#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_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_NTotCov	i_NVarCov	i_ORegAnno_bin	i_TTotCov	i_TVarCov	i_Transcript_Id	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_dbSNP_AF	i_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
GPBP1L1	60313	hgsc.bcm.edu	37	1	46124754	46124754	+	Silent	SNP	C	C	A	rs144406702		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr1:46124754C>A	ENST00000290795.3	-	3	1227	c.6G>T	c.(4-6)gcG>gcT	p.A2A	GPBP1L1_ENST00000355105.3_Silent_p.A2A			Q9HC44	GPBL1_HUMAN	GC-rich promoter binding protein 1-like 1	2					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)		GPBP1L1/MAST2_ENST00000361297(2)	breast(1)|endometrium(2)|large_intestine(4)|lung(10)|ovary(1)|skin(2)|stomach(1)	21	Acute lymphoblastic leukemia(166;0.155)					AATCATGCTGCGCCATTTAGG	0.413																																					p.A2A		Atlas-SNP	.											GPBP1L1,colon,carcinoma,0,1	GPBP1L1	43	.	0			c.G6T						.						142.0	132.0	136.0					1																	46124754		2203	4300	6503	SO:0001819	synonymous_variant	60313	exon4			ATGCTGCGCCATT		CCDS528.1	1p34.1	2008-02-05			ENSG00000159592	ENSG00000159592			28843	protein-coding gene	gene with protein product						12477932	Standard	NM_021639		Approved	SP192	uc001coq.3	Q9HC44	OTTHUMG00000040990	ENST00000290795.3:c.6G>T	chr1.hg19:g.46124754C>A		112.0	0.0		51.0	3.0	NM_021639	D3DQ10|Q9H751	Silent	SNP	ENST00000290795.3	hg19	CCDS528.1																																																																																			.	C|1.000;T|0.000		0.413	GPBP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098375.1	NM_021639	
INSRR	3645	hgsc.bcm.edu	37	1	156815550	156815550	+	Missense_Mutation	SNP	G	G	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr1:156815550G>T	ENST00000368195.3	-	10	2431	c.2035C>A	c.(2035-2037)Cct>Act	p.P679T	NTRK1_ENST00000392302.2_Intron	NM_014215.2	NP_055030.1	P14616	INSRR_HUMAN	insulin receptor-related receptor	679	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				actin cytoskeleton reorganization (GO:0031532)|cellular response to alkaline pH (GO:0071469)|male sex determination (GO:0030238)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(8)|lung(13)|ovary(7)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)	42	all_hematologic(923;0.0839)|Hepatocellular(266;0.158)					TCGGCCTCAGGATCCCCGTCT	0.652																																					p.P679T		Atlas-SNP	.											.	INSRR	309	.	0			c.C2035A						.						40.0	36.0	37.0					1																	156815550		2203	4300	6503	SO:0001583	missense	3645	exon10			CCTCAGGATCCCC	J05046	CCDS1160.1	1q21-q23	2013-02-11			ENSG00000027644	ENSG00000027644		"""Fibronectin type III domain containing"""	6093	protein-coding gene	gene with protein product		147671				2768234, 2249481	Standard	NM_014215		Approved	IRR	uc010pht.2	P14616	OTTHUMG00000041291	ENST00000368195.3:c.2035C>A	chr1.hg19:g.156815550G>T	ENSP00000357178:p.Pro679Thr	76.0	0.0		81.0	4.0	NM_014215	O60724|Q5VZS3	Missense_Mutation	SNP	ENST00000368195.3	hg19	CCDS1160.1	.	.	.	.	.	.	.	.	.	.	G	2.916	-0.224202	0.06061	.	.	ENSG00000027644	ENST00000368195	T	0.43688	0.94	4.58	2.66	0.31614	Fibronectin, type III (3);	0.520885	0.16212	N	0.224460	T	0.10423	0.0255	.	.	.	0.31210	N	0.698806	B	0.02656	0.0	B	0.01281	0.0	T	0.22208	-1.0223	9	0.22706	T	0.39	.	8.0	0.30291	0.0914:0.1623:0.7462:0.0	.	679	P14616	INSRR_HUMAN	T	679	ENSP00000357178:P679T	ENSP00000357178:P679T	P	-	1	0	INSRR	155082174	0.107000	0.21998	0.009000	0.14445	0.021000	0.10359	2.842000	0.48230	0.635000	0.30488	-0.305000	0.09177	CCT	.	.		0.652	INSRR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098929.1	NM_014215	
POU2F1	5451	hgsc.bcm.edu	37	1	167384897	167384897	+	Silent	SNP	T	T	C			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr1:167384897T>C	ENST00000541643.3	+	17	2244	c.2082T>C	c.(2080-2082)tcT>tcC	p.S694S	POU2F1_ENST00000367862.5_Silent_p.S706S|POU2F1_ENST00000420254.3_Intron|POU2F1_ENST00000367865.1_3'UTR|POU2F1_ENST00000429375.2_Silent_p.S654S|POU2F1_ENST00000367866.2_Silent_p.S717S			P14859	PO2F1_HUMAN	POU class 2 homeobox 1	694					gene expression (GO:0010467)|negative regulation of transcription, DNA-templated (GO:0045892)|transcription from RNA polymerase III promoter (GO:0006383)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(2)|large_intestine(3)|liver(2)|lung(7)|ovary(2)|prostate(2)|skin(3)|urinary_tract(1)	30						GCTTGGTCTCTGCCGCCGCAG	0.592																																					p.S717S		Atlas-SNP	.											.	POU2F1	120	.	0			c.T2151C						.						146.0	134.0	138.0					1																	167384897		2203	4300	6503	SO:0001819	synonymous_variant	5451	exon16			GGTCTCTGCCGCC	BC001664	CCDS1259.1, CCDS1259.2, CCDS55655.1, CCDS55656.1	1q24.2	2011-06-20	2007-07-13		ENSG00000143190	ENSG00000143190		"""Homeoboxes / POU class"""	9212	protein-coding gene	gene with protein product		164175	"""POU domain class 2, transcription factor 1"""	OTF1		1887216	Standard	NM_002697		Approved	OCT1	uc001gee.3	P14859	OTTHUMG00000034436	ENST00000541643.3:c.2082T>C	chr1.hg19:g.167384897T>C		133.0	0.0		80.0	21.0	NM_002697	B1AL91|B1AL93|B4E029|J3KP77|Q5TBT7|Q6PK46|Q8NEU9|Q9BPV1	Silent	SNP	ENST00000541643.3	hg19																																																																																				.	.		0.592	POU2F1-203	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_002697	
PKP1	5317	hgsc.bcm.edu	37	1	201294914	201294914	+	Missense_Mutation	SNP	T	T	C			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr1:201294914T>C	ENST00000352845.3	+	13	2117	c.2117T>C	c.(2116-2118)cTt>cCt	p.L706P	PKP1_ENST00000367324.3_Missense_Mutation_p.L685P|PKP1_ENST00000263946.3_Missense_Mutation_p.L706P			Q13835	PKP1_HUMAN	plakophilin 1	706					apoptotic process (GO:0006915)|cell adhesion (GO:0007155)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|intermediate filament bundle assembly (GO:0045110)|multicellular organismal development (GO:0007275)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)	desmosome (GO:0030057)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intermediate filament binding (GO:0019215)|lamin binding (GO:0005521)|signal transducer activity (GO:0004871)|structural constituent of epidermis (GO:0030280)			NS(2)|breast(1)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(4)|ovary(5)|prostate(1)	22						GCTGCCCGGCTTCTCCTGTCT	0.562																																					p.L706P		Atlas-SNP	.											.	PKP1	127	.	0			c.T2117C						.						67.0	62.0	64.0					1																	201294914		2203	4300	6503	SO:0001583	missense	5317	exon13			CCCGGCTTCTCCT	X79293	CCDS30966.1, CCDS30967.1	1q32	2014-06-18	2014-06-18		ENSG00000081277	ENSG00000081277		"""Armadillo repeat containing"""	9023	protein-coding gene	gene with protein product	"""ectodermal dysplasia/skin fragility syndrome"""	601975	"""plakophilin 1 (ectodermal dysplasia/skin fragility syndrome)"""			9272178	Standard	NM_001005337		Approved	B6P	uc001gwd.3	Q13835	OTTHUMG00000035729	ENST00000352845.3:c.2117T>C	chr1.hg19:g.201294914T>C	ENSP00000295597:p.Leu706Pro	139.0	0.0		116.0	25.0	NM_000299	O00645|Q14CA0|Q15152	Missense_Mutation	SNP	ENST00000352845.3	hg19	CCDS30966.1	.	.	.	.	.	.	.	.	.	.	T	21.2	4.110130	0.77210	.	.	ENSG00000081277	ENST00000367324;ENST00000263946;ENST00000352845	T;T;T	0.50277	0.75;0.75;0.75	5.29	5.29	0.74685	Armadillo-like helical (1);Armadillo-type fold (1);	0.149594	0.44483	D	0.000451	T	0.63295	0.2499	L	0.53249	1.67	0.80722	D	1	D;D;D	0.89917	0.997;1.0;1.0	D;D;D	0.76575	0.968;0.988;0.982	T	0.61840	-0.6980	10	0.37606	T	0.19	-2.7201	15.2179	0.73285	0.0:0.0:0.0:1.0	.	293;685;706	Q14BN3;Q13835-2;Q13835	.;.;PKP1_HUMAN	P	685;706;706	ENSP00000356293:L685P;ENSP00000263946:L706P;ENSP00000295597:L706P	ENSP00000263946:L706P	L	+	2	0	PKP1	199561537	0.999000	0.42202	0.985000	0.45067	0.926000	0.56050	5.471000	0.66762	1.992000	0.58205	0.533000	0.62120	CTT	.	.		0.562	PKP1-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000086897.1	NM_000299	
USH2A	7399	hgsc.bcm.edu	37	1	215802343	215802343	+	Missense_Mutation	SNP	G	G	A			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr1:215802343G>A	ENST00000307340.3	-	71	15718	c.15332C>T	c.(15331-15333)aCa>aTa	p.T5111I	SNORD116_ENST00000365628.1_RNA|USH2A_ENST00000366943.2_Missense_Mutation_p.T5135I	NM_206933.2	NP_996816	O75445	USH2A_HUMAN	Usher syndrome 2A (autosomal recessive, mild)	5111					hair cell differentiation (GO:0035315)|inner ear receptor cell differentiation (GO:0060113)|maintenance of organ identity (GO:0048496)|photoreceptor cell maintenance (GO:0045494)|response to stimulus (GO:0050896)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|visual perception (GO:0007601)	apical plasma membrane (GO:0016324)|basement membrane (GO:0005604)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|stereocilia ankle link complex (GO:0002142)|stereocilium bundle (GO:0032421)|stereocilium membrane (GO:0060171)	collagen binding (GO:0005518)|myosin binding (GO:0017022)			NS(7)|breast(20)|central_nervous_system(3)|cervix(2)|endometrium(32)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(71)|liver(2)|lung(282)|ovary(25)|pancreas(2)|prostate(12)|skin(22)|stomach(7)|upper_aerodigestive_tract(20)|urinary_tract(3)	527				OV - Ovarian serous cystadenocarcinoma(81;0.0547)|all cancers(67;0.0875)		ACTCACAGGTGTCCCAGACCG	0.498										HNSCC(13;0.011)																											p.T5111I		Atlas-SNP	.											.	USH2A	1168	.	0			c.C15332T						.						111.0	114.0	113.0					1																	215802343		2203	4300	6503	SO:0001583	missense	7399	exon71			ACAGGTGTCCCAG	AF055580	CCDS1516.1, CCDS31025.1	1q41	2013-02-11			ENSG00000042781	ENSG00000042781		"""Fibronectin type III domain containing"""	12601	protein-coding gene	gene with protein product	"""usherin"""	608400		USH2		9624053, 10729113	Standard	NM_007123		Approved	RP39	uc001hku.1	O75445	OTTHUMG00000037079	ENST00000307340.3:c.15332C>T	chr1.hg19:g.215802343G>A	ENSP00000305941:p.Thr5111Ile	164.0	0.0		109.0	13.0	NM_206933	Q5VVM9|Q6S362|Q9NS27	Missense_Mutation	SNP	ENST00000307340.3	hg19	CCDS31025.1	.	.	.	.	.	.	.	.	.	.	G	21.0	4.081370	0.76528	.	.	ENSG00000042781	ENST00000307340;ENST00000366943	T;T	0.13778	2.59;2.56	5.67	5.67	0.87782	.	0.202390	0.24187	U	0.040742	T	0.22666	0.0547	L	0.60455	1.87	0.40500	D	0.980631	P	0.50272	0.933	P	0.44860	0.462	T	0.01071	-1.1461	10	0.62326	D	0.03	.	19.7686	0.96352	0.0:0.0:1.0:0.0	.	5111	O75445	USH2A_HUMAN	I	5111;5135	ENSP00000305941:T5111I;ENSP00000355910:T5135I	ENSP00000305941:T5111I	T	-	2	0	USH2A	213868966	0.992000	0.36948	0.971000	0.41717	0.811000	0.45836	4.681000	0.61663	2.665000	0.90641	0.591000	0.81541	ACA	.	.		0.498	USH2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000128138.1	NM_007123	
AMMECR1L	83607	hgsc.bcm.edu	37	2	128628831	128628831	+	Silent	SNP	C	C	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr2:128628831C>T	ENST00000272647.5	-	4	770	c.510G>A	c.(508-510)acG>acA	p.T170T	AMMECR1L_ENST00000393001.1_Silent_p.T170T	NM_001199140.1	NP_001186069.1	Q6DCA0	AMERL_HUMAN	AMMECR1-like	170	AMMECR1. {ECO:0000255|PROSITE- ProRule:PRU00467}.									central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)	9	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.07)		ACCTGGTTAACGTGTATTCCC	0.458																																					p.T170T		Atlas-SNP	.											.	AMMECR1L	22	.	0			c.G510A						.						74.0	72.0	73.0					2																	128628831		2203	4300	6503	SO:0001819	synonymous_variant	83607	exon4			GGTTAACGTGTAT		CCDS2152.1	2q21	2012-11-15	2012-11-15		ENSG00000144233	ENSG00000144233			28658	protein-coding gene	gene with protein product			"""AMME chromosomal region gene 1-like"""				Standard	NM_001199140		Approved	MGC4268	uc002tpl.3	Q6DCA0	OTTHUMG00000131535	ENST00000272647.5:c.510G>A	chr2.hg19:g.128628831C>T		74.0	0.0		44.0	10.0	NM_031445	B4E276	Silent	SNP	ENST00000272647.5	hg19	CCDS2152.1																																																																																			.	.		0.458	AMMECR1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254392.1	NM_031445	
IL5RA	3568	hgsc.bcm.edu	37	3	3137002	3137002	+	Missense_Mutation	SNP	G	G	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr3:3137002G>T	ENST00000446632.2	-	8	1410	c.836C>A	c.(835-837)aCa>aAa	p.T279K	IL5RA_ENST00000256452.3_Missense_Mutation_p.T279K|IL5RA_ENST00000418488.2_Intron|IL5RA_ENST00000430514.2_Missense_Mutation_p.T279K|IL5RA_ENST00000445864.2_Intron|IL5RA_ENST00000438560.1_Missense_Mutation_p.T279K|IL5RA_ENST00000383846.1_Missense_Mutation_p.T279K|IL5RA_ENST00000456302.1_Missense_Mutation_p.T279K|IL5RA_ENST00000311981.8_Missense_Mutation_p.T279K	NM_175726.3	NP_783853.1	Q01344	IL5RA_HUMAN	interleukin 5 receptor, alpha	279	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell proliferation (GO:0008283)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-5-mediated signaling pathway (GO:0038043)|regulation of interleukin-5 production (GO:0032674)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	interleukin-5 receptor activity (GO:0004914)			cervix(1)|endometrium(2)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	24				Epithelial(13;0.00278)|all cancers(10;0.00809)|OV - Ovarian serous cystadenocarcinoma(96;0.00944)		TCCATTCCTTGTATTGTGTAT	0.328																																					p.T279K	GBM(169;430 2801 24955 28528)	Atlas-SNP	.											.	IL5RA	55	.	0			c.C836A						.						72.0	72.0	72.0					3																	3137002		2203	4300	6503	SO:0001583	missense	3568	exon8			TTCCTTGTATTGT	M96652	CCDS2559.1, CCDS2560.1, CCDS46739.1, CCDS58813.1	3p26-p24	2008-01-11			ENSG00000091181	ENSG00000091181		"""Interleukins and interleukin receptors"", ""CD molecules"""	6017	protein-coding gene	gene with protein product		147851		IL5R		1732409	Standard	NM_175727		Approved	CDw125, CD125	uc010hbs.3	Q01344	OTTHUMG00000090245	ENST00000446632.2:c.836C>A	chr3.hg19:g.3137002G>T	ENSP00000412209:p.Thr279Lys	161.0	0.0		116.0	51.0	NM_001243099	B3IU77|B4E2G0|Q14633|Q15469|Q6ISX9	Missense_Mutation	SNP	ENST00000446632.2	hg19	CCDS2559.1	.	.	.	.	.	.	.	.	.	.	G	4.694	0.129079	0.08981	.	.	ENSG00000091181	ENST00000446632;ENST00000438560;ENST00000256452;ENST00000383846;ENST00000311981;ENST00000430514;ENST00000456302	D;D;D;D;D;D;D	0.85484	-1.99;-1.99;-1.99;-1.99;-1.99;-1.99;-1.99	5.0	0.227	0.15359	Fibronectin, type III (1);Immunoglobulin-like fold (1);	0.788201	0.11359	N	0.572071	T	0.77870	0.4195	L	0.56396	1.775	0.09310	N	1	B;P;P;B	0.49090	0.418;0.919;0.763;0.177	B;B;B;B	0.43052	0.068;0.406;0.293;0.049	T	0.66118	-0.6003	10	0.06236	T	0.91	-1.3347	6.7952	0.23721	0.5903:0.0:0.4097:0.0	.	279;279;279;279	B4E2G0;Q01344-3;Q01344-2;Q01344	.;.;.;IL5RA_HUMAN	K	279	ENSP00000412209:T279K;ENSP00000390753:T279K;ENSP00000256452:T279K;ENSP00000373358:T279K;ENSP00000309196:T279K;ENSP00000400400:T279K;ENSP00000392059:T279K	ENSP00000256452:T279K	T	-	2	0	IL5RA	3112002	0.004000	0.15560	0.001000	0.08648	0.027000	0.11550	0.569000	0.23638	0.098000	0.17522	-0.345000	0.07892	ACA	.	.		0.328	IL5RA-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337537.2		
