#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_ACHILLES_Lineage_Results_Top_Genes	i_Annotation_Transcript	i_CCLE_ONCOMAP_overlapping_mutations	i_CCLE_ONCOMAP_total_mutations_in_gene	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_Mutation_Type	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Other_Diseases	i_CGC_Tissue Type	i_CGC_Translocation_Partner	i_CGC_Tumor_Types_Germline	i_CGC_Tumor_Types_Somatic	i_COSMIC_fusion_genes	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_mutations	i_COSMIC_overlapping_primary_sites	i_COSMIC_tissue_types_affected	i_COSMIC_total_alterations_in_gene	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Codon_Change	i_DNARepairGenes_Role	i_Description	i_DrugBank	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_FamilialCancerDatabase_Syndromes	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_GO_Biological_Process	i_GO_Cellular_Component	i_GO_Molecular_Function	i_Genome_Change	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_MUTSIG_Published_Results	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_SwissProt_acc_Id	i_SwissProt_entry_Id	i_TCGAscape_Amplification_Peaks	i_TCGAscape_Deletion_Peaks	i_Transcript_Exon	i_Transcript_Position	i_Transcript_Strand	i_Tumorscape_Amplification_Peaks	i_Tumorscape_Deletion_Peaks	i_UniProt_AApos	i_UniProt_Experimental_Info	i_UniProt_Natural_Variations	i_UniProt_Region	i_UniProt_Site	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_cDNA_Change	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_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
CASZ1	54897	broad.mit.edu	37	1	10713867	10713867	+	Silent	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:10713867C>T	ENST00000377022.3	-	11	2564	c.2247G>A	c.(2245-2247)gcG>gcA	p.A749A	RP4-734G22.3_ENST00000606802.1_RNA|CASZ1_ENST00000344008.5_Silent_p.A749A	NM_001079843.2	NP_001073312.1	Q86V15	CASZ1_HUMAN	castor zinc finger 1	749					multicellular organismal development (GO:0007275)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(2)|cervix(1)|endometrium(9)|large_intestine(13)|lung(18)|ovary(2)|prostate(5)|skin(2)|urinary_tract(1)	54	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)		CAGCCAGGGACGCAGAGGACT	0.667																																						uc001aro.2																			0				skin(1)	1						c.(2245-2247)GCG>GCA		castor homolog 1, zinc finger isoform a							33.0	42.0	39.0					1																	10713867		2203	4300	6503	SO:0001819	synonymous_variant	54897				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	DNA binding|zinc ion binding	g.chr1:10713867C>T	AK000328	CCDS120.2, CCDS41246.1	1p36.22	2013-01-07	2007-02-02		ENSG00000130940	ENSG00000130940		"""Zinc fingers, C2H2-type"""	26002	protein-coding gene	gene with protein product	"""zinc finger protein 693"", ""survival related gene"""	609895	"""castor homolog 1, zinc finger (Drosophila)"""			16631614, 21252912	Standard	NM_001079843		Approved	FLJ20321, ZNF693, castor, cst, SRG	uc001aro.4	Q86V15	OTTHUMG00000002035	ENST00000377022.3:c.2247G>A	1.37:g.10713867C>T						CASZ1_uc001arp.1_Silent_p.A749A|CASZ1_uc009vmx.2_Silent_p.A773A	p.A749A	NM_001079843	NP_001073312	Q86V15	CASZ1_HUMAN	STAD - Stomach adenocarcinoma(5;0.0224)	UCEC - Uterine corpus endometrioid carcinoma (279;0.0265)|Colorectal(212;3.54e-08)|COAD - Colon adenocarcinoma(227;9.56e-06)|BRCA - Breast invasive adenocarcinoma(304;0.000219)|Kidney(185;0.00142)|KIRC - Kidney renal clear cell carcinoma(229;0.00381)|READ - Rectum adenocarcinoma(331;0.0419)|STAD - Stomach adenocarcinoma(132;0.0623)	11	2567	-	Ovarian(185;0.203)|all_lung(157;0.204)	Lung NSC(185;4.96e-06)|all_lung(284;1.22e-05)|Renal(390;0.000147)|Breast(348;0.00093)|Colorectal(325;0.00212)|Hepatocellular(190;0.00913)|Ovarian(437;0.0229)|Myeloproliferative disorder(586;0.0255)	749					Q078S9|Q2EN02|Q5T9S1|Q6ZNM8|Q8WX49|Q8WX50|Q9BT16|Q9NXC6	Silent	SNP	ENST00000377022.3	37	c.2247G>A	CCDS41246.1																																																																																				0.667	CASZ1-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000005673.2	NM_017766	
GLIS1	148979	broad.mit.edu	37	1	54059816	54059816	+	Nonsense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:54059816G>A	ENST00000312233.2	-	3	1326	c.760C>T	c.(760-762)Cga>Tga	p.R254*		NM_147193.2	NP_671726.2			GLIS family zinc finger 1											endometrium(3)|kidney(2)|large_intestine(3)|liver(1)|lung(7)|ovary(1)|skin(3)|urinary_tract(4)	24						GAGTGCACTCGCATGTGGATG	0.652																																						uc001cvr.1																			0				skin(1)	1						c.(760-762)CGA>TGA		GLIS family zinc finger 1							66.0	63.0	64.0					1																	54059816		2203	4300	6503	SO:0001587	stop_gained	148979				negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|transcription from RNA polymerase II promoter	nucleus	DNA binding|zinc ion binding	g.chr1:54059816G>A	AK093474	CCDS582.1	1p32.3	2008-02-05			ENSG00000174332	ENSG00000174332		"""Zinc fingers, C2H2-type"""	29525	protein-coding gene	gene with protein product		610378				12042312, 14500813	Standard	NM_147193		Approved	FLJ36155	uc001cvr.1	Q8NBF1	OTTHUMG00000008079	ENST00000312233.2:c.760C>T	1.37:g.54059816G>A	ENSP00000309653:p.Arg254*						p.R254*	NM_147193	NP_671726	Q8NBF1	GLIS1_HUMAN			3	1327	-			254			C2H2-type 2; atypical.			Nonsense_Mutation	SNP	ENST00000312233.2	37	c.760C>T	CCDS582.1	.	.	.	.	.	.	.	.	.	.	G	42	9.216320	0.99103	.	.	ENSG00000174332	ENST00000312233	.	.	.	5.13	-0.995	0.10222	.	0.000000	0.64402	D	0.000020	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.5369	0.76011	0.0:0.0:0.5472:0.4527	.	.	.	.	X	254	.	ENSP00000309653:R254X	R	-	1	2	GLIS1	53832404	1.000000	0.71417	0.999000	0.59377	0.989000	0.77384	1.008000	0.29872	0.028000	0.15324	-0.262000	0.10625	CGA		0.652	GLIS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000022109.1	NM_147193	
INADL	10207	broad.mit.edu	37	1	62228837	62228837	+	Frame_Shift_Del	DEL	C	C	-			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:62228837delC	ENST00000371158.2	+	3	289	c.175delC	c.(175-177)caafs	p.Q59fs	INADL_ENST00000316485.6_Frame_Shift_Del_p.Q59fs	NM_176877.2	NP_795352	Q8NI35	INADL_HUMAN	InaD-like (Drosophila)	59	L27. {ECO:0000255|PROSITE- ProRule:PRU00365}.				cell junction assembly (GO:0034329)|cell-cell junction organization (GO:0045216)|intracellular signal transduction (GO:0035556)|tight junction assembly (GO:0070830)	apical part of cell (GO:0045177)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|tight junction (GO:0005923)				breast(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(11)|large_intestine(8)|liver(1)|lung(51)|ovary(3)|pancreas(1)|prostate(7)|skin(5)|stomach(1)|upper_aerodigestive_tract(3)	103						GTCCATCAAGCAACTGAAGGG	0.363																																						uc001dab.2																			0				ovary(3)|skin(1)	4						c.(175-177)CAAfs		InaD-like							57.0	54.0	55.0					1																	62228837		2203	4300	6503	SO:0001589	frameshift_variant	10207				intracellular signal transduction|tight junction assembly	apical plasma membrane|perinuclear region of cytoplasm|tight junction	protein binding	g.chr1:62228837delC	AB044807	CCDS617.2	1p31	2008-02-05			ENSG00000132849	ENSG00000132849			28881	protein-coding gene	gene with protein product		603199				9280290, 11374908	Standard	NM_176877		Approved	Cipp, PATJ	uc001dab.3	Q8NI35	OTTHUMG00000008560	ENST00000371158.2:c.175delC	1.37:g.62228837delC	ENSP00000360200:p.Gln59fs					INADL_uc009waf.1_Frame_Shift_Del_p.Q59fs|INADL_uc001daa.2_Frame_Shift_Del_p.Q59fs	p.Q59fs	NM_176877	NP_795352	Q8NI35	INADL_HUMAN			3	289	+			59			L27.		O15249|O43742|O60833|Q5VUA5|Q5VUA6|Q5VUA7|Q5VUA8|Q5VUA9|Q5VUB0|Q8WU78|Q9H3N9	Frame_Shift_Del	DEL	ENST00000371158.2	37	c.175delC	CCDS617.2																																																																																				0.363	INADL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000023639.2	NM_170605	
ITGA10	8515	broad.mit.edu	37	1	145532131	145532131	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:145532131C>T	ENST00000369304.3	+	8	950	c.775C>T	c.(775-777)Cag>Tag	p.Q259*	ITGA10_ENST00000481236.1_3'UTR|ITGA10_ENST00000538811.1_Nonsense_Mutation_p.Q128*|ITGA10_ENST00000539363.1_Nonsense_Mutation_p.Q116*	NM_003637.3	NP_003628.2	O75578	ITA10_HUMAN	integrin, alpha 10	259	VWFA. {ECO:0000255|PROSITE- ProRule:PRU00219}.				axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell-matrix adhesion (GO:0007160)|extracellular matrix organization (GO:0030198)|integrin-mediated signaling pathway (GO:0007229)	integrin alpha10-beta1 complex (GO:0034680)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)	collagen binding (GO:0005518)|collagen binding involved in cell-matrix adhesion (GO:0098639)|metal ion binding (GO:0046872)			NS(1)|breast(2)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	59	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)					AGGGTTCAGTCAGTCCCATGG	0.542																																						uc001eoa.2																			0				lung(2)|ovary(2)|kidney(2)|large_intestine(1)|skin(1)	8						c.(775-777)CAG>TAG		integrin, alpha 10 precursor							94.0	93.0	93.0					1																	145532131		2203	4300	6503	SO:0001587	stop_gained	8515				cell-matrix adhesion|integrin-mediated signaling pathway	integrin complex	collagen binding|receptor activity	g.chr1:145532131C>T	AF074015	CCDS72869.1	1q21.1	2010-03-23			ENSG00000143127	ENSG00000143127		"""Integrins"""	6135	protein-coding gene	gene with protein product		604042				9685391, 10702680	Standard	NM_003637		Approved		uc001eoa.3	O75578	OTTHUMG00000013751	ENST00000369304.3:c.775C>T	1.37:g.145532131C>T	ENSP00000358310:p.Gln259*					NBPF10_uc001emp.3_Intron|ITGA10_uc010oyv.1_Nonsense_Mutation_p.Q128*|ITGA10_uc009wiw.2_Nonsense_Mutation_p.Q116*|ITGA10_uc010oyw.1_Nonsense_Mutation_p.Q204*	p.Q259*	NM_003637	NP_003628	O75578	ITA10_HUMAN			8	851	+	all_hematologic(18;0.0187)|Acute lymphoblastic leukemia(18;0.0786)		259			VWFA.|Extracellular (Potential).		B2RAM4|B2RTV5|Q6UXJ6|Q9UHZ8	Nonsense_Mutation	SNP	ENST00000369304.3	37	c.775C>T	CCDS918.1	.	.	.	.	.	.	.	.	.	.	C	25.4	4.633562	0.87660	.	.	ENSG00000143127	ENST00000369304;ENST00000543043;ENST00000539363;ENST00000538811	.	.	.	5.2	3.25	0.37280	.	1.045980	0.07450	N	0.898914	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	12.2335	0.54500	0.0:0.6725:0.3275:0.0	.	.	.	.	X	259;225;116;128	.	ENSP00000358310:Q259X	Q	+	1	0	ITGA10	144243488	0.807000	0.29009	0.995000	0.50966	0.981000	0.71138	1.679000	0.37597	0.646000	0.30693	0.511000	0.50034	CAG		0.542	ITGA10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000038537.2	NM_003637	
CRTC2	200186	broad.mit.edu	37	1	153923904	153923904	+	Silent	SNP	G	G	A	rs201148360		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:153923904G>A	ENST00000368633.1	-	11	1363	c.1236C>T	c.(1234-1236)ggC>ggT	p.G412G	CRTC2_ENST00000368630.3_Silent_p.G92G|CRTC2_ENST00000476883.1_5'Flank	NM_181715.2	NP_859066.1	Q53ET0	CRTC2_HUMAN	CREB regulated transcription coactivator 2	412					gluconeogenesis (GO:0006094)|glucose homeostasis (GO:0042593)|histone H3-K9 acetylation (GO:0043970)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	cAMP response element binding protein binding (GO:0008140)			NS(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|lung(8)|ovary(3)|skin(1)|upper_aerodigestive_tract(2)	27	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)			AAGAGGGGGCGCCCAAAACAG	0.672													G|||	1	0.000199681	0.0	0.0	5008	,	,		14971	0.0		0.0	False		,,,				2504	0.001					uc010ped.1																			0				ovary(2)	2						c.(1234-1236)GGC>GGT		CREB regulated transcription coactivator 2		G		1,4401		0,1,2200	16.0	18.0	17.0		1236	-9.3	0.5	1		17	0,8598		0,0,4299	no	coding-synonymous	CRTC2	NM_181715.2		0,1,6499	AA,AG,GG		0.0,0.0227,0.0077		412/694	153923904	1,12999	2201	4299	6500	SO:0001819	synonymous_variant	200186				interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|nucleus	protein binding	g.chr1:153923904G>A	AY360172	CCDS30875.1	1q21.3	2008-02-05			ENSG00000160741	ENSG00000160741			27301	protein-coding gene	gene with protein product		608972				14506290, 14536081	Standard	NM_181715		Approved	TORC2	uc021pab.1	Q53ET0	OTTHUMG00000037156	ENST00000368633.1:c.1236C>T	1.37:g.153923904G>A						CRTC2_uc001fde.3_RNA|CRTC2_uc001fdf.3_Intron	p.G412G	NM_181715	NP_859066	Q53ET0	CRTC2_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.151)		11	1306	-	all_lung(78;3.05e-32)|Lung NSC(65;3.74e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		412					Q6UUV8|Q7Z3X7|Q8N332	Silent	SNP	ENST00000368633.1	37	c.1236C>T	CCDS30875.1																																																																																				0.672	CRTC2-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090272.3	NM_181715	
IBA57	200205	broad.mit.edu	37	1	228362896	228362896	+	Silent	SNP	C	C	T	rs375524486		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:228362896C>T	ENST00000366711.3	+	3	755	c.753C>T	c.(751-753)aaC>aaT	p.N251N	IBA57_ENST00000484749.1_3'UTR|IBA57_ENST00000546123.1_Silent_p.N58N	NM_001010867.2	NP_001010867.1	Q5T440	CAF17_HUMAN	IBA57, iron-sulfur cluster assembly homolog (S. cerevisiae)	251					glycine catabolic process (GO:0006546)|heme biosynthetic process (GO:0006783)	mitochondrion (GO:0005739)	aminomethyltransferase activity (GO:0004047)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(7)|prostate(1)	11						CCTTCATGAACGGCGTGAGCT	0.647																																						uc001hsl.3																			0					0						c.(751-753)AAC>AAT		hypothetical protein LOC200205 precursor							66.0	67.0	66.0					1																	228362896		2203	4298	6501	SO:0001819	synonymous_variant	200205				glycine catabolic process|heme biosynthetic process	mitochondrion	aminomethyltransferase activity	g.chr1:228362896C>T	AK022796	CCDS31046.1	1q42.13	2011-03-11	2011-03-11	2011-03-11	ENSG00000181873	ENSG00000181873			27302	protein-coding gene	gene with protein product	"""iron-sulfur cluster assembly factor for biotin synthase- and aconitase-like mitochondrial proteins, with a mass of 57kDa"""	615316	"""chromosome 1 open reading frame 69"""	C1orf69			Standard	NM_001010867		Approved	FLJ12734	uc001hsl.4	Q5T440	OTTHUMG00000039769	ENST00000366711.3:c.753C>T	1.37:g.228362896C>T						C1orf69_uc010pvw.1_Silent_p.N58N	p.N251N	NM_001010867	NP_001010867	Q5T440	CAF17_HUMAN			3	842	+		Prostate(94;0.0405)	251						Silent	SNP	ENST00000366711.3	37	c.753C>T	CCDS31046.1																																																																																				0.647	IBA57-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000095980.1	NM_001010867	
ZNF496	84838	broad.mit.edu	37	1	247464120	247464120	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:247464120C>T	ENST00000294753.4	-	9	1929	c.1465G>A	c.(1465-1467)Gac>Aac	p.D489N	ZNF496_ENST00000462139.1_5'UTR|ZNF496_ENST00000366498.2_Missense_Mutation_p.D525N	NM_032752.1	NP_116141.1	Q96IT1	ZN496_HUMAN	zinc finger protein 496	489					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription from RNA polymerase II promoter (GO:0006366)	nuclear body (GO:0016604)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)			NS(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(5)|lung(13)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	36	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		OV - Ovarian serous cystadenocarcinoma(106;0.00703)			TGGAGTCTGTCCGGCTGCAGG	0.642																																						uc001ico.2																			0				ovary(1)|central_nervous_system(1)	2						c.(1465-1467)GAC>AAC		zinc finger protein 496							53.0	59.0	57.0					1																	247464120		2203	4300	6503	SO:0001583	missense	84838				positive regulation of transcription, DNA-dependent|viral reproduction		DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr1:247464120C>T	BC007263	CCDS1631.1	1q44	2013-01-09			ENSG00000162714	ENSG00000162714		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	23713	protein-coding gene	gene with protein product		613911				12477932	Standard	NM_032752		Approved	ZKSCAN17, MGC15548, ZSCAN49	uc001ico.3	Q96IT1	OTTHUMG00000041164	ENST00000294753.4:c.1465G>A	1.37:g.247464120C>T	ENSP00000294753:p.Asp489Asn					ZNF496_uc009xgv.2_Missense_Mutation_p.D525N|ZNF496_uc001icp.2_Missense_Mutation_p.D489N	p.D489N	NM_032752	NP_116141	Q96IT1	ZN496_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.00703)		9	1930	-	all_cancers(71;0.000136)|all_epithelial(71;2.62e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)		489					Q8TBS2	Missense_Mutation	SNP	ENST00000294753.4	37	c.1465G>A	CCDS1631.1	.	.	.	.	.	.	.	.	.	.	C	13.21	2.168989	0.38315	.	.	ENSG00000162714	ENST00000294753;ENST00000366498	T;T	0.07444	3.19;3.19	4.05	1.11	0.20524	Zinc finger, C2H2 (1);	1.417150	0.04430	N	0.369108	T	0.04770	0.0129	N	0.08118	0	0.09310	N	1	P;B	0.41848	0.763;0.244	B;B	0.37144	0.242;0.04	T	0.37619	-0.9698	10	0.32370	T	0.25	-8.1882	7.4466	0.27215	0.0:0.684:0.0:0.316	.	525;489	Q96IT1-2;Q96IT1	.;ZN496_HUMAN	N	489;525	ENSP00000294753:D489N;ENSP00000355454:D525N	ENSP00000294753:D489N	D	-	1	0	ZNF496	245530743	0.000000	0.05858	0.000000	0.03702	0.009000	0.06853	0.390000	0.20768	0.462000	0.27095	0.655000	0.94253	GAC		0.642	ZNF496-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000098655.2	NM_032752	
OR2G6	391211	broad.mit.edu	37	1	248685052	248685052	+	Silent	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr1:248685052C>T	ENST00000343414.4	+	1	137	c.105C>T	c.(103-105)taC>taT	p.Y35Y		NM_001013355.1	NP_001013373.1	Q5TZ20	OR2G6_HUMAN	olfactory receptor, family 2, subfamily G, member 6	35						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			NS(1)|cervix(1)|endometrium(2)|large_intestine(7)|lung(40)|ovary(3)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	61	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	OV - Ovarian serous cystadenocarcinoma(106;0.0265)			TGTACTTCTACGTCTTGAGCC	0.463																																						uc001ien.1																			0				ovary(2)|skin(1)	3						c.(103-105)TAC>TAT		olfactory receptor, family 2, subfamily G,							169.0	152.0	157.0					1																	248685052		2203	4300	6503	SO:0001819	synonymous_variant	391211				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr1:248685052C>T		CCDS31119.1	1q44	2012-08-09			ENSG00000188558	ENSG00000188558		"""GPCR / Class A : Olfactory receptors"""	27019	protein-coding gene	gene with protein product							Standard	NM_001013355		Approved		uc001ien.1	Q5TZ20	OTTHUMG00000040462	ENST00000343414.4:c.105C>T	1.37:g.248685052C>T							p.Y35Y	NM_001013355	NP_001013373	Q5TZ20	OR2G6_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.0265)		1	105	+	all_cancers(71;0.000108)|all_epithelial(71;1.03e-05)|Breast(184;0.00909)|Ovarian(71;0.0377)|all_lung(81;0.127)|Lung NSC(105;0.136)	all_cancers(173;0.0156)	35			Helical; Name=1; (Potential).		B2RP33	Silent	SNP	ENST00000343414.4	37	c.105C>T	CCDS31119.1																																																																																				0.463	OR2G6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097358.1	XM_372842	
PTEN	5728	broad.mit.edu	37	10	89720831	89720831	+	Frame_Shift_Del	DEL	G	G	-			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr10:89720831delG	ENST00000371953.3	+	8	2339	c.982delG	c.(982-984)gcafs	p.A328fs	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	328	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				activation of mitotic anaphase-promoting complex activity (GO:0007092)|aging (GO:0007568)|angiogenesis (GO:0001525)|apoptotic process (GO:0006915)|brain morphogenesis (GO:0048854)|canonical Wnt signaling pathway (GO:0060070)|cardiac muscle tissue development (GO:0048738)|cell migration (GO:0016477)|cell proliferation (GO:0008283)|central nervous system development (GO:0007417)|central nervous system myelin maintenance (GO:0032286)|central nervous system neuron axonogenesis (GO:0021955)|dendritic spine morphogenesis (GO:0060997)|dentate gyrus development (GO:0021542)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|innate immune response (GO:0045087)|inositol phosphate dephosphorylation (GO:0046855)|inositol phosphate metabolic process (GO:0043647)|learning or memory (GO:0007611)|locomotor rhythm (GO:0045475)|locomotory behavior (GO:0007626)|long term synaptic depression (GO:0060292)|long-term synaptic potentiation (GO:0060291)|male mating behavior (GO:0060179)|maternal behavior (GO:0042711)|memory (GO:0007613)|multicellular organismal response to stress (GO:0033555)|negative regulation of apoptotic process (GO:0043066)|negative regulation of axonogenesis (GO:0050771)|negative regulation of cell aging (GO:0090344)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell size (GO:0045792)|negative regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031658)|negative regulation of dendritic spine morphogenesis (GO:0061002)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of excitatory postsynaptic membrane potential (GO:0090394)|negative regulation of focal adhesion assembly (GO:0051895)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of myelination (GO:0031642)|negative regulation of organ growth (GO:0046621)|negative regulation of phagocytosis (GO:0050765)|negative regulation of phosphatidylinositol 3-kinase signaling (GO:0014067)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of ribosome biogenesis (GO:0090071)|negative regulation of synaptic vesicle clustering (GO:2000808)|neuron-neuron synaptic transmission (GO:0007270)|neurotrophin TRK receptor signaling pathway (GO:0048011)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell proliferation (GO:0008284)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:2000060)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|postsynaptic density assembly (GO:0097107)|prepulse inhibition (GO:0060134)|presynaptic membrane assembly (GO:0097105)|prostate gland growth (GO:0060736)|protein dephosphorylation (GO:0006470)|protein kinase B signaling (GO:0043491)|protein stabilization (GO:0050821)|regulation of B cell apoptotic process (GO:0002902)|regulation of cellular component size (GO:0032535)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)|regulation of myeloid cell apoptotic process (GO:0033032)|regulation of neuron projection development (GO:0010975)|regulation of protein stability (GO:0031647)|response to arsenic-containing substance (GO:0046685)|response to ATP (GO:0033198)|response to drug (GO:0042493)|response to estradiol (GO:0032355)|response to ethanol (GO:0045471)|response to glucose (GO:0009749)|response to nutrient (GO:0007584)|response to zinc ion (GO:0010043)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|social behavior (GO:0035176)|synapse assembly (GO:0007416)|synapse maturation (GO:0060074)|T cell receptor signaling pathway (GO:0050852)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|mitochondrion (GO:0005739)|myelin sheath adaxonal region (GO:0035749)|neuron projection (GO:0043005)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|Schmidt-Lanterman incisure (GO:0043220)	anaphase-promoting complex binding (GO:0010997)|enzyme binding (GO:0019899)|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity (GO:0051717)|lipid binding (GO:0008289)|magnesium ion binding (GO:0000287)|PDZ domain binding (GO:0030165)|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity (GO:0016314)|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity (GO:0051800)|phosphatidylinositol-3-phosphatase activity (GO:0004438)|phosphoprotein phosphatase activity (GO:0004721)|protein serine/threonine phosphatase activity (GO:0004722)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.0?(37)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.T319_K332del(1)|p.G165_*404del(1)|p.W274_F341del(1)|p.A328fs*1(1)|p.D326_K342del(1)		NS(28)|autonomic_ganglia(2)|biliary_tract(6)|bone(5)|breast(92)|central_nervous_system(676)|cervix(26)|endometrium(1068)|eye(8)|haematopoietic_and_lymphoid_tissue(137)|kidney(24)|large_intestine(98)|liver(20)|lung(91)|meninges(2)|oesophagus(2)|ovary(82)|pancreas(6)|prostate(129)|salivary_gland(5)|skin(127)|soft_tissue(19)|stomach(30)|testis(1)|thyroid(29)|upper_aerodigestive_tract(29)|urinary_tract(12)|vulva(17)	2771		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)		TCTTGACAAAGCAAATAAAGA	0.333		31	"""D, Mis, N, F, S"""		"""glioma,  prostate, endometrial"""	"""harmartoma, glioma,  prostate, endometrial"""			Proteus syndrome;Juvenile Polyposis;Hereditary Mixed Polyposis Syndrome type 1;Cowden syndrome;Bannayan-Riley-Ruvalcaba syndrome	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)																												uc001kfb.2		31	yes	Rec	yes	"""Cowden Syndrome, Bannayan-Riley-Ruvalcaba syndrome"""	10	10q23.3	5728	D|Mis|N|F|S	phosphatase and tensin homolog gene			"""L, E, M, O"""		harmartoma|glioma| prostate|endometrial	glioma| prostate|endometrial		53	Whole gene deletion(37)|Deletion - Frameshift(10)|Deletion - In frame(4)|Unknown(2)	p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.T319_K332del(1)|p.G165_*404del(1)|p.G165_K342del(1)|p.A328fs*15(1)|p.W274_F341del(1)|p.A328fs*1(1)|p.D326_K342del(1)	prostate(16)|central_nervous_system(13)|skin(6)|lung(4)|haematopoietic_and_lymphoid_tissue(3)|breast(3)|ovary(3)|endometrium(2)|urinary_tract(2)|soft_tissue(1)	endometrium(831)|central_nervous_system(657)|skin(121)|haematopoietic_and_lymphoid_tissue(101)|large_intestine(99)|prostate(97)|breast(73)|lung(65)|ovary(58)|thyroid(29)|stomach(29)|upper_aerodigestive_tract(25)|cervix(24)|liver(20)|vulva(17)|kidney(15)|NS(14)|soft_tissue(13)|urinary_tract(12)|eye(8)|pancreas(6)|salivary_gland(5)|bone(5)|biliary_tract(4)|autonomic_ganglia(2)|meninges(2)|testis(1)|oesophagus(1)	2334						c.(982-984)GCAfs		phosphatase and tensin homolog							75.0	77.0	76.0					10																	89720831		2203	4299	6502	SO:0001589	frameshift_variant	5728	Proteus_syndrome|Cowden_syndrome|Juvenile_Polyposis|Hereditary_Mixed_Polyposis_Syndrome_type_1|Bannayan-Riley-Ruvalcaba_syndrome	Familial Cancer Database	Incl.: Encephalocraniocutaneous Lipomatosis, ECCL, Proteus-like s.;incl.: Juvenile Polyposis of the Stomach;HMPS1, Colorectal Adenoma Carcinoma syndrome, CRAC, CRAC1;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;subset of PTEN-Hamartoma Tumor Syndrome; incl.: Ruvalcaba-Myhre-Smith s.	activation of mitotic anaphase-promoting complex activity|apoptosis|canonical Wnt receptor signaling pathway|cell proliferation|central nervous system development|induction of apoptosis|inositol phosphate dephosphorylation|negative regulation of cell migration|negative regulation of cyclin-dependent protein kinase activity involved in G1/S|negative regulation of focal adhesion assembly|negative regulation of G1/S transition of mitotic cell cycle|negative regulation of protein kinase B signaling cascade|negative regulation of protein phosphorylation|nerve growth factor receptor signaling pathway|phosphatidylinositol dephosphorylation|phosphatidylinositol-mediated signaling|positive regulation of protein ubiquitination involved in ubiquitin-dependent protein catabolic process|positive regulation of sequence-specific DNA binding transcription factor activity|protein stabilization|regulation of neuron projection development|T cell receptor signaling pathway	cytosol|internal side of plasma membrane|PML body	anaphase-promoting complex binding|enzyme binding|inositol-1,3,4,5-tetrakisphosphate 3-phosphatase activity|lipid binding|magnesium ion binding|PDZ domain binding|phosphatidylinositol-3,4,5-trisphosphate 3-phosphatase activity|phosphatidylinositol-3,4-bisphosphate 3-phosphatase activity|phosphatidylinositol-3-phosphatase activity|protein serine/threonine phosphatase activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	g.chr10:89720831delG	U92436	CCDS31238.1	10q23	2014-09-17	2008-07-31		ENSG00000171862	ENSG00000171862		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	9588	protein-coding gene	gene with protein product	"""mutated in multiple advanced cancers 1"""	601728		BZS, MHAM		9090379	Standard	NM_000314		Approved	MMAC1, TEP1, PTEN1	uc001kfb.3	P60484	OTTHUMG00000018688	ENST00000371953.3:c.982delG	10.37:g.89720831delG	ENSP00000361021:p.Ala328fs	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)					p.A328fs	NM_000314	NP_000305	P60484	PTEN_HUMAN	KIRC - Kidney renal clear cell carcinoma(1;0.214)	UCEC - Uterine corpus endometrioid carcinoma (6;0.000228)|all cancers(1;4.16e-84)|GBM - Glioblastoma multiforme(1;7.77e-49)|Epithelial(1;7.67e-41)|OV - Ovarian serous cystadenocarcinoma(1;6.22e-15)|BRCA - Breast invasive adenocarcinoma(1;1.1e-06)|Lung(2;3.18e-06)|Colorectal(12;4.88e-06)|LUSC - Lung squamous cell carcinoma(2;4.97e-06)|COAD - Colon adenocarcinoma(12;1.13e-05)|Kidney(1;0.000288)|KIRC - Kidney renal clear cell carcinoma(1;0.00037)|STAD - Stomach adenocarcinoma(243;0.218)	9	2013	+		all_cancers(4;3.61e-31)|all_epithelial(4;3.96e-23)|Prostate(4;8.12e-23)|Breast(4;0.000111)|Melanoma(5;0.00146)|all_hematologic(4;0.00227)|Colorectal(252;0.00494)|all_neural(4;0.00513)|Acute lymphoblastic leukemia(4;0.0116)|Glioma(4;0.0274)|all_lung(38;0.132)	328	KANKDKANR->AAGADAANA: Reduces growth suppression activity and promotes anchorage-independent growth. Reduces binding to phospholipid membranes in vitro; phosphatase activity towards PtdIns(3,4,5)P3 is not affected.		C2 tensin-type.		B2R904|F2YHV0|O00633|O02679|Q6ICT7	Frame_Shift_Del	DEL	ENST00000371953.3	37	c.982delG	CCDS31238.1																																																																																				0.333	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
