#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
COL8A2	1296	broad.mit.edu	37	1	36565672	36565672	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr1:36565672C>T	ENST00000397799.1	-	3	396	c.172G>A	c.(172-174)Gag>Aag	p.E58K	COL8A2_ENST00000481785.1_Intron|COL8A2_ENST00000303143.4_Missense_Mutation_p.E58K			P25067	CO8A2_HUMAN	collagen, type VIII, alpha 2	58	Nonhelical region (NC2).				angiogenesis (GO:0001525)|camera-type eye morphogenesis (GO:0048593)|collagen catabolic process (GO:0030574)|epithelial cell proliferation (GO:0050673)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|single organismal cell-cell adhesion (GO:0016337)	basement membrane (GO:0005604)|collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)|protein binding, bridging (GO:0030674)			NS(2)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(1)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	17		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				CCTTTGCCCTCACGGAAGGGC	0.662											OREG0013361	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc001bzv.1																			0				central_nervous_system(1)	1						c.(172-174)GAG>AAG		collagen, type VIII, alpha 2 precursor							61.0	59.0	60.0					1																	36565672		2203	4300	6503	SO:0001583	missense	1296				angiogenesis|cell-cell adhesion|extracellular matrix organization	basement membrane|collagen	extracellular matrix structural constituent|protein binding, bridging	g.chr1:36565672C>T	M60832	CCDS403.1, CCDS72756.1	1p34.2-p32.3	2014-02-14			ENSG00000171812	ENSG00000171812		"""Collagens"""	2216	protein-coding gene	gene with protein product		120252		FECD		11689488	Standard	XM_005270477		Approved	PPCD, FECD1, PPCD2	uc001bzv.2	P25067	OTTHUMG00000007665	ENST00000397799.1:c.172G>A	1.37:g.36565672C>T	ENSP00000380901:p.Glu58Lys		OREG0013361	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	863	COL8A2_uc001bzw.1_Intron	p.E58K	NM_005202	NP_005193	P25067	CO8A2_HUMAN			1	179	-		Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)	58			Nonhelical region (NC2).		Q5JV31|Q8TEJ5	Missense_Mutation	SNP	ENST00000397799.1	37	c.172G>A	CCDS403.1	.	.	.	.	.	.	.	.	.	.	C	19.16	3.774202	0.69992	.	.	ENSG00000171812	ENST00000303143;ENST00000397799;ENST00000373172	D;D	0.91180	-2.8;-2.8	4.37	4.37	0.52481	.	0.122714	0.53938	D	0.000059	D	0.86990	0.6066	N	0.05050	-0.12	0.80722	D	1	D	0.63880	0.993	D	0.68192	0.956	T	0.82723	-0.0316	10	0.07325	T	0.83	.	14.8617	0.70387	0.0:1.0:0.0:0.0	.	58	P25067	CO8A2_HUMAN	K	58	ENSP00000305913:E58K;ENSP00000380901:E58K	ENSP00000305913:E58K	E	-	1	0	COL8A2	36338259	1.000000	0.71417	0.988000	0.46212	0.973000	0.67179	5.066000	0.64351	2.282000	0.76494	0.491000	0.48974	GAG		0.662	COL8A2-003	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313674.1	NM_005202	
CYP4A11	1579	broad.mit.edu	37	1	47406941	47406941	+	Silent	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr1:47406941G>A	ENST00000310638.4	-	1	196	c.165C>T	c.(163-165)ccC>ccT	p.P55P	CYP4A11_ENST00000457840.2_5'UTR|CYP4A11_ENST00000462347.1_Silent_p.P55P|CYP4A11_ENST00000371905.1_Silent_p.P55P|CYP4A11_ENST00000371904.4_Silent_p.P55P	NM_000778.3	NP_000769.2	Q02928	CP4AB_HUMAN	cytochrome P450, family 4, subfamily A, polypeptide 11	55					arachidonic acid metabolic process (GO:0019369)|cellular lipid metabolic process (GO:0044255)|epoxygenase P450 pathway (GO:0019373)|fatty acid metabolic process (GO:0006631)|leukotriene B4 catabolic process (GO:0036101)|leukotriene metabolic process (GO:0006691)|long-chain fatty acid metabolic process (GO:0001676)|omega-hydroxylase P450 pathway (GO:0097267)|oxidation-reduction process (GO:0055114)|positive regulation of icosanoid secretion (GO:0032305)|pressure natriuresis (GO:0003095)|renal water homeostasis (GO:0003091)|small molecule metabolic process (GO:0044281)|sodium ion homeostasis (GO:0055078)|xenobiotic metabolic process (GO:0006805)	apical plasma membrane (GO:0016324)|cytoplasm (GO:0005737)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)	alkane 1-monooxygenase activity (GO:0018685)|arachidonic acid epoxygenase activity (GO:0008392)|arachidonic acid omega-hydroxylase activity (GO:0052869)|heme binding (GO:0020037)|iron ion binding (GO:0005506)|leukotriene-B4 20-monooxygenase activity (GO:0050051)			endometrium(2)|kidney(5)|large_intestine(6)|lung(6)|ovary(5)|prostate(3)|skin(6)|soft_tissue(1)|upper_aerodigestive_tract(2)	36					Cisplatin(DB00515)|Clofibrate(DB00636)|Dexamethasone(DB01234)|Estrone(DB00655)|Ethanol(DB00898)|Lansoprazole(DB00448)|Pegvisomant(DB00082)|Pentamidine(DB00738)|Phenobarbital(DB01174)|Rifampicin(DB01045)|Tretinoin(DB00755)	GCCAGTGGGAGGGAGGGCACG	0.597																																						uc001cqp.3																			0				ovary(2)|skin(2)	4						c.(163-165)CCC>CCT		cytochrome P450, family 4, subfamily A,	NADH(DB00157)						64.0	57.0	59.0					1																	47406941		2203	4298	6501	SO:0001819	synonymous_variant	1579				long-chain fatty acid metabolic process|xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	alkane 1-monooxygenase activity|electron carrier activity|heme binding|oxygen binding	g.chr1:47406941G>A	L04751	CCDS543.1	1p33	2008-02-05	2003-01-14		ENSG00000187048	ENSG00000187048		"""Cytochrome P450s"""	2642	protein-coding gene	gene with protein product		601310	"""cytochrome P450, subfamily IVA, polypeptide 11"""	CYP4A2		7679927	Standard	NM_000778		Approved	CYP4AII	uc001cqp.4	Q02928	OTTHUMG00000008020	ENST00000310638.4:c.165C>T	1.37:g.47406941G>A						CYP4A11_uc001cqq.2_Silent_p.P55P|CYP4A11_uc010omm.1_RNA	p.P55P	NM_000778	NP_000769	Q02928	CP4AB_HUMAN			1	216	-			55					Q06766|Q16865|Q16866|Q5VSP8|Q86SU6|Q8IWY5	Silent	SNP	ENST00000310638.4	37	c.165C>T	CCDS543.1																																																																																				0.597	CYP4A11-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000022022.1	NM_000778	
LHX8	431707	broad.mit.edu	37	1	75614357	75614357	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr1:75614357G>A	ENST00000294638.5	+	8	1464	c.800G>A	c.(799-801)cGt>cAt	p.R267H	LHX8_ENST00000356261.3_Missense_Mutation_p.R257H	NM_001001933.1	NP_001001933.1	Q68G74	LHX8_HUMAN	LIM homeobox 8	267					female gonad development (GO:0008585)|forebrain neuron development (GO:0021884)|learning or memory (GO:0007611)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	female germ cell nucleus (GO:0001674)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)			NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(4)|lung(18)|ovary(3)|urinary_tract(1)	30						TTGAGCAGACGTGTGATACAG	0.383																																						uc001dgo.2																			0				ovary(3)	3						c.(799-801)CGT>CAT		LIM homeobox 8							157.0	153.0	154.0					1																	75614357		2203	4300	6503	SO:0001583	missense	431707					nucleus	sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr1:75614357G>A	AB050476	CCDS30756.1, CCDS58008.1	1p31.1	2011-06-20			ENSG00000162624	ENSG00000162624		"""Homeoboxes / LIM class"""	28838	protein-coding gene	gene with protein product		604425				9598319	Standard	NM_001256114		Approved	Lhx7	uc031pmx.1	Q68G74	OTTHUMG00000009692	ENST00000294638.5:c.800G>A	1.37:g.75614357G>A	ENSP00000294638:p.Arg267His					LHX8_uc001dgq.2_Missense_Mutation_p.R206H	p.R267H	NM_001001933	NP_001001933	Q68G74	LHX8_HUMAN			8	1464	+			267			Homeobox.		E9PGE3	Missense_Mutation	SNP	ENST00000294638.5	37	c.800G>A	CCDS30756.1	.	.	.	.	.	.	.	.	.	.	G	31	5.089784	0.94149	.	.	ENSG00000162624	ENST00000294638;ENST00000356261	D;D	0.96802	-4.13;-4.13	5.55	5.55	0.83447	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);Homeobox, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.98400	0.9468	M	0.87456	2.885	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98922	1.0784	10	0.87932	D	0	.	19.8575	0.96767	0.0:0.0:1.0:0.0	.	267	Q68G74	LHX8_HUMAN	H	267;257	ENSP00000294638:R267H;ENSP00000348597:R257H	ENSP00000294638:R267H	R	+	2	0	LHX8	75386945	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.439000	0.97543	2.767000	0.95098	0.563000	0.77884	CGT		0.383	LHX8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000026700.1	NM_001001933	
MCOLN2	255231	broad.mit.edu	37	1	85422200	85422200	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr1:85422200C>T	ENST00000370608.3	-	4	546	c.479G>A	c.(478-480)gGc>gAc	p.G160D	MCOLN2_ENST00000284027.5_Missense_Mutation_p.G132D|MCOLN2_ENST00000531325.1_5'UTR	NM_153259.2	NP_694991.2	Q8IZK6	MCLN2_HUMAN	mucolipin 2	160					calcium ion transmembrane transport (GO:0070588)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)	18				all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)		GACTTTTAAGCCAATTCTATT	0.373																																						uc001dkm.2																			0				ovary(3)|upper_aerodigestive_tract(1)	4						c.(478-480)GGC>GAC		mucolipin 2							213.0	205.0	208.0					1																	85422200		2203	4300	6503	SO:0001583	missense	255231					integral to membrane	ion channel activity	g.chr1:85422200C>T	AK094010	CCDS30762.1	1p22	2011-12-16			ENSG00000153898	ENSG00000153898		"""Voltage-gated ion channels / Transient receptor potential cation channels"""	13357	protein-coding gene	gene with protein product		607399				16382100	Standard	XM_005270719		Approved	TRPML2, FLJ36691, TRP-ML2	uc001dkm.3	Q8IZK6	OTTHUMG00000009954	ENST00000370608.3:c.479G>A	1.37:g.85422200C>T	ENSP00000359640:p.Gly160Asp					MCOLN2_uc001dkn.2_RNA	p.G160D	NM_153259	NP_694991	Q8IZK6	MCLN2_HUMAN		all cancers(265;0.0111)|Epithelial(280;0.0263)|OV - Ovarian serous cystadenocarcinoma(397;0.217)	4	720	-			160					A6NI99|Q2M3I6|Q5TAG5|Q8N9R3	Missense_Mutation	SNP	ENST00000370608.3	37	c.479G>A	CCDS30762.1	.	.	.	.	.	.	.	.	.	.	C	14.22	2.470862	0.43942	.	.	ENSG00000153898	ENST00000370608;ENST00000284027	T;T	0.61158	0.13;0.13	5.16	4.24	0.50183	.	0.178876	0.49916	D	0.000138	T	0.52948	0.1766	M	0.73598	2.24	0.49687	D	0.999819	D	0.54047	0.964	P	0.46629	0.522	T	0.60772	-0.7197	10	0.49607	T	0.09	-40.8037	15.652	0.77104	0.0:0.862:0.138:0.0	.	160	Q8IZK6	MCLN2_HUMAN	D	160;132	ENSP00000359640:G160D;ENSP00000284027:G132D	ENSP00000284027:G132D	G	-	2	0	MCOLN2	85194788	0.997000	0.39634	1.000000	0.80357	0.992000	0.81027	1.130000	0.31393	1.290000	0.44636	0.650000	0.86243	GGC		0.373	MCOLN2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000027567.2	NM_153259	
COL24A1	255631	broad.mit.edu	37	1	86289377	86289379	+	In_Frame_Del	DEL	TTG	TTG	-			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr1:86289377_86289379delTTG	ENST00000370571.2	-	44	4090_4092	c.3724_3726delCAA	c.(3724-3726)caadel	p.Q1242del	COL24A1_ENST00000436319.1_In_Frame_Del_p.Q1242del	NM_152890.5	NP_690850.2	Q17RW2	COOA1_HUMAN	collagen, type XXIV, alpha 1	1242	Collagen-like 13.				extracellular matrix organization (GO:0030198)|hematopoietic progenitor cell differentiation (GO:0002244)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix structural constituent (GO:0005201)			NS(3)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(9)|liver(1)|lung(56)|ovary(4)|prostate(2)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	101				all cancers(265;0.0627)|Epithelial(280;0.0689)		CTGGGGGTCCTTGTTGTCCAGTG	0.34																																						uc001dlj.2																			0				ovary(3)|central_nervous_system(1)|skin(1)	5						c.(3724-3726)CAAdel		collagen, type XXIV, alpha 1 precursor																																				SO:0001651	inframe_deletion	255631				cell adhesion	collagen	extracellular matrix structural constituent	g.chr1:86289377_86289379delTTG	AF410793	CCDS41353.1	1p22.3-p22.2	2013-01-16			ENSG00000171502	ENSG00000171502		"""Collagens"""	20821	protein-coding gene	gene with protein product		610025					Standard	NM_152890		Approved		uc001dlj.3	Q17RW2	OTTHUMG00000010629	ENST00000370571.2:c.3724_3726delCAA	1.37:g.86289380_86289382delTTG	ENSP00000359603:p.Gln1242del					COL24A1_uc001dli.2_In_Frame_Del_p.Q378del|COL24A1_uc010osd.1_In_Frame_Del_p.Q542del|COL24A1_uc001dlk.2_RNA|COL24A1_uc010ose.1_RNA|COL24A1_uc010osf.1_RNA	p.Q1242del	NM_152890	NP_690850	Q17RW2	COOA1_HUMAN		all cancers(265;0.0627)|Epithelial(280;0.0689)	44	3766_3768	-			1242			Collagen-like 13.		C9J1X6|Q14BD7|Q59EX5|Q5VY50|Q7Z5L5	In_Frame_Del	DEL	ENST00000370571.2	37	c.3724_3726delCAA	CCDS41353.1																																																																																				0.340	COL24A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029335.4	NM_152890	
NBPF10	100132406	broad.mit.edu	37	1	145367767	145367767	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr1:145367767G>A	ENST00000342960.5	+	83	10398	c.10363G>A	c.(10363-10365)Gaa>Aaa	p.E3455K	NBPF10_ENST00000369339.3_Intron|NBPF10_ENST00000369338.1_Intron	NM_001039703.4	NP_001034792.4	Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	755						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.E3455K(5)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		atcaaagaaggaaagaagaag	0.423																																						uc001end.3																			5	Substitution - Missense(5)		skin(2)|urinary_tract(1)|kidney(1)|central_nervous_system(1)		0						c.(10588-10590)GAA>AAA		hypothetical protein LOC100132406																																				SO:0001583	missense	100132406							g.chr1:145367767G>A	BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000342960.5:c.10363G>A	1.37:g.145367767G>A	ENSP00000345684:p.Glu3455Lys					NBPF9_uc010oye.1_Intron|NBPF10_uc001emp.3_Intron|NBPF10_uc010oyi.1_Intron|NBPF10_uc010oyk.1_Intron|NBPF10_uc010oyl.1_Intron	p.E3530K	NM_001039703	NP_001034792	A6NDV3	A6NDV3_HUMAN		Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)	85	10623	+	all_hematologic(923;0.032)		3455					Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000342960.5	37	c.10588G>A	CCDS53355.1	.	.	.	.	.	.	.	.	.	.	.	0.008	-1.929795	0.00488	.	.	ENSG00000163386	ENST00000369339;ENST00000342960	T	0.02552	4.25	.	.	.	.	.	.	.	.	T	0.00784	0.0026	L	0.51422	1.61	0.09310	N	1	.	.	.	.	.	.	T	0.46162	-0.9211	4	0.02654	T	1	.	.	.	.	.	.	.	.	K	575;3455	ENSP00000345684:E3455K	ENSP00000345684:E3455K	E	+	1	0	NBPF10	144079124	0.039000	0.19947	.	.	.	.	0.000000	0.12993	.	.	.	.	GAA		0.423	NBPF10-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		NM_001039703	
ACP6	51205	broad.mit.edu	37	1	147131584	147131584	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr1:147131584C>T	ENST00000369238.6	-	3	853	c.406G>A	c.(406-408)Gga>Aga	p.G136R	ACP6_ENST00000392988.2_Missense_Mutation_p.G136R	NM_016361.3	NP_057445.4	Q9NPH0	PPA6_HUMAN	acid phosphatase 6, lysophosphatidic	136	Substrate binding. {ECO:0000250}.				dephosphorylation (GO:0016311)|lysobisphosphatidic acid metabolic process (GO:2001311)|phospholipid metabolic process (GO:0006644)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	acid phosphatase activity (GO:0003993)|lysophosphatidic acid phosphatase activity (GO:0052642)			breast(1)|cervix(2)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)|ovary(4)|prostate(1)	16	all_hematologic(923;0.0276)					AGTCTCTCTCCCAAGGCAAAC	0.483																																						uc001epr.2																			0				ovary(4)	4						c.(406-408)GGA>AGA		acid phosphatase 6, lysophosphatidic precursor							122.0	111.0	115.0					1																	147131584		2203	4300	6503	SO:0001583	missense	51205				lipid metabolic process	extracellular region|mitochondrion	acid phosphatase activity|protein binding	g.chr1:147131584C>T	BC009965	CCDS928.1	1q21	2008-02-05			ENSG00000162836	ENSG00000162836			29609	protein-coding gene	gene with protein product		611471				12010880, 10506173	Standard	NM_016361		Approved	LPAP, ACPL1	uc001epr.2	Q9NPH0	OTTHUMG00000014019	ENST00000369238.6:c.406G>A	1.37:g.147131584C>T	ENSP00000358241:p.Gly136Arg					ACP6_uc009wjj.1_Missense_Mutation_p.G93R	p.G136R	NM_016361	NP_057445	Q9NPH0	PPA6_HUMAN			3	870	-	all_hematologic(923;0.0276)		136					Q59G61|Q5T490|Q6IAQ3|Q7LG81|Q9UIG6	Missense_Mutation	SNP	ENST00000369238.6	37	c.406G>A	CCDS928.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.648756	0.87958	.	.	ENSG00000162836	ENST00000369238;ENST00000392988	D;D	0.86497	-2.13;-2.13	5.66	5.66	0.87406	.	0.000000	0.85682	D	0.000000	D	0.95098	0.8412	M	0.92317	3.295	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.95583	0.8648	10	0.87932	D	0	.	19.7559	0.96291	0.0:1.0:0.0:0.0	.	136;136	Q9NPH0-2;Q9NPH0	.;PPA6_HUMAN	R	136	ENSP00000358241:G136R;ENSP00000376714:G136R	ENSP00000358241:G136R	G	-	1	0	ACP6	145598208	1.000000	0.71417	1.000000	0.80357	0.735000	0.41995	7.015000	0.76387	2.656000	0.90262	0.655000	0.94253	GGA		0.483	ACP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039420.2	NM_016361	