ATP2B2	491	hgsc.bcm.edu	37	3	10417206	10417206	+	Missense_Mutation	SNP	T	T	C			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr3:10417206T>C	ENST00000352432.4	-	10	1393	c.1324A>G	c.(1324-1326)Aag>Gag	p.K442E	ATP2B2_ENST00000397077.1_Missense_Mutation_p.K397E|ATP2B2_ENST00000360273.2_Missense_Mutation_p.K442E|ATP2B2_ENST00000343816.4_Missense_Mutation_p.K428E|ATP2B2_ENST00000383800.4_Missense_Mutation_p.K397E			Q01814	AT2B2_HUMAN	ATPase, Ca++ transporting, plasma membrane 2	442					auditory receptor cell stereocilium organization (GO:0060088)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cerebellar granule cell differentiation (GO:0021707)|cerebellar Purkinje cell differentiation (GO:0021702)|cGMP metabolic process (GO:0046068)|cochlea development (GO:0090102)|cytosolic calcium ion homeostasis (GO:0051480)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotion (GO:0040011)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neuron differentiation (GO:0030182)|organelle organization (GO:0006996)|otolith mineralization (GO:0045299)|positive regulation of calcium ion transport (GO:0051928)|regulation of cell size (GO:0008361)|regulation of synaptic plasticity (GO:0048167)|sensory perception of sound (GO:0007605)|serotonin metabolic process (GO:0042428)|synapse organization (GO:0050808)|transmembrane transport (GO:0055085)|transport (GO:0006810)	apical plasma membrane (GO:0016324)|cilium (GO:0005929)|cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-dependent ATPase activity (GO:0030899)|calcium-transporting ATPase activity (GO:0005388)|calmodulin binding (GO:0005516)|metal ion binding (GO:0046872)|PDZ domain binding (GO:0030165)|protein C-terminus binding (GO:0008022)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(7)|large_intestine(19)|lung(29)|ovary(5)|prostate(2)|skin(4)|stomach(2)|urinary_tract(2)	74						ATGAAGAACTTGACAAAGTAC	0.587																																					p.K442E	Ovarian(125;1619 1709 15675 19819 38835)	Atlas-SNP	.											.	ATP2B2	304	.	0			c.A1324G						.						96.0	89.0	91.0					3																	10417206		2203	4300	6503	SO:0001583	missense	491	exon11			AGAACTTGACAAA	X63575	CCDS2601.1, CCDS33701.1	3p25.3	2010-04-20	2001-12-04		ENSG00000157087	ENSG00000157087	3.6.3.8	"""ATPases / P-type"""	815	protein-coding gene	gene with protein product	"""plasma membrane Ca2+ pump 2"", ""plasma membrane calcium-transporting ATPase 2"""	108733				1313367	Standard	NM_001001331		Approved	PMCA2	uc003bvt.3	Q01814	OTTHUMG00000128679	ENST00000352432.4:c.1324A>G	chr3.hg19:g.10417206T>C	ENSP00000324172:p.Lys442Glu	135.0	0.0		126.0	13.0	NM_001001331	O00766|Q12994|Q16818	Missense_Mutation	SNP	ENST00000352432.4	hg19	CCDS33701.1	.	.	.	.	.	.	.	.	.	.	T	26.7	4.760115	0.89932	.	.	ENSG00000157087	ENST00000352432;ENST00000383800;ENST00000397077;ENST00000360273;ENST00000343816;ENST00000535386;ENST00000452124;ENST00000342354	D;D;D;D;D;D	0.88741	-2.42;-2.42;-2.42;-2.42;-2.42;-2.42	4.48	4.48	0.54585	ATPase, P-type, ATPase-associated domain (1);	0.096864	0.64402	D	0.000001	D	0.82416	0.5032	N	0.20483	0.58	0.80722	D	1	P;B;B	0.48089	0.905;0.099;0.233	B;B;B	0.43508	0.422;0.042;0.245	D	0.83890	0.0284	10	0.45353	T	0.12	-28.7124	13.9721	0.64247	0.0:0.0:0.0:1.0	.	377;409;442	F5H7F7;Q4LE63;Q01814	.;.;AT2B2_HUMAN	E	442;397;397;442;428;377;298;442	ENSP00000324172:K442E;ENSP00000373311:K397E;ENSP00000380267:K397E;ENSP00000353414:K442E;ENSP00000344677:K428E;ENSP00000414854:K298E	ENSP00000342954:K442E	K	-	1	0	ATP2B2	10392206	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.868000	0.87116	1.884000	0.54569	0.459000	0.35465	AAG	.	.		0.587	ATP2B2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000250576.2	NM_001683	
PXK	54899	hgsc.bcm.edu	37	3	58395296	58395296	+	Missense_Mutation	SNP	A	A	G			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr3:58395296A>G	ENST00000356151.2	+	15	1455	c.1346A>G	c.(1345-1347)cAc>cGc	p.H449R	PXK_ENST00000479241.1_Missense_Mutation_p.H432R|PXK_ENST00000302779.5_Missense_Mutation_p.H432R|PXK_ENST00000536660.1_Missense_Mutation_p.H312R|PXK_ENST00000484288.1_Missense_Mutation_p.H449R|PXK_ENST00000383715.4_Missense_Mutation_p.H432R|PXK_ENST00000463280.1_Missense_Mutation_p.H416R|PXK_ENST00000383716.3_Missense_Mutation_p.H416R	NM_017771.3	NP_060241.2			PX domain containing serine/threonine kinase											cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(10)|ovary(1)|skin(1)|urinary_tract(1)	19				BRCA - Breast invasive adenocarcinoma(55;0.000249)|KIRC - Kidney renal clear cell carcinoma(10;0.00346)|Kidney(10;0.00368)|OV - Ovarian serous cystadenocarcinoma(275;0.22)		GCTCAGTCCCACCATGGATCT	0.418																																					p.H449R		Atlas-SNP	.											.	PXK	89	.	0			c.A1346G						.						62.0	62.0	62.0					3																	58395296		2203	4300	6503	SO:0001583	missense	54899	exon15			AGTCCCACCATGG	AY274811	CCDS2889.1, CCDS74952.1, CCDS74954.1, CCDS74955.1	3p21.2	2008-02-05			ENSG00000168297	ENSG00000168297			23326	protein-coding gene	gene with protein product		611450					Standard	XM_005265255		Approved	FLJ20335	uc003djz.1	Q7Z7A4	OTTHUMG00000159149	ENST00000356151.2:c.1346A>G	chr3.hg19:g.58395296A>G	ENSP00000348472:p.His449Arg	253.0	1.0		196.0	93.0	NM_017771		Missense_Mutation	SNP	ENST00000356151.2	hg19	CCDS2889.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	19.52|19.52	3.843105|3.843105	0.71488|0.71488	.|.	.|.	ENSG00000168297|ENSG00000168297	ENST00000356151;ENST00000302779;ENST00000383716;ENST00000463280;ENST00000383715;ENST00000484288;ENST00000479241;ENST00000536660;ENST00000536750|ENST00000479134;ENST00000495557	T;T;T;T;T;T;T;T|.	0.32023|.	3.11;3.11;3.11;1.5;1.48;1.5;1.47;3.11|.	5.75|5.75	5.75|5.75	0.90469|0.90469	Protein kinase, catalytic domain (1);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.71476|0.71476	0.3344|0.3344	M|M	0.64997|0.64997	1.995|1.995	0.80722|0.80722	D|D	1|1	D;D;D;D;D;D|.	0.71674|.	0.997;0.996;0.994;0.998;0.996;0.996|.	D;D;D;D;D;P|.	0.70016|.	0.933;0.918;0.917;0.967;0.918;0.89|.	T|T	0.70498|0.70498	-0.4855|-0.4855	10|5	0.23302|.	T|.	0.38|.	-14.7244|-14.7244	14.9154|14.9154	0.70792|0.70792	1.0:0.0:0.0:0.0|1.0:0.0:0.0:0.0	.|.	416;416;416;449;432;449|.	E9PD56;Q7Z7A4-6;B4DID9;Q7Z7A4;Q7Z7A4-4;Q7Z7A4-2|.	.;.;.;PXK_HUMAN;.;.|.	R|A	449;432;416;416;432;449;432;312;312|204;21	ENSP00000348472:H449R;ENSP00000305045:H432R;ENSP00000373222:H416R;ENSP00000417903:H416R;ENSP00000373221:H432R;ENSP00000417915:H449R;ENSP00000419049:H432R;ENSP00000438356:H312R|.	ENSP00000305045:H432R|.	H|T	+|+	2|1	0|0	PXK|PXK	58370336|58370336	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.787000|0.787000	0.44495|0.44495	6.908000|6.908000	0.75730|0.75730	2.315000|2.315000	0.78130|0.78130	0.519000|0.519000	0.50382|0.50382	CAC|ACC	.	.		0.418	PXK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353499.1	NM_017771	
FGFR3	2261	hgsc.bcm.edu	37	4	1807577	1807577	+	Silent	SNP	C	C	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr4:1807577C>T	ENST00000260795.2	+	12	1848	c.1746C>T	c.(1744-1746)tgC>tgT	p.C582C	FGFR3_ENST00000440486.2_Silent_p.C582C|FGFR3_ENST00000481110.2_Silent_p.C583C|FGFR3_ENST00000352904.1_Silent_p.C470C|FGFR3_ENST00000412135.2_Silent_p.C470C|FGFR3_ENST00000340107.4_Silent_p.C584C			P22607	FGFR3_HUMAN	fibroblast growth factor receptor 3	582	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				alveolar secondary septum development (GO:0061144)|axonogenesis involved in innervation (GO:0060385)|bone maturation (GO:0070977)|bone mineralization (GO:0030282)|bone morphogenesis (GO:0060349)|cell-cell signaling (GO:0007267)|central nervous system myelination (GO:0022010)|chondrocyte differentiation (GO:0002062)|chondrocyte proliferation (GO:0035988)|cochlea development (GO:0090102)|digestive tract morphogenesis (GO:0048546)|endochondral bone growth (GO:0003416)|endochondral ossification (GO:0001958)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial cell fate commitment (GO:0072148)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor apoptotic signaling pathway (GO:1902178)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inner ear receptor cell differentiation (GO:0060113)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade (GO:0007259)|lens fiber cell development (GO:0070307)|lens morphogenesis in camera-type eye (GO:0002089)|MAPK cascade (GO:0000165)|morphogenesis of an epithelium (GO:0002009)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of developmental growth (GO:0048640)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of mitosis (GO:0045839)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of cell differentiation (GO:0045597)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phospholipase activity (GO:0010518)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of tyrosine phosphorylation of Stat1 protein (GO:0042511)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|response to axon injury (GO:0048678)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|substantia nigra development (GO:0021762)	cell surface (GO:0009986)|cytoplasmic side of plasma membrane (GO:0009898)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|lysosome (GO:0005764)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|fibroblast growth factor binding (GO:0017134)|fibroblast growth factor-activated receptor activity (GO:0005007)|protein tyrosine kinase activity (GO:0004713)			NS(1)|central_nervous_system(5)|cervix(6)|endometrium(2)|haematopoietic_and_lymphoid_tissue(40)|kidney(1)|large_intestine(5)|lung(9)|ovary(1)|pancreas(2)|prostate(9)|skin(339)|soft_tissue(4)|testis(2)|upper_aerodigestive_tract(58)|urinary_tract(2607)	3091		Breast(71;0.212)|all_epithelial(65;0.241)	all cancers(2;0.000145)|OV - Ovarian serous cystadenocarcinoma(23;0.0019)|Epithelial(3;0.00221)|GBM - Glioblastoma multiforme(2;0.234)		Palifermin(DB00039)|Pazopanib(DB06589)|Ponatinib(DB08901)	TCGACACCTGCAAGCCGCCCG	0.682		1	"""Mis, T"""	"""IGH@, ETV6"""	"""bladder, MM, T-cell lymphoma"""		"""Hypochondroplasia, Thanatophoric dysplasia"""		Saethre-Chotzen syndrome;Muenke syndrome																												p.C584C		Atlas-SNP	.		Dom	yes		4	4p16.3	2261	fibroblast growth factor receptor 3	yes	"""L, E"""	.	FGFR3	3320	.	0			c.C1752T						.						43.0	53.0	50.0					4																	1807577		2203	4298	6501	SO:0001819	synonymous_variant	2261	exon13	Familial Cancer Database	Acrocephalosyndactyly type III;Muenke Nonsyndromic Coronal Craniosynostosis, FGFR3-related Craniosynostosis	CACCTGCAAGCCG	M64347	CCDS3353.1, CCDS3354.1, CCDS54706.1	4p16.3	2013-01-11	2008-08-01		ENSG00000068078	ENSG00000068078		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	3690	protein-coding gene	gene with protein product		134934	"""achondroplasia, thanatophoric dwarfism"""	ACH		1847508	Standard	NM_000142		Approved	CEK2, JTK4, CD333	uc003gdu.2	P22607	OTTHUMG00000121148	ENST00000260795.2:c.1746C>T	chr4.hg19:g.1807577C>T		76.0	0.0		54.0	16.0	NM_001163213	D3DVP9|D3DVQ0|Q14308|Q16294|Q16608|Q59FL9	Silent	SNP	ENST00000260795.2	hg19	CCDS3353.1																																																																																			.	.		0.682	FGFR3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000241632.2	NM_000142	
SH3BP2	6452	hgsc.bcm.edu	37	4	2829348	2829348	+	Missense_Mutation	SNP	A	A	G			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr4:2829348A>G	ENST00000356331.5	+	7	794	c.533A>G	c.(532-534)gAt>gGt	p.D178G	SH3BP2_ENST00000435136.2_Missense_Mutation_p.D178G|SH3BP2_ENST00000511747.1_Missense_Mutation_p.D178G|SH3BP2_ENST00000442312.2_Missense_Mutation_p.D206G|SH3BP2_ENST00000503393.2_Missense_Mutation_p.D235G|SH3BP2_ENST00000452765.2_Missense_Mutation_p.D178G|SH3BP2_ENST00000515183.1_3'UTR	NM_003023.4	NP_003014.3	P78314	3BP2_HUMAN	SH3-domain binding protein 2	178					positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)		SH3/SH2 adaptor activity (GO:0005070)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	20				UCEC - Uterine corpus endometrioid carcinoma (64;0.164)		GAGCACGACGATGAGGATGAC	0.652									Cherubism																												p.D235G		Atlas-SNP	.											.	SH3BP2	43	.	0			c.A704G						.						52.0	37.0	42.0					4																	2829348		2201	4298	6499	SO:0001583	missense	6452	exon7	Familial Cancer Database	Familial Benign Giant-cell Tumor of the Jaw, Familial Multilocular Cystic Disease	ACGACGATGAGGA	BC022996	CCDS33944.1, CCDS54715.1, CCDS54716.1	4p16.3	2013-02-14				ENSG00000087266		"""Pleckstrin homology (PH) domain containing"", ""SH2 domain containing"""	10825	protein-coding gene	gene with protein product		602104	"""Cherubism"""			9299232, 11381256	Standard	NM_003023		Approved	RES4-23, CRBM	uc003gfj.4	P78314		ENST00000356331.5:c.533A>G	chr4.hg19:g.2829348A>G	ENSP00000348685:p.Asp178Gly	127.0	0.0		67.0	30.0	NM_001145856	A6NNC2|B2R5R6|B4DT04|D3DVR0|D6R919|O00500|O15373|P78315	Missense_Mutation	SNP	ENST00000356331.5	hg19	CCDS33944.1	.	.	.	.	.	.	.	.	.	.	a	14.47	2.544300	0.45280	.	.	ENSG00000087266	ENST00000452765;ENST00000508385;ENST00000512014;ENST00000442312;ENST00000435136;ENST00000511747;ENST00000503393;ENST00000356331	D;T;T;D;D;D;D;D	0.95171	-3.63;1.87;1.82;-3.63;-3.63;-3.63;-3.63;-3.63	4.8	4.8	0.61643	.	0.106622	0.64402	D	0.000010	D	0.95956	0.8683	M	0.64997	1.995	0.80722	D	1	D;D;D;D;D	0.71674	0.993;0.997;0.998;0.997;0.997	P;D;D;D;D	0.81914	0.853;0.989;0.995;0.989;0.989	D	0.95349	0.8445	10	0.46703	T	0.11	-21.8009	10.749	0.46198	1.0:0.0:0.0:0.0	.	206;153;153;235;178	B4DT04;Q6ZVU3;Q6ZTK4;D6R919;P78314	.;.;.;.;3BP2_HUMAN	G	178;178;178;206;178;178;235;178	ENSP00000409746:D178G;ENSP00000424917:D178G;ENSP00000424105:D178G;ENSP00000388152:D206G;ENSP00000403231:D178G;ENSP00000424846:D178G;ENSP00000422168:D235G;ENSP00000348685:D178G	ENSP00000348685:D178G	D	+	2	0	SH3BP2	2799146	0.994000	0.37717	0.046000	0.18839	0.083000	0.17756	4.982000	0.63825	1.806000	0.52798	0.392000	0.25879	GAT	.	.		0.652	SH3BP2-007	KNOWN	alternative_5_UTR|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000362406.2	NM_003023	
FHDC1	85462	hgsc.bcm.edu	37	4	153896514	153896514	+	Nonsense_Mutation	SNP	G	G	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr4:153896514G>T	ENST00000511601.1	+	12	2259	c.2071G>T	c.(2071-2073)Gag>Tag	p.E691*	FHDC1_ENST00000260008.3_Nonsense_Mutation_p.E691*			Q9C0D6	FHDC1_HUMAN	FH2 domain containing 1	691									ARFIP1/FHDC1(2)	NS(2)|breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|liver(2)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	43	all_hematologic(180;0.093)					CCAGGGCATGGAGGAGACCTC	0.617																																					p.E691X		Atlas-SNP	.											.	FHDC1	102	.	0			c.G2071T						.						44.0	46.0	46.0					4																	153896514		2203	4300	6503	SO:0001587	stop_gained	85462	exon11			GGCATGGAGGAGA	AB051514	CCDS34081.1	4q31.3	2014-02-12	2007-11-29		ENSG00000137460	ENSG00000137460			29363	protein-coding gene	gene with protein product						15138637	Standard	NM_033393		Approved	KIAA1727	uc003inf.2	Q9C0D6	OTTHUMG00000161452	ENST00000511601.1:c.2071G>T	chr4.hg19:g.153896514G>T	ENSP00000427567:p.Glu691*	71.0	0.0		29.0	12.0	NM_033393		Nonsense_Mutation	SNP	ENST00000511601.1	hg19	CCDS34081.1	.	.	.	.	.	.	.	.	.	.	G	37	6.463344	0.97585	.	.	ENSG00000137460	ENST00000511601;ENST00000260008	.	.	.	5.19	1.17	0.20885	.	0.740846	0.13614	N	0.374944	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.72032	D	0.01	.	17.3028	0.87187	0.0:0.4784:0.5216:0.0	.	.	.	.	X	691	.	ENSP00000260008:E691X	E	+	1	0	FHDC1	154115964	0.162000	0.22906	0.003000	0.11579	0.007000	0.05969	1.423000	0.34837	-0.035000	0.13691	0.563000	0.77884	GAG	.	.		0.617	FHDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364981.2	NM_033393	
CYFIP2	26999	hgsc.bcm.edu	37	5	156712348	156712348	+	Splice_Site	SNP	G	G	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr5:156712348G>T	ENST00000521420.1	+	2	68		c.e2-1		CYFIP2_ENST00000347377.6_Splice_Site|CYFIP2_ENST00000318218.6_Splice_Site|CYFIP2_ENST00000442283.2_Splice_Site|CYFIP2_ENST00000541131.1_5'Flank|CYFIP2_ENST00000377576.3_Splice_Site|CYFIP2_ENST00000522463.1_Splice_Site					cytoplasmic FMR1 interacting protein 2											breast(1)|endometrium(12)|kidney(2)|lung(23)	38	Renal(175;0.00212)	Medulloblastoma(196;0.0306)|all_neural(177;0.0897)	Kidney(164;0.000171)|KIRC - Kidney renal clear cell carcinoma(164;0.000785)			CTTCCCTTCAGTGCAGAATAC	0.522																																					.		Atlas-SNP	.											.	CYFIP2	354	.	0			.						.						28.0	32.0	31.0					5																	156712348		2040	4144	6184	SO:0001630	splice_region_variant	26999	.			CCTTCAGTGCAGA	AF160973	CCDS75364.1	5q34	2008-07-18				ENSG00000055163			13760	protein-coding gene	gene with protein product	"""p53 inducible protein"""	606323				11438699	Standard	NM_001037333		Approved	PIR121	uc021ygm.1	Q96F07		ENST00000521420.1:c.-23-1G>T	chr5.hg19:g.156712348G>T		39.0	0.0		39.0	6.0	.		Splice_Site	SNP	ENST00000521420.1	hg19																																																																																				.	.		0.522	CYFIP2-001	NOVEL	basic	protein_coding	protein_coding	OTTHUMT00000373710.1	NM_001037332	Intron