MUC5B	727897	broad.mit.edu	37	11	1283520	1283520	+	IGR	SNP	A	A	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr11:1283520A>C	ENST00000529681.1	+	0	17911					NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming						cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		GCAGTCCAGGACCCCCAGCAG	0.657																																						uc009ycr.1																			0					0						c.(18277-18279)GAC>GCC		SubName: Full=Mucin 5AC, oligomeric mucus/gel-forming;							49.0	58.0	55.0					11																	1283520		872	1990	2862	SO:0001628	intergenic_variant	727897				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding	g.chr11:1283520A>C	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84			11.37:g.1283520A>C							p.D6093A	NM_017511	NP_059981	Q9HC84	MUC5B_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)	72	18404	+		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)	Error:Variant_position_missing_in_Q9HC84_after_alignment					O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	c.18278A>C	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	A	1.978	-0.434742	0.04669	.	.	ENSG00000117983	ENST00000406844	.	.	.	1.35	-2.7	0.06004	.	.	.	.	.	T	0.22936	0.0554	.	.	.	.	.	.	B	0.18461	0.028	B	0.09377	0.004	T	0.11792	-1.0573	6	0.33141	T	0.24	.	3.8118	0.08799	0.2134:0.4206:0.366:0.0	.	6093	A7Y9J9	.	A	5468	.	ENSP00000384815:D5468A	D	+	2	0	MUC5B	1240096	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.549000	0.06041	-1.384000	0.02103	-0.425000	0.05940	GAC		0.657	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093	
LRRC32	2615	broad.mit.edu	37	11	76371805	76371805	+	Missense_Mutation	SNP	G	G	A	rs576424220		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr11:76371805G>A	ENST00000407242.2	-	3	1074	c.832C>T	c.(832-834)Cgg>Tgg	p.R278W	LRRC32_ENST00000404995.1_Missense_Mutation_p.R278W|LRRC32_ENST00000464145.1_Intron|LRRC32_ENST00000260061.5_Missense_Mutation_p.R278W|AP001189.4_ENST00000447519.1_RNA	NM_005512.2	NP_005503.1	Q14392	LRC32_HUMAN	leucine rich repeat containing 32	278					negative regulation of activated T cell proliferation (GO:0046007)|negative regulation of cytokine secretion (GO:0050710)|positive regulation of gene expression (GO:0010628)	integral component of plasma membrane (GO:0005887)				endometrium(1)|large_intestine(3)|lung(26)|upper_aerodigestive_tract(1)	31						GTGGGGAGCCGGATGAGGTTG	0.652																																						uc001oxq.3																			0					0						c.(832-834)CGG>TGG		leucine rich repeat containing 32 precursor							53.0	51.0	52.0					11																	76371805		2200	4292	6492	SO:0001583	missense	2615					integral to plasma membrane		g.chr11:76371805G>A	Z24680	CCDS8245.1	11q13.5-q14	2008-02-05	2005-02-25	2005-02-25	ENSG00000137507	ENSG00000137507			4161	protein-coding gene	gene with protein product		137207	"""glycoprotein A repetitions predominant"""	D11S833E, GARP		8180135, 1543912	Standard	NM_005512		Approved		uc001oxq.4	Q14392	OTTHUMG00000133687	ENST00000407242.2:c.832C>T	11.37:g.76371805G>A	ENSP00000384126:p.Arg278Trp					LRRC32_uc001oxr.3_Missense_Mutation_p.R278W|LRRC32_uc010rsf.1_Missense_Mutation_p.R278W	p.R278W	NM_005512	NP_005503	Q14392	LRC32_HUMAN			3	1075	-			278			LRR 10.|Extracellular (Potential).		Q86V06	Missense_Mutation	SNP	ENST00000407242.2	37	c.832C>T	CCDS8245.1	.	.	.	.	.	.	.	.	.	.	G	16.75	3.209483	0.58343	.	.	ENSG00000137507	ENST00000260061;ENST00000407242;ENST00000404995	T;T;T	0.80214	-1.35;-1.35;-1.35	4.42	3.49	0.39957	.	0.553031	0.19168	N	0.121012	T	0.81716	0.4881	M	0.67517	2.055	0.40347	D	0.979097	D	0.76494	0.999	P	0.47528	0.549	D	0.84164	0.0430	10	0.72032	D	0.01	.	13.7074	0.62648	0.0:0.0:0.8447:0.1553	.	278	Q14392	LRC32_HUMAN	W	278	ENSP00000260061:R278W;ENSP00000384126:R278W;ENSP00000385766:R278W	ENSP00000260061:R278W	R	-	1	2	LRRC32	76049453	1.000000	0.71417	0.995000	0.50966	0.744000	0.42396	4.531000	0.60602	1.055000	0.40461	0.455000	0.32223	CGG		0.652	LRRC32-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257926.2	NM_005512	
GRAMD1B	57476	broad.mit.edu	37	11	123485469	123485469	+	Silent	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr11:123485469G>A	ENST00000529750.1	+	16	2142	c.1815G>A	c.(1813-1815)cgG>cgA	p.R605R	GRAMD1B_ENST00000450171.2_Silent_p.R296R|GRAMD1B_ENST00000456860.2_Silent_p.R612R|GRAMD1B_ENST00000322282.7_Silent_p.R605R	NM_020716.1	NP_065767.1	Q3KR37	GRM1B_HUMAN	GRAM domain containing 1B	605						integral component of membrane (GO:0016021)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|large_intestine(5)|lung(17)|ovary(2)|prostate(1)|upper_aerodigestive_tract(2)	30		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)		CACAGACGCGGCATATCCCGG	0.537																																						uc001pyx.2																			0				ovary(1)	1						c.(1813-1815)CGG>CGA		GRAM domain containing 1B							61.0	61.0	61.0					11																	123485469		1964	4142	6106	SO:0001819	synonymous_variant	57476					integral to membrane		g.chr11:123485469G>A	AB033027	CCDS53720.1, CCDS66253.1, CCDS66254.1	11q24.1	2005-11-02				ENSG00000023171			29214	protein-coding gene	gene with protein product						10574462	Standard	NM_001286564		Approved	KIAA1201	uc001pyx.2	Q3KR37		ENST00000529750.1:c.1815G>A	11.37:g.123485469G>A						GRAMD1B_uc001pyw.2_Silent_p.R612R|GRAMD1B_uc010rzw.1_Silent_p.R565R|GRAMD1B_uc010rzx.1_Silent_p.R565R|GRAMD1B_uc001pyy.2_Silent_p.R296R	p.R605R	NM_020716	NP_065767	Q3KR37	GRM1B_HUMAN		BRCA - Breast invasive adenocarcinoma(274;7.32e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0394)	16	2144	+		Breast(109;0.00204)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)	605					Q6UW85|Q9ULL9	Silent	SNP	ENST00000529750.1	37	c.1815G>A	CCDS53720.1																																																																																				0.537	GRAMD1B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000387404.2	XM_370660	
DDX11	1663	broad.mit.edu	37	12	31236988	31236988	+	Missense_Mutation	SNP	G	G	T	rs369920569		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr12:31236988G>T	ENST00000407793.2	+	3	637	c.386G>T	c.(385-387)cGa>cTa	p.R129L	DDX11_ENST00000542838.1_Missense_Mutation_p.R129L|DDX11_ENST00000350437.4_Missense_Mutation_p.R129L|DDX11_ENST00000545668.1_Missense_Mutation_p.R129L|DDX11_ENST00000251758.5_Missense_Mutation_p.R129L|DDX11_ENST00000228264.6_Missense_Mutation_p.R103L	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	129	Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					CTGGTGGACCGACTAAAGGTG	0.587										Multiple Myeloma(12;0.14)																												uc001rjt.1																			0				breast(3)	3						c.(385-387)CGA>CTA		DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11							55.0	67.0	63.0					12																	31236988		2202	4299	6501	SO:0001583	missense	1663				G2/M transition of mitotic cell cycle|interspecies interaction between organisms|mitotic sister chromatid segregation|positive regulation of cell proliferation|S phase of mitotic cell cycle|sister chromatid cohesion	midbody|nuclear chromatin|nucleolus|spindle pole	ATP binding|ATP-dependent DNA helicase activity|DNA binding|protein binding|RNA binding	g.chr12:31236988G>T	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.386G>T	12.37:g.31236988G>T	ENSP00000384703:p.Arg129Leu	Multiple Myeloma(12;0.14)				DDX11_uc010sjw.1_Missense_Mutation_p.R129L|DDX11_uc010sjx.1_RNA|DDX11_uc001rjr.1_Missense_Mutation_p.R129L|DDX11_uc001rjs.1_Missense_Mutation_p.R129L|DDX11_uc001rju.1_5'UTR|DDX11_uc001rjv.1_Missense_Mutation_p.R129L|DDX11_uc001rjw.1_Missense_Mutation_p.R103L	p.R129L	NM_152438	NP_689651	Q96FC9	DDX11_HUMAN			3	637	+	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)		129			Helicase ATP-binding.		Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Missense_Mutation	SNP	ENST00000407793.2	37	c.386G>T	CCDS44856.1	.	.	.	.	.	.	.	.	.	.	G	13.39	2.223219	0.39300	.	.	ENSG00000013573	ENST00000542838;ENST00000407793;ENST00000251758;ENST00000228264;ENST00000438391;ENST00000415475;ENST00000545668;ENST00000350437;ENST00000535317	T;T;T;T;T;T;T;T;T	0.59772	4.04;4.04;4.04;4.04;0.24;4.04;4.04;4.04;4.04	4.57	3.68	0.42216	Helicase-like, DEXD box c2 type (1);Helicase, superfamily 1/2, ATP-binding domain, DinG/Rad3-type (1);	0.112857	0.64402	D	0.000014	T	0.68210	0.2976	M	0.75777	2.31	0.44908	D	0.997929	D;D;D;D	0.63880	0.993;0.986;0.985;0.993	P;P;P;P	0.61722	0.884;0.714;0.844;0.893	T	0.68300	-0.5445	10	0.51188	T	0.08	.	7.1205	0.25442	0.2017:0.0:0.7983:0.0	.	129;129;129;129	B4DZY1;Q96FC9;Q96FC9-4;Q96FC9-2	.;DDX11_HUMAN;.;.	L	129;129;129;103;129;103;129;129;165	ENSP00000443426:R129L;ENSP00000384703:R129L;ENSP00000251758:R129L;ENSP00000228264:R103L;ENSP00000407646:R129L;ENSP00000406457:R103L;ENSP00000440402:R129L;ENSP00000309965:R129L;ENSP00000440171:R165L	ENSP00000228264:R103L	R	+	2	0	DDX11	31128255	1.000000	0.71417	0.217000	0.23759	0.118000	0.20060	3.409000	0.52657	1.149000	0.42402	-0.424000	0.05967	CGA		0.587	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000399728.1	NM_030653	
PTPN11	5781	broad.mit.edu	37	12	112926909	112926909	+	Missense_Mutation	SNP	A	A	T	rs121918470		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr12:112926909A>T	ENST00000351677.2	+	13	1727	c.1529A>T	c.(1528-1530)cAg>cTg	p.Q510L		NM_002834.3	NP_002825.3	Q06124	PTN11_HUMAN	protein tyrosine phosphatase, non-receptor type 11	514	Tyrosine-protein phosphatase. {ECO:0000255|PROSITE-ProRule:PRU00160}.		Q -> P (in LEOPARD1). {ECO:0000269|PubMed:14961557, ECO:0000269|PubMed:15121796, ECO:0000269|PubMed:15690106}.|Q -> R (in NS1). {ECO:0000269|PubMed:15948193}.		abortive mitotic cell cycle (GO:0033277)|activation of MAPK activity (GO:0000187)|atrioventricular canal development (GO:0036302)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|brain development (GO:0007420)|cytokine-mediated signaling pathway (GO:0019221)|DNA damage checkpoint (GO:0000077)|ephrin receptor signaling pathway (GO:0048013)|epidermal growth factor receptor signaling pathway (GO:0007173)|ERBB signaling pathway (GO:0038127)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|genitalia development (GO:0048806)|glucose homeostasis (GO:0042593)|heart development (GO:0007507)|hormone metabolic process (GO:0042445)|hormone-mediated signaling pathway (GO:0009755)|innate immune response (GO:0045087)|inner ear development (GO:0048839)|insulin receptor signaling pathway (GO:0008286)|integrin-mediated signaling pathway (GO:0007229)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte migration (GO:0050900)|megakaryocyte development (GO:0035855)|multicellular organismal reproductive process (GO:0048609)|negative regulation of cell adhesion mediated by integrin (GO:0033629)|negative regulation of cortisol secretion (GO:0051463)|negative regulation of growth hormone secretion (GO:0060125)|negative regulation of insulin secretion (GO:0046676)|neurotrophin TRK receptor signaling pathway (GO:0048011)|organ growth (GO:0035265)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet formation (GO:0030220)|positive regulation of glucose import in response to insulin stimulus (GO:2001275)|positive regulation of hormone secretion (GO:0046887)|regulation of cell adhesion mediated by integrin (GO:0033628)|regulation of interferon-gamma-mediated signaling pathway (GO:0060334)|regulation of multicellular organism growth (GO:0040014)|regulation of protein export from nucleus (GO:0046825)|regulation of type I interferon-mediated signaling pathway (GO:0060338)|T cell costimulation (GO:0031295)|triglyceride metabolic process (GO:0006641)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)	insulin receptor binding (GO:0005158)|non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)|phosphoprotein phosphatase activity (GO:0004721)|protein tyrosine phosphatase activity (GO:0004725)|SH3/SH2 adaptor activity (GO:0005070)			NS(1)|autonomic_ganglia(2)|breast(1)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(406)|kidney(2)|large_intestine(6)|lung(16)|ovary(1)|skin(1)|soft_tissue(3)|stomach(3)	451						ACAGAAGCACAGTACCGATTT	0.498			Mis		"""JMML, AML, MDS"""		Noonan Syndrome		Noonan syndrome																													uc001ttx.2				Dom	yes		12	12q24.1	5781	Mis	"""protein tyrosine phosphatase, non-receptor type 11"""	yes	Noonan Syndrome	L			JMML|AML|MDS		0		p.Q510K(2)|p.Q510H(1)		haematopoietic_and_lymphoid_tissue(375)|lung(6)|autonomic_ganglia(2)|soft_tissue(2)|central_nervous_system(2)|large_intestine(1)|skin(1)|ovary(1)|NS(1)|kidney(1)	392	GRCh37	CM043070|CM052358	PTPN11	M	rs121918470	c.(1528-1530)CAG>CTG		protein tyrosine phosphatase, non-receptor type							182.0	170.0	174.0					12																	112926909		2203	4300	6503	SO:0001583	missense	5781	Noonan_syndrome	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome	axon guidance|cell junction assembly|ephrin receptor signaling pathway|epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|interferon-gamma-mediated signaling pathway|leukocyte migration|platelet activation|regulation of cell adhesion mediated by integrin|regulation of interferon-gamma-mediated signaling pathway|regulation of type I interferon-mediated signaling pathway|T cell costimulation|type I interferon-mediated signaling pathway	cytosol	non-membrane spanning protein tyrosine phosphatase activity|protein binding	g.chr12:112926909A>T	D13540	CCDS9163.1, CCDS58280.1	12q24.1	2014-09-17	2008-07-31		ENSG00000179295	ENSG00000179295		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"", ""SH2 domain containing"""	9644	protein-coding gene	gene with protein product		176876	"""Noonan syndrome 1"""	NS1		7894486, 1280823	Standard	NM_080601		Approved	BPTP3, SH-PTP2, SHP-2, PTP2C, SHP2	uc001ttx.3	Q06124	OTTHUMG00000134334	ENST00000351677.2:c.1529A>T	12.37:g.112926909A>T	ENSP00000340944:p.Gln510Leu						p.Q510L	NM_002834	NP_002825	Q06124	PTN11_HUMAN			13	1909	+			514		Q -> P (in LEOPARD1).	Tyrosine-protein phosphatase.		A8K1D9|Q96HD7	Missense_Mutation	SNP	ENST00000351677.2	37	c.1529A>T	CCDS9163.1	.	.	.	.	.	.	.	.	.	.	A	32	5.128559	0.94473	.	.	ENSG00000179295	ENST00000351677	D	0.99663	-6.33	5.13	5.13	0.70059	.	0.000000	0.85682	D	0.000000	D	0.99764	0.9904	H	0.97051	3.93	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.96994	0.9724	10	0.87932	D	0	.	15.2256	0.73348	1.0:0.0:0.0:0.0	.	510	Q06124-2	.	L	510	ENSP00000340944:Q510L	ENSP00000340944:Q510L	Q	+	2	0	PTPN11	111411292	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	8.910000	0.92685	2.064000	0.61679	0.528000	0.53228	CAG		0.498	PTPN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259496.2		
DIAPH3	81624	broad.mit.edu	37	13	60686198	60686198	+	Missense_Mutation	SNP	G	G	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr13:60686198G>T	ENST00000400324.4	-	3	556	c.336C>A	c.(334-336)aaC>aaA	p.N112K	DIAPH3_ENST00000400320.1_Missense_Mutation_p.N101K|DIAPH3_ENST00000377908.2_Missense_Mutation_p.N101K|DIAPH3_ENST00000400319.1_Intron|DIAPH3_ENST00000267215.4_Missense_Mutation_p.N112K|DIAPH3_ENST00000400330.1_Missense_Mutation_p.N112K	NM_001042517.1|NM_001258366.1	NP_001035982.1|NP_001245295.1	Q9NSV4	DIAP3_HUMAN	diaphanous-related formin 3	112					actin cytoskeleton organization (GO:0030036)|spermatogenesis (GO:0007283)	cytoplasm (GO:0005737)|nucleus (GO:0005634)				cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|liver(1)|lung(20)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	46		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)		GBM - Glioblastoma multiforme(99;2.77e-05)		GCTTTGGAAAGTTCTCCATCA	0.403																																						uc001vht.2																			0				ovary(2)	2						c.(334-336)AAC>AAA		diaphanous homolog 3 isoform a							170.0	158.0	162.0					13																	60686198		1845	4100	5945	SO:0001583	missense	81624				actin cytoskeleton organization		actin binding|Rho GTPase binding	g.chr13:60686198G>T	AL137718	CCDS41898.1, CCDS58294.1, CCDS58295.1, CCDS58296.1, CCDS58297.1, CCDS73579.1, CCDS73580.1	13q21.2	2013-05-24	2013-05-24		ENSG00000139734	ENSG00000139734			15480	protein-coding gene	gene with protein product		614567	"""diaphanous (Drosophila, homolog) 3"", ""auditory neuropathy, autosomal dominant 1"", ""diaphanous homolog 3 (Drosophila)"""	AUNA1		14767582, 20624953	Standard	NM_030932		Approved	DRF3, FLJ34705, AN, NSDAN	uc001vht.4	Q9NSV4	OTTHUMG00000017004	ENST00000400324.4:c.336C>A	13.37:g.60686198G>T	ENSP00000383178:p.Asn112Lys					DIAPH3_uc001vhw.1_Missense_Mutation_p.N101K|DIAPH3_uc010aed.1_Missense_Mutation_p.N101K|DIAPH3_uc010aee.1_Intron	p.N112K	NM_001042517	NP_001035982	Q9NSV4	DIAP3_HUMAN		GBM - Glioblastoma multiforme(99;2.77e-05)	3	555	-		Breast(118;0.052)|Prostate(109;0.103)|Hepatocellular(98;0.132)	112					A2A3B8|A2A3B9|A2A3C0|Q18P99|Q18PA0|Q18PA1|Q2KPB6|Q3ZK23|Q5JTP8|Q5T2S7|Q5XKF6|Q6MZF0|Q6NUP0|Q86VS4|Q8NAV4	Missense_Mutation	SNP	ENST00000400324.4	37	c.336C>A	CCDS41898.1	.	.	.	.	.	.	.	.	.	.	G	5.648	0.304272	0.10678	.	.	ENSG00000139734	ENST00000400324;ENST00000400330;ENST00000400327;ENST00000413168;ENST00000377908;ENST00000400320;ENST00000267215;ENST00000453990	T;T;T;D;T	0.82526	-1.4;-1.4;-1.41;-1.62;-1.39	5.82	0.602	0.17535	.	0.366869	0.28606	N	0.014746	T	0.74869	0.3773	L	0.40543	1.245	0.09310	N	1	P;P;P	0.50528	0.936;0.867;0.454	P;B;B	0.44673	0.457;0.267;0.084	T	0.66590	-0.5885	10	0.27082	T	0.32	.	10.5631	0.45156	0.4462:0.0:0.5538:0.0	.	101;101;112	C9JL55;C9JDG1;Q9NSV4	.;.;DIAP3_HUMAN	K	112;112;101;101;101;101;112;112	ENSP00000383178:N112K;ENSP00000383184:N112K;ENSP00000367141:N101K;ENSP00000383174:N101K;ENSP00000267215:N112K	ENSP00000267215:N112K	N	-	3	2	DIAPH3	59584199	0.015000	0.18098	0.029000	0.17559	0.084000	0.17831	0.114000	0.15520	0.119000	0.18210	0.655000	0.94253	AAC		0.403	DIAPH3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000045166.3	NM_001042517	
MAP3K9	4293	broad.mit.edu	37	14	71205013	71205013	+	Missense_Mutation	SNP	G	G	A	rs572761925		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr14:71205013G>A	ENST00000554752.2	-	8	1792	c.1793C>T	c.(1792-1794)aCg>aTg	p.T598M	MAP3K9_ENST00000553414.1_Missense_Mutation_p.T340M|MAP3K9_ENST00000554146.1_Missense_Mutation_p.T335M|MAP3K9_ENST00000381250.4_Missense_Mutation_p.T598M|MAP3K9_ENST00000555993.2_Missense_Mutation_p.T598M	NM_001284230.1	NP_001271159.1	P80192	M3K9_HUMAN	mitogen-activated protein kinase kinase kinase 9	598					activation of JNKK activity (GO:0007256)|activation of JUN kinase activity (GO:0007257)|apoptotic process (GO:0006915)|positive regulation of apoptotic process (GO:0043065)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		ATP binding (GO:0005524)|JUN kinase kinase kinase activity (GO:0004706)|MAP kinase kinase activity (GO:0004708)|protein homodimerization activity (GO:0042803)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)			breast(1)|central_nervous_system(3)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(25)|ovary(2)|prostate(1)|skin(3)|stomach(2)	46				all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)		TGGCCCCCACGTCCGTCCCTT	0.557													G|||	1	0.000199681	0.0	0.0	5008	,	,		17354	0.001		0.0	False		,,,				2504	0.0				GBM(114;411 1587 13539 28235 50070)	uc001xmm.2																			0				stomach(2)|lung(1)|central_nervous_system(1)|skin(1)	5						c.(1792-1794)ACG>ATG		mitogen-activated protein kinase kinase kinase							123.0	113.0	116.0					14																	71205013		2203	4300	6503	SO:0001583	missense	4293				activation of JUN kinase activity|protein autophosphorylation		ATP binding|JUN kinase kinase kinase activity|MAP kinase kinase activity|protein homodimerization activity	g.chr14:71205013G>A	AF251442	CCDS32112.1, CCDS61485.1, CCDS61488.1, CCDS73650.1	14q24.2	2012-10-02			ENSG00000006432	ENSG00000006432		"""Mitogen-activated protein kinase cascade / Kinase kinase kinases"""	6861	protein-coding gene	gene with protein product		600136		MLK1			Standard	NM_001284231		Approved	PRKE1, MEKK9	uc001xml.3	P80192	OTTHUMG00000171249	ENST00000554752.2:c.1793C>T	14.37:g.71205013G>A	ENSP00000451612:p.Thr598Met					MAP3K9_uc010ttk.1_Missense_Mutation_p.T335M|MAP3K9_uc001xmk.2_Missense_Mutation_p.T340M|MAP3K9_uc001xml.2_Missense_Mutation_p.T598M	p.T598M	NM_033141	NP_149132	P80192	M3K9_HUMAN		all cancers(60;0.00779)|BRCA - Breast invasive adenocarcinoma(234;0.00884)|OV - Ovarian serous cystadenocarcinoma(108;0.08)	8	1793	-			598					A3KN85|Q0D2G7|Q6EH31|Q9H2N5	Missense_Mutation	SNP	ENST00000554752.2	37	c.1793C>T		.	.	.	.	.	.	.	.	.	.	G	22.8	4.341792	0.81911	.	.	ENSG00000006432	ENST00000554752;ENST00000005198;ENST00000553414;ENST00000381250;ENST00000554146;ENST00000542284	T;T;T;T	0.13657	2.57;2.57;2.57;2.57	5.97	5.97	0.96955	.	0.104409	0.64402	D	0.000005	T	0.42131	0.1189	M	0.73962	2.25	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.87578	0.996;0.996;0.998;0.998	T	0.12041	-1.0563	10	0.72032	D	0.01	.	20.428	0.99075	0.0:0.0:1.0:0.0	.	335;598;598;340	G3V4P9;P80192;P80192-4;G3V347	.;M3K9_HUMAN;.;.	M	598;598;340;598;335;326	ENSP00000451612:T598M;ENSP00000451038:T340M;ENSP00000370649:T598M;ENSP00000451921:T335M	ENSP00000005198:T598M	T	-	2	0	MAP3K9	70274766	1.000000	0.71417	0.974000	0.42286	0.342000	0.28953	7.996000	0.88334	2.837000	0.97791	0.655000	0.94253	ACG		0.557	MAP3K9-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000412550.2		
AHSA1	10598	broad.mit.edu	37	14	77930956	77930956	+	Missense_Mutation	SNP	T	T	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr14:77930956T>A	ENST00000216479.3	+	5	648	c.488T>A	c.(487-489)aTg>aAg	p.M163K	SNORA46_ENST00000391069.1_RNA|AHSA1_ENST00000535854.2_Missense_Mutation_p.M163K|AHSA1_ENST00000555457.1_Intron	NM_012111.2	NP_036243.1	O95433	AHSA1_HUMAN	AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast)	163					positive regulation of ATPase activity (GO:0032781)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)			endometrium(1)|kidney(3)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)	8			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		ACCCAGGGCATGATCTTACCT	0.468																																						uc001xtw.2																			0					0						c.(487-489)ATG>AAG		activator of heat shock 90kDa protein ATPase							81.0	80.0	80.0					14																	77930956		2203	4300	6503	SO:0001583	missense	10598				protein folding|response to stress	cytosol|endoplasmic reticulum	ATPase activator activity|chaperone binding	g.chr14:77930956T>A	AJ243310	CCDS9863.1	14q	2008-02-05	2003-04-04	2003-04-11		ENSG00000100591			1189	protein-coding gene	gene with protein product		608466	"""chromosome 14 open reading frame 3"""	C14orf3			Standard	NM_012111		Approved	p38	uc001xtw.3	O95433		ENST00000216479.3:c.488T>A	14.37:g.77930956T>A	ENSP00000216479:p.Met163Lys					AHSA1_uc010tvk.1_Missense_Mutation_p.M163K	p.M163K	NM_012111	NP_036243	O95433	AHSA1_HUMAN	Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	5	648	+			163					B2R9L2|B4DUR9|Q96IL6|Q9P060	Missense_Mutation	SNP	ENST00000216479.3	37	c.488T>A	CCDS9863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	21.4|21.4	4.149308|4.149308	0.78001|0.78001	.|.	.|.	ENSG00000100591|ENSG00000100591	ENST00000553374|ENST00000555133;ENST00000216479;ENST00000535854	.|.	.|.	.|.	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	T|T	0.77377|0.77377	0.4121|0.4121	M|M	0.76170|0.76170	2.325|2.325	0.80722|0.80722	D|D	1|1	.|D;D	.|0.71674	.|0.997;0.998	.|D;D	.|0.75484	.|0.943;0.986	T|T	0.75033|0.75033	-0.3460|-0.3460	5|9	.|0.26408	.|T	.|0.33	-27.4274|-27.4274	14.9676|14.9676	0.71208|0.71208	0.0:0.0:0.0:1.0|0.0:0.0:0.0:1.0	.|.	.|163;163	.|B4DUR9;O95433	.|.;AHSA1_HUMAN	Q|K	108|28;163;163	.|.	.|ENSP00000216479:M163K	H|M	+|+	3|2	2|0	AHSA1|AHSA1	77000709|77000709	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.317000|7.317000	0.79018|0.79018	2.330000|2.330000	0.79161|0.79161	0.533000|0.533000	0.62120|0.62120	CAT|ATG		0.468	AHSA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414017.1	NM_012111	
AHSA1	10598	broad.mit.edu	37	14	77930997	77930997	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr14:77930997G>A	ENST00000216479.3	+	5	689	c.529G>A	c.(529-531)Ggg>Agg	p.G177R	SNORA46_ENST00000391069.1_RNA|AHSA1_ENST00000535854.2_Missense_Mutation_p.G177R|AHSA1_ENST00000555457.1_Intron	NM_012111.2	NP_036243.1	O95433	AHSA1_HUMAN	AHA1, activator of heat shock 90kDa protein ATPase homolog 1 (yeast)	177					positive regulation of ATPase activity (GO:0032781)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	ATPase activator activity (GO:0001671)|chaperone binding (GO:0051087)			endometrium(1)|kidney(3)|large_intestine(1)|prostate(1)|skin(1)|stomach(1)	8			Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)		AGACCCAGTGGGGCAGCCAGC	0.473																																						uc001xtw.2																			0					0						c.(529-531)GGG>AGG		activator of heat shock 90kDa protein ATPase							73.0	73.0	73.0					14																	77930997		2203	4300	6503	SO:0001583	missense	10598				protein folding|response to stress	cytosol|endoplasmic reticulum	ATPase activator activity|chaperone binding	g.chr14:77930997G>A	AJ243310	CCDS9863.1	14q	2008-02-05	2003-04-04	2003-04-11		ENSG00000100591			1189	protein-coding gene	gene with protein product		608466	"""chromosome 14 open reading frame 3"""	C14orf3			Standard	NM_012111		Approved	p38	uc001xtw.3	O95433		ENST00000216479.3:c.529G>A	14.37:g.77930997G>A	ENSP00000216479:p.Gly177Arg					AHSA1_uc010tvk.1_Missense_Mutation_p.G177R	p.G177R	NM_012111	NP_036243	O95433	AHSA1_HUMAN	Kidney(204;0.164)	BRCA - Breast invasive adenocarcinoma(234;0.0281)	5	689	+			177					B2R9L2|B4DUR9|Q96IL6|Q9P060	Missense_Mutation	SNP	ENST00000216479.3	37	c.529G>A	CCDS9863.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	11.45|11.45	1.642980|1.642980	0.29246|0.29246	.|.	.|.	ENSG00000100591|ENSG00000100591	ENST00000553374|ENST00000555133;ENST00000216479;ENST00000535854	.|.	.|.	.|.	6.08|6.08	1.95|1.95	0.26073|0.26073	.|.	0.542697|0.542697	0.21954|0.21954	N|N	0.066695|0.066695	T|T	0.26085|0.26085	0.0636|0.0636	L|L	0.34521|0.34521	1.04|1.04	0.09310|0.09310	N|N	0.999997|0.999997	.|B;B	.|0.02656	.|0.0;0.0	.|B;B	.|0.04013	.|0.001;0.0	T|T	0.18304|0.18304	-1.0341|-1.0341	6|9	.|0.17369	.|T	.|0.5	-2.5832|-2.5832	7.103|7.103	0.25348|0.25348	0.1852:0.4478:0.367:0.0|0.1852:0.4478:0.367:0.0	.|.	.|177;177	.|B4DUR9;O95433	.|.;AHSA1_HUMAN	E|R	122|42;177;177	.|.	.|ENSP00000216479:G177R	G|G	+|+	2|1	0|0	AHSA1|AHSA1	77000750|77000750	0.216000|0.216000	0.23585|0.23585	0.113000|0.113000	0.21522|0.21522	0.981000|0.981000	0.71138|0.71138	0.644000|0.644000	0.24766|0.24766	0.403000|0.403000	0.25479|0.25479	0.655000|0.655000	0.94253|0.94253	GGG|GGG		0.473	AHSA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000414017.1	NM_012111	
RPS6KA5	9252	broad.mit.edu	37	14	91372576	91372576	+	Missense_Mutation	SNP	G	G	A	rs534048620		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr14:91372576G>A	ENST00000261991.3	-	8	1047	c.874C>T	c.(874-876)Cgt>Tgt	p.R292C	RPS6KA5_ENST00000556304.1_5'UTR|RPS6KA5_ENST00000536315.2_Missense_Mutation_p.R213C|RPS6KA5_ENST00000418736.2_Missense_Mutation_p.R292C	NM_004755.2	NP_004746.2	O75582	KS6A5_HUMAN	ribosomal protein S6 kinase, 90kDa, polypeptide 5	292	Protein kinase 1. {ECO:0000255|PROSITE- ProRule:PRU00159}.				axon guidance (GO:0007411)|epidermal growth factor receptor signaling pathway (GO:0007173)|histone H2A-S1 phosphorylation (GO:0043990)|histone H3-S10 phosphorylation (GO:0043987)|histone H3-S28 phosphorylation (GO:0043988)|histone phosphorylation (GO:0016572)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|interleukin-1-mediated signaling pathway (GO:0070498)|intracellular signal transduction (GO:0035556)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of cytokine production (GO:0001818)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of histone acetylation (GO:0035066)|positive regulation of histone phosphorylation (GO:0033129)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|regulation of transcription, DNA-templated (GO:0006355)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			endometrium(2)|large_intestine(8)|lung(8)|ovary(1)|prostate(1)|skin(2)|urinary_tract(2)	24		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)		ATCAAAAGACGCTGAATTAGG	0.383													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18748	0.0		0.0	False		,,,				2504	0.0					uc001xys.2																			0				ovary(1)	1						c.(874-876)CGT>TGT		ribosomal protein S6 kinase, polypeptide 5							111.0	104.0	106.0					14																	91372576		2203	4300	6503	SO:0001583	missense	9252				axon guidance|epidermal growth factor receptor signaling pathway|histone phosphorylation|innate immune response|interleukin-1-mediated signaling pathway|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|nerve growth factor receptor signaling pathway|positive regulation of histone acetylation|positive regulation of histone phosphorylation|positive regulation of transcription from RNA polymerase II promoter|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cytoplasm|nucleoplasm	ATP binding|magnesium ion binding|protein binding|protein serine/threonine kinase activity	g.chr14:91372576G>A	AF074393	CCDS9893.1, CCDS45149.1	14q31-q32.1	2011-04-05	2002-08-29			ENSG00000100784			10434	protein-coding gene	gene with protein product		603607	"""ribosomal protein S6 kinase, 90kD, polypeptide 5"""			9687510, 10702687	Standard	NM_004755		Approved	MSK1, RLPK	uc001xys.2	O75582		ENST00000261991.3:c.874C>T	14.37:g.91372576G>A	ENSP00000261991:p.Arg292Cys					RPS6KA5_uc010twi.1_Missense_Mutation_p.R213C|RPS6KA5_uc001xyt.2_Missense_Mutation_p.R292C|RPS6KA5_uc010att.1_RNA	p.R292C	NM_004755	NP_004746	O75582	KS6A5_HUMAN		Epithelial(152;0.182)|BRCA - Breast invasive adenocarcinoma(234;0.201)	8	1089	-		all_cancers(154;0.0148)|Melanoma(154;0.099)|all_epithelial(191;0.146)	292			Protein kinase 1.		O95316|Q96AF7	Missense_Mutation	SNP	ENST00000261991.3	37	c.874C>T	CCDS9893.1	.	.	.	.	.	.	.	.	.	.	G	15.59	2.879614	0.51801	.	.	ENSG00000100784	ENST00000261991;ENST00000536315;ENST00000418736	T;T;T	0.53423	0.62;0.62;0.62	5.33	5.33	0.75918	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.225560	0.47093	D	0.000243	T	0.42017	0.1184	M	0.71296	2.17	0.80722	D	1	P;B	0.35959	0.53;0.375	B;B	0.24974	0.057;0.047	T	0.46775	-0.9167	10	0.52906	T	0.07	.	9.9904	0.41868	0.1514:0.0:0.8486:0.0	.	292;292	O75582-2;O75582	.;KS6A5_HUMAN	C	292;213;292	ENSP00000261991:R292C;ENSP00000442803:R213C;ENSP00000402787:R292C	ENSP00000261991:R292C	R	-	1	0	RPS6KA5	90442329	1.000000	0.71417	0.899000	0.35326	0.916000	0.54674	3.104000	0.50306	2.640000	0.89533	0.585000	0.79938	CGT		0.383	RPS6KA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411442.2	NM_004755	