FLG	2312	broad.mit.edu	37	1	152275520	152275520	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr1:152275520C>A	ENST00000368799.1	-	3	11877	c.11842G>T	c.(11842-11844)Ggc>Tgc	p.G3948C	FLG-AS1_ENST00000420707.1_RNA|FLG-AS1_ENST00000593011.1_RNA	NM_002016.1	NP_002007.1	P20930	FILA_HUMAN	filaggrin	3948	Ser-rich.				establishment of skin barrier (GO:0061436)|keratinocyte differentiation (GO:0030216)|multicellular organismal development (GO:0007275)	cytoplasmic membrane-bounded vesicle (GO:0016023)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	calcium ion binding (GO:0005509)|structural molecule activity (GO:0005198)			autonomic_ganglia(1)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(38)|haematopoietic_and_lymphoid_tissue(1)|kidney(16)|large_intestine(57)|lung(211)|ovary(13)|pancreas(1)|prostate(15)|skin(24)|stomach(5)|upper_aerodigestive_tract(10)|urinary_tract(12)	424	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		LUSC - Lung squamous cell carcinoma(543;0.206)			TGAGGACTGCCACGTGACTGT	0.438									Ichthyosis																													uc001ezu.1																			0				ovary(9)|skin(4)|upper_aerodigestive_tract(3)	16						c.(11842-11844)GGC>TGC		filaggrin							150.0	140.0	143.0					1																	152275520		2203	4300	6503	SO:0001583	missense	2312	Ichthyosis	Familial Cancer Database	X-linked Ichthyosis, Steroid Sulfatase Deficiency, Ichthyosis Vulgaris	keratinocyte differentiation	cytoplasmic membrane-bounded vesicle|intermediate filament	calcium ion binding|structural molecule activity	g.chr1:152275520C>A	XM_048104	CCDS30860.1	1q21.3	2013-01-10			ENSG00000143631	ENSG00000143631		"""EF-hand domain containing"""	3748	protein-coding gene	gene with protein product		135940				2740331, 2248957, 16444271	Standard	NM_002016		Approved		uc001ezu.1	P20930	OTTHUMG00000012202	ENST00000368799.1:c.11842G>T	1.37:g.152275520C>A	ENSP00000357789:p.Gly3948Cys						p.G3948C	NM_002016	NP_002007	P20930	FILA_HUMAN	LUSC - Lung squamous cell carcinoma(543;0.206)		3	11878	-	Hepatocellular(266;0.0877)|Melanoma(130;0.116)|all_hematologic(923;0.127)		3948			Ser-rich.		Q01720|Q5T583|Q9UC71	Missense_Mutation	SNP	ENST00000368799.1	37	c.11842G>T	CCDS30860.1	.	.	.	.	.	.	.	.	.	.	C	2.382	-0.341837	0.05243	.	.	ENSG00000143631	ENST00000368799	T	0.00873	5.59	2.39	-4.77	0.03219	.	.	.	.	.	T	0.00271	0.0008	L	0.36672	1.1	0.09310	N	1	B	0.21309	0.054	B	0.15870	0.014	T	0.41179	-0.9523	9	0.52906	T	0.07	.	2.7928	0.05393	0.34:0.237:0.0:0.4229	.	3948	P20930	FILA_HUMAN	C	3948	ENSP00000357789:G3948C	ENSP00000357789:G3948C	G	-	1	0	FLG	150542144	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-2.067000	0.01383	-1.807000	0.01236	-1.506000	0.00953	GGC		0.438	FLG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033742.1	NM_002016	
SH2D1B	117157	broad.mit.edu	37	1	162368720	162368720	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr1:162368720G>A	ENST00000367929.2	-	3	465	c.356C>T	c.(355-357)aCa>aTa	p.T119I	SH2D1B_ENST00000359567.3_Intron	NM_053282.4	NP_444512.2	O14796	SH21B_HUMAN	SH2 domain containing 1B	119					leukocyte activation involved in immune response (GO:0002366)|negative regulation of natural killer cell mediated cytotoxicity (GO:0045953)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of innate immune response (GO:0045089)|positive regulation of natural killer cell mediated cytotoxicity (GO:0045954)|positive regulation of natural killer cell mediated immunity (GO:0002717)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|regulation of natural killer cell activation (GO:0032814)	intracellular (GO:0005622)	protein binding, bridging (GO:0030674)			kidney(1)|large_intestine(1)|lung(4)|pancreas(1)	7	all_hematologic(112;0.115)		BRCA - Breast invasive adenocarcinoma(70;0.126)			TACCACAAATGTTTCCAACTC	0.393																																						uc001gbz.1																			0				pancreas(1)	1						c.(355-357)ACA>ATA		SH2 domain containing 1B							85.0	80.0	82.0					1																	162368720		2203	4300	6503	SO:0001583	missense	117157							g.chr1:162368720G>A	AF484964	CCDS30928.1	1q23.3	2013-02-14			ENSG00000198574	ENSG00000198574		"""SH2 domain containing"""	30416	protein-coding gene	gene with protein product		608510				9000139, 11689425	Standard	NM_053282		Approved	EAT2	uc001gbz.1	O14796	OTTHUMG00000031377	ENST00000367929.2:c.356C>T	1.37:g.162368720G>A	ENSP00000356906:p.Thr119Ile					SH2D1B_uc001gca.1_Intron	p.T119I	NM_053282	NP_444512	O14796	SH21B_HUMAN	BRCA - Breast invasive adenocarcinoma(70;0.126)		3	478	-	all_hematologic(112;0.115)		119					B2RBN6|Q5T0L1|Q8NI18|Q969K9	Missense_Mutation	SNP	ENST00000367929.2	37	c.356C>T	CCDS30928.1	.	.	.	.	.	.	.	.	.	.	G	6.253	0.414874	0.11870	.	.	ENSG00000198574	ENST00000367929	T	0.81163	-1.46	4.47	0.489	0.16854	.	2.144800	0.03176	N	0.171360	T	0.36166	0.0957	N	0.04508	-0.205	0.22684	N	0.99886	B	0.06786	0.001	B	0.04013	0.001	T	0.22836	-1.0205	9	0.32370	T	0.25	-53.2558	3.0729	0.06236	0.4144:0.2418:0.3439:0.0	.	119	O14796	SH21B_HUMAN	I	119	ENSP00000356906:T119I	ENSP00000356906:T119I	T	-	2	0	SH2D1B	160635344	0.000000	0.05858	0.001000	0.08648	0.018000	0.09664	-0.480000	0.06559	0.322000	0.23283	0.655000	0.94253	ACA		0.393	SH2D1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076794.1	NM_053282	
MYOC	4653	broad.mit.edu	37	1	171621317	171621317	+	Silent	SNP	G	G	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr1:171621317G>T	ENST00000037502.6	-	1	506	c.435C>A	c.(433-435)ctC>ctA	p.L145L		NM_000261.1	NP_000252.1	Q99972	MYOC_HUMAN	myocilin, trabecular meshwork inducible glucocorticoid response	145					bone development (GO:0060348)|clustering of voltage-gated sodium channels (GO:0045162)|ERBB2-ERBB3 signaling pathway (GO:0038133)|myelination in peripheral nervous system (GO:0022011)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of Rho protein signal transduction (GO:0035024)|negative regulation of stress fiber assembly (GO:0051497)|neuron projection development (GO:0031175)|non-canonical Wnt signaling pathway via JNK cascade (GO:0038031)|osteoblast differentiation (GO:0001649)|positive regulation of cell migration (GO:0030335)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of mitochondrial depolarization (GO:0051901)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of stress fiber assembly (GO:0051496)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of MAPK cascade (GO:0043408)|skeletal muscle hypertrophy (GO:0014734)	cilium (GO:0005929)|cytoplasmic vesicle (GO:0031410)|endoplasmic reticulum (GO:0005783)|extracellular matrix (GO:0031012)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial outer membrane (GO:0005741)|node of Ranvier (GO:0033268)|proteinaceous extracellular matrix (GO:0005578)	fibronectin binding (GO:0001968)|frizzled binding (GO:0005109)|myosin light chain binding (GO:0032027)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|prostate(1)|urinary_tract(2)	28	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)					TGTCTCGGAGGAGGTTGCTGT	0.577																																						uc001ghu.2																			0				lung(1)	1						c.(433-435)CTC>CTA		myocilin precursor							119.0	130.0	126.0					1																	171621317		2203	4300	6503	SO:0001819	synonymous_variant	4653				anatomical structure morphogenesis	cilium|extracellular space|rough endoplasmic reticulum	structural molecule activity	g.chr1:171621317G>T	BC029261	CCDS1297.1	1q23-q24	2008-02-05			ENSG00000034971	ENSG00000034971			7610	protein-coding gene	gene with protein product		601652		GLC1A		9169133, 9005853	Standard	NM_000261		Approved	TIGR, JOAG1	uc001ghu.3	Q99972	OTTHUMG00000034789	ENST00000037502.6:c.435C>A	1.37:g.171621317G>T						MYOC_uc010pmk.1_Silent_p.L87L	p.L145L	NM_000261	NP_000252	Q99972	MYOC_HUMAN			1	457	-	all_cancers(6;5.47e-10)|all_hematologic(923;0.088)|Acute lymphoblastic leukemia(37;0.181)		145			Potential.		B2RD84|O00620|Q7Z6Q9	Silent	SNP	ENST00000037502.6	37	c.435C>A	CCDS1297.1																																																																																				0.577	MYOC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084178.2	NM_000261	
RBBP5	5929	broad.mit.edu	37	1	205065948	205065948	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr1:205065948G>A	ENST00000264515.6	-	12	1399	c.1258C>T	c.(1258-1260)Ccg>Tcg	p.P420S	RBBP5_ENST00000367164.1_Missense_Mutation_p.P420S	NM_001193273.1|NM_005057.3	NP_001180202.1|NP_005048.2	Q15291	RBBP5_HUMAN	retinoblastoma binding protein 5	420					cellular response to DNA damage stimulus (GO:0006974)|histone H3-K4 methylation (GO:0051568)|regulation of transcription, DNA-templated (GO:0006355)|response to estrogen (GO:0043627)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|MLL1 complex (GO:0071339)|nucleolus (GO:0005730)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	methylated histone binding (GO:0035064)|transcription regulatory region DNA binding (GO:0044212)			cervix(1)|kidney(3)|large_intestine(4)|lung(14)|ovary(1)|pancreas(1)|prostate(2)|upper_aerodigestive_tract(1)	27	Breast(84;0.0505)		BRCA - Breast invasive adenocarcinoma(75;0.0923)			ACTGCATCCGGTGGGGGGCCG	0.498																																						uc001hbu.1																			0				lung(1)	1						c.(1258-1260)CCG>TCG		retinoblastoma binding protein 5							122.0	129.0	126.0					1																	205065948		2203	4300	6503	SO:0001583	missense	5929				histone H3-K4 methylation|regulation of transcription, DNA-dependent|response to estrogen stimulus|transcription, DNA-dependent	MLL1 complex|Set1C/COMPASS complex	methylated histone residue binding|transcription regulatory region DNA binding	g.chr1:205065948G>A	BC053856	CCDS30983.1, CCDS53463.1	1q32	2013-01-10	2001-11-28		ENSG00000117222	ENSG00000117222		"""WD repeat domain containing"""	9888	protein-coding gene	gene with protein product	"""SWD1, Set1c WD40 repeat protein, homolog (S. cerevisiae)"""	600697	"""retinoblastoma-binding protein 5"""			7558034	Standard	NM_005057		Approved	RBQ3, SWD1	uc001hbu.2	Q15291	OTTHUMG00000037104	ENST00000264515.6:c.1258C>T	1.37:g.205065948G>A	ENSP00000264515:p.Pro420Ser					RBBP5_uc010prd.1_Missense_Mutation_p.P455S|RBBP5_uc001hbv.1_Missense_Mutation_p.P420S|RBBP5_uc010pre.1_Missense_Mutation_p.P287S	p.P420S	NM_005057	NP_005048	Q15291	RBBP5_HUMAN	BRCA - Breast invasive adenocarcinoma(75;0.0923)		12	1388	-	Breast(84;0.0505)		420					A8K272|Q7Z6D8|Q8NDZ7	Missense_Mutation	SNP	ENST00000264515.6	37	c.1258C>T	CCDS30983.1	.	.	.	.	.	.	.	.	.	.	G	15.66	2.900551	0.52227	.	.	ENSG00000117222	ENST00000264515;ENST00000367164	T;T	0.57595	0.39;0.42	5.77	5.77	0.91146	.	0.000000	0.85682	D	0.000000	T	0.41926	0.1180	L	0.40543	1.245	0.80722	D	1	P;B;B;P	0.36990	0.519;0.06;0.037;0.577	B;B;B;B	0.31495	0.131;0.022;0.017;0.085	T	0.35500	-0.9786	10	0.07813	T	0.8	.	19.59	0.95506	0.0:0.0:1.0:0.0	.	293;455;420;420	B4DLF8;B4DMM7;Q15291-2;Q15291	.;.;.;RBBP5_HUMAN	S	420	ENSP00000264515:P420S;ENSP00000356132:P420S	ENSP00000264515:P420S	P	-	1	0	RBBP5	203332571	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.443000	0.97568	2.727000	0.93392	0.655000	0.94253	CCG		0.498	RBBP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090077.1	NM_005057	
SYT14	255928	broad.mit.edu	37	1	210267700	210267700	+	Missense_Mutation	SNP	C	C	T	rs77686387	byFrequency	TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr1:210267700C>T	ENST00000472886.1	+	5	490	c.476C>T	c.(475-477)cCg>cTg	p.P159L	SYT14_ENST00000422431.1_Missense_Mutation_p.P204L|SYT14_ENST00000537238.1_Missense_Mutation_p.P121L|SYT14_ENST00000399639.2_Missense_Mutation_p.P159L|SYT14_ENST00000367015.1_Missense_Mutation_p.P121L|SYT14_ENST00000534859.1_Missense_Mutation_p.P159L|SYT14_ENST00000367019.1_Missense_Mutation_p.P159L|SYT14_ENST00000271745.7_3'UTR			Q8NB59	SYT14_HUMAN	synaptotagmin XIV	159					cell death (GO:0008219)	integral component of membrane (GO:0016021)	phospholipid binding (GO:0005543)			endometrium(4)|large_intestine(11)|lung(17)|ovary(1)|prostate(1)|skin(3)	37				OV - Ovarian serous cystadenocarcinoma(81;0.085)		AGAACACCCCCGCTGGATGAA	0.428													C|||	11	0.00219649	0.0	0.0	5008	,	,		17284	0.0089		0.001	False		,,,				2504	0.001					uc009xcv.2																			0				ovary(1)|skin(1)	2						c.(475-477)CCG>CTG		synaptotagmin XIV isoform 4		C	LEU/PRO,LEU/PRO,LEU/PRO,LEU/PRO	0,4406		0,0,2203	75.0	79.0	78.0		611,476,611,476	5.6	1.0	1	dbSNP_132	78	2,8598	2.2+/-6.3	0,2,4298	yes	missense,missense,missense,missense	SYT14	NM_001146261.1,NM_001146262.1,NM_001146264.1,NM_153262.2	98,98,98,98	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	probably-damaging,probably-damaging,probably-damaging,probably-damaging	204/620,159/575,204/601,159/556	210267700	2,13004	2203	4300	6503	SO:0001583	missense	255928					integral to membrane		g.chr1:210267700C>T	AK091517	CCDS31014.1, CCDS53470.1, CCDS58058.1	1q32.2	2013-01-21			ENSG00000143469	ENSG00000143469		"""Synaptotagmins"""	23143	protein-coding gene	gene with protein product		610949					Standard	NM_001256006		Approved	sytXIV, FLJ34198	uc001hhs.5	Q8NB59	OTTHUMG00000036652	ENST00000472886.1:c.476C>T	1.37:g.210267700C>T	ENSP00000418901:p.Pro159Leu					SYT14_uc001hhs.3_Missense_Mutation_p.P204L|SYT14_uc001hht.3_Missense_Mutation_p.P159L|SYT14_uc001hhu.3_RNA|SYT14_uc010psn.1_Missense_Mutation_p.P204L|SYT14_uc010pso.1_Missense_Mutation_p.P121L	p.P159L	NM_153262	NP_694994	Q8NB59	SYT14_HUMAN		OV - Ovarian serous cystadenocarcinoma(81;0.085)	5	548	+			159			Cytoplasmic (Potential).		B1AJU0|B1AJU1|F5H426|Q5THX7|Q707N3|Q707N4|Q707N5|Q707N6|Q707N7	Missense_Mutation	SNP	ENST00000472886.1	37	c.476C>T	CCDS31014.1	4	0.0018315018315018315	0	0.0	0	0.0	3	0.005244755244755245	1	0.0013192612137203166	C	26.1	4.708507	0.89018	0.0	2.33E-4	ENSG00000143469	ENST00000422431;ENST00000534859;ENST00000399639;ENST00000537238;ENST00000367019;ENST00000472886;ENST00000367015	T;T;T;T;T;T;T	0.17854	3.39;3.25;2.25;3.53;3.26;3.52;3.53	5.62	5.62	0.85841	.	0.113614	0.64402	D	0.000011	T	0.20414	0.0491	M	0.61703	1.905	0.80722	D	1	P;B;D;D	0.62365	0.875;0.035;0.989;0.991	B;B;P;P	0.49708	0.083;0.004;0.477;0.62	T	0.01652	-1.1303	10	0.17832	T	0.49	-12.6577	17.813	0.88622	0.0:1.0:0.0:0.0	.	187;159;159;204	A1L3Y1;Q8NB59;Q8NB59-6;F5H426	.;SYT14_HUMAN;.;.	L	204;159;159;121;159;159;121	ENSP00000389039:P204L;ENSP00000442891:P159L;ENSP00000445837:P159L;ENSP00000437423:P121L;ENSP00000355986:P159L;ENSP00000418901:P159L;ENSP00000355982:P121L	ENSP00000355982:P121L	P	+	2	0	SYT14	208334323	1.000000	0.71417	0.998000	0.56505	0.984000	0.73092	5.608000	0.67654	2.650000	0.89964	0.591000	0.81541	CCG		0.428	SYT14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089124.1	NM_153262	
MPP7	143098	broad.mit.edu	37	10	28420514	28420514	+	Missense_Mutation	SNP	C	C	T	rs200656300		TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr10:28420514C>T	ENST00000375732.1	-	6	681	c.422G>A	c.(421-423)cGt>cAt	p.R141H	MPP7_ENST00000540098.1_Missense_Mutation_p.R141H|MPP7_ENST00000375719.3_Missense_Mutation_p.R141H|MPP7_ENST00000445954.2_Missense_Mutation_p.R16H|MPP7_ENST00000337532.5_Missense_Mutation_p.R141H|MPP7_ENST00000481244.1_5'UTR			Q5T2T1	MPP7_HUMAN	membrane protein, palmitoylated 7 (MAGUK p55 subfamily member 7)	141	PDZ. {ECO:0000255|PROSITE- ProRule:PRU00143}.				establishment of cell polarity (GO:0030010)|positive regulation of protein complex assembly (GO:0031334)|positive regulation of signal transduction (GO:0009967)|protein localization to adherens junction (GO:0071896)|tight junction assembly (GO:0070830)	adherens junction (GO:0005912)|cell junction (GO:0030054)|mitochondrion (GO:0005739)|MPP7-DLG1-LIN7 complex (GO:0097025)|tight junction (GO:0005923)	protein complex scaffold (GO:0032947)|protein domain specific binding (GO:0019904)|protein heterodimerization activity (GO:0046982)|signaling adaptor activity (GO:0035591)	p.R141H(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(4)|lung(8)|ovary(1)|skin(1)|stomach(1)	22						TTTGACCAGACGGATTATTTT	0.423																																						uc001iua.1																			1	Substitution - Missense(1)		endometrium(1)	ovary(1)	1						c.(421-423)CGT>CAT		palmitoylated membrane protein 7		C	HIS/ARG	0,4406		0,0,2203	133.0	121.0	125.0		422	5.7	1.0	10		125	1,8599	1.2+/-3.3	0,1,4299	no	missense	MPP7	NM_173496.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	141/577	28420514	1,13005	2203	4300	6503	SO:0001583	missense	143098				establishment of cell polarity|positive regulation of protein complex assembly|protein localization to adherens junction|tight junction assembly	MPP7-DLG1-LIN7 complex|tight junction	protein complex scaffold|protein domain specific binding|protein heterodimerization activity|signaling adaptor activity	g.chr10:28420514C>T	BC038105	CCDS7158.1	10p12.1	2004-01-15			ENSG00000150054	ENSG00000150054			26542	protein-coding gene	gene with protein product		610973				14719143	Standard	NM_173496		Approved	FLJ32798	uc001iua.1	Q5T2T1	OTTHUMG00000017868	ENST00000375732.1:c.422G>A	10.37:g.28420514C>T	ENSP00000364884:p.Arg141His					MPP7_uc009xkz.1_RNA|MPP7_uc001iub.1_Missense_Mutation_p.R141H|MPP7_uc009xla.2_Missense_Mutation_p.R141H|MPP7_uc010qdv.1_RNA	p.R141H	NM_173496	NP_775767	Q5T2T1	MPP7_HUMAN			8	826	-			141			PDZ.		B2RCC9|B4DWL9|B5MDZ3|D3DRW3|Q5T2T0|Q8IY28	Missense_Mutation	SNP	ENST00000375732.1	37	c.422G>A	CCDS7158.1	.	.	.	.	.	.	.	.	.	.	C	33	5.202861	0.94997	0.0	1.16E-4	ENSG00000150054	ENST00000375732;ENST00000337532;ENST00000540098;ENST00000375719;ENST00000445954	T;T;T;T;T	0.27720	1.65;1.65;1.65;1.65;1.65	5.74	5.74	0.90152	PDZ/DHR/GLGF (3);	0.000000	0.85682	D	0.000000	T	0.57592	0.2064	M	0.70842	2.15	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.54125	-0.8340	10	0.46703	T	0.11	.	19.513	0.95151	0.0:1.0:0.0:0.0	.	141	Q5T2T1	MPP7_HUMAN	H	141;141;141;141;16	ENSP00000364884:R141H;ENSP00000337907:R141H;ENSP00000438693:R141H;ENSP00000364871:R141H;ENSP00000405397:R16H	ENSP00000337907:R141H	R	-	2	0	MPP7	28460520	1.000000	0.71417	0.998000	0.56505	0.861000	0.49209	7.620000	0.83070	2.716000	0.92895	0.561000	0.74099	CGT		0.423	MPP7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047345.1	NM_173496	