CCNJL	79616	hgsc.bcm.edu	37	5	159686508	159686508	+	Missense_Mutation	SNP	T	T	G			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr5:159686508T>G	ENST00000393977.3	-	5	980	c.695A>C	c.(694-696)tAt>tCt	p.Y232S	CCNJL_ENST00000519673.1_Missense_Mutation_p.Y184S|CCNJL_ENST00000257536.7_Missense_Mutation_p.Y184S|CCNJL_ENST00000377503.2_5'UTR|CCNJL_ENST00000541762.1_Missense_Mutation_p.Y183S	NM_024565.5	NP_078841.3	Q8IV13	CCNJL_HUMAN	cyclin J-like	232						nucleus (GO:0005634)				endometrium(2)|kidney(5)|large_intestine(2)|lung(6)|skin(1)|upper_aerodigestive_tract(1)	17	Renal(175;0.00196)	Medulloblastoma(196;0.0354)|all_neural(177;0.116)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GTAATGGGCATACTCCTTGAG	0.637																																					p.Y232S		Atlas-SNP	.											.	CCNJL	36	.	0			c.A695C						.						68.0	73.0	71.0					5																	159686508		2068	4189	6257	SO:0001583	missense	79616	exon5			TGGGCATACTCCT	BC013353	CCDS4350.2	5q33.3	2008-10-31			ENSG00000135083	ENSG00000135083			25876	protein-coding gene	gene with protein product						12477932	Standard	XM_005265982		Approved	FLJ14166	uc003lyb.1	Q8IV13	OTTHUMG00000130325	ENST00000393977.3:c.695A>C	chr5.hg19:g.159686508T>G	ENSP00000377547:p.Tyr232Ser	48.0	0.0		31.0	7.0	NM_024565	Q6ZN43|Q9H7W8	Missense_Mutation	SNP	ENST00000393977.3	hg19	CCDS4350.2	.	.	.	.	.	.	.	.	.	.	T	20.5	4.001583	0.74818	.	.	ENSG00000135083	ENST00000393977;ENST00000257536;ENST00000519673;ENST00000541762	T;T;T;T	0.21734	1.99;1.99;1.99;1.99	5.41	4.22	0.49857	Cyclin, C-terminal (1);Cyclin-like (3);	0.064020	0.64402	D	0.000004	T	0.41880	0.1178	M	0.62723	1.935	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.97110	0.995;0.999;1.0	T	0.25012	-1.0144	10	0.87932	D	0	-11.5958	11.3202	0.49417	0.1365:0.0:0.0:0.8635	.	184;184;232	E7EN43;B4DZA8;Q8IV13	.;.;CCNJL_HUMAN	S	232;184;184;183	ENSP00000377547:Y232S;ENSP00000257536:Y184S;ENSP00000427960:Y184S;ENSP00000446367:Y183S	ENSP00000257536:Y184S	Y	-	2	0	CCNJL	159619086	1.000000	0.71417	0.473000	0.27253	0.946000	0.59487	5.018000	0.64054	0.842000	0.35045	0.533000	0.62120	TAT	.	.		0.637	CCNJL-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000252674.1	NM_024565	
EYS	346007	hgsc.bcm.edu	37	6	65612320	65612320	+	Silent	SNP	A	A	G			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr6:65612320A>G	ENST00000370621.3	-	17	3241	c.2715T>C	c.(2713-2715)tgT>tgC	p.C905C	EYS_ENST00000503581.1_Silent_p.C905C|EYS_ENST00000370616.2_Silent_p.C905C			Q5T1H1	EYS_HUMAN	eyes shut homolog (Drosophila)	905	EGF-like 13. {ECO:0000255|PROSITE- ProRule:PRU00076}.				detection of light stimulus involved in visual perception (GO:0050908)|skeletal muscle tissue regeneration (GO:0043403)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(12)|lung(42)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	69						CCATATCTTCACAGTCACCAT	0.343																																					p.C905C		Atlas-SNP	.											.	EYS	527	.	0			c.T2715C						.						153.0	127.0	135.0					6																	65612320		692	1591	2283	SO:0001819	synonymous_variant	346007	exon17			ATCTTCACAGTCA		CCDS4967.1, CCDS47445.1, CCDS47446.1	6q12	2014-01-28	2008-10-20	2008-10-20	ENSG00000188107	ENSG00000188107			21555	protein-coding gene	gene with protein product		612424	"""chromosome 6 open reading frame 180"", ""EGF-like-domain, multiple 11"", ""retinitis pigmentosa 25 (autosomal recessive)"", ""EGF-like-domain, multiple 10"", ""chromosome 6 open reading frame 178"", ""chromosome 6 open reading frame 179"""	C6orf180, EGFL11, RP25, EGFL10, C6orf178, C6orf179		18836446, 18976725	Standard	NM_001142800		Approved	dJ1018A4.2, bA166P24.2, SPAM, bA307F22.3, dJ303F19.1, bA74E24.1	uc011dxu.1	Q5T1H1	OTTHUMG00000014971	ENST00000370621.3:c.2715T>C	chr6.hg19:g.65612320A>G		203.0	0.0		121.0	26.0	NM_001142800	A2RUR2|A8MVE7|B7TYK8|B7UUQ3|B7ZBE7|B7ZBE8|B7ZBR3|B9ZVD2|Q5SZM4|Q5T3C8|Q5T669|Q5TEL3|Q5TEL4|Q5VVG4|Q6UY05|Q9H557|Q9NQ15	Silent	SNP	ENST00000370621.3	hg19																																																																																				.	.		0.343	EYS-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000351351.3	XM_294050	
CSMD1	64478	hgsc.bcm.edu	37	8	3165845	3165845	+	Missense_Mutation	SNP	G	G	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr8:3165845G>T	ENST00000520002.1	-	25	4370	c.3815C>A	c.(3814-3816)cCt>cAt	p.P1272H	CSMD1_ENST00000542608.1_Missense_Mutation_p.P1271H|CSMD1_ENST00000539096.1_Missense_Mutation_p.P1271H|CSMD1_ENST00000537824.1_Missense_Mutation_p.P1271H|CSMD1_ENST00000602723.1_Missense_Mutation_p.P1272H|CSMD1_ENST00000602557.1_Missense_Mutation_p.P1272H|CSMD1_ENST00000400186.3_Missense_Mutation_p.P1272H			Q96PZ7	CSMD1_HUMAN	CUB and Sushi multiple domains 1	1272	Sushi 7. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)				breast(20)|large_intestine(5)	25		all_cancers(1;5.7e-41)|all_epithelial(1;2.54e-36)|Lung NSC(1;7.54e-11)|all_lung(1;3.2e-10)|Hepatocellular(1;3.78e-05)|Breast(1;0.000196)|Myeloproliferative disorder(4;0.000374)|Esophageal squamous(1;0.0157)|Ovarian(12;0.091)|Renal(68;0.144)|Colorectal(14;0.234)		all cancers(1;5.03e-41)|Epithelial(1;4.78e-31)|Lung(1;1.14e-14)|LUSC - Lung squamous cell carcinoma(1;2.34e-14)|GBM - Glioblastoma multiforme(1;4.49e-10)|Colorectal(4;1.18e-07)|OV - Ovarian serous cystadenocarcinoma(1;3.2e-07)|BRCA - Breast invasive adenocarcinoma(1;6.17e-07)|COAD - Colon adenocarcinoma(4;0.000539)|READ - Rectum adenocarcinoma(4;0.00896)|Kidney(5;0.00957)|KIRC - Kidney renal clear cell carcinoma(5;0.0689)		TATGCACGAAGGTAGTGGTTT	0.502																																					p.P1271H		Atlas-SNP	.											.	CSMD1	1469	.	0			c.C3812A						.						118.0	112.0	114.0					8																	3165845		2095	4225	6320	SO:0001583	missense	64478	exon24			CACGAAGGTAGTG			8p23.2	2012-04-17			ENSG00000183117	ENSG00000183117		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	14026	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 24"""	608397					Standard	NM_033225		Approved	KIAA1890, PPP1R24	uc022aqr.1	Q96PZ7	OTTHUMG00000163605	ENST00000520002.1:c.3815C>A	chr8.hg19:g.3165845G>T	ENSP00000430733:p.Pro1272His	71.0	0.0		22.0	4.0	NM_033225	Q0H0J5|Q96QU9|Q96RM4	Missense_Mutation	SNP	ENST00000520002.1	hg19		.	.	.	.	.	.	.	.	.	.	G	16.01	3.000811	0.54254	.	.	ENSG00000183117	ENST00000400186;ENST00000520002;ENST00000318252;ENST00000537824;ENST00000542608;ENST00000539096	T;T;T;T;T	0.77620	-1.11;-1.11;-1.11;-1.11;-1.11	5.22	4.31	0.51392	Complement control module (2);Sushi/SCR/CCP (3);	0.068318	0.64402	N	0.000014	D	0.93171	0.7825	H	0.99555	4.625	0.80722	D	1	D;D;D	0.89917	0.992;1.0;1.0	P;D;D	0.81914	0.873;0.995;0.985	D	0.95834	0.8860	10	0.87932	D	0	.	15.1701	0.72865	0.0:0.0:0.8586:0.1414	.	1272;1272;1272	E5RIG2;Q96PZ7;Q96PZ7-4	.;CSMD1_HUMAN;.	H	1272;1272;1134;1271;1271;1271	ENSP00000383047:P1272H;ENSP00000430733:P1272H;ENSP00000441462:P1271H;ENSP00000446243:P1271H;ENSP00000441675:P1271H	ENSP00000320445:P1134H	P	-	2	0	CSMD1	3153252	1.000000	0.71417	0.851000	0.33527	0.204000	0.24138	7.663000	0.83820	2.414000	0.81942	0.561000	0.74099	CCT	.	.		0.502	CSMD1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000374500.2	NM_033225	
MTMR7	9108	hgsc.bcm.edu	37	8	17163407	17163407	+	Missense_Mutation	SNP	T	T	G			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr8:17163407T>G	ENST00000180173.5	-	11	1245	c.1211A>C	c.(1210-1212)gAg>gCg	p.E404A	MTMR7_ENST00000398099.3_5'UTR|MTMR7_ENST00000521857.1_Missense_Mutation_p.E404A	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	404	Myotubularin phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00669}.				inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)			breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		CCAAACACACTCAATGAACTG	0.363																																					p.E404A		Atlas-SNP	.											.	MTMR7	75	.	0			c.A1211C						.						102.0	101.0	101.0					8																	17163407		2203	4300	6503	SO:0001583	missense	9108	exon11			ACACACTCAATGA	AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.1211A>C	chr8.hg19:g.17163407T>G	ENSP00000180173:p.Glu404Ala	142.0	0.0		33.0	14.0	NM_004686	A1L4K9|B4DG87|Q68DX4	Missense_Mutation	SNP	ENST00000180173.5	hg19	CCDS34851.1	.	.	.	.	.	.	.	.	.	.	T	24.2	4.506771	0.85282	.	.	ENSG00000003987	ENST00000180173;ENST00000521857	D;D	0.93426	-3.22;-3.22	4.87	4.87	0.63330	Myotubularin phosphatase domain (1);	0.000000	0.85682	D	0.000000	D	0.97340	0.9130	M	0.92122	3.275	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;0.999	D	0.98342	1.0539	10	0.87932	D	0	.	14.9478	0.71047	0.0:0.0:0.0:1.0	.	404;404	Q9Y216-2;Q9Y216	.;MTMR7_HUMAN	A	404	ENSP00000180173:E404A;ENSP00000429733:E404A	ENSP00000180173:E404A	E	-	2	0	MTMR7	17207778	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	7.868000	0.87116	2.180000	0.69256	0.460000	0.39030	GAG	.	.		0.363	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1	NM_004686	
RFX3	5991	hgsc.bcm.edu	37	9	3247979	3247979	+	Intron	SNP	T	T	A			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr9:3247979T>A	ENST00000382004.3	-	16	2280				RFX3_ENST00000358730.2_Missense_Mutation_p.E674V|RFX3_ENST00000302303.1_Missense_Mutation_p.E674V	NM_001282116.1|NM_134428.1	NP_001269045.1|NP_602304.1	P48380	RFX3_HUMAN	regulatory factor X, 3 (influences HLA class II expression)						cell maturation (GO:0048469)|cilium assembly (GO:0042384)|cilium-dependent cell motility (GO:0060285)|endocrine pancreas development (GO:0031018)|epithelial cilium movement involved in determination of left/right asymmetry (GO:0060287)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of type B pancreatic cell development (GO:2000078)|regulation of insulin secretion (GO:0050796)|regulation of transcription, DNA-templated (GO:0006355)|transcription from RNA polymerase II promoter (GO:0006366)|type B pancreatic cell maturation (GO:0072560)	nuclear chromatin (GO:0000790)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			central_nervous_system(1)|cervix(2)|endometrium(2)|kidney(11)|large_intestine(3)|lung(14)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	40				GBM - Glioblastoma multiforme(50;0.00124)|Lung(2;0.0337)		GAAGTGTAATTCTGGCTTATT	0.453																																					p.E674V		Atlas-SNP	.											.	RFX3	156	.	0			c.A2021T						.						95.0	100.0	98.0					9																	3247979		2203	4300	6503	SO:0001627	intron_variant	5991	exon16			TGTAATTCTGGCT	AI811824	CCDS6449.1, CCDS6450.1, CCDS75809.1	9p24.2	2008-02-05			ENSG00000080298	ENSG00000080298			9984	protein-coding gene	gene with protein product		601337				8289803	Standard	XM_005251534		Approved		uc003zhr.3	P48380	OTTHUMG00000019456	ENST00000382004.3:c.1968+52A>T	chr9.hg19:g.3247979T>A		66.0	0.0		32.0	12.0	NM_002919	A8K0H5|D3DRH8|D3DRH9|Q5JTL7|Q5JTL8|Q6NW13|Q8WTU4|Q95HL5|Q95HL6	Missense_Mutation	SNP	ENST00000382004.3	hg19	CCDS6449.1	.	.	.	.	.	.	.	.	.	.	T	10.92	1.486314	0.26686	.	.	ENSG00000080298	ENST00000358730;ENST00000302303	T;T	0.59906	0.23;0.23	4.08	2.92	0.33932	.	.	.	.	.	T	0.43344	0.1243	.	.	.	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.27297	-1.0078	8	0.32370	T	0.25	.	9.4539	0.38743	0.0:0.0:0.1935:0.8065	.	674	P48380-2	.	V	674	ENSP00000351574:E674V;ENSP00000303847:E674V	ENSP00000303847:E674V	E	-	2	0	RFX3	3237979	0.960000	0.32886	0.003000	0.11579	0.040000	0.13550	2.298000	0.43602	0.688000	0.31529	0.402000	0.26972	GAA	.	.		0.453	RFX3-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051545.1	NM_002919	
PLAA	9373	hgsc.bcm.edu	37	9	26905887	26905887	+	Missense_Mutation	SNP	C	C	G			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr9:26905887C>G	ENST00000397292.3	-	14	2427	c.2010G>C	c.(2008-2010)caG>caC	p.Q670H		NM_001031689.2	NP_001026859.1	Q9Y263	PLAP_HUMAN	phospholipase A2-activating protein	670	PUL. {ECO:0000255|PROSITE- ProRule:PRU00729}.				inflammatory response (GO:0006954)|phospholipid metabolic process (GO:0006644)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	phospholipase A2 activator activity (GO:0016005)			breast(1)|endometrium(7)|kidney(2)|large_intestine(3)|lung(3)|prostate(1)	17		all_neural(3;3.53e-10)|Glioma(3;2.71e-09)		Lung(218;1.32e-05)|LUSC - Lung squamous cell carcinoma(38;0.00011)		TTTGTCCTGCCTGGCCAACAA	0.443																																					p.Q670H	Melanoma(175;2670 2735 14091 35526)	Atlas-SNP	.											.	PLAA	48	.	0			c.G2010C						.						83.0	79.0	80.0					9																	26905887		2203	4300	6503	SO:0001583	missense	9373	exon14			TCCTGCCTGGCCA	AF083395	CCDS35000.1	9p21	2013-01-10			ENSG00000137055	ENSG00000137055		"""WD repeat domain containing"""	9043	protein-coding gene	gene with protein product	"""DOA1 homolog (S. cerevisiae)"""	603873				9931468, 10644453	Standard	NM_001031689		Approved	PLAP, PLA2P, FLJ11281, FLJ12699, DOA1	uc003zqd.3	Q9Y263	OTTHUMG00000019708	ENST00000397292.3:c.2010G>C	chr9.hg19:g.26905887C>G	ENSP00000380460:p.Gln670His	198.0	0.0		93.0	22.0	NM_001031689	Q53EU5|Q5VY33|Q9NUL8|Q9NVE9|Q9UF53|Q9Y5L1	Missense_Mutation	SNP	ENST00000397292.3	hg19	CCDS35000.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	10.48|10.48	1.362073|1.362073	0.24684|0.24684	.|.	.|.	ENSG00000137055|ENSG00000137055	ENST00000517642|ENST00000397292	.|T	.|0.49432	.|0.78	6.07|6.07	6.07|6.07	0.98685|0.98685	.|PUL (2);	.|0.402261	.|0.31495	.|N	.|0.007554	T|T	0.34745|0.34745	0.0908|0.0908	L|L	0.40543|0.40543	1.245|1.245	0.80722|0.80722	D|D	1|1	.|B	.|0.02656	.|0.0	.|B	.|0.06405	.|0.002	T|T	0.36407|0.36407	-0.9749|-0.9749	5|10	.|0.48119	.|T	.|0.1	-3.1398|-3.1398	4.1806|4.1806	0.10374|0.10374	0.1536:0.5945:0.1479:0.104|0.1536:0.5945:0.1479:0.104	.|.	.|670	.|Q9Y263	.|PLAP_HUMAN	R|H	288|670	.|ENSP00000380460:Q670H	.|ENSP00000380460:Q670H	G|Q	-|-	1|3	0|2	PLAA|PLAA	26895887|26895887	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.990000|0.990000	0.78478|0.78478	0.868000|0.868000	0.27982|0.27982	2.885000|2.885000	0.99019|0.99019	0.655000|0.655000	0.94253|0.94253	GGC|CAG	.	.		0.443	PLAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051958.2	NM_001031689	
GRIN3A	116443	hgsc.bcm.edu	37	9	104499796	104499796	+	Missense_Mutation	SNP	C	C	G			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr9:104499796C>G	ENST00000361820.3	-	1	1066	c.466G>C	c.(466-468)Gca>Cca	p.A156P		NM_133445.2	NP_597702.2	Q8TCU5	NMD3A_HUMAN	glutamate receptor, ionotropic, N-methyl-D-aspartate 3A	156					calcium ion transport (GO:0006816)|dendrite development (GO:0016358)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|prepulse inhibition (GO:0060134)|response to ethanol (GO:0045471)|rhythmic process (GO:0048511)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|N-methyl-D-aspartate selective glutamate receptor complex (GO:0017146)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)|synapse (GO:0045202)	calcium channel activity (GO:0005262)|extracellular-glutamate-gated ion channel activity (GO:0005234)|glycine binding (GO:0016594)|identical protein binding (GO:0042802)|N-methyl-D-aspartate selective glutamate receptor activity (GO:0004972)|neurotransmitter binding (GO:0042165)|protein phosphatase 2A binding (GO:0051721)			breast(2)|central_nervous_system(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(44)|ovary(4)|pancreas(1)|skin(7)|upper_aerodigestive_tract(1)	80		Acute lymphoblastic leukemia(62;0.0568)			Acamprosate(DB00659)|Acetylcysteine(DB06151)|Amantadine(DB00915)|Atomoxetine(DB00289)|Chloroprocaine(DB01161)|Dextromethorphan(DB00514)|Ethanol(DB00898)|Ethopropazine(DB00392)|Felbamate(DB00949)|Gabapentin(DB00996)|Halothane(DB01159)|Ketamine(DB01221)|Ketobemidone(DB06738)|Memantine(DB01043)|Methadone(DB00333)|Milnacipran(DB04896)|Orphenadrine(DB01173)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Procaine(DB00721)|Secobarbital(DB00418)|Tramadol(DB00193)	CCCAGGCCTGCCTCGATGGCC	0.587																																					p.A156P		Atlas-SNP	.											.	GRIN3A	186	.	0			c.G466C						.						102.0	96.0	98.0					9																	104499796		2203	4300	6503	SO:0001583	missense	116443	exon1			GGCCTGCCTCGAT		CCDS6758.1	9q31.1	2012-08-29			ENSG00000198785	ENSG00000198785		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	16767	protein-coding gene	gene with protein product		606650					Standard	NM_133445		Approved	GluN3A	uc004bbp.2	Q8TCU5	OTTHUMG00000020387	ENST00000361820.3:c.466G>C	chr9.hg19:g.104499796C>G	ENSP00000355155:p.Ala156Pro	108.0	0.0		54.0	19.0	NM_133445	B3DLF9|Q5VTR3|Q8TF29|Q8WXI6	Missense_Mutation	SNP	ENST00000361820.3	hg19	CCDS6758.1	.	.	.	.	.	.	.	.	.	.	C	19.12	3.765044	0.69878	.	.	ENSG00000198785	ENST00000361820	D	0.86562	-2.14	4.98	4.98	0.66077	.	0.206037	0.42548	N	0.000699	D	0.88190	0.6370	L	0.48642	1.525	0.52099	D	0.999943	D	0.60575	0.988	P	0.51657	0.676	D	0.87667	0.2538	10	0.38643	T	0.18	.	18.2597	0.90031	0.0:1.0:0.0:0.0	.	156	Q8TCU5	NMD3A_HUMAN	P	156	ENSP00000355155:A156P	ENSP00000355155:A156P	A	-	1	0	GRIN3A	103539617	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	2.853000	0.48317	2.304000	0.77564	0.655000	0.94253	GCA	.	.		0.587	GRIN3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053453.1		
