGTGATT	X01630	CCDS6933.1	9q34.1	2012-10-02	2010-04-20	2006-08-24	ENSG00000130707	ENSG00000130707	6.3.4.5		758	protein-coding gene	gene with protein product		603470	"""argininosuccinate synthetase"""	ASS		3513483, 852520	Standard	NM_054012		Approved	CTLN1	uc004bzm.3	P00966	OTTHUMG00000020806	ENST00000372394.1:c.1141G>A	9.37:g.133374905G>A	ENSP00000361471:p.Gly381Ser	Somatic	161	0	0		WXS	Illumina HiSeq	Phase_I	155	2	0.0129032	NM_054012	Q6LDL2|Q86UZ0|Q96GT4	Missense_Mutation	SNP	ENST00000372394.1	37	CCDS6933.1	.	.	.	.	.	.	.	.	.	.	G	15.76	2.929294	0.52759	.	.	ENSG00000130707	ENST00000334909;ENST00000352480;ENST00000372394;ENST00000372393;ENST00000372386	D;D;D;D	0.99070	-5.39;-5.39;-5.39;-4.95	3.56	3.56	0.40772	.	0.298040	0.30639	U	0.009193	D	0.97813	0.9282	L	0.41632	1.29	0.58432	D	0.999999	D;D;P;P	0.62365	0.991;0.991;0.844;0.844	P;P;P;P	0.50270	0.636;0.636;0.499;0.499	D	0.97476	1.0044	10	0.48119	T	0.1	.	14.2592	0.66073	0.0:0.0:1.0:0.0	.	264;264;381;381	B4E395;E9PDT0;Q5T6L4;P00966	.;.;.;ASSY_HUMAN	S	381;381;381;381;138	ENSP00000253004:G381S;ENSP00000361471:G381S;ENSP00000361469:G381S;ENSP00000361461:G138S	ENSP00000361470:G381S	G	+	1	0	ASS1	132364726	1.000000	0.71417	0.985000	0.45067	0.242000	0.25591	7.601000	0.82783	1.981000	0.57761	0.555000	0.69702	GGT	.	.	none		0.582	ASS1-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054652.1	NM_000050	
COPB1	1315	hgsc.bcm.edu	37	11	14504615	14504615	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:14504615T>C	ENST00000249923.3	-	8	1220	c.920A>G	c.(919-921)gAa>gGa	p.E307G	COPB1_ENST00000439561.2_Missense_Mutation_p.E307G	NM_016451.4	NP_057535.1	P53618	COPB_HUMAN	coatomer protein complex, subunit beta 1	307					COPI coating of Golgi vesicle (GO:0048205)|intra-Golgi vesicle-mediated transport (GO:0006891)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|retrograde vesicle-mediated transport, Golgi to ER (GO:0006890)|viral process (GO:0016032)	COPI vesicle coat (GO:0030126)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi-associated vesicle (GO:0005798)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|plasma membrane (GO:0005886)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(9)|lung(12)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(2)	36						CTCTTTTAATTCTATCAAGCG	0.318																																					p.E307G		Atlas-SNP	.											.	COPB1	81	.	0			c.A920G						PASS	.						82.0	77.0	79.0					11																	14504615		2199	4293	6492	SO:0001583	missense	1315	exon8			TTTAATTCTATCA	BC037280	CCDS7815.1	11p15.2	2011-05-20	2006-06-30	2006-06-30	ENSG00000129083	ENSG00000129083			2231	protein-coding gene	gene with protein product		600959	"""coatomer protein complex, subunit beta"""	COPB		7982906	Standard	NM_016451		Approved		uc001mlg.2	P53618	OTTHUMG00000165824	ENST00000249923.3:c.920A>G	11.37:g.14504615T>C	ENSP00000249923:p.Glu307Gly	Somatic	53	0	0		WXS	Illumina HiSeq	Phase_I	40	4	0.1	NM_001144062	D3DQX0|Q6GTT7|Q9NTK2|Q9UNW7	Missense_Mutation	SNP	ENST00000249923.3	37	CCDS7815.1	.	.	.	.	.	.	.	.	.	.	T	20.6	4.011321	0.75046	.	.	ENSG00000129083	ENST00000249923;ENST00000439561;ENST00000534234	T;T;T	0.26957	1.7;1.7;1.7	5.56	5.56	0.83823	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.30008	0.0751	L	0.56769	1.78	0.80722	D	1	B	0.20459	0.045	B	0.26614	0.071	T	0.04053	-1.0981	10	0.33940	T	0.23	.	15.7137	0.77652	0.0:0.0:0.0:1.0	.	307	P53618	COPB_HUMAN	G	307	ENSP00000249923:E307G;ENSP00000397873:E307G;ENSP00000436383:E307G	ENSP00000249923:E307G	E	-	2	0	COPB1	14461191	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	8.018000	0.88722	2.118000	0.64928	0.482000	0.46254	GAA	.	.	none		0.318	COPB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386410.1	NM_016451	
FKBP9	11328	hgsc.bcm.edu	37	7	33014908	33014908	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:33014908G>A	ENST00000242209.4	+	3	651	c.482G>A	c.(481-483)cGg>cAg	p.R161Q	FKBP9_ENST00000538443.1_Missense_Mutation_p.R23Q|AVL9_ENST00000404479.1_Intron|FKBP9_ENST00000538336.1_Missense_Mutation_p.R214Q	NM_001284343.1|NM_007270.3	NP_001271272.1|NP_009201.2	O95302	FKBP9_HUMAN	FK506 binding protein 9, 63 kDa	161					chaperone-mediated protein folding (GO:0061077)|protein folding (GO:0006457)|protein peptidyl-prolyl isomerization (GO:0000413)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)	calcium ion binding (GO:0005509)|FK506 binding (GO:0005528)|peptidyl-prolyl cis-trans isomerase activity (GO:0003755)			central_nervous_system(13)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(6)|lung(9)|ovary(2)|upper_aerodigestive_tract(1)	39			GBM - Glioblastoma multiforme(11;0.0156)			AGTTGCCCTCGGACCATCCAG	0.473																																					p.R161Q		Atlas-SNP	.											FKBP9,brain,glioma,0,9	FKBP9	335	9	0			c.G482A						scavenged	.						99.0	87.0	91.0					7																	33014908		2203	4300	6503	SO:0001583	missense	11328	exon3			GCCCTCGGACCAT	AF089745	CCDS5439.1, CCDS64622.1, CCDS64623.1	7p11.1	2013-01-10	2002-08-29		ENSG00000122642	ENSG00000122642		"""EF-hand domain containing"""	3725	protein-coding gene	gene with protein product			"""FK506-binding protein 9 (63 kD)"""			12036304	Standard	NM_007270		Approved	FKBP60, FKBP63	uc003tdh.3	O95302	OTTHUMG00000097847	ENST00000242209.4:c.482G>A	7.37:g.33014908G>A	ENSP00000242209:p.Arg161Gln	Somatic	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	121	7	0.0578512	NM_007270	B3KY35|B7Z1G9|B7Z6H3|Q2M2A1|Q3MIR7|Q6IN76|Q6P2N1|Q96EX5|Q96IJ9	Missense_Mutation	SNP	ENST00000242209.4	37	CCDS5439.1	.	.	.	.	.	.	.	.	.	.	G	26.3	4.720086	0.89205	.	.	ENSG00000122642	ENST00000242209;ENST00000538336;ENST00000538443	D;D;D	0.86164	-2.08;-2.08;-2.08	5.36	5.36	0.76844	Peptidyl-prolyl cis-trans isomerase, FKBP-type, domain (1);	0.000000	0.85682	D	0.000000	D	0.92714	0.7684	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.999	D	0.92752	0.6217	10	0.56958	D	0.05	-4.2611	19.0957	0.93249	0.0:0.0:1.0:0.0	.	214;161;161	B7Z6H3;O95302;B3KQQ0	.;FKBP9_HUMAN;.	Q	161;214;23	ENSP00000242209:R161Q;ENSP00000439250:R214Q;ENSP00000437504:R23Q	ENSP00000242209:R161Q	R	+	2	0	FKBP9	32981433	1.000000	0.71417	1.000000	0.80357	0.456000	0.32438	9.809000	0.99208	2.524000	0.85096	0.650000	0.86243	CGG	.	.	none		0.473	FKBP9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000215137.1	NM_007270	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240804	39240804	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:39240804C>A	ENST00000391417.4	+	1	346	c.346C>A	c.(346-348)Cgc>Agc	p.R116S		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	141	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		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						cagctgctgccgcccctgctg	0.672																																					p.R116S		Atlas-SNP	.											KRTAP4-7,caecum,carcinoma,0,1	KRTAP4-7	49	1	0			c.C346A						scavenged	.						15.0	16.0	16.0					17																	39240804		692	1588	2280	SO:0001583	missense	100132476	exon1			TGCTGCCGCCCCT	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.346C>A	17.37:g.39240804C>A	ENSP00000375236:p.Arg116Ser	Somatic	63	1	0.015873		WXS	Illumina HiSeq	Phase_I	54	5	0.0925926	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	.	.	.	.	.	.	.	.	.	.	.	0.016	-1.524493	0.00959	.	.	ENSG00000240871	ENST00000391417	T	0.00596	6.32	3.15	-6.29	0.02013	.	0.163808	0.19966	U	0.102091	T	0.00241	0.0007	.	.	.	0.09310	N	0.999997	B	0.33748	0.423	B	0.29524	0.103	T	0.47661	-0.9100	9	0.11794	T	0.64	.	1.8893	0.03244	0.1228:0.1811:0.2435:0.4526	.	171	Q9BYR0	KRA47_HUMAN	S	116	ENSP00000375236:R116S	ENSP00000375236:R116S	R	+	1	0	KRTAP4-7	36494330	0.000000	0.05858	0.002000	0.10522	0.468000	0.32798	-3.208000	0.00557	-2.496000	0.00513	-0.734000	0.03567	CGC	.	.	none		0.672	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
CDC42BPG	55561	hgsc.bcm.edu	37	11	64597205	64597205	+	Silent	SNP	G	G	T	rs7936466	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:64597205G>T	ENST00000342711.5	-	30	3704	c.3705C>A	c.(3703-3705)ggC>ggA	p.G1235G	CDC42BPG_ENST00000491280.1_5'Flank	NM_017525.2	NP_059995.2			CDC42 binding protein kinase gamma (DMPK-like)											central_nervous_system(1)|lung(3)	4						ATAGCCGGTCGCCCAGCAGCC	0.716													G|||	1371	0.273762	0.0439	0.2147	5008	,	,		14616	0.4931		0.2555	False		,,,				2504	0.4192				p.G1235G		Atlas-SNP	.											.	CDC42BPG	101	.	0			c.C3705A						PASS	.	G		328,3866		16,296,1785	7.0	9.0	8.0		3705	-0.6	1.0	11	dbSNP_116	8	1926,6434		211,1504,2465	no	coding-synonymous	CDC42BPG	NM_017525.2		227,1800,4250	TT,TG,GG		23.0383,7.8207,17.9544		1235/1552	64597205	2254,10300	2097	4180	6277	SO:0001819	synonymous_variant	55561	exon30			CCGGTCGCCCAGC	AY648038	CCDS31601.1	11q13	2013-01-10			ENSG00000171219	ENSG00000171219		"""Pleckstrin homology (PH) domain containing"""	29829	protein-coding gene	gene with protein product		613991				9341881, 15194684	Standard	NM_017525		Approved	HSMDPKIN, MRCKgamma, DMPK2, kappa-200	uc001obs.4	Q6DT37	OTTHUMG00000045365	ENST00000342711.5:c.3705C>A	11.37:g.64597205G>T		Somatic	0	0	.		WXS	Illumina HiSeq	Phase_I	8	5	0.625	NM_017525		Silent	SNP	ENST00000342711.5	37	CCDS31601.1																																																																																			G|0.734;T|0.266	0.266	strong		0.716	CDC42BPG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000105352.4	XM_290516	
ARMC8	25852	hgsc.bcm.edu	37	3	138009387	138009387	+	Splice_Site	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:138009387G>A	ENST00000469044.1	+	21	2165		c.e21-1		ARMC8_ENST00000538260.1_Splice_Site|ARMC8_ENST00000461822.1_Splice_Site|NME9_ENST00000341790.5_Intron|NME9_ENST00000536478.1_Intron|NME9_ENST00000317876.4_Intron|ARMC8_ENST00000491704.1_Splice_Site|NME9_ENST00000484930.1_Intron|ARMC8_ENST00000485396.1_Splice_Site|NME9_ENST00000383180.2_Intron|ARMC8_ENST00000481646.1_Splice_Site|ARMC8_ENST00000393058.3_Splice_Site	NM_001267041.1|NM_001267042.1	NP_001253970.1|NP_001253971.1	Q8IUR7	ARMC8_HUMAN	armadillo repeat containing 8											endometrium(2)|kidney(1)|large_intestine(7)|lung(5)|upper_aerodigestive_tract(1)	16						TAATCGTTTAGGTTCACAAGA	0.428																																					.		Atlas-SNP	.											.	ARMC8	79	.	0			c.1853-1G>A						PASS	.						68.0	64.0	65.0					3																	138009387		1918	4126	6044	SO:0001630	splice_region_variant	25852	exon22			CGTTTAGGTTCAC		CCDS3098.1, CCDS54646.1, CCDS58853.1, CCDS58854.1, CCDS75020.1	3q22	2013-02-14			ENSG00000114098	ENSG00000114098		"""Armadillo repeat containing"""	24999	protein-coding gene	gene with protein product	"""GID complex subunit 5, VID28 homolog (S. cerevisiae)"""					11042152	Standard	NM_014154		Approved	HSPC056, DKFZP434A043, GID5, VID28	uc003esa.2	Q8IUR7	OTTHUMG00000159821	ENST00000469044.1:c.1895-1G>A	3.37:g.138009387G>A		Somatic	83	0	0		WXS	Illumina HiSeq	Phase_I	147	44	0.29932	NM_015396	A8K0L2|B7Z441|B7Z453|D3DNE6|F5GWK4|Q6PIL2|Q96D19|Q96HZ5|Q9NV02|Q9NV94|Q9Y4R9	Splice_Site	SNP	ENST00000469044.1	37		.	.	.	.	.	.	.	.	.	.	G	17.36	3.370690	0.61624	.	.	ENSG00000114098	ENST00000481646;ENST00000469044;ENST00000491704;ENST00000461822;ENST00000485396;ENST00000538260;ENST00000393058;ENST00000539459	.	.	.	5.02	5.02	0.67125	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.834	0.78782	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	ARMC8	139492077	1.000000	0.71417	0.966000	0.40874	0.711000	0.40976	9.281000	0.95811	2.305000	0.77605	0.442000	0.29010	.	.	.	none		0.428	ARMC8-003	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000357560.1	NM_015396	Intron
UBE2A	7319	hgsc.bcm.edu	37	X	118708868	118708868	+	Nonsense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:118708868C>T	ENST00000371558.2	+	2	223	c.49C>T	c.(49-51)Cag>Tag	p.Q17*	UBE2A_ENST00000469205.1_3'UTR|UBE2A_ENST00000346330.3_Nonsense_Mutation_p.Q17*	NM_001282161.1|NM_003336.2|NM_181762.1	NP_001269090.1|NP_003327.2|NP_861427.1	P49459	UBE2A_HUMAN	ubiquitin-conjugating enzyme E2A	17					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|DNA repair (GO:0006281)|histone H2A ubiquitination (GO:0033522)|in utero embryonic development (GO:0001701)|maternal process involved in female pregnancy (GO:0060135)|positive regulation of cell proliferation (GO:0008284)|postreplication repair (GO:0006301)|protein autoubiquitination (GO:0051865)|protein K11-linked ubiquitination (GO:0070979)|protein K48-linked ubiquitination (GO:0070936)|protein polyubiquitination (GO:0000209)|response to UV (GO:0009411)|ubiquitin-dependent protein catabolic process (GO:0006511)	chromatin (GO:0000785)|cytosol (GO:0005829)|HULC complex (GO:0033503)|nuclear chromatin (GO:0000790)|XY body (GO:0001741)	acid-amino acid ligase activity (GO:0016881)|ATP binding (GO:0005524)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin-protein transferase activity (GO:0004842)			haematopoietic_and_lymphoid_tissue(1)|lung(7)	8						CCGAAGGTTGCAGGAGGATCC	0.701								Rad6 pathway																													p.Q17X		Atlas-SNP	.											.	UBE2A	43	.	0			c.C49T						PASS	.						137.0	111.0	120.0					X																	118708868		2203	4300	6503	SO:0001587	stop_gained	7319	exon2			AGGTTGCAGGAGG	AK223045	CCDS14580.1, CCDS14581.1	Xq24	2011-05-19	2011-05-19		ENSG00000077721	ENSG00000077721		"""Ubiquitin-conjugating enzymes E2"""	12472	protein-coding gene	gene with protein product		312180	"""ubiquitin-conjugating enzyme E2A (RAD6 homolog)"""			1559696	Standard	NM_003336		Approved	UBC2, HHR6A, RAD6A	uc004erl.3	P49459	OTTHUMG00000022275	ENST00000371558.2:c.49C>T	X.37:g.118708868C>T	ENSP00000360613:p.Gln17*	Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	106	81	0.764151	NM_003336	A6NFE9|A6NGR2|A6NMF5|B2R7R9|D3DWI1|Q4TTG1|Q96FX4	Nonsense_Mutation	SNP	ENST00000371558.2	37	CCDS14580.1	.	.	.	.	.	.	.	.	.	.	C	33	5.277119	0.95459	.	.	ENSG00000077721	ENST00000371558;ENST00000346330	.	.	.	4.6	4.6	0.57074	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.52906	T	0.07	-3.7589	15.601	0.76626	0.0:1.0:0.0:0.0	.	.	.	.	X	17	.	ENSP00000335027:Q17X	Q	+	1	0	UBE2A	118592896	1.000000	0.71417	0.999000	0.59377	0.572000	0.35998	7.145000	0.77365	2.131000	0.65755	0.529000	0.55759	CAG	.	.	none		0.701	UBE2A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058036.1	NM_003336	
DDX52	11056	hgsc.bcm.edu	37	17	36003419	36003419	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:36003419C>T	ENST00000349699.2	-	1	74	c.31G>A	c.(31-33)Ggc>Agc	p.G11S	DDX52_ENST00000394367.3_5'UTR|RP11-697E22.2_ENST00000586950.1_RNA|RP11-697E22.2_ENST00000586163.1_RNA	NM_007010.3	NP_008941.2	Q9Y2R4	DDX52_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 52	11						membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)			biliary_tract(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(5)|ovary(1)|skin(3)	17		Breast(25;0.00637)|Ovarian(249;0.15)				GCCCCCGCGCCGAGCCGGCGA	0.632																																					p.G11S		Atlas-SNP	.											.	DDX52	40	.	0			c.G31A						PASS	.						44.0	45.0	45.0					17																	36003419		2203	4300	6503	SO:0001583	missense	11056	exon1			CCGCGCCGAGCCG	AF077033	CCDS11323.1	17q21.1	2014-05-06			ENSG00000141141	ENSG00000278053		"""DEAD-boxes"""	20038	protein-coding gene	gene with protein product		612500				11124703	Standard	XM_006721650		Approved	ROK1	uc002hoi.2	Q9Y2R4	OTTHUMG00000188475	ENST00000349699.2:c.31G>A	17.37:g.36003419C>T	ENSP00000268854:p.Gly11Ser	Somatic	40	0	0		WXS	Illumina HiSeq	Phase_I	53	4	0.0754717	NM_007010	Q86YG1|Q8N213|Q9NVE0|Q9Y482	Missense_Mutation	SNP	ENST00000349699.2	37	CCDS11323.1	.	.	.	.	.	.	.	.	.	.	C	12.22	1.871577	0.33069	.	.	ENSG00000141141	ENST00000349699	T	0.13778	2.56	5.5	4.53	0.55603	.	2.488010	0.00945	N	0.002898	T	0.13970	0.0338	L	0.41710	1.295	0.80722	D	1	B	0.26672	0.156	B	0.18263	0.021	T	0.43637	-0.9379	10	0.07990	T	0.79	.	11.6948	0.51538	0.1761:0.8239:0.0:0.0	.	11	Q9Y2R4	DDX52_HUMAN	S	11	ENSP00000268854:G11S	ENSP00000268854:G11S	G	-	1	0	DDX52	33077532	0.436000	0.25586	0.246000	0.24233	0.197000	0.23852	2.315000	0.43752	1.555000	0.49500	-0.152000	0.13540	GGC	.	.	none		0.632	DDX52-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256795.1	NM_152300	
ZNF33A	7581	hgsc.bcm.edu	37	10	38345000	38345000	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:38345000T>C	ENST00000458705.2	+	5	2103	c.1945T>C	c.(1945-1947)Tca>Cca	p.S649P	ZNF33A_ENST00000469037.2_Intron|ZNF33A_ENST00000374618.3_Missense_Mutation_p.S650P|ZNF33A_ENST00000432900.2_Missense_Mutation_p.S656P|ZNF33A_ENST00000307441.9_Missense_Mutation_p.S649P			Q06730	ZN33A_HUMAN	zinc finger protein 33A	649					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)			cervix(2)|endometrium(2)|large_intestine(8)|liver(2)|lung(27)|ovary(2)|prostate(1)|skin(2)	46						CTGCCATAAGTCAGCTCTAAT	0.378																																					p.S650P		Atlas-SNP	.											ZNF33A,NS,carcinoma,-1,1	ZNF33A	103	1	0			c.T1948C						scavenged	.						99.0	104.0	102.0					10																	38345000		2203	4300	6503	SO:0001583	missense	7581	exon5			CATAAGTCAGCTC	D31763	CCDS31182.1, CCDS60514.1, CCDS73088.1, CCDS73089.1	10p11.2	2013-01-08	2005-03-18		ENSG00000189180	ENSG00000189180		"""Zinc fingers, C2H2-type"", ""-"""	13096	protein-coding gene	gene with protein product	"""zinc finger and ZAK associated protein with KRAB domain"""	194521	"""zinc finger protein 33a (KOX 31)"", ""zinc finger protein 11A"""	ZNF33, ZNF11A		2014798, 8464732	Standard	NM_006974		Approved	KOX5, KOX31, KIAA0065, FLJ23404, ZZAPK	uc031pui.1	Q06730	OTTHUMG00000017983	ENST00000458705.2:c.1945T>C	10.37:g.38345000T>C	ENSP00000387713:p.Ser649Pro	Somatic	60	0	0		WXS	Illumina HiSeq	Phase_I	53	2	0.0377358	NM_006954	A8K9X9|B4E0M8|F6TH33|F8WAJ5|P17013|Q5VZ86	Missense_Mutation	SNP	ENST00000458705.2	37	CCDS31182.1	.	.	.	.	.	.	.	.	.	.	T	11.72	1.722832	0.30503	.	.	ENSG00000189180	ENST00000374618;ENST00000432900;ENST00000458705;ENST00000307441	T;T;T;T	0.36878	1.23;1.23;1.23;1.23	1.69	1.69	0.24217	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.28933	N	0.013667	T	0.48187	0.1486	L	0.53729	1.69	0.09310	N	1	D;D;D	0.89917	0.999;0.999;1.0	D;D;D	0.79108	0.943;0.937;0.992	T	0.18650	-1.0330	10	0.66056	D	0.02	.	7.0172	0.24895	0.0:0.0:0.0:1.0	.	656;649;650	F6TH33;Q06730;F8WAJ5	.;ZN33A_HUMAN;.	P	650;656;649;649	ENSP00000363747:S650P;ENSP00000402467:S656P;ENSP00000387713:S649P;ENSP00000304268:S649P	ENSP00000304268:S649P	S	+	1	0	ZNF33A	38385006	0.000000	0.05858	1.000000	0.80357	0.773000	0.43773	-0.888000	0.04148	0.750000	0.32877	0.260000	0.18958	TCA	.	.	none		0.378	ZNF33A-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000047614.1	NM_006974	
PHACTR2	9749	hgsc.bcm.edu	37	6	144104401	144104401	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:144104401G>A	ENST00000427704.2	+	10	1788	c.1658G>A	c.(1657-1659)cGc>cAc	p.R553H	PHACTR2_ENST00000305766.6_Missense_Mutation_p.R473H|PHACTR2_ENST00000440869.2_Missense_Mutation_p.R564H|PHACTR2_ENST00000367584.4_Missense_Mutation_p.R541H|PHACTR2_ENST00000367582.3_Missense_Mutation_p.R484H	NM_001100166.1|NM_014721.2	NP_001093636.1|NP_055536.2	O75167	PHAR2_HUMAN	phosphatase and actin regulator 2	553							protein phosphatase inhibitor activity (GO:0004864)			NS(3)|breast(1)|cervix(1)|endometrium(3)|large_intestine(4)|lung(13)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30				OV - Ovarian serous cystadenocarcinoma(155;1.58e-05)|GBM - Glioblastoma multiforme(68;0.0386)		GAACTTAAACGCAGACTCAGC	0.299																																					p.R564H	Pancreas(12;292 433 7358 48260 52635)|Ovarian(20;501 618 3485 36581 49208)	Atlas-SNP	.											PHACTR2_ENST00000440869,colon,carcinoma,+1,2	PHACTR2	99	2	0			c.G1691A						scavenged	.						68.0	68.0	68.0					6																	144104401		1962	4142	6104	SO:0001583	missense	9749	exon10			TTAAACGCAGACT	AB014580	CCDS43512.1, CCDS47492.1, CCDS47493.1, CCDS47494.1	6q24.1	2013-01-24	2004-05-20	2004-05-20	ENSG00000112419	ENSG00000112419		"""Phosphatase and actin regulators"""	20956	protein-coding gene	gene with protein product		608724	"""chromosome 6 open reading frame 56"""	C6orf56		9734811, 15107502	Standard	NM_001100164		Approved	KIAA0680	uc010khi.3	O75167	OTTHUMG00000015732	ENST00000427704.2:c.1658G>A	6.37:g.144104401G>A	ENSP00000391763:p.Arg553His	Somatic	102	0	0		WXS	Illumina HiSeq	Phase_I	132	2	0.0151515	NM_001100164	A6NKP5|A7MCZ5|A8MZC0|B2RWP7|B4DN76|B4DPB5|B4DTH7|Q5TFA0|Q68DM2	Missense_Mutation	SNP	ENST00000427704.2	37	CCDS47492.1	.	.	.	.	.	.	.	.	.	.	G	34	5.353550	0.95830	.	.	ENSG00000112419	ENST00000367584;ENST00000427704;ENST00000305766;ENST00000440869;ENST00000367582	T;T;T;T;T	0.36520	1.25;1.66;1.27;1.66;1.27	6.16	6.16	0.99307	.	0.092126	0.85682	D	0.000000	T	0.60077	0.2241	M	0.78916	2.43	0.80722	D	1	D;D;D;D	0.89917	0.999;1.0;1.0;1.0	D;D;D;D	0.91635	0.965;0.999;0.999;0.988	T	0.60742	-0.7203	10	0.87932	D	0	.	20.8598	0.99761	0.0:0.0:1.0:0.0	.	564;473;484;553	O75167-4;O75167-5;O75167-2;O75167	.;.;.;PHAR2_HUMAN	H	541;553;473;564;484	ENSP00000356556:R541H;ENSP00000391763:R553H;ENSP00000305530:R473H;ENSP00000417038:R564H;ENSP00000356554:R484H	ENSP00000305530:R473H	R	+	2	0	PHACTR2	144146094	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.988000	0.93501	2.937000	0.99478	0.650000	0.86243	CGC	.	.	none		0.299	PHACTR2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000042528.2	NM_014721	
NBPF10	100132406	hgsc.bcm.edu	37	1	145293535	145293535	+	Missense_Mutation	SNP	C	C	G	rs55936365		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:145293535C>G	ENST00000369339.3	+	3	383	c.130C>G	c.(130-132)Cta>Gta	p.L44V	RP11-458D21.5_ENST00000468030.1_3'UTR|NBPF10_ENST00000342960.5_Missense_Mutation_p.L44V|NBPF10_ENST00000369338.1_Intron			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	315						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.L44V(2)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		GAAATGTTTTCTAACTCAACT	0.443																																					p.L44V		Atlas-SNP	.											NBPF10,NS,carcinoma,0,2	NBPF10	221	2	2	Substitution - Missense(2)	kidney(2)	c.C130G						scavenged	.																																			SO:0001583	missense	100132406	exon1			TGTTTTCTAACTC	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.130C>G	1.37:g.145293535C>G	ENSP00000358345:p.Leu44Val	Somatic	98	1	0.0102041		WXS	Illumina HiSeq	Phase_I	142	7	0.0492958	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	0.027|0.027	-1.360141|-1.360141	0.01245|0.01245	.|.	.|.	ENSG00000163386|ENSG00000163386	ENST00000369339;ENST00000342960|ENST00000448873	T|.	0.02837|.	4.14|.	0.687|0.687	-1.37|-1.37	0.09056|0.09056	.|.	.|.	.|.	.|.	.|.	T|T	0.01765|0.01765	0.0056|0.0056	N|N	0.01122|0.01122	-1.005|-1.005	0.09310|0.09310	N|N	1|1	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.33007|0.33007	-0.9885|-0.9885	9|6	0.02654|0.33141	T|T	1|0.24	.|.	3.2142|3.2142	0.06692|0.06692	0.3787:0.2355:0.3858:0.0|0.3787:0.2355:0.3858:0.0	rs55936365|rs55936365	44|.	A8MQ30|.	.|.	V|C	44|3	ENSP00000345684:L44V|.	ENSP00000345684:L44V|ENSP00000414194:S3C	L|S	+|+	1|2	2|0	NBPF10|NBPF10	144004892|144004892	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.000000|0.000000	0.00434|0.00434	-3.451000|-3.451000	0.00466|0.00466	-3.626000|-3.626000	0.00130|0.00130	-3.729000|-3.729000	0.00022|0.00022	CTA|TCT	.	.	weak		0.443	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3	NM_001039703	