ZNF239	8187	broad.mit.edu	37	10	44052995	44052995	+	Missense_Mutation	SNP	G	G	T	rs199750361	byFrequency	TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr10:44052995G>T	ENST00000306006.6	-	2	1185	c.533C>A	c.(532-534)cCc>cAc	p.P178H	ZNF239_ENST00000426961.1_Missense_Mutation_p.P178H|ZNF239_ENST00000535642.1_Missense_Mutation_p.P178H|ZNF239_ENST00000374446.2_Missense_Mutation_p.P178H|ZNF239_ENST00000491188.1_5'UTR	NM_005674.2	NP_005665.2	Q16600	ZN239_HUMAN	zinc finger protein 239	178					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|sequence-specific DNA binding transcription factor activity (GO:0003700)			endometrium(5)|large_intestine(5)|lung(7)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						ATGGTCACAGGGTTTCTCCTC	0.428																																						uc001jaw.3																			0					0						c.(532-534)CCC>CAC		zinc finger protein 239							145.0	132.0	137.0					10																	44052995		1951	4150	6101	SO:0001583	missense	8187				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	DNA binding|RNA binding|zinc ion binding	g.chr10:44052995G>T	X82125	CCDS41502.1	10q11.22-q11.23	2013-01-08			ENSG00000196793	ENSG00000196793		"""Zinc fingers, C2H2-type"""	13031	protein-coding gene	gene with protein product		601069				8903737, 8587123	Standard	NM_005674		Approved	MOK2, HOK-2	uc009xmk.3	Q16600	OTTHUMG00000018033	ENST00000306006.6:c.533C>A	10.37:g.44052995G>T	ENSP00000307774:p.Pro178His					ZNF239_uc001jax.3_Missense_Mutation_p.P178H|ZNF239_uc009xmj.2_Missense_Mutation_p.P178H|ZNF239_uc009xmk.2_Missense_Mutation_p.P178H	p.P178H	NM_005674	NP_005665	Q16600	ZN239_HUMAN			2	1186	-			178					Q5T1G9|Q8TAS5	Missense_Mutation	SNP	ENST00000306006.6	37	c.533C>A	CCDS41502.1	.	.	.	.	.	.	.	.	.	.	G	19.39	3.817989	0.71028	.	.	ENSG00000196793	ENST00000306006;ENST00000374446;ENST00000426961;ENST00000535642;ENST00000339962	T;T;T;T	0.34859	1.34;1.34;1.34;1.34	3.98	2.13	0.27403	.	.	.	.	.	T	0.43322	0.1242	M	0.79926	2.475	0.28014	N	0.934789	D	0.61080	0.989	P	0.45998	0.5	T	0.42832	-0.9428	9	0.87932	D	0	-3.229	8.3809	0.32470	0.1959:0.0:0.8041:0.0	.	178	Q16600	ZN239_HUMAN	H	178	ENSP00000307774:P178H;ENSP00000363569:P178H;ENSP00000398202:P178H;ENSP00000443907:P178H	ENSP00000307774:P178H	P	-	2	0	ZNF239	43373001	0.965000	0.33210	0.002000	0.10522	0.204000	0.24138	3.503000	0.53340	0.644000	0.30656	0.655000	0.94253	CCC		0.428	ZNF239-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047710.1		
PTEN	5728	broad.mit.edu	37	10	89720852	89720852	+	Nonsense_Mutation	SNP	C	C	T	rs121909231		TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr10:89720852C>T	ENST00000371953.3	+	8	2360	c.1003C>T	c.(1003-1005)Cga>Tga	p.R335*	PTEN_ENST00000472832.1_3'UTR	NM_000314.4	NP_000305.3	P60484	PTEN_HUMAN	phosphatase and tensin homolog	335	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.R335*(25)|p.R55fs*1(5)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.G165_*404del(1)|p.R335G(1)|p.W274_F341del(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)		CAAAGCCAACCGATACTTTTC	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		77	Whole gene deletion(37)|Substitution - Nonsense(25)|Deletion - Frameshift(9)|Deletion - In frame(3)|Unknown(2)|Substitution - Missense(1)	p.R335*(21)|p.R55fs*1(4)|p.?(2)|p.N212fs*1(2)|p.Y27fs*1(2)|p.R335fs*8(1)|p.G165_*404del(1)|p.G165_K342del(1)|p.R335fs*4(1)|p.R335fs*7(1)|p.W274_F341del(1)|p.R335R(1)|p.D326_K342del(1)	central_nervous_system(25)|prostate(16)|skin(8)|haematopoietic_and_lymphoid_tissue(7)|endometrium(6)|lung(4)|breast(3)|ovary(3)|urinary_tract(2)|upper_aerodigestive_tract(1)|stomach(1)|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	GRCh37	CM971278	PTEN	M	rs121909231	c.(1003-1005)CGA>TGA		phosphatase and tensin homolog							60.0	63.0	62.0					10																	89720852		2203	4298	6501	SO:0001587	stop_gained	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.chr10:89720852C>T	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.1003C>T	10.37:g.89720852C>T	ENSP00000361021:p.Arg335*	HNSCC(9;0.0022)|TCGA GBM(2;<1E-08)|TSP Lung(26;0.18)					p.R335*	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	2034	+		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)	335	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	Nonsense_Mutation	SNP	ENST00000371953.3	37	c.1003C>T	CCDS31238.1	.	.	.	.	.	.	.	.	.	.	C	48	14.209601	0.99784	.	.	ENSG00000171862	ENST00000371953	.	.	.	5.37	4.39	0.52855	.	0.053988	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	.	.	.	0.4934	12.825	0.57714	0.2831:0.7169:0.0:0.0	.	.	.	.	X	335	.	.	R	+	1	2	PTEN	89710832	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	2.629000	0.46485	2.516000	0.84829	0.591000	0.81541	CGA		0.333	PTEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049241.1	NM_000314	
TCF7L2	6934	broad.mit.edu	37	10	114925317	114925317	+	Frame_Shift_Del	DEL	A	A	-			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr10:114925317delA	ENST00000355995.4	+	15	1953	c.1446delA	c.(1444-1446)agafs	p.R482fs	TCF7L2_ENST00000466338.1_3'UTR|TCF7L2_ENST00000543371.1_Frame_Shift_Del_p.R465fs|TCF7L2_ENST00000542695.1_Frame_Shift_Del_p.R198fs|TCF7L2_ENST00000369386.1_3'UTR|TCF7L2_ENST00000369397.4_Frame_Shift_Del_p.R459fs|TCF7L2_ENST00000369389.1_Frame_Shift_Del_p.E152fs|TCF7L2_ENST00000538897.1_Frame_Shift_Del_p.E458fs|TCF7L2_ENST00000536810.1_Frame_Shift_Del_p.R465fs|TCF7L2_ENST00000355717.4_Frame_Shift_Del_p.E465fs|TCF7L2_ENST00000545257.1_Frame_Shift_Del_p.R482fs|TCF7L2_ENST00000352065.5_3'UTR			Q9NQB0	TF7L2_HUMAN	transcription factor 7-like 2 (T-cell specific, HMG-box)	482	Promoter-specific activation domain.				blood vessel development (GO:0001568)|bone mineralization (GO:0030282)|brain development (GO:0007420)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in positive regulation of epithelial to mesenchymal transition (GO:0044334)|catenin import into nucleus (GO:0035411)|cell cycle arrest (GO:0007050)|cell proliferation (GO:0008283)|cellular response to starvation (GO:0009267)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic genitalia morphogenesis (GO:0030538)|embryonic hindgut morphogenesis (GO:0048619)|face morphogenesis (GO:0060325)|fat cell differentiation (GO:0045444)|generation of neurons (GO:0048699)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|glycogen metabolic process (GO:0005977)|insulin metabolic process (GO:1901142)|maintenance of DNA repeat elements (GO:0043570)|multicellular organism growth (GO:0035264)|myoblast fate commitment (GO:0048625)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of extrinsic apoptotic signaling pathway (GO:2001237)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of fibroblast growth factor receptor signaling pathway (GO:0040037)|negative regulation of organ growth (GO:0046621)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of type B pancreatic cell apoptotic process (GO:2000675)|neural tube development (GO:0021915)|odontogenesis of dentin-containing tooth (GO:0042475)|oligodendrocyte development (GO:0014003)|pancreas development (GO:0031016)|pituitary gland development (GO:0021983)|positive regulation of apoptotic process (GO:0043065)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of gluconeogenesis (GO:0045722)|positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909)|positive regulation of insulin secretion (GO:0032024)|positive regulation of protein binding (GO:0032092)|positive regulation of protein export from nucleus (GO:0046827)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of triglyceride biosynthetic process (GO:0010867)|post-embryonic development (GO:0009791)|regulation of hormone metabolic process (GO:0032350)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|regulation of myelination (GO:0031641)|regulation of oligodendrocyte differentiation (GO:0048713)|regulation of skeletal muscle tissue development (GO:0048641)|regulation of smooth muscle cell proliferation (GO:0048660)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|response to glucose (GO:0009749)|secretory granule localization (GO:0032252)|skin development (GO:0043588)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)	beta-catenin-TCF7L2 complex (GO:0070369)|cytoplasm (GO:0005737)|nuclear chromatin (GO:0000790)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein-DNA complex (GO:0032993)|transcription factor complex (GO:0005667)	armadillo repeat domain binding (GO:0070016)|beta-catenin binding (GO:0008013)|chromatin binding (GO:0003682)|gamma-catenin binding (GO:0045295)|nuclear hormone receptor binding (GO:0035257)|protein kinase binding (GO:0019901)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II repressing transcription factor binding (GO:0001103)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)		VTI1A/TCF7L2(8)	central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(24)|liver(2)|lung(8)|ovary(1)|skin(1)	41		Breast(234;0.058)|Colorectal(252;0.0615)		Epithelial(162;0.00554)|all cancers(201;0.02)		TTTCTAGGAGAAAAAAAAAGT	0.522			T	VTI1A	colorectal																																	uc001lae.3				Dom	yes		10	10q25.3	6934		transcription factor 7-like 2			E					0		p.R465C(1)		large_intestine(3)|ovary(1)	4						c.(1393-1395)AGAfs		transcription factor 7-like 2 isoform 1							94.0	102.0	99.0					10																	114925317		2203	4300	6503	SO:0001589	frameshift_variant	6934				anti-apoptosis|blood vessel development|canonical Wnt receptor signaling pathway involved in positive regulation of epithelial to mesenchymal transition|cell cycle arrest|cell proliferation|fat cell differentiation|glucose homeostasis|maintenance of DNA repeat elements|myoblast cell fate commitment|negative regulation of canonical Wnt receptor signaling pathway|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of transcription from RNA polymerase II promoter|pancreas development|positive regulation of heparan sulfate proteoglycan biosynthetic process|positive regulation of insulin secretion|positive regulation of protein binding|positive regulation of protein export from nucleus|positive regulation of protein kinase B signaling cascade|positive regulation of transcription from RNA polymerase II promoter|regulation of hormone metabolic process|regulation of smooth muscle cell proliferation|response to glucose stimulus	beta-catenin-TCF7L2 complex|PML body|protein-DNA complex	armadillo repeat domain binding|beta-catenin binding|gamma-catenin binding|nuclear hormone receptor binding|protein kinase binding|sequence-specific DNA binding|sequence-specific DNA binding transcription factor activity|transcription factor binding|transcription regulatory region DNA binding	g.chr10:114925317delA	X62871	CCDS7576.1, CCDS53578.1, CCDS55729.1, CCDS73196.1, CCDS73197.1, CCDS73198.1	10q25.3	2006-11-24			ENSG00000148737	ENSG00000148737			11641	protein-coding gene	gene with protein product		602228		TCF4		1741298	Standard	NM_001146283		Approved	TCF-4	uc001lae.4	Q9NQB0	OTTHUMG00000019070	ENST00000355995.4:c.1446delA	10.37:g.114925317delA	ENSP00000348274:p.Arg482fs					TCF7L2_uc001lac.3_Frame_Shift_Del_p.R459fs|TCF7L2_uc010qrk.1_Frame_Shift_Del_p.E435fs|TCF7L2_uc010qrl.1_Frame_Shift_Del_p.R442fs|TCF7L2_uc010qrm.1_Frame_Shift_Del_p.E441fs|TCF7L2_uc010qrn.1_Frame_Shift_Del_p.E384fs|TCF7L2_uc001lad.3_Frame_Shift_Del_p.E431fs|TCF7L2_uc001lag.3_Frame_Shift_Del_p.E465fs|TCF7L2_uc001laf.3_Frame_Shift_Del_p.R442fs|TCF7L2_uc010qro.1_Frame_Shift_Del_p.E418fs|TCF7L2_uc001lah.2_3'UTR|TCF7L2_uc010qrp.1_3'UTR|TCF7L2_uc010qrq.1_3'UTR|TCF7L2_uc010qrr.1_Frame_Shift_Del_p.R397fs|TCF7L2_uc010qrs.1_Frame_Shift_Del_p.R353fs|TCF7L2_uc010qrt.1_Frame_Shift_Del_p.R353fs|TCF7L2_uc010qru.1_Frame_Shift_Del_p.E357fs|TCF7L2_uc010qrv.1_3'UTR|TCF7L2_uc010qrw.1_3'UTR|TCF7L2_uc010qrx.1_3'UTR	p.R465fs	NM_001146274	NP_001139746	Q9NQB0	TF7L2_HUMAN		Epithelial(162;0.00554)|all cancers(201;0.02)	14	1902	+		Breast(234;0.058)|Colorectal(252;0.0615)	482			Promoter-specific activation domain.		B4DRJ8|B9X074|C6ZRJ8|C6ZRK0|E2GH14|E2GH19|E2GH20|E2GH24|E2GH25|E9PFH9|F8W742|F8W7T5|O00185|Q9NQB1|Q9NQB2|Q9NQB3|Q9NQB4|Q9NQB5|Q9NQB6|Q9NQB7|Q9ULC2	Frame_Shift_Del	DEL	ENST00000355995.4	37	c.1395delA																																																																																					0.522	TCF7L2-203	KNOWN	basic	protein_coding	protein_coding		NM_030756	
KNDC1	85442	broad.mit.edu	37	10	135038289	135038289	+	Silent	SNP	C	C	G			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr10:135038289C>G	ENST00000304613.3	+	30	5166	c.5145C>G	c.(5143-5145)tcC>tcG	p.S1715S	KNDC1_ENST00000368572.2_Silent_p.S1717S			Q76NI1	VKIND_HUMAN	kinase non-catalytic C-lobe domain (KIND) containing 1	1715	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				cerebellar granule cell differentiation (GO:0021707)|positive regulation of protein phosphorylation (GO:0001934)|regulation of dendrite morphogenesis (GO:0048814)|small GTPase mediated signal transduction (GO:0007264)	dendrite (GO:0030425)|guanyl-nucleotide exchange factor complex (GO:0032045)|neuronal cell body (GO:0043025)	protein serine/threonine kinase activity (GO:0004674)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)			NS(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(27)|ovary(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	60		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)		CCGACATTTCCACACTCGCCG	0.582																																						uc001llz.1																			0				upper_aerodigestive_tract(1)|ovary(1)	2						c.(5143-5145)TCC>TCG		kinase non-catalytic C-lobe domain (KIND)							79.0	67.0	71.0					10																	135038289		2203	4300	6503	SO:0001819	synonymous_variant	85442				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction			g.chr10:135038289C>G	AK074179	CCDS7674.1	10q26.3	2004-09-14	2004-04-07		ENSG00000171798	ENSG00000171798			29374	protein-coding gene	gene with protein product			"""RasGEF domain family, member 2"""	RASGEF2, C10orf23		11214970	Standard	NM_152643		Approved	KIAA1768, bB439H18.3, FLJ25027	uc001llz.1	Q76NI1	OTTHUMG00000019303	ENST00000304613.3:c.5145C>G	10.37:g.135038289C>G							p.S1715S	NM_152643	NP_689856	Q76NI1	VKIND_HUMAN		OV - Ovarian serous cystadenocarcinoma(35;8.77e-06)|Epithelial(32;1.13e-05)|all cancers(32;1.51e-05)	30	5146	+		all_cancers(35;4.16e-10)|all_epithelial(44;2.07e-08)|Lung NSC(174;0.000845)|all_lung(145;0.00145)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.173)|Glioma(114;0.203)	1715			Ras-GEF.		B0QZC5|Q5T233|Q6ZNH8|Q8TEE5|Q96LV7|Q9C095	Silent	SNP	ENST00000304613.3	37	c.5145C>G	CCDS7674.1																																																																																				0.582	KNDC1-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000277044.3	NM_152643	