TMEM38B	55151	hgsc.bcm.edu	37	9	108536210	108536210	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr9:108536210G>A	ENST00000374692.3	+	6	842	c.725G>A	c.(724-726)tGg>tAg	p.W242*	TMEM38B_ENST00000374688.1_Nonsense_Mutation_p.W188*	NM_018112.1	NP_060582.1	Q9NVV0	TM38B_HUMAN	transmembrane protein 38B	242						integral component of membrane (GO:0016021)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|sarcoplasmic reticulum membrane (GO:0033017)	potassium channel activity (GO:0005267)			kidney(1)|large_intestine(3)|lung(5)|ovary(1)|skin(1)|upper_aerodigestive_tract(2)	13						ACATTGAGTTGGATGCTATTT	0.408																																					p.W242X		Atlas-SNP	.											.	TMEM38B	31	.	0			c.G725A						.						117.0	113.0	114.0					9																	108536210		2203	4300	6503	SO:0001587	stop_gained	55151	exon6			TGAGTTGGATGCT	BC031938	CCDS6768.1	9q31.3	2013-05-23	2004-12-21	2004-12-22	ENSG00000095209	ENSG00000095209			25535	protein-coding gene	gene with protein product		611236	"""chromosome 9 open reading frame 87"""	C9orf87		17611541, 23316006	Standard	NM_018112		Approved	FLJ10493, bA219P18.1, D4Ertd89e, TRIC-B	uc004bcu.2	Q9NVV0	OTTHUMG00000020429	ENST00000374692.3:c.725G>A	chr9.hg19:g.108536210G>A	ENSP00000363824:p.Trp242*	158.0	0.0		95.0	34.0	NM_018112	Q5JR63|Q5SVN5|Q5SVN6|Q5VTE2|Q6IA97	Nonsense_Mutation	SNP	ENST00000374692.3	hg19	CCDS6768.1	.	.	.	.	.	.	.	.	.	.	G	14.26	2.481203	0.44147	.	.	ENSG00000095209	ENST00000374692;ENST00000374688	.	.	.	4.81	4.81	0.61882	.	0.609679	0.17087	N	0.187523	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.38643	T	0.18	-3.5522	13.5504	0.61728	0.0:0.0:1.0:0.0	.	.	.	.	X	242;188	.	ENSP00000363820:W188X	W	+	2	0	TMEM38B	107576031	1.000000	0.71417	0.843000	0.33291	0.129000	0.20672	2.106000	0.41835	2.641000	0.89580	0.585000	0.79938	TGG	.	.		0.408	TMEM38B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053517.1	NM_018112	
SVEP1	79987	hgsc.bcm.edu	37	9	113312149	113312149	+	Missense_Mutation	SNP	G	G	C			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr9:113312149G>C	ENST00000401783.2	-	2	1103	c.767C>G	c.(766-768)gCt>gGt	p.A256G	SVEP1_ENST00000374469.1_Missense_Mutation_p.A233G|SVEP1_ENST00000374461.1_Missense_Mutation_p.A233G|SVEP1_ENST00000302728.8_Missense_Mutation_p.A256G|SVEP1_ENST00000467821.1_5'UTR	NM_153366.3	NP_699197.3	Q4LDE5	SVEP1_HUMAN	sushi, von Willebrand factor type A, EGF and pentraxin domain containing 1	256	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				cell adhesion (GO:0007155)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|chromatin binding (GO:0003682)			NS(1)|autonomic_ganglia(1)|breast(5)|central_nervous_system(1)|cervix(2)|endometrium(19)|kidney(8)|large_intestine(24)|lung(58)|ovary(7)|prostate(7)|skin(1)|stomach(4)|upper_aerodigestive_tract(5)|urinary_tract(4)	147						TGCCCGGCGAGCTAAAGCCTC	0.473																																					p.A256G		Atlas-SNP	.											.	SVEP1	326	.	0			c.C767G						.						66.0	62.0	63.0					9																	113312149		1920	4123	6043	SO:0001583	missense	79987	exon2			CGGCGAGCTAAAG	AK027870		9q31-q32	2008-02-05	2005-03-15	2005-03-17	ENSG00000165124	ENSG00000165124			15985	protein-coding gene	gene with protein product		611691	"""chromosome 9 open reading frame 13"""	C9orf13			Standard	NM_153366		Approved	bA427L11.3, POLYDOM, FLJ13529	uc010mtz.3	Q4LDE5	OTTHUMG00000020482	ENST00000401783.2:c.767C>G	chr9.hg19:g.113312149G>C	ENSP00000384917:p.Ala256Gly	171.0	0.0		83.0	16.0	NM_153366	Q0P675|Q5D213|Q5T938|Q5VTE4|Q5VTE5|Q7Z387|Q7Z3G3|Q8NBT9|Q96JU7|Q9H284|Q9H8J9	Missense_Mutation	SNP	ENST00000401783.2	hg19	CCDS48004.1	.	.	.	.	.	.	.	.	.	.	G	33	5.224356	0.95139	.	.	ENSG00000165124	ENST00000401783;ENST00000374469;ENST00000302728;ENST00000374461	T;T;T;T	0.78364	-1.17;-1.17;-1.17;-1.17	5.38	5.38	0.77491	von Willebrand factor, type A (2);	0.000000	0.85682	D	0.000000	D	0.88440	0.6437	M	0.75447	2.3	0.50467	D	0.999879	P;P;D	0.89917	0.892;0.928;1.0	P;P;D	0.83275	0.579;0.809;0.996	D	0.89042	0.3449	10	0.72032	D	0.01	.	19.497	0.95077	0.0:0.0:1.0:0.0	.	256;256;256	E9PBN8;Q4LDE5;Q4LDE5-2	.;SVEP1_HUMAN;.	G	256;233;256;233	ENSP00000384917:A256G;ENSP00000363593:A233G;ENSP00000304118:A256G;ENSP00000363585:A233G	ENSP00000304118:A256G	A	-	2	0	SVEP1	112351970	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.420000	0.97426	2.677000	0.91161	0.563000	0.77884	GCT	.	.		0.473	SVEP1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			
FAM78A	286336	hgsc.bcm.edu	37	9	134136583	134136583	+	Missense_Mutation	SNP	C	C	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr9:134136583C>T	ENST00000372271.3	-	2	845	c.478G>A	c.(478-480)Gac>Aac	p.D160N	FAM78A_ENST00000247295.4_5'UTR|FAM78A_ENST00000372269.3_Missense_Mutation_p.D157N	NM_033387.3	NP_203745.2	Q5JUQ0	FA78A_HUMAN	family with sequence similarity 78, member A	160										NS(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|skin(1)	9	all_hematologic(7;0.0028)	Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;2.15e-05)|Epithelial(140;0.000267)		TAAAAGTTGTCATTCATGCTG	0.582																																					p.D160N		Atlas-SNP	.											.	FAM78A	28	.	0			c.G478A						.						127.0	117.0	120.0					9																	134136583		2203	4300	6503	SO:0001583	missense	286336	exon2			AGTTGTCATTCAT	AK095423	CCDS6941.2	9q34	2008-02-05	2005-07-18	2005-07-18	ENSG00000126882	ENSG00000126882			25465	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 59"""	C9orf59		11214971	Standard	NM_033387		Approved	FLJ00024	uc004cak.3	Q5JUQ0	OTTHUMG00000020821	ENST00000372271.3:c.478G>A	chr9.hg19:g.134136583C>T	ENSP00000361345:p.Asp160Asn	57.0	0.0		30.0	7.0	NM_033387	Q86VQ9|Q9H7P4	Missense_Mutation	SNP	ENST00000372271.3	hg19	CCDS6941.2	.	.	.	.	.	.	.	.	.	.	C	27.4	4.828590	0.90955	.	.	ENSG00000126882	ENST00000372269;ENST00000372271;ENST00000464831	.	.	.	4.75	4.75	0.60458	.	0.000000	0.85682	D	0.000000	T	0.79233	0.4411	M	0.75777	2.31	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.83275	0.996;0.996	T	0.82364	-0.0494	9	0.87932	D	0	-41.4748	17.1064	0.86664	0.0:1.0:0.0:0.0	.	160;157	Q5JUQ0;Q5JUQ2	FA78A_HUMAN;.	N	157;160;129	.	ENSP00000361343:D157N	D	-	1	0	FAM78A	133126404	1.000000	0.71417	1.000000	0.80357	0.717000	0.41224	7.776000	0.85560	2.337000	0.79520	0.462000	0.41574	GAC	.	.		0.582	FAM78A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054720.1	NM_033387	
RET	5979	hgsc.bcm.edu	37	10	43600449	43600449	+	Silent	SNP	G	G	A			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr10:43600449G>A	ENST00000355710.3	+	4	907	c.675G>A	c.(673-675)acG>acA	p.T225T	RET_ENST00000340058.5_Silent_p.T225T	NM_020975.4	NP_066124.1	P07949	RET_HUMAN	ret proto-oncogene	225	Cadherin. {ECO:0000255|PROSITE- ProRule:PRU00043}.				activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|cellular response to retinoic acid (GO:0071300)|embryonic epithelial tube formation (GO:0001838)|enteric nervous system development (GO:0048484)|homophilic cell adhesion (GO:0007156)|innervation (GO:0060384)|lymphocyte migration into lymphoid organs (GO:0097021)|MAPK cascade (GO:0000165)|membrane protein proteolysis (GO:0033619)|neural crest cell migration (GO:0001755)|neuron cell-cell adhesion (GO:0007158)|neuron maturation (GO:0042551)|peptidyl-tyrosine phosphorylation (GO:0018108)|Peyer's patch morphogenesis (GO:0061146)|positive regulation of cell adhesion mediated by integrin (GO:0033630)|positive regulation of cell migration (GO:0030335)|positive regulation of cell size (GO:0045793)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of metanephric glomerulus development (GO:0072300)|positive regulation of neuron maturation (GO:0014042)|positive regulation of neuron projection development (GO:0010976)|positive regulation of transcription, DNA-templated (GO:0045893)|posterior midgut development (GO:0007497)|protein phosphorylation (GO:0006468)|regulation of axonogenesis (GO:0050770)|regulation of cell adhesion (GO:0030155)|response to drug (GO:0042493)|response to pain (GO:0048265)|retina development in camera-type eye (GO:0060041)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|ureter maturation (GO:0035799)|ureteric bud development (GO:0001657)	endosome membrane (GO:0010008)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|protein tyrosine kinase activity (GO:0004713)|receptor activity (GO:0004872)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)		CCDC6/RET(4)|KIF5B/RET(79)	NS(2)|adrenal_gland(26)|breast(5)|central_nervous_system(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(7)|kidney(2)|large_intestine(14)|lung(27)|ovary(5)|prostate(3)|skin(1)|thyroid(504)|upper_aerodigestive_tract(1)|urinary_tract(1)	607		Ovarian(717;0.0423)			Cabozantinib(DB08875)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sorafenib(DB00398)	AGGTGAGCACGCGCTGGGCCC	0.731		1	"""T, Mis, N, F"""	"""H4, PRKAR1A, NCOA4, PCM1, GOLGA5, TRIM33, KTN1, TRIM27, HOOK3, KIF5B, CCDC6"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma, NSCLC"""	"""medullary thyroid,  papillary thyroid, pheochromocytoma"""	Hirschsprung disease		Multiple Endocrine Neoplasia, type 2B;Multiple Endocrine Neoplasia, type 2A;Familial Medullary Thyroid Carcinoma																												p.T225T	Melanoma(102;360 522 3376 9752 9881 14372 17251 18341 20876 24662 34807 43144 48149)	Atlas-SNP	.	yes	Dom	yes	Multiple endocrine neoplasia 2A/2B	10	10q11.2	5979	ret proto-oncogene	yes	"""E, O"""	.	RET	916	.	0			c.G675A						.						22.0	21.0	22.0					10																	43600449		2192	4283	6475	SO:0001819	synonymous_variant	5979	exon4	Familial Cancer Database	MEN2B, Wagenmann-Froboese s.;MEN2A, Sipple disease, incl MEN2C;FMTC	GAGCACGCGCTGG	BC004257	CCDS7200.1, CCDS53525.1	10q11.2	2014-09-17	2007-02-16		ENSG00000165731	ENSG00000165731		"""Cadherins / Cadherin-related"""	9967	protein-coding gene	gene with protein product	"""cadherin-related family member 16"""	164761	"""multiple endocrine neoplasia and medullary thyroid carcinoma 1"", ""Hirschsprung disease 1"""	HSCR1, MEN2A, MTC1, MEN2B		2687772, 1611909	Standard	NM_020975		Approved	PTC, CDHF12, RET51, CDHR16	uc001jal.3	P07949	OTTHUMG00000018024	ENST00000355710.3:c.675G>A	chr10.hg19:g.43600449G>A		59.0	0.0		40.0	13.0	NM_020630	A8K6Z2|Q15250|Q9BTB0|Q9H4A2	Silent	SNP	ENST00000355710.3	hg19	CCDS7200.1																																																																																			.	.		0.731	RET-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000047694.2	NM_020975	
RBP3	5949	hgsc.bcm.edu	37	10	48389747	48389747	+	Silent	SNP	C	C	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr10:48389747C>T	ENST00000224600.4	-	1	1244	c.1131G>A	c.(1129-1131)caG>caA	p.Q377Q	AL731561.2_ENST00000581861.1_RNA	NM_002900.2	NP_002891.1	P10745	RET3_HUMAN	retinol binding protein 3, interstitial	377	4 X approximate tandem repeats.				lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|transport (GO:0006810)|visual perception (GO:0007601)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|interphotoreceptor matrix (GO:0033165)|vesicle (GO:0031982)	retinal binding (GO:0016918)|retinoid binding (GO:0005501)|retinol binding (GO:0019841)|serine-type peptidase activity (GO:0008236)			central_nervous_system(3)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(8)|lung(30)|ovary(1)|prostate(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	59					Vitamin A(DB00162)	CAGACGCAGCCTGCAGGCCGG	0.652																																					p.Q377Q		Atlas-SNP	.											.	RBP3	152	.	0			c.G1131A						.						33.0	36.0	35.0					10																	48389747		2202	4300	6502	SO:0001819	synonymous_variant	5949	exon1			CGCAGCCTGCAGG	M22453	CCDS73119.1	10q11.2	2014-05-06	2001-11-28		ENSG00000107618	ENSG00000265203			9921	protein-coding gene	gene with protein product		180290	"""retinol-binding protein 3, interstitial"""				Standard	NM_002900		Approved	D10S64, D10S65, D10S66, RP66	uc001jez.3	P10745	OTTHUMG00000188321	ENST00000224600.4:c.1131G>A	chr10.hg19:g.48389747C>T		57.0	0.0		41.0	15.0	NM_002900	Q0QD34|Q5VSR0|Q8IXN0	Silent	SNP	ENST00000224600.4	hg19	CCDS7218.1																																																																																			.	.		0.652	RBP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047888.1	NM_002900	
CTSD	1509	hgsc.bcm.edu	37	11	1778644	1778644	+	Missense_Mutation	SNP	C	C	T	rs371522391		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr11:1778644C>T	ENST00000236671.2	-	5	746	c.614G>A	c.(613-615)cGc>cAc	p.R205H	RP11-295K3.1_ENST00000427721.1_Missense_Mutation_p.A76T|AC068580.6_ENST00000449248.1_RNA	NM_001909.4	NP_001900.1	P07339	CATD_HUMAN	cathepsin D	205					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|autophagic vacuole assembly (GO:0000045)|cell death (GO:0008219)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)|lysosome (GO:0005764)|mitochondrion (GO:0005739)	aspartic-type endopeptidase activity (GO:0004190)			endometrium(1)|large_intestine(4)|lung(8)	13		all_epithelial(84;0.00018)|Ovarian(85;0.0014)|Breast(177;0.00147)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00136)|Lung(200;0.0684)|LUSC - Lung squamous cell carcinoma(625;0.0822)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	GACGGAGATGCGGGGGTAGGC	0.587																																					p.R205H		Atlas-SNP	.											.	CTSD	26	.	0			c.G614A						.	C	HIS/ARG	1,4403	2.1+/-5.4	0,1,2201	194.0	126.0	149.0		614	-2.9	1.0	11		149	0,8598		0,0,4299	no	missense	CTSD	NM_001909.4	29	0,1,6500	TT,TC,CC		0.0,0.0227,0.0077	benign	205/413	1778644	1,13001	2202	4299	6501	SO:0001583	missense	1509	exon5			GAGATGCGGGGGT	M11233	CCDS7725.1	11p15.5	2009-06-26	2006-12-05		ENSG00000117984	ENSG00000117984	3.4.23.5	"""Cathepsins"""	2529	protein-coding gene	gene with protein product	"""ceroid-lipofuscinosis, neuronal 10"""	116840	"""cathepsin D (lysosomal aspartyl protease)"""	CPSD		3927292	Standard	NM_001909		Approved	CLN10	uc001luc.2	P07339	OTTHUMG00000044760	ENST00000236671.2:c.614G>A	chr11.hg19:g.1778644C>T	ENSP00000236671:p.Arg205His	61.0	0.0		68.0	34.0	NM_001909	Q6IB57	Missense_Mutation	SNP	ENST00000236671.2	hg19	CCDS7725.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	c|c	14.78|14.78	2.637977|2.637977	0.47153|0.47153	2.27E-4|2.27E-4	0.0|0.0	ENSG00000250644|ENSG00000117984	ENST00000427721|ENST00000236671;ENST00000438213;ENST00000367196	.|T;T;T	.|0.58358	.|0.34;0.34;0.38	4.11|4.11	-2.92|-2.92	0.05615|0.05615	.|Peptidase aspartic (1);Peptidase aspartic, catalytic (1);	.|0.778438	.|0.12176	.|N	.|0.492528	T|T	0.38026|0.38026	0.1025|0.1025	L|L	0.56280|0.56280	1.765|1.765	0.26796|0.26796	N|N	0.969301|0.969301	.|B	.|0.23249	.|0.082	.|B	.|0.13407	.|0.009	T|T	0.28073|0.28073	-1.0055|-1.0055	5|10	.|0.39692	.|T	.|0.17	.|.	3.7053|3.7053	0.08398|0.08398	0.3688:0.2628:0.0:0.3683|0.3688:0.2628:0.0:0.3683	.|.	.|205	.|P07339	.|CATD_HUMAN	T|H	76|205;190;170	.|ENSP00000236671:R205H;ENSP00000415036:R190H;ENSP00000356164:R170H	.|ENSP00000236671:R205H	A|R	-|-	1|2	0|0	RP11-295K3.1|CTSD	1735220|1735220	0.010000|0.010000	0.17322|0.17322	0.960000|0.960000	0.40013|0.40013	0.752000|0.752000	0.42762|0.42762	-0.155000|-0.155000	0.10115|0.10115	-0.137000|-0.137000	0.11455|0.11455	0.472000|0.472000	0.43445|0.43445	GCA|CGC	.	.		0.587	CTSD-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000104272.5	NM_001909	