PLEKHO2	80301	hgsc.bcm.edu	37	15	65157677	65157677	+	Missense_Mutation	SNP	C	C	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:65157677C>G	ENST00000323544.4	+	6	1191	c.1063C>G	c.(1063-1065)Ccc>Gcc	p.P355A	AC069368.3_ENST00000437723.1_Intron	NM_001195059.1|NM_025201.4	NP_001181988.1|NP_079477.2	Q8TD55	PKHO2_HUMAN	pleckstrin homology domain containing, family O member 2	355	Pro-rich.									NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	25						GCCTGCCAAGCCCTCTCAGGC	0.612																																					p.P355A		Atlas-SNP	.											.	PLEKHO2	50	.	0			c.C1063G						PASS	.						70.0	70.0	70.0					15																	65157677		2202	4299	6501	SO:0001583	missense	80301	exon6			GCCAAGCCCTCTC	AF318373	CCDS10196.1, CCDS73739.1	15q22.31	2013-01-10	2007-12-14	2007-12-14	ENSG00000241839	ENSG00000241839		"""Pleckstrin homology (PH) domain containing"""	30026	protein-coding gene	gene with protein product			"""pleckstrin homology domain containing, family Q member 1"""	PLEKHQ1		12477932	Standard	NM_025201		Approved	DKFZp761K2312, PP1628, pp9099	uc002anv.3	Q8TD55	OTTHUMG00000133050	ENST00000323544.4:c.1063C>G	15.37:g.65157677C>G	ENSP00000326706:p.Pro355Ala	Somatic	22	0	0		WXS	Illumina HiSeq	Phase_I	29	14	0.482759	NM_025201	Q7L4H4|Q8WYS8	Missense_Mutation	SNP	ENST00000323544.4	37	CCDS10196.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.120411	0.00346	.	.	ENSG00000241839	ENST00000323544	T	0.34275	1.37	5.05	2.03	0.26663	.	0.935404	0.09141	N	0.842938	T	0.16727	0.0402	N	0.11560	0.145	0.09310	N	1	B;B	0.09022	0.002;0.001	B;B	0.09377	0.004;0.002	T	0.32561	-0.9902	10	0.12430	T	0.62	.	4.9907	0.14213	0.0:0.5785:0.1598:0.2617	.	305;355	Q8TD55-2;Q8TD55	.;PKHO2_HUMAN	A	355	ENSP00000326706:P355A	ENSP00000326706:P355A	P	+	1	0	PLEKHO2	62944730	0.000000	0.05858	0.007000	0.13788	0.112000	0.19704	0.094000	0.15107	0.497000	0.27926	0.655000	0.94253	CCC	.	.	none		0.612	PLEKHO2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256659.1	NM_025201	
MUC4	4585	hgsc.bcm.edu	37	3	195509579	195509579	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:195509579C>T	ENST00000463781.3	-	2	9331	c.8872G>A	c.(8872-8874)Gcc>Acc	p.A2958T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.A2958T	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)		AGAGAGGTGGCGTGACCTGTG	0.592																																					p.A2958T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	0			c.G8872A						scavenged	.																																			SO:0001583	missense	4585	exon2			AGGTGGCGTGACC	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.8872G>A	3.37:g.195509579C>T	ENSP00000417498:p.Ala2958Thr	Somatic	123	1	0.00813008		WXS	Illumina HiSeq	Phase_I	153	3	0.0196078	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	3.910	-0.020251	0.07634	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.34275	1.38;1.37	.	.	.	.	.	.	.	.	T	0.17704	0.0425	N	0.19112	0.55	0.09310	N	1	P	0.50710	0.938	B	0.39379	0.298	T	0.14117	-1.0484	7	.	.	.	.	4.6129	0.12411	0.0:0.5198:0.0:0.4802	.	2830	E7ESK3	.	T	2958	ENSP00000417498:A2958T;ENSP00000420243:A2958T	.	A	-	1	0	MUC4	196994358	0.001000	0.12720	0.003000	0.11579	0.000000	0.00434	-0.021000	0.12504	-0.437000	0.07243	0.000000	0.15137	GCC	.	.	none		0.592	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
DOCK9	23348	hgsc.bcm.edu	37	13	99537314	99537314	+	Missense_Mutation	SNP	C	C	T	rs370847473		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr13:99537314C>T	ENST00000376460.1	-	21	2373	c.2293G>A	c.(2293-2295)Gga>Aga	p.G765R	DOCK9_ENST00000448493.2_Missense_Mutation_p.G777R|DOCK9_ENST00000442173.1_Missense_Mutation_p.G765R|DOCK9_ENST00000339416.2_Missense_Mutation_p.G766R	NM_001130048.1|NM_015296.2	NP_001123520.1|NP_056111.1	Q9BZ29	DOCK9_HUMAN	dedicator of cytokinesis 9	766	DHR-1.				blood coagulation (GO:0007596)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|membrane (GO:0016020)	Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(12)|lung(18)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_neural(89;0.101)|Medulloblastoma(90;0.18)|Lung SC(71;0.184)					ACCACCCTTCCGTCTTTCAGG	0.512																																					p.G766R		Atlas-SNP	.											DOCK9_ENST00000448493,left_upper_lobe,carcinoma,+1,3	DOCK9	311	3	0			c.G2296A						scavenged	.	C	ARG/GLY,ARG/GLY,ARG/GLY,ARG/GLY	0,3882		0,0,1941	50.0	50.0	50.0		2293,2296,2293,2296	6.0	1.0	13		50	1,8283		0,1,4141	no	missense,missense,missense,missense	DOCK9	NM_001130048.1,NM_001130049.1,NM_001130050.1,NM_015296.2	125,125,125,125	0,1,6082	TT,TC,CC		0.0121,0.0,0.0082	probably-damaging,probably-damaging,probably-damaging,probably-damaging	765/2069,766/1255,765/1254,766/2070	99537314	1,12165	1941	4142	6083	SO:0001583	missense	23348	exon21			CCCTTCCGTCTTT	AF527605	CCDS45062.1	13q32.3	2013-01-10			ENSG00000088387	ENSG00000088387		"""Pleckstrin homology (PH) domain containing"""	14132	protein-coding gene	gene with protein product	"""zizimin1"""	607325				12172552, 12432077	Standard	NM_015296		Approved	KIAA1058, ZIZ1	uc001vnt.2	Q9BZ29	OTTHUMG00000017260	ENST00000376460.1:c.2293G>A	13.37:g.99537314C>T	ENSP00000365643:p.Gly765Arg	Somatic	57	0	0		WXS	Illumina HiSeq	Phase_I	60	3	0.05	NM_001130049	B3KX25|E9PFM9|Q5JUD4|Q5JUD6|Q5T2Q1|Q5TAN8|Q9BZ25|Q9BZ26|Q9BZ27|Q9BZ28|Q9UPU4	Missense_Mutation	SNP	ENST00000376460.1	37	CCDS45062.1	.	.	.	.	.	.	.	.	.	.	C	34	5.398347	0.96030	0.0	1.21E-4	ENSG00000088387	ENST00000376460;ENST00000357329;ENST00000376455;ENST00000400235;ENST00000428223;ENST00000339416;ENST00000448493;ENST00000442173	T;T;T;T	0.24350	1.86;1.86;1.86;1.86	5.96	5.96	0.96718	.	0.000000	0.85682	D	0.000000	T	0.57301	0.2044	M	0.81239	2.535	0.80722	D	1	D;D;D;P;D	0.89917	0.995;1.0;0.995;0.921;1.0	P;D;P;P;D	0.97110	0.88;1.0;0.819;0.479;1.0	T	0.57528	-0.7796	10	0.62326	D	0.03	.	20.422	0.99049	0.0:1.0:0.0:0.0	.	766;765;765;765;766	A6H8Z6;E9PFM9;B3KX25;Q9BZ29-5;Q9BZ29	.;.;.;.;DOCK9_HUMAN	R	765;766;766;766;765;766;777;765	ENSP00000365643:G765R;ENSP00000341086:G766R;ENSP00000401958:G777R;ENSP00000406883:G765R	ENSP00000341086:G766R	G	-	1	0	DOCK9	98335315	1.000000	0.71417	0.999000	0.59377	0.942000	0.58702	7.281000	0.78621	2.832000	0.97577	0.655000	0.94253	GGA	.	.	weak		0.512	DOCK9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045566.1	NM_015296	
MYC	4609	hgsc.bcm.edu	37	8	128750820	128750820	+	Silent	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr8:128750820G>A	ENST00000259523.6	+	2	1517	c.312G>A	c.(310-312)gaG>gaA	p.E104E	MYC_ENST00000377970.2_Silent_p.E119E|MYC_ENST00000524013.1_Silent_p.E118E			P01106	MYC_HUMAN	v-myc avian myelocytomatosis viral oncogene homolog	104					branching involved in ureteric bud morphogenesis (GO:0001658)|canonical Wnt signaling pathway (GO:0060070)|cell cycle arrest (GO:0007050)|cellular iron ion homeostasis (GO:0006879)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to UV (GO:0034644)|chromatin remodeling (GO:0006338)|chromosome organization (GO:0051276)|energy reserve metabolic process (GO:0006112)|fibroblast apoptotic process (GO:0044346)|gene expression (GO:0010467)|MAPK cascade (GO:0000165)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell division (GO:0051782)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of monocyte differentiation (GO:0045656)|negative regulation of stress-activated MAPK cascade (GO:0032873)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|Notch signaling pathway (GO:0007219)|oxygen transport (GO:0015671)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of DNA biosynthetic process (GO:2000573)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of metanephric cap mesenchymal cell proliferation (GO:0090096)|positive regulation of response to DNA damage stimulus (GO:2001022)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of gene expression (GO:0010468)|regulation of telomere maintenance (GO:0032204)|response to drug (GO:0042493)|response to gamma radiation (GO:0010332)|response to growth factor (GO:0070848)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)|E-box binding (GO:0070888)|protein complex binding (GO:0032403)|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 positive regulation of transcription (GO:0001077)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)			central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	16	all_cancers(1;6.19e-134)|all_epithelial(1;1.75e-119)|all_lung(1;5.66e-51)|Breast(1;1.08e-22)|all_neural(1;4.45e-21)|Medulloblastoma(1;1.88e-20)|Colorectal(1;1.92e-09)|Lung SC(1;4.52e-07)|Ovarian(5;0.000122)|Esophageal squamous(12;0.000995)|Renal(1;0.0921)|Hepatocellular(40;0.108)|Myeloproliferative disorder(2;0.135)|Melanoma(291;0.185)	Myeloproliferative disorder(644;0.0255)|Ovarian(118;0.0654)|Breast(495;0.212)|Acute lymphoblastic leukemia(644;0.22)	Epithelial(1;1.63e-94)|all cancers(1;5.82e-87)|OV - Ovarian serous cystadenocarcinoma(1;2.12e-71)|BRCA - Breast invasive adenocarcinoma(1;4.3e-14)|Lung(2;0.000381)|Colorectal(2;0.0102)|LUAD - Lung adenocarcinoma(14;0.0172)|READ - Rectum adenocarcinoma(2;0.0723)|LUSC - Lung squamous cell carcinoma(258;0.151)	KIRC - Kidney renal clear cell carcinoma(542;0.248)	Nadroparin(DB08813)	TGGTGACCGAGCTGCTGGGAG	0.602		3	"""A, T"""	"""IGK@, BCL5, BCL7A , BTG1, TRA@, IGH@"""	"""Burkitt lymphoma,  amplified in other cancers, B-CLL"""						OREG0018982	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																									p.E119E		Atlas-SNP	.		Dom	yes		8	8q24.12-q24.13	4609	v-myc myelocytomatosis viral oncogene homolog (avian)		"""L, E"""	.	MYC	168	.	0			c.G357A						PASS	.						52.0	52.0	52.0					8																	128750820		2203	4300	6503	SO:0001819	synonymous_variant	4609	exon2			GACCGAGCTGCTG		CCDS6359.2	8q24	2013-07-09	2013-07-09		ENSG00000136997	ENSG00000136997		"""Basic helix-loop-helix proteins"""	7553	protein-coding gene	gene with protein product		190080					Standard	NM_002467		Approved	c-Myc, bHLHe39, MYCC	uc003ysi.3	P01106	OTTHUMG00000128475	ENST00000259523.6:c.312G>A	8.37:g.128750820G>A		Somatic	94	0	0	1567	WXS	Illumina HiSeq	Phase_I	122	60	0.491803	NM_002467	A8WFE7|P01107|Q14026	Silent	SNP	ENST00000259523.6	37																																																																																				.	.	none		0.602	MYC-002	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000250278.1		
FAM72B	653820	hgsc.bcm.edu	37	1	120839839	120839839	+	Silent	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:120839839T>C	ENST00000369390.3	+	1	835	c.6T>C	c.(4-6)tcT>tcC	p.S2S	RP11-439A17.7_ENST00000412759.1_RNA|FAM72B_ENST00000471903.2_Intron|FAM72B_ENST00000355228.4_Silent_p.S2S	NM_001100910.1	NP_001094380.1	Q86X60	FA72B_HUMAN	family with sequence similarity 72, member B	2										large_intestine(1)|lung(2)	3	all_neural(166;0.181)	all_lung(203;7.27e-05)|Lung NSC(69;0.000389)|all_epithelial(167;0.068)		Lung(183;0.0327)|LUSC - Lung squamous cell carcinoma(189;0.19)		ACGCCATGTCTACCAACATTT	0.443																																					p.S2S		Atlas-SNP	.											FAM72B,NS,carcinoma,0,1	FAM72B	10	1	0			c.T6C						scavenged	.						6.0	7.0	7.0					1																	120839839		1624	3651	5275	SO:0001819	synonymous_variant	653820	exon1			CATGTCTACCAAC	AL357493	CCDS72848.1	1p12	2014-05-06			ENSG00000188610	ENSG00000188610			24805	protein-coding gene	gene with protein product		614711					Standard	NM_001100910		Approved	RP11-439A17.6	uc009whp.3	Q86X60	OTTHUMG00000185025	ENST00000369390.3:c.6T>C	1.37:g.120839839T>C		Somatic	817	5	0.00611995		WXS	Illumina HiSeq	Phase_I	1083	14	0.0129271	NM_001100910	B2RPQ5|Q5QP15	Silent	SNP	ENST00000369390.3	37	CCDS41374.1																																																																																			T|0.500;C|0.500	0.500	weak		0.443	FAM72B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098437.1		
AP2S1	1175	hgsc.bcm.edu	37	19	47342811	47342811	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:47342811G>T	ENST00000263270.6	-	3	403	c.178C>A	c.(178-180)Cgc>Agc	p.R60S	AP2S1_ENST00000597020.1_Missense_Mutation_p.R40S|AP2S1_ENST00000601498.1_Missense_Mutation_p.R76S|AP2S1_ENST00000352203.4_Missense_Mutation_p.R74S|AP2S1_ENST00000599990.1_Missense_Mutation_p.R62S|AP2S1_ENST00000601649.1_Intron|AP2S1_ENST00000593442.1_Missense_Mutation_p.R10S	NM_004069.3	NP_004060.2	P53680	AP2S1_HUMAN	adaptor-related protein complex 2, sigma 1 subunit	60					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|clathrin coat assembly (GO:0048268)|endocytosis (GO:0006897)|epidermal growth factor receptor signaling pathway (GO:0007173)|intracellular protein transport (GO:0006886)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of defense response to virus by virus (GO:0050690)|regulation of endocytosis (GO:0030100)|synaptic transmission (GO:0007268)|viral process (GO:0016032)	AP-2 adaptor complex (GO:0030122)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			central_nervous_system(1)|lung(1)|urinary_tract(1)	3		all_cancers(25;1.24e-06)|all_epithelial(76;1.09e-05)|all_lung(116;0.00019)|Lung NSC(112;0.000601)|Ovarian(192;0.0221)|all_neural(266;0.0459)|Breast(70;0.128)		OV - Ovarian serous cystadenocarcinoma(262;3.86e-05)|all cancers(93;0.000107)|Epithelial(262;0.00325)|GBM - Glioblastoma multiforme(486;0.0336)		GCATAGCGGCGGTAAATGATC	0.527																																					p.R60S		Atlas-SNP	.											AP2S1,NS,lymphoid_neoplasm,+1,1	AP2S1	12	1	0			c.C178A						scavenged	.						138.0	123.0	128.0					19																	47342811		2203	4300	6503	SO:0001583	missense	1175	exon3			AGCGGCGGTAAAT	AJ010148	CCDS12693.1, CCDS33062.1	19q13.2-q13.3	2014-02-04				ENSG00000042753			565	protein-coding gene	gene with protein product		602242	"""hypocalciuric hypercalcemia 3 (Oklahoma type)"""	CLAPS2, HHC3		9040778, 9767099, 23222959	Standard	XM_005258500		Approved	FBHOk, FBH3	uc002pft.1	P53680		ENST00000263270.6:c.178C>A	19.37:g.47342811G>T	ENSP00000263270:p.Arg60Ser	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	96	3	0.03125	NM_004069	B2R4Z4|O75977|Q6PK67	Missense_Mutation	SNP	ENST00000263270.6	37	CCDS33062.1	.	.	.	.	.	.	.	.	.	.	G	19.81	3.895791	0.72639	.	.	ENSG00000042753	ENST00000263270	.	.	.	4.94	1.57	0.23409	Clathrin adaptor complex, small chain (1);Longin-like (1);AP complex, mu/sigma subunit (1);	0.000000	0.85682	D	0.000000	T	0.81259	0.4785	H	0.95328	3.655	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	T	0.78929	-0.2010	9	0.87932	D	0	.	6.2344	0.20754	0.1646:0.0:0.6849:0.1505	.	60	P53680	AP2S1_HUMAN	S	60	.	ENSP00000263270:R60S	R	-	1	0	AP2S1	52034651	1.000000	0.71417	0.902000	0.35471	0.865000	0.49528	4.741000	0.62095	0.245000	0.21373	0.460000	0.39030	CGC	.	.	none		0.527	AP2S1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000466643.1		
CDC27	996	hgsc.bcm.edu	37	17	45234463	45234463	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:45234463A>C	ENST00000066544.3	-	7	751	c.658T>G	c.(658-660)Tcc>Gcc	p.S220A	CDC27_ENST00000528748.1_5'UTR|CDC27_ENST00000531206.1_Missense_Mutation_p.S220A|CDC27_ENST00000446365.2_Missense_Mutation_p.S159A|CDC27_ENST00000527547.1_Missense_Mutation_p.S220A	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	220					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						TTTGAATTGGAAGATTCTAAA	0.323																																					p.S220A		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,2	CDC27	337	2	0			c.T658G						scavenged	.						25.0	27.0	26.0					17																	45234463		2153	4281	6434	SO:0001583	missense	996	exon7			AATTGGAAGATTC	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.658T>G	17.37:g.45234463A>C	ENSP00000066544:p.Ser220Ala	Somatic	31	0	0		WXS	Illumina HiSeq	Phase_I	45	3	0.0666667	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	A	13.62	2.291146	0.40494	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68331	-0.32;-0.27;-0.05;-0.32;0.81	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.48150	0.1484	N	0.19112	0.55	0.58432	D	0.999998	B;B;B;B	0.21225	0.013;0.023;0.053;0.031	B;B;B;B	0.15484	0.004;0.004;0.013;0.009	T	0.45086	-0.9285	10	0.07175	T	0.84	-13.9867	13.9377	0.64034	1.0:0.0:0.0:0.0	.	159;220;220;220	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	A	220;220;159;220;220	ENSP00000066544:S220A;ENSP00000434614:S220A;ENSP00000392802:S159A;ENSP00000437339:S220A;ENSP00000432105:S220A	ENSP00000066544:S220A	S	-	1	0	CDC27	42589462	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.754000	0.91642	2.180000	0.69256	0.455000	0.32223	TCC	.	.	none		0.323	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
POTEC	388468	hgsc.bcm.edu	37	18	14542916	14542916	+	Missense_Mutation	SNP	G	G	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr18:14542916G>T	ENST00000358970.5	-	1	229	c.230C>A	c.(229-231)aCg>aAg	p.T77K	POTEC_ENST00000389891.4_5'UTR	NM_001137671.1	NP_001131143.1	B2RU33	POTEC_HUMAN	POTE ankyrin domain family, member C	77										NS(2)|breast(1)|endometrium(9)|kidney(13)|lung(14)|prostate(3)|skin(6)|soft_tissue(1)|urinary_tract(3)	52						CACGTTGCTCGTGCCGCTCCC	0.577																																					p.T77K		Atlas-SNP	.											POTEC,NS,carcinoma,+1,1	POTEC	129	1	0			c.C230A						scavenged	.						42.0	51.0	48.0					18																	14542916		692	1591	2283	SO:0001583	missense	388468	exon1			TTGCTCGTGCCGC	BX649118	CCDS45835.1	18p11.21	2013-01-10	2008-11-26	2008-11-26	ENSG00000183206	ENSG00000183206		"""POTE ankyrin domain containing"", ""Ankyrin repeat domain containing"""	33894	protein-coding gene	gene with protein product	"""cancer/testis antigen family 104, member 6"""		"""ANKRD26-like family B, member 2"""	A26B2			Standard	NM_001137671		Approved	POTE18, POTE-18, DKFZp686J0529, CT104.6	uc010dln.3	B2RU33	OTTHUMG00000162963	ENST00000358970.5:c.230C>A	18.37:g.14542916G>T	ENSP00000351856:p.Thr77Lys	Somatic	413	4	0.00968523		WXS	Illumina HiSeq	Phase_I	423	10	0.0236407	NM_001137671		Missense_Mutation	SNP	ENST00000358970.5	37	CCDS45835.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.707401	0.00096	.	.	ENSG00000183206	ENST00000358970;ENST00000389891	T	0.22743	1.94	0.429	-0.857	0.10693	.	.	.	.	.	T	0.03827	0.0108	N	0.00841	-1.15	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.19614	-1.0300	8	0.02654	T	1	.	.	.	.	.	77	B2RU33	POTEC_HUMAN	K	77	ENSP00000351856:T77K	ENSP00000351856:T77K	T	-	2	0	POTEC	14532916	0.000000	0.05858	0.000000	0.03702	0.005000	0.04900	-1.710000	0.01888	-2.489000	0.00518	-1.883000	0.00544	ACG	G|1.000;|0.000	.	weak		0.577	POTEC-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371179.1	XM_496269	
NBPF10	100132406	hgsc.bcm.edu	37	1	145323656	145323656	+	Missense_Mutation	SNP	A	A	T	rs75252120	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:145323656A>T	ENST00000342960.5	+	27	3528	c.3493A>T	c.(3493-3495)Att>Ttt	p.I1165F	NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000369338.1_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	752						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.I1165F(3)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		TATTGCAGGAATTAAAAAGGA	0.473																																					p.I1165F		Atlas-SNP	.											NBPF10,NS,carcinoma,0,7	NBPF10	221	7	3	Substitution - Missense(3)	endometrium(2)|kidney(1)	c.A3493T						scavenged	.																																			SO:0001583	missense	100132406	exon27			GCAGGAATTAAAA	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.3493A>T	1.37:g.145323656A>T	ENSP00000345684:p.Ile1165Phe	Somatic	43	1	0.0232558		WXS	Illumina HiSeq	Phase_I	71	12	0.169014	NM_001039703	Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	7.524	0.657305	0.14580	.	.	ENSG00000163386	ENST00000342960	T	0.03441	3.93	.	.	.	.	.	.	.	.	T	0.02342	0.0072	M	0.67953	2.075	0.09310	N	1	.	.	.	.	.	.	T	0.44065	-0.9352	5	0.28530	T	0.3	.	.	.	.	.	.	.	.	F	1165	ENSP00000345684:I1165F	ENSP00000345684:I1165F	I	+	1	0	NBPF10	144035013	0.353000	0.24904	0.005000	0.12908	0.123000	0.20343	1.122000	0.31295	0.386000	0.24997	0.128000	0.15822	ATT	A|0.625;T|0.375	0.375	strong		0.473	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
FLG	2312	hgsc.bcm.edu	37	1	152280691	152280691	+	Missense_Mutation	SNP	A	A	T	rs117945779	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:152280691A>T	ENST00000368799.1	-	3	6706	c.6671T>A	c.(6670-6672)cTg>cAg	p.L2224Q	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	2224	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)			CTGGCCCACCAGTGAGTGTCT	0.542									Ichthyosis				-|||	959	0.191494	0.1936	0.1873	5008	,	,		22319	0.3026		0.0706	False		,,,				2504	0.2014				p.L2224Q		Atlas-SNP	.											FLG,NS,malignant_melanoma,+1,1	FLG	900	1	0			c.T6671A						scavenged	.						260.0	255.0	257.0					1																	152280691		2203	4300	6503	SO:0001583	missense	2312	exon3	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	CCCACCAGTGAGT	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.6671T>A	1.37:g.152280691A>T	ENSP00000357789:p.Leu2224Gln	Somatic	328	33	0.10061		WXS	Illumina HiSeq	Phase_I	591	70	0.118443	NM_002016	Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	t	2.028	-0.423196	0.04734	.	.	ENSG00000143631	ENST00000368799	T	0.02656	4.21	0.883	-0.332	0.12675	.	.	.	.	.	T	0.00144	0.0004	N	0.00034	-2.56	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.30119	-0.9989	9	0.08381	T	0.77	.	1.4068	0.02283	0.3248:0.2503:0.0:0.4249	.	2224	P20930	FILA_HUMAN	Q	2224	ENSP00000357789:L2224Q	ENSP00000357789:L2224Q	L	-	2	0	FLG	150547315	0.313000	0.24554	0.000000	0.03702	0.001000	0.01503	-0.556000	0.05992	-0.732000	0.04856	-0.721000	0.03606	CTG	.	.	weak		0.542	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
OR52R1	119695	hgsc.bcm.edu	37	11	4825192	4825192	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:4825192G>A	ENST00000356069.2	-	1	418	c.419C>T	c.(418-420)aCc>aTc	p.T140I	MMP26_ENST00000477339.1_Intron|MMP26_ENST00000380390.1_Intron|OR52R1_ENST00000380382.1_Missense_Mutation_p.T219I	NM_001005177.3	NP_001005177.3	Q8NGF1	O52R1_HUMAN	olfactory receptor, family 52, subfamily R, member 1	140						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(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(14)|prostate(1)|skin(3)	29		Medulloblastoma(188;0.0025)|Breast(177;0.0184)|all_neural(188;0.0227)		Epithelial(150;4.77e-12)|BRCA - Breast invasive adenocarcinoma(625;0.00435)|LUSC - Lung squamous cell carcinoma(625;0.19)		GACCGATGGGGTCAGGATGCT	0.567																																					p.T140I		Atlas-SNP	.											.	OR52R1	81	.	0			c.C419T						PASS	.						105.0	93.0	97.0					11																	4825192		2201	4298	6499	SO:0001583	missense	119695	exon1			GATGGGGTCAGGA	BK004282	CCDS31360.1, CCDS31360.2	11p15.4	2012-08-09			ENSG00000176937	ENSG00000176937		"""GPCR / Class A : Olfactory receptors"""	15235	protein-coding gene	gene with protein product							Standard	NM_001005177		Approved		uc021qcs.1	Q8NGF1	OTTHUMG00000066510	ENST00000356069.2:c.419C>T	11.37:g.4825192G>A	ENSP00000348368:p.Thr140Ile	Somatic	52	0	0		WXS	Illumina HiSeq	Phase_I	56	27	0.482143	NM_001005177	Q6IFI0	Missense_Mutation	SNP	ENST00000356069.2	37	CCDS31360.2	.	.	.	.	.	.	.	.	.	.	G	14.60	2.582644	0.46006	.	.	ENSG00000176937	ENST00000356069;ENST00000380382	T;T	0.00381	7.63;7.63	5.42	5.42	0.78866	GPCR, rhodopsin-like superfamily (1);	0.133368	0.33670	N	0.004668	T	0.01661	0.0053	H	0.97611	4.04	0.32673	N	0.51654	D	0.60160	0.987	P	0.57776	0.827	T	0.01961	-1.1239	10	0.87932	D	0	.	17.9523	0.89057	0.0:0.0:1.0:0.0	.	140	Q8NGF1	O52R1_HUMAN	I	140;219	ENSP00000348368:T140I;ENSP00000369742:T219I	ENSP00000348368:T140I	T	-	2	0	OR52R1	4781768	0.021000	0.18746	0.396000	0.26296	0.137000	0.21094	1.265000	0.33027	2.826000	0.97356	0.650000	0.86243	ACC	.	.	none		0.567	OR52R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142183.1	NM_001005177	