OR5L2	26338	broad.mit.edu	37	11	55594994	55594994	+	Silent	SNP	A	A	G			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr11:55594994A>G	ENST00000378397.1	+	1	300	c.300A>G	c.(298-300)caA>caG	p.Q100Q		NM_001004739.1	NP_001004739.1	Q8NGL0	OR5L2_HUMAN	olfactory receptor, family 5, subfamily L, member 2	100						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|kidney(1)|large_intestine(1)|lung(42)|ovary(1)|prostate(3)|skin(1)|stomach(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	59		all_epithelial(135;0.208)				GCATGGTGCAATTCTACTTGT	0.473										HNSCC(27;0.073)																												uc001nhy.1																			0				ovary(1)	1						c.(298-300)CAA>CAG		olfactory receptor, family 5, subfamily L,							191.0	180.0	184.0					11																	55594994		2200	4296	6496	SO:0001819	synonymous_variant	26338				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:55594994A>G	AB065782	CCDS31511.1	11q11	2012-08-09			ENSG00000205030	ENSG00000205030		"""GPCR / Class A : Olfactory receptors"""	8351	protein-coding gene	gene with protein product						1370859	Standard	NM_001004739		Approved	HTPCRX16, HSHTPCRX16	uc001nhy.1	Q8NGL0	OTTHUMG00000166812	ENST00000378397.1:c.300A>G	11.37:g.55594994A>G		HNSCC(27;0.073)					p.Q100Q	NM_001004739	NP_001004739	Q8NGL0	OR5L2_HUMAN			1	300	+		all_epithelial(135;0.208)	100			Helical; Name=3; (Potential).		Q6IF66|Q96RB2	Silent	SNP	ENST00000378397.1	37	c.300A>G	CCDS31511.1																																																																																				0.473	OR5L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391516.1	NM_001004739	
GLYATL1	92292	broad.mit.edu	37	11	58723492	58723492	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr11:58723492C>T	ENST00000317391.4	+	8	1241	c.901C>T	c.(901-903)Cca>Tca	p.P301S	RP11-142C4.6_ENST00000525714.1_RNA|GLYATL1_ENST00000300079.5_Missense_Mutation_p.P332S|RP11-142C4.6_ENST00000533954.1_RNA	NM_001220494.1	NP_001207423.1	Q969I3	GLYL1_HUMAN	glycine-N-acyltransferase-like 1	301						mitochondrion (GO:0005739)	glutamine N-acyltransferase activity (GO:0047946)|glycine N-acyltransferase activity (GO:0047961)			NS(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(19)|ovary(1)|skin(4)|urinary_tract(1)	34					Glycine(DB00145)	GAATCTAGTTCCATTTTAGAC	0.418																																						uc001nnf.2																			0				ovary(1)	1						c.(901-903)CCA>TCA		SubName: Full=Glycine acyltransferase family-C; SubName: Full=Glycine-N-acyltransferase-like 1, isoform CRA_a;	Glycine(DB00145)						49.0	50.0	50.0					11																	58723492		2201	4293	6494	SO:0001583	missense	92292					mitochondrion	glycine N-acyltransferase activity	g.chr11:58723492C>T	AK091965	CCDS31556.1, CCDS55768.1	11q12.1	2014-08-12			ENSG00000166840	ENSG00000166840			30519	protein-coding gene	gene with protein product		614761				12477932	Standard	NM_080661		Approved	MGC15397, FLJ34646	uc001nnh.2	Q969I3	OTTHUMG00000167221	ENST00000317391.4:c.901C>T	11.37:g.58723492C>T	ENSP00000322223:p.Pro301Ser					uc001nng.1_Intron|GLYATL1_uc001nnh.1_Missense_Mutation_p.P332S|GLYATL1_uc001nni.1_Missense_Mutation_p.P301S|GLYATL1_uc001nnj.1_Missense_Mutation_p.P301S	p.P301S			Q969I3	GLYL1_HUMAN			8	1277	+			301					A6NDT0|Q7Z510|Q8NAW8	Missense_Mutation	SNP	ENST00000317391.4	37	c.901C>T	CCDS55768.1	.	.	.	.	.	.	.	.	.	.	.	8.688	0.906668	0.17833	.	.	ENSG00000166840	ENST00000444580;ENST00000317391;ENST00000300079	T;T	0.25414	2.38;1.8	1.67	1.67	0.24075	.	1.908140	0.04412	U	0.366123	T	0.19565	0.0470	L	0.36672	1.1	0.09310	N	1	P;B	0.38800	0.648;0.244	B;B	0.31290	0.127;0.025	T	0.29671	-1.0004	10	0.66056	D	0.02	.	6.6757	0.23093	0.0:1.0:0.0:0.0	.	332;301	Q969I3-2;Q969I3	.;GLYL1_HUMAN	S	278;301;332	ENSP00000322223:P301S;ENSP00000300079:P332S	ENSP00000300079:P332S	P	+	1	0	GLYATL1	58480068	0.003000	0.15002	0.029000	0.17559	0.085000	0.17905	0.499000	0.22546	0.886000	0.36113	0.411000	0.27672	CCA		0.418	GLYATL1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393783.1	NM_080661	
FAT3	120114	broad.mit.edu	37	11	92532317	92532317	+	Silent	SNP	A	A	G			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr11:92532317A>G	ENST00000298047.6	+	9	6155	c.6138A>G	c.(6136-6138)gaA>gaG	p.E2046E	FAT3_ENST00000409404.2_Silent_p.E2046E|FAT3_ENST00000525166.1_Silent_p.E1896E			Q8TDW7	FAT3_HUMAN	FAT atypical cadherin 3	2046	Cadherin 18. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|multicellular organismal development (GO:0007275)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|endometrium(10)|kidney(4)|large_intestine(11)|liver(2)|lung(37)|ovary(5)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(5)	85		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)				ACCGTGAAGAACAAGAGTTAT	0.463										TCGA Ovarian(4;0.039)																												uc001pdj.3																			0				ovary(4)|pancreas(1)	5						c.(6136-6138)GAA>GAG		FAT tumor suppressor homolog 3							57.0	59.0	58.0					11																	92532317		1929	4140	6069	SO:0001819	synonymous_variant	120114				homophilic cell adhesion|multicellular organismal development	integral to membrane|plasma membrane	calcium ion binding	g.chr11:92532317A>G	AB076400		11q14.3	2013-05-31	2013-05-31		ENSG00000165323	ENSG00000165323		"""Cadherins / Cadherin-related"""	23112	protein-coding gene	gene with protein product	"""cadherin-related family member 10"""	612483	"""FAT tumor suppressor homolog 3 (Drosophila)"""			11811999	Standard	NM_001008781		Approved	KIAA1989, CDHF15, CDHR10	uc001pdj.4	Q8TDW7	OTTHUMG00000154468	ENST00000298047.6:c.6138A>G	11.37:g.92532317A>G		TCGA Ovarian(4;0.039)					p.E2046E	NM_001008781	NP_001008781	Q8TDW7	FAT3_HUMAN			9	6155	+		Acute lymphoblastic leukemia(157;3.01e-05)|all_hematologic(158;0.00858)	2046			Extracellular (Potential).|Cadherin 18.		B5MDB0|Q96AU6	Silent	SNP	ENST00000298047.6	37	c.6138A>G																																																																																					0.463	FAT3-201	KNOWN	basic	protein_coding	protein_coding		NM_001008781	
TTC12	54970	broad.mit.edu	37	11	113233171	113233171	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr11:113233171G>A	ENST00000529221.1	+	19	1768	c.1663G>A	c.(1663-1665)Gtt>Att	p.V555I	TTC12_ENST00000393020.1_Missense_Mutation_p.V555I|TTC12_ENST00000314756.3_Missense_Mutation_p.V555I|TTC12_ENST00000483239.2_Missense_Mutation_p.V561I	NM_017868.3	NP_060338.3	Q9H892	TTC12_HUMAN	tetratricopeptide repeat domain 12	555										breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(1)|large_intestine(6)|lung(12)|pancreas(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	32		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)		TCTGAAAATTGTTGAGGAGGC	0.428																																						uc001pnu.2																			0				pancreas(2)|upper_aerodigestive_tract(1)|central_nervous_system(1)	4						c.(1663-1665)GTT>ATT		tetratricopeptide repeat domain 12							98.0	104.0	102.0					11																	113233171		2201	4296	6497	SO:0001583	missense	54970						binding	g.chr11:113233171G>A	AK000542	CCDS8360.2	11q23.2	2013-01-10			ENSG00000149292	ENSG00000149292		"""Tetratricopeptide (TTC) repeat domain containing"""	23700	protein-coding gene	gene with protein product		610732				12964006	Standard	XM_005271607		Approved	FLJ13859, FLJ20535, TPARM	uc001pnu.3	Q9H892	OTTHUMG00000142832	ENST00000529221.1:c.1663G>A	11.37:g.113233171G>A	ENSP00000433757:p.Val555Ile					TTC12_uc001pnv.2_Missense_Mutation_p.V561I|TTC12_uc001pnw.2_RNA|TTC12_uc001pnx.2_Missense_Mutation_p.V405I	p.V555I	NM_017868	NP_060338	Q9H892	TTC12_HUMAN		BRCA - Breast invasive adenocarcinoma(274;5.3e-06)|Epithelial(105;8.37e-05)|all cancers(92;0.000694)	19	1768	+		all_cancers(61;2.73e-16)|all_epithelial(67;8.64e-10)|Melanoma(852;1.46e-05)|all_hematologic(158;0.00014)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0101)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)|Prostate(24;0.183)|Renal(330;0.187)	555					Q8N5H9|Q9NWY3	Missense_Mutation	SNP	ENST00000529221.1	37	c.1663G>A	CCDS8360.2	.	.	.	.	.	.	.	.	.	.	G	6.115	0.389424	0.11581	.	.	ENSG00000149292	ENST00000529221;ENST00000314756;ENST00000393020;ENST00000483239	T;T;T;T	0.48836	0.8;0.8;0.8;0.8	5.05	-7.15	0.01521	Armadillo-like helical (1);Armadillo-type fold (1);	2.331600	0.01435	N	0.014866	T	0.35740	0.0942	L	0.34521	1.04	0.09310	N	1	B;B	0.13145	0.007;0.007	B;B	0.15052	0.012;0.012	T	0.23404	-1.0189	10	0.37606	T	0.19	-0.161	11.1305	0.48343	0.697:0.0:0.2107:0.0922	.	555;555	A8K8G6;Q9H892	.;TTC12_HUMAN	I	555;555;555;561	ENSP00000433757:V555I;ENSP00000315160:V555I;ENSP00000376743:V555I;ENSP00000419652:V561I	ENSP00000315160:V555I	V	+	1	0	TTC12	112738381	0.000000	0.05858	0.000000	0.03702	0.085000	0.17905	-0.543000	0.06084	-1.426000	0.01994	-0.345000	0.07892	GTT		0.428	TTC12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286455.2	NM_017868	
SRPR	6734	broad.mit.edu	37	11	126137085	126137085	+	Missense_Mutation	SNP	C	C	G			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr11:126137085C>G	ENST00000332118.6	-	4	665	c.511G>C	c.(511-513)Ggg>Cgg	p.G171R	FOXRED1_ENST00000263578.5_5'Flank|FOXRED1_ENST00000532125.1_5'Flank|SRPR_ENST00000532259.1_Missense_Mutation_p.G143R|SRPR_ENST00000530680.1_5'Flank|FOXRED1_ENST00000442061.2_5'Flank	NM_003139.3	NP_003130.2	P08240	SRPR_HUMAN	signal recognition particle receptor (docking protein)	171					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|cotranslational protein targeting to membrane (GO:0006613)|endoplasmic reticulum unfolded protein response (GO:0030968)|gene expression (GO:0010467)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|signal recognition particle receptor complex (GO:0005785)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|poly(A) RNA binding (GO:0044822)|signal recognition particle binding (GO:0005047)			endometrium(7)|large_intestine(2)|lung(9)|ovary(2)|prostate(1)	21	all_hematologic(175;0.145)			BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)		TTCTTGGCCCCCTTTTTTTTG	0.438																																						uc001qdh.2																			0					0						c.(511-513)GGG>CGG		signal recognition particle receptor							354.0	346.0	348.0					11																	126137085		2201	4299	6500	SO:0001583	missense	6734				SRP-dependent cotranslational protein targeting to membrane	integral to membrane|signal recognition particle receptor complex	GTP binding|GTPase activity|receptor activity|signal recognition particle binding	g.chr11:126137085C>G	BC001162	CCDS31717.1, CCDS53722.1	11q24-q25	2012-10-02	2008-10-29		ENSG00000182934	ENSG00000182934			11307	protein-coding gene	gene with protein product		182180	"""signal recognition particle receptor ('docking protein')"""			3340536, 1312991	Standard	NM_001177842		Approved	SRP-alpha, Sralpha	uc001qdh.3	P08240	OTTHUMG00000165826	ENST00000332118.6:c.511G>C	11.37:g.126137085C>G	ENSP00000328023:p.Gly171Arg					SRPR_uc010sbm.1_Missense_Mutation_p.G143R|FOXRED1_uc001qdi.2_5'Flank|FOXRED1_uc010sbn.1_5'Flank|FOXRED1_uc010sbo.1_5'Flank|FOXRED1_uc010sbp.1_5'Flank|FOXRED1_uc010sbq.1_5'Flank|FOXRED1_uc001qdj.2_5'Flank|FOXRED1_uc010sbr.1_5'Flank	p.G171R	NM_003139	NP_003130	P08240	SRPR_HUMAN		BRCA - Breast invasive adenocarcinoma(274;1.1e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0736)	4	562	-	all_hematologic(175;0.145)		171					A6NIB3|B2R5Z8|B4E0H3|E9PJS4|Q9BVJ4	Missense_Mutation	SNP	ENST00000332118.6	37	c.511G>C	CCDS31717.1	.	.	.	.	.	.	.	.	.	.	C	11.94	1.790053	0.31685	.	.	ENSG00000182934	ENST00000332118;ENST00000532259	.	.	.	4.92	4.92	0.64577	Signal recognition particle receptor, alpha subunit, N-terminal (1);	0.213531	0.49916	D	0.000125	T	0.49745	0.1575	L	0.29908	0.895	0.47153	D	0.999332	B;B	0.34372	0.31;0.451	B;B	0.39299	0.296;0.173	T	0.39522	-0.9610	9	0.13108	T	0.6	-12.9188	18.3148	0.90217	0.0:1.0:0.0:0.0	.	143;171	E9PJS4;P08240	.;SRPR_HUMAN	R	171;143	.	ENSP00000328023:G171R	G	-	1	0	SRPR	125642295	1.000000	0.71417	1.000000	0.80357	0.914000	0.54420	3.577000	0.53885	2.546000	0.85860	0.305000	0.20034	GGG		0.438	SRPR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000386425.2	NM_003139	
ACAD8	27034	broad.mit.edu	37	11	134129623	134129623	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr11:134129623G>T	ENST00000281182.4	+	6	795	c.689G>T	c.(688-690)gGc>gTc	p.G230V	ACAD8_ENST00000537423.1_Missense_Mutation_p.G153V|ACAD8_ENST00000374752.4_Missense_Mutation_p.G103V|ACAD8_ENST00000543332.1_Missense_Mutation_p.G132V|ACAD8_ENST00000524547.1_3'UTR	NM_014384.2	NP_055199.1	Q9UKU7	ACAD8_HUMAN	acyl-CoA dehydrogenase family, member 8	230					branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|lipid metabolic process (GO:0006629)|regulation of transcription, DNA-templated (GO:0006355)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|valine catabolic process (GO:0006574)	mitochondrial matrix (GO:0005759)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)			endometrium(4)|large_intestine(3)|lung(5)|ovary(1)|urinary_tract(1)	14	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	Flavin adenine dinucleotide(DB03147)	CTCAGCTTTGGCAAGAAGGAG	0.517																																					GBM(65;238 1125 33403 41853 48889)	uc001qhk.2																			0					0						c.(688-690)GGC>GTC		acyl-Coenzyme A dehydrogenase family, member 8							89.0	92.0	91.0					11																	134129623		2201	4297	6498	SO:0001583	missense	27034				branched chain family amino acid catabolic process|lipid metabolic process|regulation of transcription, DNA-dependent|transcription, DNA-dependent	mitochondrial matrix	acyl-CoA dehydrogenase activity|flavin adenine dinucleotide binding	g.chr11:134129623G>T	AF126245	CCDS8498.1	11q25	2014-09-17	2010-04-30		ENSG00000151498	ENSG00000151498			87	protein-coding gene	gene with protein product		604773	"""acyl-Coenzyme A dehydrogenase family, member 8"""			10524212	Standard	NM_014384		Approved		uc001qhk.3	Q9UKU7	OTTHUMG00000167177	ENST00000281182.4:c.689G>T	11.37:g.134129623G>T	ENSP00000281182:p.Gly230Val					ACAD8_uc009zdc.2_3'UTR|ACAD8_uc010sco.1_Missense_Mutation_p.G132V|ACAD8_uc010scp.1_RNA|ACAD8_uc010scq.1_Missense_Mutation_p.G153V|ACAD8_uc001qhl.2_Missense_Mutation_p.G103V|ACAD8_uc010scr.1_Missense_Mutation_p.G192V|ACAD8_uc009zde.1_Missense_Mutation_p.G103V	p.G230V	NM_014384	NP_055199	Q9UKU7	ACAD8_HUMAN		Epithelial(10;1.92e-10)|all cancers(11;2.26e-09)|BRCA - Breast invasive adenocarcinoma(10;8.73e-09)|OV - Ovarian serous cystadenocarcinoma(99;0.00154)|Lung(977;0.21)	6	750	+	all_hematologic(175;0.127)	all_cancers(12;8e-23)|all_epithelial(12;2.59e-16)|all_lung(97;1.19e-05)|Lung NSC(97;2.76e-05)|Breast(109;0.000182)|all_neural(223;0.0189)|Medulloblastoma(222;0.0245)|Esophageal squamous(93;0.0559)	230					B7Z5W4|Q6ZWP6|Q9BUS8	Missense_Mutation	SNP	ENST00000281182.4	37	c.689G>T	CCDS8498.1	.	.	.	.	.	.	.	.	.	.	G	28.6	4.930891	0.92389	.	.	ENSG00000151498	ENST00000281182;ENST00000537423;ENST00000543332;ENST00000374752;ENST00000537915	D;D;D;D	0.99150	-5.49;-5.49;-5.49;-5.49	5.83	5.83	0.93111	Acyl-CoA dehydrogenase/oxidase (1);Acyl-CoA oxidase/dehydrogenase, central domain (1);	0.044369	0.85682	D	0.000000	D	0.99524	0.9830	M	0.93854	3.465	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	0.97110	1.0;0.994;1.0;1.0;1.0	D	0.98438	1.0585	10	0.87932	D	0	.	20.1067	0.97897	0.0:0.0:1.0:0.0	.	171;153;132;103;230	B7Z767;B7Z5W4;B7Z9L5;Q6ZWP6;Q9UKU7	.;.;.;.;ACAD8_HUMAN	V	230;153;132;103;192	ENSP00000281182:G230V;ENSP00000443763:G153V;ENSP00000438302:G132V;ENSP00000363884:G103V	ENSP00000281182:G230V	G	+	2	0	ACAD8	133634833	1.000000	0.71417	1.000000	0.80357	0.974000	0.67602	9.869000	0.99810	2.753000	0.94483	0.655000	0.94253	GGC		0.517	ACAD8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393607.1	NM_014384	
CD163L1	283316	broad.mit.edu	37	12	7586265	7586265	+	Silent	SNP	C	C	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr12:7586265C>T	ENST00000313599.3	-	3	207	c.150G>A	c.(148-150)ctG>ctA	p.L50L	CD163L1_ENST00000396630.1_Silent_p.L50L|CD163L1_ENST00000416109.2_Silent_p.L50L			Q9NR16	C163B_HUMAN	CD163 molecule-like 1	50	SRCR 1. {ECO:0000255|PROSITE- ProRule:PRU00196}.					extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	scavenger receptor activity (GO:0005044)			breast(5)|central_nervous_system(3)|endometrium(8)|kidney(3)|large_intestine(18)|lung(37)|ovary(8)|prostate(3)|skin(6)|stomach(1)|urinary_tract(4)	96						CTCCATTGACCAGCCTCAACT	0.473																																						uc001qsy.2																			0				ovary(8)|skin(2)|central_nervous_system(1)	11						c.(148-150)CTG>CTA		scavenger receptor cysteine-rich type 1							141.0	115.0	124.0					12																	7586265		2203	4300	6503	SO:0001819	synonymous_variant	283316					extracellular region|integral to membrane|plasma membrane	scavenger receptor activity	g.chr12:7586265C>T	AF264014	CCDS8577.1, CCDS73434.1	12p13.31	2006-03-28	2006-03-28			ENSG00000177675			30375	protein-coding gene	gene with protein product		606079	"""CD163 antigen-like 1"""			11124526, 11086079	Standard	XM_005253348		Approved	M160, CD163B	uc001qsy.3	Q9NR16		ENST00000313599.3:c.150G>A	12.37:g.7586265C>T						CD163L1_uc010sge.1_Silent_p.L50L	p.L50L	NM_174941	NP_777601	Q9NR16	C163B_HUMAN			3	176	-			50			SRCR 1.|Extracellular (Potential).		B4E0G7|C9JHR7|E7EVK4|Q2M3B7|Q6UWC2	Silent	SNP	ENST00000313599.3	37	c.150G>A	CCDS8577.1																																																																																				0.473	CD163L1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000399329.1	NM_174941	