OR52N4	390072	hgsc.bcm.edu	37	11	5776243	5776243	+	Silent	SNP	C	C	G			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr11:5776243C>G	ENST00000317254.3	+	1	321	c.273C>G	c.(271-273)ctC>ctG	p.L91L	TRIM5_ENST00000380027.1_Intron	NM_001005175.2	NP_001005175.3	Q8NGI2	O52N4_HUMAN	olfactory receptor, family 52, subfamily N, member 4 (gene/pseudogene)	91						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	26		Medulloblastoma(188;0.0075)|all_neural(188;0.0577)|Breast(177;0.086)		Epithelial(150;1.87e-10)|LUSC - Lung squamous cell carcinoma(625;0.114)|BRCA - Breast invasive adenocarcinoma(625;0.135)|Lung(200;0.197)		GGTTTCATCTCAAGGACATTG	0.468																																					p.L91L		Atlas-SNP	.											OR52N4,right_upper_lobe,carcinoma,0,1	OR52N4	55	.	0			c.C273G						.						145.0	148.0	147.0					11																	5776243		2201	4297	6498	SO:0001819	synonymous_variant	390072	exon1			TCATCTCAAGGAC	AB065813	CCDS44528.1	11p15.4	2013-10-10	2013-10-10		ENSG00000181074	ENSG00000181074		"""GPCR / Class A : Olfactory receptors"""	15230	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily N, member 4"""				Standard	NM_001005175		Approved		uc001mbu.3	Q8NGI2	OTTHUMG00000066887	ENST00000317254.3:c.273C>G	chr11.hg19:g.5776243C>G		123.0	0.0		74.0	12.0	NM_001005175	B2RNP8|Q6IF77	Silent	SNP	ENST00000317254.3	hg19	CCDS44528.1																																																																																			.	.		0.468	OR52N4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000143350.1	NM_001005175	
NRXN2	9379	hgsc.bcm.edu	37	11	64434901	64434901	+	Missense_Mutation	SNP	C	C	A	rs143130600		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr11:64434901C>A	ENST00000377551.1	-	8	1830	c.1619G>T	c.(1618-1620)gGt>gTt	p.G540V	NRXN2_ENST00000377559.3_Missense_Mutation_p.G509V|NRXN2_ENST00000409571.1_Missense_Mutation_p.G533V|NRXN2_ENST00000265459.6_Missense_Mutation_p.G540V			Q9P2S2	NRX2A_HUMAN	neurexin 2	540	Laminin G-like 3. {ECO:0000255|PROSITE- ProRule:PRU00122}.				adult behavior (GO:0030534)|gephyrin clustering (GO:0097116)|neuroligin clustering (GO:0097118)|neuron cell-cell adhesion (GO:0007158)|neurotransmitter secretion (GO:0007269)|postsynaptic density protein 95 clustering (GO:0097119)|postsynaptic membrane assembly (GO:0097104)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|vocal learning (GO:0042297)|vocalization behavior (GO:0071625)	integral component of membrane (GO:0016021)	calcium channel regulator activity (GO:0005246)|cell adhesion molecule binding (GO:0050839)|metal ion binding (GO:0046872)|neuroligin family protein binding (GO:0097109)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(6)|liver(1)|lung(34)|ovary(6)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(6)|urinary_tract(1)	71						GCCAGCTCCACCCCCAGCCCG	0.657																																					p.G540V		Atlas-SNP	.											.	NRXN2	247	.	0			c.G1619T						.						49.0	52.0	51.0					11																	64434901		2201	4297	6498	SO:0001583	missense	9379	exon9			GCTCCACCCCCAG		CCDS8077.1, CCDS31597.1, CCDS8078.1	11q13	2008-07-18			ENSG00000110076	ENSG00000110076			8009	protein-coding gene	gene with protein product	"""neurexin II"""	600566				1621094	Standard	NM_015080		Approved		uc021qkw.1	P58401	OTTHUMG00000045214	ENST00000377551.1:c.1619G>T	chr11.hg19:g.64434901C>A	ENSP00000366774:p.Gly540Val	81.0	0.0		49.0	11.0	NM_015080	A7E2C1|Q9Y2D6	Missense_Mutation	SNP	ENST00000377551.1	hg19	CCDS8077.1	.	.	.	.	.	.	.	.	.	.	C	4.594	0.110325	0.08780	.	.	ENSG00000110076	ENST00000377551;ENST00000377559;ENST00000265459;ENST00000345863;ENST00000409571	T;T;T;T	0.62788	0.0;0.12;0.0;0.12	4.3	-1.63	0.08345	Concanavalin A-like lectin/glucanase (1);Concanavalin A-like lectin/glucanase, subgroup (1);Laminin G domain (2);Laminin G, subdomain 2 (1);	1.182110	0.06903	N	0.806307	T	0.38081	0.1027	N	0.03608	-0.345	0.09310	N	0.999998	B;B;B	0.28605	0.217;0.008;0.0	B;B;B	0.31946	0.138;0.065;0.002	T	0.37267	-0.9713	10	0.52906	T	0.07	.	7.6893	0.28559	0.1966:0.5605:0.2429:0.0	.	509;540;286	Q9P2S2-2;Q9P2S2;E7EV67	.;NRX2A_HUMAN;.	V	540;509;540;509;533	ENSP00000366774:G540V;ENSP00000366782:G509V;ENSP00000265459:G540V;ENSP00000386416:G533V	ENSP00000265459:G540V	G	-	2	0	NRXN2	64191477	0.000000	0.05858	0.042000	0.18584	0.282000	0.26991	0.093000	0.15086	-0.128000	0.11641	-0.502000	0.04539	GGT	.	C|1.000;T|0.000		0.657	NRXN2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104967.3	NM_015080	
NLRX1	79671	hgsc.bcm.edu	37	11	119052990	119052990	+	Missense_Mutation	SNP	G	G	A			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr11:119052990G>A	ENST00000409109.1	+	9	3129	c.2542G>A	c.(2542-2544)Ggt>Agt	p.G848S	NLRX1_ENST00000525863.1_Missense_Mutation_p.G848S|NLRX1_ENST00000409265.4_Missense_Mutation_p.G848S|NLRX1_ENST00000292199.2_Missense_Mutation_p.G848S|NLRX1_ENST00000409991.1_Missense_Mutation_p.G848S	NM_001282144.1	NP_001269073.1	Q86UT6	NLRX1_HUMAN	NLR family member X1	848	Required for the repression of MAVS- induced interferon signaling.				innate immune response (GO:0045087)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of inflammatory response (GO:0050728)|negative regulation of innate immune response (GO:0045824)|negative regulation of interferon-beta production (GO:0032688)|negative regulation of interleukin-6 production (GO:0032715)|negative regulation of RIG-I signaling pathway (GO:0039536)|negative regulation of type I interferon production (GO:0032480)|viral process (GO:0016032)	mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)			cervix(1)|endometrium(2)|kidney(2)|lung(10)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	22	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.7e-05)		CAACGGTGCTGGTGACACAGC	0.682																																					p.G848S		Atlas-SNP	.											.	NLRX1	128	.	0			c.G2542A						.						60.0	63.0	62.0					11																	119052990		2200	4295	6495	SO:0001583	missense	79671	exon9			GGTGCTGGTGACA	AB094095	CCDS8416.1	11q23.3	2007-02-07			ENSG00000160703	ENSG00000160703		"""Nucleotide-binding domain and leucine rich repeat containing"""	29890	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat containing X1"", ""NOD-like receptor X1"", ""NLR family, X1"""	611947				12766759	Standard	XM_005271669		Approved	NOD9, CLR11.3	uc001pvw.3	Q86UT6	OTTHUMG00000154476	ENST00000409109.1:c.2542G>A	chr11.hg19:g.119052990G>A	ENSP00000387334:p.Gly848Ser	56.0	0.0		25.0	7.0	NM_024618	A8K6Q1|B3KPK2|B3KTA2|Q7RTR3|Q96D51|Q9H724	Missense_Mutation	SNP	ENST00000409109.1	hg19	CCDS8416.1	.	.	.	.	.	.	.	.	.	.	G	14.71	2.617421	0.46736	.	.	ENSG00000160703	ENST00000409991;ENST00000292199;ENST00000409265;ENST00000409109;ENST00000525863	T;T;T;T;T	0.53206	0.63;0.63;0.63;0.63;0.63	4.52	2.58	0.30949	.	0.216054	0.37012	N	0.002285	T	0.46908	0.1417	L	0.55743	1.74	0.21416	N	0.999691	D;B	0.55800	0.973;0.386	P;B	0.53593	0.73;0.079	T	0.26780	-1.0093	10	0.33940	T	0.23	.	3.9576	0.09396	0.312:0.188:0.5:0.0	.	848;848	Q86UT6-2;Q86UT6	.;NLRX1_HUMAN	S	848	ENSP00000386851:G848S;ENSP00000292199:G848S;ENSP00000386858:G848S;ENSP00000387334:G848S;ENSP00000433442:G848S	ENSP00000292199:G848S	G	+	1	0	NLRX1	118558200	1.000000	0.71417	0.631000	0.29282	0.912000	0.54170	2.704000	0.47118	1.131000	0.42111	0.407000	0.27541	GGT	.	.		0.682	NLRX1-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335403.1	NM_170722	
EEA1	8411	hgsc.bcm.edu	37	12	93205205	93205205	+	Silent	SNP	T	T	C			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr12:93205205T>C	ENST00000322349.8	-	17	2313	c.2049A>G	c.(2047-2049)ttA>ttG	p.L683L		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	683	Gln/Glu/Lys-rich.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						TAATCTTATTTAACTCCTTTA	0.313																																					p.L683L		Atlas-SNP	.											.	EEA1	104	.	0			c.A2049G						.						51.0	51.0	51.0					12																	93205205		2201	4298	6499	SO:0001819	synonymous_variant	8411	exon17			CTTATTTAACTCC	L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"""Zinc fingers, FYVE domain containing"""	3185	protein-coding gene	gene with protein product		605070	"""early endosome antigen 1, 162kD"""			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.2049A>G	chr12.hg19:g.93205205T>C		48.0	0.0		43.0	11.0	NM_003566	Q14221	Silent	SNP	ENST00000322349.8	hg19	CCDS31874.1																																																																																			.	.		0.313	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1	NM_003566	
MAP4K5	11183	hgsc.bcm.edu	37	14	50911780	50911780	+	Missense_Mutation	SNP	C	C	A			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr14:50911780C>A	ENST00000013125.4	-	18	1636	c.1318G>T	c.(1318-1320)Gtg>Ttg	p.V440L		NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	440					activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					GTCTCTGCCACAGGCCCACAA	0.423																																					p.V440L		Atlas-SNP	.											.	MAP4K5	48	.	0			c.G1318T						.						100.0	94.0	96.0					14																	50911780		1856	4092	5948	SO:0001583	missense	11183	exon18			CTGCCACAGGCCC	U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6867	protein-coding gene	gene with protein product	"""germinal center kinase-related"""	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.1318G>T	chr14.hg19:g.50911780C>A	ENSP00000013125:p.Val440Leu	122.0	0.0		73.0	16.0	NM_006575	Q8IYF6	Missense_Mutation	SNP	ENST00000013125.4	hg19		.	.	.	.	.	.	.	.	.	.	C	7.563	0.665175	0.14710	.	.	ENSG00000012983	ENST00000013125	T	0.13538	2.58	5.39	0.0837	0.14434	Protein kinase-like domain (1);	1.242570	0.05155	N	0.496721	T	0.05502	0.0145	N	0.08118	0	0.09310	N	1	B;B;B	0.14438	0.01;0.008;0.01	B;B;B	0.10450	0.004;0.005;0.002	T	0.35724	-0.9777	10	0.08381	T	0.77	.	1.8258	0.03120	0.1142:0.3798:0.2568:0.2492	.	114;440;440	B3KWC4;B2R928;Q9Y4K4	.;.;M4K5_HUMAN	L	440	ENSP00000013125:V440L	ENSP00000013125:V440L	V	-	1	0	MAP4K5	49981530	0.506000	0.26139	0.469000	0.27204	0.924000	0.55760	0.366000	0.20365	-0.003000	0.14444	-0.152000	0.13540	GTG	.	.		0.423	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1	NM_006575	
CYLD	1540	hgsc.bcm.edu	37	16	50815217	50815217	+	Missense_Mutation	SNP	G	G	A			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr16:50815217G>A	ENST00000427738.3	+	9	1784	c.1579G>A	c.(1579-1581)Gcc>Acc	p.A527T	CYLD_ENST00000566206.1_Missense_Mutation_p.A524T|CYLD_ENST00000569418.1_Missense_Mutation_p.A524T|RP11-327F22.4_ENST00000564510.1_RNA|CYLD_ENST00000564326.1_Missense_Mutation_p.A524T|CYLD_ENST00000311559.9_Missense_Mutation_p.A527T|CYLD_ENST00000568704.2_Intron|CYLD_ENST00000398568.2_Missense_Mutation_p.A524T|CYLD_ENST00000540145.1_Missense_Mutation_p.A527T|RP11-327F22.4_ENST00000575917.1_RNA			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	527	CAP-Gly 3. {ECO:0000255|PROSITE- ProRule:PRU00045}.|Interaction with IKBKG/NEMO.|Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				TTTCACCTGTGCCCTGAAGAA	0.483			"""Mis, N, F, S"""		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																												p.A527T		Atlas-SNP	.	yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	.	CYLD	150	.	0			c.G1579A						.						102.0	98.0	100.0					16																	50815217		1932	4141	6073	SO:0001583	missense	1540	exon11	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	ACCTGTGCCCTGA	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"""ubiquitin specific peptidase like 2"""	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.1579G>A	chr16.hg19:g.50815217G>A	ENSP00000392025:p.Ala527Thr	105.0	0.0		55.0	17.0	NM_015247	O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	hg19	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.174382	0.57692	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	T;T;T	0.74526	-0.85;-0.85;-0.85	6.02	6.02	0.97574	Cytoskeleton-associated protein, Gly-rich domain (4);	0.046658	0.85682	D	0.000000	T	0.76169	0.3950	L	0.28014	0.82	0.58432	D	0.999997	D;D;P;P	0.59767	0.98;0.986;0.867;0.891	P;P;B;B	0.58721	0.818;0.844;0.288;0.412	T	0.69323	-0.5175	10	0.16896	T	0.51	-5.9624	20.5407	0.99260	0.0:0.0:1.0:0.0	.	524;527;524;527	A8KAB0;F5H2R7;Q9NQC7-2;Q9NQC7	.;.;.;CYLD_HUMAN	T	527;527;524;524	ENSP00000445447:A527T;ENSP00000308928:A527T;ENSP00000381574:A524T	ENSP00000308928:A527T	A	+	1	0	CYLD	49372718	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	6.934000	0.75880	2.865000	0.98341	0.655000	0.94253	GCC	.	.		0.483	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2		
TAF1C	9013	hgsc.bcm.edu	37	16	84214736	84214736	+	Missense_Mutation	SNP	C	C	A			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr16:84214736C>A	ENST00000567759.1	-	11	1481	c.1299G>T	c.(1297-1299)caG>caT	p.Q433H	TAF1C_ENST00000341690.6_Missense_Mutation_p.Q340H|TAF1C_ENST00000541676.1_Missense_Mutation_p.Q340H|TAF1C_ENST00000378541.4_Missense_Mutation_p.Q433H|TAF1C_ENST00000570117.1_Missense_Mutation_p.Q101H|TAF1C_ENST00000566732.1_Missense_Mutation_p.Q407H	NM_005679.3	NP_005670	Q15572	TAF1C_HUMAN	TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kDa	433					gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of RNA polymerase I transcription (GO:0006363)|transcription elongation from RNA polymerase I promoter (GO:0006362)|transcription from RNA polymerase I promoter (GO:0006360)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase I promoter (GO:0006361)	nucleoplasm (GO:0005654)	DNA binding (GO:0003677)			endometrium(1)|kidney(3)|large_intestine(3)|lung(11)|ovary(3)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)	26						GTTCCCCTTTCTGGCACGAAG	0.612																																					p.Q433H		Atlas-SNP	.											.	TAF1C	60	.	0			c.G1299T						.						84.0	87.0	86.0					16																	84214736		2200	4300	6500	SO:0001583	missense	9013	exon11			CCCTTTCTGGCAC	L39059	CCDS32496.1, CCDS45535.1, CCDS58488.1, CCDS58489.1	16q24	2008-02-05	2002-08-29			ENSG00000103168			11534	protein-coding gene	gene with protein product		604905	"""TATA box binding protein (TBP)-associated factor, RNA polymerase I, C, 110kD"""			7801123	Standard	NM_005679		Approved	TAFI110, TAFI95, SL1, MGC:39976	uc010vnx.2	Q15572		ENST00000567759.1:c.1299G>T	chr16.hg19:g.84214736C>A	ENSP00000455265:p.Gln433His	114.0	0.0		54.0	28.0	NM_005679	B7Z5K5|B7Z5S4|B7Z908|B7Z9L7|Q59F67|Q8N6V3	Missense_Mutation	SNP	ENST00000567759.1	hg19	CCDS32496.1	.	.	.	.	.	.	.	.	.	.	C	9.568	1.120224	0.20877	.	.	ENSG00000103168	ENST00000378541;ENST00000541676;ENST00000341690	T;T;T	0.62498	0.02;0.02;0.02	4.56	3.61	0.41365	.	0.115077	0.38436	N	0.001681	T	0.74313	0.3700	M	0.70595	2.14	0.31335	N	0.684381	D;D;D	0.76494	0.997;0.999;0.997	D;D;D	0.85130	0.995;0.997;0.995	T	0.75476	-0.3304	10	0.59425	D	0.04	-29.1612	8.6093	0.33793	0.0:0.8957:0.0:0.1043	.	407;433;340	Q15572-6;Q15572;Q15572-2	.;TAF1C_HUMAN;.	H	433;340;340	ENSP00000367802:Q433H;ENSP00000437900:Q340H;ENSP00000345305:Q340H	ENSP00000345305:Q340H	Q	-	3	2	TAF1C	82772237	1.000000	0.71417	1.000000	0.80357	0.099000	0.18886	1.118000	0.31246	1.141000	0.42275	-0.137000	0.14449	CAG	.	.		0.612	TAF1C-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000433045.2	NM_139353	