ARHGAP28	79822	hgsc.bcm.edu	37	18	6882194	6882194	+	Missense_Mutation	SNP	T	T	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr18:6882194T>A	ENST00000383472.4	+	11	1453	c.1349T>A	c.(1348-1350)aTg>aAg	p.M450K	ARHGAP28_ENST00000314319.3_Missense_Mutation_p.M291K|ARHGAP28_ENST00000418986.1_Missense_Mutation_p.M291K|ARHGAP28_ENST00000400091.2_Missense_Mutation_p.M450K|ARHGAP28_ENST00000531294.1_Missense_Mutation_p.M286K|ARHGAP28_ENST00000419673.2_Missense_Mutation_p.M291K|ARHGAP28_ENST00000262227.3_Missense_Mutation_p.M398K|ARHGAP28_ENST00000532996.1_Missense_Mutation_p.M273K			Q9P2N2	RHG28_HUMAN	Rho GTPase activating protein 28	450	Rho-GAP. {ECO:0000255|PROSITE- ProRule:PRU00172}.				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)				TGGGACAAAATGTGCCATAGA	0.383																																					p.M291K		Atlas-SNP	.											.	ARHGAP28	181	.	0			c.T872A						PASS	.						174.0	167.0	169.0					18																	6882194		2203	4300	6503	SO:0001583	missense	79822	exon10			ACAAAATGTGCCA	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.1349T>A	18.37:g.6882194T>A	ENSP00000372964:p.Met450Lys	Somatic	172	0	0		WXS	Illumina HiSeq	Phase_I	101	83	0.821782	NM_001010000	A8MQB7|A8MU88|Q6P160|Q8N4T3|Q9NW53	Missense_Mutation	SNP	ENST00000383472.4	37		.	.	.	.	.	.	.	.	.	.	T	25.4	4.633106	0.87660	.	.	ENSG00000088756	ENST00000400091;ENST00000262227;ENST00000419673;ENST00000531294;ENST00000314319;ENST00000418986;ENST00000532996;ENST00000383472	T;T;T;T;T;T	0.41065	1.01;1.01;1.01;1.01;1.01;1.01	5.68	5.68	0.88126	Rho GTPase-activating protein domain (4);Rho GTPase activation protein (1);	0.048511	0.85682	D	0.000000	T	0.42063	0.1186	N	0.22421	0.69	0.44409	D	0.997329	P;P;P;B	0.49961	0.93;0.8;0.762;0.239	P;P;P;B	0.50270	0.631;0.636;0.503;0.249	T	0.42032	-0.9475	10	0.72032	D	0.01	.	15.9369	0.79717	0.0:0.0:0.0:1.0	.	450;282;291;398	Q9P2N2;E9PRP2;F6VKJ9;Q9P2N2-2	RHG28_HUMAN;.;.;.	K	450;398;291;286;291;291;282;273	ENSP00000382963:M450K;ENSP00000262227:M398K;ENSP00000392660:M291K;ENSP00000437262:M286K;ENSP00000313506:M291K;ENSP00000406907:M291K	ENSP00000262227:M398K	M	+	2	0	ARHGAP28	6872194	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.655000	0.74392	2.172000	0.68678	0.533000	0.62120	ATG	.	.	none		0.383	ARHGAP28-006	NOVEL	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000442123.3	XM_371108	
EEF2K	29904	hgsc.bcm.edu	37	16	22291669	22291669	+	Nonsense_Mutation	SNP	C	C	A	rs150317840		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr16:22291669C>A	ENST00000263026.5	+	17	2514	c.2040C>A	c.(2038-2040)taC>taA	p.Y680*		NM_013302.3	NP_037434	O00418	EF2K_HUMAN	eukaryotic elongation factor-2 kinase	680					insulin receptor signaling pathway (GO:0008286)|protein autophosphorylation (GO:0046777)|regulation of protein autophosphorylation (GO:0031952)|translational elongation (GO:0006414)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|elongation factor-2 kinase activity (GO:0004686)|protein kinase activity (GO:0004672)|translation factor activity, nucleic acid binding (GO:0008135)			breast(1)|central_nervous_system(1)|endometrium(8)|large_intestine(2)|lung(13)|ovary(1)|prostate(1)|skin(2)	29				GBM - Glioblastoma multiforme(48;0.0223)		CAGGAGGCTACGGGCTGGAGA	0.622																																					p.Y680X	NSCLC(195;1411 2157 20319 27471 51856)	Atlas-SNP	.											EEF2K_ENST00000263026,NS,carcinoma,0,2	EEF2K	142	2	0			c.C2040A						scavenged	.						64.0	47.0	53.0					16																	22291669		2197	4300	6497	SO:0001587	stop_gained	29904	exon17			AGGCTACGGGCTG	U93850	CCDS10604.1	16p12	2008-02-05			ENSG00000103319	ENSG00000103319			24615	protein-coding gene	gene with protein product		606968				9144159, 12051769	Standard	NM_013302		Approved	eEF-2K	uc002dki.3	O00418	OTTHUMG00000094771	ENST00000263026.5:c.2040C>A	16.37:g.22291669C>A	ENSP00000263026:p.Tyr680*	Somatic	59	0	0		WXS	Illumina HiSeq	Phase_I	91	2	0.021978	NM_013302	Q8N588	Nonsense_Mutation	SNP	ENST00000263026.5	37	CCDS10604.1	.	.	.	.	.	.	.	.	.	.	C	36	5.731940	0.96856	.	.	ENSG00000103319	ENST00000263026	.	.	.	5.58	-7.59	0.01308	.	0.407571	0.31809	N	0.007022	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.5859	15.2201	0.73306	0.0:0.4341:0.0:0.5659	.	.	.	.	X	680	.	ENSP00000263026:Y680X	Y	+	3	2	EEF2K	22199170	0.000000	0.05858	0.000000	0.03702	0.008000	0.06430	-0.792000	0.04594	-2.102000	0.00845	-1.267000	0.01435	TAC	C|1.000;T|0.000	.	alt		0.622	EEF2K-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000211580.2	NM_013302	
PIWIL1	9271	hgsc.bcm.edu	37	12	130847589	130847589	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:130847589G>A	ENST00000245255.3	+	18	2367	c.2095G>A	c.(2095-2097)Gtg>Atg	p.V699M		NM_001190971.1|NM_004764.4	NP_001177900.1|NP_004755.2	Q96J94	PIWL1_HUMAN	piwi-like RNA-mediated gene silencing 1	699	Piwi. {ECO:0000255|PROSITE- ProRule:PRU00150}.				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)|spermatid development (GO:0007286)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mRNA cap binding complex (GO:0005845)|P granule (GO:0043186)|polysome (GO:0005844)	mRNA binding (GO:0003729)|piRNA binding (GO:0034584)|single-stranded RNA binding (GO:0003727)			breast(6)|cervix(1)|endometrium(2)|kidney(4)|large_intestine(8)|lung(26)|ovary(2)|prostate(4)|skin(3)|urinary_tract(1)	57	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;3.02e-06)|Epithelial(86;3.85e-05)|all cancers(50;4.65e-05)		CCGGATCATCGTGTACCGCGA	0.488																																					p.V699M		Atlas-SNP	.											.	PIWIL1	157	.	0			c.G2095A						PASS	.						114.0	112.0	113.0					12																	130847589		2203	4300	6503	SO:0001583	missense	9271	exon18			ATCATCGTGTACC	AF104260	CCDS9268.1	12q24.33	2014-01-21	2013-02-15		ENSG00000125207	ENSG00000125207		"""Argonaute/PIWI family"""	9007	protein-coding gene	gene with protein product		605571	"""piwi (Drosophila)-like 1"", ""piwi-like 1 (Drosophila)"""			9851978, 12906857	Standard	NM_004764		Approved	PIWI, HIWI, CT80.1	uc001uik.3	Q96J94	OTTHUMG00000168382	ENST00000245255.3:c.2095G>A	12.37:g.130847589G>A	ENSP00000245255:p.Val699Met	Somatic	139	0	0		WXS	Illumina HiSeq	Phase_I	130	43	0.330769	NM_004764	A4F266|O95404|Q8NA60|Q8TBY5|Q96JD5	Missense_Mutation	SNP	ENST00000245255.3	37	CCDS9268.1	.	.	.	.	.	.	.	.	.	.	G	18.80	3.700418	0.68501	.	.	ENSG00000125207	ENST00000245255	T	0.16597	2.33	5.66	5.66	0.87406	Stem cell self-renewal protein Piwi (3);Ribonuclease H-like (1);	0.056584	0.64402	D	0.000001	T	0.37785	0.1016	M	0.79258	2.445	0.58432	D	0.999999	D;D	0.71674	0.998;0.994	P;P	0.59546	0.859;0.815	T	0.14699	-1.0463	10	0.66056	D	0.02	-15.817	12.0926	0.53736	0.0782:0.0:0.9218:0.0	.	699;699	Q96J94;Q96J94-2	PIWL1_HUMAN;.	M	699	ENSP00000245255:V699M	ENSP00000245255:V699M	V	+	1	0	PIWIL1	129413542	1.000000	0.71417	0.960000	0.40013	0.456000	0.32438	5.444000	0.66587	2.663000	0.90544	0.591000	0.81541	GTG	.	.	none		0.488	PIWIL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399510.1		
SLC35F4	341880	hgsc.bcm.edu	37	14	58060834	58060834	+	Nonsense_Mutation	SNP	T	T	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr14:58060834T>A	ENST00000339762.6	-	2	219	c.220A>T	c.(220-222)Aga>Tga	p.R74*	SLC35F4_ENST00000557430.1_5'UTR|SLC35F4_ENST00000556826.1_Nonsense_Mutation_p.R38*|SLC35F4_ENST00000554729.1_5'UTR			A4IF30	S35F4_HUMAN	solute carrier family 35, member F4	74					transport (GO:0006810)	integral component of membrane (GO:0016021)				breast(1)|endometrium(4)|large_intestine(3)|lung(12)|ovary(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	24						ACTGATGATCTGGAGGTACCT	0.438																																					p.R38X		Atlas-SNP	.											SLC35F4_ENST00000339762,NS,carcinoma,0,2	SLC35F4	105	2	0			c.A112T						scavenged	.						64.0	64.0	64.0					14																	58060834		1919	4122	6041	SO:0001587	stop_gained	341880	exon2			ATGATCTGGAGGT			14q22.3	2013-05-22		2003-11-28	ENSG00000151812	ENSG00000151812		"""Solute carriers"""	19845	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 36"""	C14orf36			Standard	NM_001206920		Approved	FLJ37712	uc021rtp.1	A4IF30	OTTHUMG00000171317	ENST00000339762.6:c.220A>T	14.37:g.58060834T>A	ENSP00000342518:p.Arg74*	Somatic	81	1	0.0123457		WXS	Illumina HiSeq	Phase_I	74	2	0.027027	NM_001206920	A6NDQ3	Nonsense_Mutation	SNP	ENST00000339762.6	37		.	.	.	.	.	.	.	.	.	.	T	25.5	4.647311	0.87958	.	.	ENSG00000151812	ENST00000556826;ENST00000339762	.	.	.	5.83	3.3	0.37823	.	0.057562	0.64402	D	0.000003	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-16.7166	11.4724	0.50278	0.0:0.0:0.4577:0.5423	.	.	.	.	X	38;74	.	ENSP00000342518:R74X	R	-	1	2	SLC35F4	57130587	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	2.437000	0.44828	1.006000	0.39211	0.477000	0.44152	AGA	.	.	none		0.438	SLC35F4-201	KNOWN	basic	protein_coding	protein_coding		XM_292260	
TRMT13	54482	hgsc.bcm.edu	37	1	100606488	100606488	+	Silent	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:100606488A>G	ENST00000370141.2	+	7	588	c.582A>G	c.(580-582)ggA>ggG	p.G194G		NM_019083.2	NP_061956.2	Q9NUP7	TRM13_HUMAN	tRNA methyltransferase 13 homolog (S. cerevisiae)	194					tRNA processing (GO:0008033)		metal ion binding (GO:0046872)|methyltransferase activity (GO:0008168)										CGGGAAAGGGAAAATTATCTC	0.363																																					p.G194G		Atlas-SNP	.											CCDC76,NS,carcinoma,+2,1	.	.	1	0			c.A582G						scavenged	.						131.0	126.0	128.0					1																	100606488		2203	4300	6503	SO:0001819	synonymous_variant	54482	exon7			AAAGGGAAAATTA	BC075811	CCDS765.1	1p21.2	2012-06-07	2012-06-07	2012-06-07	ENSG00000122435	ENSG00000122435			25502	protein-coding gene	gene with protein product			"""coiled-coil domain containing 76"""	CCDC76		11799066	Standard	NM_019083		Approved	FLJ10287, FLJ11219	uc001dsv.3	Q9NUP7	OTTHUMG00000010841	ENST00000370141.2:c.582A>G	1.37:g.100606488A>G		Somatic	143	1	0.00699301		WXS	Illumina HiSeq	Phase_I	77	2	0.025974	NM_019083	Q5VVL0|Q9NW65	Silent	SNP	ENST00000370141.2	37	CCDS765.1																																																																																			.	.	none		0.363	TRMT13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029919.1	NM_019083	
KIAA1244	57221	hgsc.bcm.edu	37	6	138531058	138531058	+	Silent	SNP	G	G	A	rs138636575		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:138531058G>A	ENST00000251691.4	+	4	397	c.231G>A	c.(229-231)tcG>tcA	p.S77S		NM_020340.4	NP_065073.3			KIAA1244									p.S6S(1)		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)		AGCTTCTGTCGGAAGAGAGGT	0.458																																					p.S77S		Atlas-SNP	.											KIAA1244,NS,carcinoma,0,1	KIAA1244	236	1	1	Substitution - coding silent(1)	lung(1)	c.G231A						scavenged	.	G		1,4405	2.1+/-5.4	0,1,2202	139.0	133.0	135.0		231	-11.1	0.3	6	dbSNP_134	135	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	KIAA1244	NM_020340.4		0,2,6501	AA,AG,GG		0.0116,0.0227,0.0154		77/2178	138531058	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	57221	exon4			TCTGTCGGAAGAG	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.231G>A	6.37:g.138531058G>A		Somatic	175	0	0		WXS	Illumina HiSeq	Phase_I	174	4	0.0229885	NM_020340		Silent	SNP	ENST00000251691.4	37	CCDS5189.2																																																																																			G|1.000;A|0.000	0.000	weak		0.458	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
MAPK8IP1	9479	hgsc.bcm.edu	37	11	45926727	45926727	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:45926727C>T	ENST00000241014.2	+	11	2160	c.1990C>T	c.(1990-1992)Ccc>Tcc	p.P664S	MAPK8IP1_ENST00000395629.2_Missense_Mutation_p.P654S|RP11-618K13.2_ENST00000533218.1_RNA	NM_005456.3	NP_005447.1	Q9UQF2	JIP1_HUMAN	mitogen-activated protein kinase 8 interacting protein 1	664	PID. {ECO:0000255|PROSITE- ProRule:PRU00148}.				JUN phosphorylation (GO:0007258)|negative regulation of apoptotic process (GO:0043066)|negative regulation of intrinsic apoptotic signaling pathway (GO:2001243)|negative regulation of JNK cascade (GO:0046329)|negative regulation of JUN kinase activity (GO:0043508)|positive regulation of signal transduction (GO:0009967)|regulation of JNK cascade (GO:0046328)|regulation of transcription, DNA-templated (GO:0006355)|vesicle-mediated transport (GO:0016192)	axonal growth cone (GO:0044295)|cell body (GO:0044297)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic growth cone (GO:0044294)|dentate gyrus mossy fiber (GO:0044302)|endoplasmic reticulum (GO:0005783)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|synapse (GO:0045202)	kinesin binding (GO:0019894)|MAP-kinase scaffold activity (GO:0005078)|protein kinase inhibitor activity (GO:0004860)			breast(1)|endometrium(2)|kidney(2)|large_intestine(7)|lung(7)|ovary(2)|prostate(1)|skin(2)	24				GBM - Glioblastoma multiforme(35;0.231)		CACCAAGCACCCCGCCGACCA	0.632																																					p.P664S		Atlas-SNP	.											MAPK8IP1,hand,carcinoma,-1,3	MAPK8IP1	51	3	0			c.C1990T						scavenged	.						62.0	60.0	61.0					11																	45926727		2203	4299	6502	SO:0001583	missense	9479	exon11			AAGCACCCCGCCG		CCDS7916.1	11p11.2	2009-07-24			ENSG00000121653	ENSG00000121653			6882	protein-coding gene	gene with protein product		604641		PRKM8IP		9235893, 9442013	Standard	NM_005456		Approved	IB1, JIP-1, JIP1	uc001nbr.3	Q9UQF2	OTTHUMG00000134324	ENST00000241014.2:c.1990C>T	11.37:g.45926727C>T	ENSP00000241014:p.Pro664Ser	Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	120	4	0.0333333	NM_005456	D3DQP4|O43407	Missense_Mutation	SNP	ENST00000241014.2	37	CCDS7916.1	.	.	.	.	.	.	.	.	.	.	C	30	5.053254	0.93793	.	.	ENSG00000121653	ENST00000241014;ENST00000395629	T;T	0.15139	2.45;2.45	5.02	5.02	0.67125	Phosphotyrosine interaction domain (3);Pleckstrin homology-type (1);	0.056060	0.64402	D	0.000001	T	0.36908	0.0984	L	0.60455	1.87	0.80722	D	1	D	0.54397	0.966	P	0.59643	0.861	T	0.06356	-1.0831	10	0.87932	D	0	-10.9472	18.8901	0.92397	0.0:1.0:0.0:0.0	.	664	Q9UQF2	JIP1_HUMAN	S	664;654	ENSP00000241014:P664S;ENSP00000378991:P654S	ENSP00000241014:P664S	P	+	1	0	MAPK8IP1	45883303	1.000000	0.71417	0.999000	0.59377	0.959000	0.62525	7.589000	0.82641	2.775000	0.95449	0.655000	0.94253	CCC	.	.	none		0.632	MAPK8IP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259405.1	NM_005456	
TREML2	79865	hgsc.bcm.edu	37	6	41166119	41166119	+	Missense_Mutation	SNP	T	T	C	rs76984414		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:41166119T>C	ENST00000483722.1	-	2	289	c.104A>G	c.(103-105)gAg>gGg	p.E35G		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	35	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					AGACAGAGTCTCCCCTTCAAG	0.498																																					p.E35G		Atlas-SNP	.											TREML2,colon,carcinoma,0,2	TREML2	41	2	0			c.A104G						scavenged	.						132.0	135.0	134.0					6																	41166119		2203	4300	6503	SO:0001583	missense	79865	exon2			AGAGTCTCCCCTT	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.104A>G	6.37:g.41166119T>C	ENSP00000418767:p.Glu35Gly	Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	99	9	0.0909091	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	37	CCDS4853.2	.	.	.	.	.	.	.	.	.	.	.	7.815	0.716447	0.15306	.	.	ENSG00000112195	ENST00000483722	T	0.20598	2.06	4.75	3.58	0.41010	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.462226	0.19397	N	0.115265	T	0.05410	0.0143	L	0.33245	0.995	0.26220	N	0.979173	B	0.14438	0.01	B	0.12156	0.007	T	0.37596	-0.9699	10	0.29301	T	0.29	-14.8097	9.5481	0.39293	0.0:0.0923:0.0:0.9077	.	35	Q5T2D2	TRML2_HUMAN	G	35	ENSP00000418767:E35G	ENSP00000418767:E35G	E	-	2	0	TREML2	41274097	1.000000	0.71417	0.999000	0.59377	0.017000	0.09413	1.360000	0.34125	0.283000	0.22279	-1.195000	0.01675	GAG	.	.	weak		0.498	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807	
MED27	9442	hgsc.bcm.edu	37	9	134736013	134736013	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:134736013C>T	ENST00000292035.5	-	8	911	c.848G>A	c.(847-849)cGc>cAc	p.R283H	MED27_ENST00000357028.2_Missense_Mutation_p.R247H	NM_004269.3	NP_004260.2	Q6P2C8	MED27_HUMAN	mediator complex subunit 27	283					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)	cytoplasm (GO:0005737)|mediator complex (GO:0016592)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	transcription coactivator activity (GO:0003713)			breast(1)|endometrium(4)|kidney(3)|large_intestine(3)|lung(5)|skin(1)|urinary_tract(1)	18		Myeloproliferative disorder(178;0.206)		OV - Ovarian serous cystadenocarcinoma(145;6.82e-06)|Epithelial(140;0.000193)		CTTCCCGCAGCGCTGGCACGG	0.562																																					p.R283H	Colon(41;784 923 6932 42329 52483)	Atlas-SNP	.											.	MED27	37	.	0			c.G848A						PASS	.						33.0	32.0	32.0					9																	134736013		2203	4300	6503	SO:0001583	missense	9442	exon8			CCGCAGCGCTGGC	AF104252	CCDS6945.1, CCDS59153.1, CCDS69689.1	9q34.13	2008-02-05	2007-07-30	2007-07-30	ENSG00000160563	ENSG00000160563			2377	protein-coding gene	gene with protein product		605044	"""cofactor required for Sp1 transcriptional activation, subunit 8, 34kDa"""	CRSP8		9989412	Standard	NM_004269		Approved	TRAP37, CRSP34	uc004cbe.2	Q6P2C8	OTTHUMG00000020833	ENST00000292035.5:c.848G>A	9.37:g.134736013C>T	ENSP00000292035:p.Arg283His	Somatic	141	0	0		WXS	Illumina HiSeq	Phase_I	121	9	0.0743802	NM_004269	O95401|Q4F964|Q5VTA4|Q5VTA5|Q9BU57|Q9NYR4|V9GYV9	Missense_Mutation	SNP	ENST00000292035.5	37	CCDS6945.1	.	.	.	.	.	.	.	.	.	.	C	33	5.219164	0.95104	.	.	ENSG00000160563	ENST00000292035;ENST00000357028;ENST00000372184	.	.	.	5.3	5.3	0.74995	.	0.000000	0.85682	D	0.000000	T	0.78572	0.4304	M	0.73598	2.24	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.74674	0.984;0.96	T	0.80600	-0.1310	9	0.62326	D	0.03	0.0762	16.105	0.81213	0.0:1.0:0.0:0.0	.	247;283	Q6P2C8-2;Q6P2C8	.;MED27_HUMAN	H	283;209;247	.	ENSP00000292035:R283H	R	-	2	0	MED27	133725834	1.000000	0.71417	1.000000	0.80357	1.000000	0.99986	7.611000	0.82962	2.472000	0.83506	0.655000	0.94253	CGC	.	.	none		0.562	MED27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054770.2	NM_004269	
ABLIM1	3983	hgsc.bcm.edu	37	10	116331143	116331143	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:116331143G>A	ENST00000277895.5	-	4	683	c.586C>T	c.(586-588)Cga>Tga	p.R196*	ABLIM1_ENST00000533213.2_Nonsense_Mutation_p.R136*|ABLIM1_ENST00000369252.4_Nonsense_Mutation_p.R136*	NM_002313.5	NP_002304.3	O14639	ABLM1_HUMAN	actin binding LIM protein 1	196	LIM zinc-binding 2. {ECO:0000255|PROSITE- ProRule:PRU00125}.				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)		AATGTGACTCGGTCTCCGGGT	0.537																																					p.R196X		Atlas-SNP	.											.	ABLIM1	131	.	0			c.C586T						PASS	.						121.0	118.0	119.0					10																	116331143		2203	4300	6503	SO:0001587	stop_gained	3983	exon4			TGACTCGGTCTCC	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.586C>T	10.37:g.116331143G>A	ENSP00000277895:p.Arg196*	Somatic	85	0	0		WXS	Illumina HiSeq	Phase_I	106	52	0.490566	NM_002313	A6NI16|A6NJ06|A8MXA9|B3KVH2|Q15039|Q5JVV1|Q5JVV2|Q5T6N2|Q5T6N3|Q5T6N5|Q68CQ9|Q9BUP1	Nonsense_Mutation	SNP	ENST00000277895.5	37	CCDS7590.1	.	.	.	.	.	.	.	.	.	.	G	39	7.324017	0.98210	.	.	ENSG00000099204	ENST00000336585;ENST00000369252;ENST00000369267;ENST00000533213;ENST00000369262;ENST00000369263;ENST00000369256;ENST00000369260;ENST00000277895	.	.	.	5.97	5.02	0.67125	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	13.8323	0.63389	0.0:0.0:0.7325:0.2675	.	.	.	.	X	196;136;136;136;196;120;120;120;196	.	ENSP00000277895:R196X	R	-	1	2	ABLIM1	116321133	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.205000	0.58466	2.836000	0.97738	0.655000	0.94253	CGA	.	.	none		0.537	ABLIM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050469.3		
MUC2	4583	hgsc.bcm.edu	37	11	1093072	1093072	+	Missense_Mutation	SNP	G	G	C	rs12575990	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:1093072G>C	ENST00000441003.2	+	30	4918	c.4891G>C	c.(4891-4893)Gcc>Ccc	p.A1631P	MUC2_ENST00000361558.6_Intron|MUC2_ENST00000359061.5_Missense_Mutation_p.A1598P|MUC2_ENST00000333592.6_5'Flank	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)	aaccccaacagccatcaccac	0.627																																					p.A1631P		Atlas-SNP	.											MUC2_ENST00000441003,NS,carcinoma,0,2	MUC2	614	2	0			c.G4891C						scavenged	.						113.0	159.0	143.0					11																	1093072		1870	3587	5457	SO:0001583	missense	4583	exon30			CCAACAGCCATCA	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.4891G>C	11.37:g.1093072G>C	ENSP00000415183:p.Ala1631Pro	Somatic	39	9	0.230769		WXS	Illumina HiSeq	Phase_I	69	12	0.173913	NM_002457	Q14878	Missense_Mutation	SNP	ENST00000441003.2	37		.	.	.	.	.	.	.	.	.	.	C	1.747	-0.490205	0.04322	.	.	ENSG00000198788	ENST00000441003;ENST00000359061	T;T	0.11385	2.78;3.19	1.75	-3.51	0.04696	.	.	.	.	.	T	0.06234	0.0161	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.28522	-1.0041	8	0.31617	T	0.26	.	4.9505	0.14011	0.473:0.205:0.3219:0.0	rs12575990;rs57525069	1631	E7EUV1	.	P	1631;1598	ENSP00000415183:A1631P;ENSP00000351956:A1598P	ENSP00000351956:A1598P	A	+	1	0	MUC2	1083072	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-1.737000	0.01843	-2.884000	0.00318	-2.023000	0.00429	GCC	.	.	weak		0.627	MUC2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000345894.2	NM_002457	
TTN	7273	hgsc.bcm.edu	37	2	179398481	179398481	+	Silent	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:179398481A>G	ENST00000591111.1	-	308	98162	c.97938T>C	c.(97936-97938)ccT>ccC	p.P32646P	TTN-AS1_ENST00000588244.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN_ENST00000342992.6_Silent_p.P31719P|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN_ENST00000589042.1_Silent_p.P34287P|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN_ENST00000342175.6_Silent_p.P25414P|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN_ENST00000460472.2_Silent_p.P25222P|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN_ENST00000359218.5_Silent_p.P25347P			Q8WZ42	TITIN_HUMAN	titin	32646	Ig-like 144.				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)			ATGTTACATGAGGCTCTGGGT	0.403																																					p.P34287P		Atlas-SNP	.											TTN_ENST00000359218,NS,carcinoma,-1,4	TTN	18412	4	0			c.T102861C						scavenged	.						113.0	103.0	106.0					2																	179398481		1907	4116	6023	SO:0001819	synonymous_variant	7273	exon358			TACATGAGGCTCT	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.97938T>C	2.37:g.179398481A>G		Somatic	91	0	0		WXS	Illumina HiSeq	Phase_I	136	2	0.0147059	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																																																																																				.	.	none		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
WIPI1	55062	hgsc.bcm.edu	37	17	66449072	66449072	+	Silent	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:66449072G>A	ENST00000262139.5	-	2	141	c.142C>T	c.(142-144)Ctg>Ttg	p.L48L	WIPI1_ENST00000589459.1_Intron|WIPI1_ENST00000546360.1_Intron	NM_017983.5	NP_060453.3	Q5MNZ9	WIPI1_HUMAN	WD repeat domain, phosphoinositide interacting 1	48					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|autophagy (GO:0006914)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|vesicle targeting, trans-Golgi to endosome (GO:0048203)	autophagic vacuole membrane (GO:0000421)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytoskeleton (GO:0005856)|endosome membrane (GO:0010008)|Golgi membrane (GO:0000139)|pre-autophagosomal structure (GO:0000407)|pre-autophagosomal structure membrane (GO:0034045)|trans-Golgi network (GO:0005802)	androgen receptor binding (GO:0050681)|estrogen receptor binding (GO:0030331)|phosphatidylinositol-3,5-bisphosphate binding (GO:0080025)|phosphatidylinositol-3-phosphate binding (GO:0032266)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(4)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	18						ACTTGATCCAGCTGCTCCACA	0.502																																					p.L48L		Atlas-SNP	.											.	WIPI1	46	.	0			c.C142T						PASS	.						121.0	106.0	111.0					17																	66449072		2203	4300	6503	SO:0001819	synonymous_variant	55062	exon2			GATCCAGCTGCTC		CCDS11677.1	17q24.2	2014-02-12				ENSG00000070540		"""WD repeat domain containing"""	25471	protein-coding gene	gene with protein product		609224				15020712, 15602573	Standard	NM_017983		Approved	FLJ10055, WIPI49, Atg18, ATG18A	uc010dey.3	Q5MNZ9		ENST00000262139.5:c.142C>T	17.37:g.66449072G>A		Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	68	4	0.0588235	NM_017983	Q8IXM5|Q9NWF8	Silent	SNP	ENST00000262139.5	37	CCDS11677.1																																																																																			.	.	none		0.502	WIPI1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000448739.1	NM_017983	