PIK3C2G	5288	broad.mit.edu	37	12	18435035	18435035	+	Missense_Mutation	SNP	C	C	T	rs191077735	byFrequency	TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr12:18435035C>T	ENST00000266497.5	+	1	58	c.20C>T	c.(19-21)aCg>aTg	p.T7M	PIK3C2G_ENST00000538779.1_Missense_Mutation_p.T7M|PIK3C2G_ENST00000433979.1_Missense_Mutation_p.T7M|PIK3C2G_ENST00000535651.1_Missense_Mutation_p.T7M|RERGL_ENST00000541632.1_Intron			O75747	P3C2G_HUMAN	phosphatidylinositol-4-phosphate 3-kinase, catalytic subunit type 2 gamma	7					chemotaxis (GO:0006935)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol-3-phosphate biosynthetic process (GO:0036092)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	1-phosphatidylinositol-3-kinase activity (GO:0016303)|1-phosphatidylinositol-4-phosphate 3-kinase activity (GO:0035005)|ATP binding (GO:0005524)|phosphatidylinositol binding (GO:0035091)|phosphatidylinositol phosphate kinase activity (GO:0016307)	p.T7M(1)		breast(5)|central_nervous_system(6)|endometrium(2)|kidney(4)|large_intestine(8)|lung(31)|ovary(2)|prostate(1)|skin(2)|stomach(4)|upper_aerodigestive_tract(1)	66		Hepatocellular(102;0.194)				TCTTGGCAAACGGATCCAAAT	0.353													.|||	4	0.000798722	0.0	0.0014	5008	,	,		17294	0.001		0.0	False		,,,				2504	0.002					uc001rdt.2																			1	Substitution - Missense(1)	p.T7M(1)	central_nervous_system(1)	lung(8)|central_nervous_system(6)|breast(3)|stomach(2)|ovary(2)	21						c.(19-21)ACG>ATG		phosphoinositide-3-kinase, class 2 gamma		C	MET/THR	1,3665		0,1,1832	46.0	42.0	44.0		20	3.4	1.0	12		44	3,8171		0,3,4084	yes	missense	PIK3C2G	NM_004570.4	81	0,4,5916	TT,TC,CC		0.0367,0.0273,0.0338	probably-damaging	7/1446	18435035	4,11836	1833	4087	5920	SO:0001583	missense	5288				cell communication|phosphatidylinositol-mediated signaling	membrane|phosphatidylinositol 3-kinase complex	1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol binding|phosphatidylinositol-4-phosphate 3-kinase activity	g.chr12:18435035C>T	AJ000008	CCDS44839.1, CCDS73452.1	12p12	2012-07-13	2012-07-13		ENSG00000139144	ENSG00000139144	2.7.1.154		8973	protein-coding gene	gene with protein product		609001	"""phosphoinositide-3-kinase, class 2, gamma polypeptide"""			9878262	Standard	XM_005253393		Approved		uc001rdt.3	O75747	OTTHUMG00000168841	ENST00000266497.5:c.20C>T	12.37:g.18435035C>T	ENSP00000266497:p.Thr7Met					PIK3C2G_uc010sia.1_RNA|PIK3C2G_uc010sib.1_Missense_Mutation_p.T7M|PIK3C2G_uc010sic.1_Translation_Start_Site	p.T7M	NM_004570	NP_004561	O75747	P3C2G_HUMAN			2	136	+		Hepatocellular(102;0.194)	7					A1L3U0	Missense_Mutation	SNP	ENST00000266497.5	37	c.20C>T	CCDS44839.1	2	9.157509157509158E-4	0	0.0	1	0.0027624309392265192	1	0.0017482517482517483	0	0.0	C	15.13	2.743150	0.49151	2.73E-4	3.67E-4	ENSG00000139144	ENST00000535651;ENST00000433979;ENST00000266497;ENST00000538779	T;T;T;T	0.67171	1.1;-0.25;-0.25;-0.21	4.29	3.39	0.38822	.	0.918343	0.09112	N	0.846971	T	0.64735	0.2625	L	0.34521	1.04	0.24625	N	0.993656	D;D	0.59767	0.986;0.976	P;P	0.50896	0.653;0.451	T	0.55218	-0.8175	10	0.87932	D	0	-6.2815	10.1647	0.42873	0.0:0.7796:0.2204:0.0	.	7;7	F5H369;O75747	.;P3C2G_HUMAN	M	7	ENSP00000443850:T7M;ENSP00000404845:T7M;ENSP00000266497:T7M;ENSP00000445381:T7M	ENSP00000266497:T7M	T	+	2	0	PIK3C2G	18326302	0.019000	0.18553	0.994000	0.49952	0.723000	0.41478	-0.434000	0.06939	1.390000	0.46547	0.655000	0.94253	ACG		0.353	PIK3C2G-002	KNOWN	NAGNAG_splice_site|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000401316.1	NM_004570	
KRT7	3855	broad.mit.edu	37	12	52642505	52642505	+	Silent	SNP	C	C	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr12:52642505C>A	ENST00000331817.5	+	9	1554	c.1371C>A	c.(1369-1371)atC>atA	p.I457I	KRT7_ENST00000552322.1_3'UTR|RP3-416H24.1_ENST00000546686.1_RNA|KRT86_ENST00000544024.1_5'Flank|KRT121P_ENST00000529785.1_RNA	NM_005556.3	NP_005547.3	P08729	K2C7_HUMAN	keratin 7	457	Tail.				viral process (GO:0016032)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.I457M(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(5)|prostate(2)|stomach(1)|urinary_tract(1)	14				BRCA - Breast invasive adenocarcinoma(357;0.105)	Primaquine(DB01087)	CTTATTCCATCCGGACCGCAT	0.647																																						uc001saa.1																			1	Substitution - Missense(1)		urinary_tract(1)		0						c.(1369-1371)ATC>ATA		keratin 7							36.0	40.0	39.0					12																	52642505		2203	4300	6503	SO:0001819	synonymous_variant	3855				cytoskeleton organization|DNA replication|interphase|interspecies interaction between organisms|regulation of translation	Golgi apparatus|keratin filament|nucleus	protein binding|structural molecule activity	g.chr12:52642505C>A		CCDS8822.1	12q13.13	2013-01-16			ENSG00000135480	ENSG00000135480		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6445	protein-coding gene	gene with protein product	"""keratin, type II cytoskeletal 7"", ""cytokeratin 7"", ""sarcolectin"", ""keratin, 55K type II cytoskeletal"""	148059				1713141, 16831889	Standard	XR_245927		Approved	K7, CK7, K2C7, SCL	uc001saa.1	P08729	OTTHUMG00000169580	ENST00000331817.5:c.1371C>A	12.37:g.52642505C>A						KRT86_uc010snq.1_5'Flank	p.I457I	NM_005556	NP_005547	P08729	K2C7_HUMAN		BRCA - Breast invasive adenocarcinoma(357;0.105)	9	1498	+			457			Tail.		Q92676|Q9BUD8|Q9Y3R7	Silent	SNP	ENST00000331817.5	37	c.1371C>A	CCDS8822.1																																																																																				0.647	KRT7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000404897.1	NM_005556	
KRT2	3849	broad.mit.edu	37	12	53039092	53039092	+	Missense_Mutation	SNP	C	C	T	rs142557360	byFrequency	TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr12:53039092C>T	ENST00000309680.3	-	9	1652	c.1631G>A	c.(1630-1632)cGa>cAa	p.R544Q		NM_000423.2	NP_000414.2	P35908	K22E_HUMAN	keratin 2	544	Tail.				epidermis development (GO:0008544)|keratinization (GO:0031424)|keratinocyte activation (GO:0032980)|keratinocyte migration (GO:0051546)|keratinocyte proliferation (GO:0043616)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|membrane (GO:0016020)|nucleus (GO:0005634)	structural constituent of cytoskeleton (GO:0005200)			endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(18)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	32				BRCA - Breast invasive adenocarcinoma(357;0.19)		GCCAGACTGTCGGCCTCCAGA	0.572													C|||	2	0.000399361	0.0	0.0	5008	,	,		19432	0.0		0.001	False		,,,				2504	0.001					uc001sat.2																			0				ovary(2)	2						c.(1630-1632)CGA>CAA		keratin 2		C	GLN/ARG	2,4404	4.2+/-10.8	0,2,2201	118.0	123.0	121.0		1631	4.1	0.4	12	dbSNP_134	121	1,8599	1.2+/-3.3	0,1,4299	yes	missense	KRT2	NM_000423.2	43	0,3,6500	TT,TC,CC		0.0116,0.0454,0.0231	probably-damaging	544/640	53039092	3,13003	2203	4300	6503	SO:0001583	missense	3849				keratinization|keratinocyte activation|keratinocyte migration|keratinocyte proliferation	Golgi apparatus|keratin filament	protein binding|structural constituent of cytoskeleton	g.chr12:53039092C>T		CCDS8835.1	12q13.13	2013-01-16	2008-08-01	2006-07-17	ENSG00000172867	ENSG00000172867		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6439	protein-coding gene	gene with protein product	"""epidermal ichthyosis bullosa of Siemens"""	600194	"""keratin 2A (epidermal ichthyosis bullosa of Siemens)"""	KRT2A		7524919, 16831889	Standard	NM_000423		Approved	KRTE	uc001sat.3	P35908	OTTHUMG00000169748	ENST00000309680.3:c.1631G>A	12.37:g.53039092C>T	ENSP00000310861:p.Arg544Gln						p.R544Q	NM_000423	NP_000414	P35908	K22E_HUMAN		BRCA - Breast invasive adenocarcinoma(357;0.19)	9	1664	-			544			Tail.		Q4VAQ2	Missense_Mutation	SNP	ENST00000309680.3	37	c.1631G>A	CCDS8835.1	.	.	.	.	.	.	.	.	.	.	C	13.97	2.396595	0.42512	4.54E-4	1.16E-4	ENSG00000172867	ENST00000309680	D	0.90955	-2.76	4.06	4.06	0.47325	.	.	.	.	.	T	0.81513	0.4838	N	0.08118	0	0.38928	D	0.957874	D	0.61080	0.989	P	0.45377	0.478	T	0.80612	-0.1305	9	0.13108	T	0.6	.	15.3543	0.74415	0.0:1.0:0.0:0.0	.	544	P35908	K22E_HUMAN	Q	544	ENSP00000310861:R544Q	ENSP00000310861:R544Q	R	-	2	0	KRT2	51325359	0.001000	0.12720	0.431000	0.26735	0.315000	0.28087	1.267000	0.33050	2.281000	0.76405	0.561000	0.74099	CGA		0.572	KRT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405704.1	NM_000423	
DCN	1634	broad.mit.edu	37	12	91552214	91552214	+	Nonsense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr12:91552214G>A	ENST00000052754.5	-	4	898	c.397C>T	c.(397-399)Cga>Tga	p.R133*	DCN_ENST00000456569.2_Intron|DCN_ENST00000547568.2_Intron|DCN_ENST00000393155.1_Nonsense_Mutation_p.R133*|DCN_ENST00000303320.3_Intron|DCN_ENST00000420120.2_Intron|DCN_ENST00000228329.5_Intron|DCN_ENST00000425043.1_Intron|DCN_ENST00000441303.2_Intron|DCN_ENST00000552962.1_Nonsense_Mutation_p.R133*	NM_001920.3	NP_001911.1	P07585	PGS2_HUMAN	decorin	133					aging (GO:0007568)|carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|glycosaminoglycan metabolic process (GO:0030203)|kidney development (GO:0001822)|organ morphogenesis (GO:0009887)|peptide cross-linking via chondroitin 4-sulfate glycosaminoglycan (GO:0019800)|placenta development (GO:0001890)|response to lipopolysaccharide (GO:0032496)|response to mechanical stimulus (GO:0009612)|skeletal muscle tissue development (GO:0007519)|small molecule metabolic process (GO:0044281)|wound healing (GO:0042060)	collagen type VI trimer (GO:0005589)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|lysosomal lumen (GO:0043202)|proteinaceous extracellular matrix (GO:0005578)	extracellular matrix binding (GO:0050840)|glycosaminoglycan binding (GO:0005539)|poly(A) RNA binding (GO:0044822)	p.R133*(1)		central_nervous_system(2)|cervix(1)|kidney(2)|large_intestine(4)|liver(1)|lung(8)|ovary(1)|skin(1)	20						AGATAAAGTCGTTCCAACTTC	0.408																																						uc001tbs.2																			1	Substitution - Nonsense(1)	p.R133*(1)	central_nervous_system(1)	central_nervous_system(2)|ovary(1)|lung(1)	4						c.(397-399)CGA>TGA		decorin isoform a preproprotein							131.0	127.0	128.0					12																	91552214		2203	4300	6503	SO:0001587	stop_gained	1634				organ morphogenesis	extracellular space		g.chr12:91552214G>A	AF138300	CCDS9039.1, CCDS9040.1, CCDS9041.1, CCDS9042.1, CCDS44951.1	12q21.33	2014-04-16			ENSG00000011465	ENSG00000011465		"""Proteoglycans / Extracellular Matrix : Small leucine-rich repeats"""	2705	protein-coding gene	gene with protein product	"""decorin proteoglycan"""	125255				8432526	Standard	NM_133507		Approved	DSPG2, SLRR1B	uc001tbt.3	P07585	OTTHUMG00000169998	ENST00000052754.5:c.397C>T	12.37:g.91552214G>A	ENSP00000052754:p.Arg133*					DCN_uc001tbo.2_Intron|DCN_uc001tbp.2_Intron|DCN_uc001tbq.2_Intron|DCN_uc001tbr.2_Intron|DCN_uc001tbt.2_Nonsense_Mutation_p.R133*|DCN_uc001tbu.2_Nonsense_Mutation_p.R133*	p.R133*	NM_133503	NP_598010	P07585	PGS2_HUMAN			3	491	-			133			LRR 3.		Q9P0Z0|Q9P0Z1|Q9Y5N8|Q9Y5N9	Nonsense_Mutation	SNP	ENST00000052754.5	37	c.397C>T	CCDS9039.1	.	.	.	.	.	.	.	.	.	.	G	27.8	4.860018	0.91433	.	.	ENSG00000011465	ENST00000052754;ENST00000393155;ENST00000552962;ENST00000547937;ENST00000552145;ENST00000550563	.	.	.	5.69	1.07	0.20283	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07325	T	0.83	.	15.2272	0.73359	0.0:0.0:0.2263:0.7737	.	.	.	.	X	133	.	ENSP00000052754:R133X	R	-	1	2	DCN	90076345	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.109000	0.31135	0.276000	0.22118	0.650000	0.86243	CGA		0.408	DCN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406799.3	NM_133507	
POLR3B	55703	broad.mit.edu	37	12	106824234	106824234	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr12:106824234G>A	ENST00000228347.4	+	14	1669	c.1447G>A	c.(1447-1449)Gac>Aac	p.D483N	POLR3B_ENST00000539066.1_Missense_Mutation_p.D425N	NM_018082.5	NP_060552.4	Q9NW08	RPC2_HUMAN	polymerase (RNA) III (DNA directed) polypeptide B	483					defense response to virus (GO:0051607)|gene expression (GO:0010467)|innate immune response (GO:0045087)|positive regulation of innate immune response (GO:0045089)|positive regulation of interferon-beta production (GO:0032728)|positive regulation of type I interferon production (GO:0032481)|termination of RNA polymerase III transcription (GO:0006386)|transcription elongation from RNA polymerase III promoter (GO:0006385)|transcription from RNA polymerase III promoter (GO:0006383)	cytosol (GO:0005829)|DNA-directed RNA polymerase III complex (GO:0005666)|nucleoplasm (GO:0005654)	DNA binding (GO:0003677)|DNA-directed RNA polymerase activity (GO:0003899)|metal ion binding (GO:0046872)|ribonucleoside binding (GO:0032549)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(22)|ovary(1)|prostate(3)|skin(3)|urinary_tract(2)	57						GTGTCCTTCGGACACTCCTGA	0.522																																						uc001tlp.2																			0				ovary(1)|central_nervous_system(1)	2						c.(1447-1449)GAC>AAC		DNA-directed RNA polymerase III B isoform 1							84.0	78.0	80.0					12																	106824234		2203	4300	6503	SO:0001583	missense	55703				innate immune response|positive regulation of innate immune response|positive regulation of interferon-beta production|response to virus|termination of RNA polymerase III transcription|transcription elongation from RNA polymerase III promoter	nucleoplasm	DNA binding|DNA-directed RNA polymerase activity|metal ion binding|ribonucleoside binding	g.chr12:106824234G>A	AY092084	CCDS9105.1, CCDS53824.1	12q23.3	2014-08-12			ENSG00000013503	ENSG00000013503		"""RNA polymerase subunits"""	30348	protein-coding gene	gene with protein product		614366				12391170	Standard	NM_018082		Approved	RPC2, FLJ10388	uc001tlp.3	Q9NW08	OTTHUMG00000170077	ENST00000228347.4:c.1447G>A	12.37:g.106824234G>A	ENSP00000228347:p.Asp483Asn					POLR3B_uc001tlq.2_Missense_Mutation_p.D425N	p.D483N	NM_018082	NP_060552	Q9NW08	RPC2_HUMAN			14	1669	+			483					A8K6H0|B3KV73|F5H1E6|Q9NW59	Missense_Mutation	SNP	ENST00000228347.4	37	c.1447G>A	CCDS9105.1	.	.	.	.	.	.	.	.	.	.	G	35	5.445693	0.96187	.	.	ENSG00000013503	ENST00000228347;ENST00000551370;ENST00000539066	T;T	0.79141	-1.24;-1.24	5.56	5.56	0.83823	RNA polymerase Rpb2, domain 3 (1);	0.000000	0.85682	D	0.000000	D	0.90776	0.7104	M	0.90595	3.13	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.92210	0.5775	10	0.87932	D	0	-29.4701	19.5257	0.95206	0.0:0.0:1.0:0.0	.	483	Q9NW08	RPC2_HUMAN	N	483;483;425	ENSP00000228347:D483N;ENSP00000445721:D425N	ENSP00000228347:D483N	D	+	1	0	POLR3B	105348364	1.000000	0.71417	0.968000	0.41197	0.993000	0.82548	9.429000	0.97481	2.589000	0.87451	0.655000	0.94253	GAC		0.522	POLR3B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407166.1	NM_018082	
RIMBP2	23504	broad.mit.edu	37	12	130921520	130921520	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr12:130921520G>A	ENST00000261655.4	-	10	2085	c.1922C>T	c.(1921-1923)cCg>cTg	p.P641L	RIMBP2_ENST00000536002.1_Missense_Mutation_p.P549L|RIMBP2_ENST00000535703.1_Missense_Mutation_p.P549L	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	641	Pro-rich.				negative regulation of phosphatase activity (GO:0010923)	cell junction (GO:0030054)|plasma membrane (GO:0005886)|synapse (GO:0045202)				NS(2)|breast(1)|central_nervous_system(5)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(33)|ovary(3)|pancreas(1)|prostate(3)|skin(6)|upper_aerodigestive_tract(5)|urinary_tract(1)	96	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)		GCCCACGGGCGGCTCCAGCAT	0.711																																						uc001uil.2																			0				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11						c.(1921-1923)CCG>CTG		RIM-binding protein 2							36.0	36.0	36.0					12																	130921520		2201	4298	6499	SO:0001583	missense	23504					cell junction|synapse		g.chr12:130921520G>A	AB002316	CCDS31925.1	12q24.33	2014-06-13				ENSG00000060709			30339	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 133"""	611602				10748113	Standard	NM_015347		Approved	KIAA0318, RBP2, MGC15831, RIM-BP2, PPP1R133	uc001uil.2	O15034		ENST00000261655.4:c.1922C>T	12.37:g.130921520G>A	ENSP00000261655:p.Pro641Leu					RIMBP2_uc001uim.2_Missense_Mutation_p.P549L|RIMBP2_uc001uin.1_Missense_Mutation_p.P300L	p.P641L	NM_015347	NP_056162	O15034	RIMB2_HUMAN		OV - Ovarian serous cystadenocarcinoma(86;4.29e-06)|all cancers(50;4.56e-05)|Epithelial(86;5.41e-05)	10	2086	-	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)	641			Pro-rich.		Q96ID2	Missense_Mutation	SNP	ENST00000261655.4	37	c.1922C>T	CCDS31925.1	.	.	.	.	.	.	.	.	.	.	G	11.80	1.748029	0.30955	.	.	ENSG00000060709	ENST00000261655;ENST00000392375;ENST00000535703;ENST00000536002	T;T;T	0.21191	2.02;2.76;2.76	4.63	4.63	0.57726	.	0.136669	0.49916	D	0.000137	T	0.41673	0.1169	M	0.63843	1.955	0.80722	D	1	B;B;D	0.89917	0.063;0.428;1.0	B;B;D	0.64506	0.008;0.06;0.926	T	0.17167	-1.0378	10	0.29301	T	0.29	-13.3458	17.4987	0.87725	0.0:0.0:1.0:0.0	.	549;549;641	C9JWN3;O15034-2;O15034	.;.;RIMB2_HUMAN	L	641;549;549;549	ENSP00000261655:P641L;ENSP00000440347:P549L;ENSP00000439159:P549L	ENSP00000261655:P641L	P	-	2	0	RIMBP2	129487473	1.000000	0.71417	0.910000	0.35882	0.048000	0.14542	5.301000	0.65727	2.121000	0.65114	0.561000	0.74099	CCG		0.711	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347	