SENP8	123228	broad.mit.edu	37	15	72432087	72432090	+	Frame_Shift_Del	DEL	CAGT	CAGT	-			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr15:72432087_72432090delCAGT	ENST00000542035.2	+	2	456_459	c.123_126delCAGT	c.(121-126)aacagtfs	p.NS41fs	SENP8_ENST00000544171.1_Frame_Shift_Del_p.NS41fs|SENP8_ENST00000340912.4_Frame_Shift_Del_p.NS41fs|SENP8_ENST00000544411.1_Frame_Shift_Del_p.NS41fs|RP11-2I17.4_ENST00000568984.1_RNA	NM_001166340.1	NP_001159812.1	Q96LD8	SENP8_HUMAN	SUMO/sentrin specific peptidase family member 8	41	Protease.						cysteine-type peptidase activity (GO:0008234)			breast(1)|kidney(2)|lung(1)|ovary(1)|skin(1)	6						ACTTTGCCAACAGTCAGTTTCATG	0.475																																						uc002atp.2																			0				ovary(1)|skin(1)	2						c.(121-126)AACAGTfs		SUMO/sentrin specific peptidase family member 8																																				SO:0001589	frameshift_variant	123228				proteolysis		cysteine-type peptidase activity|protein binding	g.chr15:72432087_72432090delCAGT	BC031411	CCDS10240.1	15q22.33	2005-08-17	2005-08-17	2004-01-30	ENSG00000166192	ENSG00000166192			22992	protein-coding gene	gene with protein product	"""NEDD8-specific protease 1"", ""sentrin/SUMO-specific protease SENP8"", ""deneddylase 1"""	608659	"""protease, cysteine, 2 (NEDD8 specific)"", ""SUMO/sentrin specific protease family member 8"""	PRSC2		12730221, 12759362	Standard	NM_145204		Approved	NEDP1, DEN1, HsT17512	uc021spt.1	Q96LD8	OTTHUMG00000133441	ENST00000542035.2:c.123_126delCAGT	15.37:g.72432091_72432094delCAGT	ENSP00000446057:p.Asn41fs						p.N41fs	NM_145204	NP_660205	Q96LD8	SENP8_HUMAN			2	222_225	+			41_42			Protease.		Q96QA4	Frame_Shift_Del	DEL	ENST00000542035.2	37	c.123_126delCAGT	CCDS10240.1																																																																																				0.475	SENP8-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420036.1	NM_145204	
RHBDL1	9028	broad.mit.edu	37	16	726867	726867	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr16:726867G>A	ENST00000219551.2	+	2	619	c.592G>A	c.(592-594)Gtg>Atg	p.V198M	LA16c-313D11.9_ENST00000567091.1_RNA|RHBDL1_ENST00000352681.3_Missense_Mutation_p.V133M|LA16c-313D11.9_ENST00000571933.1_RNA			O75783	RHBL1_HUMAN	rhomboid, veinlet-like 1 (Drosophila)	198					signal transduction (GO:0007165)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			endometrium(1)|kidney(1)|lung(4)|urinary_tract(3)	9		Hepatocellular(780;0.0218)				CCCACCCCCCGTGTTCATGGC	0.667																																						uc002cis.1																			0					0						c.(592-594)GTG>ATG		rhomboid protease 1							83.0	76.0	78.0					16																	726867		2201	4300	6501	SO:0001583	missense	9028				proteolysis|signal transduction	integral to plasma membrane|membrane fraction	calcium ion binding|serine-type endopeptidase activity	g.chr16:726867G>A	Y17108	CCDS61779.1	16p13.3	2008-02-05	2001-11-28	2003-04-11	ENSG00000103269	ENSG00000103269			10007	protein-coding gene	gene with protein product		603264	"""rhomboid (veinlet, Drosophila)-like"""	RHBDL		9662444	Standard	NM_001278720		Approved	RRP	uc002cis.1	O75783	OTTHUMG00000121141	ENST00000219551.2:c.592G>A	16.37:g.726867G>A	ENSP00000219551:p.Val198Met					RHBDL1_uc002cir.1_Missense_Mutation_p.V133M|RHBDL1_uc010uun.1_Missense_Mutation_p.V133M	p.V198M	NM_003961	NP_003952	O75783	RHBL1_HUMAN			2	619	+		Hepatocellular(780;0.0218)	198			Helical; (Potential).		A2IDC0|A2IDC1|Q0VAX4|Q9NQ85	Missense_Mutation	SNP	ENST00000219551.2	37	c.592G>A	CCDS10418.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.407879	0.62399	.	.	ENSG00000103269	ENST00000352681;ENST00000450775;ENST00000219551	T;T	0.12039	2.72;2.72	4.01	4.01	0.46588	.	0.082827	0.49305	D	0.000149	T	0.10766	0.0263	N	0.14661	0.345	0.51012	D	0.999904	D;D;P	0.63046	0.992;0.966;0.93	P;P;P	0.48840	0.584;0.483;0.592	T	0.04752	-1.0929	10	0.52906	T	0.07	-29.4608	8.8043	0.34927	0.1048:0.0:0.8952:0.0	.	133;198;133	B4DFK3;O75783;O75783-2	.;RHBL1_HUMAN;.	M	133;133;198	ENSP00000344206:V133M;ENSP00000219551:V198M	ENSP00000219551:V198M	V	+	1	0	RHBDL1	666868	0.998000	0.40836	0.969000	0.41365	0.981000	0.71138	2.727000	0.47311	2.079000	0.62486	0.462000	0.41574	GTG		0.667	RHBDL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000241619.1	NM_003961	
NOD2	64127	broad.mit.edu	37	16	50733737	50733737	+	Missense_Mutation	SNP	C	C	G	rs184502667		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr16:50733737C>G	ENST00000300589.2	+	2	517	c.412C>G	c.(412-414)Cgg>Ggg	p.R138G	NOD2_ENST00000526417.2_3'UTR	NM_022162.1	NP_071445.1	Q9HC29	NOD2_HUMAN	nucleotide-binding oligomerization domain containing 2	138	CARD 2. {ECO:0000255|PROSITE- ProRule:PRU00046}.				activation of MAPK activity (GO:0000187)|activation of MAPK activity involved in innate immune response (GO:0035419)|cellular response to muramyl dipeptide (GO:0071225)|cellular response to peptidoglycan (GO:0071224)|cytokine production involved in immune response (GO:0002367)|defense response (GO:0006952)|defense response to bacterium (GO:0042742)|defense response to Gram-positive bacterium (GO:0050830)|detection of bacterium (GO:0016045)|detection of biotic stimulus (GO:0009595)|detection of muramyl dipeptide (GO:0032498)|immunoglobulin production involved in immunoglobulin mediated immune response (GO:0002381)|innate immune response (GO:0045087)|innate immune response in mucosa (GO:0002227)|intracellular signal transduction (GO:0035556)|JNK cascade (GO:0007254)|macrophage inflammatory protein-1 alpha production (GO:0071608)|maintenance of gastrointestinal epithelium (GO:0030277)|microglial cell activation involved in immune response (GO:0002282)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of inflammatory response to antigenic stimulus (GO:0002862)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of interleukin-12 production (GO:0032695)|negative regulation of interleukin-18 production (GO:0032701)|negative regulation of interleukin-2 production (GO:0032703)|negative regulation of macrophage apoptotic process (GO:2000110)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of T cell mediated immunity (GO:0002710)|negative regulation of toll-like receptor 2 signaling pathway (GO:0034136)|negative regulation of tumor necrosis factor production (GO:0032720)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing 2 signaling pathway (GO:0070431)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|pathogen-associated molecular pattern dependent induction by symbiont of host innate immune response (GO:0052033)|positive regulation of B cell activation (GO:0050871)|positive regulation of biosynthetic process of antibacterial peptides active against Gram-positive bacteria (GO:0006965)|positive regulation of dendritic cell antigen processing and presentation (GO:0002606)|positive regulation of dendritic cell cytokine production (GO:0002732)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of gamma-delta T cell activation (GO:0046645)|positive regulation of humoral immune response mediated by circulating immunoglobulin (GO:0002925)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of interleukin-1 beta production (GO:0032731)|positive regulation of interleukin-1 beta secretion (GO:0050718)|positive regulation of interleukin-10 production (GO:0032733)|positive regulation of interleukin-12 production (GO:0032735)|positive regulation of interleukin-17 production (GO:0032740)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of JNK cascade (GO:0046330)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of Notch signaling pathway (GO:0045747)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phagocytosis (GO:0050766)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of prostaglandin-E synthase activity (GO:2000363)|positive regulation of prostaglandin-endoperoxide synthase activity (GO:0060585)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of stress-activated MAPK cascade (GO:0032874)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|positive regulation of type 2 immune response (GO:0002830)|protein oligomerization (GO:0051259)|regulation of inflammatory response (GO:0050727)|regulation of neutrophil chemotaxis (GO:0090022)|response to exogenous dsRNA (GO:0043330)|response to lipopolysaccharide (GO:0032496)|response to muramyl dipeptide (GO:0032495)|response to nutrient (GO:0007584)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|vesicle (GO:0031982)	ATP binding (GO:0005524)|CARD domain binding (GO:0050700)|enzyme binding (GO:0019899)|muramyl dipeptide binding (GO:0032500)|peptidoglycan binding (GO:0042834)|protein kinase binding (GO:0019901)			cervix(1)|endometrium(5)|kidney(3)|large_intestine(7)|lung(30)|ovary(3)|skin(3)	52		all_cancers(37;0.0156)				GCAGAGTCACCGGCCAGCCAT	0.632																																						uc002egm.1																			0				ovary(3)|skin(1)	4						c.(412-414)CGG>GGG		nucleotide-binding oligomerization domain							43.0	44.0	43.0					16																	50733737		2198	4300	6498	SO:0001583	missense	64127				activation of MAPK activity involved in innate immune response|cytokine production involved in immune response|detection of bacterium|detection of muramyl dipeptide|JNK cascade|MyD88-dependent toll-like receptor signaling pathway|MyD88-independent toll-like receptor signaling pathway|negative regulation of macrophage apoptosis|nucleotide-binding oligomerization domain containing 2 signaling pathway|positive regulation of B cell activation|positive regulation of dendritic cell antigen processing and presentation|positive regulation of epithelial cell proliferation|positive regulation of ERK1 and ERK2 cascade|positive regulation of gamma-delta T cell activation|positive regulation of I-kappaB kinase/NF-kappaB cascade|positive regulation of interleukin-1 beta secretion|positive regulation of interleukin-10 production|positive regulation of interleukin-17 production|positive regulation of interleukin-6 production|positive regulation of JNK cascade|positive regulation of NF-kappaB transcription factor activity|positive regulation of nitric-oxide synthase biosynthetic process|positive regulation of Notch signaling pathway|positive regulation of phosphatidylinositol 3-kinase activity|positive regulation of prostaglandin-E synthase activity|positive regulation of prostaglandin-endoperoxide synthase activity|positive regulation of stress-activated MAPK cascade|positive regulation of tumor necrosis factor production|positive regulation of type 2 immune response|protein oligomerization|stress-activated MAPK cascade|Toll signaling pathway|toll-like receptor 1 signaling pathway|toll-like receptor 2 signaling pathway|toll-like receptor 3 signaling pathway|toll-like receptor 4 signaling pathway	cell surface|cytosol|plasma membrane|vesicle	ATP binding|CARD domain binding|muramyl dipeptide binding|protein kinase binding	g.chr16:50733737C>G	AF178930	CCDS10746.1	16q12	2014-09-17	2006-12-08	2006-12-08	ENSG00000167207	ENSG00000167207		"""Nucleotide-binding domain and leucine rich repeat containing"""	5331	protein-coding gene	gene with protein product	"""nucleotide-binding oligomerization domain, leucine rich repeat and CARD domain containing 2"", ""NOD-like receptor C2"", ""NLR family, CARD domain containing 2"""	605956	"""caspase recruitment domain family, member 15"""	IBD1, CARD15		7809109, 8587604	Standard	XM_005256084		Approved	BLAU, CD, PSORAS1, CLR16.3, NLRC2	uc002egm.1	Q9HC29	OTTHUMG00000133171	ENST00000300589.2:c.412C>G	16.37:g.50733737C>G	ENSP00000300589:p.Arg138Gly					NOD2_uc010cbj.1_Missense_Mutation_p.R111G|NOD2_uc010cbk.1_Missense_Mutation_p.R111G|NOD2_uc002egl.1_5'UTR	p.R138G	NM_022162	NP_071445	Q9HC29	NOD2_HUMAN			2	517	+		all_cancers(37;0.0156)	138			CARD 2.		E2JEQ6|Q96RH5|Q96RH6|Q96RH8	Missense_Mutation	SNP	ENST00000300589.2	37	c.412C>G	CCDS10746.1	.	.	.	.	.	.	.	.	.	.	C	19.26	3.792885	0.70452	.	.	ENSG00000167207	ENST00000526417;ENST00000531674;ENST00000300589	T;T	0.35048	1.76;1.33	5.29	4.28	0.50868	DEATH-like (2);Caspase Recruitment (2);	0.000000	0.49916	D	0.000136	T	0.51092	0.1654	M	0.65498	2.005	0.50632	D	0.999884	D	0.56287	0.975	P	0.60682	0.878	T	0.53401	-0.8444	10	0.87932	D	0	.	9.4899	0.38953	0.2644:0.7356:0.0:0.0	.	138	Q9HC29	NOD2_HUMAN	G	111;111;138	ENSP00000431681:R111G;ENSP00000300589:R138G	ENSP00000300589:R138G	R	+	1	2	NOD2	49291238	0.999000	0.42202	1.000000	0.80357	0.966000	0.64601	2.557000	0.45871	2.482000	0.83794	0.591000	0.81541	CGG		0.632	NOD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256876.2	NM_022162	
GPR56	9289	broad.mit.edu	37	16	57688009	57688009	+	Silent	SNP	C	C	T	rs374209597		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr16:57688009C>T	ENST00000388812.4	+	5	1172	c.732C>T	c.(730-732)gcC>gcT	p.A244A	GPR56_ENST00000388813.5_Silent_p.A244A|GPR56_ENST00000379696.3_Silent_p.A244A|GPR56_ENST00000379694.4_Silent_p.A74A|GPR56_ENST00000544297.1_Silent_p.A69A|GPR56_ENST00000568908.1_Silent_p.A244A|GPR56_ENST00000540164.2_Silent_p.A244A|GPR56_ENST00000562631.1_Silent_p.A244A|GPR56_ENST00000567835.1_Silent_p.A244A|GPR56_ENST00000562558.1_Silent_p.A244A|GPR56_ENST00000568909.1_Silent_p.A244A|GPR56_ENST00000538815.1_Silent_p.A244A|GPR56_ENST00000456916.1_Silent_p.A244A			Q9Y653	GPR56_HUMAN	G protein-coupled receptor 56	244					angiogenesis (GO:0001525)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|cerebral cortex radial glia guided migration (GO:0021801)|G-protein coupled receptor signaling pathway (GO:0007186)|layer formation in cerebral cortex (GO:0021819)|negative regulation of cell proliferation (GO:0008285)|negative regulation of neuron migration (GO:2001223)|neuropeptide signaling pathway (GO:0007218)|positive regulation of cell adhesion (GO:0045785)|positive regulation of Rho protein signal transduction (GO:0035025)|protein kinase C signaling (GO:0070528)|Rho protein signal transduction (GO:0007266)|vascular endothelial growth factor production (GO:0010573)	extracellular vesicular exosome (GO:0070062)|glial limiting end-foot (GO:0097451)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	collagen binding (GO:0005518)|extracellular matrix binding (GO:0050840)|G-protein coupled receptor activity (GO:0004930)			kidney(1)|large_intestine(3)|lung(9)|prostate(1)|skin(1)	15						AGCCCACAGCCGGCCTCCAGG	0.662													C|||	1	0.000199681	0.0	0.0014	5008	,	,		14729	0.0		0.0	False		,,,				2504	0.0					uc002emb.2																			0					0						c.(730-732)GCC>GCT		G protein-coupled receptor 56 isoform a		C	,,,,,,,	1,4395	2.1+/-5.4	0,1,2197	42.0	44.0	43.0		732,732,732,747,732,732,732,732	-4.2	0.0	16		43	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	GPR56	NM_001145770.1,NM_001145771.1,NM_001145772.1,NM_001145773.1,NM_001145774.1,NM_005682.5,NM_201524.2,NM_201525.2	,,,,,,,	0,2,6496	TT,TC,CC		0.0116,0.0227,0.0154	,,,,,,,	244/688,244/694,244/688,249/693,244/688,244/694,244/688,244/688	57688009	2,12994	2198	4300	6498	SO:0001819	synonymous_variant	9289				brain development|cell adhesion|cell-cell signaling|neuropeptide signaling pathway	integral to plasma membrane	G-protein coupled receptor activity	g.chr16:57688009C>T	AJ011001	CCDS32460.1, CCDS32461.1, CCDS73893.1	16q13	2014-08-08				ENSG00000205336		"""-"", ""GPCR / Class B : Orphans"""	4512	protein-coding gene	gene with protein product		604110				10049584, 10100861	Standard	XM_005256237		Approved	TM7LN4, TM7XN1	uc002emb.2	Q9Y653		ENST00000388812.4:c.732C>T	16.37:g.57688009C>T						GPR56_uc002elz.1_Silent_p.A74A|GPR56_uc002ema.1_Silent_p.A69A|GPR56_uc002emc.2_Silent_p.A244A|GPR56_uc002emf.2_Silent_p.A244A|GPR56_uc010vhs.1_Silent_p.A244A|GPR56_uc002emd.2_Silent_p.A244A|GPR56_uc002eme.2_Silent_p.A244A|GPR56_uc010vht.1_Silent_p.A249A|GPR56_uc002emg.3_Silent_p.A244A|GPR56_uc010vhu.1_Silent_p.A69A	p.A244A	NM_005682	NP_005673	Q9Y653	GPR56_HUMAN			6	1024	+			244			Extracellular (Potential).		A6NIT7|A6NJV9|B0M0K4|B4DR54|O95966|Q6ZMP1|Q8NGB3|Q96HB4	Silent	SNP	ENST00000388812.4	37	c.732C>T	CCDS32460.1																																																																																				0.662	GPR56-203	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000433436.3		
NF1	4763	broad.mit.edu	37	17	29652976	29652979	+	Frame_Shift_Del	DEL	TCTC	TCTC	-			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr17:29652976_29652979delTCTC	ENST00000358273.4	+	37	5357_5360	c.4974_4977delTCTC	c.(4972-4977)tttctcfs	p.FL1658fs	NF1_ENST00000356175.3_Frame_Shift_Del_p.FL1637fs|NF1_ENST00000581113.2_3'UTR	NM_001042492.2	NP_001035957.1	P21359	NF1_HUMAN	neurofibromin 1	1658	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.|Lipid binding.				actin cytoskeleton organization (GO:0030036)|adrenal gland development (GO:0030325)|artery morphogenesis (GO:0048844)|brain development (GO:0007420)|camera-type eye morphogenesis (GO:0048593)|cell communication (GO:0007154)|cerebral cortex development (GO:0021987)|cognition (GO:0050890)|collagen fibril organization (GO:0030199)|extracellular matrix organization (GO:0030198)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|forebrain astrocyte development (GO:0021897)|forebrain morphogenesis (GO:0048853)|heart development (GO:0007507)|liver development (GO:0001889)|MAPK cascade (GO:0000165)|metanephros development (GO:0001656)|myelination in peripheral nervous system (GO:0022011)|negative regulation of angiogenesis (GO:0016525)|negative regulation of astrocyte differentiation (GO:0048712)|negative regulation of cell migration (GO:0030336)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of endothelial cell proliferation (GO:0001937)|negative regulation of fibroblast proliferation (GO:0048147)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of neuroblast proliferation (GO:0007406)|negative regulation of neurotransmitter secretion (GO:0046929)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of osteoclast differentiation (GO:0045671)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of Rac protein signal transduction (GO:0035021)|negative regulation of Ras protein signal transduction (GO:0046580)|negative regulation of transcription factor import into nucleus (GO:0042992)|neural tube development (GO:0021915)|osteoblast differentiation (GO:0001649)|peripheral nervous system development (GO:0007422)|phosphatidylinositol 3-kinase signaling (GO:0014065)|pigmentation (GO:0043473)|positive regulation of adenylate cyclase activity (GO:0045762)|positive regulation of apoptotic process (GO:0043065)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|positive regulation of neuron apoptotic process (GO:0043525)|positive regulation of Ras GTPase activity (GO:0032320)|Ras protein signal transduction (GO:0007265)|regulation of angiogenesis (GO:0045765)|regulation of blood vessel endothelial cell migration (GO:0043535)|regulation of bone resorption (GO:0045124)|regulation of cell-matrix adhesion (GO:0001952)|regulation of glial cell differentiation (GO:0045685)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of Ras GTPase activity (GO:0032318)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to hypoxia (GO:0001666)|Schwann cell development (GO:0014044)|skeletal muscle tissue development (GO:0007519)|smooth muscle tissue development (GO:0048745)|spinal cord development (GO:0021510)|sympathetic nervous system development (GO:0048485)|visual learning (GO:0008542)|wound healing (GO:0042060)	axon (GO:0030424)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|membrane (GO:0016020)|nucleus (GO:0005634)	phosphatidylcholine binding (GO:0031210)|phosphatidylethanolamine binding (GO:0008429)|Ras GTPase activator activity (GO:0005099)	p.0?(8)|p.?(3)|p.S1660fs*37(2)	NF1/ACCN1(2)	autonomic_ganglia(12)|breast(11)|central_nervous_system(72)|cervix(6)|endometrium(12)|haematopoietic_and_lymphoid_tissue(59)|kidney(9)|large_intestine(39)|liver(1)|lung(80)|ovary(20)|pancreas(2)|prostate(2)|skin(8)|soft_tissue(249)|stomach(2)|thyroid(1)|upper_aerodigestive_tract(5)|urinary_tract(9)	599		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)		AAACAGACTTTCTCTCTAAGTGGT	0.422			"""D, Mis, N, F, S, O"""		"""neurofibroma, glioma"""	"""neurofibroma, glioma"""			Neurofibromatosis, type 1	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)																												uc002hgg.2			yes	Rec	yes	Neurofibromatosis type 1	17	17q12	4763	D|Mis|N|F|S|O	neurofibromatosis type 1 gene			O		neurofibroma|glioma	neurofibroma|glioma		13	Whole gene deletion(8)|Unknown(3)|Deletion - Frameshift(2)	p.S1660fs*37(2)	soft_tissue(7)|autonomic_ganglia(2)|central_nervous_system(2)|lung(1)|large_intestine(1)	soft_tissue(159)|central_nervous_system(56)|lung(28)|large_intestine(27)|haematopoietic_and_lymphoid_tissue(18)|ovary(18)|autonomic_ganglia(12)|breast(3)|skin(3)|stomach(2)|thyroid(1)|prostate(1)|kidney(1)|pancreas(1)	330	GRCh37	CD972357	NF1	D		c.(4972-4977)TTTCTCfs		neurofibromin isoform 1																																				SO:0001589	frameshift_variant	4763	Neurofibromatosis_type_1	Familial Cancer Database	NF1, von Recklinghausen disease, incl.: Hereditary Spinal Neurofibromatosis, Neurofibromatosis-Noonan syndrome	actin cytoskeleton organization|adrenal gland development|artery morphogenesis|camera-type eye morphogenesis|cerebral cortex development|collagen fibril organization|forebrain astrocyte development|forebrain morphogenesis|heart development|liver development|MAPKKK cascade|metanephros development|myelination in peripheral nervous system|negative regulation of cell migration|negative regulation of endothelial cell proliferation|negative regulation of MAP kinase activity|negative regulation of MAPKKK cascade|negative regulation of neuroblast proliferation|negative regulation of oligodendrocyte differentiation|negative regulation of transcription factor import into nucleus|osteoblast differentiation|phosphatidylinositol 3-kinase cascade|pigmentation|positive regulation of adenylate cyclase activity|positive regulation of neuron apoptosis|Ras protein signal transduction|regulation of blood vessel endothelial cell migration|regulation of bone resorption|response to hypoxia|smooth muscle tissue development|spinal cord development|sympathetic nervous system development|visual learning|wound healing	axon|cytoplasm|dendrite|intrinsic to internal side of plasma membrane|nucleus	protein binding|Ras GTPase activator activity	g.chr17:29652976_29652979delTCTC		CCDS11264.1, CCDS42292.1, CCDS45645.1	17q11.2	2014-09-17	2008-07-31		ENSG00000196712	ENSG00000196712			7765	protein-coding gene	gene with protein product	"""neurofibromatosis"", ""von Recklinghausen disease"", ""Watson disease"""	613113				1715669	Standard	NM_000267		Approved		uc002hgg.3	P21359	OTTHUMG00000132871	ENST00000358273.4:c.4974_4977delTCTC	17.37:g.29652976_29652979delTCTC	ENSP00000351015:p.Phe1658fs	TCGA GBM(6;<1E-08)|TSP Lung(7;0.0071)|TCGA Ovarian(3;0.0088)				NF1_uc002hgh.2_Frame_Shift_Del_p.F1637fs|NF1_uc002hgi.1_Frame_Shift_Del_p.F670fs|NF1_uc010cso.2_5'UTR	p.F1658fs	NM_001042492	NP_001035957	P21359	NF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (4;4.38e-05)|all cancers(4;1.64e-26)|Epithelial(4;9.15e-23)|OV - Ovarian serous cystadenocarcinoma(4;3.58e-21)|GBM - Glioblastoma multiforme(4;0.00146)	37	5307_5310	+		all_cancers(10;1.29e-12)|all_epithelial(10;0.00347)|all_hematologic(16;0.00556)|Acute lymphoblastic leukemia(14;0.00593)|Breast(31;0.014)|Myeloproliferative disorder(56;0.0255)|all_lung(9;0.0321)|Lung NSC(157;0.0659)	1658_1659			CRAL-TRIO.		O00662|Q14284|Q14930|Q14931|Q9UMK3	Frame_Shift_Del	DEL	ENST00000358273.4	37	c.4974_4977delTCTC	CCDS42292.1																																																																																				0.422	NF1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256351.2	NM_000267	
KRT35	3886	broad.mit.edu	37	17	39637191	39637191	+	Silent	SNP	T	T	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr17:39637191T>A	ENST00000393989.1	-	1	201	c.159A>T	c.(157-159)tcA>tcT	p.S53S	KRT35_ENST00000246639.2_Silent_p.S23S	NM_002280.4	NP_002271.3	Q92764	KRT35_HUMAN	keratin 35	53	Head.				anatomical structure morphogenesis (GO:0009653)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)	structural molecule activity (GO:0005198)			NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(2)|large_intestine(3)|lung(9)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	29		Breast(137;0.000286)				CCAGACCCACTGAGCAGGCAG	0.632																																						uc002hws.2																			0				ovary(1)|skin(1)	2						c.(157-159)TCA>TCT		keratin 35							36.0	43.0	41.0					17																	39637191		2079	4221	6300	SO:0001819	synonymous_variant	3886				anatomical structure morphogenesis	intermediate filament	protein binding|structural molecule activity	g.chr17:39637191T>A	X90762	CCDS11394.2	17q21.2	2013-01-16	2006-07-17	2006-07-17	ENSG00000197079	ENSG00000197079		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6453	protein-coding gene	gene with protein product	"""hard keratin type I 5"""	602764	"""keratin, hair, acidic, 5"""	KRTHA5		8823373, 16831889	Standard	NM_002280		Approved	Ha-5	uc002hws.3	Q92764	OTTHUMG00000133425	ENST00000393989.1:c.159A>T	17.37:g.39637191T>A							p.S53S	NM_002280	NP_002271	Q92764	KRT35_HUMAN			1	202	-		Breast(137;0.000286)	53			Head.		O76012|Q92651	Silent	SNP	ENST00000393989.1	37	c.159A>T	CCDS11394.2																																																																																				0.632	KRT35-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_002280	
PTPRM	5797	broad.mit.edu	37	18	8244151	8244151	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr18:8244151G>A	ENST00000332175.8	+	15	3433	c.2396G>A	c.(2395-2397)gGc>gAc	p.G799D	PTPRM_ENST00000400053.4_Missense_Mutation_p.G737D|PTPRM_ENST00000444013.1_Missense_Mutation_p.G586D|PTPRM_ENST00000400060.4_Missense_Mutation_p.G799D|PTPRM_ENST00000580170.1_Missense_Mutation_p.G799D	NM_002845.3	NP_002836.3	P28827	PTPRM_HUMAN	protein tyrosine phosphatase, receptor type, M	799					homophilic cell adhesion (GO:0007156)|negative regulation of angiogenesis (GO:0016525)|negative regulation of endothelial cell migration (GO:0010596)|negative regulation of endothelial cell proliferation (GO:0001937)|neuron projection development (GO:0031175)|peptidyl-tyrosine dephosphorylation (GO:0035335)|positive regulation of vasodilation (GO:0045909)|protein dephosphorylation (GO:0006470)|response to drug (GO:0042493)|retina layer formation (GO:0010842)|retinal ganglion cell axon guidance (GO:0031290)|signal transduction (GO:0007165)	cell-cell adherens junction (GO:0005913)|cell-cell junction (GO:0005911)|cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)	cadherin binding (GO:0045296)|identical protein binding (GO:0042802)|protein tyrosine phosphatase activity (GO:0004725)|transmembrane receptor protein tyrosine phosphatase activity (GO:0005001)			breast(3)|central_nervous_system(1)|cervix(3)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(32)|lung(25)|ovary(2)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	90		Colorectal(10;0.234)				GCTGAGCAGGGCACAAACTGC	0.483																																						uc002knn.3																			0				lung(3)|ovary(2)|central_nervous_system(1)	6						c.(2395-2397)GGC>GAC		protein tyrosine phosphatase, receptor type, M							162.0	146.0	151.0					18																	8244151		2203	4300	6503	SO:0001583	missense	5797				homophilic cell adhesion|negative regulation of angiogenesis|negative regulation of endothelial cell migration|negative regulation of endothelial cell proliferation|response to drug|retina layer formation|retinal ganglion cell axon guidance	cell-cell adherens junction|integral to plasma membrane|lamellipodium|perinuclear region of cytoplasm	cadherin binding|transmembrane receptor protein tyrosine phosphatase activity	g.chr18:8244151G>A	X58288	CCDS11840.1, CCDS58613.1	18p11.2	2013-02-11			ENSG00000173482	ENSG00000173482		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	9675	protein-coding gene	gene with protein product		176888		PTPRL1		1655529, 8404049	Standard	NM_002845		Approved	RPTPU, hR-PTPu	uc010dkv.3	P28827	OTTHUMG00000131575	ENST00000332175.8:c.2396G>A	18.37:g.8244151G>A	ENSP00000331418:p.Gly799Asp					PTPRM_uc010dkv.2_Missense_Mutation_p.G799D|PTPRM_uc010wzl.1_Missense_Mutation_p.G586D	p.G799D	NM_002845	NP_002836	P28827	PTPRM_HUMAN			15	2899	+		Colorectal(10;0.234)	799			Cytoplasmic (Potential).		A7MBN1|D3DUH8|J3QL11	Missense_Mutation	SNP	ENST00000332175.8	37	c.2396G>A	CCDS11840.1	.	.	.	.	.	.	.	.	.	.	G	34	5.369959	0.95900	.	.	ENSG00000173482	ENST00000332175;ENST00000400060;ENST00000400053;ENST00000444013	T;T;T;T	0.47177	1.19;1.21;1.02;0.85	5.82	5.82	0.92795	.	0.050962	0.85682	D	0.000000	T	0.50786	0.1636	L	0.57536	1.79	0.80722	D	1	B;P;P	0.40970	0.071;0.734;0.734	B;B;B	0.40329	0.045;0.326;0.326	T	0.47749	-0.9093	10	0.39692	T	0.17	.	20.1178	0.97943	0.0:0.0:1.0:0.0	.	586;799;799	E7EVX9;A7MBN1;P28827	.;.;PTPRM_HUMAN	D	799;799;737;586	ENSP00000331418:G799D;ENSP00000382933:G799D;ENSP00000382927:G737D;ENSP00000387608:G586D	ENSP00000331418:G799D	G	+	2	0	PTPRM	8234151	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	9.869000	0.99810	2.759000	0.94783	0.557000	0.71058	GGC		0.483	PTPRM-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254456.1		