FASN	2194	hgsc.bcm.edu	37	17	80051623	80051623	+	Missense_Mutation	SNP	C	C	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr17:80051623C>T	ENST00000306749.2	-	4	523	c.305G>A	c.(304-306)gGa>gAa	p.G102E		NM_004104.4	NP_004095.4	P49327	FAS_HUMAN	fatty acid synthase	102	Beta-ketoacyl synthase. {ECO:0000250}.				acetyl-CoA metabolic process (GO:0006084)|cellular lipid metabolic process (GO:0044255)|cellular response to interleukin-4 (GO:0071353)|energy reserve metabolic process (GO:0006112)|fatty acid biosynthetic process (GO:0006633)|fatty acid metabolic process (GO:0006631)|long-chain fatty-acyl-CoA biosynthetic process (GO:0035338)|osteoblast differentiation (GO:0001649)|pantothenate metabolic process (GO:0015939)|positive regulation of cellular metabolic process (GO:0031325)|small molecule metabolic process (GO:0044281)|triglyceride biosynthetic process (GO:0019432)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|glycogen granule (GO:0042587)|Golgi apparatus (GO:0005794)|membrane (GO:0016020)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	3-hydroxyoctanoyl-[acyl-carrier-protein] dehydratase activity (GO:0047451)|3-hydroxypalmitoyl-[acyl-carrier-protein] dehydratase activity (GO:0004317)|3-oxoacyl-[acyl-carrier-protein] reductase (NADPH) activity (GO:0004316)|3-oxoacyl-[acyl-carrier-protein] synthase activity (GO:0004315)|[acyl-carrier-protein] S-acetyltransferase activity (GO:0004313)|[acyl-carrier-protein] S-malonyltransferase activity (GO:0004314)|drug binding (GO:0008144)|enoyl-[acyl-carrier-protein] reductase (NADPH, A-specific) activity (GO:0047117)|enoyl-[acyl-carrier-protein] reductase (NADPH, B-specific) activity (GO:0004319)|fatty acid synthase activity (GO:0004312)|myristoyl-[acyl-carrier-protein] hydrolase activity (GO:0016295)|NADPH binding (GO:0070402)|oleoyl-[acyl-carrier-protein] hydrolase activity (GO:0004320)|palmitoyl-[acyl-carrier-protein] hydrolase activity (GO:0016296)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)			central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(12)|prostate(3)|skin(2)|urinary_tract(1)	34	all_neural(118;0.0878)|Ovarian(332;0.227)|all_lung(278;0.246)		OV - Ovarian serous cystadenocarcinoma(97;0.0211)|BRCA - Breast invasive adenocarcinoma(99;0.0237)		Cerulenin(DB01034)|Orlistat(DB01083)	AGTGTGTGTTCCTCGGAGTGA	0.677																																					p.G102E	Colon(59;314 1043 11189 28578 32273)	Atlas-SNP	.											.	FASN	154	.	0			c.G305A						.						55.0	51.0	53.0					17																	80051623		2200	4295	6495	SO:0001583	missense	2194	exon4			TGTGTTCCTCGGA	U26644	CCDS11801.1	17q25	2012-01-31			ENSG00000169710	ENSG00000169710	2.3.1.85	"""Short chain dehydrogenase/reductase superfamily / Atypical members"""	3594	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 27X, member 1"""	600212				7835891, 7567999, 19027726	Standard	NM_004104		Approved	FAS, SDR27X1	uc002kdu.3	P49327		ENST00000306749.2:c.305G>A	chr17.hg19:g.80051623C>T	ENSP00000304592:p.Gly102Glu	45.0	0.0		68.0	40.0	NM_004104	Q13479|Q16702|Q4LE83|Q6P4U5|Q6SS02|Q969R1|Q96C68|Q96IT0	Missense_Mutation	SNP	ENST00000306749.2	hg19	CCDS11801.1	.	.	.	.	.	.	.	.	.	.	C	24.3	4.518479	0.85495	.	.	ENSG00000169710	ENST00000306749	T	0.38077	1.16	4.38	4.38	0.52667	Beta-ketoacyl synthase, N-terminal (1);Thiolase-like, subgroup (1);Thiolase-like (1);	0.066543	0.64402	D	0.000014	T	0.63885	0.2549	M	0.82517	2.595	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.71873	-0.4461	10	0.87932	D	0	-42.0902	16.5418	0.84386	0.0:1.0:0.0:0.0	.	102	P49327	FAS_HUMAN	E	102	ENSP00000304592:G102E	ENSP00000304592:G102E	G	-	2	0	FASN	77644912	1.000000	0.71417	0.381000	0.26106	0.805000	0.45488	5.836000	0.69375	2.006000	0.58801	0.561000	0.74099	GGA	.	.		0.677	FASN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000442369.1	NM_004104	
FOXK2	3607	hgsc.bcm.edu	37	17	80477826	80477826	+	Missense_Mutation	SNP	G	G	C			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr17:80477826G>C	ENST00000335255.5	+	1	236	c.62G>C	c.(61-63)gGg>gCg	p.G21A		NM_004514.3	NP_004505.2	Q01167	FOXK2_HUMAN	forkhead box K2	21	Gly-rich.			AAAAALSGAGTPPAGGGAGGGGAGGGGSPPGGWAVARLEGR EFEYLMKKRSVTIGRNSSQGSVDVSMGHSSFISRRHLEIFT PPGGGGHGGAAPELPPAQPRPDAGGDFYLRCLGKNG -> Q (in Ref. 1; CAA43200). {ECO:0000305}.	positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)	intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	magnesium ion binding (GO:0000287)|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 (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(5)|prostate(1)|urinary_tract(1)	17	Breast(20;0.00106)|all_neural(118;0.0952)		OV - Ovarian serous cystadenocarcinoma(97;0.0371)|BRCA - Breast invasive adenocarcinoma(99;0.0415)			ggcggggccgggggcggcggg	0.846																																					p.G21A		Atlas-SNP	.											FOXK2,NS,carcinoma,0,1	FOXK2	46	.	0			c.G62C						.						1.0	1.0	1.0					17																	80477826		122	223	345	SO:0001583	missense	3607	exon1			GGGCCGGGGGCGG	U58196	CCDS11813.1	17q25	2006-12-15	2004-03-09	2004-03-10	ENSG00000141568	ENSG00000141568		"""Forkhead boxes"""	6036	protein-coding gene	gene with protein product		147685	"""interleukin enhancer binding factor 1"""	ILF, ILF1		3260003	Standard	NM_004514		Approved		uc002kfn.3	Q01167	OTTHUMG00000140374	ENST00000335255.5:c.62G>C	chr17.hg19:g.80477826G>C	ENSP00000335677:p.Gly21Ala	1.0	0.0		4.0	2.0	NM_004514	A6NEP5|Q13622|Q13623|Q13624	Missense_Mutation	SNP	ENST00000335255.5	hg19	CCDS11813.1	.	.	.	.	.	.	.	.	.	.	.	2.177	-0.388435	0.04932	.	.	ENSG00000141568	ENST00000335255;ENST00000335241	D	0.93076	-3.16	1.8	1.8	0.24995	.	.	.	.	.	D	0.89375	0.6697	N	0.08118	0	0.25222	N	0.98989	D;D;D	0.71674	0.998;0.996;0.998	D;D;D	0.68621	0.959;0.91;0.959	T	0.80350	-0.1419	9	0.14252	T	0.57	.	6.724	0.23346	0.0:0.0:1.0:0.0	.	21;21;21	Q01167-3;Q01167;Q01167-2	.;FOXK2_HUMAN;.	A	21	ENSP00000335677:G21A	ENSP00000334321:G21A	G	+	2	0	FOXK2	78071115	0.917000	0.31117	0.403000	0.26384	0.773000	0.43773	0.923000	0.28757	0.820000	0.34516	0.486000	0.48141	GGG	.	.		0.846	FOXK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000277099.2	NM_181430	
LAMA1	284217	hgsc.bcm.edu	37	18	7002349	7002349	+	Silent	SNP	A	A	G			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr18:7002349A>G	ENST00000389658.3	-	30	4389	c.4296T>C	c.(4294-4296)gaT>gaC	p.D1432D		NM_005559.3	NP_005550.2	P25391	LAMA1_HUMAN	laminin, alpha 1	1432	Laminin EGF-like 15. {ECO:0000255|PROSITE-ProRule:PRU00460}.				axon guidance (GO:0007411)|branching involved in salivary gland morphogenesis (GO:0060445)|cell adhesion (GO:0007155)|cell surface receptor signaling pathway (GO:0007166)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|establishment of epithelial cell apical/basal polarity (GO:0045198)|extracellular matrix organization (GO:0030198)|morphogenesis of an epithelial sheet (GO:0002011)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of embryonic development (GO:0045995)|retinal blood vessel morphogenesis (GO:0061304)	basement membrane (GO:0005604)|cell-cell junction (GO:0005911)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|laminin-1 complex (GO:0005606)|laminin-3 complex (GO:0005608)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|glycosphingolipid binding (GO:0043208)			NS(4)|breast(7)|central_nervous_system(3)|cervix(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(49)|liver(1)|lung(71)|ovary(9)|pancreas(3)|prostate(5)|skin(11)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(3)	205		Colorectal(10;0.172)				AAGTACACACATCACAATGGT	0.507																																					p.D1432D		Atlas-SNP	.											.	LAMA1	458	.	0			c.T4296C						.						227.0	183.0	198.0					18																	7002349		2203	4300	6503	SO:0001819	synonymous_variant	284217	exon30			ACACACATCACAA	X58531	CCDS32787.1	18p11.3	2013-03-01			ENSG00000101680	ENSG00000101680		"""Laminins"""	6481	protein-coding gene	gene with protein product		150320		LAMA		2591971	Standard	NM_005559		Approved		uc002knm.3	P25391	OTTHUMG00000133478	ENST00000389658.3:c.4296T>C	chr18.hg19:g.7002349A>G		52.0	0.0		37.0	9.0	NM_005559		Silent	SNP	ENST00000389658.3	hg19	CCDS32787.1																																																																																			.	.		0.507	LAMA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257369.1	NM_005559	
CPAMD8	27151	hgsc.bcm.edu	37	19	17040002	17040002	+	Missense_Mutation	SNP	T	T	A			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr19:17040002T>A	ENST00000443236.1	-	24	3066	c.3035A>T	c.(3034-3036)cAg>cTg	p.Q1012L		NM_015692.2	NP_056507.2	Q8IZJ3	CPMD8_HUMAN	C3 and PZP-like, alpha-2-macroglobulin domain containing 8	965						extracellular space (GO:0005615)|plasma membrane (GO:0005886)	serine-type endopeptidase inhibitor activity (GO:0004867)			breast(11)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(17)|lung(14)|ovary(7)|pancreas(2)|prostate(4)|skin(5)	82						CAGTGGCCGCTGCACATACTG	0.587																																					p.Q1012L		Atlas-SNP	.											.	CPAMD8	192	.	0			c.A3035T						.						48.0	55.0	53.0					19																	17040002		2096	4227	6323	SO:0001583	missense	27151	exon24			GGCCGCTGCACAT	AY101765	CCDS42519.1	19p13.12	2008-02-05			ENSG00000160111	ENSG00000160111			23228	protein-coding gene	gene with protein product		608841				10574462	Standard	NM_015692		Approved	KIAA1283, VIP, K-CAP	uc002nfb.3	Q8IZJ3	OTTHUMG00000133549	ENST00000443236.1:c.3035A>T	chr19.hg19:g.17040002T>A	ENSP00000402505:p.Gln1012Leu	37.0	0.0		30.0	5.0	NM_015692	Q8NC09|Q9ULD7	Missense_Mutation	SNP	ENST00000443236.1	hg19	CCDS42519.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.98|15.98	2.992975|2.992975	0.54041|0.54041	.|.	.|.	ENSG00000160111|ENSG00000160111	ENST00000291440|ENST00000443236	.|.	.|.	.|.	3.4|3.4	2.32|2.32	0.28847|0.28847	.|.	0.196250|.	0.33364|.	U|.	0.004989|.	T|T	0.59487|0.59487	0.2197|0.2197	L|L	0.57536|0.57536	1.79|1.79	0.80722|0.80722	D|D	1|1	P|.	0.44195|.	0.828|.	B|.	0.33750|.	0.169|.	T|T	0.52343|0.52343	-0.8588|-0.8588	9|5	0.28530|.	T|.	0.3|.	.|.	9.3067|9.3067	0.37878|0.37878	0.0:0.0:0.1819:0.8181|0.0:0.0:0.1819:0.8181	.|.	965|.	Q8IZJ3|.	CPMD8_HUMAN|.	L|C	1012|1023	.|.	ENSP00000291440:Q1012L|.	Q|S	-|-	2|1	0|0	CPAMD8|CPAMD8	16901002|16901002	1.000000|1.000000	0.71417|0.71417	0.509000|0.509000	0.27700|0.27700	0.897000|0.897000	0.52465|0.52465	3.063000|3.063000	0.49978|0.49978	0.213000|0.213000	0.20722|0.20722	0.533000|0.533000	0.62120|0.62120	CAG|AGC	.	.		0.587	CPAMD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257531.2	NM_015692	
CILP2	148113	hgsc.bcm.edu	37	19	19655201	19655201	+	Missense_Mutation	SNP	C	C	A			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr19:19655201C>A	ENST00000291495.5	+	8	1932	c.1847C>A	c.(1846-1848)aCc>aAc	p.T616N	CILP2_ENST00000586018.1_Missense_Mutation_p.T622N	NM_153221.2	NP_694953.2	Q8IUL8	CILP2_HUMAN	cartilage intermediate layer protein 2	616						extracellular vesicular exosome (GO:0070062)|proteinaceous extracellular matrix (GO:0005578)				NS(1)|breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(3)|lung(17)|ovary(2)|prostate(2)|skin(1)|urinary_tract(1)	32						CGAGACCTCACCTCGGCGGCG	0.692																																					p.T616N		Atlas-SNP	.											.	CILP2	84	.	0			c.C1847A						.						46.0	55.0	52.0					19																	19655201		2200	4298	6498	SO:0001583	missense	148113	exon8			ACCTCACCTCGGC	AF542080	CCDS12405.1	19p13.11	2013-01-14				ENSG00000160161		"""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	24213	protein-coding gene	gene with protein product		612419				12477932	Standard	NM_153221		Approved	MGC45771	uc002nmv.4	Q8IUL8		ENST00000291495.5:c.1847C>A	chr19.hg19:g.19655201C>A	ENSP00000291495:p.Thr616Asn	71.0	0.0		41.0	17.0	NM_153221	Q6NV88|Q8N4A6|Q8WV21	Missense_Mutation	SNP	ENST00000291495.5	hg19	CCDS12405.1	.	.	.	.	.	.	.	.	.	.	C	12.32	1.902375	0.33628	.	.	ENSG00000160161	ENST00000291495	T	0.44881	0.91	4.37	3.32	0.38043	.	0.539436	0.19585	N	0.110752	T	0.29256	0.0728	N	0.19112	0.55	0.26737	N	0.970478	B;B	0.24092	0.097;0.097	B;B	0.26094	0.051;0.066	T	0.26883	-1.0090	10	0.66056	D	0.02	-13.3451	11.028	0.47757	0.0:0.6349:0.3651:0.0	.	616;616	B2RAJ0;Q8IUL8	.;CILP2_HUMAN	N	616	ENSP00000291495:T616N	ENSP00000291495:T616N	T	+	2	0	CILP2	19516201	0.355000	0.24921	0.014000	0.15608	0.785000	0.44390	3.087000	0.50167	0.819000	0.34492	0.485000	0.47835	ACC	.	.		0.692	CILP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000459738.3	NM_153221	
RBM42	79171	hgsc.bcm.edu	37	19	36120133	36120133	+	Silent	SNP	G	G	T	rs371589146		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr19:36120133G>T	ENST00000262633.4	+	1	183	c.78G>T	c.(76-78)ccG>ccT	p.P26P	RBM42_ENST00000589559.1_Silent_p.P26P|RBM42_ENST00000589871.1_Silent_p.P26P|RBM42_ENST00000592202.1_Silent_p.P26P|RBM42_ENST00000586618.1_Silent_p.P26P|RBM42_ENST00000588161.1_Silent_p.P26P|RBM42_ENST00000360475.4_Silent_p.P26P	NM_024321.3	NP_077297.2	Q9BTD8	RBM42_HUMAN	RNA binding motif protein 42	26						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)			CTGGCATCCCGGGCAAAAGCG	0.687																																					p.P26P		Atlas-SNP	.											.	RBM42	40	.	0			c.G78T						.						11.0	12.0	11.0					19																	36120133		1960	3804	5764	SO:0001819	synonymous_variant	79171	exon1			CATCCCGGGCAAA	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.78G>T	chr19.hg19:g.36120133G>T		35.0	0.0		27.0	11.0	NM_024321	O00320|Q8N5R7|Q9BU66	Silent	SNP	ENST00000262633.4	hg19	CCDS12468.1																																																																																			.	.		0.687	RBM42-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000459057.2	NM_024321	
ZBTB32	27033	hgsc.bcm.edu	37	19	36207170	36207170	+	Missense_Mutation	SNP	A	A	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr19:36207170A>T	ENST00000392197.2	+	6	1478	c.1160A>T	c.(1159-1161)cAg>cTg	p.Q387L	KMT2B_ENST00000420124.1_5'Flank|KMT2B_ENST00000222270.7_5'Flank|ZBTB32_ENST00000262630.3_Missense_Mutation_p.Q387L|KMT2B_ENST00000341701.1_5'Flank|KMT2B_ENST00000607650.1_RNA			Q9Y2Y4	ZBT32_HUMAN	zinc finger and BTB domain containing 32	387					DNA repair (GO:0006281)|hemopoiesis (GO:0030097)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of cytokine production (GO:0001817)|T cell proliferation (GO:0042098)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transcription corepressor activity (GO:0003714)|zinc ion binding (GO:0008270)			large_intestine(5)|lung(1)|ovary(1)|prostate(2)|skin(2)|stomach(1)|urinary_tract(2)	14	all_lung(56;2.22e-07)|Lung NSC(56;3.47e-07)|Esophageal squamous(110;0.162)		LUSC - Lung squamous cell carcinoma(66;0.0515)			CTCAAGCATCAGATGGAGACG	0.627																																					p.Q387L		Atlas-SNP	.											.	ZBTB32	33	.	0			c.A1160T						.						36.0	33.0	34.0					19																	36207170		2203	4300	6503	SO:0001583	missense	27033	exon5			AGCATCAGATGGA	AF130255	CCDS12471.1	19q13.1	2013-01-08			ENSG00000011590	ENSG00000011590		"""-"", ""Zinc fingers, C2H2-type"", ""BTB/POZ domain containing"""	16763	protein-coding gene	gene with protein product	"""repressor of GATA"""	605859				10572087	Standard	XM_005258739		Approved	TZFP, FAZF, FAXF, Rog, ZNF538	uc002oay.3	Q9Y2Y4	OTTHUMG00000048118	ENST00000392197.2:c.1160A>T	chr19.hg19:g.36207170A>T	ENSP00000376035:p.Gln387Leu	82.0	0.0		81.0	27.0	NM_014383	Q8WVP2	Missense_Mutation	SNP	ENST00000392197.2	hg19	CCDS12471.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.442828	0.83993	.	.	ENSG00000011590	ENST00000262630;ENST00000392197	T;T	0.07327	3.2;3.2	4.72	4.72	0.59763	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.45867	D	0.000321	T	0.15435	0.0372	N	0.21142	0.635	0.49130	D	0.999756	D	0.76494	0.999	D	0.87578	0.998	T	0.05582	-1.0876	10	0.39692	T	0.17	-14.3215	12.206	0.54353	1.0:0.0:0.0:0.0	.	387	Q9Y2Y4	ZBT32_HUMAN	L	387	ENSP00000262630:Q387L;ENSP00000376035:Q387L	ENSP00000262630:Q387L	Q	+	2	0	ZBTB32	40899010	1.000000	0.71417	1.000000	0.80357	0.930000	0.56654	7.085000	0.76875	1.983000	0.57843	0.459000	0.35465	CAG	.	.		0.627	ZBTB32-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000109491.3	NM_014383	