PARP4	143	broad.mit.edu	37	13	25016086	25016086	+	Silent	SNP	A	A	G	rs113538547		TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr13:25016086A>G	ENST00000381989.3	-	30	3669	c.3564T>C	c.(3562-3564)ttT>ttC	p.F1188F		NM_006437.3	NP_006428.2	Q9UKK3	PARP4_HUMAN	poly (ADP-ribose) polymerase family, member 4	1188					cell death (GO:0008219)|cellular protein modification process (GO:0006464)|cellular response to DNA damage stimulus (GO:0006974)|DNA repair (GO:0006281)|inflammatory response (GO:0006954)|protein ADP-ribosylation (GO:0006471)|response to drug (GO:0042493)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle microtubule (GO:0005876)	DNA binding (GO:0003677)|enzyme binding (GO:0019899)|NAD+ ADP-ribosyltransferase activity (GO:0003950)	p.F1188F(1)		autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|endometrium(5)|kidney(3)|large_intestine(14)|lung(18)|ovary(3)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	63		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)		GAATATCAGGAAAAGGCGACT	0.413																																						uc001upl.2																			1	Substitution - coding silent(1)		prostate(1)	ovary(3)|skin(1)	4						c.(3562-3564)TTT>TTC		poly (ADP-ribose) polymerase family, member 4							42.0	45.0	44.0					13																	25016086		2203	4300	6503	SO:0001819	synonymous_variant	143				cell death|DNA repair|inflammatory response|protein ADP-ribosylation|response to drug|transport	cytoplasm|nucleus|ribonucleoprotein complex|spindle microtubule	DNA binding|enzyme binding|NAD+ ADP-ribosyltransferase activity	g.chr13:25016086A>G	AF057160	CCDS9307.1	13q11	2010-09-29	2004-08-20	2004-08-26	ENSG00000102699	ENSG00000102699		"""Poly (ADP-ribose) polymerases"""	271	protein-coding gene	gene with protein product	"""von Willebrand factor A domain containing 5C"""	607519	"""ADP-ribosyltransferase (NAD+; poly (ADP-ribose) polymerase)-like 1"""	ADPRTL1		10644454	Standard	NM_006437		Approved	VAULT3, p193, VPARP, VWA5C	uc001upl.3	Q9UKK3	OTTHUMG00000016582	ENST00000381989.3:c.3564T>C	13.37:g.25016086A>G							p.F1188F	NM_006437	NP_006428	Q9UKK3	PARP4_HUMAN		all cancers(112;0.000127)|Epithelial(112;0.000778)|Kidney(163;0.039)|OV - Ovarian serous cystadenocarcinoma(117;0.0578)|KIRC - Kidney renal clear cell carcinoma(186;0.135)|Lung(94;0.195)	30	3670	-		all_epithelial(30;7.67e-16)|Lung SC(185;0.0225)|Breast(139;0.052)	1188					O75903|Q14682|Q5QNZ9|Q9H1M6	Silent	SNP	ENST00000381989.3	37	c.3564T>C	CCDS9307.1																																																																																				0.413	PARP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044189.1	NM_006437	
RB1	5925	broad.mit.edu	37	13	49030485	49030485	+	Splice_Site	SNP	G	G	C	rs483352690		TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr13:49030485G>C	ENST00000267163.4	+	19	2098	c.1960G>C	c.(1960-1962)Gtg>Ctg	p.V654L		NM_000321.2	NP_000312.2	P06400	RB_HUMAN	retinoblastoma 1	654	Domain B.|Pocket; binds T and E1A.		V -> E (in RB). {ECO:0000269|PubMed:7795591}.		androgen receptor signaling pathway (GO:0030521)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell morphogenesis involved in neuron differentiation (GO:0048667)|chromatin remodeling (GO:0006338)|digestive tract development (GO:0048565)|enucleate erythrocyte differentiation (GO:0043353)|G1/S transition of mitotic cell cycle (GO:0000082)|glial cell apoptotic process (GO:0034349)|hepatocyte apoptotic process (GO:0097284)|maintenance of mitotic sister chromatid cohesion (GO:0034088)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|myoblast differentiation (GO:0045445)|negative regulation of epithelial cell proliferation (GO:0050680)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of smoothened signaling pathway (GO:0045879)|negative regulation of transcription from RNA polymerase II promoter during mitosis (GO:0007070)|negative regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0071930)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron apoptotic process (GO:0051402)|neuron maturation (GO:0042551)|neuron projection development (GO:0031175)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to chromosome, centromeric region (GO:0071459)|Ras protein signal transduction (GO:0007265)|regulation of centromere complex assembly (GO:0090230)|regulation of cohesin localization to chromatin (GO:0071922)|regulation of lipid kinase activity (GO:0043550)|regulation of mitotic cell cycle (GO:0007346)|regulation of transcription involved in G1/S transition of mitotic cell cycle (GO:0000083)|sister chromatid biorientation (GO:0031134)|skeletal muscle cell differentiation (GO:0035914)|striated muscle cell differentiation (GO:0051146)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	chromatin (GO:0000785)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|PML body (GO:0016605)|Rb-E2F complex (GO:0035189)|spindle (GO:0005819)|SWI/SNF complex (GO:0016514)	androgen receptor binding (GO:0050681)|core promoter binding (GO:0001047)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|kinase binding (GO:0019900)|phosphoprotein binding (GO:0051219)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)|ubiquitin protein ligase binding (GO:0031625)	p.0?(15)|p.?(10)|p.V654M(3)|p.V654fs*4(1)|p.V654L(1)		NS(3)|adrenal_gland(1)|bone(22)|breast(30)|central_nervous_system(48)|cervix(3)|endometrium(14)|eye(95)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(20)|kidney(3)|large_intestine(10)|liver(3)|lung(153)|oesophagus(1)|ovary(13)|pancreas(5)|pituitary(1)|prostate(14)|salivary_gland(2)|skin(9)|soft_tissue(9)|stomach(4)|upper_aerodigestive_tract(1)|urinary_tract(31)	496		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	"""""""Insulin(DB00071)|Insulin Regular(DB00030)"""	TTATAAAAAAGGTTAGTAGAT	0.403		6	"""D, Mis, N, F, S"""		"""retinoblastoma, sarcoma, breast, small cell lung"""	"""retinoblastoma, sarcoma, breast, small cell lung"""			Hereditary Retinoblastoma	TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)																												uc001vcb.2		6	yes	Rec	yes	Familial retinoblastoma	13	13q14	5925	D|Mis|N|F|S	retinoblastoma gene			"""L, E, M, O"""		retinoblastoma|sarcoma|breast|small cell lung	retinoblastoma|sarcoma|breast|small cell lung		30	Whole gene deletion(15)|Unknown(10)|Substitution - Missense(4)|Deletion - Frameshift(1)	p.?(6)|p.V654fs*4(1)|p.V654fs*6(1)|p.V654L(1)	bone(10)|breast(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|adrenal_gland(1)|eye(1)|soft_tissue(1)|central_nervous_system(1)|endometrium(1)|urinary_tract(1)|lung(1)|skin(1)|liver(1)	lung(94)|eye(89)|central_nervous_system(47)|bone(22)|breast(21)|urinary_tract(17)|haematopoietic_and_lymphoid_tissue(14)|ovary(10)|prostate(9)|soft_tissue(8)|skin(7)|endometrium(5)|cervix(3)|liver(3)|salivary_gland(2)|stomach(2)|oesophagus(1)|adrenal_gland(1)|kidney(1)|gastrointestinal_tract_(site_indeterminate)(1)|pituitary(1)	358	GRCh37	CM034902|CS050405|CS081965|CS083261	RB1	M|S		c.(1960-1962)GTG>CTG		retinoblastoma 1	Insulin Glargine recombinant(DB00047)|Insulin Lyspro recombinant(DB00046)|Insulin recombinant(DB00030)|Insulin, porcine(DB00071)						53.0	51.0	51.0					13																	49030485		2203	4300	6503	SO:0001630	splice_region_variant	5925	Hereditary_Retinoblastoma	Familial Cancer Database		androgen receptor signaling pathway|cell cycle arrest|chromatin remodeling|G1 phase of mitotic cell cycle|interspecies interaction between organisms|maintenance of mitotic sister chromatid cohesion|mitotic cell cycle G1/S transition checkpoint|myoblast differentiation|negative regulation of cell growth|negative regulation of protein kinase activity|negative regulation of S phase of mitotic cell cycle|negative regulation of sequence-specific DNA binding transcription factor activity|positive regulation of mitotic metaphase/anaphase transition|protein localization to chromosome, centromeric region|Ras protein signal transduction|regulation of centromere complex assembly|regulation of cohesin localization to chromatin|regulation of lipid kinase activity|regulation of transcription involved in G1/S phase of mitotic cell cycle|S phase of mitotic cell cycle|sister chromatid biorientation	chromatin|PML body|Rb-E2F complex|SWI/SNF complex	androgen receptor binding|DNA binding|kinase binding|phosphoprotein binding|sequence-specific DNA binding transcription factor activity|transcription coactivator activity|transcription factor binding|ubiquitin protein ligase binding	g.chr13:49030485G>C	M15400	CCDS31973.1	13q14.2	2014-09-17	2008-07-31		ENSG00000139687	ENSG00000139687		"""Endogenous ligands"""	9884	protein-coding gene	gene with protein product	"""prepro-retinoblastoma-associated protein"", ""protein phosphatase 1, regulatory subunit 130"""	614041	"""osteosarcoma"""	OSRC		1857421, 15057823	Standard	NM_000321		Approved	RB, PPP1R130	uc001vcb.3	P06400	OTTHUMG00000016900	ENST00000267163.4:c.1960+1G>C	13.37:g.49030485G>C		TCGA GBM(7;6.82e-08)|TSP Lung(12;0.097)|TCGA Ovarian(6;0.080)					p.V654L	NM_000321	NP_000312	P06400	RB_HUMAN		GBM - Glioblastoma multiforme(2;9.98e-18)|LUSC - Lung squamous cell carcinoma(3;0.013)	19	2126	+		all_cancers(8;6.9e-71)|all_epithelial(8;4.61e-22)|Acute lymphoblastic leukemia(8;1.1e-21)|all_hematologic(8;2.3e-21)|all_lung(13;1.51e-09)|Lung NSC(96;7.03e-07)|Breast(56;1.53e-05)|Prostate(109;0.000493)|Myeloproliferative disorder(33;0.0179)|Hepatocellular(98;0.0207)|all_neural(104;0.0227)|Glioma(44;0.0286)|Lung SC(185;0.0301)	654		V -> E (in RB).	Pocket; binds T and E1A.|Domain B.		A8K5E3|P78499|Q5VW46|Q8IZL4	Missense_Mutation	SNP	ENST00000267163.4	37	c.1960G>C	CCDS31973.1	.	.	.	.	.	.	.	.	.	.	G	15.51	2.854399	0.51270	.	.	ENSG00000139687	ENST00000542917;ENST00000267163	D	0.93019	-3.15	5.97	5.97	0.96955	Retinoblastoma-associated protein, B-box (1);Cyclin-like (2);	0.216802	0.41097	D	0.000945	D	0.89842	0.6832	L	0.28115	0.83	0.52099	D	0.999941	B	0.31968	0.349	B	0.33799	0.17	D	0.86416	0.1751	10	0.27785	T	0.31	.	20.4214	0.99039	0.0:0.0:1.0:0.0	.	654	P06400	RB_HUMAN	L	633;654	ENSP00000267163:V654L	ENSP00000267163:V654L	V	+	1	0	RB1	47928486	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	5.809000	0.69172	2.820000	0.97059	0.655000	0.94253	GTG		0.403	RB1-002	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000044884.1		Missense_Mutation
ADAM21P1	145241	broad.mit.edu	37	14	70713534	70713534	+	RNA	SNP	G	G	A	rs546315157	byFrequency	TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr14:70713534G>A	ENST00000530196.1	-	0	984					NR_003951.1				ADAM metallopeptidase domain 21 pseudogene 1																		ATTTGTTTCCGTTGAGAGAAA	0.358													G|||	2	0.000399361	0.0	0.0	5008	,	,		23828	0.0		0.002	False		,,,				2504	0.0					uc010ttg.1																			0					0						c.(334-336)CGG>TGG		SubName: Full=ADAM21-like protein;																																						145241							g.chr14:70713534G>A			14q24.2	2014-03-25	2010-01-12	2010-01-12	ENSG00000235812	ENSG00000235812			19822	pseudogene	pseudogene			"""a disintegrin and metalloproteinase domain 21 pseudogene"", ""ADAM metallopeptidase domain 21 pseudogene"""	ADAM21P			Standard	NR_003951		Approved		uc010ttg.2		OTTHUMG00000166565		14.37:g.70713534G>A							p.R112W	NR_003951						1	985	-									Missense_Mutation	SNP	ENST00000530196.1	37	c.334C>T																																																																																					0.358	ADAM21P1-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000390451.1	NG_002467	
RIN3	79890	broad.mit.edu	37	14	93118565	93118565	+	Missense_Mutation	SNP	G	G	A	rs145578489		TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr14:93118565G>A	ENST00000216487.7	+	6	1330	c.1171G>A	c.(1171-1173)Gtt>Att	p.V391I	RIN3_ENST00000418924.2_3'UTR	NM_024832.3	NP_079108.3	Q8TB24	RIN3_HUMAN	Ras and Rab interactor 3	391	Pro-rich.				endocytosis (GO:0006897)|positive regulation of Rab GTPase activity (GO:0032851)|signal transduction (GO:0007165)	cytoplasmic vesicle (GO:0031410)|early endosome (GO:0005769)	GTPase activator activity (GO:0005096)|Rab GTPase binding (GO:0017137)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)			endometrium(4)|kidney(2)|large_intestine(7)|lung(19)|ovary(1)|prostate(1)|skin(1)|urinary_tract(1)	36		all_cancers(154;0.0701)				CAGACGCCGCGTTTCCGAGAG	0.667													G|||	1	0.000199681	0.0	0.0014	5008	,	,		12188	0.0		0.0	False		,,,				2504	0.0					uc001yap.2																			0				lung(2)|ovary(1)	3						c.(1171-1173)GTT>ATT		Ras and Rab interactor 3		G	ILE/VAL	12,4394	17.9+/-39.9	0,12,2191	37.0	39.0	38.0		1171	-8.2	0.0	14	dbSNP_134	38	1,8597	1.2+/-3.3	0,1,4298	yes	missense	RIN3	NM_024832.3	29	0,13,6489	AA,AG,GG		0.0116,0.2724,0.1	benign	391/986	93118565	13,12991	2203	4299	6502	SO:0001583	missense	79890				endocytosis|signal transduction	cytoplasmic membrane-bounded vesicle|early endosome	GTPase activator activity|Ras GTPase binding	g.chr14:93118565G>A	BC025248	CCDS32144.1	14q32.13	2008-08-29				ENSG00000100599			18751	protein-coding gene	gene with protein product		610223				11733506	Standard	NM_024832		Approved	FLJ22439	uc001yap.3	Q8TB24		ENST00000216487.7:c.1171G>A	14.37:g.93118565G>A	ENSP00000216487:p.Val391Ile					RIN3_uc010auk.2_Missense_Mutation_p.V53I|RIN3_uc001yaq.2_Missense_Mutation_p.V316I|RIN3_uc001yar.1_Missense_Mutation_p.V53I|RIN3_uc001yas.1_Missense_Mutation_p.V53I	p.V391I	NM_024832	NP_079108	Q8TB24	RIN3_HUMAN			6	1323	+		all_cancers(154;0.0701)	391			Pro-rich.		Q76LB3|Q8NF30|Q8TEE8|Q8WYP4|Q9H6A5|Q9HAG1	Missense_Mutation	SNP	ENST00000216487.7	37	c.1171G>A	CCDS32144.1	0	0.0	0	0.0	0	0.0	0	0.0	0	0.0	G	0.012	-1.654297	0.00779	0.002724	1.16E-4	ENSG00000100599	ENST00000216487;ENST00000428147	T	0.05199	3.48	4.08	-8.16	0.01061	.	1.273530	0.06078	N	0.661334	T	0.01254	0.0041	N	0.00237	-1.79	0.19945	N	0.999949	B;B;B;B	0.23128	0.08;0.0;0.0;0.024	B;B;B;B	0.16722	0.016;0.0;0.0;0.004	T	0.49476	-0.8936	10	0.15066	T	0.55	-10.3308	7.5813	0.27965	0.4216:0.3115:0.2669:0.0	.	391;437;316;391	Q8TB24-4;Q86U22;Q6ZRC2;Q8TB24	.;.;.;RIN3_HUMAN	I	391;315	ENSP00000216487:V391I	ENSP00000216487:V391I	V	+	1	0	RIN3	92188318	0.000000	0.05858	0.003000	0.11579	0.124000	0.20399	-2.702000	0.00823	-1.861000	0.01153	-1.800000	0.00619	GTT		0.667	RIN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412269.1		
RCOR1	23186	broad.mit.edu	37	14	103174815	103174815	+	Missense_Mutation	SNP	C	C	G			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr14:103174815C>G	ENST00000570597.1	+	6	665	c.665C>G	c.(664-666)tCt>tGt	p.S222C	RCOR1_ENST00000262241.6_Missense_Mutation_p.S225C			Q9UKL0	RCOR1_HUMAN	REST corepressor 1	222	Interaction with HDAC1.|SANT 1. {ECO:0000255|PROSITE- ProRule:PRU00624}.				blood coagulation (GO:0007596)|histone H4 deacetylation (GO:0070933)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|viral process (GO:0016032)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	chromatin binding (GO:0003682)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(6)|ovary(1)|upper_aerodigestive_tract(1)	12						CCAGATAAATCTATAGCAAGT	0.393																																						uc001ymb.2																			0				ovary(1)	1						c.(664-666)TCT>TGT		REST corepressor 1							131.0	150.0	144.0					14																	103174815		2203	4300	6503	SO:0001583	missense	23186				blood coagulation|histone H4 deacetylation|interspecies interaction between organisms	transcriptional repressor complex	protein binding|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription|transcription regulatory region DNA binding	g.chr14:103174815C>G	AF155595	CCDS9974.1, CCDS9974.2	14q32.33	2004-04-16	2004-04-16	2004-04-16		ENSG00000089902			17441	protein-coding gene	gene with protein product		607675	"""REST corepressor"""	RCOR		10449787	Standard	NM_015156		Approved	COREST, KIAA0071	uc001ymb.4	Q9UKL0		ENST00000570597.1:c.665C>G	14.37:g.103174815C>G	ENSP00000459789:p.Ser222Cys						p.S222C	NM_015156	NP_055971	Q9UKL0	RCOR1_HUMAN			6	665	+			222			Interaction with HDAC1.|SANT 1.		Q15044|Q6P2I9|Q86VG5	Missense_Mutation	SNP	ENST00000570597.1	37	c.665C>G		.	.	.	.	.	.	.	.	.	.	C	25.4	4.632785	0.87660	.	.	ENSG00000089902	ENST00000262241	.	.	.	5.88	5.88	0.94601	SANT domain, DNA binding (1);Homeodomain-like (1);SANT, eukarya (1);	0.052434	0.85682	D	0.000000	D	0.84497	0.5485	M	0.87971	2.92	0.80722	D	1	D	0.76494	0.999	D	0.65573	0.936	D	0.86042	0.1520	9	0.72032	D	0.01	-17.8216	20.2279	0.98344	0.0:1.0:0.0:0.0	.	222	Q9UKL0	RCOR1_HUMAN	C	222	.	ENSP00000262241:S222C	S	+	2	0	RCOR1	102244568	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.702000	0.68332	2.778000	0.95560	0.655000	0.94253	TCT		0.393	RCOR1-201	KNOWN	basic|appris_candidate	protein_coding	protein_coding		NM_015156	