PPP4R1	9989	broad.mit.edu	37	18	9570482	9570482	+	Nonsense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr18:9570482G>A	ENST00000400556.3	-	11	1319	c.1246C>T	c.(1246-1248)Cag>Tag	p.Q416*	PPP4R1_ENST00000400555.3_Nonsense_Mutation_p.Q399*	NM_001042388.2	NP_001035847.1	Q8TF05	PP4R1_HUMAN	protein phosphatase 4, regulatory subunit 1	416					dephosphorylation (GO:0016311)|protein phosphorylation (GO:0006468)|regulation of catalytic activity (GO:0050790)|signal transduction (GO:0007165)	protein phosphatase 4 complex (GO:0030289)	protein phosphatase type 4 regulator activity (GO:0030362)			large_intestine(1)|skin(2)	3						GCTGCTTCCTGGTGAGATTCT	0.443																																					Melanoma(188;1232 2082 5061 11948 35994)	uc002koe.1																			0				skin(1)	1						c.(1246-1248)CAG>TAG		protein phosphatase 4, regulatory subunit 1							73.0	71.0	72.0					18																	9570482		1869	4103	5972	SO:0001587	stop_gained	9989				protein phosphorylation|signal transduction	protein phosphatase 4 complex	protein binding|protein phosphatase type 4 regulator activity	g.chr18:9570482G>A	AF111106	CCDS42412.1, CCDS42413.1	18p11.22	2010-06-18			ENSG00000154845	ENSG00000154845		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	9320	protein-coding gene	gene with protein product		604908				10026142	Standard	NM_001042388		Approved	PP4R1	uc002koe.2	Q8TF05	OTTHUMG00000137466	ENST00000400556.3:c.1246C>T	18.37:g.9570482G>A	ENSP00000383402:p.Gln416*					PPP4R1_uc002kof.2_5'UTR|PPP4R1_uc010wzo.1_Nonsense_Mutation_p.Q262*|PPP4R1_uc002kod.1_Nonsense_Mutation_p.Q399*|PPP4R1_uc010wzp.1_RNA	p.Q416*	NM_001042388	NP_001035847	Q8TF05	PP4R1_HUMAN			11	1364	-			416					Q99774|Q9UNQ7	Nonsense_Mutation	SNP	ENST00000400556.3	37	c.1246C>T	CCDS42412.1	.	.	.	.	.	.	.	.	.	.	G	39	7.450131	0.98292	.	.	ENSG00000154845	ENST00000400556;ENST00000400555;ENST00000285124	.	.	.	5.32	5.32	0.75619	.	0.323970	0.25780	N	0.028353	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	-4.3753	9.6963	0.40158	0.0:0.1615:0.6918:0.1467	.	.	.	.	X	416;399;327	.	.	Q	-	1	0	PPP4R1	9560482	0.375000	0.25089	0.874000	0.34290	0.941000	0.58515	2.298000	0.43602	2.638000	0.89438	0.591000	0.81541	CAG		0.443	PPP4R1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268571.1	NM_005134	
NPC1	4864	broad.mit.edu	37	18	21120489	21120489	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr18:21120489C>T	ENST00000269228.5	-	17	3081	c.2527G>A	c.(2527-2529)Gtg>Atg	p.V843M	NPC1_ENST00000540608.1_5'UTR|NPC1_ENST00000412552.2_Missense_Mutation_p.V525M	NM_000271.4	NP_000262.2	O15118	NPC1_HUMAN	Niemann-Pick disease, type C1	843					adult walking behavior (GO:0007628)|autophagy (GO:0006914)|bile acid metabolic process (GO:0008206)|cellular response to low-density lipoprotein particle stimulus (GO:0071404)|cellular response to steroid hormone stimulus (GO:0071383)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|endocytosis (GO:0006897)|establishment of protein localization to membrane (GO:0090150)|lysosomal transport (GO:0007041)|membrane raft organization (GO:0031579)|negative regulation of cell death (GO:0060548)|negative regulation of macroautophagy (GO:0016242)|protein glycosylation (GO:0006486)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|signal transduction (GO:0007165)	endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|membrane raft (GO:0045121)|nuclear envelope (GO:0005635)|perinuclear region of cytoplasm (GO:0048471)	cholesterol binding (GO:0015485)|hedgehog receptor activity (GO:0008158)|receptor activity (GO:0004872)|sterol transporter activity (GO:0015248)|transmembrane signaling receptor activity (GO:0004888)			breast(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(10)|lung(13)|ovary(2)|stomach(1)	38	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)					AGAACACCCACAAATATTGCT	0.363																																						uc002kum.3																			0				ovary(2)	2						c.(2527-2529)GTG>ATG		Niemann-Pick disease, type C1 precursor							94.0	85.0	88.0					18																	21120489		2203	4300	6503	SO:0001583	missense	4864				autophagy|bile acid metabolic process|cholesterol efflux|cholesterol homeostasis|lysosomal transport	endoplasmic reticulum|integral to plasma membrane|late endosome membrane|lysosomal membrane|nuclear envelope|perinuclear region of cytoplasm	hedgehog receptor activity|protein binding|sterol transporter activity	g.chr18:21120489C>T	AF002020	CCDS11878.1	18q11.2	2014-06-17			ENSG00000141458	ENSG00000141458			7897	protein-coding gene	gene with protein product		607623				8446622	Standard	NM_000271		Approved		uc002kum.4	O15118	OTTHUMG00000131873	ENST00000269228.5:c.2527G>A	18.37:g.21120489C>T	ENSP00000269228:p.Val843Met					NPC1_uc010xaz.1_Missense_Mutation_p.V576M|NPC1_uc010xba.1_Missense_Mutation_p.V688M	p.V843M	NM_000271	NP_000262	O15118	NPC1_HUMAN			17	2801	-	all_cancers(21;0.000106)|all_epithelial(16;6.57e-07)|Lung NSC(20;0.00166)|all_lung(20;0.00536)|Colorectal(14;0.0202)|Ovarian(20;0.127)		843			Helical; (Potential).		B4DET3|Q9P130	Missense_Mutation	SNP	ENST00000269228.5	37	c.2527G>A	CCDS11878.1	.	.	.	.	.	.	.	.	.	.	C	26.5	4.740050	0.89573	.	.	ENSG00000141458	ENST00000269228;ENST00000412552;ENST00000540608	D;D	0.94138	-3.36;-3.36	6.07	5.2	0.72013	.	0.000000	0.85682	D	0.000000	D	0.93488	0.7922	M	0.73962	2.25	0.80722	D	1	P;P	0.38800	0.648;0.476	B;B	0.41466	0.358;0.231	D	0.93161	0.6558	10	0.51188	T	0.08	-24.8818	15.4893	0.75593	0.0:0.9339:0.0:0.0661	.	854;843	Q59GR1;O15118	.;NPC1_HUMAN	M	843;525;688	ENSP00000269228:V843M;ENSP00000408606:V525M	ENSP00000269228:V843M	V	-	1	0	NPC1	19374487	1.000000	0.71417	0.988000	0.46212	0.943000	0.58893	5.905000	0.69893	1.575000	0.49775	0.655000	0.94253	GTG		0.363	NPC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254823.2	NM_000271	
TRAPPC8	22878	broad.mit.edu	37	18	29487454	29487454	+	Missense_Mutation	SNP	T	T	G			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr18:29487454T>G	ENST00000283351.4	-	9	1693	c.1358A>C	c.(1357-1359)gAt>gCt	p.D453A	TRAPPC8_ENST00000582539.1_Missense_Mutation_p.D399A|TRAPPC8_ENST00000582513.1_Missense_Mutation_p.D453A	NM_014939.3	NP_055754	Q9Y2L5	TPPC8_HUMAN	trafficking protein particle complex 8	453					vesicle-mediated transport (GO:0016192)	Golgi apparatus (GO:0005794)				breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(6)|large_intestine(7)|liver(2)|lung(13)|ovary(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	47						CATTGCTTGATCATTAAGAAA	0.338																																						uc002kxc.3																			0					0						c.(1357-1359)GAT>GCT		hypothetical protein LOC22878							80.0	81.0	81.0					18																	29487454		2203	4300	6503	SO:0001583	missense	22878				ER to Golgi vesicle-mediated transport	cis-Golgi network		g.chr18:29487454T>G	AB023229	CCDS11901.1	18q12.1	2011-10-10	2010-06-29	2010-06-29	ENSG00000153339	ENSG00000153339		"""Trafficking protein particle complex"""	29169	protein-coding gene	gene with protein product	"""general sporulation gene 1 homolog (S. cerevisiae)"""	614136	"""KIAA1012"""	KIAA1012		10231032, 11230166	Standard	NM_014939		Approved	HsT2706, TRS85, GSG1	uc002kxc.4	Q9Y2L5	OTTHUMG00000132267	ENST00000283351.4:c.1358A>C	18.37:g.29487454T>G	ENSP00000283351:p.Asp453Ala					KIAA1012_uc002kxb.3_Missense_Mutation_p.D399A|KIAA1012_uc002kxd.3_RNA|KIAA1012_uc002kxe.2_Missense_Mutation_p.D453A	p.D453A	NM_014939	NP_055754	Q9Y2L5	TPPC8_HUMAN			9	1722	-			453					A0JP15|B3KME5|Q9H0L2	Missense_Mutation	SNP	ENST00000283351.4	37	c.1358A>C	CCDS11901.1	.	.	.	.	.	.	.	.	.	.	T	14.06	2.423015	0.43020	.	.	ENSG00000153339	ENST00000283351	T	0.55234	0.53	5.36	5.36	0.76844	.	0.160182	0.53938	D	0.000056	T	0.73583	0.3605	M	0.82823	2.61	0.80722	D	1	D;D	0.76494	0.999;0.998	D;D	0.74023	0.982;0.976	T	0.78168	-0.2309	10	0.72032	D	0.01	.	13.9178	0.63911	0.0:0.0:0.0:1.0	.	453;453	Q6PCC9;Q9Y2L5	.;TPPC8_HUMAN	A	453	ENSP00000283351:D453A	ENSP00000283351:D453A	D	-	2	0	TRAPPC8	27741452	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.636000	0.83301	2.021000	0.59480	0.528000	0.53228	GAT		0.338	TRAPPC8-001	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255355.1	NM_014939	
CREB3L3	84699	broad.mit.edu	37	19	4164609	4164609	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr19:4164609C>T	ENST00000078445.2	+	5	833	c.686C>T	c.(685-687)aCc>aTc	p.T229I	CREB3L3_ENST00000602257.1_Missense_Mutation_p.T227I|CREB3L3_ENST00000252587.3_Missense_Mutation_p.T169I|CREB3L3_ENST00000595923.1_Missense_Mutation_p.T228I|CREB3L3_ENST00000602147.1_Missense_Mutation_p.T229I	NM_001271995.1|NM_001271996.1|NM_032607.1	NP_001258924.1|NP_001258925.1|NP_115996.1	Q68CJ9	CR3L3_HUMAN	cAMP responsive element binding protein 3-like 3	229					positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to unfolded protein (GO:0006986)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)	RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001228)			breast(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(1)|skin(2)|urinary_tract(3)	24				UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)		GAAGGCATCACCCTGCCCACT	0.617																																						uc002lzl.2																			0				ovary(1)|skin(1)	2						c.(685-687)ACC>ATC		cAMP responsive element binding protein 3-like							81.0	63.0	69.0					19																	4164609		2203	4300	6503	SO:0001583	missense	84699				response to unfolded protein	endoplasmic reticulum membrane|integral to membrane|nucleus	protein dimerization activity|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity	g.chr19:4164609C>T		CCDS12121.1, CCDS62498.1, CCDS62499.1, CCDS62500.1	19p13.3	2013-01-10				ENSG00000060566		"""basic leucine zipper proteins"""	18855	protein-coding gene	gene with protein product		611998				11353085	Standard	NM_032607		Approved	CREB-H	uc002lzl.4	Q68CJ9		ENST00000078445.2:c.686C>T	19.37:g.4164609C>T	ENSP00000078445:p.Thr229Ile					CREB3L3_uc002lzm.2_Missense_Mutation_p.T219I|CREB3L3_uc010xib.1_Missense_Mutation_p.T218I|CREB3L3_uc010xic.1_Missense_Mutation_p.T220I	p.T229I	NM_032607	NP_115996	Q68CJ9	CR3L3_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|BRCA - Breast invasive adenocarcinoma(158;0.0232)|STAD - Stomach adenocarcinoma(1328;0.18)	5	802	+			229			Cytoplasmic (Potential).		B2R7S6|B7ZL69|M0QYW7|Q6ZMC5|Q96TB9	Missense_Mutation	SNP	ENST00000078445.2	37	c.686C>T	CCDS12121.1	.	.	.	.	.	.	.	.	.	.	C	8.745	0.919895	0.17982	.	.	ENSG00000060566	ENST00000078445;ENST00000381943;ENST00000252587	T;T	0.75260	-0.92;-0.92	4.99	3.96	0.45880	Eukaryotic transcription factor, Skn-1-like, DNA-binding (1);	0.377451	0.29059	N	0.013267	T	0.77003	0.4067	L	0.59436	1.845	0.40443	D	0.980067	P;D;B;B	0.59357	0.923;0.985;0.3;0.199	P;P;B;B	0.52159	0.504;0.691;0.253;0.128	T	0.78478	-0.2188	10	0.52906	T	0.07	-5.1333	12.136	0.53972	0.0:0.9151:0.0:0.0849	.	229;227;228;229	Q68CJ9-3;B7ZL69;Q68CJ9-2;Q68CJ9	.;.;.;CR3L3_HUMAN	I	229;229;169	ENSP00000078445:T229I;ENSP00000252587:T169I	ENSP00000078445:T229I	T	+	2	0	CREB3L3	4115609	0.085000	0.21516	0.916000	0.36221	0.102000	0.19082	0.892000	0.28322	1.098000	0.41479	0.561000	0.74099	ACC		0.617	CREB3L3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000457922.1	NM_032607	
DNAJB1	3337	broad.mit.edu	37	19	14627500	14627500	+	Silent	SNP	T	T	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr19:14627500T>C	ENST00000254322.2	-	2	640	c.570A>G	c.(568-570)ctA>ctG	p.L190L	DNAJB1_ENST00000396969.4_Silent_p.L90L	NM_006145.1	NP_006136.1	P25685	DNJB1_HUMAN	DnaJ (Hsp40) homolog, subfamily B, member 1	190					chaperone cofactor-dependent protein refolding (GO:0070389)|chaperone mediated protein folding requiring cofactor (GO:0051085)|negative regulation of inclusion body assembly (GO:0090084)|positive regulation of ATPase activity (GO:0032781)|response to unfolded protein (GO:0006986)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)	ATPase activator activity (GO:0001671)|ATPase binding (GO:0051117)|chaperone binding (GO:0051087)|Hsp70 protein binding (GO:0030544)|unfolded protein binding (GO:0051082)	p.L190L(1)		NS(1)|breast(1)|cervix(3)|endometrium(1)|kidney(1)|lung(7)|prostate(1)|urinary_tract(1)	16				GBM - Glioblastoma multiforme(1328;0.0476)		CGTCGGGGTTTAGCCGCTTGT	0.483																																						uc002myz.1																			1	Substitution - coding silent(1)		prostate(1)		0						c.(568-570)CTA>CTG		DnaJ (Hsp40) homolog, subfamily B, member 1							168.0	167.0	168.0					19																	14627500		2203	4300	6503	SO:0001819	synonymous_variant	3337				chaperone cofactor-dependent protein refolding|response to unfolded protein	cytoplasm|nucleolus	heat shock protein binding|unfolded protein binding	g.chr19:14627500T>C	D49547	CCDS12312.1, CCDS74295.1	19p13.12	2014-08-12			ENSG00000132002	ENSG00000132002		"""Heat shock proteins / DNAJ (HSP40)"""	5270	protein-coding gene	gene with protein product	"""radial spoke 16 homolog B (Chlamydomonas)"""	604572		HSPF1		8975727, 8250930	Standard	XM_006722733		Approved	Hsp40, Sis1, RSPH16B	uc002myz.1	P25685	OTTHUMG00000183289	ENST00000254322.2:c.570A>G	19.37:g.14627500T>C						DNAJB1_uc010xnr.1_Silent_p.L90L	p.L190L	NM_006145	NP_006136	P25685	DNJB1_HUMAN		GBM - Glioblastoma multiforme(1328;0.0476)	2	610	-			190					B4DX52	Silent	SNP	ENST00000254322.2	37	c.570A>G	CCDS12312.1																																																																																				0.483	DNAJB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465987.1	NM_006145	
LILRB5	10990	broad.mit.edu	37	19	54760357	54760357	+	Missense_Mutation	SNP	G	G	A	rs201274171	byFrequency	TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr19:54760357G>A	ENST00000316219.5	-	3	457	c.350C>T	c.(349-351)gCg>gTg	p.A117V	LILRB5_ENST00000345866.6_Missense_Mutation_p.A117V|LILRB5_ENST00000450632.1_Missense_Mutation_p.A117V|LILRB5_ENST00000449561.2_Missense_Mutation_p.A117V	NM_001081442.1|NM_006840.3	NP_001074911.1|NP_006831.1	O75023	LIRB5_HUMAN	leukocyte immunoglobulin-like receptor, subfamily B (with TM and ITIM domains), member 5	117	Ig-like C2-type 2.				cell surface receptor signaling pathway (GO:0007166)|defense response (GO:0006952)|immune system process (GO:0002376)	integral component of membrane (GO:0016021)	transmembrane signaling receptor activity (GO:0004888)	p.A117V(2)		NS(1)|breast(1)|endometrium(3)|kidney(5)|large_intestine(12)|lung(25)|ovary(1)|pancreas(1)|prostate(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	56	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)			GBM - Glioblastoma multiforme(193;0.105)		CTCACCTGTCGCCACCAGCTC	0.637													.|||	5	0.000998403	0.0	0.0	5008	,	,		15249	0.005		0.0	False		,,,				2504	0.0					uc002qex.2																			2	Substitution - Missense(2)		large_intestine(2)	ovary(1)|pancreas(1)	2						c.(349-351)GCG>GTG		leukocyte immunoglobulin-like receptor,		G	VAL/ALA,VAL/ALA,VAL/ALA	2,4404	4.2+/-10.8	0,2,2201	70.0	73.0	72.0		350,350,350	2.3	1.0	19		72	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense	LILRB5	NM_001081442.1,NM_001081443.1,NM_006840.3	64,64,64	0,3,6500	AA,AG,GG		0.0116,0.0454,0.0231	benign,benign,benign	117/592,117/492,117/591	54760357	3,13003	2203	4300	6503	SO:0001583	missense	10990				cell surface receptor linked signaling pathway|defense response	integral to membrane	transmembrane receptor activity	g.chr19:54760357G>A	AF025534	CCDS12885.1, CCDS42611.1, CCDS46176.1	19q13.4	2013-01-11			ENSG00000105609	ENSG00000105609		"""Leukocyte immunoglobulin-like receptors"", ""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	6609	protein-coding gene	gene with protein product		604814				9548455	Standard	NM_006840		Approved	LIR-8, LIR8, CD85c	uc002qey.3	O75023	OTTHUMG00000066636	ENST00000316219.5:c.350C>T	19.37:g.54760357G>A	ENSP00000320390:p.Ala117Val					LILRA6_uc002qew.1_Intron|LILRB5_uc010yer.1_Missense_Mutation_p.A117V|LILRB5_uc002qey.2_Missense_Mutation_p.A117V|LILRB5_uc002qez.2_Missense_Mutation_p.A117V|LILRB5_uc002qfa.1_Missense_Mutation_p.A107V|LILRB5_uc010yes.1_RNA	p.A117V	NM_006840	NP_006831	O75023	LIRB5_HUMAN		GBM - Glioblastoma multiforme(193;0.105)	3	461	-	all_cancers(19;0.00681)|all_epithelial(19;0.00368)|all_lung(19;0.016)|Lung NSC(19;0.0296)|Ovarian(34;0.19)		117			Extracellular (Potential).|Ig-like C2-type 2.		Q8N760	Missense_Mutation	SNP	ENST00000316219.5	37	c.350C>T	CCDS12885.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	0.008	-1.912117	0.00508	4.54E-4	1.16E-4	ENSG00000105609	ENST00000316219;ENST00000450632;ENST00000449561;ENST00000345866	T;T;T;T	0.05925	3.37;3.37;3.37;3.37	3.29	2.26	0.28386	Immunoglobulin-like fold (1);	0.284575	0.24833	N	0.035231	T	0.00754	0.0025	N	0.00019	-2.8	0.20703	N	0.999868	B;B;B;B;B	0.25235	0.004;0.121;0.005;0.005;0.002	B;B;B;B;B	0.15870	0.003;0.014;0.002;0.0;0.003	T	0.42258	-0.9462	10	0.02654	T	1	.	5.5078	0.16864	0.8642:0.0:0.1358:0.0	.	117;108;117;117;117	C9JMK7;Q8NF80;O75023-2;O75023-3;O75023	.;.;.;.;LIRB5_HUMAN	V	117	ENSP00000320390:A117V;ENSP00000414225:A117V;ENSP00000406478:A117V;ENSP00000263430:A117V	ENSP00000320390:A117V	A	-	2	0	LILRB5	59452169	0.441000	0.25626	0.953000	0.39169	0.029000	0.11900	1.138000	0.31491	0.452000	0.26830	-0.385000	0.06624	GCG		0.637	LILRB5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000142877.2		
DPP10	57628	broad.mit.edu	37	2	116593818	116593818	+	Missense_Mutation	SNP	A	A	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr2:116593818A>T	ENST00000410059.1	+	22	2516	c.2036A>T	c.(2035-2037)gAc>gTc	p.D679V	DPP10_ENST00000310323.8_Missense_Mutation_p.D672V|DPP10_ENST00000409163.1_Missense_Mutation_p.D629V|DPP10_ENST00000393147.2_Missense_Mutation_p.D683V	NM_001178037.1|NM_020868.3	NP_001171508.1|NP_065919	Q8N608	DPP10_HUMAN	dipeptidyl-peptidase 10 (non-functional)	679						integral component of membrane (GO:0016021)|membrane (GO:0016020)	serine-type peptidase activity (GO:0008236)			breast(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(24)|liver(2)|lung(48)|ovary(6)|prostate(1)|skin(5)|soft_tissue(1)	101						CCTATCACAGACTTGAAATTG	0.368																																						uc002tla.1																			0				ovary(5)|large_intestine(2)|skin(2)|breast(1)	10						c.(2035-2037)GAC>GTC		dipeptidyl peptidase 10 isoform long							88.0	85.0	86.0					2																	116593818		2203	4300	6503	SO:0001583	missense	57628				proteolysis	integral to membrane|membrane fraction	serine-type peptidase activity	g.chr2:116593818A>T	AY172661	CCDS33278.1, CCDS46400.1, CCDS54388.1, CCDS54389.1	2q14.1	2010-05-04	2010-05-04		ENSG00000175497	ENSG00000175497			20823	protein-coding gene	gene with protein product		608209	"""dipeptidylpeptidase 10"", ""dipeptidyl-peptidase 10"""			10819331, 12662155	Standard	NM_020868		Approved	DPRP3	uc002tle.3	Q8N608	OTTHUMG00000153294	ENST00000410059.1:c.2036A>T	2.37:g.116593818A>T	ENSP00000386565:p.Asp679Val					DPP10_uc002tlb.1_Missense_Mutation_p.D629V|DPP10_uc002tlc.1_Missense_Mutation_p.D675V|DPP10_uc002tle.2_Missense_Mutation_p.D683V|DPP10_uc002tlf.1_Missense_Mutation_p.D672V	p.D679V	NM_020868	NP_065919	Q8N608	DPP10_HUMAN			22	2493	+			679			Extracellular (Potential).		A8K1Q2|J3KPP2|J3KQ46|Q0GLB8|Q53QT3|Q53S86|Q53SL8|Q53SS4|Q6TTV4|Q86YR9|Q9P236	Missense_Mutation	SNP	ENST00000410059.1	37	c.2036A>T	CCDS46400.1	.	.	.	.	.	.	.	.	.	.	A	20.8	4.046145	0.75846	.	.	ENSG00000175497	ENST00000410059;ENST00000409163;ENST00000393147;ENST00000310323	T;T;T;T	0.44881	0.91;0.91;0.91;0.91	5.81	5.81	0.92471	Peptidase S9, prolyl oligopeptidase, catalytic domain (1);	0.000000	0.85682	D	0.000000	T	0.73505	0.3595	M	0.94101	3.495	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;1.0;1.0	D;D;D;D	0.97110	0.999;1.0;0.999;0.999	T	0.81272	-0.1008	10	0.87932	D	0	-31.1628	15.3479	0.74355	1.0:0.0:0.0:0.0	.	672;683;675;679	Q8N608-2;Q0GLB8;Q0GLB9;Q8N608	.;.;.;DPP10_HUMAN	V	679;629;683;672	ENSP00000386565:D679V;ENSP00000387038:D629V;ENSP00000376855:D683V;ENSP00000309066:D672V	ENSP00000309066:D672V	D	+	2	0	DPP10	116310288	1.000000	0.71417	1.000000	0.80357	0.975000	0.68041	7.479000	0.81095	2.210000	0.71456	0.533000	0.62120	GAC		0.368	DPP10-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000330580.4	NM_020868	
WDR33	55339	broad.mit.edu	37	2	128484320	128484320	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr2:128484320C>T	ENST00000322313.4	-	8	914	c.756G>A	c.(754-756)tgG>tgA	p.W252*		NM_018383.4	NP_060853.3	Q9C0J8	WDR33_HUMAN	WD repeat domain 33	252					mRNA processing (GO:0006397)|postreplication repair (GO:0006301)|spermatogenesis (GO:0007283)	collagen trimer (GO:0005581)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			NS(1)|breast(3)|endometrium(2)|kidney(2)|large_intestine(9)|lung(17)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	39	Colorectal(110;0.1)			BRCA - Breast invasive adenocarcinoma(221;0.0695)		TGGTTGGATGCCAGTCTACAC	0.408																																						uc002tpg.1																			0					0						c.(754-756)TGG>TGA		WD repeat domain 33 isoform 1							175.0	172.0	173.0					2																	128484320		2203	4300	6503	SO:0001587	stop_gained	55339				postreplication repair|spermatogenesis	collagen|nucleus	protein binding	g.chr2:128484320C>T		CCDS2150.1, CCDS42746.1, CCDS46407.1	2q21.1	2013-01-09			ENSG00000136709	ENSG00000136709		"""WD repeat domain containing"""	25651	protein-coding gene	gene with protein product						11162572	Standard	NM_001006622		Approved	FLJ11294, WDC146, NET14	uc002tpg.2	Q9C0J8	OTTHUMG00000131534	ENST00000322313.4:c.756G>A	2.37:g.128484320C>T	ENSP00000325377:p.Trp252*						p.W252*	NM_018383	NP_060853	Q9C0J8	WDR33_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.0695)	8	939	-	Colorectal(110;0.1)		252			WD 4.		Q05DP8|Q53FG9|Q587J1|Q69YF7|Q6NUQ0|Q9NUL1	Nonsense_Mutation	SNP	ENST00000322313.4	37	c.756G>A	CCDS2150.1	.	.	.	.	.	.	.	.	.	.	C	36	5.675019	0.96764	.	.	ENSG00000136709	ENST00000322313;ENST00000436787	.	.	.	5.52	5.52	0.82312	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-5.1042	19.4285	0.94755	0.0:1.0:0.0:0.0	.	.	.	.	X	252;174	.	ENSP00000325377:W252X	W	-	3	0	WDR33	128200790	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.590000	0.87494	0.591000	0.81541	TGG		0.408	WDR33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331141.2	NM_018383	
HOXD10	3236	broad.mit.edu	37	2	176981726	176981726	+	Silent	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr2:176981726G>A	ENST00000249501.4	+	1	420	c.165G>A	c.(163-165)ccG>ccA	p.P55P	HOXD10_ENST00000490088.2_Intron	NM_002148.3	NP_002139.2	P28358	HXD10_HUMAN	homeobox D10	55					adult locomotory behavior (GO:0008344)|anterior/posterior pattern specification (GO:0009952)|embryonic limb morphogenesis (GO:0030326)|embryonic skeletal system morphogenesis (GO:0048704)|forelimb morphogenesis (GO:0035136)|hindlimb morphogenesis (GO:0035137)|neuromuscular process (GO:0050905)|peripheral nervous system neuron development (GO:0048935)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|proximal/distal pattern formation (GO:0009954)|single fertilization (GO:0007338)|skeletal muscle tissue development (GO:0007519)|spinal cord motor neuron cell fate specification (GO:0021520)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	chromatin binding (GO:0003682)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.P55P(2)		endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|ovary(3)|upper_aerodigestive_tract(1)	17			OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)		GACTGCTCCCGTCTCTGGCCA	0.488																																						uc002ukj.2																			2	Substitution - coding silent(2)		large_intestine(1)|endometrium(1)	ovary(1)	1						c.(163-165)CCG>CCA		homeobox D10							109.0	109.0	109.0					2																	176981726		2203	4300	6503	SO:0001819	synonymous_variant	3236					nucleus	sequence-specific DNA binding	g.chr2:176981726G>A		CCDS2266.1	2q31.1	2014-09-17	2005-12-22		ENSG00000128710	ENSG00000128710		"""Homeoboxes / ANTP class : HOXL subclass"""	5133	protein-coding gene	gene with protein product		142984	"""homeo box D10"""	HOX4, HOX4D		1973146, 1358459	Standard	NM_002148		Approved		uc002ukj.3	P28358	OTTHUMG00000132511	ENST00000249501.4:c.165G>A	2.37:g.176981726G>A							p.P55P	NM_002148	NP_002139	P28358	HXD10_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0207)|Epithelial(96;0.18)	Colorectal(32;0.0226)|READ - Rectum adenocarcinoma(9;0.0556)	1	235	+			55					Q6NT10	Silent	SNP	ENST00000249501.4	37	c.165G>A	CCDS2266.1																																																																																				0.488	HOXD10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255692.2		
PLEKHM3	389072	broad.mit.edu	37	2	208841462	208841462	+	Missense_Mutation	SNP	G	G	A	rs200329503		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr2:208841462G>A	ENST00000427836.2	-	3	1948	c.1459C>T	c.(1459-1461)Cgc>Tgc	p.R487C	PLEKHM3_ENST00000457206.1_Missense_Mutation_p.R487C|PLEKHM3_ENST00000389247.4_Missense_Mutation_p.R487C	NM_001080475.2	NP_001073944.1	Q6ZWE6	PKHM3_HUMAN	pleckstrin homology domain containing, family M, member 3	487					intracellular signal transduction (GO:0035556)		metal ion binding (GO:0046872)			central_nervous_system(1)|cervix(1)|endometrium(2)|large_intestine(1)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	19						ACAGATTGGCGTTTGTTCTTC	0.478													G|||	1	0.000199681	0.0	0.0	5008	,	,		20469	0.0		0.0	False		,,,				2504	0.001					uc002vcl.2																			0				ovary(1)	1						c.(1459-1461)CGC>TGC		pleckstrin homology domain containing, family M,							98.0	97.0	97.0					2																	208841462		1998	4187	6185	SO:0001583	missense	389072				intracellular signal transduction		metal ion binding	g.chr2:208841462G>A	AK057612	CCDS42808.1	2q33.3	2013-01-10	2008-04-03	2008-04-03	ENSG00000178385	ENSG00000178385		"""Pleckstrin homology (PH) domain containing"""	34006	protein-coding gene	gene with protein product	"""differentiation associated protein"""		"""pleckstrin homology domain containing, family M, member 1-like"""	PLEKHM1L		19028694	Standard	NM_001080475		Approved	DAPR	uc002vcl.2	Q6ZWE6	OTTHUMG00000154781	ENST00000427836.2:c.1459C>T	2.37:g.208841462G>A	ENSP00000417003:p.Arg487Cys					PLEKHM3_uc002vcm.2_Missense_Mutation_p.R487C	p.R487C	NM_001080475	NP_001073944	Q6ZWE6	PKHM3_HUMAN			3	1949	-			487					B9EKV2|Q8WW68	Missense_Mutation	SNP	ENST00000427836.2	37	c.1459C>T	CCDS42808.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	22.0|22.0	4.228534|4.228534	0.79576|0.79576	.|.	.|.	ENSG00000178385|ENSG00000178385	ENST00000427836;ENST00000389247;ENST00000457206|ENST00000447645	D;D;D|.	0.86097|.	-2.02;-2.03;-2.07|.	5.52|5.52	5.52|5.52	0.82312|0.82312	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.65133|0.65133	0.2662|0.2662	L|L	0.34521|0.34521	1.04|1.04	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.85130|.	0.997;0.997|.	T|T	0.58994|0.58994	-0.7537|-0.7537	10|5	0.87932|.	D|.	0|.	.|.	19.8024|19.8024	0.96513|0.96513	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	487;487|.	C9J119;Q6ZWE6|.	.;PKHM3_HUMAN|.	C|M	487|238	ENSP00000417003:R487C;ENSP00000373899:R487C;ENSP00000400150:R487C|.	ENSP00000373899:R487C|.	R|T	-|-	1|2	0|0	PLEKHM3|PLEKHM3	208549707|208549707	1.000000|1.000000	0.71417|0.71417	0.915000|0.915000	0.36163|0.36163	0.782000|0.782000	0.44232|0.44232	9.174000|9.174000	0.94824|0.94824	2.752000|2.752000	0.94435|0.94435	0.655000|0.655000	0.94253|0.94253	CGC|ACG		0.478	PLEKHM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337036.1	NM_001080475	