PTOV1	53635	hgsc.bcm.edu	37	19	50361895	50361895	+	Silent	SNP	C	C	A	rs376020024		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr19:50361895C>A	ENST00000601675.1	+	10	1130	c.1026C>A	c.(1024-1026)atC>atA	p.I342I	PTOV1_ENST00000601638.1_Silent_p.I310I|AC018766.5_ENST00000599259.1_RNA|AC018766.5_ENST00000593654.1_RNA|PTOV1_ENST00000600603.1_Silent_p.I310I|PTOV1_ENST00000599732.1_Silent_p.I342I|PTOV1_ENST00000598325.1_3'UTR|AC018766.4_ENST00000596624.1_RNA|PTOV1_ENST00000221557.9_Silent_p.I310I|AC018766.5_ENST00000601893.1_RNA|PTOV1_ENST00000391842.1_Silent_p.I342I			Q86YD1	PTOV1_HUMAN	prostate tumor overexpressed 1	342	Interaction with FLOT1.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				endometrium(5)|kidney(3)|large_intestine(2)|lung(5)|ovary(1)	16		all_lung(116;1.05e-05)|Lung NSC(112;3.77e-05)|all_neural(266;0.107)|Ovarian(192;0.231)		GBM - Glioblastoma multiforme(134;0.0116)|OV - Ovarian serous cystadenocarcinoma(262;0.0132)		TGTGCCGGATCATGGACAATG	0.662																																					p.I342I		Atlas-SNP	.											.	PTOV1	41	.	0			c.C1026A						.	C		2,4404		0,2,2201	42.0	28.0	33.0		1026	2.4	0.9	19		33	0,8600		0,0,4300	no	coding-synonymous	PTOV1	NM_017432.3		0,2,6501	AA,AC,CC		0.0,0.0454,0.0154		342/417	50361895	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	53635	exon10			CCGGATCATGGAC	AF238381	CCDS12782.1	19q13.33	2014-08-28	2008-09-12		ENSG00000104960	ENSG00000104960			9632	protein-coding gene	gene with protein product		610195				12598323, 15713644	Standard	XM_005258998		Approved		uc002pqf.1	Q86YD1	OTTHUMG00000183162	ENST00000601675.1:c.1026C>A	chr19.hg19:g.50361895C>A		81.0	0.0		52.0	25.0	NM_017432	Q6UXX7|Q96BU3|Q9HBN4|Q9NYL1	Silent	SNP	ENST00000601675.1	hg19	CCDS12782.1																																																																																			.	.		0.662	PTOV1-007	KNOWN	alternative_3_UTR|NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465347.1	NM_017432	
SYNDIG1	79953	hgsc.bcm.edu	37	20	24565510	24565510	+	Missense_Mutation	SNP	A	A	G			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr20:24565510A>G	ENST00000376862.3	+	3	1132	c.499A>G	c.(499-501)Aca>Gca	p.T167A		NM_024893.1	NP_079169.1	Q9H7V2	SYNG1_HUMAN	synapse differentiation inducing 1	167					intracellular protein transport (GO:0006886)|positive regulation of synapse assembly (GO:0051965)|response to biotic stimulus (GO:0009607)|synaptic vesicle clustering (GO:0097091)	cell body (GO:0044297)|cell junction (GO:0030054)|dendritic shaft (GO:0043198)|dendritic spine (GO:0043197)|early endosome membrane (GO:0031901)|excitatory synapse (GO:0060076)|integral component of plasma membrane (GO:0005887)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)	glutamate receptor binding (GO:0035254)|protein homodimerization activity (GO:0042803)	p.T167A(1)		breast(2)|endometrium(1)|large_intestine(3)|lung(14)|prostate(1)|skin(3)	24						CTCAAGCGACACAGAGAGTGA	0.562																																					p.T167A		Atlas-SNP	.											SYNDIG1,NS,carcinoma,0,1	SYNDIG1	58	.	1	Substitution - Missense(1)	lung(1)	c.A499G						.						140.0	132.0	135.0					20																	24565510		2203	4300	6503	SO:0001583	missense	79953	exon3			AGCGACACAGAGA	AK024282	CCDS13164.1	20p11.21	2011-06-30	2011-06-30	2011-06-30	ENSG00000101463	ENSG00000101463			15885	protein-coding gene	gene with protein product	"""interferon induced transmembrane protein domain containing 5"", ""synapse differentiation induced gene 1"""	614311	"""chromosome 20 open reading frame 39"", ""transmembrane protein 90B"""	C20orf39, TMEM90B		20152115	Standard	NM_024893		Approved	FLJ14220, IFITMD5, SynDIG1	uc002wtw.1	Q9H7V2	OTTHUMG00000032104	ENST00000376862.3:c.499A>G	chr20.hg19:g.24565510A>G	ENSP00000366058:p.Thr167Ala	60.0	1.0		64.0	29.0	NM_024893	Q6IA30|Q9H514	Missense_Mutation	SNP	ENST00000376862.3	hg19	CCDS13164.1	.	.	.	.	.	.	.	.	.	.	A	13.58	2.278997	0.40294	.	.	ENSG00000101463	ENST00000376862	D	0.90620	-2.7	5.1	5.1	0.69264	.	0.078921	0.52532	D	0.000063	D	0.88746	0.6520	L	0.47716	1.5	0.41539	D	0.988501	P	0.47762	0.9	P	0.45538	0.484	D	0.89491	0.3757	10	0.56958	D	0.05	-16.4836	12.8475	0.57837	1.0:0.0:0.0:0.0	.	167	Q9H7V2	SYNG1_HUMAN	A	167	ENSP00000366058:T167A	ENSP00000366058:T167A	T	+	1	0	SYNDIG1	24513510	0.992000	0.36948	0.997000	0.53966	0.670000	0.39368	3.706000	0.54830	1.930000	0.55929	0.459000	0.35465	ACA	.	.		0.562	SYNDIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078376.1	NM_024893	
DSCAM	1826	hgsc.bcm.edu	37	21	42080424	42080424	+	Missense_Mutation	SNP	T	T	A			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr21:42080424T>A	ENST00000400454.1	-	2	794	c.317A>T	c.(316-318)aAt>aTt	p.N106I		NM_001271534.1|NM_001389.3	NP_001258463.1|NP_001380.2	O60469	DSCAM_HUMAN	Down syndrome cell adhesion molecule	106	Ig-like C2-type 1.				cell adhesion (GO:0007155)|dendrite morphogenesis (GO:0048813)|dendrite self-avoidance (GO:0070593)|locomotory behavior (GO:0007626)|negative regulation of cell adhesion (GO:0007162)|nervous system development (GO:0007399)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of phosphorylation (GO:0042327)|post-embryonic retina morphogenesis in camera-type eye (GO:0060060)	axon (GO:0030424)|extracellular region (GO:0005576)|growth cone (GO:0030426)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)				NS(2)|breast(1)|central_nervous_system(1)|cervix(1)|endometrium(22)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(22)|lung(47)|ovary(7)|pancreas(2)|prostate(3)|skin(14)|upper_aerodigestive_tract(6)|urinary_tract(4)	142		all_cancers(19;0.186)|Prostate(19;1.15e-05)|all_epithelial(19;0.0103)				CCCTGAAGGATTTTCAGCTGT	0.463																																					p.N106I	Melanoma(134;970 1778 1785 21664 32388)	Atlas-SNP	.											.	DSCAM	347	.	0			c.A317T						.						114.0	109.0	111.0					21																	42080424		1885	4110	5995	SO:0001583	missense	1826	exon2			GAAGGATTTTCAG	AF023449	CCDS42929.1	21q22.2-q22.3	2013-02-11			ENSG00000171587	ENSG00000171587		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	3039	protein-coding gene	gene with protein product		602523				9426258	Standard	NM_001271534		Approved	CHD2-42, CHD2-52	uc002yyq.1	O60469	OTTHUMG00000086732	ENST00000400454.1:c.317A>T	chr21.hg19:g.42080424T>A	ENSP00000383303:p.Asn106Ile	69.0	0.0		46.0	15.0	NM_001271534	O60468	Missense_Mutation	SNP	ENST00000400454.1	hg19	CCDS42929.1	.	.	.	.	.	.	.	.	.	.	T	22.3	4.272051	0.80469	.	.	ENSG00000171587	ENST00000400454	T	0.56941	0.43	5.22	5.22	0.72569	Immunoglobulin-like fold (1);	0.000000	0.85682	D	0.000000	T	0.78149	0.4238	M	0.91818	3.245	0.53688	D	0.999977	D	0.76494	0.999	D	0.87578	0.998	D	0.83855	0.0265	10	0.87932	D	0	.	15.1068	0.72326	0.0:0.0:0.0:1.0	.	106	O60469	DSCAM_HUMAN	I	106	ENSP00000383303:N106I	ENSP00000383303:N106I	N	-	2	0	DSCAM	41002294	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.603000	0.82811	1.980000	0.57719	0.477000	0.44152	AAT	.	.		0.463	DSCAM-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195029.1	NM_001389	
SIK1	150094	hgsc.bcm.edu	37	21	44841639	44841639	+	Silent	SNP	C	C	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr21:44841639C>T	ENST00000270162.6	-	5	510	c.378G>A	c.(376-378)gcG>gcA	p.A126A		NM_173354.3	NP_775490.2	P57059	SIK1_HUMAN	salt-inducible kinase 1	126	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cardiac muscle cell differentiation (GO:0055007)|cell cycle (GO:0007049)|entrainment of circadian clock by photoperiod (GO:0043153)|intracellular signal transduction (GO:0035556)|negative regulation of CREB transcription factor activity (GO:0032792)|negative regulation of gluconeogenesis (GO:0045721)|negative regulation of triglyceride biosynthetic process (GO:0010868)|positive regulation of anoikis (GO:2000210)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of cell differentiation (GO:0045595)|regulation of mitotic cell cycle (GO:0007346)|regulation of myotube differentiation (GO:0010830)|regulation of sodium ion transport (GO:0002028)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	14-3-3 protein binding (GO:0071889)|ATP binding (GO:0005524)|cAMP response element binding protein binding (GO:0008140)|magnesium ion binding (GO:0000287)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)			breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(6)|ovary(1)|prostate(1)|skin(2)|testis(2)|urinary_tract(1)	21					Dabrafenib(DB08912)	ACTTCTTCCGCGCCTCGTTCT	0.572																																					p.A126A		Atlas-SNP	.											SIK1,caecum,carcinoma,0,1	SIK1	65	.	0			c.G378A						.						67.0	61.0	63.0					21																	44841639		2203	4300	6503	SO:0001819	synonymous_variant	150094	exon5			CTTCCGCGCCTCG	BC038504	CCDS33575.1	21q22.3	2008-12-23	2008-12-23	2008-12-23	ENSG00000142178	ENSG00000142178			11142	protein-coding gene	gene with protein product	"""myocardial SNF1-like kinase"""	605705	"""SNF1-like kinase"""	SNF1LK		7893599	Standard	NM_173354		Approved	msk	uc002zdf.2	P57059	OTTHUMG00000086874	ENST00000270162.6:c.378G>A	chr21.hg19:g.44841639C>T		111.0	0.0		78.0	24.0	NM_173354	A6NC84|Q5R2V5|Q6ZNL8|Q86YJ2	Silent	SNP	ENST00000270162.6	hg19	CCDS33575.1																																																																																			.	.		0.572	SIK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195654.1	NM_173354	
SHROOM4	57477	hgsc.bcm.edu	37	X	50350826	50350826	+	Missense_Mutation	SNP	G	G	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	G	G	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chrX:50350826G>T	ENST00000289292.7	-	6	3599	c.3316C>A	c.(3316-3318)Cct>Act	p.P1106T	SHROOM4_ENST00000460112.3_Missense_Mutation_p.P990T|SHROOM4_ENST00000376020.2_Missense_Mutation_p.P1106T			Q9ULL8	SHRM4_HUMAN	shroom family member 4	1106	Poly-Pro.				actin cytoskeleton organization (GO:0030036)|actin filament organization (GO:0007015)|brain development (GO:0007420)|cognition (GO:0050890)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|myosin II complex (GO:0016460)|stress fiber (GO:0001725)	actin filament binding (GO:0051015)			breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(5)|large_intestine(6)|liver(1)|lung(20)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(1)	52	Ovarian(276;0.236)					CAGTTGGGAGGAGGAGGGCGA	0.587																																					p.P1106T		Atlas-SNP	.											.	SHROOM4	171	.	0			c.C3316A						.						39.0	34.0	35.0					X																	50350826		2203	4300	6503	SO:0001583	missense	57477	exon6			TGGGAGGAGGAGG	AB033028	CCDS35277.1	Xp11.22	2008-02-05			ENSG00000158352	ENSG00000158352			29215	protein-coding gene	gene with protein product		300579				10574462, 16615870	Standard	NR_027121		Approved	KIAA1202	uc004dpe.2	Q9ULL8	OTTHUMG00000021521	ENST00000289292.7:c.3316C>A	chrX.hg19:g.50350826G>T	ENSP00000289292:p.Pro1106Thr	92.0	0.0		30.0	17.0	NM_020717	A7E2X9|D6RFW0|Q96LA0	Missense_Mutation	SNP	ENST00000289292.7	hg19	CCDS35277.1	.	.	.	.	.	.	.	.	.	.	G	15.86	2.958479	0.53400	.	.	ENSG00000158352	ENST00000289292;ENST00000376020;ENST00000460112	T;T;T	0.25250	2.24;2.24;1.81	5.74	5.74	0.90152	.	0.193727	0.44483	D	0.000447	T	0.34919	0.0914	L	0.34521	1.04	0.49213	D	0.999763	D	0.58268	0.982	P	0.55112	0.769	T	0.07009	-1.0795	10	0.87932	D	0	.	16.1551	0.81657	0.0:0.0:1.0:0.0	.	1106	Q9ULL8	SHRM4_HUMAN	T	1106;1106;990	ENSP00000289292:P1106T;ENSP00000365188:P1106T;ENSP00000421450:P990T	ENSP00000289292:P1106T	P	-	1	0	SHROOM4	50367566	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.125000	0.77193	2.418000	0.82041	0.513000	0.50165	CCT	.	.		0.587	SHROOM4-001	KNOWN	NMD_exception|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056564.4	NM_020717	
PABPC5	140886	hgsc.bcm.edu	37	X	90690699	90690699	+	Silent	SNP	T	T	A			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chrX:90690699T>A	ENST00000312600.3	+	2	337	c.123T>A	c.(121-123)gcT>gcA	p.A41A	PABPC5-AS1_ENST00000456187.1_RNA|PABPC5_ENST00000373105.1_Intron	NM_080832.2	NP_543022.1	Q96DU9	PABP5_HUMAN	poly(A) binding protein, cytoplasmic 5	41	RRM 1. {ECO:0000255|PROSITE- ProRule:PRU00176}.					mitochondrion (GO:0005739)	nucleotide binding (GO:0000166)|RNA binding (GO:0003723)			central_nervous_system(2)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(20)|ovary(1)|pancreas(1)	42						TCAGGCCTGCTGGCCCTCTGC	0.572																																					p.A41A		Atlas-SNP	.											.	PABPC5	92	.	0			c.T123A						.						53.0	41.0	45.0					X																	90690699		2203	4300	6503	SO:0001819	synonymous_variant	140886	exon2			GCCTGCTGGCCCT	AJ278963	CCDS14460.1	Xq21.3	2013-02-12	2001-11-28		ENSG00000174740	ENSG00000174740		"""RNA binding motif (RRM) containing"""	13629	protein-coding gene	gene with protein product		300407	"""poly(A)-binding protein, cytoplasmic 5"""			11374897	Standard	NM_080832		Approved	PABP5	uc004efg.3	Q96DU9	OTTHUMG00000021959	ENST00000312600.3:c.123T>A	chrX.hg19:g.90690699T>A		53.0	0.0		16.0	10.0	NM_080832	A8K240|Q5JQF4|Q6P529|Q9UFE5	Silent	SNP	ENST00000312600.3	hg19	CCDS14460.1																																																																																			.	.		0.572	PABPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057429.1	NM_080832	
GLRA4	441509	hgsc.bcm.edu	37	X	102978843	102978843	+	Missense_Mutation	SNP	A	A	C			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	A	A	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chrX:102978843A>C	ENST00000372617.4	-	5	938	c.518T>G	c.(517-519)cTg>cGg	p.L173R	GLRA4_ENST00000469567.1_5'Flank	NM_001024452.2	NP_001019623.2	Q5JXX5	GLRA4_HUMAN	glycine receptor, alpha 4	173						cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)			cervix(1)|endometrium(2)|large_intestine(2)|lung(13)|upper_aerodigestive_tract(2)|urinary_tract(1)	21						GAGGTCCATCAGGCAGGACAA	0.527																																					p.L173R		Atlas-SNP	.											.	GLRA4	86	.	0			c.T518G						.						117.0	110.0	112.0					X																	102978843		2034	4174	6208	SO:0001583	missense	441509	exon5			TCCATCAGGCAGG	Z93848	CCDS43980.2	Xq22.2	2012-01-16			ENSG00000188828	ENSG00000188828		"""Ligand-gated ion channels / Glycine receptors"""	31715	protein-coding gene	gene with protein product							Standard	NM_001024452		Approved		uc011mse.2	Q5JXX5	OTTHUMG00000022110	ENST00000372617.4:c.518T>G	chrX.hg19:g.102978843A>C	ENSP00000361700:p.Leu173Arg	280.0	1.0		102.0	69.0	NM_001024452		Missense_Mutation	SNP	ENST00000372617.4	hg19	CCDS43980.2	.	.	.	.	.	.	.	.	.	.	G	14.46	2.541146	0.45280	.	.	ENSG00000188828	ENST00000372617	T	0.78364	-1.17	5.46	5.46	0.80206	Neurotransmitter-gated ion-channel ligand-binding (3);Neurotransmitter-gated ion-channel, conserved site (1);	0.000000	0.85682	D	0.000000	T	0.61060	0.2317	N	0.10874	0.06	0.32898	D	0.512749	B;B	0.02656	0.0;0.0	B;B	0.06405	0.0;0.002	T	0.64162	-0.6472	10	0.59425	D	0.04	.	11.2816	0.49197	0.0905:0.0:0.9095:0.0	.	173;132	Q5JXX5;B9WSA6	GLRA4_HUMAN;.	R	173	ENSP00000361700:L173R	ENSP00000361700:L173R	L	-	2	0	GLRA4	102865499	1.000000	0.71417	0.888000	0.34837	0.570000	0.35934	6.795000	0.75140	1.085000	0.41206	-0.170000	0.13304	CTG	.	.		0.527	GLRA4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057742.2	NM_001024452	
RAB9B	51209	hgsc.bcm.edu	37	X	103080318	103080318	+	Missense_Mutation	SNP	C	C	T			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chrX:103080318C>T	ENST00000243298.2	-	3	681	c.397G>A	c.(397-399)Gtg>Atg	p.V133M		NM_016370.2	NP_057454.1	Q9NP90	RAB9B_HUMAN	RAB9B, member RAS oncogene family	133					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	phagocytic vesicle (GO:0045335)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GTP binding (GO:0005525)			endometrium(1)|kidney(1)|large_intestine(1)|lung(11)	14						TCAGTAGTCACTTGCCTATCC	0.433																																					p.V133M		Atlas-SNP	.											.	RAB9B	24	.	0			c.G397A						.						230.0	220.0	223.0					X																	103080318		2203	4300	6503	SO:0001583	missense	51209	exon3			TAGTCACTTGCCT	AB036693	CCDS14515.1	Xq22.1-q22.3	2010-04-19			ENSG00000123570	ENSG00000123570		"""RAB, member RAS oncogene"""	14090	protein-coding gene	gene with protein product		300285				11043518	Standard	NM_016370		Approved	RAB9L	uc004ell.2	Q9NP90	OTTHUMG00000022112	ENST00000243298.2:c.397G>A	chrX.hg19:g.103080318C>T	ENSP00000243298:p.Val133Met	91.0	0.0		24.0	17.0	NM_016370	B2R8M0|Q52LX2	Missense_Mutation	SNP	ENST00000243298.2	hg19	CCDS14515.1	.	.	.	.	.	.	.	.	.	.	C	16.53	3.148687	0.57151	.	.	ENSG00000123570	ENST00000243298	D	0.83914	-1.78	5.51	5.51	0.81932	Small GTP-binding protein domain (1);	0.056566	0.64402	D	0.000001	D	0.91744	0.7389	M	0.91818	3.245	0.58432	D	0.999999	D	0.89917	1.0	D	0.77004	0.989	D	0.92703	0.6176	10	0.87932	D	0	0.0455	9.3971	0.38408	0.0:0.9014:0.0:0.0986	.	133	Q9NP90	RAB9B_HUMAN	M	133	ENSP00000243298:V133M	ENSP00000243298:V133M	V	-	1	0	RAB9B	102966974	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.088000	0.71371	2.311000	0.77944	0.600000	0.82982	GTG	.	.		0.433	RAB9B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057746.1		