JAG2	3714	broad.mit.edu	37	14	105617967	105617967	+	Silent	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr14:105617967G>A	ENST00000331782.3	-	8	1552	c.1149C>T	c.(1147-1149)gcC>gcT	p.A383A	RP11-44N21.4_ENST00000548203.1_RNA|JAG2_ENST00000347004.2_Silent_p.A383A	NM_002226.4	NP_002217.3	Q9Y219	JAG2_HUMAN	jagged 2	383	EGF-like 4. {ECO:0000255|PROSITE- ProRule:PRU00076}.				auditory receptor cell fate commitment (GO:0009912)|cell cycle (GO:0007049)|cell differentiation (GO:0030154)|epithelial cell apoptotic process involved in palatal shelf morphogenesis (GO:1990134)|gamma-delta T cell differentiation (GO:0042492)|in utero embryonic development (GO:0001701)|morphogenesis of embryonic epithelium (GO:0016331)|Notch receptor processing (GO:0007220)|Notch signaling pathway (GO:0007219)|odontogenesis of dentin-containing tooth (GO:0042475)|regulation of cell adhesion (GO:0030155)|regulation of cell migration (GO:0030334)|regulation of cell proliferation (GO:0042127)|respiratory system process (GO:0003016)|skeletal system development (GO:0001501)|spermatogenesis (GO:0007283)|T cell differentiation (GO:0030217)|thymic T cell selection (GO:0045061)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|growth factor activity (GO:0008083)|Notch binding (GO:0005112)			breast(2)|endometrium(2)|kidney(3)|large_intestine(1)|lung(7)|prostate(2)|skin(5)	22		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)		ACTCACCAAGGGCACAGGTGG	0.652																																						uc001yqg.2																			0				lung(3)|breast(2)	5						c.(1147-1149)GCC>GCT		jagged 2 isoform a precursor							22.0	21.0	21.0					14																	105617967		2195	4298	6493	SO:0001819	synonymous_variant	3714				auditory receptor cell fate commitment|cell communication|cell cycle|Notch receptor processing|Notch signaling pathway|regulation of cell migration|regulation of cell proliferation|spermatogenesis|thymic T cell selection	integral to plasma membrane	calcium ion binding|growth factor activity|Notch binding	g.chr14:105617967G>A	AF020201	CCDS9998.1, CCDS9999.1	14q32	2008-08-01			ENSG00000184916	ENSG00000184916			6189	protein-coding gene	gene with protein product		602570				9315665, 10662552	Standard	NM_002226		Approved		uc001yqg.4	Q9Y219	OTTHUMG00000140172	ENST00000331782.3:c.1149C>T	14.37:g.105617967G>A						JAG2_uc001yqf.2_5'Flank|JAG2_uc001yqh.2_Silent_p.A383A	p.A383A	NM_002226	NP_002217	Q9Y219	JAG2_HUMAN	OV - Ovarian serous cystadenocarcinoma(23;0.00989)|all cancers(16;0.0114)|Epithelial(46;0.0272)	Epithelial(152;0.047)|OV - Ovarian serous cystadenocarcinoma(161;0.148)|all cancers(159;0.208)	8	1553	-		all_cancers(154;0.0336)|all_epithelial(191;0.0729)|Melanoma(154;0.155)	383			EGF-like 4.|Extracellular (Potential).		Q9UE17|Q9UE99|Q9UNK8|Q9Y6P9|Q9Y6Q0	Silent	SNP	ENST00000331782.3	37	c.1149C>T	CCDS9998.1																																																																																				0.652	JAG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276506.2		
TMC3	342125	broad.mit.edu	37	15	81624852	81624852	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr15:81624852G>A	ENST00000359440.5	-	22	3346	c.3211C>T	c.(3211-3213)Ccg>Tcg	p.P1071S	RP11-761I4.3_ENST00000560851.1_RNA|TMC3_ENST00000558726.1_Missense_Mutation_p.P1072S|RP11-761I4.3_ENST00000559781.1_RNA|RP11-761I4.3_ENST00000560973.1_RNA	NM_001080532.1	NP_001074001.1			transmembrane channel-like 3											autonomic_ganglia(2)|breast(1)|endometrium(4)|kidney(1)|large_intestine(7)|liver(1)|lung(11)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	34						ACGGACCTCGGGAACCTGCCC	0.612																																						uc002bgo.1																			0				ovary(1)|liver(1)	2						c.(3211-3213)CCG>TCG		transmembrane channel-like 3							23.0	27.0	26.0					15																	81624852		2093	4226	6319	SO:0001583	missense	342125					integral to membrane		g.chr15:81624852G>A	AY263163	CCDS45324.1	15q24.3	2006-11-24				ENSG00000188869			22995	protein-coding gene	gene with protein product						12906855, 12812529	Standard	NM_001080532		Approved		uc021ssk.1	Q7Z5M5		ENST00000359440.5:c.3211C>T	15.37:g.81624852G>A	ENSP00000352413:p.Pro1071Ser					TMC3_uc010blr.1_RNA	p.P1071S	NM_001080532	NP_001074001	Q7Z5M5	TMC3_HUMAN			22	3211	-			1071			Cytoplasmic (Potential).			Missense_Mutation	SNP	ENST00000359440.5	37	c.3211C>T	CCDS45324.1	.	.	.	.	.	.	.	.	.	.	G	13.38	2.220545	0.39201	.	.	ENSG00000188869	ENST00000359440	T	0.64085	-0.08	5.2	0.964	0.19655	.	0.407073	0.17843	U	0.160132	T	0.42086	0.1187	L	0.29908	0.895	0.09310	N	1	B	0.13594	0.008	B	0.08055	0.003	T	0.23261	-1.0193	10	0.45353	T	0.12	-11.9835	3.1124	0.06363	0.1432:0.2566:0.4681:0.1322	.	1071	Q7Z5M5	TMC3_HUMAN	S	1071	ENSP00000352413:P1071S	ENSP00000352413:P1071S	P	-	1	0	TMC3	79411907	0.193000	0.23313	0.138000	0.22173	0.088000	0.18126	2.493000	0.45320	0.208000	0.20626	0.655000	0.94253	CCG		0.612	TMC3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000417795.3	NM_181841	
NPRL3	8131	broad.mit.edu	37	16	167362	167362	+	Missense_Mutation	SNP	C	C	G			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr16:167362C>G	ENST00000399953.3	-	4	733	c.331G>C	c.(331-333)Gat>Cat	p.D111H	NPRL3_ENST00000405960.3_5'UTR|NPRL3_ENST00000399951.3_Intron	NM_001077350.2|NM_001243247.1|NM_001243248.1|NM_001243249.1	NP_001070818.1|NP_001230176.1|NP_001230177.1|NP_001230178.1	Q12980	NPRL3_HUMAN	nitrogen permease regulator-like 3 (S. cerevisiae)	111					aorta morphogenesis (GO:0035909)|cardiac muscle tissue development (GO:0048738)|palate development (GO:0060021)|ventricular septum development (GO:0003281)		GTPase activator activity (GO:0005096)			endometrium(1)|large_intestine(3)|ovary(2)	6						GGGGAAGGATCTGTTTTGGAG	0.393																																						uc002cfr.2																			0				ovary(1)	1						c.(331-333)GAT>CAT		conserved gene telomeric to alpha globin cluster							58.0	56.0	56.0					16																	167362		1849	4085	5934	SO:0001583	missense	8131						protein binding	g.chr16:167362C>G		CCDS73794.1, CCDS73795.1	16p13.3	2011-01-06	2010-03-30	2010-03-30	ENSG00000103148	ENSG00000103148			14124	protein-coding gene	gene with protein product	"""conserved gene telomeric to alpha globin cluster"""	600928	"""chromosome 16 open reading frame 35"""	C16orf35		8575760	Standard	NM_001243247		Approved	CGTHBA, RMD11, NPR3, MARE, HS-40	uc002cfr.3	Q12980	OTTHUMG00000047792	ENST00000399953.3:c.331G>C	16.37:g.167362C>G	ENSP00000382834:p.Asp111His					NPRL3_uc010uua.1_Intron|NPRL3_uc002cfp.1_RNA|NPRL3_uc002cfq.2_Intron|NPRL3_uc010uub.1_Intron|NPRL3_uc010uuc.1_Missense_Mutation_p.D33H|NPRL3_uc002cfs.1_Intron	p.D111H	NM_001077350	NP_001070818	Q12980	NPRL3_HUMAN			5	430	-			111					D3DU40|Q1W6H0|Q4TT56|Q92469	Missense_Mutation	SNP	ENST00000399953.3	37	c.331G>C		.	.	.	.	.	.	.	.	.	.	C	25.5	4.645748	0.87958	.	.	ENSG00000103148	ENST00000399953;ENST00000419636	.	.	.	5.37	5.37	0.77165	Galactose-binding domain-like (1);	0.000000	0.85682	D	0.000000	T	0.80369	0.4610	.	.	.	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.979;0.999	T	0.81373	-0.0962	8	0.56958	D	0.05	-3.7903	18.4759	0.90792	0.0:1.0:0.0:0.0	.	33;111	B7Z220;Q12980	.;NPRL3_HUMAN	H	111;124	.	ENSP00000382834:D111H	D	-	1	0	NPRL3	107362	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	7.689000	0.84165	2.673000	0.90976	0.655000	0.94253	GAT		0.393	NPRL3-202	KNOWN	basic|appris_principal	protein_coding	protein_coding		NM_001039476	
SLC6A10P	386757	broad.mit.edu	37	16	32890954	32890954	+	RNA	SNP	C	C	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr16:32890954C>A	ENST00000330048.5	-	0	3012					NR_003083.2				solute carrier family 6 (neurotransmitter transporter), member 10, pseudogene																		ACCCAGACCACCACCACGCAC	0.632																																						uc002edh.1																			0					0						c.(100-102)GTG>TTG		RecName: Full=Transporter;																																						386757							g.chr16:32890954C>A	U41163		16p11.2	2013-07-19	2013-07-19	2013-07-19	ENSG00000214617	ENSG00000214617		"""Solute carriers"""	11043	pseudogene	pseudogene	"""creatine transporter-2"""		"""solute carrier family 6 (neurotransmitter transporter, creatine), member 10"""	SLC6A10		9154116	Standard	NR_003083		Approved	CT-2	uc002edh.1		OTTHUMG00000132481		16.37:g.32890954C>A						SLC6A10P_uc002edi.1_RNA	p.V34L							3	276	-									Missense_Mutation	SNP	ENST00000330048.5	37	c.100G>T																																																																																					0.632	SLC6A10P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000432081.2		
CX3CL1	6376	broad.mit.edu	37	16	57416501	57416501	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr16:57416501G>A	ENST00000006053.6	+	3	862	c.751G>A	c.(751-753)Gga>Aga	p.G251R	CX3CL1_ENST00000565912.1_Missense_Mutation_p.G213R|CX3CL1_ENST00000563383.1_Missense_Mutation_p.G257R	NM_002996.3	NP_002987.1	P78423	X3CL1_HUMAN	chemokine (C-X3-C motif) ligand 1	251	Mucin-like stalk.				angiogenesis involved in wound healing (GO:0060055)|cell adhesion (GO:0007155)|chemotaxis (GO:0006935)|cytokine-mediated signaling pathway (GO:0019221)|defense response (GO:0006952)|immune response (GO:0006955)|leukocyte adhesive activation (GO:0050902)|leukocyte chemotaxis (GO:0030595)|lymphocyte chemotaxis (GO:0048247)|macrophage chemotaxis (GO:0048246)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|neutrophil chemotaxis (GO:0030593)|positive regulation of angiogenesis (GO:0045766)|positive regulation of calcium-independent cell-cell adhesion (GO:0051041)|positive regulation of inflammatory response (GO:0050729)|positive regulation of transforming growth factor beta1 production (GO:0032914)	cell surface (GO:0009986)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	chemokine activity (GO:0008009)|receptor binding (GO:0005102)			breast(1)|endometrium(1)|large_intestine(1)|lung(2)	5						GTGGGGTCAGGGACAGAGCCC	0.692																																						uc002eli.2																			0					0						c.(751-753)GGA>AGA		chemokine (C-X3-C motif) ligand 1 precursor							35.0	40.0	39.0					16																	57416501		2198	4300	6498	SO:0001583	missense	6376				cell adhesion|cytokine-mediated signaling pathway|defense response|immune response|leukocyte adhesive activation|positive regulation of calcium-independent cell-cell adhesion|positive regulation of inflammatory response	cell surface|extracellular space|integral to membrane|plasma membrane	chemokine activity	g.chr16:57416501G>A	U84487	CCDS10779.1	16q13	2013-02-25	2002-08-22	2002-08-23	ENSG00000006210	ENSG00000006210		"""Endogenous ligands"""	10647	protein-coding gene	gene with protein product		601880	"""small inducible cytokine subfamily D (Cys-X3-Cys), member 1 (fractalkine, neurotactin)"""	SCYD1		9177350, 9024663	Standard	NM_002996		Approved	NTN, C3Xkine, ABCD-3, CXC3C, CXC3, fractalkine, neurotactin	uc002eli.3	P78423	OTTHUMG00000133469	ENST00000006053.6:c.751G>A	16.37:g.57416501G>A	ENSP00000006053:p.Gly251Arg						p.G251R	NM_002996	NP_002987	P78423	X3CL1_HUMAN			3	818	+			251			Mucin-like stalk.|Extracellular (Potential).		O00672	Missense_Mutation	SNP	ENST00000006053.6	37	c.751G>A	CCDS10779.1	.	.	.	.	.	.	.	.	.	.	G	11.00	1.510062	0.27036	.	.	ENSG00000006210	ENST00000006053	T	0.04809	3.55	4.23	3.26	0.37387	.	3.482270	0.02239	U	0.065559	T	0.04815	0.0130	L	0.27053	0.805	0.09310	N	1	P	0.36616	0.561	B	0.27500	0.08	T	0.38200	-0.9672	10	0.87932	D	0	-15.0125	8.2808	0.31900	0.1139:0.0:0.8861:0.0	.	251	P78423	X3CL1_HUMAN	R	251	ENSP00000006053:G251R	ENSP00000006053:G251R	G	+	1	0	CX3CL1	55974002	0.003000	0.15002	0.001000	0.08648	0.006000	0.05464	1.234000	0.32660	0.871000	0.35750	0.558000	0.71614	GGA		0.692	CX3CL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257345.3	NM_002996	
SCN4A	6329	broad.mit.edu	37	17	62018566	62018566	+	Silent	SNP	C	C	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr17:62018566C>T	ENST00000435607.1	-	24	5152	c.5076G>A	c.(5074-5076)ggG>ggA	p.G1692G	SCN4A_ENST00000578147.1_Silent_p.G1692G	NM_000334.4	NP_000325.4	P35499	SCN4A_HUMAN	sodium channel, voltage-gated, type IV, alpha subunit	1692					membrane depolarization during action potential (GO:0086010)|muscle contraction (GO:0006936)|neuronal action potential (GO:0019228)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	voltage-gated sodium channel activity (GO:0005248)			breast(4)|central_nervous_system(3)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(40)|ovary(3)|pancreas(1)|prostate(6)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	101					Diclofenac(DB00586)|Flecainide(DB01195)|Propofol(DB00818)|Valproic Acid(DB00313)|Zonisamide(DB00909)	CGTCCATTTCCCCAGAGTCAC	0.577																																						uc002jds.1																			0				ovary(1)|pancreas(1)|skin(1)	3						c.(5074-5076)GGG>GGA		voltage-gated sodium channel type 4 alpha	Lamotrigine(DB00555)						128.0	124.0	125.0					17																	62018566		2081	4211	6292	SO:0001819	synonymous_variant	6329				muscle contraction	voltage-gated sodium channel complex	voltage-gated sodium channel activity	g.chr17:62018566C>T	U24693		17q23.3	2012-02-26	2007-01-23					"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10591	protein-coding gene	gene with protein product		603967		HYKPP		1654742, 1659948, 16382098	Standard	XM_005257566		Approved	Nav1.4, HYPP, SkM1	uc002jds.1	P35499		ENST00000435607.1:c.5076G>A	17.37:g.62018566C>T							p.G1692G	NM_000334	NP_000325	P35499	SCN4A_HUMAN			24	5153	-			1692					Q15478|Q16447|Q7Z6B1	Silent	SNP	ENST00000435607.1	37	c.5076G>A	CCDS45761.1																																																																																				0.577	SCN4A-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		NM_000334	
ITGB4	3691	broad.mit.edu	37	17	73745120	73745120	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr17:73745120G>A	ENST00000200181.3	+	27	3497	c.3310G>A	c.(3310-3312)Gac>Aac	p.D1104N	ITGB4_ENST00000449880.2_Missense_Mutation_p.D1104N|ITGB4_ENST00000450894.3_Missense_Mutation_p.D1104N|ITGB4_ENST00000579662.1_Missense_Mutation_p.D1104N|ITGB4_ENST00000339591.3_Missense_Mutation_p.D1104N	NM_000213.3	NP_000204.3	P16144	ITB4_HUMAN	integrin, beta 4	1104					amelogenesis (GO:0097186)|autophagy (GO:0006914)|cell adhesion (GO:0007155)|cell junction assembly (GO:0034329)|cell motility (GO:0048870)|cell-matrix adhesion (GO:0007160)|digestive tract development (GO:0048565)|extracellular matrix organization (GO:0030198)|filopodium assembly (GO:0046847)|hemidesmosome assembly (GO:0031581)|integrin-mediated signaling pathway (GO:0007229)|mesodermal cell differentiation (GO:0048333)|nail development (GO:0035878)|renal system development (GO:0072001)|response to wounding (GO:0009611)|skin development (GO:0043588)	basal plasma membrane (GO:0009925)|basement membrane (GO:0005604)|cell leading edge (GO:0031252)|cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|hemidesmosome (GO:0030056)|integrin complex (GO:0008305)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	G-protein coupled receptor binding (GO:0001664)|receptor activity (GO:0004872)			breast(2)|central_nervous_system(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(3)|liver(1)|lung(25)|skin(1)|urinary_tract(1)	43	all_cancers(13;1.5e-07)		all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)			CATCATCAGGGACCCAGGTAG	0.617																																						uc002jpg.2																			0				lung(4)	4						c.(3310-3312)GAC>AAC		integrin beta 4 isoform 1 precursor							20.0	23.0	22.0					17																	73745120		2202	4298	6500	SO:0001583	missense	3691				cell communication|cell motility|cell-matrix adhesion|hemidesmosome assembly|integrin-mediated signaling pathway|multicellular organismal development|response to wounding	cell leading edge|cell surface|hemidesmosome|integrin complex	protein binding|receptor activity	g.chr17:73745120G>A		CCDS11727.1, CCDS32736.1, CCDS58599.1	17q25.1	2013-09-19			ENSG00000132470	ENSG00000132470		"""CD molecules"", ""Integrins"", ""Fibronectin type III domain containing"""	6158	protein-coding gene	gene with protein product		147557				2070796	Standard	XM_005257309		Approved	CD104	uc002jpg.3	P16144	OTTHUMG00000179814	ENST00000200181.3:c.3310G>A	17.37:g.73745120G>A	ENSP00000200181:p.Asp1104Asn					ITGB4_uc002jph.2_Missense_Mutation_p.D1104N|ITGB4_uc002jpi.3_Missense_Mutation_p.D1104N|ITGB4_uc002jpj.2_Missense_Mutation_p.D1104N	p.D1104N	NM_000213	NP_000204	P16144	ITB4_HUMAN	all cancers(21;8.32e-07)|Epithelial(20;1.92e-06)|BRCA - Breast invasive adenocarcinoma(9;0.00194)|Lung(188;0.132)|LUSC - Lung squamous cell carcinoma(166;0.154)		27	3497	+	all_cancers(13;1.5e-07)		1104			Cytoplasmic (Potential).		A0AVL6|O14690|O14691|O15339|O15340|O15341|Q0VF97|Q9UIQ4	Missense_Mutation	SNP	ENST00000200181.3	37	c.3310G>A	CCDS11727.1	.	.	.	.	.	.	.	.	.	.	G	11.60	1.686922	0.29962	.	.	ENSG00000132470	ENST00000200181;ENST00000339591;ENST00000449880	T;T;T	0.34275	1.37;1.37;1.37	5.24	4.06	0.47325	.	0.202568	0.40302	N	0.001140	T	0.25082	0.0609	N	0.14661	0.345	0.46241	D	0.998941	P;P;P	0.43788	0.817;0.722;0.586	B;B;B	0.41299	0.353;0.193;0.193	T	0.13899	-1.0492	10	0.59425	D	0.04	.	14.7111	0.69232	0.082:0.0:0.918:0.0	.	1104;1104;1104	P16144-3;A0AVL6;P16144	.;.;ITB4_HUMAN	N	1104	ENSP00000200181:D1104N;ENSP00000344079:D1104N;ENSP00000400217:D1104N	ENSP00000200181:D1104N	D	+	1	0	ITGB4	71256715	1.000000	0.71417	0.871000	0.34182	0.194000	0.23727	2.840000	0.48215	2.458000	0.83093	0.650000	0.86243	GAC		0.617	ITGB4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000448334.1		