CCDC108	255101	broad.mit.edu	37	2	219874081	219874081	+	Missense_Mutation	SNP	G	G	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr2:219874081G>C	ENST00000341552.5	-	28	4637	c.4554C>G	c.(4552-4554)gaC>gaG	p.D1518E	CCDC108_ENST00000441968.1_Missense_Mutation_p.D1518E|AC097468.4_ENST00000441450.1_RNA|CCDC108_ENST00000453220.1_Missense_Mutation_p.D1518E	NM_194302.2	NP_919278.2	Q6ZU64	CC108_HUMAN	coiled-coil domain containing 108	1518						integral component of membrane (GO:0016021)	poly(A) RNA binding (GO:0044822)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(18)|liver(1)|lung(34)|ovary(2)|pancreas(1)|prostate(6)|skin(5)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	80		Renal(207;0.0915)		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		TGCATACCAGGTCTGCACTGT	0.587																																						uc002vjl.1																			0				ovary(2)|upper_aerodigestive_tract(1)|pancreas(1)	4						c.(4552-4554)GAC>GAG		coiled-coil domain containing 108 isoform 1							63.0	60.0	61.0					2																	219874081		2200	4293	6493	SO:0001583	missense	255101					integral to membrane	structural molecule activity	g.chr2:219874081G>C	NM_194302, AL833882, AK127189	CCDS2430.2, CCDS2431.2, CCDS63125.1, CCDS63126.1	2q35	2008-02-05			ENSG00000181378	ENSG00000181378			25325	protein-coding gene	gene with protein product		614270				12477932	Standard	NM_194302		Approved	DKFZp434O0527, MGC35338	uc002vjl.2	Q6ZU64	OTTHUMG00000133013	ENST00000341552.5:c.4554C>G	2.37:g.219874081G>C	ENSP00000340776:p.Asp1518Glu						p.D1518E	NM_194302	NP_919278	Q6ZU64	CC108_HUMAN		Epithelial(149;1.12e-06)|all cancers(144;0.000196)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	28	4638	-		Renal(207;0.0915)	1518					A2BDD8|E9PCR1|E9PG25|E9PG72|Q6ZSR8|Q8N0T4|Q8NDJ3	Missense_Mutation	SNP	ENST00000341552.5	37	c.4554C>G	CCDS2430.2	.	.	.	.	.	.	.	.	.	.	G	8.976	0.974130	0.18736	.	.	ENSG00000181378	ENST00000341552;ENST00000441968;ENST00000453220	T;T;T	0.05382	3.45;3.45;3.45	5.33	2.42	0.29668	.	0.151725	0.30584	N	0.009303	T	0.09468	0.0233	M	0.74258	2.255	0.58432	D	0.999999	P	0.35745	0.518	B	0.38020	0.263	T	0.05273	-1.0895	10	0.51188	T	0.08	-17.2367	6.5715	0.22541	0.16:0.3404:0.4996:0.0	.	1518	Q6ZU64	CC108_HUMAN	E	1518	ENSP00000340776:D1518E;ENSP00000413377:D1518E;ENSP00000409117:D1518E	ENSP00000340776:D1518E	D	-	3	2	CCDC108	219582325	1.000000	0.71417	0.428000	0.26697	0.115000	0.19883	1.386000	0.34419	0.181000	0.19994	0.555000	0.69702	GAC		0.587	CCDC108-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256598.4	NM_194302	
RBM44	375316	broad.mit.edu	37	2	238738022	238738022	+	Silent	SNP	G	G	A	rs376575329		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr2:238738022G>A	ENST00000409864.1	+	13	3020	c.2766G>A	c.(2764-2766)tcG>tcA	p.S922S	RBM44_ENST00000316997.4_Silent_p.S922S			Q6ZP01	RBM44_HUMAN	RNA binding motif protein 44	921						cytoplasm (GO:0005737)|intercellular bridge (GO:0045171)	nucleotide binding (GO:0000166)|protein homodimerization activity (GO:0042803)|RNA binding (GO:0003723)			breast(1)|endometrium(4)|kidney(4)|large_intestine(11)|lung(7)|ovary(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	33		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)		GAATTAGTTCGAATAATTTAG	0.388																																						uc002vxi.3																			0				ovary(4)	4						c.(2764-2766)TCG>TCA		RNA binding motif protein 44		G		0,3646		0,0,1823	96.0	94.0	94.0		2766	-2.3	0.0	2		94	2,8158		0,2,4078	no	coding-synonymous	RBM44	NM_001080504.2		0,2,5901	AA,AG,GG		0.0245,0.0,0.0169		922/1053	238738022	2,11804	1823	4080	5903	SO:0001819	synonymous_variant	375316						nucleotide binding|RNA binding	g.chr2:238738022G>A	AK097730	CCDS46554.1	2q37.3	2013-02-12			ENSG00000177483	ENSG00000177483		"""RNA binding motif (RRM) containing"""	24756	protein-coding gene	gene with protein product							Standard	NM_001080504		Approved	FLJ40411	uc002vxi.4	Q6ZP01	OTTHUMG00000152937	ENST00000409864.1:c.2766G>A	2.37:g.238738022G>A							p.S922S	NM_001080504	NP_001073973	Q6ZP01	RBM44_HUMAN		Epithelial(121;3.74e-22)|OV - Ovarian serous cystadenocarcinoma(60;5.3e-11)|Kidney(56;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(57;6.5e-08)|BRCA - Breast invasive adenocarcinoma(100;0.000118)|Lung(119;0.0112)|LUSC - Lung squamous cell carcinoma(224;0.0266)	13	2898	+		Breast(86;0.0042)|Renal(207;0.00571)|Ovarian(221;0.17)|all_hematologic(139;0.182)	921					A0AUW3	Silent	SNP	ENST00000409864.1	37	c.2766G>A	CCDS46554.1																																																																																				0.388	RBM44-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328733.2	NM_001080504	
NOP56	10528	broad.mit.edu	37	20	2633552	2633552	+	Missense_Mutation	SNP	A	A	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr20:2633552A>T	ENST00000329276.5	+	2	584	c.68A>T	c.(67-69)gAg>gTg	p.E23V	MIR1292_ENST00000408135.1_RNA|SNORD110_ENST00000408189.1_RNA|SNORA51_ENST00000606420.1_RNA	NM_006392.3	NP_006383.2	O00567	NOP56_HUMAN	NOP56 ribonucleoprotein	23					cell death (GO:0008219)|rRNA processing (GO:0006364)	box C/D snoRNP complex (GO:0031428)|cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleolus (GO:0005730)|pre-snoRNP complex (GO:0070761)|small nucleolar ribonucleoprotein complex (GO:0005732)	poly(A) RNA binding (GO:0044822)|RNA binding (GO:0003723)|snoRNA binding (GO:0030515)			breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|pancreas(1)|skin(2)|urinary_tract(1)	25						AAGGAAGTGGAGGAGATCAGT	0.677																																						uc002wgh.2																			0				ovary(1)|pancreas(1)	2						c.(67-69)GAG>GTG		nucleolar protein 5A							24.0	27.0	26.0					20																	2633552		2201	4300	6501	SO:0001583	missense	10528				rRNA processing	box C/D snoRNP complex|pre-snoRNP complex	protein binding|snoRNA binding	g.chr20:2633552A>T	Y12065	CCDS13030.1	20p13	2012-12-10	2012-12-10	2009-01-13	ENSG00000101361	ENSG00000101361			15911	protein-coding gene	gene with protein product	"""spinocerebellar ataxia 36"""	614154	"""nucleolar protein 5A (56kD with KKE/D repeat)"", ""nucleolar protein 5A (56kDa with KKE/D repeat)"", ""NOP56 ribonucleoprotein homolog (yeast)"""	NOL5A		9372940, 21683323	Standard	NR_027700		Approved	SCA36	uc002wgh.3	O00567	OTTHUMG00000031703	ENST00000329276.5:c.68A>T	20.37:g.2633552A>T	ENSP00000370589:p.Glu23Val					NOP56_uc010zpy.1_RNA|NOP56_uc002wgi.2_5'Flank|SNORD110_uc002wgj.2_5'Flank|SNORA51_uc002wgk.1_5'Flank|NOP56_uc002wgm.1_5'Flank	p.E23V	NM_006392	NP_006383	O00567	NOP56_HUMAN			2	121	+			23					Q2M3T6|Q9NQ05	Missense_Mutation	SNP	ENST00000329276.5	37	c.68A>T	CCDS13030.1	.	.	.	.	.	.	.	.	.	.	A	37	6.133652	0.97310	.	.	ENSG00000101361	ENST00000329276;ENST00000445139	T;T	0.60424	0.19;0.77	5.77	5.77	0.91146	NOP5, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.80014	0.4546	M	0.91406	3.205	0.80722	D	1	D	0.67145	0.996	D	0.68621	0.959	D	0.84672	0.0712	10	0.87932	D	0	-24.3054	14.0969	0.65029	1.0:0.0:0.0:0.0	.	23	O00567	NOP56_HUMAN	V	23	ENSP00000370589:E23V;ENSP00000388497:E23V	ENSP00000370589:E23V	E	+	2	0	NOP56	2581552	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.586000	0.90806	2.210000	0.71456	0.472000	0.43445	GAG		0.677	NOP56-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077631.2	NM_006392	
LBP	3929	broad.mit.edu	37	20	36992652	36992652	+	Missense_Mutation	SNP	G	G	A	rs545550026		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr20:36992652G>A	ENST00000217407.2	+	7	837	c.676G>A	c.(676-678)Gcc>Acc	p.A226T		NM_004139.3	NP_004130.2	P18428	LBP_HUMAN	lipopolysaccharide binding protein	226					acute-phase response (GO:0006953)|cellular defense response (GO:0006968)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to lipoteichoic acid (GO:0071223)|defense response to Gram-negative bacterium (GO:0050829)|defense response to Gram-positive bacterium (GO:0050830)|detection of molecule of bacterial origin (GO:0032490)|innate immune response (GO:0045087)|leukocyte chemotaxis involved in inflammatory response (GO:0002232)|lipopolysaccharide transport (GO:0015920)|lipopolysaccharide-mediated signaling pathway (GO:0031663)|macrophage activation involved in immune response (GO:0002281)|negative regulation of growth of symbiont in host (GO:0044130)|negative regulation of tumor necrosis factor production (GO:0032720)|opsonization (GO:0008228)|positive regulation of chemokine production (GO:0032722)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of interleukin-8 production (GO:0032757)|positive regulation of macrophage activation (GO:0043032)|positive regulation of neutrophil chemotaxis (GO:0090023)|positive regulation of respiratory burst involved in inflammatory response (GO:0060265)|positive regulation of toll-like receptor 4 signaling pathway (GO:0034145)|positive regulation of tumor necrosis factor biosynthetic process (GO:0042535)|positive regulation of tumor necrosis factor production (GO:0032760)|response to lipopolysaccharide (GO:0032496)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	lipopolysaccharide binding (GO:0001530)|lipoteichoic acid binding (GO:0070891)|receptor binding (GO:0005102)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(2)|lung(16)|ovary(2)|prostate(1)|urinary_tract(1)	28		Myeloproliferative disorder(115;0.00878)				TGACAGTTTCGCCGACATTGA	0.562																																						uc002xic.1																			0				ovary(1)|central_nervous_system(1)	2						c.(676-678)GCC>ACC		lipopolysaccharide-binding protein precursor							89.0	87.0	88.0					20																	36992652		2203	4300	6503	SO:0001583	missense	3929				acute-phase response|cellular defense response|cellular response to lipoteichoic acid|defense response to Gram-negative bacterium|defense response to Gram-positive bacterium|detection of molecule of bacterial origin|innate immune response|lipid transport|lipopolysaccharide transport|lipopolysaccharide-mediated signaling pathway|macrophage activation involved in immune response|negative regulation of tumor necrosis factor production|opsonization|positive regulation of interleukin-6 production|positive regulation of interleukin-8 production|positive regulation of macrophage activation|positive regulation of respiratory burst involved in inflammatory response|positive regulation of toll-like receptor 4 signaling pathway|positive regulation of tumor necrosis factor production|Toll signaling pathway	extracellular space	Gram-negative bacterial cell surface binding|Gram-positive bacterial cell surface binding|lipid binding|lipopolysaccharide binding|lipoteichoic acid binding|receptor binding	g.chr20:36992652G>A		CCDS13304.1	20q11.23	2011-08-16	2001-11-28		ENSG00000129988	ENSG00000129988		"""BPI fold containing"""	6517	protein-coding gene	gene with protein product	"""BPI fold containing family D, member 2"""	151990	"""lipopolysaccharide-binding protein"""			8432532	Standard	NM_004139		Approved	BPIFD2	uc002xic.2	P18428	OTTHUMG00000032447	ENST00000217407.2:c.676G>A	20.37:g.36992652G>A	ENSP00000217407:p.Ala226Thr						p.A226T	NM_004139	NP_004130	P18428	LBP_HUMAN			7	711	+		Myeloproliferative disorder(115;0.00878)	226					B2R938|O43438|Q92672|Q9H403|Q9UD66	Missense_Mutation	SNP	ENST00000217407.2	37	c.676G>A	CCDS13304.1	.	.	.	.	.	.	.	.	.	.	G	12.07	1.827892	0.32329	.	.	ENSG00000129988	ENST00000217407;ENST00000538599	T	0.04917	3.53	5.2	-8.58	0.00897	Lipid-binding serum glycoprotein, N-terminal (1);Bactericidal permeability-increasing protein, alpha/beta domain (1);	2.297420	0.01727	N	0.028620	T	0.03178	0.0093	L	0.31926	0.97	0.09310	N	1	P	0.35656	0.514	B	0.28139	0.086	T	0.41610	-0.9499	10	0.16896	T	0.51	0.425	1.7423	0.02955	0.413:0.0939:0.1379:0.3552	.	226	P18428	LBP_HUMAN	T	226	ENSP00000217407:A226T	ENSP00000217407:A226T	A	+	1	0	LBP	36426066	0.000000	0.05858	0.000000	0.03702	0.001000	0.01503	-1.631000	0.02026	-1.175000	0.02751	-0.218000	0.12543	GCC		0.562	LBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079174.2	NM_004139	
WFDC9	259240	broad.mit.edu	37	20	44237357	44237357	+	Missense_Mutation	SNP	G	G	A	rs139643257	byFrequency	TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr20:44237357G>A	ENST00000326000.1	-	4	401	c.184C>T	c.(184-186)Cgt>Tgt	p.R62C		NM_147198.3	NP_671731.1	Q8NEX5	WFDC9_HUMAN	WAP four-disulfide core domain 9	62						extracellular region (GO:0005576)				breast(1)|large_intestine(1)|liver(1)|lung(1)|prostate(1)|stomach(1)	6		Myeloproliferative disorder(115;0.0122)				TGATTTGGACGTACACAAGTC	0.453													G|||	3	0.000599042	0.0	0.0	5008	,	,		20344	0.0		0.003	False		,,,				2504	0.0					uc002xoy.2																			0					0						c.(184-186)CGT>TGT		protease inhibitor WAP9 precursor		G	CYS/ARG	7,4399	12.9+/-30.5	0,7,2196	248.0	193.0	212.0		184	-7.9	0.0	20	dbSNP_134	212	42,8558	26.8+/-75.7	0,42,4258	yes	missense	WFDC9	NM_147198.3	180	0,49,6454	AA,AG,GG		0.4884,0.1589,0.3767	possibly-damaging	62/90	44237357	49,12957	2203	4300	6503	SO:0001583	missense	259240					extracellular region		g.chr20:44237357G>A	AL031671	CCDS13362.1	20q13.12	2013-01-21			ENSG00000180205	ENSG00000180205		"""WAP four-disulfide core domain containing"""	20380	protein-coding gene	gene with protein product						12206714	Standard	NM_147198		Approved	WAP9, dJ688G8.2	uc002xoy.3	Q8NEX5	OTTHUMG00000046332	ENST00000326000.1:c.184C>T	20.37:g.44237357G>A	ENSP00000320532:p.Arg62Cys						p.R62C	NM_147198	NP_671731	Q8NEX5	WFDC9_HUMAN			4	402	-		Myeloproliferative disorder(115;0.0122)	62					Q3MIX6|Q5TGZ8	Missense_Mutation	SNP	ENST00000326000.1	37	c.184C>T	CCDS13362.1	3	0.0013736263736263737	0	0.0	0	0.0	0	0.0	3	0.00395778364116095	G	11.55	1.672168	0.29693	0.001589	0.004884	ENSG00000180205	ENST00000326000	T	0.31510	1.49	3.94	-7.88	0.01178	.	2.894430	0.01286	N	0.009898	T	0.20251	0.0487	.	.	.	0.09310	N	1	P	0.52692	0.955	B	0.41723	0.365	T	0.42292	-0.9460	9	0.37606	T	0.19	6.5972	6.0654	0.19860	0.3528:0.0:0.1337:0.5134	.	62	Q8NEX5	WFDC9_HUMAN	C	62	ENSP00000320532:R62C	ENSP00000320532:R62C	R	-	1	0	WFDC9	43670771	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-1.804000	0.01738	-2.513000	0.00502	-0.188000	0.12872	CGT		0.453	WFDC9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000106945.1		
TP53RK	112858	broad.mit.edu	37	20	45315631	45315631	+	3'UTR	SNP	C	C	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr20:45315631C>A	ENST00000372102.3	-	0	553				RP1-28H20.3_ENST00000606362.1_lincRNA			Q96S44	PRPK_HUMAN	TP53 regulating kinase						lipopolysaccharide biosynthetic process (GO:0009103)|protein phosphorylation (GO:0006468)|tRNA processing (GO:0008033)	membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|hydrolase activity (GO:0016787)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)			kidney(1)|large_intestine(1)|lung(4)|skin(1)	7		Myeloproliferative disorder(115;0.0122)				TTCAGCTGTTCCAGGGGGGGT	0.498																																						uc002xsk.2																			0					0						c.(523-525)GAA>TAA		p53-related protein kinase							109.0	110.0	109.0					20																	45315631		2203	4300	6503	SO:0001624	3_prime_UTR_variant	112858				lipopolysaccharide biosynthetic process	membrane|nucleus	ATP binding|p53 binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	g.chr20:45315631C>A		CCDS13401.1	20q13.2	2014-05-14	2004-05-10	2004-05-12	ENSG00000172315	ENSG00000172315			16197	protein-coding gene	gene with protein product		608679	"""chromosome 20 open reading frame 64"""	C20orf64		11546806, 12914926	Standard	NM_033550		Approved	dJ101A2.2, prpk, Nori-2p, BUD32	uc002xsk.3	Q96S44	OTTHUMG00000085887	ENST00000372102.3:c.*162G>T	20.37:g.45315631C>A						SLC13A3_uc002xsg.1_5'Flank|SLC13A3_uc010gho.1_5'Flank|TP53RK_uc002xsj.2_3'UTR	p.E175*	NM_033550	NP_291028	Q96S44	PRPK_HUMAN			2	746	-		Myeloproliferative disorder(115;0.0122)	175			Protein kinase.		B3KU44|Q3T977|Q5JZ01|Q6NZ60|Q96FM7|Q9NQE6	Nonsense_Mutation	SNP	ENST00000372102.3	37	c.523G>T		.	.	.	.	.	.	.	.	.	.	C	29.9	5.045403	0.93685	.	.	ENSG00000172315	ENST00000372114	.	.	.	5.16	5.16	0.70880	.	0.507958	0.23261	N	0.050128	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.11182	T	0.66	-2.8912	18.8467	0.92210	0.0:1.0:0.0:0.0	.	.	.	.	X	175	.	ENSP00000361186:E175X	E	-	1	0	TP53RK	44749038	0.999000	0.42202	0.045000	0.18777	0.036000	0.12997	4.583000	0.60964	2.664000	0.90586	0.655000	0.94253	GAA		0.498	TP53RK-002	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000193688.1	NM_033550	
SCAF4	57466	broad.mit.edu	37	21	33074598	33074598	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr21:33074598C>T	ENST00000286835.7	-	5	798	c.416G>A	c.(415-417)aGt>aAt	p.S139N	SCAF4_ENST00000434667.3_Missense_Mutation_p.S124N|SCAF4_ENST00000399804.1_Missense_Mutation_p.S139N	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4	139	CID. {ECO:0000255|PROSITE- ProRule:PRU00724}.					nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						GGCTGCATTACTGGTTCCCGC	0.388																																						uc002ypd.2																			0					0						c.(415-417)AGT>AAT		splicing factor, arginine/serine-rich 15 isoform							162.0	138.0	146.0					21																	33074598		2203	4300	6503	SO:0001583	missense	57466					nucleus	nucleotide binding|RNA binding	g.chr21:33074598C>T	AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"""RNA binding motif (RRM) containing"""	19304	protein-coding gene	gene with protein product			"""splicing factor, arginine/serine-rich 15"""	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.416G>A	21.37:g.33074598C>T	ENSP00000286835:p.Ser139Asn					SFRS15_uc002ype.2_Missense_Mutation_p.S139N|SFRS15_uc010glu.2_Missense_Mutation_p.S124N|SFRS15_uc002ypf.1_5'Flank|SFRS15_uc002ypg.2_Missense_Mutation_p.S139N	p.S139N	NM_020706	NP_065757	O95104	SFR15_HUMAN			5	842	-			139			CID.		C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Missense_Mutation	SNP	ENST00000286835.7	37	c.416G>A	CCDS33537.1	.	.	.	.	.	.	.	.	.	.	C	15.73	2.919698	0.52653	.	.	ENSG00000156304	ENST00000434667;ENST00000286835;ENST00000399804	T;T;T	0.48201	0.86;0.82;0.82	5.51	4.58	0.56647	ENTH/VHS (1);RNA polymerase II, large subunit, CTD (1);	0.241273	0.43579	D	0.000550	T	0.39332	0.1074	N	0.22421	0.69	0.42527	D	0.993027	P;P;P;P	0.43094	0.546;0.799;0.675;0.546	B;B;B;B	0.43658	0.244;0.205;0.426;0.244	T	0.13953	-1.0490	10	0.21014	T	0.42	-17.2752	17.9369	0.89015	0.0:0.8687:0.1313:0.0	.	124;139;139;139	C9JLZ0;Q0P607;O95104-2;O95104	.;.;.;SFR15_HUMAN	N	124;139;139	ENSP00000402377:S124N;ENSP00000286835:S139N;ENSP00000382703:S139N	ENSP00000286835:S139N	S	-	2	0	SCAF4	31996469	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	4.523000	0.60545	2.582000	0.87167	0.484000	0.47621	AGT		0.388	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1	XM_047889	
CAND2	23066	broad.mit.edu	37	3	12858462	12858462	+	Silent	SNP	C	C	T	rs377443431		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr3:12858462C>T	ENST00000456430.2	+	10	2072	c.2031C>T	c.(2029-2031)gaC>gaT	p.D677D	CAND2_ENST00000295989.5_Silent_p.D584D	NM_001162499.1	NP_001155971.1	O75155	CAND2_HUMAN	cullin-associated and neddylation-dissociated 2 (putative)	677					positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	intracellular (GO:0005622)|nucleus (GO:0005634)		p.D584D(2)		breast(3)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(10)|lung(8)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	37						CAGCCCTGGACGCCCTGGCCC	0.662																																					GBM(43;676 868 1633 6395 37496)	uc003bxk.2																			2	Substitution - coding silent(2)		large_intestine(1)|prostate(1)	skin(3)|pancreas(1)	4						c.(2029-2031)GAC>GAT		TBP-interacting protein isoform 1		C	,	2,4054		0,2,2026	24.0	26.0	25.0		2031,1752	-9.9	0.2	3		25	0,8374		0,0,4187	no	coding-synonymous,coding-synonymous	CAND2	NM_001162499.1,NM_012298.2	,	0,2,6213	TT,TC,CC		0.0,0.0493,0.0161	,	677/1237,584/1120	12858462	2,12428	2028	4187	6215	SO:0001819	synonymous_variant	23066				positive regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein binding	g.chr3:12858462C>T		CCDS43053.1, CCDS54554.1	3p25.2	2008-02-05			ENSG00000144712	ENSG00000144712			30689	protein-coding gene	gene with protein product	"""TBP interacting protein"""	610403				9734811, 10441524	Standard	NM_012298		Approved	TIP120B, KIAA0667, Tp120b	uc003bxk.2	O75155	OTTHUMG00000155397	ENST00000456430.2:c.2031C>T	3.37:g.12858462C>T						CAND2_uc003bxj.2_Silent_p.D584D	p.D677D	NM_001162499	NP_001155971	O75155	CAND2_HUMAN			10	2080	+			677			HEAT 14.		B9EGM9|E9KL24	Silent	SNP	ENST00000456430.2	37	c.2031C>T	CCDS54554.1																																																																																				0.662	CAND2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000339856.4	XM_371617	
ZIC4	84107	broad.mit.edu	37	3	147113783	147113783	+	Missense_Mutation	SNP	C	C	G			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr3:147113783C>G	ENST00000383075.3	-	3	1056	c.544G>C	c.(544-546)Gga>Cga	p.G182R	ZIC4_ENST00000425731.3_Missense_Mutation_p.G220R|ZIC4_ENST00000473123.1_Missense_Mutation_p.G182R|ZIC4_ENST00000484399.1_Missense_Mutation_p.G182R|ZIC4_ENST00000525172.2_Missense_Mutation_p.G232R|ZIC4_ENST00000491672.1_Intron	NM_032153.5	NP_115529.2	Q8N9L1	ZIC4_HUMAN	Zic family member 4	182						nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(9)|lung(34)|upper_aerodigestive_tract(4)	57						AAGGGCTTTCCCTGGCGCGGA	0.597																																						uc003ewd.1																			0				upper_aerodigestive_tract(1)|central_nervous_system(1)	2						c.(544-546)GGA>CGA		zinc finger protein of the cerebellum 4							118.0	129.0	125.0					3																	147113783		2203	4300	6503	SO:0001583	missense	84107					nucleus	DNA binding|zinc ion binding	g.chr3:147113783C>G	AF332509	CCDS43160.1, CCDS54652.1, CCDS54653.1, CCDS58857.1	3q24	2013-01-08	2003-02-21		ENSG00000174963	ENSG00000174963		"""Zinc fingers, C2H2-type"""	20393	protein-coding gene	gene with protein product		608948	"""zinc finger protein of the cerebellum 4"""				Standard	NM_001168378		Approved		uc011bno.2	Q8N9L1	OTTHUMG00000037281	ENST00000383075.3:c.544G>C	3.37:g.147113783C>G	ENSP00000372553:p.Gly182Arg					ZIC4_uc003ewc.1_Missense_Mutation_p.G112R|ZIC4_uc011bno.1_Missense_Mutation_p.G232R	p.G182R	NM_032153	NP_115529	Q8N9L1	ZIC4_HUMAN			3	817	-			182			C2H2-type 2; atypical.		A0AVA2|B2RMQ8|B4DF89|B7Z2L2|C9J7D5|J3KQG1|Q4G157|Q9BZ94	Missense_Mutation	SNP	ENST00000383075.3	37	c.544G>C	CCDS43160.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.911009	0.92178	.	.	ENSG00000174963	ENST00000383075;ENST00000425731;ENST00000525172;ENST00000484399;ENST00000473123;ENST00000462748	D;D;D;D;D;D	0.94376	-3.41;-3.41;-3.41;-3.41;-3.41;-3.41	5.2	5.2	0.72013	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.47093	D	0.000256	D	0.96116	0.8734	M	0.62723	1.935	0.80722	D	1	P;D	0.76494	0.946;0.999	P;D	0.76071	0.593;0.987	D	0.96326	0.9240	10	0.62326	D	0.03	.	18.7355	0.91753	0.0:1.0:0.0:0.0	.	232;182	B7Z2L2;Q8N9L1	.;ZIC4_HUMAN	R	182;220;232;182;182;182	ENSP00000372553:G182R;ENSP00000397695:G220R;ENSP00000435509:G232R;ENSP00000417855:G182R;ENSP00000420775:G182R;ENSP00000420627:G182R	ENSP00000372553:G182R	G	-	1	0	ZIC4	148596473	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.818000	0.86416	2.425000	0.82216	0.511000	0.50034	GGA		0.597	ZIC4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355504.1		
MECOM	2122	broad.mit.edu	37	3	168834185	168834185	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr3:168834185G>A	ENST00000464456.1	-	7	2111	c.911C>T	c.(910-912)cCt>cTt	p.P304L	MECOM_ENST00000472280.1_Missense_Mutation_p.P305L|MECOM_ENST00000468789.1_Missense_Mutation_p.P304L|MECOM_ENST00000460814.1_Missense_Mutation_p.P304L|MECOM_ENST00000392736.3_Missense_Mutation_p.P304L|MECOM_ENST00000494292.1_Missense_Mutation_p.P492L|MECOM_ENST00000433243.2_Missense_Mutation_p.P305L|MECOM_ENST00000264674.3_Missense_Mutation_p.P369L	NM_001164000.1	NP_001157472.1	Q13465	MDS1_HUMAN	MDS1 and EVI1 complex locus	0					regulation of transcription, DNA-templated (GO:0006355)		sequence-specific DNA binding transcription factor activity (GO:0003700)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(9)|kidney(4)|large_intestine(13)|liver(1)|lung(28)|ovary(2)|pancreas(1)|prostate(2)|skin(12)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(4)	85						AAACAGACCAGGGAAGCTAAA	0.473																																						uc003ffi.3																			0				lung(5)|skin(5)|upper_aerodigestive_tract(1)|central_nervous_system(1)|ovary(1)|pancreas(1)	14						c.(910-912)CCT>CTT		MDS1 and EVI1 complex locus isoform b							311.0	276.0	288.0					3																	168834185		2203	4300	6503	SO:0001583	missense	2122				apoptosis|cell differentiation|hemopoietic stem cell proliferation|negative regulation of JNK cascade|negative regulation of programmed cell death|negative regulation of transcription, DNA-dependent|regulation of cell cycle	nuclear speck	DNA binding|protein binding|protein homodimerization activity|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr3:168834185G>A	S82592, AF164154	CCDS3205.1, CCDS54669.1, CCDS54670.1	3q26.2	2013-01-08	2009-08-07	2009-08-07	ENSG00000085276	ENSG00000085276		"""Zinc fingers, C2H2-type"""	3498	protein-coding gene	gene with protein product		165215	"""myelodysplasia syndrome 1"", ""ecotropic viral integration site 1"""	MDS1, EVI1		2115646, 8171026, 8643684	Standard	NM_001105077		Approved	MDS1-EVI1, PRDM3	uc011bpj.1	Q03112	OTTHUMG00000158596	ENST00000464456.1:c.911C>T	3.37:g.168834185G>A	ENSP00000419770:p.Pro304Leu					MECOM_uc010hwk.1_Missense_Mutation_p.P327L|MECOM_uc003ffj.3_Missense_Mutation_p.P369L|MECOM_uc011bpi.1_Missense_Mutation_p.P305L|MECOM_uc003ffn.3_Missense_Mutation_p.P304L|MECOM_uc003ffk.2_Missense_Mutation_p.P304L|MECOM_uc003ffl.2_Missense_Mutation_p.P464L|MECOM_uc011bpj.1_Missense_Mutation_p.P492L|MECOM_uc011bpk.1_Missense_Mutation_p.P294L|MECOM_uc010hwn.2_Missense_Mutation_p.P492L	p.P304L	NM_005241	NP_005232	Q03112	EVI1_HUMAN			7	1180	-			304					Q13466|Q6FH90	Missense_Mutation	SNP	ENST00000464456.1	37	c.911C>T	CCDS54669.1	.	.	.	.	.	.	.	.	.	.	G	19.15	3.771825	0.69992	.	.	ENSG00000085276	ENST00000264674;ENST00000392736;ENST00000464456;ENST00000472280;ENST00000494292;ENST00000468789;ENST00000460814;ENST00000433243	T;T;T;T;T;T;T;T	0.09723	3.02;3.06;2.95;3.15;2.97;3.06;3.01;3.15	5.93	5.93	0.95920	.	0.348800	0.28476	N	0.015208	T	0.33498	0.0865	L	0.60455	1.87	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.999;0.999;0.997;0.999;0.997	T	0.00512	-1.1696	10	0.87932	D	0	-11.4591	20.3368	0.98748	0.0:0.0:1.0:0.0	.	492;305;492;369;304	Q03112-3;Q03112-6;E7EQ57;Q03112-4;Q03112	.;.;.;.;EVI1_HUMAN	L	369;304;304;305;492;304;304;305	ENSP00000264674:P369L;ENSP00000376493:P304L;ENSP00000419770:P304L;ENSP00000420048:P305L;ENSP00000417899:P492L;ENSP00000419995:P304L;ENSP00000420466:P304L;ENSP00000394302:P305L	ENSP00000264674:P369L	P	-	2	0	MECOM	170316879	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.476000	0.97823	2.805000	0.96524	0.655000	0.94253	CCT		0.473	MECOM-020	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000351519.1	NM_005241, NM_004991	
NAALADL2	254827	broad.mit.edu	37	3	174951839	174951839	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr3:174951839G>A	ENST00000454872.1	+	3	792	c.664G>A	c.(664-666)Gat>Aat	p.D222N	NAALADL2_ENST00000473253.1_3'UTR|NAALADL2-AS2_ENST00000424690.1_RNA	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	222						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		TGTGCTGCTTGATCTGCCAGG	0.443																																						uc003fit.2																			0				pancreas(1)	1						c.(664-666)GAT>AAT		N-acetylated alpha-linked acidic dipeptidase 2							107.0	104.0	105.0					3																	174951839		1973	4155	6128	SO:0001583	missense	254827				proteolysis	integral to membrane	peptidase activity	g.chr3:174951839G>A		CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase II-type non-peptidase homologue"""	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.664G>A	3.37:g.174951839G>A	ENSP00000404705:p.Asp222Asn					NAALADL2_uc003fiu.1_Missense_Mutation_p.D215N|NAALADL2_uc010hwy.1_Missense_Mutation_p.D44N	p.D222N	NM_207015	NP_996898	Q58DX5	NADL2_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)	3	751	+	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	222			Extracellular (Potential).		Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Missense_Mutation	SNP	ENST00000454872.1	37	c.664G>A	CCDS46960.1	.	.	.	.	.	.	.	.	.	.	A	5.460	0.269932	0.10349	.	.	ENSG00000177694	ENST00000454872;ENST00000316366	T	0.38077	1.16	5.72	2.08	0.27032	.	1.165910	0.06219	N	0.686412	T	0.18215	0.0437	N	0.03324	-0.35	0.09310	N	1	B;B	0.09022	0.002;0.0	B;B	0.12837	0.008;0.0	T	0.29701	-1.0003	10	0.13853	T	0.58	-3.9209	10.4096	0.44285	0.4657:0.0:0.5343:0.0	.	205;222	Q58DX5-2;Q58DX5	.;NADL2_HUMAN	N	222;29	ENSP00000404705:D222N	ENSP00000314951:D29N	D	+	1	0	NAALADL2	176434533	0.000000	0.05858	0.001000	0.08648	0.108000	0.19459	0.704000	0.25661	-0.087000	0.12528	-1.079000	0.02226	GAT		0.443	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347390.2	NM_207015	