MUC4	4585	hgsc.bcm.edu	37	3	195509622	195509622	+	Silent	SNP	G	G	C	rs199744021	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:195509622G>C	ENST00000463781.3	-	2	9288	c.8829C>G	c.(8827-8829)acC>acG	p.T2943T	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Silent_p.T2943T	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.T2943T(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)		CAGGAAGAGGGGTGGTGTCAC	0.597													.|||	7	0.00139776	0.003	0.0014	5008	,	,		9829	0.0		0.0	False		,,,				2504	0.002				p.T2943T		Atlas-SNP	.											MUC4_ENST00000463781,NS,carcinoma,0,1	MUC4	1505	1	1	Substitution - coding silent(1)	endometrium(1)	c.C8829G						scavenged	.																																			SO:0001819	synonymous_variant	4585	exon2			AAGAGGGGTGGTG	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.8829C>G	3.37:g.195509622G>C		Somatic	150	6	0.04		WXS	Illumina HiSeq	Phase_I	185	19	0.102703	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		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
CYP2F1	1572	hgsc.bcm.edu	37	19	41633809	41633809	+	Missense_Mutation	SNP	G	G	A	rs139951793	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:41633809G>A	ENST00000331105.2	+	10	1370	c.1298G>A	c.(1297-1299)cGc>cAc	p.R433H		NM_000774.3	NP_000765.2	P24903	CP2F1_HUMAN	cytochrome P450, family 2, subfamily F, polypeptide 1	433					naphthalene metabolic process (GO:0018931)|response to toxic substance (GO:0009636)|small molecule metabolic process (GO:0044281)|trichloroethylene metabolic process (GO:0018979)|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, 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)			central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(11)|ovary(2)|skin(2)	29						CCTGCAGGGCGCCGTCTGTGC	0.612																																					p.R433H		Atlas-SNP	.											CYP2F1,NS,lymphoid_neoplasm,0,2	CYP2F1	60	2	0			c.G1298A						scavenged	.						14.0	16.0	15.0					19																	41633809		2197	4288	6485	SO:0001583	missense	1572	exon10			CAGGGCGCCGTCT	J02906	CCDS12572.1	19q13.1-q13.2	2008-02-05	2003-01-14		ENSG00000197446	ENSG00000197446		"""Cytochrome P450s"""	2632	protein-coding gene	gene with protein product		124070	"""cytochrome P450, subfamily IIF, polypeptide 1"""	CYP2F			Standard	NM_000774		Approved		uc002opu.1	P24903	OTTHUMG00000167412	ENST00000331105.2:c.1298G>A	19.37:g.41633809G>A	ENSP00000333534:p.Arg433His	Somatic	225	24	0.106667		WXS	Illumina HiSeq	Phase_I	197	16	0.0812183	NM_000774	A7KAU6|A7KAU7|A7KAU8|A7KAU9|A7KAV0|Q32MN5|Q8WWJ2	Missense_Mutation	SNP	ENST00000331105.2	37	CCDS12572.1	.	.	.	.	.	.	.	.	.	.	g	12.45	1.941510	0.34283	.	.	ENSG00000197446	ENST00000331105	T	0.70631	-0.5	3.1	2.05	0.26809	Cytochrome P450, conserved site (1);	0.176601	0.41194	U	0.000921	T	0.56202	0.1969	L	0.58510	1.815	0.09310	N	1	P	0.40515	0.719	B	0.29862	0.108	T	0.55661	-0.8106	10	0.87932	D	0	.	5.1896	0.15203	0.2785:0.0:0.7215:0.0	.	433	P24903	CP2F1_HUMAN	H	433	ENSP00000333534:R433H	ENSP00000333534:R433H	R	+	2	0	CYP2F1	46325649	0.000000	0.05858	0.010000	0.14722	0.328000	0.28507	0.452000	0.21795	0.529000	0.28599	0.089000	0.15464	CGC	G|0.994;A|0.006	0.006	strong		0.612	CYP2F1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394527.2		
TM9SF2	9375	hgsc.bcm.edu	37	13	100204538	100204538	+	Silent	SNP	G	G	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr13:100204538G>C	ENST00000376387.4	+	13	1636	c.1446G>C	c.(1444-1446)gtG>gtC	p.V482V		NM_004800.1	NP_004791.1	Q99805	TM9S2_HUMAN	transmembrane 9 superfamily member 2	482					transport (GO:0006810)	endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)				endometrium(3)|kidney(1)|large_intestine(5)|lung(5)|ovary(1)|prostate(2)	17	all_neural(89;0.0837)|Medulloblastoma(90;0.18)|Lung SC(71;0.218)					GCATATCTGTGCCTCTGACGT	0.388																																					p.V482V		Atlas-SNP	.											.	TM9SF2	52	.	0			c.G1446C						PASS	.						213.0	195.0	201.0					13																	100204538		2203	4300	6503	SO:0001819	synonymous_variant	9375	exon13			ATCTGTGCCTCTG	U81006	CCDS9493.1	13q32.2	2011-03-28			ENSG00000125304	ENSG00000125304			11865	protein-coding gene	gene with protein product		604678				9729438	Standard	NM_004800		Approved	P76	uc001voj.2	Q99805	OTTHUMG00000017272	ENST00000376387.4:c.1446G>C	13.37:g.100204538G>C		Somatic	177	0	0		WXS	Illumina HiSeq	Phase_I	234	25	0.106838	NM_004800	A8K399|Q2TAY5	Silent	SNP	ENST00000376387.4	37	CCDS9493.1																																																																																			.	.	none		0.388	TM9SF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045602.3		
NEK1	4750	hgsc.bcm.edu	37	4	170400567	170400567	+	Missense_Mutation	SNP	T	T	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:170400567T>A	ENST00000439128.2	-	22	2682	c.2042A>T	c.(2041-2043)aAa>aTa	p.K681I	NEK1_ENST00000507142.1_Missense_Mutation_p.K709I|NEK1_ENST00000512193.1_Missense_Mutation_p.K612I|NEK1_ENST00000511633.1_Missense_Mutation_p.K665I|NEK1_ENST00000510533.1_Missense_Mutation_p.K637I	NM_012224.2	NP_036356.1	Q96PY6	NEK1_HUMAN	NIMA-related kinase 1	681					cellular response to DNA damage stimulus (GO:0006974)|cilium assembly (GO:0042384)|mitotic nuclear division (GO:0007067)|response to ionizing radiation (GO:0010212)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|pericentriolar material (GO:0000242)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			NS(1)|breast(3)|endometrium(3)|kidney(2)|large_intestine(13)|lung(18)|ovary(2)|prostate(2)|stomach(1)	45		Prostate(90;0.00601)|Renal(120;0.0183)		GBM - Glioblastoma multiforme(119;0.0287)|KIRC - Kidney renal clear cell carcinoma(143;0.0325)|Kidney(143;0.0385)|LUSC - Lung squamous cell carcinoma(193;0.14)		GCCAACTTCTTTCAAAGCTGA	0.353																																					p.K709I		Atlas-SNP	.											.	NEK1	203	.	0			c.A2126T						PASS	.						75.0	73.0	74.0					4																	170400567		1843	4074	5917	SO:0001583	missense	4750	exon24			ACTTCTTTCAAAG	AB067488	CCDS47162.1, CCDS56348.1, CCDS56349.1, CCDS56350.1, CCDS56351.1	4q32.3	2012-11-15	2012-11-15		ENSG00000137601	ENSG00000137601			7744	protein-coding gene	gene with protein product		604588	"""NIMA (never in mitosis gene a)-related kinase 1"""			1382974, 8274451	Standard	NM_012224		Approved	NY-REN-55, KIAA1901	uc003isd.2	Q96PY6	OTTHUMG00000160963	ENST00000439128.2:c.2042A>T	4.37:g.170400567T>A	ENSP00000408020:p.Lys681Ile	Somatic	152	0	0		WXS	Illumina HiSeq	Phase_I	109	92	0.844037	NM_001199397	G5E9Z3|Q05DG5|Q14CB7|Q5H9T1|Q6PIB8|Q96SS2|Q9H6P7|Q9Y594	Missense_Mutation	SNP	ENST00000439128.2	37	CCDS47162.1	.	.	.	.	.	.	.	.	.	.	T	20.3	3.970361	0.74246	.	.	ENSG00000137601	ENST00000439128;ENST00000511633;ENST00000510533;ENST00000507142;ENST00000512193	T;T;T;T;T	0.74842	-0.88;-0.81;-0.81;-0.8;-0.83	4.74	4.74	0.60224	.	0.191168	0.36482	N	0.002565	D	0.82802	0.5116	M	0.64997	1.995	0.46078	D	0.998856	D;D;D;D;D	0.63880	0.993;0.993;0.993;0.993;0.987	D;P;D;P;P	0.68353	0.957;0.898;0.957;0.898;0.907	D	0.84491	0.0611	10	0.66056	D	0.02	.	12.9491	0.58389	0.0:0.0:0.0:1.0	.	612;665;709;637;681	Q96PY6-4;G5E9Z3;Q96PY6-3;Q96PY6-2;Q96PY6	.;.;.;.;NEK1_HUMAN	I	681;665;637;709;612	ENSP00000408020:K681I;ENSP00000423332:K665I;ENSP00000427653:K637I;ENSP00000424757:K709I;ENSP00000424938:K612I	ENSP00000408020:K681I	K	-	2	0	NEK1	170637142	1.000000	0.71417	1.000000	0.80357	0.935000	0.57460	3.033000	0.49743	1.988000	0.58038	0.397000	0.26171	AAA	.	.	none		0.353	NEK1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000363157.3		
MUC4	4585	hgsc.bcm.edu	37	3	195508418	195508418	+	Missense_Mutation	SNP	C	C	G	rs548345415	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:195508418C>G	ENST00000463781.3	-	2	10492	c.10033G>C	c.(10033-10035)Gtg>Ctg	p.V3345L	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_Missense_Mutation_p.V3345L	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)		GTGACAGGCACAGGGGTGGTG	0.597													.|||	1317	0.262979	0.3646	0.2075	5008	,	,		12766	0.2976		0.2336	False		,,,				2504	0.1595				p.V3345L		Atlas-SNP	.											MUC4_ENST00000463781,rectum,carcinoma,+2,1	MUC4	1505	1	0			c.G10033C						scavenged	.						31.0	24.0	26.0					3																	195508418		666	1575	2241	SO:0001583	missense	4585	exon2			CAGGCACAGGGGT	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.10033G>C	3.37:g.195508418C>G	ENSP00000417498:p.Val3345Leu	Somatic	151	7	0.0463576		WXS	Illumina HiSeq	Phase_I	171	10	0.0584795	NM_018406	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	Missense_Mutation	SNP	ENST00000463781.3	37	CCDS54700.1	.	.	.	.	.	.	.	.	.	.	N	0.014	-1.600585	0.00849	.	.	ENSG00000145113	ENST00000463781;ENST00000475231	T;T	0.37584	1.26;1.19	1.03	-2.05	0.07321	.	.	.	.	.	T	0.10680	0.0261	N	0.02539	-0.55	0.09310	N	1	B	0.09022	0.002	B	0.01281	0.0	T	0.08411	-1.0723	8	.	.	.	.	0.4737	0.00536	0.1854:0.3006:0.1852:0.3288	.	3217	E7ESK3	.	L	3345	ENSP00000417498:V3345L;ENSP00000420243:V3345L	.	V	-	1	0	MUC4	196993197	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-5.422000	0.00123	-4.572000	0.00041	-4.097000	0.00011	GTG	.	.	none		0.597	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6	NM_018406	
TREML2	79865	hgsc.bcm.edu	37	6	41166098	41166098	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:41166098G>A	ENST00000483722.1	-	2	310	c.125C>T	c.(124-126)tCc>tTc	p.S42F		NM_024807.2	NP_079083.2	Q5T2D2	TRML2_HUMAN	triggering receptor expressed on myeloid cells-like 2	42	Ig-like V-type.				T cell activation (GO:0042110)	cell surface (GO:0009986)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	receptor activity (GO:0004872)			breast(1)|central_nervous_system(1)|large_intestine(1)|lung(13)|ovary(1)|prostate(1)	18	Ovarian(28;0.0418)|Colorectal(47;0.196)					GCCCTTATAGGAGCACTGCAC	0.512																																					p.S42F		Atlas-SNP	.											TREML2,colon,carcinoma,0,1	TREML2	41	1	0			c.C125T						PASS	.						155.0	164.0	161.0					6																	41166098		2203	4300	6503	SO:0001583	missense	79865	exon2			TTATAGGAGCACT	AK023755	CCDS4853.1, CCDS4853.2	6p21.1	2013-01-11	2004-04-14	2004-04-16	ENSG00000112195	ENSG00000112195		"""Immunoglobulin superfamily / V-set domain containing"""	21092	protein-coding gene	gene with protein product	"""TREM-like transcript 2"""	609715	"""chromosome 6 open reading frame 76"""	C6orf76		12645956	Standard	NM_024807		Approved	FLJ13693, TLT2, dJ238O23.1	uc010jxm.1	Q5T2D2	OTTHUMG00000016349	ENST00000483722.1:c.125C>T	6.37:g.41166098G>A	ENSP00000418767:p.Ser42Phe	Somatic	66	0	0		WXS	Illumina HiSeq	Phase_I	93	6	0.0645161	NM_024807	Q08AP8|Q08AP9|Q8IWY0|Q9H8E9	Missense_Mutation	SNP	ENST00000483722.1	37	CCDS4853.2	.	.	.	.	.	.	.	.	.	.	.	13.82	2.351464	0.41700	.	.	ENSG00000112195	ENST00000483722	T	0.64803	-0.12	4.75	3.85	0.44370	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.487586	0.17816	N	0.161037	T	0.59224	0.2178	L	0.43757	1.38	0.32993	D	0.525191	D	0.76494	0.999	D	0.72982	0.979	T	0.60682	-0.7215	10	0.48119	T	0.1	-10.0883	10.3616	0.43998	0.0:0.0:0.8036:0.1964	.	42	Q5T2D2	TRML2_HUMAN	F	42	ENSP00000418767:S42F	ENSP00000418767:S42F	S	-	2	0	TREML2	41274076	1.000000	0.71417	1.000000	0.80357	0.316000	0.28119	0.753000	0.26376	1.079000	0.41038	0.563000	0.77884	TCC	.	.	none		0.512	TREML2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043756.3	NM_024807	
USP18	11274	hgsc.bcm.edu	37	22	18650682	18650682	+	Missense_Mutation	SNP	C	C	T	rs3180408	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr22:18650682C>T	ENST00000215794.7	+	6	936	c.506C>T	c.(505-507)aCg>aTg	p.T169M		NM_017414.3	NP_059110.2	Q9UMW8	UBP18_HUMAN	ubiquitin specific peptidase 18	169	USP.		T -> M (in dbSNP:rs3180408). {ECO:0000269|Ref.7}.		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)	p.T169M(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|stomach(1)	10						GCCCTGTATACGATCCGGGTG	0.547													c|||	1489	0.297324	0.3979	0.2997	5008	,	,		16115	0.1637		0.3072	False		,,,				2504	0.2873				p.T169M		Atlas-SNP	.											USP18,NS,carcinoma,0,1	USP18	22	1	1	Substitution - Missense(1)	stomach(1)	c.C506T						scavenged	.	C	MET/THR	1709,2697		320,1069,814	121.0	94.0	103.0		506	-3.1	0.0	22	dbSNP_105	103	2965,5635		496,1973,1831	no	missense	USP18	NM_017414.3	81	816,3042,2645	TT,TC,CC		34.4767,38.788,35.9373	benign	169/373	18650682	4674,8332	2203	4300	6503	SO:0001583	missense	11274	exon6			TGTATACGATCCG	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.506C>T	22.37:g.18650682C>T	ENSP00000215794:p.Thr169Met	Somatic	225	1	0.00444444		WXS	Illumina HiSeq	Phase_I	254	3	0.011811	NM_017414	Q53Y90|Q6IAD9|Q9NY71	Missense_Mutation	SNP	ENST00000215794.7	37	CCDS13752.1	614	0.28113553113553114	173	0.3516260162601626	107	0.2955801104972376	92	0.16083916083916083	242	0.31926121372031663	.	2.520	-0.311064	0.05458	0.38788	0.344767	ENSG00000184979	ENST00000215794;ENST00000441683	T	0.31769	1.48	5.62	-3.07	0.05363	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.540147	0.20380	N	0.093467	T	0.00012	0.0000	L	0.50333	1.59	0.80722	P	0.0	P	0.36789	0.57	B	0.33521	0.165	T	0.40270	-0.9572	9	0.46703	T	0.11	.	7.1474	0.25591	0.0:0.5396:0.1135:0.347	rs3180408;rs3210451;rs3180408	169	Q9UMW8	UBP18_HUMAN	M	169;1	ENSP00000215794:T169M	ENSP00000215794:T169M	T	+	2	0	USP18	17030682	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.076000	0.11412	-0.757000	0.04697	-1.789000	0.00628	ACG	C|0.674;N|0.000	.	strong		0.547	USP18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316368.1		
KMT2A	4297	hgsc.bcm.edu	37	11	118371761	118371761	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:118371761A>G	ENST00000389506.5	+	25	6209	c.6209A>G	c.(6208-6210)aAg>aGg	p.K2070R	KMT2A_ENST00000534358.1_Missense_Mutation_p.K2073R|KMT2A_ENST00000354520.4_Missense_Mutation_p.K2032R			Q03164	KMT2A_HUMAN	lysine (K)-specific methyltransferase 2A	2070	FYR N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00875}.				anterior/posterior pattern specification (GO:0009952)|apoptotic process (GO:0006915)|DNA methylation (GO:0006306)|embryonic hemopoiesis (GO:0035162)|histone H3-K4 methylation (GO:0051568)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|negative regulation of cell proliferation (GO:0008285)|positive regulation of cellular response to drug (GO:2001040)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of transporter activity (GO:0032411)|protein complex assembly (GO:0006461)|regulation of histone H3-K4 methylation (GO:0051569)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)	AT DNA binding (GO:0003680)|chromatin binding (GO:0003682)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|identical protein binding (GO:0042802)|lysine-acetylated histone binding (GO:0070577)|protein homodimerization activity (GO:0042803)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)|unmethylated CpG binding (GO:0045322)|zinc ion binding (GO:0008270)										TATACATGCAAGATAGTGGAG	0.468																																					p.K2073R		Atlas-SNP	.											.	MLL	548	.	0			c.A6218G						PASS	.						150.0	118.0	129.0					11																	118371761		2200	4296	6496	SO:0001583	missense	4297	exon25			CATGCAAGATAGT	L04284	CCDS31686.1, CCDS55791.1	11q23	2014-09-17	2013-05-09	2013-05-09	ENSG00000118058	ENSG00000118058		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	7132	protein-coding gene	gene with protein product		159555	"""myeloid/lymphoid or mixed-lineage leukemia (trithorax (Drosophila) homolog)"", ""myeloid/lymphoid or mixed-lineage leukemia (trithorax homolog, Drosophila)"""	MLL		1720549	Standard	NM_001197104		Approved	TRX1, HRX, ALL-1, HTRX1, CXXC7, MLL1A		Q03164	OTTHUMG00000166337	ENST00000389506.5:c.6209A>G	11.37:g.118371761A>G	ENSP00000374157:p.Lys2070Arg	Somatic	112	0	0		WXS	Illumina HiSeq	Phase_I	121	25	0.206612	NM_001197104	E9PQG7|Q13743|Q13744|Q14845|Q16364|Q59FF2|Q6UBD1|Q9HBJ3|Q9UD94|Q9UMA3	Missense_Mutation	SNP	ENST00000389506.5	37	CCDS31686.1	.	.	.	.	.	.	.	.	.	.	A	17.83	3.485424	0.63962	.	.	ENSG00000118058	ENST00000534358;ENST00000389506;ENST00000354520;ENST00000359313	T;T;T	0.77358	-1.09;-1.09;-1.09	5.83	5.83	0.93111	FY-rich, N-terminal (1);FY-rich, N-terminal subgroup (1);	0.047613	0.85682	D	0.000000	T	0.56124	0.1964	N	0.02842	-0.48	0.53005	D	0.999968	B;B	0.30326	0.276;0.219	B;B	0.35278	0.199;0.138	T	0.60383	-0.7274	10	0.02654	T	1	.	16.2011	0.82078	1.0:0.0:0.0:0.0	.	2073;2070	E9PQG7;Q03164	.;MLL1_HUMAN	R	2073;2070;2032;980	ENSP00000436786:K2073R;ENSP00000374157:K2070R;ENSP00000346516:K2032R	ENSP00000346516:K2032R	K	+	2	0	MLL	117876971	1.000000	0.71417	1.000000	0.80357	0.869000	0.49853	6.135000	0.71696	2.219000	0.72066	0.482000	0.46254	AAG	.	.	none		0.468	KMT2A-015	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399085.2	NM_005933	
CNNM3	26505	hgsc.bcm.edu	37	2	97483238	97483238	+	Splice_Site	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:97483238A>G	ENST00000305510.3	+	1	1252	c.1224A>G	c.(1222-1224)cgA>cgG	p.R408R	CNNM3_ENST00000377060.3_Splice_Site_p.R408R	NM_017623.4	NP_060093.3	Q8NE01	CNNM3_HUMAN	cyclin and CBS domain divalent metal cation transport mediator 3	408	CBS 2. {ECO:0000255|PROSITE- ProRule:PRU00703}.				ion transport (GO:0006811)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	adenyl nucleotide binding (GO:0030554)	p.R408R(1)		NS(1)|kidney(2)|large_intestine(2)|lung(3)|ovary(2)|skin(1)|urinary_tract(2)	13						AATTCAAGCGAGGTAACGGCC	0.602																																					p.R408R		Atlas-SNP	.											CNNM3,NS,carcinoma,0,1	CNNM3	33	1	1	Substitution - coding silent(1)	kidney(1)	c.A1224G						scavenged	.						103.0	99.0	100.0					2																	97483238		2203	4300	6503	SO:0001630	splice_region_variant	26505	exon1			CAAGCGAGGTAAC	AF216965	CCDS2025.1, CCDS2026.1	2q11.2	2014-08-08	2014-08-07		ENSG00000168763	ENSG00000168763			104	protein-coding gene	gene with protein product		607804	"""cyclin M3"""	ACDP3		21393841, 24632616	Standard	XM_005263917		Approved		uc002swy.3	Q8NE01	OTTHUMG00000130531	ENST00000305510.3:c.1225+1A>G	2.37:g.97483238A>G		Somatic	70	1	0.0142857		WXS	Illumina HiSeq	Phase_I	66	3	0.0454545	NM_199078	B3KX67|Q8TBV4|Q96IW4|Q9NRK4|Q9NXW6	Silent	SNP	ENST00000305510.3	37	CCDS2025.1																																																																																			.	.	none		0.602	CNNM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252952.2	NM_017623	Silent
HRNR	388697	hgsc.bcm.edu	37	1	152186042	152186042	+	Missense_Mutation	SNP	A	A	G	rs12751022	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:152186042A>G	ENST00000368801.2	-	3	8138	c.8063T>C	c.(8062-8064)tTg>tCg	p.L2688S	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_001009931.1	NP_001009931.1	Q86YZ3	HORN_HUMAN	hornerin	2688				L -> S (in Ref. 1; BAC57496). {ECO:0000305}.	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)	p.L2688S(1)		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)			AGAGTGACCCAAGCGAGACTC	0.582													G|||	2279	0.455072	0.3336	0.5908	5008	,	,		10987	0.6181		0.3718	False		,,,				2504	0.4407				p.L2688S		Atlas-SNP	.											HRNR,NS,carcinoma,0,1	HRNR	403	1	1	Substitution - Missense(1)	prostate(1)	c.T8063C						scavenged	.						30.0	26.0	28.0					1																	152186042		1929	3848	5777	SO:0001583	missense	388697	exon3			TGACCCAAGCGAG	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.8063T>C	1.37:g.152186042A>G	ENSP00000357791:p.Leu2688Ser	Somatic	80	5	0.0625		WXS	Illumina HiSeq	Phase_I	83	15	0.180723	NM_001009931	Q5DT20|Q5U1F4	Missense_Mutation	SNP	ENST00000368801.2	37	CCDS30859.1	1136	0.5201465201465202	216	0.43902439024390244	226	0.6243093922651933	348	0.6083916083916084	346	0.45646437994722955	G	3.703	-0.061145	0.07317	.	.	ENSG00000197915	ENST00000368801	T	0.01484	4.84	2.89	1.85	0.25348	.	.	.	.	.	T	0.00178	0.0005	N	0.00308	-1.67	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.14755	-1.0461	8	0.08381	T	0.77	.	5.4214	0.16402	0.4598:0.0:0.5402:0.0	rs12751022	2688	Q86YZ3	HORN_HUMAN	S	2688	ENSP00000357791:L2688S	ENSP00000357791:L2688S	L	-	2	0	HRNR	150452666	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-0.091000	0.11146	0.047000	0.15862	-0.291000	0.09656	TTG	A|0.478;G|0.522	0.522	strong		0.582	HRNR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000034016.1	XM_373868	
C21orf2	755	hgsc.bcm.edu	37	21	45753051	45753051	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr21:45753051G>A	ENST00000339818.4	-	4	445	c.238C>T	c.(238-240)Ctc>Ttc	p.L80F	C21orf2_ENST00000496321.1_5'UTR|C21orf2_ENST00000397956.3_Missense_Mutation_p.L80F|AP001062.7_ENST00000448927.1_RNA|C21orf2_ENST00000325223.7_Missense_Mutation_p.L80F	NM_001271440.1|NM_004928.2	NP_001258369.1|NP_004919.1	O43822	CU002_HUMAN	chromosome 21 open reading frame 2	80					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)		AGGTAGAAGAGCTCAGCCAGG	0.677																																					p.L80F		Atlas-SNP	.											.	C21orf2	10	.	0			c.C238T						PASS	.						23.0	24.0	24.0					21																	45753051		2202	4300	6502	SO:0001583	missense	755	exon4			AGAAGAGCTCAGC	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.238C>T	21.37:g.45753051G>A	ENSP00000344566:p.Leu80Phe	Somatic	100	0	0		WXS	Illumina HiSeq	Phase_I	129	56	0.434109	NM_004928	A8MPS9|O14993|Q8N5X6|Q99837|Q99838	Missense_Mutation	SNP	ENST00000339818.4	37	CCDS13709.1	.	.	.	.	.	.	.	.	.	.	G	29.9	5.041713	0.93685	.	.	ENSG00000160226	ENST00000339818;ENST00000380160;ENST00000397956;ENST00000325223	T;T;T	0.25085	1.82;1.82;1.82	4.99	4.99	0.66335	.	0.000000	0.85682	D	0.000000	T	0.60470	0.2271	M	0.92317	3.295	0.80722	D	1	D;D;D;D	0.89917	1.0;0.988;1.0;1.0	D;P;D;D	0.97110	0.999;0.908;1.0;0.999	T	0.69483	-0.5133	10	0.54805	T	0.06	-34.0877	15.5737	0.76359	0.0:0.0:1.0:0.0	.	80;80;80;39	G5E952;Q8N5X6;O43822;O43822-2	.;.;CU002_HUMAN;.	F	80;116;80;80	ENSP00000344566:L80F;ENSP00000381047:L80F;ENSP00000317302:L80F	ENSP00000317302:L80F	L	-	1	0	C21orf2	44577479	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	9.037000	0.93765	2.482000	0.83794	0.655000	0.94253	CTC	.	.	none		0.677	C21orf2-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000195799.1	NM_004928	
IGLL5	100423062	hgsc.bcm.edu	37	22	23230278	23230278	+	Silent	SNP	G	G	A	rs544778929	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr22:23230278G>A	ENST00000526893.1	+	1	319	c.45G>A	c.(43-45)gaG>gaA	p.E15E	IGLL5_ENST00000531372.1_Silent_p.E15E|IGLL5_ENST00000532223.2_Silent_p.E15E|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	15						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						CCCCTGAGGAGCTGGGCCCTG	0.672													G|||	6	0.00119808	0.0023	0.0029	5008	,	,		13267	0.0		0.0	False		,,,				2504	0.001				p.E15E		Atlas-SNP	.											IGLL5,NS,lymphoid_neoplasm,0,1	IGLL5	26	1	0			c.G45A						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			TGAGGAGCTGGGC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.45G>A	22.37:g.23230278G>A		Somatic	159	0	0		WXS	Illumina HiSeq	Phase_I	75	65	0.866667	NM_001178126		Silent	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.672	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