HGS	9146	hgsc.bcm.edu	37	17	79660939	79660939	+	Frame_Shift_Del	DEL	C	C	-			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	C	C	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr17:79660939delC	ENST00000329138.4	+	11	1015	c.880delC	c.(880-882)cccfs	p.P294fs		NM_004712.4	NP_004703.1	O14964	HGS_HUMAN	hepatocyte growth factor-regulated tyrosine kinase substrate	294	Interaction with SNX1. {ECO:0000250}.				endosomal transport (GO:0016197)|endosome to lysosome transport (GO:0008333)|epidermal growth factor receptor signaling pathway (GO:0007173)|membrane invagination (GO:0010324)|membrane organization (GO:0061024)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of JAK-STAT cascade (GO:0046426)|positive regulation of gene expression (GO:0010628)|protein localization to membrane (GO:0072657)|protein targeting to lysosome (GO:0006622)|regulation of protein catabolic process (GO:0042176)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|secretory granule (GO:0030141)	metal ion binding (GO:0046872)|protein domain specific binding (GO:0019904)			endometrium(2)|kidney(3)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)	12	all_neural(118;0.0878)|all_lung(278;0.23)		BRCA - Breast invasive adenocarcinoma(99;0.0101)|OV - Ovarian serous cystadenocarcinoma(97;0.0955)			CAAGGCGGAGCCCATGCCCTC	0.662																																					p.E293fs		Atlas-Indel,Pindel	.											.	HGS	54	.	0			c.879delG						.						38.0	42.0	41.0					17																	79660939		2202	4300	6502	SO:0001589	frameshift_variant	9146	exon11			.	D84064	CCDS11784.1	17q25	2009-04-29				ENSG00000185359		"""Zinc fingers, FYVE domain containing"""	4897	protein-coding gene	gene with protein product		604375				9407053, 9630564	Standard	NM_004712		Approved	Hrs, ZFYVE8, Vps27	uc002kbg.3	O14964		ENST00000329138.4:c.880delC	chr17.hg19:g.79660939delC	ENSP00000331201:p.Pro294fs	28.0	0.0		54.0	15.0	NM_004712	Q9NR36	Frame_Shift_Del	DEL	ENST00000329138.4	hg19	CCDS11784.1																																																																																			.	.		0.662	HGS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440541.1	NM_004712	
TP53	7157	hgsc.bcm.edu	37	17	7579389	7579399	+	Frame_Shift_Del	DEL	GGGAAGGGACA	GGGAAGGGACA	-			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	GGGAAGGGACA	GGGAAGGGACA	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr17:7579389_7579399delGGGAAGGGACA	ENST00000269305.4	-	4	477_487	c.288_298delTGTCCCTTCCC	c.(286-300)tctgtcccttcccagfs	p.VPSQ97fs	TP53_ENST00000420246.2_Frame_Shift_Del_p.VPSQ97fs|TP53_ENST00000413465.2_Frame_Shift_Del_p.VPSQ97fs|TP53_ENST00000574684.1_5'Flank|TP53_ENST00000445888.2_Frame_Shift_Del_p.VPSQ97fs|TP53_ENST00000455263.2_Frame_Shift_Del_p.VPSQ97fs|TP53_ENST00000359597.4_Frame_Shift_Del_p.VPSQ97fs	NM_000546.5|NM_001126112.2|NM_001126118.1|NM_001276760.1|NM_001276761.1	NP_000537.3|NP_001119584.1|NP_001119590.1|NP_001263689.1|NP_001263690.1	P04637	P53_HUMAN	tumor protein p53	97	Interaction with WWOX.		V -> A (in a sporadic cancer; somatic mutation).|V -> F (in a sporadic cancer; somatic mutation).|V -> I (in familial cancer not matching LFS; germline mutation and in a sporadic cancer; somatic mutation).		apoptotic process (GO:0006915)|B cell lineage commitment (GO:0002326)|base-excision repair (GO:0006284)|blood coagulation (GO:0007596)|cell aging (GO:0007569)|cell cycle arrest (GO:0007050)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cellular protein localization (GO:0034613)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to drug (GO:0035690)|cellular response to glucose starvation (GO:0042149)|cellular response to hypoxia (GO:0071456)|cellular response to ionizing radiation (GO:0071479)|cellular response to UV (GO:0034644)|cerebellum development (GO:0021549)|chromatin assembly (GO:0031497)|determination of adult lifespan (GO:0008340)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA strand renaturation (GO:0000733)|double-strand break repair (GO:0006302)|embryonic organ development (GO:0048568)|ER overload response (GO:0006983)|gastrulation (GO:0007369)|in utero embryonic development (GO:0001701)|intrinsic apoptotic signaling pathway (GO:0097193)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|mitotic cell cycle arrest (GO:0071850)|mitotic G1 DNA damage checkpoint (GO:0031571)|multicellular organism growth (GO:0035264)|multicellular organismal development (GO:0007275)|necroptotic process (GO:0070266)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of DNA replication (GO:0008156)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of helicase activity (GO:0051097)|negative regulation of macromitophagy (GO:1901525)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of reactive oxygen species metabolic process (GO:2000378)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|neuron apoptotic process (GO:0051402)|Notch signaling pathway (GO:0007219)|nucleotide-excision repair (GO:0006289)|oligodendrocyte apoptotic process (GO:0097252)|oxidative stress-induced premature senescence (GO:0090403)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cardiac muscle cell apoptotic process (GO:0010666)|positive regulation of cell aging (GO:0090343)|positive regulation of cell cycle arrest (GO:0071158)|positive regulation of histone deacetylation (GO:0031065)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|positive regulation of mitochondrial membrane permeability (GO:0035794)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:1900740)|positive regulation of protein oligomerization (GO:0032461)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|positive regulation of thymocyte apoptotic process (GO:0070245)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein complex assembly (GO:0006461)|protein import into nucleus, translocation (GO:0000060)|protein localization (GO:0008104)|protein tetramerization (GO:0051262)|Ras protein signal transduction (GO:0007265)|regulation of apoptotic process (GO:0042981)|regulation of mitochondrial membrane permeability (GO:0046902)|regulation of mitochondrial membrane permeability involved in apoptotic process (GO:1902108)|regulation of tissue remodeling (GO:0034103)|regulation of transcription, DNA-templated (GO:0006355)|release of cytochrome c from mitochondria (GO:0001836)|replicative senescence (GO:0090399)|response to antibiotic (GO:0046677)|response to gamma radiation (GO:0010332)|response to ischemia (GO:0002931)|response to salt stress (GO:0009651)|response to X-ray (GO:0010165)|rRNA transcription (GO:0009303)|somitogenesis (GO:0001756)|T cell differentiation in thymus (GO:0033077)|T cell lineage commitment (GO:0002360)|T cell proliferation involved in immune response (GO:0002309)|transforming growth factor beta receptor signaling pathway (GO:0007179)|viral process (GO:0016032)	chromatin (GO:0000785)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|nuclear chromatin (GO:0000790)|nuclear matrix (GO:0016363)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|protein complex (GO:0043234)|replication fork (GO:0005657)	ATP binding (GO:0005524)|chaperone binding (GO:0051087)|chromatin binding (GO:0003682)|copper ion binding (GO:0005507)|damaged DNA binding (GO:0003684)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|histone acetyltransferase binding (GO:0035035)|histone deacetylase regulator activity (GO:0035033)|identical protein binding (GO:0042802)|p53 binding (GO:0002039)|protease binding (GO:0002020)|protein heterodimerization activity (GO:0046982)|protein kinase binding (GO:0019901)|protein N-terminus binding (GO:0047485)|protein phosphatase 2A binding (GO:0051721)|protein phosphatase binding (GO:0019903)|receptor tyrosine kinase binding (GO:0030971)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II core promoter sequence-specific DNA binding (GO:0000979)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)|ubiquitin protein ligase binding (GO:0031625)|zinc ion binding (GO:0008270)	p.Q100*(12)|p.0?(8)|p.P98S(4)|p.S99fs*48(3)|p.S99fs*23(3)|p.P98L(3)|p.V97V(3)|p.Q100fs*37(3)|p.G59fs*23(3)|p.S99F(2)|p.V97I(1)|p.V73fs*9(1)|p.V97A(1)|p.P98fs*26(1)|p.S99P(1)|p.W91fs*13(1)|p.P13fs*18(1)|p.S33fs*23(1)|p.S99fs*24(1)		NS(16)|adrenal_gland(37)|autonomic_ganglia(16)|biliary_tract(273)|bone(108)|breast(2530)|central_nervous_system(1264)|cervix(68)|endometrium(223)|eye(24)|fallopian_tube(1)|gastrointestinal_tract_(site_indeterminate)(1)|genital_tract(16)|haematopoietic_and_lymphoid_tissue(1301)|kidney(96)|large_intestine(5124)|liver(897)|lung(2388)|meninges(5)|oesophagus(1473)|ovary(1659)|pancreas(452)|penis(10)|peritoneum(33)|pituitary(4)|placenta(1)|pleura(3)|prostate(235)|salivary_gland(43)|skin(791)|small_intestine(14)|soft_tissue(220)|stomach(1158)|testis(11)|thymus(21)|thyroid(54)|upper_aerodigestive_tract(2271)|urinary_tract(1259)|vagina(6)|vulva(79)	24185		all_cancers(10;1.01e-06)|Myeloproliferative disorder(207;0.0122)|Prostate(122;0.081)		GBM - Glioblastoma multiforme(2;1.59e-06)|READ - Rectum adenocarcinoma(115;0.174)	Acetylsalicylic acid(DB00945)	TAGGTTTTCTGGGAAGGGACAGAAGATGACA	0.645		111	"""Mis, N, F"""		"""breast, colorectal, lung, sarcoma, adrenocortical, glioma, multiple other tumour types"""	"""breast, sarcoma, adrenocortical carcinoma, glioma, multiple other tumour types"""		Other conserved DNA damage response genes	Osteosarcoma, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Breast-Ovarian Cancer, non-BRCA1/2;Hereditary Adrenocortical Cancer;Endometrial Cancer, Familial Clustering of	HNSCC(1;<9.43e-08)|TCGA GBM(1;<1E-08)|TSP Lung(2;<1E-08)|TCGA Ovarian(1;<1.89e-07)|Multiple Myeloma(5;0.019)																											p.97_100del	Pancreas(47;798 1329 9957 10801)	Atlas-Indel,Pindel	.	yes	Rec	yes	Li-Fraumeni syndrome	17	17p13	7157	tumor protein p53		"""L, E, M, O"""	.	TP53	33396	.	53	Deletion - Frameshift(17)|Substitution - Nonsense(12)|Substitution - Missense(12)|Whole gene deletion(8)|Substitution - coding silent(3)|Insertion - Frameshift(1)	upper_aerodigestive_tract(7)|haematopoietic_and_lymphoid_tissue(7)|ovary(5)|large_intestine(4)|lung(4)|skin(4)|bone(4)|central_nervous_system(3)|kidney(3)|adrenal_gland(2)|urinary_tract(2)|breast(2)|pancreas(2)|stomach(1)|eye(1)|oesophagus(1)|liver(1)	c.289_299del	GRCh37	CM045203	TP53	M		.																																			SO:0001589	frameshift_variant	7157	exon4	Familial Cancer Database	Familial Osteogenic Sarcoma;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;BRCAX;Familial Adrenocortical Carcinoma;	.	AF307851	CCDS11118.1, CCDS45605.1, CCDS45606.1, CCDS73963.1, CCDS73964.1, CCDS73965.1, CCDS73966.1, CCDS73967.1, CCDS73968.1, CCDS73969.1, CCDS73970.1, CCDS73971.1	17p13.1	2014-09-17	2008-01-16		ENSG00000141510	ENSG00000141510			11998	protein-coding gene	gene with protein product	"""Li-Fraumeni syndrome"""	191170				6396087, 3456488, 2047879	Standard	NM_001126115		Approved	p53, LFS1	uc002gij.3	P04637	OTTHUMG00000162125	ENST00000269305.4:c.288_298delTGTCCCTTCCC	chr17.hg19:g.7579389_7579399delGGGAAGGGACA	ENSP00000269305:p.Val97fs	190.0	0.0		64.0	23.0	NM_001126112	Q15086|Q15087|Q15088|Q16535|Q16807|Q16808|Q16809|Q16810|Q16811|Q16848|Q2XN98|Q3LRW1|Q3LRW2|Q3LRW3|Q3LRW4|Q3LRW5|Q86UG1|Q8J016|Q99659|Q9BTM4|Q9HAQ8|Q9NP68|Q9NPJ2|Q9NZD0|Q9UBI2|Q9UQ61	Frame_Shift_Del	DEL	ENST00000269305.4	hg19	CCDS11118.1																																																																																			.	.		0.645	TP53-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367397.1	NM_000546	
SUN5	140732	hgsc.bcm.edu	37	20	31577506	31577506	+	Splice_Site	DEL	T	T	-			TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	T	T	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chr20:31577506delT	ENST00000356173.3	-	9	627		c.e9-2		SUN5_ENST00000375523.3_Splice_Site	NM_080675.3	NP_542406.2	Q8TC36	SUN5_HUMAN	Sad1 and UNC84 domain containing 5						spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)				endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)	25						CATTTTTTGCTGAAAAGGCAG	0.512																																					.		Pindel	.											.	SUN5	63	.	0			c.535-1A>-						.						166.0	128.0	141.0					20																	31577506		2203	4300	6503	SO:0001630	splice_region_variant	140732	exon10			.	AL121756	CCDS13209.1	20q11.21	2010-01-27	2010-01-27	2010-01-27	ENSG00000167098	ENSG00000167098			16252	protein-coding gene	gene with protein product	"""testis and spermatogenesis related gene 4"""	613942	"""sperm associated antigen 4-like"""	SPAG4L		9691178, 10373309	Standard	NM_080675		Approved	dJ726C3.1, TSARG4	uc002wyi.3	Q8TC36	OTTHUMG00000032239	ENST00000356173.3:c.535-2A>-	chr20.hg19:g.31577506delT		79.0	0.0		66.0	18.0	NM_080675	A6NJ82|Q5T9R0	Splice_Site	DEL	ENST00000356173.3	hg19	CCDS13209.1																																																																																			.	.		0.512	SUN5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078659.1	NM_080675	Intron
MSN	4478	hgsc.bcm.edu	37	X	64951035	64951044	+	Frame_Shift_Del	DEL	ACACCGTGGC	ACACCGTGGC	-	rs373340100		TCGA-BC-A69H-01A-11D-A30V-10	TCGA-BC-A69H-10A-01D-A30V-10	ACACCGTGGC	ACACCGTGGC	.	.	.	.	Unknown	Untested	Somatic	PhaseI	WXS	none	.		Illumina HiSeq	b2e0f3c4-dcff-4718-8461-381609521e4f	371b4d98-49a4-4605-a24e-d7b92923da58	g.chrX:64951035_64951044delACACCGTGGC	ENST00000360270.5	+	5	706_715	c.534_543delACACCGTGGC	c.(532-543)gaacaccgtggcfs	p.EHRG178fs		NM_002444.2	NP_002435.1	P26038	MOES_HUMAN	moesin	178	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				cellular component movement (GO:0006928)|establishment of endothelial barrier (GO:0061028)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|positive regulation of gene expression (GO:0010628)|regulation of lymphocyte migration (GO:2000401)	apical part of cell (GO:0045177)|apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|blood microparticle (GO:0072562)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|focal adhesion (GO:0005925)|microvillus (GO:0005902)|plasma membrane (GO:0005886)|uropod (GO:0001931)|vesicle (GO:0031982)	cell adhesion molecule binding (GO:0050839)|double-stranded RNA binding (GO:0003725)|protein kinase binding (GO:0019901)|receptor binding (GO:0005102)|structural constituent of cytoskeleton (GO:0005200)	p.R180R(1)	MSN/ALK(6)	breast(4)|central_nervous_system(3)|endometrium(7)|kidney(5)|large_intestine(6)|lung(11)|ovary(3)|prostate(1)|skin(2)|urinary_tract(1)	43						GGCATGAGGAACACCGTGGCATGCTCAGGT	0.524			T	ALK	ALCL																																p.178_181del		Pindel	.		Dom	yes		X	Xq11.2-q12	4478	moesin		L	.	MSN	89	.	1	Substitution - coding silent(1)	ovary(1)	c.533_542del						.																																			SO:0001589	frameshift_variant	4478	exon5			.	M69066	CCDS14382.1	Xq11.1	2010-10-20			ENSG00000147065	ENSG00000147065			7373	protein-coding gene	gene with protein product		309845				1924289, 7628534	Standard	XM_005262269		Approved		uc004dwf.3	P26038	OTTHUMG00000021723	ENST00000360270.5:c.534_543delACACCGTGGC	chrX.hg19:g.64951035_64951044delACACCGTGGC	ENSP00000353408:p.Glu178fs	154.0	0.0		56.0	17.0	NM_002444		Frame_Shift_Del	DEL	ENST00000360270.5	hg19	CCDS14382.1																																																																																			.	.		0.524	MSN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056981.1	NM_002444	