GNRHR	2798	broad.mit.edu	37	4	68606377	68606377	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr4:68606377C>T	ENST00000226413.4	-	3	832	c.808G>A	c.(808-810)Gtt>Att	p.V270I	GNRHR_ENST00000420975.2_Missense_Mutation_p.G227D|UBA6-AS1_ENST00000500538.2_RNA|UBA6-AS1_ENST00000502758.1_RNA	NM_000406.2	NP_000397.1	P30968	GNRHR_HUMAN	gonadotropin-releasing hormone receptor	270					cellular response to gonadotropin-releasing hormone (GO:0097211)|G-protein coupled receptor signaling pathway (GO:0007186)|multicellular organismal development (GO:0007275)	integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	gonadotropin-releasing hormone receptor activity (GO:0004968)			endometrium(2)|large_intestine(4)|liver(1)|lung(4)|ovary(1)|urinary_tract(1)	13					Abarelix(DB00106)|Buserelin(DB06719)|Cetrorelix(DB00050)|Danazol(DB01406)|Degarelix(DB06699)|Gonadorelin(DB00644)|Goserelin(DB00014)|Leuprolide(DB00007)|Nafarelin(DB00666)	GCAAATGCAACCGTCATTTTT	0.408																																						uc003hdn.2																			0				ovary(1)	1						c.(808-810)GTT>ATT		gonadotropin-releasing hormone receptor isoform	Abarelix(DB00106)|Cetrorelix(DB00050)|Danazol(DB01406)|Gonadorelin(DB00644)|Leuprolide(DB00007)|Nafarelin(DB00666)						211.0	217.0	215.0					4																	68606377		2203	4300	6503	SO:0001583	missense	2798				multicellular organismal development	integral to plasma membrane	gonadotropin-releasing hormone receptor activity	g.chr4:68606377C>T		CCDS3517.1, CCDS47064.1	4q21.2	2012-08-08			ENSG00000109163	ENSG00000109163		"""GPCR / Class A : Gonadotropin-releasing hormone receptors"""	4421	protein-coding gene	gene with protein product		138850		GRHR		8386108	Standard	NM_000406		Approved	LHRHR	uc003hdn.3	P30968	OTTHUMG00000129302	ENST00000226413.4:c.808G>A	4.37:g.68606377C>T	ENSP00000226413:p.Val270Ile					LOC550112_uc003hdl.3_Intron|GNRHR_uc003hdm.2_Missense_Mutation_p.G227D|uc003hdo.1_5'Flank	p.V270I	NM_000406	NP_000397	P30968	GNRHR_HUMAN			3	2559	-			270			Cytoplasmic (Potential).		O75793|Q14D13|Q92644	Missense_Mutation	SNP	ENST00000226413.4	37	c.808G>A	CCDS3517.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	12.86|12.86	2.065628|2.065628	0.36470|0.36470	.|.	.|.	ENSG00000109163|ENSG00000109163	ENST00000420975|ENST00000226413	D|T	0.81821|0.37235	-1.54|1.21	5.43|5.43	5.43|5.43	0.79202|0.79202	.|GPCR, rhodopsin-like superfamily (1);	.|0.133510	.|0.34025	.|N	.|0.004336	T|T	0.14960|0.14960	0.0361|0.0361	.|.	.|.	.|.	0.28532|0.28532	N|N	0.912522|0.912522	B|B	0.26258|0.34329	0.145|0.449	B|B	0.24541|0.30495	0.054|0.116	T|T	0.17410|0.17410	-1.0370|-1.0370	8|9	0.36615|0.05525	T|T	0.2|0.97	-17.0486|-17.0486	10.5382|10.5382	0.45018|0.45018	0.0:0.9118:0.0:0.0882|0.0:0.9118:0.0:0.0882	.|.	227|270	P30968-2|P30968	.|GNRHR_HUMAN	D|I	227|270	ENSP00000397561:G227D|ENSP00000226413:V270I	ENSP00000397561:G227D|ENSP00000226413:V270I	G|V	-|-	2|1	0|0	GNRHR|GNRHR	68288972|68288972	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.400000|0.400000	0.30750|0.30750	2.290000|2.290000	0.43531|0.43531	2.718000|2.718000	0.92993|0.92993	0.585000|0.585000	0.79938|0.79938	GGT|GTT		0.408	GNRHR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251432.2		
PITX2	5308	broad.mit.edu	37	4	111539460	111539460	+	Missense_Mutation	SNP	T	T	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr4:111539460T>C	ENST00000354925.2	-	7	2480	c.775A>G	c.(775-777)Acg>Gcg	p.T259A	PITX2_ENST00000355080.5_Missense_Mutation_p.T213A|PITX2_ENST00000556049.1_5'Flank|PITX2_ENST00000306732.3_Missense_Mutation_p.T266A|RP11-380D23.2_ENST00000503456.1_lincRNA|PITX2_ENST00000394598.2_Missense_Mutation_p.T259A|PITX2_ENST00000394595.3_3'UTR	NM_001204397.1	NP_001191326.1	Q99697	PITX2_HUMAN	paired-like homeodomain 2	259					atrial cardiac muscle tissue morphogenesis (GO:0055009)|atrioventricular valve development (GO:0003171)|camera-type eye development (GO:0043010)|cardiac neural crest cell migration involved in outflow tract morphogenesis (GO:0003253)|cell proliferation involved in outflow tract morphogenesis (GO:0061325)|deltoid tuberosity development (GO:0035993)|determination of left/right symmetry (GO:0007368)|embryonic camera-type eye development (GO:0031076)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic hindlimb morphogenesis (GO:0035116)|endodermal digestive tract morphogenesis (GO:0061031)|extraocular skeletal muscle development (GO:0002074)|female gonad development (GO:0008585)|hair cell differentiation (GO:0035315)|hypothalamus cell migration (GO:0021855)|in utero embryonic development (GO:0001701)|iris morphogenesis (GO:0061072)|left lung morphogenesis (GO:0060460)|left/right axis specification (GO:0070986)|male gonad development (GO:0008584)|myoblast fusion (GO:0007520)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|odontogenesis (GO:0042476)|odontogenesis of dentin-containing tooth (GO:0042475)|patterning of blood vessels (GO:0001569)|positive regulation of DNA binding (GO:0043388)|positive regulation of myoblast proliferation (GO:2000288)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|prolactin secreting cell differentiation (GO:0060127)|pulmonary myocardium development (GO:0003350)|pulmonary vein morphogenesis (GO:0060577)|regulation of cell migration (GO:0030334)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|regulation of transcription, DNA-templated (GO:0006355)|response to hormone (GO:0009725)|response to vitamin A (GO:0033189)|somatotropin secreting cell differentiation (GO:0060126)|spleen development (GO:0048536)|subthalamic nucleus development (GO:0021763)|superior vena cava morphogenesis (GO:0060578)|vascular smooth muscle cell differentiation (GO:0035886)|vasculogenesis (GO:0001570)|ventricular cardiac muscle cell development (GO:0055015)|ventricular septum morphogenesis (GO:0060412)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	chromatin DNA binding (GO:0031490)|phosphoprotein binding (GO:0051219)|protein homodimerization activity (GO:0042803)|ribonucleoprotein complex binding (GO:0043021)|RNA polymerase II activating transcription factor binding (GO:0001102)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II transcription coactivator activity (GO:0001105)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region sequence-specific DNA binding (GO:0000976)			breast(1)|endometrium(3)|large_intestine(1)|lung(5)	10		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.00222)		CAGGCAGGCGTCGGCACCGCG	0.592																																						uc003iad.2																			0					0						c.(775-777)ACG>GCG		paired-like homeodomain transcription factor 2							46.0	49.0	48.0					4																	111539460		2203	4300	6503	SO:0001583	missense	5308				determination of left/right symmetry|organ morphogenesis	transcription factor complex	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription factor binding	g.chr4:111539460T>C	U69961	CCDS3692.1, CCDS3693.1, CCDS3694.1	4q25	2011-06-20	2007-07-12		ENSG00000164093	ENSG00000164093		"""Homeoboxes / PRD class"""	9005	protein-coding gene	gene with protein product		601542	"""paired-like homeodomain transcription factor 2"""	IRID2, IHG2, RIEG, RIEG1, RGS		9539779, 7581385	Standard	NM_000325		Approved	IGDS, RS, Brx1, Otlx2, ARP1	uc021xqr.1	Q99697	OTTHUMG00000132837	ENST00000354925.2:c.775A>G	4.37:g.111539460T>C	ENSP00000347004:p.Thr259Ala					PITX2_uc003iac.2_Missense_Mutation_p.T266A|PITX2_uc003iae.2_Missense_Mutation_p.T213A|PITX2_uc010iml.2_Missense_Mutation_p.T130A|PITX2_uc003iaf.2_Missense_Mutation_p.T259A	p.T259A	NM_153426	NP_700475	Q99697	PITX2_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.00222)	5	1357	-		Hepatocellular(203;0.217)	259					A8K6C6|B2RA02|B3KXS0|O60578|O60579|O60580|Q3KQX9|Q9BY17	Missense_Mutation	SNP	ENST00000354925.2	37	c.775A>G	CCDS3692.1	.	.	.	.	.	.	.	.	.	.	T	12.16	1.855518	0.32791	.	.	ENSG00000164093	ENST00000306732;ENST00000394598;ENST00000355080;ENST00000354925;ENST00000511837	D;D;D;D;D	0.92149	-2.63;-2.74;-2.9;-2.74;-2.98	5.68	5.68	0.88126	.	0.000000	0.85682	D	0.000000	D	0.87924	0.6300	N	0.02539	-0.55	0.80722	D	1	B;D;B;B	0.56035	0.0;0.974;0.0;0.001	B;D;B;B	0.67725	0.002;0.953;0.003;0.009	D	0.85345	0.1098	10	0.07990	T	0.79	.	15.9332	0.79683	0.0:0.0:0.0:1.0	.	213;213;259;266	A8K6C6;Q99697-3;Q99697;Q99697-2	.;.;PITX2_HUMAN;.	A	266;259;213;259;259	ENSP00000304169:T266A;ENSP00000378097:T259A;ENSP00000347192:T213A;ENSP00000347004:T259A;ENSP00000421454:T259A	ENSP00000304169:T266A	T	-	1	0	PITX2	111758909	1.000000	0.71417	0.993000	0.49108	0.996000	0.88848	6.088000	0.71371	2.172000	0.68678	0.533000	0.62120	ACG		0.592	PITX2-003	KNOWN	alternative_5_UTR|basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256308.2		
SLC22A4	6583	broad.mit.edu	37	5	131676327	131676327	+	Frame_Shift_Del	DEL	T	T	-	rs72552721		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr5:131676327delT	ENST00000200652.3	+	9	1688	c.1514delT	c.(1513-1515)cttfs	p.L505fs	AC034220.3_ENST00000417795.1_RNA|AC034220.3_ENST00000437091.1_RNA	NM_003059.2	NP_003050.2	Q9H015	S22A4_HUMAN	solute carrier family 22 (organic cation/zwitterion transporter), member 4	505					body fluid secretion (GO:0007589)|carnitine metabolic process (GO:0009437)|carnitine transmembrane transport (GO:1902603)|carnitine transport (GO:0015879)|cation transmembrane transport (GO:0098655)|organic cation transport (GO:0015695)|quaternary ammonium group transport (GO:0015697)|sodium ion transport (GO:0006814)|transmembrane transport (GO:0055085)|triglyceride metabolic process (GO:0006641)	apical plasma membrane (GO:0016324)|integral component of plasma membrane (GO:0005887)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|carnitine transmembrane transporter activity (GO:0015226)|cation:cation antiporter activity (GO:0015491)|nucleotide binding (GO:0000166)|PDZ domain binding (GO:0030165)|quaternary ammonium group transmembrane transporter activity (GO:0015651)|secondary active organic cation transmembrane transporter activity (GO:0008513)|symporter activity (GO:0015293)	p.E509fs*1(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|ovary(1)|urinary_tract(1)	16		all_cancers(142;0.0752)|Breast(839;0.198)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		Amiloride(DB00594)|Aminohippurate(DB00345)|Benzylpenicillin(DB01053)|Choline(DB00122)|Cimetidine(DB00501)|Clonidine(DB00575)|Desipramine(DB01151)|Guanidine(DB00536)|Imipramine(DB00458)|Ipratropium bromide(DB00332)|L-Arginine(DB00125)|L-Carnitine(DB00583)|L-Lysine(DB00123)|Levofloxacin(DB01137)|Mepyramine(DB06691)|Nicotine(DB00184)|Ofloxacin(DB01165)|Procainamide(DB01035)|Quinidine(DB00908)|Quinine(DB00468)|Spermine(DB00127)|Testosterone(DB00624)|Tiotropium(DB01409)|Verapamil(DB00661)	ATCCTCACCCTTTTTTTCCCT	0.418																																						uc003kwq.2																			1	Insertion - Frameshift(1)		ovary(1)		0						c.(1513-1515)CTTfs		solute carrier family 22 member 4	L-Carnitine(DB00583)						222.0	206.0	211.0					5																	131676327		2203	4300	6503	SO:0001589	frameshift_variant	6583				body fluid secretion|sodium ion transport	apical plasma membrane|integral to plasma membrane|mitochondrion	ATP binding|carnitine transporter activity|cation:cation antiporter activity|PDZ domain binding|secondary active organic cation transmembrane transporter activity|symporter activity	g.chr5:131676327delT	AB007448	CCDS4153.1	5q23.3	2013-07-18	2013-07-18		ENSG00000197208	ENSG00000197208		"""Solute carriers"""	10968	protein-coding gene	gene with protein product		604190	"""solute carrier family 22 (organic cation/ergothioneine transporter), member 4"""			9426230, 15795384	Standard	NM_003059		Approved	OCTN1, MGC34546	uc003kwq.3	Q9H015	OTTHUMG00000059648	ENST00000200652.3:c.1514delT	5.37:g.131676327delT	ENSP00000200652:p.Leu505fs					uc003kwr.3_Intron	p.L505fs	NM_003059	NP_003050	Q9H015	S22A4_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)		9	1679	+		all_cancers(142;0.0752)|Breast(839;0.198)	505			Helical; Name=12; (Potential).		O14546	Frame_Shift_Del	DEL	ENST00000200652.3	37	c.1514delT	CCDS4153.1																																																																																				0.418	SLC22A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000132661.1	NM_003059	
PCDHGB1	56104	broad.mit.edu	37	5	140730012	140730012	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr5:140730012G>A	ENST00000523390.1	+	1	185	c.185G>A	c.(184-186)cGa>cAa	p.R62Q	PCDHGA1_ENST00000517417.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA2_ENST00000394576.2_Intron	NM_018922.2|NM_032095.1	NP_061745.1|NP_115266.1	Q9Y5G3	PCDGD_HUMAN	protocadherin gamma subfamily B, 1	62	Cadherin 1. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(6)|lung(3)|ovary(2)|prostate(1)	16			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TTGCCAACTCGAAAACTGCGG	0.522											OREG0016856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc003ljo.1																			0					0						c.(184-186)CGA>CAA		protocadherin gamma subfamily B, 1 isoform 1							77.0	76.0	77.0					5																	140730012		1884	4101	5985	SO:0001583	missense	56104				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:140730012G>A	AF152517	CCDS54923.1, CCDS75330.1	5q31	2010-01-26				ENSG00000254221		"""Cadherins / Protocadherins : Clustered"""	8708	other	protocadherin	"""protocadherin gamma subfamily B, 1, isoform 2"""	606299				10380929	Standard	NM_018922		Approved	PCDH-GAMMA-B1		Q9Y5G3		ENST00000523390.1:c.185G>A	5.37:g.140730012G>A	ENSP00000429273:p.Arg62Gln		OREG0016856	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1658	PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc011daq.1_Missense_Mutation_p.R62Q	p.R62Q	NM_018922	NP_061745	Q9Y5G3	PCDGD_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	185	+			62			Cadherin 1.|Extracellular (Potential).		Q3SY75|Q9Y5C8	Missense_Mutation	SNP	ENST00000523390.1	37	c.185G>A	CCDS54923.1	.	.	.	.	.	.	.	.	.	.	.	28.3	4.904581	0.92035	.	.	ENSG00000254221	ENST00000523390	T	0.40225	1.04	5.52	4.65	0.58169	Cadherin, N-terminal (1);Cadherin (3);Cadherin-like (1);	.	.	.	.	T	0.73651	0.3614	H	0.98256	4.185	0.27532	N	0.951053	D;D	0.67145	0.983;0.996	B;P	0.57720	0.299;0.826	T	0.75210	-0.3398	9	0.72032	D	0.01	.	14.2571	0.66060	0.0727:0.0:0.9273:0.0	.	62;62	Q9Y5G3-2;Q9Y5G3	.;PCDGD_HUMAN	Q	62	ENSP00000429273:R62Q	ENSP00000429273:R62Q	R	+	2	0	PCDHGB1	140710196	0.896000	0.30565	0.997000	0.53966	0.994000	0.84299	3.584000	0.53936	1.462000	0.47948	0.563000	0.77884	CGA		0.522	PCDHGB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374740.1	NM_018922	
MFAP3	4238	broad.mit.edu	37	5	153432941	153432941	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr5:153432941G>A	ENST00000436816.1	+	3	976	c.757G>A	c.(757-759)Gag>Aag	p.E253K	MFAP3_ENST00000322602.5_Missense_Mutation_p.E253K|MFAP3_ENST00000439768.2_Missense_Mutation_p.E107K	NM_001242336.1|NM_005927.4	NP_001229265.1|NP_005918.1	P55082	MFAP3_HUMAN	microfibrillar-associated protein 3	253					extracellular matrix organization (GO:0030198)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(1)|kidney(2)|large_intestine(1)|lung(2)|pancreas(1)	7	Renal(175;0.00488)	Lung NSC(249;0.00145)|all_lung(500;0.00226)|all_neural(177;0.122)|Breast(839;0.14)	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;9.69e-06)|GBM - Glioblastoma multiforme(465;0.0201)		AGCCTTTGTTGAGGAGATGTT	0.453																																						uc003lvf.2																			0					0						c.(757-759)GAG>AAG		microfibrillar-associated protein 3 isoform 2							111.0	106.0	107.0					5																	153432941		2203	4300	6503	SO:0001583	missense	4238					integral to membrane|plasma membrane		g.chr5:153432941G>A		CCDS4324.1, CCDS47319.1	5q32-q33.2	2013-01-11			ENSG00000037749	ENSG00000037749		"""Immunoglobulin superfamily / I-set domain containing"""	7034	protein-coding gene	gene with protein product		600491				7782085	Standard	NM_005927		Approved		uc010jib.2	P55082	OTTHUMG00000130149	ENST00000436816.1:c.757G>A	5.37:g.153432941G>A	ENSP00000409933:p.Glu253Lys					MFAP3_uc010jib.2_Missense_Mutation_p.E253K|MFAP3_uc011ddb.1_Missense_Mutation_p.E107K	p.E253K	NM_001135037	NP_001128509	P55082	MFAP3_HUMAN	Kidney(363;0.000173)|KIRC - Kidney renal clear cell carcinoma(527;0.000785)	OV - Ovarian serous cystadenocarcinoma(192;9.69e-06)|GBM - Glioblastoma multiforme(465;0.0201)	3	1273	+	Renal(175;0.00488)	Lung NSC(249;0.00145)|all_lung(500;0.00226)|all_neural(177;0.122)|Breast(839;0.14)	253			Cytoplasmic (Potential).		B2RDK0|B4DKA1|Q9NXA7	Missense_Mutation	SNP	ENST00000436816.1	37	c.757G>A	CCDS4324.1	.	.	.	.	.	.	.	.	.	.	G	26.7	4.759713	0.89932	.	.	ENSG00000037749	ENST00000439768;ENST00000436816;ENST00000322602	T;T	0.32272	1.46;1.46	5.71	5.71	0.89125	.	0.000000	0.85682	D	0.000000	T	0.55705	0.1937	M	0.64404	1.975	0.58432	D	0.999994	D	0.89917	1.0	D	0.83275	0.996	T	0.46119	-0.9214	9	.	.	.	-19.0111	20.2245	0.98337	0.0:0.0:1.0:0.0	.	253	P55082	MFAP3_HUMAN	K	107;253;253	ENSP00000409933:E253K;ENSP00000322956:E253K	.	E	+	1	0	MFAP3	153413134	1.000000	0.71417	0.993000	0.49108	0.911000	0.54048	9.585000	0.98223	2.861000	0.98227	0.650000	0.86243	GAG		0.453	MFAP3-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252457.2	NM_005927	
EBF1	1879	broad.mit.edu	37	5	158140123	158140123	+	Silent	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr5:158140123G>A	ENST00000313708.6	-	13	1506	c.1224C>T	c.(1222-1224)gcC>gcT	p.A408A	EBF1_ENST00000517373.1_Silent_p.A400A|EBF1_ENST00000518836.1_5'UTR|EBF1_ENST00000380654.4_Silent_p.A377A	NM_024007.3	NP_076870.1	Q9UH73	COE1_HUMAN	early B-cell factor 1	408					multicellular organismal development (GO:0007275)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)		HMGA2/EBF1(2)	breast(3)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(18)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	42	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			ACAGGGCCTCGGCAATGTCGG	0.527			T	HMGA2	lipoma																																	uc010jip.2				Dom	yes		5	5q34	1879	T	early B-cell factor 1			M	HMGA2		lipoma	HMGA2/EBF1(2)	0				soft_tissue(2)|ovary(1)|central_nervous_system(1)|pancreas(1)	5						c.(1222-1224)GCC>GCT		early B-cell factor							92.0	76.0	81.0					5																	158140123		2203	4300	6503	SO:0001819	synonymous_variant	1879				multicellular organismal development	nucleus	DNA binding|metal ion binding	g.chr5:158140123G>A	AF208502	CCDS4343.1	5q34	2008-02-05	2006-09-26	2006-09-26	ENSG00000164330	ENSG00000164330			3126	protein-coding gene	gene with protein product		164343	"""early B-cell factor"""	EBF		8012110	Standard	NM_024007		Approved	OLF1	uc010jip.3	Q9UH73	OTTHUMG00000130304	ENST00000313708.6:c.1224C>T	5.37:g.158140123G>A						EBF1_uc011ddw.1_Silent_p.A276A|EBF1_uc011ddx.1_Silent_p.A409A|EBF1_uc003lxl.3_Silent_p.A377A	p.A408A	NM_024007	NP_076870	Q9UH73	COE1_HUMAN	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		13	1526	-	Renal(175;0.00196)	Acute lymphoblastic leukemia(3;2.99e-06)|all_hematologic(3;0.000772)|Medulloblastoma(196;0.037)|all_neural(177;0.143)	408					Q8IW11	Silent	SNP	ENST00000313708.6	37	c.1224C>T	CCDS4343.1																																																																																				0.527	EBF1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000252649.1	NM_024007	
BTNL3	10917	broad.mit.edu	37	5	180432547	180432547	+	Missense_Mutation	SNP	G	G	A	rs199970076		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr5:180432547G>A	ENST00000342868.6	+	8	1260	c.1076G>A	c.(1075-1077)cGg>cAg	p.R359Q	RNU6-1036P_ENST00000383959.1_RNA	NM_197975.2	NP_932079.1	Q6UXE8	BTNL3_HUMAN	butyrophilin-like 3	359	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.					integral component of membrane (GO:0016021)				NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(10)|prostate(2)|skin(1)	25	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)			GGAGTGTGTCGGGATGACGTA	0.478																																						uc003mmr.2																			0					0						c.(1075-1077)CGG>CAG		butyrophilin-like 3 precursor							190.0	207.0	201.0					5																	180432547		2192	4295	6487	SO:0001583	missense	10917				lipid metabolic process	integral to membrane		g.chr5:180432547G>A	AB020625	CCDS47358.1	5q35	2014-01-14			ENSG00000168903	ENSG00000168903		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	1143	protein-coding gene	gene with protein product	"""butyrophilin-like receptor"""	606192				10429365	Standard	NM_197975		Approved	BTNLR, BTN9.1	uc003mmr.3	Q6UXE8	OTTHUMG00000162091	ENST00000342868.6:c.1076G>A	5.37:g.180432547G>A	ENSP00000341787:p.Arg359Gln					BTNL3_uc010jlp.2_Missense_Mutation_p.R144Q	p.R359Q	NM_197975	NP_932079	Q6UXE8	BTNL3_HUMAN	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000272)		8	1204	+	all_cancers(89;3.37e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.00336)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)|all_lung(500;0.248)	359			B30.2/SPRY.|Cytoplasmic (Potential).		Q496L7|Q9Y2C7	Missense_Mutation	SNP	ENST00000342868.6	37	c.1076G>A	CCDS47358.1	.	.	.	.	.	.	.	.	.	.	G	8.000	0.755294	0.15846	.	.	ENSG00000168903	ENST00000342868;ENST00000376852	T	0.70399	-0.48	3.0	-4.32	0.03688	Concanavalin A-like lectin/glucanase (1);SPla/RYanodine receptor subgroup (1);Butyrophylin-like (1);B30.2/SPRY domain (1);SPla/RYanodine receptor SPRY (1);	.	.	.	.	T	0.58836	0.2150	L	0.46614	1.455	0.09310	N	1	B;B	0.29115	0.233;0.071	B;B	0.17722	0.019;0.008	T	0.27054	-1.0085	9	0.19147	T	0.46	.	16.2826	0.82703	0.134:0.0:0.866:0.0	.	325;359	C9JDC2;Q6UXE8	.;BTNL3_HUMAN	Q	359;325	ENSP00000341787:R359Q	ENSP00000341787:R359Q	R	+	2	0	BTNL3	180365153	0.006000	0.16342	0.000000	0.03702	0.013000	0.08279	0.258000	0.18387	-1.943000	0.01039	-1.076000	0.02234	CGG		0.478	BTNL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000367176.2	NM_197975	
ROS1	6098	broad.mit.edu	37	6	117679033	117679033	+	Missense_Mutation	SNP	G	G	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr6:117679033G>T	ENST00000368508.3	-	24	3986	c.3788C>A	c.(3787-3789)cCc>cAc	p.P1263H	ROS1_ENST00000368507.3_Missense_Mutation_p.P1258H|GOPC_ENST00000467125.1_Intron	NM_002944.2	NP_002935.2	P08922	ROS1_HUMAN	ROS proto-oncogene 1 , receptor tyrosine kinase	1263					cell differentiation (GO:0030154)|cell growth (GO:0016049)|cell proliferation (GO:0008283)|columnar/cuboidal epithelial cell development (GO:0002066)|negative regulation of gene expression (GO:0010629)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein phosphorylation (GO:0006468)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of phosphate transport (GO:0010966)|regulation of TOR signaling (GO:0032006)|spermatogenesis (GO:0007283)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)	p.P1263F(1)	TPM3_ENST00000368530/ROS1(4)|LRIG3/ROS1(2)|CD74_ENST00000009530/ROS1(32)|SLC34A2/ROS1(14)|EZR/ROS1(4)|GOPC/ROS1(14)|SDC4/ROS1(7)	NS(2)|breast(7)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(12)|large_intestine(28)|lung(56)|ovary(8)|prostate(5)|skin(19)|stomach(3)|upper_aerodigestive_tract(5)|urinary_tract(3)	162		all_cancers(87;0.00846)|all_epithelial(87;0.0242)		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)		CACCTCTCTGGGATATTTCAC	0.318			T	"""GOPC, SDC4, SLC34A2, EZR, LRIG3"""	"""glioblastoma, NSCLC"""																																	uc003pxp.1				Dom	yes		6	6q22	6098	T	v-ros UR2 sarcoma virus oncogene homolog 1 (avian)			"""O, E"""	GOPC|ROS1		glioblastoma|NSCLC		1	Substitution - Missense(1)		skin(1)	lung(8)|ovary(6)|central_nervous_system(3)|skin(3)|stomach(2)|breast(2)|large_intestine(1)	25						c.(3787-3789)CCC>CAC		proto-oncogene c-ros-1 protein precursor							94.0	91.0	92.0					6																	117679033		2202	4299	6501	SO:0001583	missense	6098				transmembrane receptor protein tyrosine kinase signaling pathway	membrane fraction|sodium:potassium-exchanging ATPase complex	ATP binding|transmembrane receptor protein tyrosine kinase activity	g.chr6:117679033G>T	M13599	CCDS5116.1	6q21-q22	2014-06-26	2014-06-26		ENSG00000047936	ENSG00000047936		"""Fibronectin type III domain containing"""	10261	protein-coding gene	gene with protein product		165020	"""v-ros avian UR2 sarcoma virus oncogene homolog 1"", ""v-ros UR2 sarcoma virus oncogene homolog 1 (avian)"", ""c-ros oncogene 1 , receptor tyrosine kinase"""			1611909	Standard	NM_002944		Approved	MCF3, ROS, c-ros-1	uc003pxp.1	P08922	OTTHUMG00000016188	ENST00000368508.3:c.3788C>A	6.37:g.117679033G>T	ENSP00000357494:p.Pro1263His					ROS1_uc011ebi.1_RNA|GOPC_uc003pxq.1_Intron	p.P1263H	NM_002944	NP_002935	P08922	ROS_HUMAN		GBM - Glioblastoma multiforme(226;0.0387)|OV - Ovarian serous cystadenocarcinoma(136;0.0954)|all cancers(137;0.137)	24	3987	-		all_cancers(87;0.00846)|all_epithelial(87;0.0242)	1263			Extracellular (Potential).		Q15368|Q5TDB5	Missense_Mutation	SNP	ENST00000368508.3	37	c.3788C>A	CCDS5116.1	.	.	.	.	.	.	.	.	.	.	G	10.86	1.468645	0.26335	.	.	ENSG00000047936	ENST00000368508;ENST00000368507	D;D	0.91124	-2.79;-2.79	5.12	3.31	0.37934	.	0.111846	0.38005	N	0.001849	T	0.74283	0.3696	L	0.27053	0.805	0.26397	N	0.976486	P	0.43412	0.806	B	0.41946	0.371	T	0.69331	-0.5173	10	0.66056	D	0.02	.	6.2462	0.20818	0.279:0.0:0.721:0.0	.	1263	P08922	ROS1_HUMAN	H	1263;1258	ENSP00000357494:P1263H;ENSP00000357493:P1258H	ENSP00000357493:P1258H	P	-	2	0	ROS1	117785726	0.907000	0.30839	0.532000	0.27989	0.232000	0.25224	2.170000	0.42443	1.296000	0.44742	-0.143000	0.13931	CCC		0.318	ROS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000043464.1		
CRHR2	1395	broad.mit.edu	37	7	30693212	30693212	+	Missense_Mutation	SNP	C	C	T	rs199502493	byFrequency	TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:30693212C>T	ENST00000471646.1	-	12	1517	c.1100G>A	c.(1099-1101)cGc>cAc	p.R367H	CRHR2_ENST00000341843.4_Missense_Mutation_p.R353H|CRHR2_ENST00000506074.2_3'UTR|CRHR2_ENST00000348438.4_Missense_Mutation_p.R394H	NM_001202482.1|NM_001202483.1|NM_001883.4	NP_001189411.1|NP_001189412.1|NP_001874.2	Q13324	CRFR2_HUMAN	corticotropin releasing hormone receptor 2	367					adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cAMP-mediated signaling (GO:0043951)|positive regulation of cAMP-mediated signaling (GO:0043950)	cell surface (GO:0009986)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	corticotrophin-releasing factor receptor activity (GO:0015056)	p.R367H(1)		breast(2)|kidney(2)|large_intestine(7)|lung(10)|ovary(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	28						CACGGCTGAGCGCACCTGTGG	0.642													C|||	3	0.000599042	0.0	0.0014	5008	,	,		16499	0.002		0.0	False		,,,				2504	0.0					uc003tbn.2																			1	Substitution - Missense(1)		stomach(1)	lung(2)|ovary(1)|skin(1)	4						c.(1099-1101)CGC>CAC		corticotropin releasing hormone receptor 2							93.0	81.0	85.0					7																	30693212		2203	4300	6503	SO:0001583	missense	1395				G-protein signaling, coupled to cAMP nucleotide second messenger	integral to plasma membrane	corticotrophin-releasing factor receptor activity|protein binding	g.chr7:30693212C>T		CCDS5429.1, CCDS56477.1, CCDS56478.1, CCDS75576.1	7p21-p15	2012-08-10			ENSG00000106113	ENSG00000106113		"""GPCR / Class B : Corticotropin-releasing factor receptors"""	2358	protein-coding gene	gene with protein product		602034				8536644	Standard	NM_001883		Approved	CRF2, CRF-RB, HM-CRF	uc003tbp.3	Q13324	OTTHUMG00000023218	ENST00000471646.1:c.1100G>A	7.37:g.30693212C>T	ENSP00000418722:p.Arg367His					CRHR2_uc010kvw.1_3'UTR|CRHR2_uc010kvx.1_Missense_Mutation_p.R366H|CRHR2_uc010kvy.1_Missense_Mutation_p.R203H|CRHR2_uc003tbo.2_Missense_Mutation_p.R353H|CRHR2_uc003tbp.2_Missense_Mutation_p.R394H	p.R367H	NM_001883	NP_001874	Q13324	CRFR2_HUMAN			12	1344	-			367			Cytoplasmic (Potential).		B2R967|B3SXS6|B3SXS7|B3SXS8|B3SXT0|F8WA81|O43461|Q4QRJ4|Q99431	Missense_Mutation	SNP	ENST00000471646.1	37	c.1100G>A	CCDS5429.1	3	0.0013736263736263737	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	1	0.0013192612137203166	C	19.07	3.756228	0.69648	.	.	ENSG00000106113	ENST00000471646;ENST00000348438;ENST00000341843	T;T;T	0.58358	0.34;0.34;0.34	4.53	4.53	0.55603	.	0.000000	0.85682	D	0.000000	T	0.73651	0.3614	M	0.83953	2.67	0.80722	D	1	D;D;D;D	0.89917	0.998;1.0;1.0;0.998	P;D;D;P	0.72982	0.87;0.979;0.969;0.87	T	0.78994	-0.1984	10	0.87932	D	0	.	15.1361	0.72566	0.0:1.0:0.0:0.0	.	366;394;353;367	B3SXT0;Q13324-2;Q13324-3;Q13324	.;.;.;CRFR2_HUMAN	H	367;394;353	ENSP00000418722:R367H;ENSP00000340943:R394H;ENSP00000344304:R353H	ENSP00000344304:R353H	R	-	2	0	CRHR2	30659737	1.000000	0.71417	0.973000	0.42090	0.013000	0.08279	7.753000	0.85153	2.236000	0.73375	0.563000	0.77884	CGC		0.642	CRHR2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250448.3		
DDX56	54606	broad.mit.edu	37	7	44611162	44611162	+	Silent	SNP	C	C	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:44611162C>A	ENST00000258772.5	-	6	925	c.819G>T	c.(817-819)cgG>cgT	p.R273R	DDX56_ENST00000431640.1_Silent_p.R273R|DDX56_ENST00000485367.1_5'UTR	NM_001257189.1|NM_019082.3	NP_001244118.1|NP_061955.1	Q9NY93	DDX56_HUMAN	DEAD (Asp-Glu-Ala-Asp) box helicase 56	273	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.				ATP catabolic process (GO:0006200)|rRNA processing (GO:0006364)	membrane (GO:0016020)|nucleolus (GO:0005730)	ATP binding (GO:0005524)|ATP-dependent RNA helicase activity (GO:0004004)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(5)|upper_aerodigestive_tract(1)	16						ACAGGCGTAGCCGGTAACTCC	0.522																																						uc003tlg.2																			0				upper_aerodigestive_tract(1)	1						c.(817-819)CGG>CGT		DEAD (Asp-Glu-Ala-Asp) box polypeptide 56							85.0	77.0	80.0					7																	44611162		2203	4300	6503	SO:0001819	synonymous_variant	54606				rRNA processing	nucleolus	ATP binding|ATP-dependent RNA helicase activity|identical protein binding|RNA binding	g.chr7:44611162C>A	AJ131712	CCDS5492.1, CCDS59053.1	7p13	2012-02-23	2012-02-23		ENSG00000136271	ENSG00000136271		"""DEAD-boxes"""	18193	protein-coding gene	gene with protein product	"""nucleolar helicase of 61 kDa"""	608023	"""DEAD (Asp-Glu-Ala-Asp) box polypeptide 56"""			10749921	Standard	NM_019082		Approved	NOH61	uc003tlg.4	Q9NY93	OTTHUMG00000129211	ENST00000258772.5:c.819G>T	7.37:g.44611162C>A						DDX56_uc003tle.2_RNA|DDX56_uc003tlf.2_Silent_p.R209R|DDX56_uc003tlh.2_RNA|DDX56_uc010kyg.2_Silent_p.R273R|DDX56_uc010kyh.1_RNA	p.R273R	NM_019082	NP_061955	Q9NY93	DDX56_HUMAN			6	1462	-			273			Helicase C-terminal.		A4D2K9|C9JV95|Q6IAE2|Q9H9I8	Silent	SNP	ENST00000258772.5	37	c.819G>T	CCDS5492.1																																																																																				0.522	DDX56-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251291.1	NM_019082	