RAD51AP1	10635	hgsc.bcm.edu	37	12	4668142	4668142	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:4668142A>G	ENST00000352618.4	+	9	1041	c.991A>G	c.(991-993)Aat>Gat	p.N331D	RAD51AP1_ENST00000543041.1_Missense_Mutation_p.N229D|RAD51AP1_ENST00000321524.7_Missense_Mutation_p.N298D|RAD51AP1_ENST00000228843.9_Missense_Mutation_p.N348D|RAD51AP1_ENST00000544931.1_3'UTR	NM_006479.4	NP_006470.1			RAD51 associated protein 1											breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|upper_aerodigestive_tract(1)	13			Colorectal(7;0.00306)|COAD - Colon adenocarcinoma(12;0.0389)			TTTGCATCCAAATGCCACTAG	0.458																																					p.N348D		Atlas-SNP	.											.	RAD51AP1	30	.	0			c.A1042G						PASS	.						128.0	118.0	121.0					12																	4668142		2203	4300	6503	SO:0001583	missense	10635	exon10			CATCCAAATGCCA	AF006259	CCDS8529.1, CCDS44805.1	12p13.2-p13.1	2004-09-16			ENSG00000111247	ENSG00000111247			16956	protein-coding gene	gene with protein product		603070				9396801	Standard	NM_001130862		Approved	PIR51	uc001qmw.3	Q96B01	OTTHUMG00000168125	ENST00000352618.4:c.991A>G	12.37:g.4668142A>G	ENSP00000309479:p.Asn331Asp	Somatic	68	0	0		WXS	Illumina HiSeq	Phase_I	70	29	0.414286	NM_001130862		Missense_Mutation	SNP	ENST00000352618.4	37	CCDS8529.1	.	.	.	.	.	.	.	.	.	.	A	13.98	2.399685	0.42512	.	.	ENSG00000111247	ENST00000321524;ENST00000543041;ENST00000228843;ENST00000352618	T;T;T;T	0.48201	1.0;1.0;0.82;0.82	4.32	4.32	0.51571	.	0.680081	0.13888	N	0.355802	T	0.42449	0.1203	L	0.58101	1.795	0.30391	N	0.780976	P;B;B;P	0.41848	0.763;0.341;0.341;0.634	B;B;B;B	0.36608	0.229;0.08;0.08;0.178	T	0.52132	-0.8616	10	0.59425	D	0.04	-4.8877	9.7988	0.40751	1.0:0.0:0.0:0.0	.	229;348;348;331	B4DUS5;Q96B01;A8K313;Q96B01-2	.;R51A1_HUMAN;.;.	D	298;229;348;331	ENSP00000323750:N298D;ENSP00000439960:N229D;ENSP00000228843:N348D;ENSP00000309479:N331D	ENSP00000228843:N348D	N	+	1	0	RAD51AP1	4538403	0.581000	0.26741	0.803000	0.32268	0.451000	0.32288	1.716000	0.37981	1.809000	0.52856	0.533000	0.62120	AAT	.	.	none		0.458	RAD51AP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398293.1	NM_006479	
UBB	7314	hgsc.bcm.edu	37	17	16285491	16285491	+	Silent	SNP	C	C	T	rs16962973		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:16285491C>T	ENST00000395837.1	+	2	451	c.270C>T	c.(268-270)acC>acT	p.T90T	UBB_ENST00000578649.1_Intron|UBB_ENST00000535788.1_Intron|UBB_ENST00000302182.3_Silent_p.T90T|UBB_ENST00000395839.1_Silent_p.T90T|RP11-138I1.4_ENST00000583934.1_RNA	NM_001281718.1|NM_001281720.1	NP_001268647.1|NP_001268649.1	P0CG47	UBB_HUMAN	ubiquitin B	90	Ubiquitin-like 2. {ECO:0000255|PROSITE- ProRule:PRU00214}.		GMQIFVKTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQ QRLIFAGKQLEDGRTLSDYNIQKESTLHLVLRLRGGMQIFV KTLTGKTITLEVEPSDTIENVKAKIQDKEGIPPDQQRLIFA GKQLEDGRTLSDYNIQKESTLHLVLRLRGGC -> YADLRE DPDRQDHHPGSGAQ (in UBB(+1); loss of polyubiquitination; impairs the ubiquitin-proteasome pathway; refractory to disassembly by DUBs; slow degradation by UCHL3).		activation of MAPK activity (GO:0000187)|anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|carbohydrate metabolic process (GO:0005975)|cellular response to hypoxia (GO:0071456)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA repair (GO:0006281)|endosomal transport (GO:0016197)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G1/S transition of mitotic cell cycle (GO:0000082)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|glucose metabolic process (GO:0006006)|glycogen biosynthetic process (GO:0005978)|I-kappaB kinase/NF-kappaB signaling (GO:0007249)|innate immune response (GO:0045087)|intracellular transport of virus (GO:0075733)|ion transmembrane transport (GO:0034220)|JNK cascade (GO:0007254)|membrane organization (GO:0061024)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|negative regulation of type I interferon production (GO:0032480)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|neurotrophin TRK receptor signaling pathway (GO:0048011)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of apoptotic process (GO:0043065)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type I interferon production (GO:0032481)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of type I interferon production (GO:0032479)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stress-activated MAPK cascade (GO:0051403)|T cell receptor signaling pathway (GO:0050852)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|transmembrane transport (GO:0055085)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)|viral life cycle (GO:0019058)|viral process (GO:0016032)|viral protein processing (GO:0019082)|virion assembly (GO:0019068)	cytosol (GO:0005829)|endocytic vesicle membrane (GO:0030666)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|nucleoplasm (GO:0005654)|plasma membrane (GO:0005886)				breast(1)|central_nervous_system(1)|endometrium(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	16				UCEC - Uterine corpus endometrioid carcinoma (92;0.0822)		AGACCATCACCCTGGAAGTGG	0.552																																					p.T90T	Melanoma(163;1126 3406 34901)	Atlas-SNP	.											UBB,bladder,carcinoma,0,2	UBB	30	2	0			c.C270T						scavenged	.						75.0	76.0	75.0					17																	16285491		2203	4297	6500	SO:0001819	synonymous_variant	7314	exon2			CATCACCCTGGAA		CCDS11177.1	17p12-p11.2	2010-11-25			ENSG00000170315	ENSG00000170315			12463	protein-coding gene	gene with protein product	"""polyubiquitin B"""	191339				2154095	Standard	NM_018955		Approved	MGC8385, FLJ25987	uc002gpx.3	P0CG47	OTTHUMG00000058987	ENST00000395837.1:c.270C>T	17.37:g.16285491C>T		Somatic	137	1	0.00729927		WXS	Illumina HiSeq	Phase_I	130	3	0.0230769	NM_018955	P02248|P02249|P02250|P62988|Q29120|Q6LBL4|Q6LDU5|Q8WYN8|Q91887|Q91888|Q9BWD6|Q9BX98|Q9UEF2|Q9UEG1|Q9UEK8|Q9UPK7	Silent	SNP	ENST00000395837.1	37	CCDS11177.1																																																																																			C|0.996;T|0.004	0.004	strong		0.552	UBB-002	NOVEL	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000130459.1	NM_018955	
FANCM	57697	hgsc.bcm.edu	37	14	45624650	45624650	+	Nonsense_Mutation	SNP	A	A	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr14:45624650A>T	ENST00000267430.5	+	8	1469	c.1384A>T	c.(1384-1386)Aag>Tag	p.K462*	FANCM_ENST00000542564.2_Nonsense_Mutation_p.K436*|FANCM_ENST00000556036.1_Nonsense_Mutation_p.K462*	NM_020937.2	NP_065988.1	Q8IYD8	FANCM_HUMAN	Fanconi anemia, complementation group M	462	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				DNA repair (GO:0006281)|replication fork processing (GO:0031297)|resolution of meiotic recombination intermediates (GO:0000712)	FANCM-MHF complex (GO:0071821)|Fanconi anaemia nuclear complex (GO:0043240)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|nuclease activity (GO:0004518)			breast(4)|central_nervous_system(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(18)|liver(2)|lung(31)|ovary(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(6)|urinary_tract(1)	85						TGAACACTTCAAGTCATGGAA	0.313								Involved in tolerance or repair of DNA crosslinks	Fanconi Anemia																												p.K462X		Atlas-SNP	.											.	FANCM	225	.	0			c.A1384T						PASS	.						69.0	73.0	72.0					14																	45624650		2202	4300	6502	SO:0001587	stop_gained	57697	exon8	Familial Cancer Database	Pancytopenia Dysmelia, FA (several complementation groups)	CACTTCAAGTCAT	AK001672	CCDS32070.1	14q21.3	2014-09-17	2005-09-01	2005-09-01		ENSG00000187790		"""Fanconi anemia, complementation groups"""	23168	protein-coding gene	gene with protein product		609644	"""KIAA1596"""	KIAA1596		10997877, 16116422	Standard	NM_020937		Approved	FAAP250	uc001wwd.4	Q8IYD8		ENST00000267430.5:c.1384A>T	14.37:g.45624650A>T	ENSP00000267430:p.Lys462*	Somatic	119	0	0		WXS	Illumina HiSeq	Phase_I	128	40	0.3125	NM_020937	B2RTQ9|Q3YFH9|Q8N9X6|Q9HCH6	Nonsense_Mutation	SNP	ENST00000267430.5	37	CCDS32070.1	.	.	.	.	.	.	.	.	.	.	A	38	6.864036	0.97893	.	.	ENSG00000187790	ENST00000556036;ENST00000267430;ENST00000542564;ENST00000556250	.	.	.	5.42	5.42	0.78866	.	0.409870	0.28834	N	0.013998	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	11.7616	0.51908	0.853:0.147:0.0:0.0	.	.	.	.	X	462;462;436;47	.	ENSP00000267430:K462X	K	+	1	0	FANCM	44694400	0.968000	0.33430	0.984000	0.44739	0.854000	0.48673	2.342000	0.43992	2.040000	0.60383	0.460000	0.39030	AAG	.	.	none		0.313	FANCM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000410474.1	XM_048128	
CBWD3	445571	hgsc.bcm.edu	37	9	70871857	70871857	+	Missense_Mutation	SNP	T	T	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr9:70871857T>A	ENST00000360171.6	+	5	1002	c.451T>A	c.(451-453)Tgg>Agg	p.W151R	CBWD3_ENST00000377342.5_Intron	NM_201453.2	NP_958861.2	Q5JTY5	CBWD3_HUMAN	COBW domain containing 3	151							ATP binding (GO:0005524)			kidney(1)|large_intestine(1)|lung(2)|prostate(1)	5				all cancers(8;0.00136)|Epithelial(8;0.0288)|GBM - Glioblastoma multiforme(74;0.0402)|OV - Ovarian serous cystadenocarcinoma(323;0.18)		TTCTATGTTTTGGGTTGATGC	0.269																																					p.W151R		Atlas-SNP	.											.	CBWD3	10	.	0			c.T451A						PASS	.						25.0	31.0	29.0					9																	70871857		2189	4258	6447	SO:0001583	missense	445571	exon5			ATGTTTTGGGTTG	BC069006	CCDS35038.1, CCDS35038.2	9q13	2014-05-06			ENSG00000196873	ENSG00000196873			18519	protein-coding gene	gene with protein product		611080				15233989, 12421752	Standard	XM_005277637		Approved	bA561O23.1	uc004aga.4	Q5JTY5	OTTHUMG00000184383	ENST00000360171.6:c.451T>A	9.37:g.70871857T>A	ENSP00000353295:p.Trp151Arg	Somatic	399	0	0		WXS	Illumina HiSeq	Phase_I	484	112	0.231405	NM_201453	B4DNG9|Q6VB91	Missense_Mutation	SNP	ENST00000360171.6	37	CCDS35038.1	.	.	.	.	.	.	.	.	.	.	.	17.24	3.338396	0.60963	.	.	ENSG00000196873	ENST00000360171;ENST00000447896;ENST00000455061;ENST00000455820;ENST00000377344	T	0.41065	1.01	3.38	3.38	0.38709	Cobalamin (vitamin B12) biosynthesis CobW-like (1);	0.000000	0.85682	D	0.000000	T	0.61578	0.2358	M	0.75264	2.295	0.80722	D	1	D;P	0.89917	1.0;0.815	D;P	0.87578	0.998;0.733	T	0.65685	-0.6108	10	0.87932	D	0	-30.7068	11.0695	0.47995	0.0:0.0:0.0:1.0	.	151;151	E7ETY5;Q5JTY5	.;CBWD3_HUMAN	R	151;151;151;151;115	ENSP00000353295:W151R	ENSP00000353295:W151R	W	+	1	0	CBWD3	70061677	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.201000	0.77847	1.311000	0.45024	0.254000	0.18369	TGG	.	.	none		0.269	CBWD3-001	KNOWN	non_canonical_polymorphism|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052526.1	NM_201453	
IL18RAP	8807	hgsc.bcm.edu	37	2	103040530	103040530	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:103040530C>T	ENST00000264260.2	+	4	919	c.330C>T	c.(328-330)acC>acT	p.T110T	IL18RAP_ENST00000409369.1_Intron	NM_003853.2	NP_003844.1	O95256	I18RA_HUMAN	interleukin 18 receptor accessory protein	110					cell surface receptor signaling pathway (GO:0007166)|immune response (GO:0006955)|inflammatory response (GO:0006954)	integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			autonomic_ganglia(1)|central_nervous_system(2)|endometrium(3)|kidney(4)|large_intestine(5)|lung(10)|ovary(2)|prostate(1)|skin(5)|urinary_tract(4)	37						ACAAATGTACCCTTCACTTTT	0.383																																					p.T110T		Atlas-SNP	.											IL18RAP,NS,carcinoma,+1,1	IL18RAP	102	1	0			c.C330T						scavenged	.						84.0	80.0	81.0					2																	103040530		2203	4300	6503	SO:0001819	synonymous_variant	8807	exon4			ATGTACCCTTCAC	AF077346	CCDS2061.1	2q12.1	2013-01-11			ENSG00000115607	ENSG00000115607		"""Interleukins and interleukin receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	5989	protein-coding gene	gene with protein product		604509				9792649	Standard	XM_005264034		Approved	AcPL, CD218b	uc002tbx.3	O95256	OTTHUMG00000130777	ENST00000264260.2:c.330C>T	2.37:g.103040530C>T		Somatic	183	0	0		WXS	Illumina HiSeq	Phase_I	244	4	0.0163934	NM_003853	B2RPJ3|Q3KPE7|Q3KPE8|Q53TT4|Q53TU5	Silent	SNP	ENST00000264260.2	37	CCDS2061.1																																																																																			.	.	none		0.383	IL18RAP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253291.2	NM_003853	
COL6A1	1291	hgsc.bcm.edu	37	21	47423737	47423737	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr21:47423737G>A	ENST00000361866.3	+	35	3011	c.2897G>A	c.(2896-2898)gGc>gAc	p.G966D	COL6A1_ENST00000498614.1_3'UTR	NM_001848.2	NP_001839.2	P12109	CO6A1_HUMAN	collagen, type VI, alpha 1	966	C-terminal globular domain.|VWFA 3. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|osteoblast differentiation (GO:0001649)|protein heterotrimerization (GO:0070208)	collagen type VI trimer (GO:0005589)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|protein complex (GO:0043234)|proteinaceous extracellular matrix (GO:0005578)|sarcolemma (GO:0042383)	platelet-derived growth factor binding (GO:0048407)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|lung(18)|ovary(1)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	33	all_hematologic(128;0.24)			Colorectal(79;0.0265)|READ - Rectum adenocarcinoma(84;0.0649)		CAGCGGGCAGGCATCGAGATC	0.672																																					p.G966D		Atlas-SNP	.											.	COL6A1	101	.	0			c.G2897A						PASS	.						39.0	40.0	39.0					21																	47423737		2200	4298	6498	SO:0001583	missense	1291	exon35			GGGCAGGCATCGA	M20776	CCDS13727.1	21q22.3	2014-09-17			ENSG00000142156	ENSG00000142156		"""Collagens"""	2211	protein-coding gene	gene with protein product		120220					Standard	XM_006723964		Approved		uc002zhu.1	P12109	OTTHUMG00000090440	ENST00000361866.3:c.2897G>A	21.37:g.47423737G>A	ENSP00000355180:p.Gly966Asp	Somatic	95	0	0		WXS	Illumina HiSeq	Phase_I	88	39	0.443182	NM_001848	O00117|O00118|Q14040|Q14041|Q16258|Q7Z645|Q9BSA8	Missense_Mutation	SNP	ENST00000361866.3	37	CCDS13727.1	.	.	.	.	.	.	.	.	.	.	G	14.47	2.544844	0.45280	.	.	ENSG00000142156	ENST00000361866	D	0.82803	-1.65	4.83	2.7	0.31948	von Willebrand factor, type A (3);	0.364959	0.27280	N	0.020091	T	0.81351	0.4804	M	0.78049	2.395	0.54753	D	0.999987	B	0.15473	0.013	B	0.20184	0.028	T	0.77035	-0.2737	10	0.44086	T	0.13	-12.9407	10.1343	0.42697	0.1868:0.0:0.8132:0.0	.	966	P12109	CO6A1_HUMAN	D	966	ENSP00000355180:G966D	ENSP00000355180:G966D	G	+	2	0	COL6A1	46248165	0.968000	0.33430	0.912000	0.35992	0.308000	0.27856	1.709000	0.37909	0.771000	0.33359	0.596000	0.82720	GGC	.	.	none		0.672	COL6A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206877.1	NM_001848	
FNDC7	163479	hgsc.bcm.edu	37	1	109270645	109270645	+	Silent	SNP	C	C	A	rs200404056		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:109270645C>A	ENST00000370017.3	+	7	1604	c.1327C>A	c.(1327-1329)Cga>Aga	p.R443R	FNDC7_ENST00000271311.2_Silent_p.R444R	NM_001144937.1	NP_001138409.1	Q5VTL7	FNDC7_HUMAN	fibronectin type III domain containing 7	443	Fibronectin type-III 5. {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)		CAATGAAGTCCGAGGCAGCAA	0.478																																					p.R443R		Atlas-SNP	.											FNDC7_ENST00000370017,NS,malignant_melanoma,-1,4	FNDC7	113	4	0			c.C1327A						scavenged	.						229.0	206.0	214.0					1																	109270645		2203	4300	6503	SO:0001819	synonymous_variant	163479	exon7			GAAGTCCGAGGCA		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.1327C>A	1.37:g.109270645C>A		Somatic	140	0	0		WXS	Illumina HiSeq	Phase_I	166	2	0.0120482	NM_001144937	A1L468|E9PAZ5|Q6PF16|Q8NA51	Silent	SNP	ENST00000370017.3	37	CCDS44185.1	.	.	.	.	.	.	.	.	.	.	C	2.709	-0.269297	0.05716	.	.	ENSG00000143107	ENST00000445274	.	.	.	5.34	3.27	0.37495	.	.	.	.	.	T	0.60130	0.2245	.	.	.	0.58432	D	0.999998	.	.	.	.	.	.	T	0.61978	-0.6951	4	.	.	.	-9.0667	14.7969	0.69884	0.3899:0.6101:0.0:0.0	.	.	.	.	Q	218	.	.	P	+	2	0	FNDC7	109072168	0.044000	0.20184	0.999000	0.59377	0.361000	0.29550	0.139000	0.16036	1.228000	0.43614	-0.521000	0.04368	CCG	C|1.000;T|0.000	.	alt		0.478	FNDC7-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030589.4	NM_173532	
KCNN3	3782	hgsc.bcm.edu	37	1	154842244	154842244	+	Missense_Mutation	SNP	A	A	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:154842244A>T	ENST00000271915.4	-	1	512	c.197T>A	c.(196-198)cTt>cAt	p.L66H	KCNN3_ENST00000358505.2_5'Flank	NM_001204087.1|NM_002249.5	NP_001191016.1|NP_002240.3	Q9UGI6	KCNN3_HUMAN	potassium intermediate/small conductance calcium-activated channel, subfamily N, member 3	66	Gln-rich.				potassium ion transmembrane transport (GO:0071805)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	calmodulin binding (GO:0005516)|small conductance calcium-activated potassium channel activity (GO:0016286)			cervix(1)|endometrium(3)|kidney(2)|large_intestine(6)|lung(11)|prostate(4)|skin(1)	28	all_lung(78;2.29e-27)|all_hematologic(923;0.088)|Hepatocellular(266;0.108)|all_neural(408;0.245)		BRCA - Breast invasive adenocarcinoma(34;0.00819)		Miconazole(DB01110)|Procaine(DB00721)	ctgctgctgaagctgcggagg	0.701																																					p.L66H		Atlas-SNP	.											KCNN3,NS,carcinoma,+1,3	KCNN3	141	3	0			c.T197A						scavenged	.																																			SO:0001583	missense	3782	exon1			TGCTGAAGCTGCG	AF031815	CCDS1072.1, CCDS30880.1, CCDS72928.1	1q21.3	2012-07-05			ENSG00000143603	ENSG00000143603		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	6292	protein-coding gene	gene with protein product		602983				9491810, 16382103	Standard	NM_002249		Approved	KCa2.3, hSK3, SKCA3	uc021pah.1	Q9UGI6	OTTHUMG00000037260	ENST00000271915.4:c.197T>A	1.37:g.154842244A>T	ENSP00000271915:p.Leu66His	Somatic	21	2	0.0952381		WXS	Illumina HiSeq	Phase_I	50	30	0.6	NM_001204087	B1ANX0|O43517|Q86VF9|Q8WXG7	Missense_Mutation	SNP	ENST00000271915.4	37	CCDS30880.1	.	.	.	.	.	.	.	.	.	.	a	9.986	1.229557	0.22542	.	.	ENSG00000143603	ENST00000271915;ENST00000539103	T	0.58060	0.36	4.47	-1.06	0.10002	.	2.530250	0.01603	N	0.022141	T	0.17152	0.0412	N	0.08118	0	0.35103	D	0.765442	.	.	.	.	.	.	T	0.03807	-1.1002	8	0.72032	D	0.01	-1.1381	4.5154	0.11932	0.5982:0.0:0.2622:0.1396	.	.	.	.	H	66;161	ENSP00000271915:L66H	ENSP00000271915:L66H	L	-	2	0	KCNN3	153108868	0.001000	0.12720	0.839000	0.33178	0.980000	0.70556	0.019000	0.13444	0.013000	0.14918	0.460000	0.39030	CTT	.	.	none		0.701	KCNN3-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090688.3	NM_002249	
ARID3B	10620	hgsc.bcm.edu	37	15	74836319	74836319	+	Silent	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:74836319A>G	ENST00000346246.5	+	2	273	c.42A>G	c.(40-42)caA>caG	p.Q14Q		NM_006465.2	NP_006456.1	Q8IVW6	ARI3B_HUMAN	AT rich interactive domain 3B (BRIGHT-like)	14	Gln-rich.					nucleus (GO:0005634)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|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)			NS(1)|breast(1)|endometrium(1)|large_intestine(2)|lung(7)|prostate(2)	14						agcagcaacaacagaagcagc	0.562																																					p.Q14Q		Atlas-SNP	.											ARID3B,right_lower_lobe,carcinoma,0,1	ARID3B	35	1	0			c.A42G						scavenged	.						18.0	21.0	20.0					15																	74836319		2196	4294	6490	SO:0001819	synonymous_variant	10620	exon2			GCAACAACAGAAG		CCDS10264.1	15q24	2013-02-07	2006-11-08		ENSG00000179361	ENSG00000179361		"""-"""	14350	protein-coding gene	gene with protein product		612457	"""AT rich interactive domain 3B (BRIGHT- like)"""				Standard	NM_006465		Approved	BDP, DRIL2	uc002ayd.3	Q8IVW6	OTTHUMG00000141321	ENST00000346246.5:c.42A>G	15.37:g.74836319A>G		Somatic	132	6	0.0454545		WXS	Illumina HiSeq	Phase_I	178	9	0.0505618	NM_006465	O95443|Q59HC9|Q6P9C9	Silent	SNP	ENST00000346246.5	37	CCDS10264.1																																																																																			.	.	none		0.562	ARID3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280688.2	NM_006465	
RIMBP3	85376	hgsc.bcm.edu	37	22	20457413	20457413	+	Missense_Mutation	SNP	T	T	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr22:20457413T>C	ENST00000426804.1	-	1	4373	c.3889A>G	c.(3889-3891)Aac>Gac	p.N1297D	SCARNA18_ENST00000516215.1_RNA|RN7SKP131_ENST00000363006.1_RNA|SCARNA17_ENST00000516762.1_RNA	NM_015672.1	NP_056487.1	Q9UFD9	RIM3A_HUMAN	RIMS binding protein 3	1297										breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(3)|lung(1)|prostate(1)|skin(1)|urinary_tract(1)	13	Colorectal(54;0.0993)|Melanoma(16;0.165)		LUSC - Lung squamous cell carcinoma(15;0.0405)|Lung(15;0.224)			GGCCTGTGGTTCTGGGGACTC	0.577																																					p.N1297D		Atlas-SNP	.											RIMBP3,NS,carcinoma,+1,1	RIMBP3	42	1	0			c.A3889G						scavenged	.						6.0	8.0	8.0					22																	20457413		871	2418	3289	SO:0001583	missense	85376	exon1			TGTGGTTCTGGGG	AB051453	CCDS46665.1	22q11.21	2014-05-06			ENSG00000196622	ENSG00000275793			29344	protein-coding gene	gene with protein product		612699				11258795, 17855024	Standard	NM_015672		Approved	KIAA1666, RIMBP3.1, RIMBP3A	uc002zsd.4	Q9UFD9	OTTHUMG00000188355	ENST00000426804.1:c.3889A>G	22.37:g.20457413T>C	ENSP00000391564:p.Asn1297Asp	Somatic	233	1	0.00429185		WXS	Illumina HiSeq	Phase_I	271	2	0.00738007	NM_015672	Q8IYP7|Q9BY94|Q9UFQ5	Missense_Mutation	SNP	ENST00000426804.1	37	CCDS46665.1	.	.	.	.	.	.	.	.	.	.	T	5.571	0.290189	0.10567	.	.	ENSG00000196622	ENST00000355186;ENST00000426804	T	0.19938	2.11	3.18	-2.83	0.05769	.	1.204890	0.05804	N	0.612853	T	0.12732	0.0309	L	0.32530	0.975	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.33317	-0.9873	10	0.14656	T	0.56	-2.6787	4.4824	0.11773	0.0:0.4004:0.1839:0.4157	.	1203	Q9UFD9	RIM3A_HUMAN	D	1203;1297	ENSP00000391564:N1297D	ENSP00000347318:N1203D	N	-	1	0	RIMBP3	18837413	0.000000	0.05858	0.001000	0.08648	0.049000	0.14656	-0.047000	0.11963	-0.825000	0.04290	-3.743000	0.00022	AAC	.	.	none		0.577	RIMBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318945.2	NM_015672	
LINS	55180	hgsc.bcm.edu	37	15	101110302	101110302	+	Missense_Mutation	SNP	C	C	G	rs2411837	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr15:101110302C>G	ENST00000314742.8	-	7	1637	c.1415G>C	c.(1414-1416)aGc>aCc	p.S472T	LINS_ENST00000559149.1_5'Flank	NM_001040616.2	NP_001035706	Q8NG48	LINES_HUMAN	lines homolog (Drosophila)	472			S -> T (in dbSNP:rs2411837).					p.S472T(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(3)|ovary(1)|prostate(1)|skin(1)|stomach(4)	21						CTGAGTCAAGCTTTCAGTGGC	0.338													C|||	1276	0.254792	0.115	0.2219	5008	,	,		17645	0.2252		0.4215	False		,,,				2504	0.3262				p.S472T		Atlas-SNP	.											LINS,NS,carcinoma,0,1	LINS	62	1	1	Substitution - Missense(1)	stomach(1)	c.G1415C						scavenged	.	C	THR/SER	691,3715	263.8+/-265.7	61,569,1573	56.0	55.0	56.0		1415	1.5	0.0	15	dbSNP_100	56	3716,4882	488.7+/-372.4	815,2086,1398	yes	missense	LINS	NM_001040616.2	58	876,2655,2971	GG,GC,CC		43.2194,15.6832,33.8896	benign	472/758	101110302	4407,8597	2203	4299	6502	SO:0001583	missense	55180	exon7			GTCAAGCTTTCAG	AK095448	CCDS10385.1	15q26.3	2010-09-08	2010-09-08	2010-09-08	ENSG00000140471	ENSG00000140471			30922	protein-coding gene	gene with protein product		610350	"""lines homolog 1 (Drosophila)"""	LINS1		12119551, 8889548	Standard	NM_001040616		Approved	WINS1	uc002bwg.3	Q8NG48	OTTHUMG00000149865	ENST00000314742.8:c.1415G>C	15.37:g.101110302C>G	ENSP00000318423:p.Ser472Thr	Somatic	2	1	0.5		WXS	Illumina HiSeq	Phase_I	6	6	1	NM_001040616	Q96FW2|Q9NVQ3	Missense_Mutation	SNP	ENST00000314742.8	37	CCDS10385.1	616	0.28205128205128205	69	0.1402439024390244	92	0.2541436464088398	132	0.23076923076923078	323	0.4261213720316623	C	6.256	0.415431	0.11870	0.156832	0.432194	ENSG00000140471	ENST00000314742	T	0.18338	2.22	5.48	1.52	0.23074	.	1.019250	0.07759	N	0.949715	T	0.00012	0.0000	L	0.44542	1.39	0.80722	P	0.0	B	0.32467	0.372	B	0.30316	0.114	T	0.47394	-0.9121	9	0.52906	T	0.07	0.0722	8.2917	0.31960	0.0:0.5925:0.0:0.4075	rs2411837;rs17777920;rs52833524;rs2411837	472	Q8NG48	LINES_HUMAN	T	472	ENSP00000318423:S472T	ENSP00000318423:S472T	S	-	2	0	LINS	98927825	0.000000	0.05858	0.025000	0.17156	0.670000	0.39368	-0.174000	0.09839	0.285000	0.22329	0.655000	0.94253	AGC	C|0.688;G|0.310	0.310	strong		0.338	LINS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313592.1	NM_018148	
ZNF648	127665	hgsc.bcm.edu	37	1	182025500	182025500	+	Missense_Mutation	SNP	C	C	T	rs559054881		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:182025500C>T	ENST00000339948.3	-	2	1853	c.1646G>A	c.(1645-1647)cGa>cAa	p.R549Q		NM_001009992.1	NP_001009992.1	Q5T619	ZN648_HUMAN	zinc finger protein 648	549					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(7)|large_intestine(10)|lung(17)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	40						GGCTCGGTGTCGTTGGAGGTG	0.587													C|||	1	0.000199681	0.0	0.0	5008	,	,		19654	0.0		0.001	False		,,,				2504	0.0				p.R549Q	NSCLC(71;908 1374 5429 20458 35642)	Atlas-SNP	.											ZNF648,colon,carcinoma,-1,1	ZNF648	111	1	0			c.G1646A						scavenged	.						195.0	157.0	170.0					1																	182025500		2203	4300	6503	SO:0001583	missense	127665	exon2			CGGTGTCGTTGGA	AK128654	CCDS30952.1	1q25.3	2013-01-08			ENSG00000179930	ENSG00000179930		"""Zinc fingers, C2H2-type"""	18190	protein-coding gene	gene with protein product							Standard	NM_001009992		Approved	FLJ46813	uc001goz.3	Q5T619	OTTHUMG00000037302	ENST00000339948.3:c.1646G>A	1.37:g.182025500C>T	ENSP00000344129:p.Arg549Gln	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	277	4	0.0144404	NM_001009992	B2RP16	Missense_Mutation	SNP	ENST00000339948.3	37	CCDS30952.1	.	.	.	.	.	.	.	.	.	.	C	9.751	1.167419	0.21621	.	.	ENSG00000179930	ENST00000339948	T	0.36157	1.27	2.63	2.63	0.31362	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.22820	0.0551	L	0.33753	1.03	0.09310	N	1	B	0.18968	0.032	B	0.13407	0.009	T	0.18555	-1.0333	9	0.12766	T	0.61	.	6.8993	0.24273	0.2745:0.7255:0.0:0.0	.	549	Q5T619	ZN648_HUMAN	Q	549	ENSP00000344129:R549Q	ENSP00000344129:R549Q	R	-	2	0	ZNF648	180292123	0.000000	0.05858	0.208000	0.23602	0.823000	0.46562	-0.144000	0.10280	1.793000	0.52555	0.655000	0.94253	CGA	.	.	none		0.587	ZNF648-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090794.1	XM_060597	
PTH2R	5746	hgsc.bcm.edu	37	2	209345848	209345848	+	Nonsense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:209345848G>A	ENST00000272847.2	+	10	1248	c.1035G>A	c.(1033-1035)tgG>tgA	p.W345*	AC019185.4_ENST00000424628.1_RNA|PTH2R_ENST00000413482.1_3'UTR	NM_005048.2	NP_005039.1	P49190	PTH2R_HUMAN	parathyroid hormone 2 receptor	345					G-protein coupled receptor signaling pathway (GO:0007186)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	parathyroid hormone receptor activity (GO:0004991)			breast(2)|endometrium(1)|kidney(2)|large_intestine(10)|lung(21)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43				Epithelial(149;0.0684)|Lung(261;0.0785)|LUSC - Lung squamous cell carcinoma(261;0.0836)	Preotact(DB05829)	CCAAAATCTGGGAGACCAATG	0.358																																					p.W345X		Atlas-SNP	.											PTH2R,NS,carcinoma,+1,2	PTH2R	92	2	0			c.G1035A						scavenged	.						101.0	99.0	99.0					2																	209345848		2203	4300	6503	SO:0001587	stop_gained	5746	exon10			AATCTGGGAGACC	BC036811	CCDS2383.1	2q33	2012-08-10	2007-08-24	2007-08-24	ENSG00000144407	ENSG00000144407		"""GPCR / Class B : Parathyroid hormone receptors"""	9609	protein-coding gene	gene with protein product		601469	"""parathyroid hormone receptor 2"""	PTHR2			Standard	NM_005048		Approved		uc002vdb.4	P49190	OTTHUMG00000132960	ENST00000272847.2:c.1035G>A	2.37:g.209345848G>A	ENSP00000272847:p.Trp345*	Somatic	206	0	0		WXS	Illumina HiSeq	Phase_I	202	3	0.0148515	NM_005048	Q8N429	Nonsense_Mutation	SNP	ENST00000272847.2	37	CCDS2383.1	.	.	.	.	.	.	.	.	.	.	G	38	6.878990	0.97904	.	.	ENSG00000144407	ENST00000272847	.	.	.	5.54	4.67	0.58626	.	0.000000	0.47093	D	0.000255	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.35	0.55143	0.0824:0.0:0.9176:0.0	.	.	.	.	X	345	.	.	W	+	3	0	PTH2R	209054093	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	2.650000	0.46665	1.484000	0.48361	0.650000	0.86243	TGG	.	.	none		0.358	PTH2R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256519.2	NM_005048	
PABPC1	26986	hgsc.bcm.edu	37	8	101724606	101724606	+	Missense_Mutation	SNP	G	G	A	rs202060459		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr8:101724606G>A	ENST00000318607.5	-	7	2084	c.956C>T	c.(955-957)aCa>aTa	p.T319I	PABPC1_ENST00000519596.1_5'UTR|PABPC1_ENST00000522387.1_Missense_Mutation_p.T287I|PABPC1_ENST00000519004.1_Missense_Mutation_p.T274I	NM_002568.3	NP_002559.2	P11940	PABP1_HUMAN	poly(A) binding protein, cytoplasmic 1	319	RRM 4. {ECO:0000255|PROSITE- ProRule:PRU00176}.				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)	p.T319I(2)		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)			ACTAGTGATTGTACCAAATGG	0.284																																					p.T319I		Atlas-SNP	.											PABPC1,NS,carcinoma,0,2	PABPC1	76	2	2	Substitution - Missense(2)	kidney(1)|endometrium(1)	c.C956T						scavenged	.						154.0	166.0	162.0					8																	101724606		2203	4298	6501	SO:0001583	missense	26986	exon7			GTGATTGTACCAA	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.956C>T	8.37:g.101724606G>A	ENSP00000313007:p.Thr319Ile	Somatic	170	0	0		WXS	Illumina HiSeq	Phase_I	253	4	0.0158103	NM_002568	Q15097|Q93004	Missense_Mutation	SNP	ENST00000318607.5	37	CCDS6289.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	26.8|26.8	4.768189|4.768189	0.90020|0.90020	.|.	.|.	ENSG00000070756|ENSG00000070756	ENST00000519100|ENST00000318607;ENST00000347137;ENST00000519004;ENST00000522387	.|T;T;T	.|0.16196	.|2.36;2.36;2.36	5.65|5.65	5.65|5.65	0.86999|0.86999	.|Nucleotide-binding, alpha-beta plait (1);RNA recognition motif domain (3);	.|0.000000	.|0.64402	.|D	.|0.000009	.|T	.|0.37652	.|0.1011	M|M	0.62154|0.62154	1.92|1.92	0.80722|0.80722	D|D	1|1	.|P;P;D	.|0.54964	.|0.917;0.784;0.969	.|P;B;P	.|0.56916	.|0.747;0.442;0.809	.|T	.|0.03784	.|-1.1004	.|10	.|0.87932	.|D	.|0	.|.	20.0919|20.0919	0.97823|0.97823	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|287;319;319	.|E7ERJ7;B3KT93;P11940	.|.;.;PABP1_HUMAN	X|I	188|319;319;274;287	.|ENSP00000313007:T319I;ENSP00000429594:T274I;ENSP00000429395:T287I	.|ENSP00000313007:T319I	Q|T	-|-	1|2	0|0	PABPC1|PABPC1	101793782|101793782	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	9.776000|9.776000	0.99001|0.99001	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	CAA|ACA	.	.	weak		0.284	PABPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380217.1	NM_002568	
TUBA3C	7278	hgsc.bcm.edu	37	13	19751463	19751463	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr13:19751463C>T	ENST00000400113.3	-	4	764	c.660G>A	c.(658-660)gaG>gaA	p.E220E		NM_006001.2	NP_005992.1	Q13748	TBA3C_HUMAN	tubulin, alpha 3c	220					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|microtubule-based process (GO:0007017)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|biliary_tract(1)|breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(12)|lung(33)|ovary(4)|prostate(7)|skin(7)|urinary_tract(1)	72		all_cancers(29;1.31e-20)|all_epithelial(30;1.59e-20)|all_lung(29;6.91e-20)|Lung NSC(5;9.25e-17)|Hepatocellular(1;0.0207)|Lung SC(185;0.0262)|Ovarian(182;0.162)		all cancers(112;6.78e-06)|Epithelial(112;3.79e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.00172)|Lung(94;0.0186)|LUSC - Lung squamous cell carcinoma(192;0.108)		ACGTGGGACGCTCGATGTCCA	0.567																																					p.E220E		Atlas-SNP	.											TUBA3C,NS,carcinoma,-2,1	TUBA3C	166	1	0			c.G660A						scavenged	.						229.0	192.0	205.0					13																	19751463		2203	4300	6503	SO:0001819	synonymous_variant	7278	exon4			GGGACGCTCGATG	AF005392	CCDS9284.1	13q12.11	2007-06-20	2007-02-12	2007-02-12	ENSG00000198033	ENSG00000198033		"""Tubulins"""	12408	protein-coding gene	gene with protein product		602528	"""tubulin, alpha 2"""	TUBA2		9465305	Standard	NM_006001		Approved	bA408E5.3	uc009zzj.3	Q13748	OTTHUMG00000016481	ENST00000400113.3:c.660G>A	13.37:g.19751463C>T		Somatic	331	1	0.00302115		WXS	Illumina HiSeq	Phase_I	309	4	0.012945	NM_006001	A6NJQ0|Q5W099|Q6PEY3|Q96F18	Silent	SNP	ENST00000400113.3	37	CCDS9284.1																																																																																			.	.	none		0.567	TUBA3C-002	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044007.2	NM_006001	
KRTAP4-11	653240	hgsc.bcm.edu	37	17	39274214	39274214	+	Missense_Mutation	SNP	G	G	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:39274214G>C	ENST00000391413.2	-	1	392	c.354C>G	c.(352-354)agC>agG	p.S118R		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	118	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)			gtctgcagcagctggacacac	0.652																																					p.S118R		Atlas-SNP	.											KRTAP4-11,right_upper_lobe,carcinoma,-1,2	KRTAP4-11	94	2	0			c.C354G						scavenged	.						4.0	8.0	7.0					17																	39274214		642	1521	2163	SO:0001583	missense	653240	exon1			GCAGCAGCTGGAC	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.354C>G	17.37:g.39274214G>C	ENSP00000375232:p.Ser118Arg	Somatic	56	1	0.0178571		WXS	Illumina HiSeq	Phase_I	76	9	0.118421	NM_033059	A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	11.65	1.702454	0.30232	.	.	ENSG00000212721	ENST00000391413	T	0.01963	4.53	3.63	2.63	0.31362	.	.	.	.	.	T	0.05914	0.0154	M	0.92691	3.335	0.25757	N	0.984995	B	0.18166	0.026	B	0.19391	0.025	T	0.23013	-1.0200	9	0.37606	T	0.19	.	5.3088	0.15819	0.1185:0.2126:0.6689:0.0	.	118	Q9BYQ6	KR411_HUMAN	R	118	ENSP00000375232:S118R	ENSP00000375232:S118R	S	-	3	2	KRTAP4-11	36527740	0.000000	0.05858	0.722000	0.30670	0.015000	0.08874	0.147000	0.16202	0.630000	0.30394	-0.413000	0.06143	AGC	.	.	none		0.652	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1		
MKI67	4288	hgsc.bcm.edu	37	10	129903685	129903685	+	Missense_Mutation	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:129903685A>G	ENST00000368654.3	-	13	6794	c.6419T>C	c.(6418-6420)cTc>cCc	p.L2140P	MKI67_ENST00000368653.3_Missense_Mutation_p.L1780P	NM_002417.4	NP_002408.3	P46013	KI67_HUMAN	marker of proliferation Ki-67	2140	16 X 122 AA approximate repeats.				cell proliferation (GO:0008283)|cellular response to heat (GO:0034605)|DNA metabolic process (GO:0006259)|hyaluronan metabolic process (GO:0030212)|meiotic nuclear division (GO:0007126)|organ regeneration (GO:0031100)|response to organic cyclic compound (GO:0014070)	chromosome, centromeric region (GO:0000775)|condensed chromosome (GO:0000793)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)			NS(2)|autonomic_ganglia(1)|breast(2)|central_nervous_system(2)|cervix(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(5)|kidney(7)|large_intestine(30)|lung(64)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|soft_tissue(1)|stomach(10)|upper_aerodigestive_tract(4)|urinary_tract(4)	159		all_epithelial(44;2.12e-05)|all_lung(145;0.00679)|Lung NSC(174;0.00998)|all_neural(114;0.0936)|Colorectal(57;0.14)|Breast(234;0.166)|Melanoma(40;0.203)				GGTCTGTGTGAGCTGCTTCAG	0.502																																					p.L2140P		Atlas-SNP	.											MKI67,NS,carcinoma,0,1	MKI67	363	1	0			c.T6419C						scavenged	.						266.0	248.0	254.0					10																	129903685		2203	4300	6503	SO:0001583	missense	4288	exon13			TGTGTGAGCTGCT	X65550	CCDS7659.1, CCDS53588.1	10q26.2	2014-06-12	2013-10-10		ENSG00000148773	ENSG00000148773			7107	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 105"""	176741	"""antigen identified by monoclonal antibody Ki-67"""			2571566, 16206250	Standard	NM_002417		Approved	MIB-, PPP1R105	uc001lke.3	P46013	OTTHUMG00000019255	ENST00000368654.3:c.6419T>C	10.37:g.129903685A>G	ENSP00000357643:p.Leu2140Pro	Somatic	490	0	0		WXS	Illumina HiSeq	Phase_I	589	7	0.0118845	NM_002417	Q5VWH2	Missense_Mutation	SNP	ENST00000368654.3	37	CCDS7659.1	.	.	.	.	.	.	.	.	.	.	A	12.33	1.905797	0.33628	.	.	ENSG00000148773	ENST00000368654;ENST00000368653;ENST00000537609	T;T	0.02369	4.32;4.32	3.96	-1.84	0.07809	.	2.418250	0.01969	N	0.043948	T	0.02727	0.0082	L	0.28608	0.87	0.09310	N	1	B;B;B	0.18741	0.022;0.026;0.03	B;B;B	0.22386	0.013;0.039;0.034	T	0.44081	-0.9351	10	0.27785	T	0.31	.	3.5257	0.07759	0.3387:0.0:0.1268:0.5346	.	2139;1780;2140	F5H4V4;P46013-2;P46013	.;.;KI67_HUMAN	P	2140;1780;2139	ENSP00000357643:L2140P;ENSP00000357642:L1780P	ENSP00000357642:L1780P	L	-	2	0	MKI67	129793675	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.022000	0.12480	-0.396000	0.07703	0.459000	0.35465	CTC	.	.	none		0.502	MKI67-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000050999.1	NM_002417	
CDC27	996	hgsc.bcm.edu	37	17	45219311	45219311	+	Missense_Mutation	SNP	T	T	C	rs140737545		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:45219311T>C	ENST00000066544.3	-	12	1552	c.1459A>G	c.(1459-1461)Att>Gtt	p.I487V	CDC27_ENST00000531206.1_Missense_Mutation_p.I493V|CDC27_ENST00000446365.2_Missense_Mutation_p.I426V|CDC27_ENST00000527547.1_Missense_Mutation_p.I486V	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	487					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						TGGCTCAAAATATTTATAGCT	0.383																																					p.I493V		Atlas-SNP	.											CDC27_ENST00000531206,NS,carcinoma,0,20	CDC27	337	20	0			c.A1477G						scavenged	.						112.0	118.0	116.0					17																	45219311		2203	4299	6502	SO:0001583	missense	996	exon12			TCAAAATATTTAT	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.1459A>G	17.37:g.45219311T>C	ENSP00000066544:p.Ile487Val	Somatic	36	1	0.0277778		WXS	Illumina HiSeq	Phase_I	39	3	0.0769231	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	T	4.731	0.135890	0.09032	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547	T;T;T;T	0.73681	-0.77;-0.77;-0.77;-0.77	5.92	3.6	0.41247	.	0.089833	0.85682	D	0.000000	T	0.53384	0.1793	L	0.31476	0.935	0.49798	D	0.999821	B;B;B;B	0.23316	0.05;0.083;0.083;0.024	B;B;B;B	0.17098	0.008;0.017;0.017;0.005	T	0.44590	-0.9318	10	0.02654	T	1	-23.2923	6.9274	0.24422	0.0:0.0792:0.1504:0.7704	.	426;486;493;487	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	V	487;493;426;486	ENSP00000066544:I487V;ENSP00000434614:I493V;ENSP00000392802:I426V;ENSP00000437339:I486V	ENSP00000066544:I487V	I	-	1	0	CDC27	42574310	1.000000	0.71417	0.998000	0.56505	0.990000	0.78478	4.907000	0.63300	1.072000	0.40860	0.528000	0.53228	ATT	.	.	weak		0.383	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
ZFHX4	79776	hgsc.bcm.edu	37	8	77766731	77766731	+	Missense_Mutation	SNP	A	A	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr8:77766731A>T	ENST00000521891.2	+	10	8022	c.7574A>T	c.(7573-7575)cAc>cTc	p.H2525L	ZFHX4_ENST00000050961.6_Missense_Mutation_p.H2480L|ZFHX4_ENST00000455469.2_Missense_Mutation_p.H2480L|ZFHX4_ENST00000518282.1_Missense_Mutation_p.H2499L	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2480					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CAATTCCTTCACTCTCCGTTC	0.498										HNSCC(33;0.089)																											p.H2525L		Atlas-SNP	.											.	ZFHX4	878	.	0			c.A7574T						PASS	.						167.0	167.0	167.0					8																	77766731		2038	4213	6251	SO:0001583	missense	79776	exon10			TCCTTCACTCTCC		CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.7574A>T	8.37:g.77766731A>T	ENSP00000430497:p.His2525Leu	Somatic	81	0	0		WXS	Illumina HiSeq	Phase_I	105	12	0.114286	NM_024721	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	A	16.66	3.184571	0.57909	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	T;T;T;T	0.53857	0.6;0.66;0.63;0.62	4.94	4.94	0.65067	.	0.000000	0.46758	U	0.000276	T	0.65554	0.2702	M	0.71581	2.175	0.80722	D	1	P;P;P	0.52316	0.92;0.896;0.952	P;P;P	0.55999	0.727;0.789;0.789	T	0.66444	-0.5922	10	0.39692	T	0.17	.	14.7648	0.69632	1.0:0.0:0.0:0.0	.	2480;2480;2525	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	L	2525;2509;2480;2480;2499	ENSP00000430497:H2525L;ENSP00000399605:H2480L;ENSP00000050961:H2480L;ENSP00000430848:H2499L	ENSP00000050961:H2480L	H	+	2	0	ZFHX4	77929286	1.000000	0.71417	0.999000	0.59377	0.960000	0.62799	9.131000	0.94446	2.077000	0.62373	0.528000	0.53228	CAC	.	.	none		0.498	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2	NM_024721	
KRTAP4-7	100132476	hgsc.bcm.edu	37	17	39240790	39240790	+	Missense_Mutation	SNP	G	G	A	rs11650261|rs553572799	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:39240790G>A	ENST00000391417.4	+	1	332	c.332G>A	c.(331-333)cGc>cAc	p.R111H		NM_033061.3	NP_149050.3	Q9BYR0	KRA47_HUMAN	keratin associated protein 4-7	136	31 X 5 AA repeats of C-C-[GIKRQVHEML]- [SPTRV]-[STVQRCP].		Missing. {ECO:0000269|PubMed:15955084}.		aging (GO:0007568)|hair cycle (GO:0042633)	keratin filament (GO:0045095)		p.R111_C115delRPSCC(1)|p.?(1)		NS(1)|endometrium(3)|kidney(1)|lung(1)|prostate(2)|urinary_tract(1)	9						acctgctgccgccccagctgc	0.657													g|||	343	0.0684904	0.0272	0.1196	5008	,	,		10689	0.0685		0.1153	False		,,,				2504	0.0399				p.R111H		Atlas-SNP	.											KRTAP4-9_ENST00000377734,NS,carcinoma,0,3	KRTAP4-7	49	3	2	Unknown(1)|Deletion - In frame(1)	NS(2)	c.G332A						scavenged	.						11.0	13.0	12.0					17																	39240790		682	1579	2261	SO:0001583	missense	100132476	exon1			GCTGCCGCCCCAG	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.332G>A	17.37:g.39240790G>A	ENSP00000375236:p.Arg111His	Somatic	68	3	0.0441176		WXS	Illumina HiSeq	Phase_I	52	2	0.0384615	NM_033061	A0AVM6|A8MQ08|A8MTL4	Missense_Mutation	SNP	ENST00000391417.4	37	CCDS45673.1	148	0.06776556776556776	22	0.044715447154471545	32	0.08839779005524862	22	0.038461538461538464	72	0.09498680738786279	.	6.498	0.460116	0.12342	.	.	ENSG00000240871	ENST00000391417	T	0.00612	6.22	3.95	-0.91	0.10511	.	8.977930	0.00616	U	0.000420	T	0.00039	0.0001	.	.	.	0.09310	N	1	D	0.60575	0.988	P	0.46389	0.515	T	0.44050	-0.9353	9	0.48119	T	0.1	.	3.4362	0.07446	0.2202:0.0:0.299:0.4808	rs11650261	166	Q9BYR0	KRA47_HUMAN	H	111	ENSP00000375236:R111H	ENSP00000375236:R111H	R	+	2	0	KRTAP4-7	36494316	0.000000	0.05858	0.005000	0.12908	0.119000	0.20118	0.218000	0.17622	0.230000	0.21059	-0.391000	0.06502	CGC	G|0.932;A|0.068	0.068	strong		0.657	KRTAP4-7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257686.1		
KRTAP4-8	728224	hgsc.bcm.edu	37	17	39254126	39254126	+	Missense_Mutation	SNP	C	C	T	rs202107241		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:39254126C>T	ENST00000333822.4	-	1	267	c.211G>A	c.(211-213)Gtg>Atg	p.V71M		NM_031960.2	NP_114166.1	Q9BYQ9	KRA48_HUMAN	keratin associated protein 4-8	71	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						CAGCTGGACACACAGCAGCTG	0.667																																					p.V71M		Atlas-SNP	.											KRTAP4-8,colon,carcinoma,+2,2	KRTAP4-8	57	2	0			c.G211A						scavenged	.						5.0	8.0	7.0					17																	39254126		619	1441	2060	SO:0001583	missense	728224	exon1			TGGACACACAGCA	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.211G>A	17.37:g.39254126C>T	ENSP00000328444:p.Val71Met	Somatic	56	4	0.0714286		WXS	Illumina HiSeq	Phase_I	62	2	0.0322581	NM_031960	A8MSH3	Missense_Mutation	SNP	ENST00000333822.4	37	CCDS45674.1	.	.	.	.	.	.	.	.	.	.	.	8.585	0.883304	0.17467	.	.	ENSG00000204880	ENST00000333822;ENST00000332991	T	0.01430	4.9	3.55	-7.1	0.01547	.	3.062900	0.01485	U	0.016837	T	0.03477	0.0100	M	0.81497	2.545	0.09310	N	1	P	0.40266	0.71	B	0.43623	0.425	T	0.15896	-1.0421	10	0.45353	T	0.12	.	7.8878	0.29661	0.0:0.5469:0.2514:0.2017	.	71	Q9BYQ9	KRA48_HUMAN	M	71	ENSP00000328444:V71M	ENSP00000414561:V71M	V	-	1	0	KRTAP4-8	36507652	0.000000	0.05858	0.019000	0.16419	0.121000	0.20230	-2.017000	0.01445	-1.974000	0.00998	-1.450000	0.01041	GTG	.	.	weak		0.667	KRTAP4-8-001	KNOWN	not_best_in_genome_evidence|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257684.1	NM_031960	
KRTAP4-3	85290	hgsc.bcm.edu	37	17	39324333	39324333	+	Missense_Mutation	SNP	T	T	A	rs12953139	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:39324333T>A	ENST00000391356.2	-	1	91	c.92A>T	c.(91-93)cAg>cTg	p.Q31L		NM_033187.1	NP_149443.1	Q9BYR4	KRA43_HUMAN	keratin associated protein 4-3	31					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)			GCAGGTGGTCTGGCAGCAGCT	0.637																																					p.Q31L		Atlas-SNP	.											KRTAP4-3,NS,carcinoma,0,1	KRTAP4-3	40	1	0			c.A92T						scavenged	.						29.0	32.0	31.0					17																	39324333		2195	4293	6488	SO:0001583	missense	85290	exon1			GTGGTCTGGCAGC	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.92A>T	17.37:g.39324333T>A	ENSP00000375151:p.Gln31Leu	Somatic	128	2	0.015625		WXS	Illumina HiSeq	Phase_I	210	49	0.233333	NM_033187		Missense_Mutation	SNP	ENST00000391356.2	37	CCDS42331.1	.	.	.	.	.	.	.	.	.	.	.	8.661	0.900435	0.17686	.	.	ENSG00000196156	ENST00000391356	T	0.01629	4.72	5.15	0.112	0.14623	.	.	.	.	.	T	0.03608	0.0103	M	0.85373	2.75	0.80722	P	0.0	B	0.34181	0.44	B	0.38378	0.272	T	0.11131	-1.0600	8	0.35671	T	0.21	.	3.821	0.08836	0.1588:0.2591:0.0:0.5822	.	31	Q9BYR4	KRA43_HUMAN	L	31	ENSP00000375151:Q31L	ENSP00000375151:Q31L	Q	-	2	0	KRTAP4-3	36577859	0.006000	0.16342	0.208000	0.23602	0.204000	0.24138	0.129000	0.15830	0.020000	0.15106	0.533000	0.62120	CAG	A|0.046;T|0.954	0.046	strong		0.637	KRTAP4-3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257784.1		
CTNND2	1501	hgsc.bcm.edu	37	5	11732341	11732341	+	Missense_Mutation	SNP	C	C	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:11732341C>A	ENST00000304623.8	-	2	270	c.81G>T	c.(79-81)aaG>aaT	p.K27N	CTNND2_ENST00000359640.2_Missense_Mutation_p.K27N|CTNND2_ENST00000458100.2_5'UTR	NM_001332.2	NP_001323.1	Q9UQB3	CTND2_HUMAN	catenin (cadherin-associated protein), delta 2	27					cell adhesion (GO:0007155)|learning (GO:0007612)|morphogenesis of a branching structure (GO:0001763)|multicellular organismal development (GO:0007275)|regulation of synaptic plasticity (GO:0048167)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|autonomic_ganglia(1)|breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(3)|kidney(3)|large_intestine(29)|liver(1)|lung(71)|ovary(4)|pancreas(2)|prostate(1)|skin(5)|upper_aerodigestive_tract(4)|urinary_tract(2)	136						GGGAACTCGTCTTCTCTGAGG	0.502																																					p.K27N		Atlas-SNP	.											.	CTNND2	289	.	0			c.G81T						PASS	.						126.0	127.0	126.0					5																	11732341		2203	4300	6503	SO:0001583	missense	1501	exon2			ACTCGTCTTCTCT	U52828	CCDS3881.1, CCDS75227.1, CCDS75228.1	5p15.2	2013-02-14	2012-08-15		ENSG00000169862	ENSG00000169862		"""Armadillo repeat containing"""	2516	protein-coding gene	gene with protein product	"""neural plakophilin-related arm-repeat protein"""	604275	"""catenin (cadherin-associated protein), delta 2 (neural plakophilin-related arm-repeat protein)"""			9342840, 9223106	Standard	XM_005248251		Approved	NPRAP, GT24	uc003jfa.1	Q9UQB3	OTTHUMG00000090511	ENST00000304623.8:c.81G>T	5.37:g.11732341C>A	ENSP00000307134:p.Lys27Asn	Somatic	45	0	0		WXS	Illumina HiSeq	Phase_I	58	25	0.431034	NM_001332	B0FTZ7|O00379|O15390|O43206|O43840|Q13589|Q9UM66|Q9UPM3	Missense_Mutation	SNP	ENST00000304623.8	37	CCDS3881.1	.	.	.	.	.	.	.	.	.	.	C	7.609	0.674382	0.14841	.	.	ENSG00000169862	ENST00000304623;ENST00000359640;ENST00000502551;ENST00000508761	T;T	0.76060	-0.94;-0.99	5.8	3.08	0.35506	.	0.000000	0.46758	D	0.000274	T	0.50034	0.1592	N	0.08118	0	0.80722	D	1	B	0.09022	0.002	B	0.09377	0.004	T	0.20874	-1.0262	10	0.12430	T	0.62	-20.7622	10.2002	0.43077	0.0:0.7052:0.0:0.2948	.	27	Q9UQB3	CTND2_HUMAN	N	27;27;13;13	ENSP00000307134:K27N;ENSP00000352661:K27N	ENSP00000307134:K27N	K	-	3	2	CTNND2	11785341	1.000000	0.71417	0.999000	0.59377	0.902000	0.53008	0.865000	0.27940	0.109000	0.17891	-0.829000	0.03081	AAG	.	.	none		0.502	CTNND2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206999.1	NM_001332	
DIAPH1	1729	hgsc.bcm.edu	37	5	140953563	140953563	+	Silent	SNP	T	T	A	rs374236039|rs3075570		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:140953563T>A	ENST00000398557.4	-	16	1994	c.1854A>T	c.(1852-1854)ccA>ccT	p.P618P	DIAPH1_ENST00000253811.6_Silent_p.P618P|DIAPH1_ENST00000389057.5_Silent_p.P609P|DIAPH1_ENST00000518047.1_Silent_p.P609P|DIAPH1_ENST00000520569.1_Silent_p.P564P|DIAPH1_ENST00000398566.3_Silent_p.P609P|DIAPH1_ENST00000389054.3_Silent_p.P618P|DIAPH1_ENST00000398562.2_Silent_p.P609P	NM_005219.4	NP_005210.3	O60610	DIAP1_HUMAN	diaphanous-related formin 1	618	FH1.				actin filament polymerization (GO:0030041)|cellular response to histamine (GO:0071420)|cytoskeleton organization (GO:0007010)|positive regulation of cell migration (GO:0030335)|protein localization to microtubule (GO:0035372)|regulation of cell shape (GO:0008360)|regulation of microtubule-based process (GO:0032886)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|sensory perception of sound (GO:0007605)	cytoplasm (GO:0005737)|mitotic spindle (GO:0072686)|ruffle membrane (GO:0032587)	ion channel binding (GO:0044325)|poly(A) RNA binding (GO:0044822)|receptor binding (GO:0005102)			breast(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(12)|pancreas(1)|skin(2)|stomach(2)	23			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			GCAAaggaggtggaggaggag	0.577																																					p.P618P		Atlas-SNP	.											DIAPH1,NS,carcinoma,0,1	DIAPH1	64	1	0			c.A1854T						scavenged	.						21.0	21.0	21.0					5																	140953563		1987	4116	6103	SO:0001819	synonymous_variant	1729	exon16			AGGAGGTGGAGGA	BC007411		5q31	2013-05-24	2013-05-24		ENSG00000131504	ENSG00000131504			2876	protein-coding gene	gene with protein product		602121	"""diaphanous (Drosophila, homolog) 1"", ""diaphanous homolog 1 (Drosophila)"""	DFNA1		9360932, 1350680	Standard	NM_005219		Approved	hDIA1, LFHL1	uc003llb.4	O60610	OTTHUMG00000149893	ENST00000398557.4:c.1854A>T	5.37:g.140953563T>A		Somatic	16	1	0.0625		WXS	Illumina HiSeq	Phase_I	35	8	0.228571	NM_005219	A6NF18|B7ZKW2|E9PEZ2|Q17RN4|Q59FH8|Q9UC76	Silent	SNP	ENST00000398557.4	37	CCDS43374.1																																																																																			.	.	weak		0.577	DIAPH1-203	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		NM_005219	