GTF2IRD2	84163	broad.mit.edu	37	7	74212399	74212399	+	Silent	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:74212399C>T	ENST00000405086.2	-	16	1641	c.1452G>A	c.(1450-1452)gaG>gaA	p.E484E	GTF2IRD2_ENST00000451013.2_Silent_p.E31E	NM_173537.2	NP_775808	Q86UP8	GTD2A_HUMAN	GTF2I repeat domain containing 2	484					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)			breast(1)|endometrium(3)|large_intestine(2)|lung(2)|ovary(2)|skin(1)	11						cgtgaagcttctcgtcacgca	0.443																																					NSCLC(40;560 1096 7501 40315 49546)	uc003ubd.1																			0				ovary(1)	1						c.(1450-1452)GAG>GAA		GTF2I repeat domain containing 2							184.0	162.0	170.0					7																	74212399		2203	4300	6503	SO:0001819	synonymous_variant	84163				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|zinc ion binding	g.chr7:74212399C>T	BC047706	CCDS5576.1, CCDS64682.1	7q11.23	2014-05-06			ENSG00000196275	ENSG00000196275			30775	protein-coding gene	gene with protein product	"""transcription factor GTF2IRD2"""	608899				15243160	Standard	NM_173537		Approved	FLJ37938, GTF2IRD2A	uc003ubd.1	Q86UP8	OTTHUMG00000181527	ENST00000405086.2:c.1452G>A	7.37:g.74212399C>T						GTF2IRD2_uc010lbt.1_Silent_p.E31E	p.E484E	NM_173537	NP_775808	Q86UP8	GTD2A_HUMAN			16	1636	-			484					A8K5W6|B3KUZ2|Q69G40|Q6EKI8|Q6EKI9|Q6NVW2|Q6P7N8|Q86WX4|Q8ND85|Q8NDE5	Silent	SNP	ENST00000405086.2	37	c.1452G>A	CCDS5576.1																																																																																				0.443	GTF2IRD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252712.3	NM_173537	
CCL24	6369	broad.mit.edu	37	7	75442664	75442664	+	Missense_Mutation	SNP	G	G	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:75442664G>C	ENST00000416943.1	-	3	244	c.151C>G	c.(151-153)Cag>Gag	p.Q51E	CCL24_ENST00000222902.2_Missense_Mutation_p.Q51E	NM_002991.2	NP_002982.2	O00175	CCL24_HUMAN	chemokine (C-C motif) ligand 24	51					cell-cell signaling (GO:0007267)|chemotaxis (GO:0006935)|cytoskeleton organization (GO:0007010)|eosinophil chemotaxis (GO:0048245)|immune response (GO:0006955)|inflammatory response (GO:0006954)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of angiogenesis (GO:0045766)|positive regulation of cell migration (GO:0030335)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of eosinophil migration (GO:2000418)|positive regulation of inflammatory response (GO:0050729)|positive regulation of Rac GTPase activity (GO:0032855)|regulation of cell shape (GO:0008360)|signal transduction (GO:0007165)	extracellular space (GO:0005615)	chemokine activity (GO:0008009)			endometrium(1)|lung(2)	3						CTGGACAGCTGGTAGCTGACC	0.562																																						uc011kga.1																			0					0						c.(151-153)CAG>GAG		small inducible cytokine A24 precursor							70.0	65.0	67.0					7																	75442664		2203	4300	6503	SO:0001583	missense	6369				cell-cell signaling|chemotaxis|immune response|inflammatory response|positive regulation of actin filament polymerization|positive regulation of cell migration|positive regulation of endothelial cell proliferation|positive regulation of Rac GTPase activity|signal transduction	extracellular space	chemokine activity	g.chr7:75442664G>C	U85768	CCDS34670.1	7q11.23	2013-02-25	2002-08-22	2002-08-23	ENSG00000106178	ENSG00000106178		"""Chemokine ligands"", ""Endogenous ligands"""	10623	protein-coding gene	gene with protein product	"""CK-beta-6"", ""myeloid progenitor inhibitory factor 2"", ""eotaxin-2"""	602495	"""small inducible cytokine subfamily A (Cys-Cys), member 24"""	SCYA24		9104803, 9598329	Standard	NM_002991		Approved	Ckb-6, MPIF-2, eotaxin-2, MPIF2	uc011kga.2	O00175	OTTHUMG00000156635	ENST00000416943.1:c.151C>G	7.37:g.75442664G>C	ENSP00000400533:p.Gln51Glu						p.Q51E	NM_002991	NP_002982	O00175	CCL24_HUMAN			2	151	-			51					B2R5K2	Missense_Mutation	SNP	ENST00000416943.1	37	c.151C>G	CCDS34670.1	.	.	.	.	.	.	.	.	.	.	G	8.460	0.855089	0.17106	.	.	ENSG00000106178	ENST00000222902;ENST00000416943	T;T	0.04015	3.73;3.73	4.14	2.16	0.27623	Chemokine interleukin-8-like domain (3);	0.150400	0.31415	N	0.007695	T	0.07188	0.0182	L	0.31207	0.915	0.28634	N	0.907524	D	0.59767	0.986	P	0.58970	0.849	T	0.12426	-1.0548	10	0.40728	T	0.16	.	5.1269	0.14890	0.1165:0.2136:0.6698:0.0	.	51	O00175	CCL24_HUMAN	E	51	ENSP00000222902:Q51E;ENSP00000400533:Q51E	ENSP00000222902:Q51E	Q	-	1	0	CCL24	75280600	0.994000	0.37717	0.944000	0.38274	0.254000	0.26022	1.502000	0.35704	1.089000	0.41292	0.655000	0.94253	CAG		0.562	CCL24-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344886.1	NM_002991	
CDHR3	222256	broad.mit.edu	37	7	105660961	105660961	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:105660961C>T	ENST00000317716.9	+	13	1876	c.1796C>T	c.(1795-1797)cCc>cTc	p.P599L	CDHR3_ENST00000470188.1_Intron|CDHR3_ENST00000542731.1_Missense_Mutation_p.P599L|CDHR3_ENST00000478080.1_Missense_Mutation_p.P511L|CDHR3_ENST00000343407.5_Intron	NM_152750.4	NP_689963.2	Q6ZTQ4	CDHR3_HUMAN	cadherin-related family member 3	599	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(1)|cervix(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(15)|ovary(1)	23						GATTCCAGCCCCAGATCTTTC	0.488																																						uc003vdl.3																			0				ovary(1)	1						c.(1795-1797)CCC>CTC		hypothetical protein LOC222256 precursor							140.0	124.0	129.0					7																	105660961		1891	4114	6005	SO:0001583	missense	222256				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr7:105660961C>T	AK126338	CCDS47684.1, CCDS75651.1	7q22.2	2011-07-01			ENSG00000128536	ENSG00000128536		"""Cadherins / Cadherin-related"""	26308	protein-coding gene	gene with protein product		615610					Standard	NM_152750		Approved	FLJ44366, FLJ23834, CDH28	uc003vdl.4	Q6ZTQ4	OTTHUMG00000157520	ENST00000317716.9:c.1796C>T	7.37:g.105660961C>T	ENSP00000325954:p.Pro599Leu					CDHR3_uc003vdk.2_Intron|CDHR3_uc003vdm.3_Missense_Mutation_p.P586L|CDHR3_uc011klt.1_Missense_Mutation_p.P511L|CDHR3_uc003vdn.2_Intron	p.P599L	NM_152750	NP_689963	Q6ZTQ4	CDHR3_HUMAN			13	1904	+			599			Cadherin 6.|Extracellular (Potential).		Q8TCI7	Missense_Mutation	SNP	ENST00000317716.9	37	c.1796C>T	CCDS47684.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.3|23.3	4.394639|4.394639	0.83011|0.83011	.|.	.|.	ENSG00000128536|ENSG00000128536	ENST00000542731;ENST00000317716;ENST00000478080|ENST00000468477	T;T;T|T	0.58358|0.58940	0.34;0.34;1.27|0.3	5.55|5.55	5.55|5.55	0.83447|0.83447	Cadherin (2);Cadherin-like (1);|.	0.335463|0.335463	0.30028|0.30028	N|N	0.010592|0.010592	T|T	0.70482|0.70482	0.3229|0.3229	M|M	0.70595|0.70595	2.14|2.14	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	0.999;1.0|.	D;D|.	0.72075|.	0.922;0.976|.	T|T	0.66224|0.66224	-0.5977|-0.5977	10|8	0.12103|0.28530	T|T	0.63|0.3	-13.8547|-13.8547	17.6826|17.6826	0.88248|0.88248	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	586;599|.	B3KYA0;Q6ZTQ4|.	.;CDHR3_HUMAN|.	L|S	599;599;511|68	ENSP00000439766:P599L;ENSP00000325954:P599L;ENSP00000417771:P511L|ENSP00000418958:P68S	ENSP00000325954:P599L|ENSP00000418958:P68S	P|P	+|+	2|1	0|0	CDHR3|CDHR3	105448197|105448197	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.964000|0.964000	0.63967|0.63967	5.359000|5.359000	0.66074|0.66074	2.615000|2.615000	0.88500|0.88500	0.655000|0.655000	0.94253|0.94253	CCC|CCA		0.488	CDHR3-004	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000349025.2	NM_152750	
SND1	27044	broad.mit.edu	37	7	127334947	127334948	+	Frame_Shift_Ins	INS	-	-	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:127334947_127334948insA	ENST00000354725.3	+	3	488_489	c.294_295insA	c.(295-297)atafs	p.I99fs		NM_014390.2	NP_055205.2	Q7KZF4	SND1_HUMAN	staphylococcal nuclease and tudor domain containing 1	99	TNase-like 1. {ECO:0000255|PROSITE- ProRule:PRU00272}.				gene silencing by RNA (GO:0031047)|osteoblast differentiation (GO:0001649)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	cytoplasm (GO:0005737)|dense body (GO:0097433)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|RISC complex (GO:0016442)	nuclease activity (GO:0004518)|poly(A) RNA binding (GO:0044822)|transcription cofactor activity (GO:0003712)			central_nervous_system(1)|endometrium(8)|kidney(1)|large_intestine(9)|lung(15)|ovary(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	41						TCTGTTTCACGATAGAAAACAA	0.465																																						uc003vmi.2																			0				ovary(2)|central_nervous_system(1)	3						c.(292-297)ACGATAfs		staphylococcal nuclease domain containing 1																																				SO:0001589	frameshift_variant	27044				gene silencing by RNA|interspecies interaction between organisms|regulation of transcription, DNA-dependent|transcription, DNA-dependent	melanosome|nucleus|RNA-induced silencing complex	nuclease activity|nucleic acid binding|protein binding|transcription cofactor activity	g.chr7:127334947_127334948insA		CCDS34747.1	7q31.3	2014-03-24			ENSG00000197157	ENSG00000197157		"""Tudor domain containing"""	30646	protein-coding gene	gene with protein product	"""p100 EBNA2 co-activator"", ""Tudor-SN"""	602181				7651391, 9003410, 12819296	Standard	NM_014390		Approved	TDRD11, p100	uc003vmi.3	Q7KZF4	OTTHUMG00000157560	ENST00000354725.3:c.295dupA	7.37:g.127334948_127334948dupA	ENSP00000346762:p.Ile99fs						p.T98fs	NM_014390	NP_055205	Q7KZF4	SND1_HUMAN			3	520_521	+			98_99			TNase-like 1.		Q13122|Q96AG0	Frame_Shift_Ins	INS	ENST00000354725.3	37	c.294_295insA	CCDS34747.1																																																																																				0.465	SND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349148.1	NM_014390	
KEL	3792	broad.mit.edu	37	7	142643377	142643377	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr7:142643377C>T	ENST00000355265.2	-	11	1705	c.1231G>A	c.(1231-1233)Gtg>Atg	p.V411M	KEL_ENST00000479768.2_5'UTR	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	411					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					GTCTCCTCCACGCACTTCATC	0.567																																						uc003wcb.2																			0				ovary(3)|central_nervous_system(1)	4						c.(1231-1233)GTG>ATG		Kell blood group, metallo-endopeptidase							87.0	74.0	78.0					7																	142643377		2203	4300	6503	SO:0001583	missense	3792				proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding	g.chr7:142643377C>T	BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"""CD molecules"", ""Blood group antigens"""	6308	protein-coding gene	gene with protein product		613883	"""Kell blood group"", ""Kell blood group, metalloendopeptidase"""			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.1231G>A	7.37:g.142643377C>T	ENSP00000347409:p.Val411Met						p.V411M	NM_000420	NP_000411	P23276	KELL_HUMAN			11	1441	-	Melanoma(164;0.059)		411			Extracellular (Potential).		B2RBV4|Q96RS8|Q99885	Missense_Mutation	SNP	ENST00000355265.2	37	c.1231G>A	CCDS34766.1	.	.	.	.	.	.	.	.	.	.	c	9.334	1.061309	0.19987	.	.	ENSG00000197993	ENST00000355265	T	0.78003	-1.14	4.48	1.54	0.23209	Peptidase M13 (1);	0.762469	0.11301	N	0.578219	T	0.62085	0.2399	L	0.41824	1.3	0.27440	N	0.953734	P	0.44006	0.824	B	0.34536	0.185	T	0.57843	-0.7741	10	0.72032	D	0.01	-1.8374	4.0324	0.09714	0.1854:0.611:0.0:0.2036	.	411	P23276	KELL_HUMAN	M	411	ENSP00000347409:V411M	ENSP00000347409:V411M	V	-	1	0	KEL	142353499	0.016000	0.18221	0.915000	0.36163	0.177000	0.22998	-0.211000	0.09332	0.475000	0.27415	-0.355000	0.07637	GTG		0.567	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420	
SOX7	83595	broad.mit.edu	37	8	10583649	10583649	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr8:10583649G>A	ENST00000304501.1	-	2	844	c.766C>T	c.(766-768)Ccc>Tcc	p.P256S	SOX7_ENST00000554914.1_Missense_Mutation_p.P308S|SOX7_ENST00000553390.1_Missense_Mutation_p.P308S	NM_031439.2	NP_113627.1	Q9BT81	SOX7_HUMAN	SRY (sex determining region Y)-box 7	256					endoderm formation (GO:0001706)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|regulation of canonical Wnt signaling pathway (GO:0060828)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription regulatory region DNA binding (GO:0044212)			breast(1)|endometrium(1)|kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	20				COAD - Colon adenocarcinoma(149;0.0732)		GAGCCCAGGGGGTGGCTACAG	0.692																																						uc003wtf.2																			0				breast(1)	1						c.(766-768)CCC>TCC		SRY-box 7							22.0	30.0	27.0					8																	10583649		2196	4280	6476	SO:0001583	missense	83595				endoderm formation|negative regulation of cell proliferation|negative regulation of transcription, DNA-dependent|positive regulation of caspase activity|regulation of canonical Wnt receptor signaling pathway	cytoplasm|nucleus	transcription regulatory region DNA binding	g.chr8:10583649G>A	AJ409320	CCDS5977.1	8p22	2013-01-25			ENSG00000171056	ENSG00000171056		"""SRY (sex determining region Y)-boxes"""	18196	protein-coding gene	gene with protein product		612202				11691915	Standard	NM_031439		Approved		uc003wtf.3	Q9BT81	OTTHUMG00000090585	ENST00000304501.1:c.766C>T	8.37:g.10583649G>A	ENSP00000301921:p.Pro256Ser					SOX7_uc011kwz.1_Missense_Mutation_p.P308S	p.P256S	NM_031439	NP_113627	Q9BT81	SOX7_HUMAN		COAD - Colon adenocarcinoma(149;0.0732)	2	845	-			256					B4DKV0|Q53YD0	Missense_Mutation	SNP	ENST00000304501.1	37	c.766C>T	CCDS5977.1	.	.	.	.	.	.	.	.	.	.	G	10.36	1.329936	0.24167	.	.	ENSG00000171056;ENSG00000171056;ENSG00000258724	ENST00000304501;ENST00000553390;ENST00000554914	T;T;T	0.75938	-0.98;-0.98;-0.98	5.05	-0.3	0.12804	.	0.242826	0.35235	N	0.003350	T	0.51415	0.1673	L	0.31526	0.94	0.26093	N	0.980923	P;B	0.45176	0.852;0.042	B;B	0.39217	0.294;0.103	T	0.50432	-0.8829	10	0.20519	T	0.43	.	3.4664	0.07552	0.2207:0.1163:0.5439:0.119	.	308;256	B4DKV0;Q9BT81	.;SOX7_HUMAN	S	256;308;308	ENSP00000301921:P256S;ENSP00000452017:P308S;ENSP00000451145:P308S	ENSP00000346908:P308S	P	-	1	0	SOX7;CTD-2135J3.4	10621059	0.994000	0.37717	0.923000	0.36655	0.616000	0.37450	0.967000	0.29344	-0.321000	0.08627	-1.598000	0.00824	CCC		0.692	SOX7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207131.1		
HGSNAT	138050	broad.mit.edu	37	8	43048945	43048945	+	Missense_Mutation	SNP	G	G	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr8:43048945G>C	ENST00000458501.2	+	14	1507	c.1507G>C	c.(1507-1509)Ggc>Cgc	p.G503R	HGSNAT_ENST00000521576.1_Missense_Mutation_p.G192R|HGSNAT_ENST00000297798.7_Missense_Mutation_p.G207R|HGSNAT_ENST00000379644.4_Missense_Mutation_p.G475R			Q68CP4	HGNAT_HUMAN	heparan-alpha-glucosaminide N-acetyltransferase	503					carbohydrate metabolic process (GO:0005975)|glycosaminoglycan catabolic process (GO:0006027)|glycosaminoglycan metabolic process (GO:0030203)|lysosomal transport (GO:0007041)|protein oligomerization (GO:0051259)|small molecule metabolic process (GO:0044281)	integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)	heparan-alpha-glucosaminide N-acetyltransferase activity (GO:0015019)|transferase activity, transferring acyl groups (GO:0016746)			cervix(1)|endometrium(2)|large_intestine(4)|lung(6)	13	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)			GGGCATCCTGGGCACCATCAA	0.428																																						uc003xpx.3																			0					0						c.(1423-1425)GGC>CGC		heparan-alpha-glucosaminide N-acetyltransferase							153.0	154.0	153.0					8																	43048945		1924	4145	6069	SO:0001583	missense	138050				lysosomal transport|protein oligomerization	integral to membrane|lysosomal membrane	heparan-alpha-glucosaminide N-acetyltransferase activity	g.chr8:43048945G>C		CCDS47852.1	8p11.1	2011-11-16	2006-09-05	2006-08-16	ENSG00000165102	ENSG00000165102	2.3.1.78		26527	protein-coding gene	gene with protein product		610453	"""transmembrane protein 76"""	TMEM76		17033958, 16960811	Standard	NM_152419		Approved	FLJ32731, HGNAT	uc003xpx.4	Q68CP4	OTTHUMG00000164102	ENST00000458501.2:c.1507G>C	8.37:g.43048945G>C	ENSP00000389524:p.Gly503Arg						p.G475R	NM_152419	NP_689632	Q68CP4	HGNAT_HUMAN	Lung(22;0.0777)|LUSC - Lung squamous cell carcinoma(45;0.17)		14	1471	+	Prostate(17;0.0119)|Ovarian(28;0.0172)|Lung SC(25;0.184)	all_cancers(86;0.000223)|all_epithelial(80;1.61e-07)|all_lung(54;0.00021)|Lung NSC(58;0.000778)|Hepatocellular(245;0.0524)|Renal(179;0.0822)|Esophageal squamous(32;0.129)	503			Helical; (Potential).		B4E2V0	Missense_Mutation	SNP	ENST00000458501.2	37	c.1423G>C		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	21.5|21.5	4.153238|4.153238	0.78114|0.78114	.|.	.|.	ENSG00000165102|ENSG00000165102	ENST00000524016|ENST00000458501;ENST00000379644;ENST00000521576;ENST00000297798	.|D;D;D;D	.|0.90069	.|-2.61;-2.61;-2.61;-2.61	5.12|5.12	5.12|5.12	0.69794|0.69794	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	D|D	0.95661|0.95661	0.8589|0.8589	M|M	0.92738|0.92738	3.34|3.34	0.80722|0.80722	D|D	1|1	.|D	.|0.89917	.|1.0	.|D	.|0.78314	.|0.991	D|D	0.96569|0.96569	0.9421|0.9421	6|10	.|0.72032	.|D	.|0.01	-15.2171|-15.2171	16.0959|16.0959	0.81123|0.81123	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|503	.|Q68CP4	.|HGNAT_HUMAN	A|R	176|503;475;192;207	.|ENSP00000389524:G503R;ENSP00000368965:G475R;ENSP00000429029:G192R;ENSP00000297798:G207R	.|ENSP00000297798:G207R	G|G	+|+	2|1	0|0	HGSNAT|HGSNAT	43168102|43168102	1.000000|1.000000	0.71417|0.71417	0.909000|0.909000	0.35828|0.35828	0.513000|0.513000	0.34164|0.34164	9.276000|9.276000	0.95745|0.95745	2.391000|2.391000	0.81399|0.81399	0.650000|0.650000	0.86243|0.86243	GGG|GGC		0.428	HGSNAT-202	KNOWN	basic	protein_coding	protein_coding		XM_372038	
ENPP2	5168	broad.mit.edu	37	8	120628516	120628516	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr8:120628516C>T	ENST00000075322.6	-	8	824	c.766G>A	c.(766-768)Gga>Aga	p.G256R	ENPP2_ENST00000522826.1_Missense_Mutation_p.G256R|ENPP2_ENST00000427067.2_Missense_Mutation_p.G252R|ENPP2_ENST00000259486.6_Missense_Mutation_p.G256R	NM_001040092.2	NP_001035181.1	Q13822	ENPP2_HUMAN	ectonucleotide pyrophosphatase/phosphodiesterase 2	256					cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|immune response (GO:0006955)|nucleic acid phosphodiester bond hydrolysis (GO:0090305)|phosphate-containing compound metabolic process (GO:0006796)|phosphatidylcholine catabolic process (GO:0034638)|phospholipid catabolic process (GO:0009395)|regulation of cell migration (GO:0030334)	extracellular space (GO:0005615)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	alkylglycerophosphoethanolamine phosphodiesterase activity (GO:0047391)|calcium ion binding (GO:0005509)|hydrolase activity (GO:0016787)|lysophospholipase activity (GO:0004622)|nucleic acid binding (GO:0003676)|nucleotide diphosphatase activity (GO:0004551)|phosphodiesterase I activity (GO:0004528)|polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)|transcription factor binding (GO:0008134)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(15)|lung(30)|ovary(2)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)	69	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		STAD - Stomach adenocarcinoma(47;0.00185)			GGTTGACCTCCCCACCATCTA	0.378																																					Melanoma(20;305 879 2501 4818 31020)	uc003yot.1																			0				ovary(2)|central_nervous_system(2)|upper_aerodigestive_tract(1)|large_intestine(1)|kidney(1)	7						c.(766-768)GGA>AGA		autotaxin isoform 2 preproprotein							151.0	133.0	139.0					8																	120628516		2203	4300	6503	SO:0001583	missense	5168				cellular component movement|chemotaxis|G-protein coupled receptor protein signaling pathway|immune response|phosphate metabolic process|phosphatidylcholine catabolic process|regulation of cell migration	extracellular space|integral to plasma membrane	alkylglycerophosphoethanolamine phosphodiesterase activity|calcium ion binding|lysophospholipase activity|nucleic acid binding|nucleotide diphosphatase activity|phosphodiesterase I activity|polysaccharide binding|scavenger receptor activity|transcription factor binding|zinc ion binding	g.chr8:120628516C>T	D45421	CCDS6329.1, CCDS34936.1, CCDS47914.1	8q24.12	2014-04-09	2008-08-01		ENSG00000136960	ENSG00000136960	3.1.4.1, 3.6.1.9		3357	protein-coding gene	gene with protein product	"""autotaxin"""	601060		PDNP2		8586446	Standard	NM_001040092		Approved	ATX, PD-IALPHA	uc003yos.2	Q13822	OTTHUMG00000164995	ENST00000075322.6:c.766G>A	8.37:g.120628516C>T	ENSP00000075322:p.Gly256Arg					ENPP2_uc003yos.1_Missense_Mutation_p.G256R|ENPP2_uc010mdd.1_Missense_Mutation_p.G256R	p.G256R	NM_001040092	NP_001035181	Q13822	ENPP2_HUMAN	STAD - Stomach adenocarcinoma(47;0.00185)		8	852	-	Lung NSC(37;5.03e-06)|Ovarian(258;0.0249)|Hepatocellular(40;0.161)		256					A8UHA1|E9PHP7|Q13827|Q14555|Q15117|Q9UCQ8|Q9UCR0|Q9UCR1|Q9UCR2|Q9UCR3|Q9UCR4	Missense_Mutation	SNP	ENST00000075322.6	37	c.766G>A	CCDS34936.1	.	.	.	.	.	.	.	.	.	.	C	20.8	4.043946	0.75732	.	.	ENSG00000136960	ENST00000259486;ENST00000427067;ENST00000522826;ENST00000075322;ENST00000520066	T;T;T;T;T	0.74632	-0.86;-0.86;-0.86;-0.86;-0.86	5.55	5.55	0.83447	Alkaline phosphatase-like, alpha/beta/alpha (1);Alkaline-phosphatase-like, core domain (1);	0.100154	0.64402	D	0.000002	D	0.84629	0.5514	L	0.60957	1.885	0.80722	D	1	D;D;D	0.89917	0.999;1.0;0.999	D;D;D	0.87578	0.995;0.998;0.989	T	0.83233	-0.0062	10	0.41790	T	0.15	.	19.5156	0.95162	0.0:1.0:0.0:0.0	.	256;256;256	E9PHP7;Q13822;Q13822-2	.;ENPP2_HUMAN;.	R	256;252;256;256;238	ENSP00000259486:G256R;ENSP00000403315:G252R;ENSP00000428291:G256R;ENSP00000075322:G256R;ENSP00000428304:G238R	ENSP00000075322:G256R	G	-	1	0	ENPP2	120697697	1.000000	0.71417	1.000000	0.80357	0.359000	0.29487	7.818000	0.86416	2.605000	0.88082	0.563000	0.77884	GGA		0.378	ENPP2-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000381390.1		
HAS2	3037	broad.mit.edu	37	8	122626452	122626452	+	Missense_Mutation	SNP	T	T	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr8:122626452T>C	ENST00000303924.4	-	4	2093	c.1556A>G	c.(1555-1557)tAt>tGt	p.Y519C		NM_005328.2	NP_005319.1	Q92819	HYAS2_HUMAN	hyaluronan synthase 2	519					atrioventricular canal development (GO:0036302)|bone morphogenesis (GO:0060349)|cellular response to fluid shear stress (GO:0071498)|cellular response to interleukin-1 (GO:0071347)|cellular response to platelet-derived growth factor stimulus (GO:0036120)|cellular response to tumor necrosis factor (GO:0071356)|endocardial cushion to mesenchymal transition (GO:0090500)|extracellular matrix assembly (GO:0085029)|extracellular polysaccharide biosynthetic process (GO:0045226)|hyaluronan biosynthetic process (GO:0030213)|kidney development (GO:0001822)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of monocyte aggregation (GO:1900625)|positive regulation of urine volume (GO:0035810)|renal water absorption (GO:0070295)|vasculogenesis (GO:0001570)	integral component of plasma membrane (GO:0005887)	hyaluronan synthase activity (GO:0050501)		HAS2/PLAG1(10)	breast(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|lung(19)|ovary(5)|skin(1)	38	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		STAD - Stomach adenocarcinoma(47;0.00503)			ATAGCATGCATAGAGCAACGT	0.418																																						uc003yph.2																		HAS2/PLAG1(10)	0				soft_tissue(10)|ovary(5)	15						c.(1555-1557)TAT>TGT		hyaluronan synthase 2							198.0	171.0	180.0					8																	122626452		2203	4300	6503	SO:0001583	missense	3037					integral to plasma membrane	hyaluronan synthase activity	g.chr8:122626452T>C	U54804	CCDS6335.1	8q24.12	2013-02-22			ENSG00000170961	ENSG00000170961	2.4.1.212	"""Glycosyltransferase family 2 domain containing"""	4819	protein-coding gene	gene with protein product		601636				9169154	Standard	NM_005328		Approved		uc003yph.2	Q92819	OTTHUMG00000164953	ENST00000303924.4:c.1556A>G	8.37:g.122626452T>C	ENSP00000306991:p.Tyr519Cys						p.Y519C	NM_005328	NP_005319	Q92819	HAS2_HUMAN	STAD - Stomach adenocarcinoma(47;0.00503)		4	2094	-	Lung NSC(37;3.12e-08)|Ovarian(258;0.0254)|Hepatocellular(40;0.0997)|all_neural(195;0.142)		519			Helical; Name=7; (Potential).		Q32MM3	Missense_Mutation	SNP	ENST00000303924.4	37	c.1556A>G	CCDS6335.1	.	.	.	.	.	.	.	.	.	.	T	17.31	3.358030	0.61403	.	.	ENSG00000170961	ENST00000303924	T	0.62498	0.02	6.17	6.17	0.99709	.	0.000000	0.85682	D	0.000000	T	0.80369	0.4610	M	0.76838	2.35	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.82458	-0.0447	10	0.87932	D	0	-16.8984	16.8222	0.85835	0.0:0.0:0.0:1.0	.	519	Q92819	HAS2_HUMAN	C	519	ENSP00000306991:Y519C	ENSP00000306991:Y519C	Y	-	2	0	HAS2	122695633	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.030000	0.88816	2.371000	0.80710	0.533000	0.62120	TAT		0.418	HAS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000381150.2	NM_005328	
FAM49B	51571	broad.mit.edu	37	8	130866513	130866513	+	Splice_Site	SNP	G	G	A	rs200940349		TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr8:130866513G>A	ENST00000519824.2	-	7	788	c.515C>T	c.(514-516)cCg>cTg	p.P172L	FAM49B_ENST00000519540.1_Splice_Site_p.P172L|FAM49B_ENST00000519110.1_Splice_Site_p.P172L|FAM49B_ENST00000522941.1_Splice_Site_p.P26L|FAM49B_ENST00000523509.1_Splice_Site_p.P172L|FAM49B_ENST00000522746.1_Splice_Site_p.P172L|FAM49B_ENST00000522250.1_Splice_Site_p.P26L|FAM49B_ENST00000517654.1_Splice_Site_p.P172L|FAM49B_ENST00000401979.2_Splice_Site_p.P172L|FAM49B_ENST00000518879.1_5'Flank	NM_016623.4	NP_057707.3	Q9NUQ9	FA49B_HUMAN	family with sequence similarity 49, member B	172						cilium (GO:0005929)|extracellular vesicular exosome (GO:0070062)				kidney(1)|large_intestine(6)|lung(4)|prostate(1)	12	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		LUAD - Lung adenocarcinoma(14;0.0989)			TTAACTTACCGGTACATTGTT	0.348													G|||	1	0.000199681	0.0	0.0	5008	,	,		17561	0.0		0.001	False		,,,				2504	0.0					uc003yss.2																			0					0						c.(514-516)CCG>CTG		hypothetical protein LOC51571							157.0	135.0	142.0					8																	130866513		2203	4300	6503	SO:0001630	splice_region_variant	51571							g.chr8:130866513G>A	AF208851	CCDS6361.1	8q24	2004-08-20				ENSG00000153310			25216	protein-coding gene	gene with protein product							Standard	NM_001256763		Approved	BM-009	uc003ysu.4	Q9NUQ9		ENST00000519824.2:c.516+1C>T	8.37:g.130866513G>A						FAM49B_uc003yst.2_Missense_Mutation_p.P172L|FAM49B_uc003ysu.2_Missense_Mutation_p.P172L|FAM49B_uc003ysv.2_Missense_Mutation_p.P26L|FAM49B_uc003ysw.2_Missense_Mutation_p.P172L|FAM49B_uc003ysx.2_Missense_Mutation_p.P172L|FAM49B_uc003ysy.1_Missense_Mutation_p.P172L	p.P172L	NM_016623	NP_057707	Q9NUQ9	FA49B_HUMAN	LUAD - Lung adenocarcinoma(14;0.0989)		10	1064	-	Ovarian(5;0.000567)|Esophageal squamous(12;0.00693)|Acute lymphoblastic leukemia(118;0.155)		172					Q96AZ5|Q9NW21|Q9NZE7	Missense_Mutation	SNP	ENST00000519824.2	37	c.515C>T	CCDS6361.1	1|1	4.578754578754579E-4|4.578754578754579E-4	0|0	0.0|0.0	0|0	0.0|0.0	0|0	0.0|0.0	1|1	0.0013192612137203166|0.0013192612137203166	G|G	16.28|16.28	3.079106|3.079106	0.55753|0.55753	.|.	.|.	ENSG00000153310|ENSG00000153310	ENST00000522746;ENST00000523509;ENST00000401979;ENST00000519110;ENST00000522250;ENST00000519824;ENST00000517654;ENST00000519540;ENST00000522941|ENST00000311292	T;T;T;T;T;T;T;T;T|.	0.41400|.	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0|.	5.8|5.8	5.8|5.8	0.92144|0.92144	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.69904|0.69904	0.3163|0.3163	L|L	0.43152|0.43152	1.355|1.355	0.80722|0.80722	D|D	1|1	P|.	0.35612|.	0.512|.	B|.	0.33568|.	0.166|.	T|T	0.70521|0.70521	-0.4849|-0.4849	10|6	0.28530|0.66056	T|D	0.3|0.02	-13.5108|-13.5108	18.6274|18.6274	0.91346|0.91346	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	172|.	Q9NUQ9|.	FA49B_HUMAN|.	L|W	172;172;172;172;26;172;172;172;26|126	ENSP00000428117:P172L;ENSP00000429802:P172L;ENSP00000384880:P172L;ENSP00000429078:P172L;ENSP00000429978:P26L;ENSP00000429150:P172L;ENSP00000430674:P172L;ENSP00000429499:P172L;ENSP00000430433:P26L|.	ENSP00000384880:P172L|ENSP00000311651:R126W	P|R	-|-	2|1	0|2	FAM49B|FAM49B	130935695|130935695	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.955000|0.955000	0.61496|0.61496	4.417000|4.417000	0.59822|0.59822	2.745000|2.745000	0.94114|0.94114	0.491000|0.491000	0.48974|0.48974	CCG|CGG		0.348	FAM49B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000380390.2	NM_016623	Missense_Mutation