APEH	327	hgsc.bcm.edu	37	3	49723296	49723296	+	IGR	SNP	G	G	A	rs2087733	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr3:49723296G>A	ENST00000296456.5	+	0	3220				MST1_ENST00000383728.3_3'UTR|AC099668.5_ENST00000563780.1_RNA|MST1_ENST00000494828.2_5'Flank|MST1_ENST00000449682.2_Missense_Mutation_p.P416L	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase						beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)	p.P402L(4)		endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		GACTCACTGCGGCTTGTGCGG	0.677													G|||	3	0.000599042	0.0	0.0	5008	,	,		23747	0.0		0.003	False		,,,				2504	0.0				p.P416L		Atlas-SNP	.											MST1,trunk,malignant_melanoma,0,3	MST1	84	3	4	Substitution - Missense(4)	NS(2)|lung(1)|skin(1)	c.C1247T						scavenged	.						67.0	64.0	65.0					3																	49723296		2197	4282	6479	SO:0001628	intergenic_variant	4485	exon10			CACTGCGGCTTGT	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882		3.37:g.49723296G>A		Somatic	113	6	0.0530973		WXS	Illumina HiSeq	Phase_I	113	10	0.0884956	NM_020998	Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	G	13.04	2.117796	0.37339	.	.	ENSG00000173531	ENST00000449682	T	0.66280	-0.2	5.1	5.1	0.69264	.	0.000000	0.42053	D	0.000772	T	0.52980	0.1768	L	0.33137	0.985	0.80722	D	1	B	0.18013	0.025	B	0.17979	0.02	T	0.48969	-0.8987	10	0.38643	T	0.18	.	16.2918	0.82756	0.0:0.0:1.0:0.0	rs2087733	416	G3XAK1	.	L	416	ENSP00000414287:P416L	ENSP00000414287:P416L	P	-	2	0	MST1	49698300	1.000000	0.71417	0.996000	0.52242	0.047000	0.14425	8.980000	0.93460	2.373000	0.80994	0.561000	0.74099	CCG	G|0.375;A|0.625	0.625	strong		0.677	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2		
SLC27A5	10998	hgsc.bcm.edu	37	19	59010920	59010920	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:59010920C>T	ENST00000263093.2	-	7	1715	c.1606G>A	c.(1606-1608)Gta>Ata	p.V536I	SLC27A5_ENST00000601355.1_Missense_Mutation_p.V452I|SLC27A5_ENST00000599700.1_5'Flank|SLC27A5_ENST00000594786.1_5'Flank	NM_012254.2	NP_036386.1	Q9Y2P5	S27A5_HUMAN	solute carrier family 27 (fatty acid transporter), member 5	536					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)		ATGGCCAGTACGTCCCCGGTG	0.687																																					p.V536I		Atlas-SNP	.											.	SLC27A5	58	.	0			c.G1606A						PASS	.						85.0	78.0	81.0					19																	59010920		2203	4300	6503	SO:0001583	missense	10998	exon7			CCAGTACGTCCCC	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.1606G>A	19.37:g.59010920C>T	ENSP00000263093:p.Val536Ile	Somatic	64	0	0		WXS	Illumina HiSeq	Phase_I	76	28	0.368421	NM_012254	B3KVP6|B4DPQ1	Missense_Mutation	SNP	ENST00000263093.2	37	CCDS12983.1	.	.	.	.	.	.	.	.	.	.	C	17.77	3.470540	0.63625	.	.	ENSG00000083807	ENST00000263093	T	0.37915	1.17	5.26	-0.904	0.10530	AMP-dependent synthetase/ligase (1);	0.216318	0.39985	N	0.001207	T	0.19886	0.0478	L	0.35414	1.06	0.26467	N	0.975346	B	0.20780	0.048	B	0.20767	0.031	T	0.10154	-1.0642	10	0.56958	D	0.05	-17.5506	1.7058	0.02881	0.1539:0.3661:0.2999:0.1802	.	536	Q9Y2P5	S27A5_HUMAN	I	536	ENSP00000263093:V536I	ENSP00000263093:V536I	V	-	1	0	SLC27A5	63702732	0.996000	0.38824	0.016000	0.15963	0.983000	0.72400	0.379000	0.20585	0.312000	0.23038	0.462000	0.41574	GTA	.	.	none		0.687	SLC27A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000467060.1	NM_012254	
MTMR1	8776	hgsc.bcm.edu	37	X	149896207	149896207	+	Missense_Mutation	SNP	A	A	C			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chrX:149896207A>C	ENST00000370390.3	+	5	632	c.475A>C	c.(475-477)Aag>Cag	p.K159Q	MTMR1_ENST00000544228.1_Missense_Mutation_p.K159Q|MTMR1_ENST00000445323.2_Missense_Mutation_p.K167Q|MTMR1_ENST00000451863.2_Missense_Mutation_p.K159Q|MTMR1_ENST00000542156.1_Missense_Mutation_p.K159Q|MTMR1_ENST00000541925.1_Missense_Mutation_p.K65Q|MTMR1_ENST00000538506.1_Missense_Mutation_p.K46Q	NM_003828.2	NP_003819.1	Q13613	MTMR1_HUMAN	myotubularin related protein 1	159	GRAM.				phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|plasma membrane (GO:0005886)	phosphatidylinositol-3-phosphatase activity (GO:0004438)|protein tyrosine phosphatase activity (GO:0004725)			central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(5)|ovary(2)|prostate(1)	23	Acute lymphoblastic leukemia(192;6.56e-05)					CAGAGTGGAGAAGATTGGAGC	0.423																																					p.K159Q		Atlas-SNP	.											.	MTMR1	82	.	0			c.A475C						PASS	.						125.0	108.0	114.0					X																	149896207		2203	4300	6503	SO:0001583	missense	8776	exon5			GTGGAGAAGATTG	U58032	CCDS14695.1	Xq28	2011-06-09			ENSG00000063601	ENSG00000063601		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7449	protein-coding gene	gene with protein product		300171				9828128	Standard	XM_005274765		Approved		uc004fei.3	Q13613	OTTHUMG00000024159	ENST00000370390.3:c.475A>C	X.37:g.149896207A>C	ENSP00000359417:p.Lys159Gln	Somatic	196	0	0		WXS	Illumina HiSeq	Phase_I	122	92	0.754098	NM_003828	A0A024RC07|Q9UBX6|Q9UEM0|Q9UQD5	Missense_Mutation	SNP	ENST00000370390.3	37	CCDS14695.1	.	.	.	.	.	.	.	.	.	.	a	20.2	3.953853	0.73902	.	.	ENSG00000063601	ENST00000541925;ENST00000493995;ENST00000439546;ENST00000429965;ENST00000434699;ENST00000542156;ENST00000370390;ENST00000490316;ENST00000445323;ENST00000544228;ENST00000451863;ENST00000438018;ENST00000436701;ENST00000538506	D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.90732	-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72;-2.72	5.08	5.08	0.68730	GRAM (2);	0.154112	0.56097	D	0.000028	D	0.94275	0.8161	M	0.80847	2.515	0.58432	D	0.999997	P;P;D	0.57899	0.921;0.904;0.981	P;P;P	0.58970	0.849;0.704;0.804	D	0.94951	0.8100	10	0.87932	D	0	.	14.1476	0.65360	1.0:0.0:0.0:0.0	.	159;167;159	Q13613;F8WA39;Q8NEC6	MTMR1_HUMAN;.;.	Q	65;65;65;65;65;159;159;176;167;159;159;123;140;46	ENSP00000441879:K65Q;ENSP00000431992:K65Q;ENSP00000404599:K65Q;ENSP00000390736:K65Q;ENSP00000405946:K65Q;ENSP00000445281:K159Q;ENSP00000359417:K159Q;ENSP00000436957:K176Q;ENSP00000414178:K167Q;ENSP00000440534:K159Q;ENSP00000387446:K159Q;ENSP00000389884:K123Q;ENSP00000414925:K140Q;ENSP00000443444:K46Q	ENSP00000359417:K159Q	K	+	1	0	MTMR1	149646865	1.000000	0.71417	1.000000	0.80357	0.950000	0.60333	5.001000	0.63946	1.787000	0.52448	0.441000	0.28932	AAG	.	.	none		0.423	MTMR1-013	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000060863.2	NM_003828, NM_176789	
KIAA1244	57221	hgsc.bcm.edu	37	6	138583857	138583857	+	Missense_Mutation	SNP	G	G	A	rs149573553	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:138583857G>A	ENST00000251691.4	+	12	1403	c.1237G>A	c.(1237-1239)Gaa>Aaa	p.E413K		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)		TGGCATGACCGAAGCATGCAT	0.473													G|||	2	0.000399361	0.0	0.0	5008	,	,		23811	0.002		0.0	False		,,,				2504	0.0				p.E413K		Atlas-SNP	.											.	KIAA1244	236	.	0			c.G1237A						PASS	.						110.0	104.0	106.0					6																	138583857		2203	4300	6503	SO:0001583	missense	57221	exon12			ATGACCGAAGCAT	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.1237G>A	6.37:g.138583857G>A	ENSP00000251691:p.Glu413Lys	Somatic	116	0	0		WXS	Illumina HiSeq	Phase_I	127	49	0.385827	NM_020340		Missense_Mutation	SNP	ENST00000251691.4	37	CCDS5189.2	2	9.157509157509158E-4	0	0.0	0	0.0	2	0.0034965034965034965	0	0.0	G	22.9	4.348964	0.82132	.	.	ENSG00000112379	ENST00000251691	T	0.04275	3.66	5.82	5.82	0.92795	.	0.000000	0.85682	D	0.000000	T	0.09468	0.0233	M	0.73962	2.25	0.58432	D	0.999992	D	0.67145	0.996	P	0.50570	0.644	T	0.01178	-1.1427	10	0.72032	D	0.01	-13.0813	18.2897	0.90126	0.0:0.0:1.0:0.0	.	413	Q5TH69	BIG3_HUMAN	K	413	ENSP00000251691:E413K	ENSP00000251691:E413K	E	+	1	0	KIAA1244	138625550	1.000000	0.71417	0.709000	0.30452	0.865000	0.49528	7.342000	0.79310	2.745000	0.94114	0.655000	0.94253	GAA	G|0.999;A|0.001	0.001	strong		0.473	KIAA1244-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042425.4	NM_020340	
KRT6A	3853	hgsc.bcm.edu	37	12	52885485	52885485	+	Missense_Mutation	SNP	T	T	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:52885485T>G	ENST00000330722.6	-	2	644	c.576A>C	c.(574-576)gaA>gaC	p.E192D		NM_005554.3	NP_005545.1	P02538	K2C6A_HUMAN	keratin 6A	192	Coil 1A.|Rod.			E -> D (in Ref. 1; AAB60696). {ECO:0000305}.	cell differentiation (GO:0030154)|positive regulation of cell proliferation (GO:0008284)	extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			breast(2)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(7)|liver(1)|lung(14)|ovary(4)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	39				BRCA - Breast invasive adenocarcinoma(357;0.189)		TCCACTTTGTTTCCAGAACCT	0.532																																					p.E192D		Atlas-SNP	.											KRT6A,NS,haematopoietic_neoplasm,0,1	KRT6A	89	1	0			c.A576C						scavenged	.						66.0	67.0	67.0					12																	52885485		2203	4300	6503	SO:0001583	missense	3853	exon2			CTTTGTTTCCAGA	BC014152, L42593, L42610	CCDS41786.1	12q13.13	2013-01-16			ENSG00000205420	ENSG00000205420		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6443	protein-coding gene	gene with protein product		148041	"""keratin 6C"", ""keratin 6D"""	KRT6C, KRT6D		1713141, 16831889	Standard	NM_005554		Approved	CK6C, K6C, CK6D, K6D	uc001sam.3	P02538	OTTHUMG00000169597	ENST00000330722.6:c.576A>C	12.37:g.52885485T>G	ENSP00000369317:p.Glu192Asp	Somatic	172	1	0.00581395		WXS	Illumina HiSeq	Phase_I	172	3	0.0174419	NM_005554	A4QPC1|P48667|Q08AR4|Q6NT67|Q96CL4	Missense_Mutation	SNP	ENST00000330722.6	37	CCDS41786.1	.	.	.	.	.	.	.	.	.	.	t	15.33	2.801841	0.50315	.	.	ENSG00000205420	ENST00000330722;ENST00000452121	T	0.78595	-1.19	5.26	-1.41	0.08941	Filament (1);	0.298035	0.28414	N	0.015426	T	0.76772	0.4034	M	0.92555	3.32	0.31174	N	0.70282	B	0.24651	0.108	B	0.31016	0.123	T	0.68059	-0.5509	10	0.40728	T	0.16	.	2.0814	0.03635	0.1319:0.2762:0.2398:0.352	.	192	P02538	K2C6A_HUMAN	D	192;148	ENSP00000369317:E192D	ENSP00000369317:E192D	E	-	3	2	KRT6A	51171752	0.999000	0.42202	0.994000	0.49952	0.965000	0.64279	0.625000	0.24477	-0.197000	0.10350	-0.302000	0.09304	GAA	.	.	none		0.532	KRT6A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404978.2	NM_005554	
TDRD6	221400	hgsc.bcm.edu	37	6	46656149	46656149	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr6:46656149G>A	ENST00000316081.6	+	1	284	c.284G>A	c.(283-285)cGt>cAt	p.R95H	RP11-446F17.3_ENST00000422284.2_RNA|TDRD6_ENST00000544460.1_Missense_Mutation_p.R95H|RP11-446F17.3_ENST00000571590.1_RNA|RP11-446F17.3_ENST00000434329.2_RNA	NM_001010870.2	NP_001010870.1	O60522	TDRD6_HUMAN	tudor domain containing 6	95	Tudor 1. {ECO:0000255|PROSITE- ProRule:PRU00211}.				germ cell development (GO:0007281)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|P granule (GO:0043186)				NS(1)|breast(9)|central_nervous_system(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(25)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	80			Lung(136;0.192)			CAGGAGAGCCGTGTCTTCCTG	0.701																																					p.R95H		Atlas-SNP	.											.	TDRD6	205	.	0			c.G284A						PASS	.						6.0	8.0	7.0					6																	46656149		2017	3951	5968	SO:0001583	missense	221400	exon1			AGAGCCGTGTCTT	AF039442	CCDS34470.1, CCDS55017.1	6p12.3	2013-01-23			ENSG00000180113	ENSG00000180113		"""Tudor domain containing"""	21339	protein-coding gene	gene with protein product	"""cancer/testis antigen 41.2"", ""spermatogenesis associated 36"""	611200				9610721	Standard	NM_001010870		Approved	NY-CO-45, bA446F17.4, CT41.2, SPATA36	uc003oyj.3	O60522	OTTHUMG00000014788	ENST00000316081.6:c.284G>A	6.37:g.46656149G>A	ENSP00000346065:p.Arg95His	Somatic	18	0	0		WXS	Illumina HiSeq	Phase_I	23	12	0.521739	NM_001168359	B3KWU2|F5H5M3|Q5HYB1|Q5VTS4|Q6ZMX5	Missense_Mutation	SNP	ENST00000316081.6	37	CCDS34470.1	.	.	.	.	.	.	.	.	.	.	G	17.05	3.289084	0.59976	.	.	ENSG00000180113	ENST00000544460;ENST00000316081	T;T	0.09723	2.95;2.95	5.31	5.31	0.75309	Maternal tudor protein (1);Tudor domain (1);	0.869952	0.10294	N	0.692000	T	0.19366	0.0465	L	0.56769	1.78	0.29552	N	0.851296	D;D	0.89917	1.0;1.0	D;D	0.76071	0.977;0.987	T	0.02411	-1.1163	10	0.51188	T	0.08	-5.4554	13.8844	0.63699	0.0:0.0:0.8474:0.1525	.	95;95	F5H5M3;O60522	.;TDRD6_HUMAN	H	95	ENSP00000443299:R95H;ENSP00000346065:R95H	ENSP00000346065:R95H	R	+	2	0	TDRD6	46764108	0.940000	0.31905	1.000000	0.80357	0.978000	0.69477	1.391000	0.34475	2.482000	0.83794	0.563000	0.77884	CGT	.	.	none		0.701	TDRD6-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040800.1	XM_166443	
MAP2K3	5606	hgsc.bcm.edu	37	17	21208440	21208440	+	Splice_Site	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:21208440G>A	ENST00000342679.4	+	9	1023	c.774G>A	c.(772-774)atG>atA	p.M258I	MAP2K3_ENST00000361818.5_Splice_Site_p.M229I|MAP2K3_ENST00000316920.6_Splice_Site_p.M229I	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	258	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|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)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)								COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		GCATCACCATGGTACTGTGGG	0.612																																					p.M258I		Atlas-SNP	.											.	MAP2K3	135	.	0			c.G774A						PASS	.						113.0	99.0	104.0					17																	21208440		2203	4300	6503	SO:0001630	splice_region_variant	5606	exon9			CACCATGGTACTG	L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6843	protein-coding gene	gene with protein product	"""MAPK/ERK kinase 3"", ""MAP kinase kinase 3"", ""dual specificity mitogen activated protein kinase kinase 3"""	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.774+1G>A	17.37:g.21208440G>A		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	124	17	0.137097	NM_145109	B3KSK7|Q99441|Q9UE71|Q9UE72	Missense_Mutation	SNP	ENST00000342679.4	37	CCDS11217.1	.	.	.	.	.	.	.	.	.	.	G	18.82	3.705218	0.68615	.	.	ENSG00000034152	ENST00000342679;ENST00000395491;ENST00000361818;ENST00000316920	T;T	0.62941	-0.01;-0.01	4.97	4.97	0.65823	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.37785	0.1016	N	0.01134	-0.995	0.80722	D	1	B	0.32160	0.358	B	0.34242	0.178	T	0.52185	-0.8609	10	0.51188	T	0.08	-50.5579	18.2339	0.89944	0.0:0.0:1.0:0.0	.	258	P46734	MP2K3_HUMAN	I	258;229;229;262	ENSP00000345083:M258I;ENSP00000355081:M229I	ENSP00000319139:M262I	M	+	3	0	MAP2K3	21149033	1.000000	0.71417	1.000000	0.80357	0.632000	0.37999	9.690000	0.98676	2.309000	0.77851	0.462000	0.41574	ATG	.	.	none		0.612	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2	NM_145109	Missense_Mutation
DNAH10	196385	hgsc.bcm.edu	37	12	124399057	124399057	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr12:124399057C>T	ENST00000409039.3	+	60	10205	c.10180C>T	c.(10180-10182)Cgg>Tgg	p.R3394W		NM_207437.3	NP_997320.2	Q8IVF4	DYH10_HUMAN	dynein, axonemal, heavy chain 10	3394					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)		CCAGCCTTTCCGGCTGGAAAG	0.592																																					p.R3394W		Atlas-SNP	.											DNAH10_same_name,colon,carcinoma,0,2	DNAH10	888	2	0			c.C10180T						scavenged	.						42.0	45.0	44.0					12																	124399057		1954	4164	6118	SO:0001583	missense	196385	exon60			CCTTTCCGGCTGG	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.10180C>T	12.37:g.124399057C>T	ENSP00000386770:p.Arg3394Trp	Somatic	52	1	0.0192308		WXS	Illumina HiSeq	Phase_I	60	2	0.0333333	NM_207437	C9JMF5|O95495|Q6ZUC9|Q6ZUP6|Q8N761	Missense_Mutation	SNP	ENST00000409039.3	37	CCDS9255.2	.	.	.	.	.	.	.	.	.	.	C	16.71	3.199144	0.58126	.	.	ENSG00000197653	ENST00000409039	T	0.22743	1.94	5.28	2.07	0.26955	.	0.207319	0.37483	N	0.002062	T	0.40645	0.1125	M	0.84326	2.69	0.21290	N	0.999737	D	0.71674	0.998	P	0.55260	0.772	T	0.40794	-0.9544	10	0.72032	D	0.01	.	13.635	0.62217	0.5743:0.4257:0.0:0.0	.	3394	Q8IVF4	DYH10_HUMAN	W	3394	ENSP00000386770:R3394W	ENSP00000386770:R3394W	R	+	1	2	DNAH10	122965010	0.120000	0.22244	0.067000	0.19924	0.571000	0.35966	0.748000	0.26305	0.525000	0.28522	0.561000	0.74099	CGG	.	.	none		0.592	DNAH10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335420.3		
ADAMTS2	9509	hgsc.bcm.edu	37	5	178552090	178552090	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr5:178552090C>T	ENST00000251582.7	-	19	2943	c.2842G>A	c.(2842-2844)Gac>Aac	p.D948N		NM_014244.4	NP_055059.2	O95450	ATS2_HUMAN	ADAM metallopeptidase with thrombospondin type 1 motif, 2	948	TSP type-1 3. {ECO:0000255|PROSITE- ProRule:PRU00210}.				collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|lung development (GO:0030324)|protein processing (GO:0016485)|skin development (GO:0043588)|spermatogenesis (GO:0007283)	extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	metalloendopeptidase activity (GO:0004222)|metallopeptidase activity (GO:0008237)|zinc ion binding (GO:0008270)			breast(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(31)|ovary(1)|pancreas(3)|prostate(2)|skin(7)	72	all_cancers(89;0.000456)|all_epithelial(37;0.000138)|Renal(175;0.000159)|Lung NSC(126;0.00184)|all_lung(126;0.00326)	all_cancers(40;0.00604)|all_neural(177;0.00411)|Medulloblastoma(196;0.00508)|Lung NSC(249;0.0569)|all_lung(500;0.129)|all_hematologic(541;0.211)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	GBM - Glioblastoma multiforme(465;0.0473)		GTGGTGTTGTCGTGTAGCGGC	0.692																																					p.D948N		Atlas-SNP	.											ADAMTS2,caecum,carcinoma,0,2	ADAMTS2	190	2	0			c.G2842A						scavenged	.						112.0	113.0	113.0					5																	178552090		2203	4300	6503	SO:0001583	missense	9509	exon19			TGTTGTCGTGTAG	AJ003125	CCDS4444.1, CCDS34311.1	5q23-q24	2008-07-18	2005-08-19		ENSG00000087116	ENSG00000087116		"""ADAM metallopeptidases with thrombospondin type 1 motif"""	218	protein-coding gene	gene with protein product	"""procollagen I N-proteinase"", ""procollagen N-endopeptidase"""	604539	"""a disintegrin-like and metalloprotease (reprolysin type) with thrombospondin type 1 motif, 2"""			10094461, 15373769	Standard	NM_014244		Approved	ADAMTS-3, hPCPNI, PCINP, ADAM-TS2, NPI	uc003mjw.3	O95450	OTTHUMG00000130915	ENST00000251582.7:c.2842G>A	5.37:g.178552090C>T	ENSP00000251582:p.Asp948Asn	Somatic	146	2	0.0136986		WXS	Illumina HiSeq	Phase_I	103	2	0.0194175	NM_014244		Missense_Mutation	SNP	ENST00000251582.7	37	CCDS4444.1	.	.	.	.	.	.	.	.	.	.	C	0.743	-0.775731	0.02951	.	.	ENSG00000087116	ENST00000251582	T	0.53857	0.6	5.31	2.0	0.26442	.	0.301971	0.27792	N	0.017833	T	0.26774	0.0655	N	0.12422	0.21	0.80722	D	1	B	0.24317	0.101	B	0.22601	0.04	T	0.10730	-1.0617	10	0.06757	T	0.87	.	8.4694	0.32975	0.0:0.7177:0.0:0.2823	.	948	O95450	ATS2_HUMAN	N	948	ENSP00000251582:D948N	ENSP00000251582:D948N	D	-	1	0	ADAMTS2	178484696	0.966000	0.33281	0.957000	0.39632	0.030000	0.12068	1.550000	0.36223	0.026000	0.15269	-1.140000	0.01884	GAC	.	.	none		0.692	ADAMTS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253507.1	NM_014244	
UPF3A	65110	hgsc.bcm.edu	37	13	115057219	115057219	+	Silent	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr13:115057219A>G	ENST00000375299.3	+	7	854	c.798A>G	c.(796-798)aaA>aaG	p.K266K	UPF3A_ENST00000475218.2_3'UTR|UPF3A_ENST00000351487.5_Silent_p.K233K	NM_023011.3	NP_075387.1	Q9H1J1	REN3A_HUMAN	UPF3 regulator of nonsense transcripts homolog A (yeast)	266					gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA transport (GO:0051028)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|nucleocytoplasmic transport (GO:0006913)|positive regulation of translation (GO:0045727)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	nucleocytoplasmic transporter activity (GO:0005487)|nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			autonomic_ganglia(1)|central_nervous_system(2)|kidney(2)|large_intestine(2)|lung(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	16	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)	OV - Ovarian serous cystadenocarcinoma(48;0.195)|Epithelial(10;0.2)		gcaaaaaaaaagagacagata	0.353																																					p.K266K		Atlas-SNP	.											.	UPF3A	47	.	0			c.A798G						PASS	.						39.0	40.0	40.0					13																	115057219		2201	4289	6490	SO:0001819	synonymous_variant	65110	exon7			AAAAAAAGAGACA	AF318575	CCDS9543.1, CCDS9544.1	13q34	2010-04-30			ENSG00000169062	ENSG00000169062			20332	protein-coding gene	gene with protein product		605530				11113196, 11163187	Standard	NM_023011		Approved	RENT3A, UPF3, HUPF3A	uc001vup.3	Q9H1J1	OTTHUMG00000017403	ENST00000375299.3:c.798A>G	13.37:g.115057219A>G		Somatic	67	0	0		WXS	Illumina HiSeq	Phase_I	103	5	0.0485437	NM_023011	A2A366|Q5T8C3|Q5T8C9|Q7Z6N3|Q86YK1|Q9BZI8	Silent	SNP	ENST00000375299.3	37	CCDS9543.1																																																																																			.	.	none		0.353	UPF3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045968.2		
KCNS3	3790	hgsc.bcm.edu	37	2	18112978	18112978	+	Missense_Mutation	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr2:18112978G>A	ENST00000403915.1	+	3	1154	c.703G>A	c.(703-705)Ggg>Agg	p.G235R	KCNS3_ENST00000465292.1_Intron|KCNS3_ENST00000304101.4_Missense_Mutation_p.G235R	NM_001282428.1	NP_001269357.1	Q9BQ31	KCNS3_HUMAN	potassium voltage-gated channel, delayed-rectifier, subfamily S, member 3	235					energy reserve metabolic process (GO:0006112)|potassium ion transport (GO:0006813)|protein homooligomerization (GO:0051260)|regulation of insulin secretion (GO:0050796)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)|potassium channel regulator activity (GO:0015459)			endometrium(5)|kidney(1)|large_intestine(7)|lung(11)|ovary(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.158)					CTGGTTCACCGGGGAGCTTGC	0.517																																					p.G235R		Atlas-SNP	.											KCNS3,caecum,carcinoma,-1,2	KCNS3	85	2	0			c.G703A						scavenged	.						87.0	86.0	86.0					2																	18112978		2203	4300	6503	SO:0001583	missense	3790	exon3			TTCACCGGGGAGC	AF043472	CCDS1692.1	2p24	2011-07-05			ENSG00000170745	ENSG00000170745		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	6302	protein-coding gene	gene with protein product		603888				10484328, 16382104	Standard	NM_002252		Approved	Kv9.3	uc002rcw.3	Q9BQ31	OTTHUMG00000044150	ENST00000403915.1:c.703G>A	2.37:g.18112978G>A	ENSP00000385968:p.Gly235Arg	Somatic	130	0	0		WXS	Illumina HiSeq	Phase_I	167	2	0.011976	NM_002252	D6W520|O43651|Q4ZFY1|Q96B56	Missense_Mutation	SNP	ENST00000403915.1	37	CCDS1692.1	.	.	.	.	.	.	.	.	.	.	G	9.954	1.220989	0.22457	.	.	ENSG00000170745	ENST00000403915;ENST00000304101	D;D	0.98437	-4.93;-4.93	6.07	4.28	0.50868	Ion transport (1);	0.484707	0.23690	N	0.045530	D	0.95551	0.8554	L	0.43923	1.385	0.09310	N	1	P	0.38167	0.621	B	0.37833	0.259	D	0.91363	0.5113	10	0.66056	D	0.02	.	6.4072	0.21670	0.1353:0.0:0.6137:0.251	.	235	Q9BQ31	KCNS3_HUMAN	R	235	ENSP00000385968:G235R;ENSP00000305824:G235R	ENSP00000305824:G235R	G	+	1	0	KCNS3	17976459	0.013000	0.17824	0.318000	0.25279	0.979000	0.70002	1.050000	0.30404	0.894000	0.36317	0.655000	0.94253	GGG	.	.	none		0.517	KCNS3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323808.1	NM_002252	
SPTBN2	6712	hgsc.bcm.edu	37	11	66472275	66472275	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:66472275C>T	ENST00000533211.1	-	15	2803	c.2472G>A	c.(2470-2472)caG>caA	p.Q824Q	SPTBN2_ENST00000309996.2_Silent_p.Q824Q|SPTBN2_ENST00000529997.1_Silent_p.Q824Q			O15020	SPTN2_HUMAN	spectrin, beta, non-erythrocytic 2	824					actin filament capping (GO:0051693)|adult behavior (GO:0030534)|antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|axon guidance (GO:0007411)|cell death (GO:0008219)|cerebellar Purkinje cell layer morphogenesis (GO:0021692)|multicellular organism growth (GO:0035264)|synapse assembly (GO:0007416)|vesicle-mediated transport (GO:0016192)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|neuronal cell body (GO:0043025)|spectrin (GO:0008091)	actin binding (GO:0003779)|phospholipid binding (GO:0005543)|structural constituent of cytoskeleton (GO:0005200)			autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(10)|kidney(5)|large_intestine(15)|liver(1)|lung(22)|ovary(2)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	74						GCACCCGGCTCTGCACCTCGG	0.716																																					p.Q824Q		Atlas-SNP	.											SPTBN2,right_lower_lobe,carcinoma,0,1	SPTBN2	188	1	0			c.G2472A						scavenged	.						13.0	14.0	14.0					11																	66472275		2184	4272	6456	SO:0001819	synonymous_variant	6712	exon14			CCGGCTCTGCACC	AB008567, AF026487, AF026488, AF079569	CCDS8150.1	11q13.2	2013-01-10			ENSG00000173898	ENSG00000173898		"""Pleckstrin homology (PH) domain containing"""	11276	protein-coding gene	gene with protein product		604985	"""spinocerebellar ataxia 5"""	SCA5		9826670, 16429157	Standard	NM_006946		Approved		uc001ojd.3	O15020	OTTHUMG00000167262	ENST00000533211.1:c.2472G>A	11.37:g.66472275C>T		Somatic	11	0	0		WXS	Illumina HiSeq	Phase_I	20	2	0.1	NM_006946	O14872|O14873	Silent	SNP	ENST00000533211.1	37	CCDS8150.1																																																																																			.	.	none		0.716	SPTBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393892.2	NM_006946	
DMKN	93099	hgsc.bcm.edu	37	19	36002404	36002404	+	Missense_Mutation	SNP	C	C	T	rs56743379|rs138902616		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr19:36002404C>T	ENST00000339686.3	-	5	1003	c.827G>A	c.(826-828)aGc>aAc	p.S276N	DMKN_ENST00000462126.1_5'Flank|DMKN_ENST00000414866.2_5'Flank|DMKN_ENST00000451297.2_Missense_Mutation_p.S276N|DMKN_ENST00000429837.1_Intron|DMKN_ENST00000467637.1_5'Flank|DMKN_ENST00000488892.1_5'Flank|DMKN_ENST00000419602.1_Intron|DMKN_ENST00000447113.2_Missense_Mutation_p.S276N|DMKN_ENST00000480502.1_5'Flank|DMKN_ENST00000392206.2_5'Flank|DMKN_ENST00000424570.2_Missense_Mutation_p.S276N|DMKN_ENST00000402589.2_5'Flank|DMKN_ENST00000440396.1_Missense_Mutation_p.S276N|DMKN_ENST00000492341.2_5'Flank|DMKN_ENST00000418261.1_Missense_Mutation_p.S276N|DMKN_ENST00000474928.1_5'Flank|DMKN_ENST00000602781.1_5'Flank|DMKN_ENST00000461300.1_5'Flank|DMKN_ENST00000436012.1_5'Flank|DMKN_ENST00000443640.1_5'Flank|DMKN_ENST00000472252.2_5'Flank|DMKN_ENST00000458071.1_5'Flank	NM_033317.4	NP_201574	Q6E0U4	DMKN_HUMAN	dermokine	276	Gly-rich.					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)			gccactgctgctgccactgct	0.647																																					p.S276N		Atlas-SNP	.											DMKN,NS,carcinoma,0,2	DMKN	116	2	1	Deletion - In frame(1)	ovary(1)	c.G827A						scavenged	.						28.0	21.0	23.0					19																	36002404		2176	4255	6431	SO:0001583	missense	93099	exon5			CTGCTGCTGCCAC	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.827G>A	19.37:g.36002404C>T	ENSP00000342012:p.Ser276Asn	Somatic	24	13	0.541667		WXS	Illumina HiSeq	Phase_I	36	17	0.472222	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	.	.	.	.	.	.	.	.	.	.	C	7.414	0.635437	0.14322	.	.	ENSG00000161249	ENST00000339686;ENST00000392207;ENST00000447113;ENST00000440396;ENST00000418261;ENST00000424570;ENST00000451297	T;T;T;T;T;T	0.39056	1.1;1.1;1.1;1.1;1.1;1.1	3.2	-1.74	0.08056	.	0.904855	0.09337	N	0.815985	T	0.30696	0.0773	L	0.48642	1.525	0.09310	N	1	B;B;B;B;B	0.06786	0.0;0.0;0.0;0.0;0.001	B;B;B;B;B	0.08055	0.001;0.001;0.001;0.001;0.003	T	0.32241	-0.9914	10	0.16896	T	0.51	5.0393	8.4003	0.32581	0.0:0.7659:0.0:0.2341	.	276;276;276;276;276	E7EUS0;Q6E0U4-7;Q6E0U4-3;Q6E0U4-5;Q6E0U4	.;.;.;.;DMKN_HUMAN	N	276	ENSP00000342012:S276N;ENSP00000394908:S276N;ENSP00000415277:S276N;ENSP00000414743:S276N;ENSP00000388404:S276N;ENSP00000409513:S276N	ENSP00000342012:S276N	S	-	2	0	DMKN	40694244	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.213000	0.09305	-0.013000	0.14199	-1.984000	0.00453	AGC	.	.	weak		0.647	DMKN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000109461.2	NM_033317	
KRTAP4-6	81871	hgsc.bcm.edu	37	17	39296167	39296167	+	Silent	SNP	A	A	G			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:39296167A>G	ENST00000345847.4	-	1	572	c.573T>C	c.(571-573)atT>atC	p.I191I		NM_030976.1	NP_112238.1	Q9BYQ5	KRA46_HUMAN	keratin associated protein 4-6	191						keratin filament (GO:0045095)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|lung(1)|prostate(1)|urinary_tract(1)	9						GGCAGGTGGAAATGACACAGG	0.627																																					p.I191I		Atlas-SNP	.											KRTAP4-6,bladder,carcinoma,0,9	KRTAP4-6	46	9	0			c.T573C						scavenged	.																																			SO:0001819	synonymous_variant	81871	exon1			GGTGGAAATGACA	AJ406938	CCDS54125.1	17q21.2	2013-06-25			ENSG00000198090	ENSG00000198090		"""Keratin associated proteins"""	18909	protein-coding gene	gene with protein product			"""keratin associated protein 4-15"""	KRTAP4-15			Standard	NM_030976		Approved	KAP4.6, KAP4.15	uc010cxk.2	Q9BYQ5	OTTHUMG00000133634	ENST00000345847.4:c.573T>C	17.37:g.39296167A>G		Somatic	147	3	0.0204082		WXS	Illumina HiSeq	Phase_I	194	5	0.0257732	NM_030976	Q9BYR1	Silent	SNP	ENST00000345847.4	37	CCDS54125.1																																																																																			.	.	none		0.627	KRTAP4-6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257779.1		
NELL1	4745	hgsc.bcm.edu	37	11	21594748	21594748	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:21594748C>T	ENST00000357134.5	+	19	2327	c.2175C>T	c.(2173-2175)tgC>tgT	p.C725C	NELL1_ENST00000298925.5_Silent_p.C753C|NELL1_ENST00000325319.5_Silent_p.C668C|NELL1_ENST00000532434.1_Silent_p.C678C|NELL1_ENST00000529218.1_3'UTR	NM_006157.3|NM_201551.1	NP_006148.2|NP_963845.1	Q92832	NELL1_HUMAN	NEL-like 1 (chicken)	725	VWFC 2. {ECO:0000255|PROSITE- ProRule:PRU00220}.				cell differentiation (GO:0030154)|negative regulation of cyclin catabolic process (GO:2000599)|negative regulation of osteoblast proliferation (GO:0033689)|nervous system development (GO:0007399)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|regulation of gene expression (GO:0010468)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	calcium ion binding (GO:0005509)			NS(1)|breast(3)|endometrium(5)|kidney(3)|large_intestine(15)|lung(36)|ovary(2)|prostate(3)|skin(1)|urinary_tract(1)	70						AGGTAGATTGCTGGCCACTCA	0.448																																					p.C725C		Atlas-SNP	.											NELL1,NS,carcinoma,0,1	NELL1	179	1	0			c.C2175T						scavenged	.						81.0	80.0	81.0					11																	21594748		2203	4300	6503	SO:0001819	synonymous_variant	4745	exon19			AGATTGCTGGCCA	AK127805	CCDS7855.1, CCDS44555.1, CCDS73267.1, CCDS73268.1	11p15.1	2008-02-01	2001-11-28		ENSG00000165973	ENSG00000165973			7750	protein-coding gene	gene with protein product		602319	"""nel (chicken)-like 1"""			8975702	Standard	NM_006157		Approved	IDH3GL, FLJ45906	uc001mqe.3	Q92832	OTTHUMG00000166042	ENST00000357134.5:c.2175C>T	11.37:g.21594748C>T		Somatic	133	0	0		WXS	Illumina HiSeq	Phase_I	148	3	0.0202703	NM_006157	B2CKC1|Q4VB90|Q4VB91|Q6NSY8|Q9Y472	Silent	SNP	ENST00000357134.5	37	CCDS7855.1																																																																																			.	.	none		0.448	NELL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387588.1	NM_006157	
AP5Z1	9907	hgsc.bcm.edu	37	7	4823361	4823361	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr7:4823361C>T	ENST00000348624.4	+	5	647	c.553C>T	c.(553-555)Cgc>Tgc	p.R185C	AP5Z1_ENST00000401897.1_Missense_Mutation_p.R185C	NM_014855.2	NP_055670.1	O43299	AP5Z1_HUMAN	adaptor-related protein complex 5, zeta 1 subunit	185					cell death (GO:0008219)|double-strand break repair via homologous recombination (GO:0000724)|endosomal transport (GO:0016197)|protein transport (GO:0015031)	AP-5 adaptor complex (GO:0044599)|AP-type membrane coat adaptor complex (GO:0030119)|cytoplasm (GO:0005737)|nucleus (GO:0005634)											CGACTGGCTGCGCTACGCCAG	0.657																																					p.R185C		Atlas-SNP	.											.	.	.	.	0			c.C553T						PASS	.						5.0	8.0	7.0					7																	4823361		1760	3730	5490	SO:0001583	missense	9907	exon5			TGGCTGCGCTACG	AB007875	CCDS47528.1	7p22.1	2012-03-20	2012-03-20	2012-03-20	ENSG00000242802	ENSG00000242802			22197	protein-coding gene	gene with protein product		613653	"""KIAA0415"""	KIAA0415		20613862, 22022230	Standard	NM_014855		Approved	SPG48, zeta	uc003sne.3	O43299	OTTHUMG00000151754	ENST00000348624.4:c.553C>T	7.37:g.4823361C>T	ENSP00000297562:p.Arg185Cys	Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	83	39	0.46988	NM_014855	Q8N3X2|Q96H80	Missense_Mutation	SNP	ENST00000348624.4	37	CCDS47528.1	.	.	.	.	.	.	.	.	.	.	C	16.11	3.029717	0.54790	.	.	ENSG00000242802	ENST00000348624;ENST00000401897	T;T	0.50277	0.76;0.75	4.37	4.37	0.52481	.	0.000000	0.85682	D	0.000000	T	0.66973	0.2844	M	0.77103	2.36	0.80722	D	1	D	0.89917	1.0	D	0.80764	0.994	T	0.71119	-0.4685	10	0.66056	D	0.02	.	11.8038	0.52143	0.1882:0.8118:0.0:0.0	.	185	O43299	K0415_HUMAN	C	185	ENSP00000297562:R185C;ENSP00000384980:R185C	ENSP00000297562:R185C	R	+	1	0	KIAA0415	4789887	0.929000	0.31497	0.969000	0.41365	0.255000	0.26057	1.781000	0.38644	1.983000	0.57843	0.462000	0.41574	CGC	.	.	none		0.657	AP5Z1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323771.1		
OR4C6	219432	hgsc.bcm.edu	37	11	55433333	55433333	+	Missense_Mutation	SNP	C	C	T	rs140747151	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr11:55433333C>T	ENST00000314259.3	+	1	720	c.691C>T	c.(691-693)Cgg>Tgg	p.R231W		NM_001004704.1	NP_001004704.1	Q8NH72	OR4C6_HUMAN	olfactory receptor, family 4, subfamily C, member 6	231						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.R231W(1)		breast(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(4)|lung(49)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	71						CTCTAAAGGGCGGCACAAAGC	0.502													c|||	2	0.000399361	0.0	0.0	5008	,	,		18006	0.0		0.002	False		,,,				2504	0.0				p.R231W		Atlas-SNP	.											OR4C6,middle_lobe,carcinoma,0,4	OR4C6	114	4	1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	c.C691T						PASS	.	C	TRP/ARG	0,4400		0,0,2200	132.0	126.0	128.0		691	-8.1	0.0	11	dbSNP_134	128	3,8589	3.0+/-9.4	0,3,4293	yes	missense	OR4C6	NM_001004704.1	101	0,3,6493	TT,TC,CC		0.0349,0.0,0.0231	benign	231/310	55433333	3,12989	2200	4296	6496	SO:0001583	missense	219432	exon1			AAAGGGCGGCACA	CR593785	CCDS31506.1	11q11	2012-08-09			ENSG00000181903	ENSG00000181903		"""GPCR / Class A : Olfactory receptors"""	14743	protein-coding gene	gene with protein product							Standard	NM_001004704		Approved		uc010rik.2	Q8NH72	OTTHUMG00000166800	ENST00000314259.3:c.691C>T	11.37:g.55433333C>T	ENSP00000324769:p.Arg231Trp	Somatic	109	0	0		WXS	Illumina HiSeq	Phase_I	172	68	0.395349	NM_001004704	B2RP11|Q6IFD2	Missense_Mutation	SNP	ENST00000314259.3	37	CCDS31506.1	2	9.157509157509158E-4	0	0.0	0	0.0	0	0.0	2	0.002638522427440633	C	5.384	0.256036	0.10185	0.0	3.49E-4	ENSG00000181903	ENST00000314259	T	0.00335	8.06	4.07	-8.14	0.01069	GPCR, rhodopsin-like superfamily (1);	0.754623	0.10587	N	0.657205	T	0.00328	0.0010	M	0.87971	2.92	0.09310	N	1	B	0.22146	0.065	B	0.26693	0.072	T	0.27773	-1.0064	10	0.72032	D	0.01	.	6.9124	0.24342	0.6124:0.1383:0.0:0.2493	.	231	Q8NH72	OR4C6_HUMAN	W	231	ENSP00000324769:R231W	ENSP00000324769:R231W	R	+	1	2	OR4C6	55189909	0.000000	0.05858	0.000000	0.03702	0.007000	0.05969	-4.913000	0.00170	-1.249000	0.02500	0.543000	0.68304	CGG	C|0.999;T|0.001	0.001	strong		0.502	OR4C6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391504.1	NM_001004704	
HSPA12A	259217	hgsc.bcm.edu	37	10	118464772	118464772	+	Silent	SNP	G	G	A			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr10:118464772G>A	ENST00000369209.3	-	3	248	c.144C>T	c.(142-144)aaC>aaT	p.N48N		NM_025015.2	NP_079291.2	O43301	HS12A_HUMAN	heat shock 70kDa protein 12A	48						extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)			breast(2)|endometrium(2)|kidney(1)|large_intestine(5)|lung(15)|ovary(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	32				all cancers(201;0.0158)		GTTCTGAGACGTTGGAGTCAG	0.582																																					p.N48N		Atlas-SNP	.											.	HSPA12A	81	.	0			c.C144T						PASS	.						177.0	188.0	185.0					10																	118464772		2150	4269	6419	SO:0001819	synonymous_variant	259217	exon3			TGAGACGTTGGAG	AB007877	CCDS41569.1	10q25.3	2011-09-02	2002-08-29		ENSG00000165868	ENSG00000165868		"""Heat shock proteins / HSP70"""	19022	protein-coding gene	gene with protein product		610701	"""heat shock 70kD protein 12A"""			12552099	Standard	NM_025015		Approved	FLJ13874, KIAA0417	uc001lct.3	O43301	OTTHUMG00000019107	ENST00000369209.3:c.144C>T	10.37:g.118464772G>A		Somatic	103	0	0		WXS	Illumina HiSeq	Phase_I	119	45	0.378151	NM_025015		Silent	SNP	ENST00000369209.3	37	CCDS41569.1																																																																																			.	.	none		0.582	HSPA12A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050530.1	NM_025015	
LIMD2	80774	hgsc.bcm.edu	37	17	61776164	61776164	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:61776164C>T	ENST00000259006.3	-	4	377	c.219G>A	c.(217-219)aaG>aaA	p.K73K	LIMD2_ENST00000578061.1_Silent_p.K73K|LIMD2_ENST00000582055.1_Silent_p.K24K|LIMD2_ENST00000583211.1_Silent_p.K24K|LIMD2_ENST00000578993.1_Silent_p.K33K|LIMD2_ENST00000578402.1_Silent_p.K73K	NM_030576.3	NP_085053.1	Q9BT23	LIMD2_HUMAN	LIM domain containing 2	73	LIM zinc-binding. {ECO:0000255|PROSITE- ProRule:PRU00125}.						zinc ion binding (GO:0008270)			kidney(1)|lung(2)	3						CGCACCTGAGCTTGGTGTGAC	0.657																																					p.K73K		Atlas-SNP	.											.	LIMD2	6	.	0			c.G219A						PASS	.						44.0	44.0	44.0					17																	61776164		2203	4300	6503	SO:0001819	synonymous_variant	80774	exon4			CCTGAGCTTGGTG	AK092301	CCDS11641.1	17q23.3	2006-02-03				ENSG00000136490			28142	protein-coding gene	gene with protein product						12477932	Standard	NM_030576		Approved	MGC10986	uc002jbj.4	Q9BT23		ENST00000259006.3:c.219G>A	17.37:g.61776164C>T		Somatic	93	0	0		WXS	Illumina HiSeq	Phase_I	91	39	0.428571	NM_030576	D3DU16|Q96S91	Silent	SNP	ENST00000259006.3	37	CCDS11641.1																																																																																			.	.	none		0.657	LIMD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000443877.1	NM_030576	
TAS1R2	80834	hgsc.bcm.edu	37	1	19175988	19175988	+	Silent	SNP	G	G	A	rs146531311	byFrequency	TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr1:19175988G>A	ENST00000375371.3	-	4	1335	c.1314C>T	c.(1312-1314)ttC>ttT	p.F438F	RP13-279N23.2_ENST00000494072.3_3'UTR	NM_152232.2	NP_689418.2	Q8TE23	TS1R2_HUMAN	taste receptor, type 1, member 2	438					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)	CTTGCGGGTCGAAGAAGATTT	0.582																																					p.F438F		Atlas-SNP	.											TAS1R2,NS,carcinoma,0,1	TAS1R2	134	1	0			c.C1314T						PASS	.	A		0,4406		0,0,2203	75.0	68.0	70.0		1314	-5.2	0.0	1	dbSNP_134	70	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous	TAS1R2	NM_152232.2		0,2,6501	AA,AG,GG		0.0233,0.0,0.0154		438/840	19175988	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	80834	exon4			CGGGTCGAAGAAG		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.1314C>T	1.37:g.19175988G>A		Somatic	113	0	0		WXS	Illumina HiSeq	Phase_I	125	54	0.432	NM_152232	Q5TZ19	Silent	SNP	ENST00000375371.3	37	CCDS187.1																																																																																			G|1.000;A|0.000	0.000	strong		0.582	TAS1R2-001	NOVEL	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000006953.1		
UFSP2	55325	hgsc.bcm.edu	37	4	186329507	186329507	+	Missense_Mutation	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr4:186329507C>T	ENST00000264689.6	-	8	1030	c.914G>A	c.(913-915)cGa>cAa	p.R305Q		NM_018359.3	NP_060829.2	Q9NUQ7	UFSP2_HUMAN	UFM1-specific peptidase 2	305						cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)	small conjugating protein-specific protease activity (GO:0019783)|thiolester hydrolase activity (GO:0016790)			endometrium(3)|kidney(1)|large_intestine(3)|lung(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	12		all_lung(41;1.3e-11)|Lung NSC(41;2.25e-11)|Melanoma(20;0.00109)|Colorectal(36;0.0215)|Renal(120;0.0246)|Hepatocellular(41;0.0268)|Prostate(90;0.0283)|all_hematologic(60;0.0749)		all cancers(43;3.4e-25)|Epithelial(43;2.23e-22)|OV - Ovarian serous cystadenocarcinoma(60;1.54e-11)|BRCA - Breast invasive adenocarcinoma(30;8.1e-05)|GBM - Glioblastoma multiforme(59;0.000148)|STAD - Stomach adenocarcinoma(60;0.000782)|LUSC - Lung squamous cell carcinoma(40;0.00939)|COAD - Colon adenocarcinoma(29;0.0108)|READ - Rectum adenocarcinoma(43;0.166)		CTGCAGAGATCGATAAGCACA	0.428																																					p.R305Q		Atlas-SNP	.											.	UFSP2	33	.	0			c.G914A						PASS	.						132.0	117.0	122.0					4																	186329507		2203	4300	6503	SO:0001583	missense	55325	exon8			AGAGATCGATAAG	AK002062	CCDS3842.1	4q35.1	2008-03-25	2008-03-25	2008-03-25	ENSG00000109775	ENSG00000109775			25640	protein-coding gene	gene with protein product		611482	"""chromosome 4 open reading frame 20"""	C4orf20		17182609	Standard	NM_018359		Approved	FLJ11200	uc003ixo.2	Q9NUQ7	OTTHUMG00000160441	ENST00000264689.6:c.914G>A	4.37:g.186329507C>T	ENSP00000264689:p.Arg305Gln	Somatic	127	0	0		WXS	Illumina HiSeq	Phase_I	73	4	0.0547945	NM_018359	Q6IA77|Q96FS3	Missense_Mutation	SNP	ENST00000264689.6	37	CCDS3842.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	33|33	5.235189|5.235189	0.95207|0.95207	.|.	.|.	ENSG00000109775|ENSG00000109775	ENST00000509180|ENST00000264689	.|T	.|0.41400	.|1.0	6.03|6.03	6.03|6.03	0.97812|0.97812	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.79287|0.79287	0.4420|0.4420	H|H	0.97611|0.97611	4.04|4.04	0.80722|0.80722	D|D	1|1	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.91635	.|0.999;0.999	D|D	0.85593|0.85593	0.1247|0.1247	5|10	.|0.87932	.|D	.|0	-8.9285|-8.9285	20.5568|20.5568	0.99304|0.99304	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|305;205	.|Q9NUQ7;B3KRI4	.|UFSP2_HUMAN;.	N|Q	34|305	.|ENSP00000264689:R305Q	.|ENSP00000264689:R305Q	D|R	-|-	1|2	0|0	UFSP2|UFSP2	186566501|186566501	1.000000|1.000000	0.71417|0.71417	0.041000|0.041000	0.18516|0.18516	0.712000|0.712000	0.41017|0.41017	7.478000|7.478000	0.81082|0.81082	2.861000|2.861000	0.98227|0.98227	0.655000|0.655000	0.94253|0.94253	GAT|CGA	.	.	none		0.428	UFSP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000360589.2	NM_018359	
CDC27	996	hgsc.bcm.edu	37	17	45234327	45234327	+	Missense_Mutation	SNP	C	C	T	rs7350889		TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr17:45234327C>T	ENST00000066544.3	-	7	887	c.794G>A	c.(793-795)gGt>gAt	p.G265D	CDC27_ENST00000528748.1_5'Flank|CDC27_ENST00000531206.1_Missense_Mutation_p.G265D|CDC27_ENST00000446365.2_Missense_Mutation_p.G204D|CDC27_ENST00000527547.1_Missense_Mutation_p.G265D	NM_001114091.1|NM_001256.3	NP_001107563.1|NP_001247.3	P30260	CDC27_HUMAN	cell division cycle 27	265					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|metaphase/anaphase transition of mitotic cell cycle (GO:0007091)|mitotic cell cycle (GO:0000278)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle (GO:0005819)	protein phosphatase binding (GO:0019903)	p.G265D(2)		NS(1)|breast(5)|central_nervous_system(3)|cervix(1)|endometrium(2)|kidney(17)|large_intestine(18)|lung(11)|ovary(5)|pancreas(1)|prostate(19)|skin(5)|upper_aerodigestive_tract(2)	90						TAAACTTCGACCAGTTTTTGG	0.368																																					p.G265D		Atlas-SNP	.											CDC27_ENST00000531206,NS,adenoma,0,4	CDC27	337	4	2	Substitution - Missense(2)	skin(2)	c.G794A						scavenged	.						60.0	65.0	63.0					17																	45234327		2201	4295	6496	SO:0001583	missense	996	exon7			CTTCGACCAGTTT	U00001	CCDS11509.1, CCDS45720.1, CCDS74090.1	17q21.32	2013-01-17	2013-01-17		ENSG00000004897	ENSG00000004897		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1728	protein-coding gene	gene with protein product	"""anaphase promoting complex subunit 3"""	116946	"""cell division cycle 27"", ""cell division cycle 27 homolog (S. cerevisiae)"""	D0S1430E, D17S978E		8234252	Standard	XM_005257892		Approved	APC3, ANAPC3, NUC2	uc002ile.4	P30260	OTTHUMG00000166429	ENST00000066544.3:c.794G>A	17.37:g.45234327C>T	ENSP00000066544:p.Gly265Asp	Somatic	40	1	0.025		WXS	Illumina HiSeq	Phase_I	58	5	0.0862069	NM_001114091	G3V1C4|Q16349|Q96F35	Missense_Mutation	SNP	ENST00000066544.3	37	CCDS11509.1	.	.	.	.	.	.	.	.	.	.	C	15.07	2.725453	0.48833	.	.	ENSG00000004897	ENST00000066544;ENST00000531206;ENST00000446365;ENST00000527547;ENST00000526866	T;T;T;T;T	0.68181	-0.31;-0.3;-0.11;-0.31;0.86	5.64	5.64	0.86602	.	0.000000	0.85682	D	0.000000	T	0.52853	0.1760	N	0.24115	0.695	0.80722	D	1	B;B;B;B	0.32350	0.251;0.366;0.247;0.251	B;B;B;B	0.27076	0.045;0.056;0.076;0.055	T	0.51694	-0.8673	10	0.33141	T	0.24	1.6987	17.2083	0.86924	0.0:1.0:0.0:0.0	rs7350889;rs7350889	204;265;265;265	B4DL80;G5EA36;G3V1C4;P30260	.;.;.;CDC27_HUMAN	D	265;265;204;265;265	ENSP00000066544:G265D;ENSP00000434614:G265D;ENSP00000392802:G204D;ENSP00000437339:G265D;ENSP00000432105:G265D	ENSP00000066544:G265D	G	-	2	0	CDC27	42589326	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.618000	0.67722	2.665000	0.90641	0.460000	0.39030	GGT	C|1.000;|0.000	.	weak		0.368	CDC27-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000389742.2		
IGLL5	100423062	hgsc.bcm.edu	37	22	23230380	23230380	+	Silent	SNP	C	C	T			TCGA-FF-8047-01A-11D-2210-10	TCGA-FF-8047-10A-01D-2210-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none	.		Illumina GAIIx	1b1780d5-06da-40ee-9e15-02631a68027b	07c3103c-94ed-4fee-968d-318721aa84a9	g.chr22:23230380C>T	ENST00000526893.1	+	1	421	c.147C>T	c.(145-147)gaC>gaT	p.D49D	IGLL5_ENST00000531372.1_Silent_p.D49D|IGLL5_ENST00000532223.2_Silent_p.D49D|hsa-mir-5571_ENST00000577998.1_RNA	NM_001178126.1	NP_001171597.1	B9A064	IGLL5_HUMAN	immunoglobulin lambda-like polypeptide 5	49						extracellular vesicular exosome (GO:0070062)				breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|lung(3)|urinary_tract(1)	7						AAAGCGGGGACCCAGACCCTG	0.682																																					p.T14I		Atlas-SNP	.											.	IGLL5	26	.	0			c.C41T						PASS	.																																			SO:0001819	synonymous_variant	100423062	exon1			CGGGGACCCAGAC	M34518, M34515	CCDS54506.1	22q11.22	2013-01-11			ENSG00000254709	ENSG00000254709		"""Immunoglobulin superfamily / C1-set domain containing"""	38476	protein-coding gene	gene with protein product							Standard	NM_001178126		Approved		uc010gtu.3	B9A064	OTTHUMG00000165670	ENST00000526893.1:c.147C>T	22.37:g.23230380C>T		Somatic	123	0	0		WXS	Illumina HiSeq	Phase_I	63	50	0.793651	NM_001256296		Missense_Mutation	SNP	ENST00000526893.1	37	CCDS54506.1																																																																																			.	.	none		0.682	IGLL5-002	KNOWN	basic|appris_candidate|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000385699.1	NM_001178126	