GSN	2934	broad.mit.edu	37	9	124062285	124062285	+	Splice_Site	SNP	T	T	G			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr9:124062285T>G	ENST00000373818.4	+	1	213		c.e1+2		GSN_ENST00000545652.1_Intron|GSN_ENST00000341272.2_Intron|GSN_ENST00000394353.2_Intron|GSN_ENST00000436847.1_Intron|GSN_ENST00000373823.3_Intron|GSN_ENST00000373808.2_Intron|GSN_ENST00000449733.1_Intron|GSN_ENST00000412819.1_Intron	NM_000177.4|NM_001258029.1	NP_000168.1|NP_001244958.1	P06396	GELS_HUMAN	gelsolin						actin filament polymerization (GO:0030041)|actin filament severing (GO:0051014)|aging (GO:0007568)|apoptotic process (GO:0006915)|barbed-end actin filament capping (GO:0051016)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)|cellular response to cadmium ion (GO:0071276)|cilium morphogenesis (GO:0060271)|oligodendrocyte development (GO:0014003)|phosphatidylinositol-mediated signaling (GO:0048015)|regulation of cell adhesion (GO:0030155)|response to ethanol (GO:0045471)|response to folic acid (GO:0051593)|tissue regeneration (GO:0042246)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|blood microparticle (GO:0072562)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|lamellipodium (GO:0030027)|perinuclear region of cytoplasm (GO:0048471)|protein complex (GO:0043234)|ruffle (GO:0001726)	calcium ion binding (GO:0005509)			NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(6)|kidney(1)|large_intestine(1)|lung(8)|ovary(1)	21						gaggcgcgggtgagtgcccgg	0.697																																						uc004blf.1																			0				breast(2)|ovary(1)	3						c.e1+2		gelsolin isoform a precursor							22.0	24.0	23.0					9																	124062285		1599	3598	5197	SO:0001630	splice_region_variant	2934				actin filament polymerization|actin filament severing|barbed-end actin filament capping|cellular component disassembly involved in apoptosis|cilium morphogenesis	actin cytoskeleton|cytosol	actin binding|calcium ion binding|protein binding	g.chr9:124062285T>G	X04412	CCDS6828.1, CCDS6829.1, CCDS48011.1, CCDS65118.1, CCDS75890.1, CCDS75891.1	9q33	2010-04-27	2010-04-27		ENSG00000148180	ENSG00000148180			4620	protein-coding gene	gene with protein product	"""amyloidosis, Finnish type"""	137350	"""gelsolin (amyloidosis, Finnish type)"""			1652889	Standard	NM_001127662		Approved	DKFZp313L0718	uc004blf.1	P06396	OTTHUMG00000020584	ENST00000373818.4:c.144+2T>G	9.37:g.124062285T>G						GSN_uc004bld.1_Intron|GSN_uc010mvq.1_Intron|GSN_uc010mvr.1_Intron|GSN_uc010mvu.1_Intron|GSN_uc010mvt.1_Intron|GSN_uc010mvs.1_Intron|GSN_uc004ble.1_Intron|GSN_uc010mvv.1_Intron|GSN_uc011lyh.1_Intron|GSN_uc011lyi.1_Intron|GSN_uc011lyj.1_5'Flank	p.R48_splice	NM_000177	NP_000168	P06396	GELS_HUMAN			1	205	+								A2A418|A8MUD1|A8MYN7|B7Z373|B7Z5V1|F5H1A8|Q5T0I2|Q8WVV7	Splice_Site	SNP	ENST00000373818.4	37	c.144_splice	CCDS6828.1																																																																																				0.697	GSN-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000053861.1	NM_000177	Intron
ABL1	25	broad.mit.edu	37	9	133760582	133760582	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr9:133760582G>A	ENST00000318560.5	+	11	3286	c.2905G>A	c.(2905-2907)Gcc>Acc	p.A969T		NM_005157.4	NP_005148.2	P00519	ABL1_HUMAN	ABL proto-oncogene 1, non-receptor tyrosine kinase	969	F-actin-binding.|Pro-rich.				actin cytoskeleton organization (GO:0030036)|autophagy (GO:0006914)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cell cycle arrest (GO:0007050)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|cellular response to dopamine (GO:1903351)|cellular response to oxidative stress (GO:0034599)|DNA damage induced protein phosphorylation (GO:0006975)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|innate immune response (GO:0045087)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|mismatch repair (GO:0006298)|mitochondrial depolarization (GO:0051882)|mitotic nuclear division (GO:0007067)|muscle cell differentiation (GO:0042692)|negative regulation of phospholipase C activity (GO:1900275)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|negative regulation of ubiquitin-protein transferase activity (GO:0051444)|peptidyl-tyrosine phosphorylation (GO:0018108)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of oxidoreductase activity (GO:0051353)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of autophagy (GO:0010506)|regulation of cell adhesion (GO:0030155)|regulation of cell motility (GO:2000145)|regulation of endocytosis (GO:0030100)|regulation of response to DNA damage stimulus (GO:2001020)|regulation of transcription, DNA-templated (GO:0006355)|response to oxidative stress (GO:0006979)|signal transduction in response to DNA damage (GO:0042770)	actin cytoskeleton (GO:0015629)|cell leading edge (GO:0031252)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	actin monomer binding (GO:0003785)|ATP binding (GO:0005524)|DNA binding (GO:0003677)|magnesium ion binding (GO:0000287)|manganese ion binding (GO:0030145)|mitogen-activated protein kinase binding (GO:0051019)|nicotinate-nucleotide adenylyltransferase activity (GO:0004515)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|proline-rich region binding (GO:0070064)|protein C-terminus binding (GO:0008022)|protein kinase activity (GO:0004672)|protein tyrosine kinase activity (GO:0004713)|SH3 domain binding (GO:0017124)|syntaxin binding (GO:0019905)			breast(3)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1149)|kidney(3)|large_intestine(7)|lung(15)|ovary(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	1195		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	Adenosine triphosphate(DB00171)|Bosutinib(DB06616)|Dasatinib(DB01254)|Imatinib(DB00619)|Nilotinib(DB04868)|Ponatinib(DB08901)|Regorafenib(DB08896)	GCCACAGTCCGCCAAGCCGTC	0.667			"""T, Mis"""	"""BCR, ETV6, NUP214"""	"""CML, ALL, T-ALL"""																																	uc004bzw.2				Dom	yes		9	9q34.1	25	T|Mis	v-abl Abelson murine leukemia viral oncogene homolog 1			L	BCR|ETV6|NUP214		CML|ALL|T-ALL		0				haematopoietic_and_lymphoid_tissue(807)|lung(5)|stomach(2)|central_nervous_system(1)|breast(1)|skin(1)	817						c.(2905-2907)GCC>ACC		c-abl oncogene 1, receptor tyrosine kinase	Adenosine triphosphate(DB00171)|Dasatinib(DB01254)|Imatinib(DB00619)						40.0	49.0	46.0					9																	133760582		2201	4297	6498	SO:0001583	missense	25				actin cytoskeleton organization|axon guidance|blood coagulation|cell adhesion|DNA damage induced protein phosphorylation|DNA damage response, signal transduction resulting in induction of apoptosis|mismatch repair|muscle cell differentiation|negative regulation of protein serine/threonine kinase activity|peptidyl-tyrosine phosphorylation|positive regulation of muscle cell differentiation|positive regulation of oxidoreductase activity|regulation of transcription involved in S phase of mitotic cell cycle	cytoskeleton|cytosol|nuclear membrane|nucleolus|perinuclear region of cytoplasm	ATP binding|DNA binding|magnesium ion binding|manganese ion binding|mitogen-activated protein kinase binding|non-membrane spanning protein tyrosine kinase activity|proline-rich region binding|protein C-terminus binding|SH3 domain binding	g.chr9:133760582G>A	M14752	CCDS35165.1, CCDS35166.1	9q34.1	2014-09-17	2014-06-26		ENSG00000097007	ENSG00000097007		"""SH2 domain containing"""	76	protein-coding gene	gene with protein product		189980	"""v-abl Abelson murine leukemia viral oncogene homolog 1"", ""c-abl oncogene 1, receptor tyrosine kinase"", ""c-abl oncogene 1, non-receptor tyrosine kinase"""	ABL		1857987, 12626632	Standard	NM_007313		Approved	JTK7, c-ABL, p150	uc004bzv.3	P00519	OTTHUMG00000020813	ENST00000318560.5:c.2905G>A	9.37:g.133760582G>A	ENSP00000323315:p.Ala969Thr					ABL1_uc004bzv.2_Missense_Mutation_p.A988T	p.A969T	NM_005157	NP_005148	P00519	ABL1_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;5.4e-05)	11	2908	+		all_hematologic(13;0.0361)|Acute lymphoblastic leukemia(5;0.0543)|Myeloproliferative disorder(178;0.204)	969			F-actin-binding.|Pro-rich.		A3KFJ3|Q13869|Q13870|Q16133|Q17R61|Q45F09	Missense_Mutation	SNP	ENST00000318560.5	37	c.2905G>A	CCDS35166.1	.	.	.	.	.	.	.	.	.	.	G	10.29	1.310473	0.23821	.	.	ENSG00000097007	ENST00000444970;ENST00000372348;ENST00000318560	T;T	0.10960	2.82;2.82	5.27	-8.63	0.00878	F-actin binding (1);	0.637464	0.17132	N	0.185799	T	0.02688	0.0081	N	0.03324	-0.35	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.08055	0.002;0.003	T	0.29882	-0.9997	10	0.21540	T	0.41	.	5.9674	0.19332	0.2866:0.1113:0.4935:0.1086	.	969;1006	P00519;Q59FK4	ABL1_HUMAN;.	T	784;988;969	ENSP00000361423:A988T;ENSP00000323315:A969T	ENSP00000323315:A969T	A	+	1	0	ABL1	132750403	0.000000	0.05858	0.009000	0.14445	0.881000	0.50899	-0.412000	0.07132	-1.679000	0.01452	-0.340000	0.08031	GCC		0.667	ABL1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000054684.1	NM_007313	
RXRA	6256	broad.mit.edu	37	9	137300840	137300840	+	Missense_Mutation	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chr9:137300840C>T	ENST00000481739.1	+	4	537	c.485C>T	c.(484-486)aCg>aTg	p.T162M	RXRA_ENST00000356384.4_3'UTR|RXRA_ENST00000540193.1_Missense_Mutation_p.T65M	NM_002957.4	NP_002948.1	P19793	RXRA_HUMAN	retinoid X receptor, alpha	162					camera-type eye development (GO:0043010)|cardiac muscle cell proliferation (GO:0060038)|cellular lipid metabolic process (GO:0044255)|cholesterol metabolic process (GO:0008203)|embryo implantation (GO:0007566)|gene expression (GO:0010467)|in utero embryonic development (GO:0001701)|maternal placenta development (GO:0001893)|modulation by virus of host morphology or physiology (GO:0019048)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peroxisome proliferator activated receptor signaling pathway (GO:0035357)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein homotetramerization (GO:0051289)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|response to retinoic acid (GO:0032526)|retinoic acid receptor signaling pathway (GO:0048384)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|small molecule metabolic process (GO:0044281)|transcription initiation from RNA polymerase II promoter (GO:0006367)|ventricular cardiac muscle cell differentiation (GO:0055012)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|vitamin metabolic process (GO:0006766)	nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	9-cis retinoic acid receptor activity (GO:0004886)|chromatin DNA binding (GO:0031490)|DNA binding (GO:0003677)|enzyme binding (GO:0019899)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|protein heterodimerization activity (GO:0046982)|retinoic acid receptor activity (GO:0003708)|retinoic acid-responsive element binding (GO:0044323)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription coactivator activity (GO:0003713)|vitamin D receptor binding (GO:0042809)|zinc ion binding (GO:0008270)			breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|prostate(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	19				OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Bexarotene(DB00307)|Etodolac(DB00749)	TTCAAGCGGACGGTGCGCAAG	0.647																																						uc004cfb.2																			0				upper_aerodigestive_tract(1)|ovary(1)	2						c.(484-486)ACG>ATG		retinoid X receptor, alpha	Acitretin(DB00459)|Adapalene(DB00210)|Alitretinoin(DB00523)|Etretinate(DB00926)						128.0	106.0	114.0					9																	137300840		2203	4300	6503	SO:0001583	missense	6256				cellular lipid metabolic process|cholesterol metabolic process|interspecies interaction between organisms|negative regulation of transcription from RNA polymerase II promoter|positive regulation of transcription from RNA polymerase II promoter|regulation of transcription from RNA polymerase II promoter by nuclear hormone receptor|response to retinoic acid|vitamin metabolic process	nuclear chromatin|nucleoplasm	enzyme binding|ligand-regulated transcription factor activity|protein heterodimerization activity|retinoic acid-responsive element binding|retinoid-X receptor activity|sequence-specific DNA binding transcription factor activity|steroid binding|steroid hormone receptor activity|transcription coactivator activity|vitamin D receptor binding|zinc ion binding	g.chr9:137300840C>T	X52773	CCDS35172.1	9q34	2013-01-16			ENSG00000186350	ENSG00000186350		"""Nuclear hormone receptors"""	10477	protein-coding gene	gene with protein product	"""nuclear receptor subfamily 2 group B member 1"""	180245				2159111	Standard	XM_005263409		Approved	NR2B1	uc004cfa.1	P19793	OTTHUMG00000020887	ENST00000481739.1:c.485C>T	9.37:g.137300840C>T	ENSP00000419692:p.Thr162Met					RXRA_uc004cfc.1_Missense_Mutation_p.T65M	p.T162M	NM_002957	NP_002948	P19793	RXRA_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;4.66e-08)|Epithelial(140;6.72e-08)|all cancers(34;2.22e-07)	4	647	+			162			Nuclear receptor.		B3KY83|Q2NL52|Q2V504	Missense_Mutation	SNP	ENST00000481739.1	37	c.485C>T	CCDS35172.1	.	.	.	.	.	.	.	.	.	.	C	19.89	3.911363	0.72983	.	.	ENSG00000186350	ENST00000481739;ENST00000540193	D;D	0.97731	-4.51;-4.51	4.25	3.34	0.38264	Zinc finger, NHR/GATA-type (1);Zinc finger, nuclear hormone receptor-type (4);	0.000000	0.85682	D	0.000000	D	0.98501	0.9500	M	0.83312	2.635	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98988	1.0807	10	0.87932	D	0	.	12.4439	0.55639	0.0:0.9158:0.0:0.0841	.	162	P19793	RXRA_HUMAN	M	162;65	ENSP00000419692:T162M;ENSP00000442123:T65M	ENSP00000419692:T162M	T	+	2	0	RXRA	136440661	1.000000	0.71417	0.955000	0.39395	0.979000	0.70002	4.532000	0.60608	0.883000	0.36040	0.561000	0.74099	ACG		0.647	RXRA-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054949.1	NM_002957	
VCX3B	425054	broad.mit.edu	37	X	8433593	8433593	+	Splice_Site	SNP	G	G	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chrX:8433593G>C	ENST00000381032.1	+	2	409	c.102G>C	c.(100-102)aaG>aaC	p.K34N	VCX3B_ENST00000453306.1_Splice_Site_p.K34N|VCX3B_ENST00000381029.4_Splice_Site_p.K34N|VCX3B_ENST00000440654.2_Splice_Site_p.K34N|VCX3B_ENST00000444481.1_Splice_Site_p.K34N	NM_001001888.3	NP_001001888.3	Q9H321	VCX3B_HUMAN	variable charge, X-linked 3B	34						nucleolus (GO:0005730)|nucleus (GO:0005634)				NS(1)|large_intestine(1)|lung(2)|prostate(1)|skin(3)|urinary_tract(3)	11						CGAAGAAGAAGGTGAGTGACC	0.632																																						uc010ndo.2																			0					0						c.(100-102)AAG>AAC		variable charge, X-linked 3B							29.0	16.0	21.0					X																	8433593		1240	2108	3348	SO:0001630	splice_region_variant	425054					nucleolus		g.chrX:8433593G>C		CCDS48077.1, CCDS48077.2	Xp22.31	2009-01-14			ENSG00000205642	ENSG00000205642			31838	protein-coding gene	gene with protein product							Standard	NM_001001888		Approved	VCX-C	uc011mht.2	Q9H321	OTTHUMG00000021106	ENST00000381032.1:c.102+1G>C	X.37:g.8433593G>C						VCX3B_uc011mht.1_Missense_Mutation_p.K34N|VCX3B_uc004csd.1_Missense_Mutation_p.K34N	p.K34N	NM_001001888	NP_001001888	Q9H321	VCX3B_HUMAN			2	409	+			34					C9JS46|Q4KN12	Missense_Mutation	SNP	ENST00000381032.1	37	c.102G>C	CCDS48077.2	.	.	.	.	.	.	.	.	.	.	G	2.315	-0.357087	0.05138	.	.	ENSG00000205642	ENST00000381032;ENST00000453306;ENST00000444481;ENST00000440654;ENST00000381029	T;T;T;T;T	0.27256	1.85;1.68;1.95;1.68;1.93	0.384	0.384	0.16244	.	.	.	.	.	T	0.26122	0.0637	N	0.19112	0.55	0.09310	N	1	D;D	0.54772	0.968;0.968	P;P	0.61874	0.895;0.895	T	0.23868	-1.0176	8	0.21014	T	0.42	.	.	.	.	.	34;34	Q9H321;E7ERZ8	VCX3B_HUMAN;.	N	34	ENSP00000370420:K34N;ENSP00000411785:K34N;ENSP00000414780:K34N;ENSP00000410372:K34N;ENSP00000370417:K34N	ENSP00000370417:K34N	K	+	3	2	VCX3B	8393593	0.977000	0.34250	0.060000	0.19600	0.060000	0.15804	0.112000	0.15479	0.422000	0.26005	0.424000	0.28305	AAG		0.632	VCX3B-001	NOVEL	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055691.1		Missense_Mutation
USP9X	8239	broad.mit.edu	37	X	41075424	41075424	+	Silent	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chrX:41075424G>A	ENST00000324545.8	+	35	6237	c.5604G>A	c.(5602-5604)gtG>gtA	p.V1868V	USP9X_ENST00000378308.2_Silent_p.V1868V	NM_001039590.2|NM_001039591.2	NP_001034679.2|NP_001034680.2	Q93008	USP9X_HUMAN	ubiquitin specific peptidase 9, X-linked	1868	USP.				axon extension (GO:0048675)|BMP signaling pathway (GO:0030509)|cerebellar cortex structural organization (GO:0021698)|chromosome segregation (GO:0007059)|female gamete generation (GO:0007292)|gene expression (GO:0010467)|hippocampus development (GO:0021766)|in utero embryonic development (GO:0001701)|mitotic nuclear division (GO:0007067)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron migration (GO:0001764)|post-embryonic development (GO:0009791)|protein deubiquitination (GO:0016579)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)|ubiquitin-dependent protein catabolic process (GO:0006511)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|growth cone (GO:0030426)|membrane (GO:0016020)	co-SMAD binding (GO:0070410)|cysteine-type endopeptidase activity (GO:0004197)|cysteine-type peptidase activity (GO:0008234)|ubiquitin thiolesterase activity (GO:0004221)			NS(3)|breast(6)|central_nervous_system(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(3)|kidney(6)|large_intestine(16)|lung(29)|ovary(2)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	87						TTGTGGGTGTGCTCGTACACA	0.448																																					Ovarian(172;1807 2695 35459 49286)	uc004dfb.2																			0				lung(3)|breast(2)|ovary(1)	6						c.(5602-5604)GTG>GTA		ubiquitin specific protease 9, X-linked isoform							104.0	110.0	108.0					X																	41075424		2195	4297	6492	SO:0001819	synonymous_variant	8239				BMP signaling pathway|cell division|chromosome segregation|female gamete generation|mitosis|protein deubiquitination|transforming growth factor beta receptor signaling pathway|ubiquitin-dependent protein catabolic process	cytoplasm	co-SMAD binding|cysteine-type endopeptidase activity|ubiquitin thiolesterase activity	g.chrX:41075424G>A	X98296	CCDS43930.1, CCDS55403.1	Xp11.4	2010-08-03	2006-02-14		ENSG00000124486	ENSG00000124486		"""Ubiquitin-specific peptidases"""	12632	protein-coding gene	gene with protein product		300072	"""ubiquitin specific protease 9, X chromosome (fat facets-like Drosophila)"", ""ubiquitin specific protease 9, X-linked (fat facets-like, Drosophila)"", ""ubiquitin specific peptidase 9, X-linked (fat facets-like, Drosophila)"""			8922996	Standard	NM_001039590		Approved	DFFRX, FAF	uc004dfb.3	Q93008	OTTHUMG00000021367	ENST00000324545.8:c.5604G>A	X.37:g.41075424G>A						USP9X_uc004dfc.2_Silent_p.V1868V	p.V1868V	NM_001039590	NP_001034679	Q93008	USP9X_HUMAN			35	6237	+			1868					O75550|Q8WWT3|Q8WX12	Silent	SNP	ENST00000324545.8	37	c.5604G>A	CCDS43930.1																																																																																				0.448	USP9X-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000056250.4	NM_004652	
TEX11	56159	broad.mit.edu	37	X	69902635	69902635	+	Missense_Mutation	SNP	G	G	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chrX:69902635G>A	ENST00000395889.2	-	15	1245	c.1090C>T	c.(1090-1092)Cgt>Tgt	p.R364C	TEX11_ENST00000374333.2_Missense_Mutation_p.R349C|TEX11_ENST00000374320.2_Missense_Mutation_p.R39C|TEX11_ENST00000344304.3_Missense_Mutation_p.R364C	NM_001003811.1	NP_001003811.1	Q8IYF3	TEX11_HUMAN	testis expressed 11	364					chiasma assembly (GO:0051026)|fertilization (GO:0009566)|male gonad development (GO:0008584)|male meiosis chromosome segregation (GO:0007060)|meiotic gene conversion (GO:0006311)|negative regulation of apoptotic process (GO:0043066)|reciprocal meiotic recombination (GO:0007131)|resolution of meiotic recombination intermediates (GO:0000712)|synaptonemal complex assembly (GO:0007130)	central element (GO:0000801)				breast(4)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(12)|lung(13)|ovary(3)|prostate(3)|skin(3)	48	Renal(35;0.156)					GACTTAAAACGTTCATGAATA	0.358																																						uc004dyl.2																			0				ovary(3)|breast(1)|skin(1)	5						c.(1090-1092)CGT>TGT		testis expressed sequence 11 isoform 1							70.0	59.0	62.0					X																	69902635		2203	4300	6503	SO:0001583	missense	56159						protein binding	g.chrX:69902635G>A	AF285594	CCDS35323.1, CCDS43968.1	Xp11	2008-02-05	2007-03-13		ENSG00000120498	ENSG00000120498			11733	protein-coding gene	gene with protein product		300311	"""testis expressed sequence 11"""			11279525	Standard	NM_001003811		Approved	TSGA3, TGC1	uc004dyl.3	Q8IYF3	OTTHUMG00000021782	ENST00000395889.2:c.1090C>T	X.37:g.69902635G>A	ENSP00000379226:p.Arg364Cys					TEX11_uc004dyk.2_Missense_Mutation_p.R39C|TEX11_uc004dym.2_Missense_Mutation_p.R349C	p.R364C	NM_001003811	NP_001003811	Q8IYF3	TEX11_HUMAN			15	1252	-	Renal(35;0.156)		364					A8K8V6|Q5JQQ8|Q96LZ4|Q96M47|Q9BXU6	Missense_Mutation	SNP	ENST00000395889.2	37	c.1090C>T	CCDS35323.1	.	.	.	.	.	.	.	.	.	.	G	9.178	1.022825	0.19433	.	.	ENSG00000120498	ENST00000374333;ENST00000395889;ENST00000374320;ENST00000344304	T;T;T;T	0.50001	1.27;1.28;0.76;1.28	4.56	2.76	0.32466	.	0.393945	0.25848	N	0.027905	T	0.44008	0.1273	L	0.38175	1.15	0.09310	N	1	D;D	0.69078	0.996;0.997	P;P	0.54815	0.648;0.761	T	0.22871	-1.0204	9	.	.	.	-2.6515	4.8485	0.13524	0.1134:0.0:0.6774:0.2092	.	349;364	Q8IYF3-3;Q8IYF3	.;TEX11_HUMAN	C	349;364;39;364	ENSP00000363453:R349C;ENSP00000379226:R364C;ENSP00000363440:R39C;ENSP00000340995:R364C	.	R	-	1	0	TEX11	69819360	0.402000	0.25311	0.166000	0.22797	0.005000	0.04900	1.561000	0.36342	0.368000	0.24481	0.415000	0.27848	CGT		0.358	TEX11-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000359072.1		
FHL1	2273	broad.mit.edu	37	X	135291466	135291466	+	Silent	SNP	C	C	T			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chrX:135291466C>T	ENST00000345434.3	+	6	834	c.753C>T	c.(751-753)caC>caT	p.H251H	FHL1_ENST00000370690.3_Intron|FHL1_ENST00000370683.1_Intron|FHL1_ENST00000535737.1_Intron|FHL1_ENST00000394153.2_Intron|FHL1_ENST00000394155.2_Silent_p.H251H|FHL1_ENST00000370676.3_Intron|FHL1_ENST00000539015.1_Intron|FHL1_ENST00000543669.1_Intron			Q13642	FHL1_HUMAN	four and a half LIM domains 1	251					cell differentiation (GO:0030154)|muscle organ development (GO:0007517)|negative regulation of cell growth (GO:0030308)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of G2/M transition of mitotic cell cycle (GO:0010972)|organ morphogenesis (GO:0009887)|positive regulation of potassium ion transport (GO:0043268)|regulation of membrane depolarization (GO:0003254)|regulation of potassium ion transmembrane transporter activity (GO:1901016)	cytoplasm (GO:0005737)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ion channel binding (GO:0044325)|zinc ion binding (GO:0008270)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(3)|lung(10)|prostate(1)|upper_aerodigestive_tract(1)	19	Acute lymphoblastic leukemia(192;0.000127)					CAGTGTGCCACGGGAAACGCT	0.552											OREG0019943	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc004ezo.2																			0					0						c.(751-753)CAC>CAT		four and a half LIM domains 1 isoform 1							58.0	53.0	54.0					X																	135291466		1568	3582	5150	SO:0001819	synonymous_variant	2273				cell differentiation|cell growth|muscle organ development|organ morphogenesis	cytosol|nucleus|plasma membrane	protein binding|zinc ion binding	g.chrX:135291466C>T	U60115	CCDS14655.1, CCDS55505.1, CCDS55506.1, CCDS55507.1, CCDS76036.1	Xq26.3	2014-09-17			ENSG00000022267	ENSG00000022267			3702	protein-coding gene	gene with protein product	"""Four-and-a-half LIM domains 1"", ""LIM protein SLIMMER"""	300163				8753811, 9714789	Standard	NM_001449		Approved	SLIM1, KYO-T, bA535K18.1, FHL1B, XMPMA, FLH1A, MGC111107	uc004ezo.3	Q13642	OTTHUMG00000022504	ENST00000345434.3:c.753C>T	X.37:g.135291466C>T			OREG0019943	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	1617	FHL1_uc010nrz.2_Intron|FHL1_uc004ezm.2_Intron|FHL1_uc004ezl.2_Intron|FHL1_uc004ezq.2_Intron|FHL1_uc011mvy.1_Intron|FHL1_uc011mvz.1_Intron|FHL1_uc004ezn.2_Intron|FHL1_uc011mwa.1_Intron|FHL1_uc011mwb.1_Intron|FHL1_uc004ezp.2_Intron|FHL1_uc004ezr.2_Intron	p.H251H	NM_001159702	NP_001153174	Q13642	FHL1_HUMAN			6	853	+	Acute lymphoblastic leukemia(192;0.000127)		251					B7Z5T4|B7Z793|O95212|Q13230|Q13645|Q5JXI7|Q5M7Y6|Q6IB30|Q9NZ40|Q9UKZ8|Q9Y630	Silent	SNP	ENST00000345434.3	37	c.753C>T	CCDS55507.1																																																																																				0.552	FHL1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000058461.1	NM_001449	
SLITRK2	84631	broad.mit.edu	37	X	144905002	144905002	+	Silent	SNP	T	T	C			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chrX:144905002T>C	ENST00000370490.1	+	1	5314	c.1059T>C	c.(1057-1059)aaT>aaC	p.N353N	SLITRK2_ENST00000447897.2_Silent_p.N353N|SLITRK2_ENST00000428560.2_Silent_p.N353N|SLITRK2_ENST00000434188.2_Silent_p.N353N|SLITRK2_ENST00000413937.2_Silent_p.N353N			Q9H156	SLIK2_HUMAN	SLIT and NTRK-like family, member 2	353	LRRNT.				axonogenesis (GO:0007409)	integral component of membrane (GO:0016021)				NS(1)|breast(3)|central_nervous_system(1)|endometrium(9)|kidney(1)|large_intestine(17)|lung(40)|ovary(5)|pancreas(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)	86	Acute lymphoblastic leukemia(192;6.56e-05)					GCTCAGACAATGGTCTGAATG	0.493																																						uc004fcd.2																			0				ovary(5)|central_nervous_system(1)|pancreas(1)	7						c.(1057-1059)AAT>AAC		SLIT and NTRK-like family, member 2 precursor							68.0	63.0	64.0					X																	144905002		2203	4300	6503	SO:0001819	synonymous_variant	84631					integral to membrane		g.chrX:144905002T>C	Y19205	CCDS14680.1	Xq27.3	2008-02-05	2004-03-11		ENSG00000185985	ENSG00000185985			13449	protein-coding gene	gene with protein product		300561	"""slit-like 1 (Drosophila)"""	SLITL1		11347906, 14557068	Standard	NM_032539		Approved	KIAA1854, CXorf2	uc011mwr.2	Q9H156	OTTHUMG00000022595	ENST00000370490.1:c.1059T>C	X.37:g.144905002T>C						SLITRK2_uc010nsp.2_Silent_p.N353N|SLITRK2_uc010nso.2_Silent_p.N353N|SLITRK2_uc011mwq.1_Silent_p.N353N|SLITRK2_uc011mwr.1_Silent_p.N353N|SLITRK2_uc011mws.1_Silent_p.N353N|SLITRK2_uc004fcg.2_Silent_p.N353N|SLITRK2_uc011mwt.1_Silent_p.N353N	p.N353N	NM_032539	NP_115928	Q9H156	SLIK2_HUMAN			5	2049	+	Acute lymphoblastic leukemia(192;6.56e-05)		353			Extracellular (Potential).|LRRNT.		A8K117|Q2KHN3|Q5JXB1|Q8NBC7|Q96JH3	Silent	SNP	ENST00000370490.1	37	c.1059T>C	CCDS14680.1																																																																																				0.493	SLITRK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058633.1	NM_032539	
PLXNA3	55558	broad.mit.edu	37	X	153689599	153689599	+	Missense_Mutation	SNP	C	C	A			TCGA-06-5412-01A-01D-1696-08	TCGA-06-5412-10A-01D-1696-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	b6be0866-b8ae-4767-8cdc-e1dd4f78f440	4cb53c96-2d07-4a8e-9749-89a4d29acc17	g.chrX:153689599C>A	ENST00000369682.3	+	3	930	c.755C>A	c.(754-756)aCa>aAa	p.T252K		NM_017514.3	NP_059984.3	P51805	PLXA3_HUMAN	plexin A3	252	Sema. {ECO:0000255|PROSITE- ProRule:PRU00352}.				axon guidance (GO:0007411)|branchiomotor neuron axon guidance (GO:0021785)|facial nerve structural organization (GO:0021612)|hippocampus development (GO:0021766)|multicellular organismal development (GO:0007275)|negative chemotaxis (GO:0050919)|negative regulation of axon extension involved in axon guidance (GO:0048843)|positive regulation of cytoskeleton organization (GO:0051495)|pyramidal neuron development (GO:0021860)|semaphorin-plexin signaling pathway (GO:0071526)|semaphorin-plexin signaling pathway involved in axon guidance (GO:1902287)|trigeminal nerve structural organization (GO:0021637)	integral component of membrane (GO:0016021)|intracellular (GO:0005622)|membrane (GO:0016020)|plasma membrane (GO:0005886)|semaphorin receptor complex (GO:0002116)	semaphorin receptor activity (GO:0017154)|transmembrane signaling receptor activity (GO:0004888)			breast(2)|central_nervous_system(2)|cervix(2)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(26)|ovary(2)|prostate(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	48	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					CTGTTGGACACAGCGGGCGAG	0.567																																						uc004flm.2																			0				upper_aerodigestive_tract(1)|ovary(1)|central_nervous_system(1)	3						c.(754-756)ACA>AAA		plexin A3 precursor							107.0	91.0	96.0					X																	153689599		2203	4300	6503	SO:0001583	missense	55558				axon guidance	integral to membrane|intracellular|plasma membrane	transmembrane receptor activity	g.chrX:153689599C>A	X74609	CCDS14752.1	Xq28	2008-02-05			ENSG00000130827	ENSG00000130827		"""Plexins"""	9101	protein-coding gene	gene with protein product		300022		PLXN4		8248200, 8733135	Standard	NM_017514		Approved	SEX, XAP-6, 6.3, Plxn3	uc004flm.3	P51805	OTTHUMG00000033290	ENST00000369682.3:c.755C>A	X.37:g.153689599C>A	ENSP00000358696:p.Thr252Lys						p.T252K	NM_017514	NP_059984	P51805	PLXA3_HUMAN			3	928	+	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)		252			Sema.|Extracellular (Potential).		Q5HY36	Missense_Mutation	SNP	ENST00000369682.3	37	c.755C>A	CCDS14752.1	.	.	.	.	.	.	.	.	.	.	C	17.97	3.518917	0.64634	.	.	ENSG00000130827	ENST00000369682	T	0.00922	5.54	5.06	5.06	0.68205	WD40/YVTN repeat-like-containing domain (1);Semaphorin/CD100 antigen (4);	0.205157	0.42053	D	0.000774	T	0.01523	0.0049	L	0.39898	1.24	0.26149	N	0.980172	B	0.32245	0.361	B	0.35770	0.21	T	0.49399	-0.8944	10	0.44086	T	0.13	.	16.2001	0.82067	0.0:1.0:0.0:0.0	.	252	P51805	PLXA3_HUMAN	K	252	ENSP00000358696:T252K	ENSP00000358696:T252K	T	+	2	0	PLXNA3	153342793	0.969000	0.33509	0.837000	0.33122	0.976000	0.68499	4.800000	0.62524	2.343000	0.79666	0.529000	0.55759	ACA		0.567	PLXNA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000081634.1	NM_017514	