PRKCSH	5589	broad.mit.edu	37	19	11559895	11559895	+	Missense_Mutation	SNP	T	T	C			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr19:11559895T>C	ENST00000589838.1	+	15	1345	c.1345T>C	c.(1345-1347)Tgg>Cgg	p.W449R	PRKCSH_ENST00000592741.1_Missense_Mutation_p.W456R|PRKCSH_ENST00000591462.1_Missense_Mutation_p.W446R|PRKCSH_ENST00000587327.1_Missense_Mutation_p.W446R|PRKCSH_ENST00000412601.1_Missense_Mutation_p.W446R|PRKCSH_ENST00000252455.2_Missense_Mutation_p.W449R			P14314	GLU2B_HUMAN	protein kinase C substrate 80K-H	449	PRKCSH.				cellular protein metabolic process (GO:0044267)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|liver development (GO:0001889)|N-glycan processing (GO:0006491)|negative regulation of neuron projection development (GO:0010977)|nitrogen compound metabolic process (GO:0006807)|post-translational protein modification (GO:0043687)|protein folding (GO:0006457)|protein heterooligomerization (GO:0051291)|protein N-linked glycosylation via asparagine (GO:0018279)|renal system development (GO:0072001)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|intracellular (GO:0005622)	calcium ion binding (GO:0005509)|ion channel binding (GO:0044325)|phosphoprotein binding (GO:0051219)|protein kinase C binding (GO:0005080)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|prostate(3)	19						TCACAGCACCTGGGGCTCATG	0.662																																						uc002mrt.2																			0					0						c.(1345-1347)TGG>CGG		protein kinase C substrate 80K-H isoform 1							51.0	53.0	52.0					19																	11559895		2203	4300	6503	SO:0001583	missense	5589				innate immune response|intracellular protein kinase cascade|post-translational protein modification|protein folding|protein N-linked glycosylation via asparagine	endoplasmic reticulum lumen	calcium ion binding|protein kinase C binding	g.chr19:11559895T>C		CCDS32911.1, CCDS45977.1, CCDS74286.1	19p13.2	2014-01-30			ENSG00000130175	ENSG00000130175	2.7.11.1	"""EF-hand domain containing"""	9411	protein-coding gene	gene with protein product		177060	"""polycystic liver disease"""	G19P1, PCLD, PLD1		12529853	Standard	NM_002743		Approved		uc002mrt.3	P14314	OTTHUMG00000182029	ENST00000589838.1:c.1345T>C	19.37:g.11559895T>C	ENSP00000465461:p.Trp449Arg					PRKCSH_uc002mru.2_Missense_Mutation_p.W446R|PRKCSH_uc010xlz.1_Missense_Mutation_p.W456R|PRKCSH_uc010dya.2_Missense_Mutation_p.W231R|PRKCSH_uc010dyb.2_Missense_Mutation_p.W446R	p.W449R	NM_002743	NP_002734	P14314	GLU2B_HUMAN			16	1681	+			449			PRKCSH.		A8K318|Q96BU9|Q96D06|Q9P0W9	Missense_Mutation	SNP	ENST00000589838.1	37	c.1345T>C	CCDS32911.1	.	.	.	.	.	.	.	.	.	.	T	12.71	2.019597	0.35606	.	.	ENSG00000130175	ENST00000252455;ENST00000412601	T;T	0.81247	-1.47;-1.47	4.67	2.54	0.30619	Mannose-6-phosphate receptor, binding (1);Glucosidase II beta subunit-like (1);	0.000000	0.85682	D	0.000000	D	0.89065	0.6609	M	0.90705	3.14	0.80722	D	1	D;D;D;D	0.89917	1.0;1.0;0.994;1.0	D;D;D;D	0.87578	0.998;0.998;0.945;0.997	D	0.86199	0.1617	10	0.87932	D	0	-15.8327	5.8542	0.18710	0.1475:0.0843:0.0:0.7682	.	456;456;446;449	E7EQZ9;B4DJQ5;A8K318;P14314	.;.;.;GLU2B_HUMAN	R	449;446	ENSP00000252455:W449R;ENSP00000395616:W446R	ENSP00000252455:W449R	W	+	1	0	PRKCSH	11420895	1.000000	0.71417	0.907000	0.35723	0.013000	0.08279	7.084000	0.76866	0.168000	0.19655	-0.256000	0.11100	TGG		0.662	PRKCSH-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000458817.1		
LRP3	4037	broad.mit.edu	37	19	33695616	33695616	+	Silent	SNP	A	A	C			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr19:33695616A>C	ENST00000253193.7	+	4	535	c.333A>C	c.(331-333)ccA>ccC	p.P111P	CTD-2540B15.13_ENST00000609744.1_RNA	NM_002333.3	NP_002324.2	O75074	LRP3_HUMAN	low density lipoprotein receptor-related protein 3	111	CUB 1. {ECO:0000255|PROSITE- ProRule:PRU00059}.				receptor-mediated endocytosis (GO:0006898)	coated pit (GO:0005905)|integral component of membrane (GO:0016021)		p.P111P(1)		breast(1)|kidney(1)|large_intestine(1)|lung(9)|ovary(1)|pancreas(2)	15	Esophageal squamous(110;0.137)					CAGCAGCCCCACCCCGCCAGG	0.662																																						uc010edh.2																			1	Substitution - coding silent(1)		lung(1)	pancreas(2)|ovary(1)	3						c.(331-333)CCA>CCC		low density lipoprotein receptor-related protein							56.0	59.0	58.0					19																	33695616		2203	4299	6502	SO:0001819	synonymous_variant	4037				receptor-mediated endocytosis	coated pit|integral to membrane	receptor activity	g.chr19:33695616A>C	AB009462	CCDS12430.1	19q13.11	2013-05-30			ENSG00000130881	ENSG00000130881		"""Low density lipoprotein receptors"""	6695	protein-coding gene	gene with protein product		603159				9693042, 7959795	Standard	NM_002333		Approved	LRP-3, hLRp105	uc010edh.3	O75074	OTTHUMG00000180343	ENST00000253193.7:c.333A>C	19.37:g.33695616A>C						LRP3_uc010xrp.1_5'UTR|LRP3_uc002nuk.3_5'UTR	p.P111P	NM_002333	NP_002324	O75074	LRP3_HUMAN			4	426	+	Esophageal squamous(110;0.137)		111			Extracellular (Potential).|CUB 1.		B3KQD6|B4DKF2	Silent	SNP	ENST00000253193.7	37	c.333A>C	CCDS12430.1																																																																																				0.662	LRP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000450842.4		
BCKDHA	593	broad.mit.edu	37	19	41932546	41932546	+	IGR	SNP	C	C	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr19:41932546C>T	ENST00000269980.2	+	0	2103				B3GNT8_ENST00000601379.1_Intron|CTC-435M10.6_ENST00000598887.1_RNA|B3GNT8_ENST00000321702.2_Silent_p.T46T	NM_000709.3|NM_001164783.1	NP_000700.1|NP_001158255.1	P12694	ODBA_HUMAN	branched chain keto acid dehydrogenase E1, alpha polypeptide						branched-chain amino acid catabolic process (GO:0009083)|cellular nitrogen compound metabolic process (GO:0034641)|response to cAMP (GO:0051591)|response to glucocorticoid (GO:0051384)|response to nutrient (GO:0007584)|small molecule metabolic process (GO:0044281)	mitochondrial alpha-ketoglutarate dehydrogenase complex (GO:0005947)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	3-methyl-2-oxobutanoate dehydrogenase (2-methylpropanoyl-transferring) activity (GO:0003863)|alpha-ketoacid dehydrogenase activity (GO:0003826)|carboxy-lyase activity (GO:0016831)|metal ion binding (GO:0046872)			central_nervous_system(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)	10						GGTTGGCTGGCGTGGGGCTTG	0.662																																						uc002oqs.2																			0					0						c.(136-138)ACG>ACA		UDP-GlcNAc:betaGal							31.0	29.0	30.0					19																	41932546		2203	4297	6500	SO:0001628	intergenic_variant	374907				poly-N-acetyllactosamine biosynthetic process|protein glycosylation	Golgi membrane|integral to membrane	galactosyltransferase activity|protein N-acetylglucosaminyltransferase activity	g.chr19:41932546C>T	J04474	CCDS12581.1	19q13.1-q13.2	2008-07-09	2005-11-29		ENSG00000248098	ENSG00000248098			986	protein-coding gene	gene with protein product	"""maple syrup urine disease"""	608348	"""branched chain keto acid dehydrogenase E1, alpha polypeptide (maple syrup urine disease)"", ""2-oxoisovalerate dehydrogenase (lipoamide)"""	OVD1A			Standard	NM_000709		Approved	MSU	uc002oqq.3	P12694	OTTHUMG00000168128		19.37:g.41932546C>T						CYP2F1_uc010xvw.1_Intron|B3GNT8_uc002oqt.1_Intron	p.T46T	NM_198540	NP_940942	Q7Z7M8	B3GN8_HUMAN			3	592	-			46			Lumenal (Potential).		B4DP47|E7EW46|Q16034|Q16472	Silent	SNP	ENST00000269980.2	37	c.138G>A	CCDS12581.1																																																																																				0.662	BCKDHA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000398313.3	NM_000709	
TRAPPC12	51112	broad.mit.edu	37	2	3392024	3392024	+	Silent	SNP	C	C	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr2:3392024C>T	ENST00000324266.5	+	2	825	c.630C>T	c.(628-630)ttC>ttT	p.F210F	TRAPPC12_ENST00000382110.2_Silent_p.F210F	NM_016030.5	NP_057114.5	Q8WVT3	TPC12_HUMAN	trafficking protein particle complex 12	210					vesicle-mediated transport (GO:0016192)												GCACGTTCTTCGGAGACACGG	0.677																																						uc002qxm.1																			0				ovary(2)|breast(1)|pancreas(1)	4						c.(628-630)TTC>TTT		tetratricopeptide repeat domain 15							32.0	38.0	36.0					2																	3392024		2203	4300	6503	SO:0001819	synonymous_variant	51112						binding	g.chr2:3392024C>T	BC017475	CCDS1652.1	2p25.3	2013-01-10	2011-12-12	2011-12-12	ENSG00000171853	ENSG00000171853		"""Trafficking protein particle complex"", ""Tetratricopeptide (TTC) repeat domain containing"""	24284	protein-coding gene	gene with protein product		614139	"""tetratricopeptide repeat domain 15"""	TTC15		10810093, 21525244, 20562859	Standard	NM_016030		Approved	CGI-87, TTC-15	uc002qxm.1	Q8WVT3	OTTHUMG00000090328	ENST00000324266.5:c.630C>T	2.37:g.3392024C>T						TTC15_uc002qxn.1_Silent_p.F210F|TTC15_uc010ewm.1_Silent_p.F210F|TTC15_uc002qxl.1_Silent_p.F210F	p.F210F	NM_016030	NP_057114	Q8WVT3	TTC15_HUMAN		OV - Ovarian serous cystadenocarcinoma(76;0.0402)|Epithelial(75;0.0986)|all cancers(51;0.149)	2	836	+	Acute lymphoblastic leukemia(172;0.0627)|all_hematologic(175;0.093)	all_cancers(51;0.214)	210					B3KV01|D6W4Y2|Q8WVW1|Q9Y395	Silent	SNP	ENST00000324266.5	37	c.630C>T	CCDS1652.1																																																																																				0.677	TRAPPC12-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206693.2	NM_016030	
GREB1	9687	broad.mit.edu	37	2	11706613	11706613	+	Silent	SNP	C	C	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr2:11706613C>T	ENST00000381486.2	+	4	585	c.285C>T	c.(283-285)tgC>tgT	p.C95C	GREB1_ENST00000389825.3_5'UTR|GREB1_ENST00000234142.5_Silent_p.C95C|GREB1_ENST00000381483.2_Silent_p.C95C|GREB1_ENST00000263834.5_Silent_p.C95C	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	95						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TAGGGTTTTGCCAGGCCGGGA	0.642																																					Ovarian(39;850 945 2785 23371 33093)	uc002rbk.1																			0				ovary(1)	1						c.(283-285)TGC>TGT		growth regulation by estrogen in breast cancer 1							47.0	47.0	47.0					2																	11706613		2203	4300	6503	SO:0001819	synonymous_variant	9687					integral to membrane		g.chr2:11706613C>T		CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.285C>T	2.37:g.11706613C>T						GREB1_uc002rbl.2_Silent_p.C95C|GREB1_uc002rbm.2_5'UTR|GREB1_uc002rbn.1_Silent_p.C95C	p.C95C	NM_014668	NP_055483	Q4ZG55	GREB1_HUMAN		Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)	4	585	+	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)		95					A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	ENST00000381486.2	37	c.285C>T	CCDS42655.1																																																																																				0.642	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280490.1	NM_014668	
BUB1	699	broad.mit.edu	37	2	111408233	111408233	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr2:111408233C>T	ENST00000302759.6	-	18	2211	c.2093G>A	c.(2092-2094)tGc>tAc	p.C698Y	BUB1_ENST00000535254.1_Missense_Mutation_p.C678Y|BUB1_ENST00000409311.1_Missense_Mutation_p.C698Y	NM_004336.3	NP_004327.1	O43683	BUB1_HUMAN	BUB1 mitotic checkpoint serine/threonine kinase	698					apoptotic process (GO:0006915)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|positive regulation of intrinsic apoptotic signaling pathway (GO:2001244)|regulation of chromosome segregation (GO:0051983)|regulation of sister chromatid cohesion (GO:0007063)|spindle assembly checkpoint (GO:0071173)|viral process (GO:0016032)	condensed chromosome kinetochore (GO:0000777)|condensed nuclear chromosome, centromeric region (GO:0000780)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)			breast(3)|endometrium(8)|kidney(4)|large_intestine(9)|lung(18)|ovary(1)|prostate(1)|stomach(1)	45		Ovarian(717;0.0822)		BRCA - Breast invasive adenocarcinoma(221;0.0556)		TGTGAGTCTGCAAGCCTCAAC	0.532																																						uc002tgc.2																			0				lung(2)|breast(2)|stomach(1)|ovary(1)|kidney(1)	7						c.(2092-2094)TGC>TAC		budding uninhibited by benzimidazoles 1							106.0	76.0	86.0					2																	111408233		2203	4300	6503	SO:0001583	missense	699				apoptosis|cell division|chromosome segregation|interspecies interaction between organisms|mitotic cell cycle spindle assembly checkpoint|mitotic prometaphase|regulation of sister chromatid cohesion	condensed chromosome kinetochore|cytosol	ATP binding|protein binding|protein serine/threonine kinase activity	g.chr2:111408233C>T	AF046078	CCDS33273.1, CCDS62984.1, CCDS62985.1	2q13	2013-01-17	2013-01-17		ENSG00000169679	ENSG00000169679			1148	protein-coding gene	gene with protein product		602452	"""budding uninhibited by benzimidazoles 1 (yeast homolog)"", ""budding uninhibited by benzimidazoles 1 homolog (yeast)"""	BUB1L			Standard	NM_004336		Approved	hBUB1, BUB1A	uc002tgc.3	O43683	OTTHUMG00000153638	ENST00000302759.6:c.2093G>A	2.37:g.111408233C>T	ENSP00000302530:p.Cys698Tyr					BUB1_uc010yxh.1_Missense_Mutation_p.C678Y|BUB1_uc010fkb.2_Missense_Mutation_p.C698Y	p.C698Y	NM_004336	NP_004327	O43683	BUB1_HUMAN		BRCA - Breast invasive adenocarcinoma(221;0.0556)	18	2205	-		Ovarian(717;0.0822)	698					E9PC26|F5GXI5|O43430|O43643|O60626|Q53QE4	Missense_Mutation	SNP	ENST00000302759.6	37	c.2093G>A	CCDS33273.1	.	.	.	.	.	.	.	.	.	.	C	2.809	-0.247304	0.05867	.	.	ENSG00000169679	ENST00000535254;ENST00000409311;ENST00000302759;ENST00000541432	T;T;T	0.31510	2.24;1.49;2.5	5.18	2.62	0.31277	.	0.422043	0.30210	N	0.010152	T	0.20007	0.0481	L	0.55481	1.735	0.09310	N	1	B;B;B	0.13145	0.004;0.007;0.007	B;B;B	0.11329	0.006;0.004;0.004	T	0.37314	-0.9711	10	0.02654	T	1	-1.0035	4.4399	0.11568	0.1846:0.6464:0.0:0.169	.	678;698;698	F5GXI5;E9PC26;O43683	.;.;BUB1_HUMAN	Y	678;698;698;698	ENSP00000441013:C678Y;ENSP00000386701:C698Y;ENSP00000302530:C698Y	ENSP00000302530:C698Y	C	-	2	0	BUB1	111124705	0.429000	0.25530	0.005000	0.12908	0.077000	0.17291	0.633000	0.24598	0.397000	0.25310	0.650000	0.86243	TGC		0.532	BUB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331925.1	NM_004336	
SCN9A	6335	broad.mit.edu	37	2	167055444	167055444	+	Missense_Mutation	SNP	C	C	G	rs180949263		TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr2:167055444C>G	ENST00000409435.1	-	26	5704	c.5705G>C	c.(5704-5706)cGt>cCt	p.R1902P	SCN9A_ENST00000375387.4_Missense_Mutation_p.R1903P|AC010127.3_ENST00000447809.2_RNA|SCN9A_ENST00000409672.1_Missense_Mutation_p.R1891P|SCN9A_ENST00000303354.6_Missense_Mutation_p.R1903P			Q15858	SCN9A_HUMAN	sodium channel, voltage-gated, type IX, alpha subunit	1902	IQ.				behavioral response to pain (GO:0048266)|inflammatory response (GO:0006954)|membrane depolarization during action potential (GO:0086010)|neuronal action potential (GO:0019228)|post-embryonic development (GO:0009791)|response to toxic substance (GO:0009636)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	plasma membrane (GO:0005886)|voltage-gated sodium channel complex (GO:0001518)	sodium ion binding (GO:0031402)|voltage-gated sodium channel activity (GO:0005248)			NS(1)|breast(5)|central_nervous_system(6)|endometrium(6)|kidney(3)|large_intestine(27)|lung(38)|ovary(6)|prostate(8)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	108					Lacosamide(DB06218)|Lidocaine(DB00281)|Ranolazine(DB00243)|Rufinamide(DB06201)|Valproic Acid(DB00313)|Zonisamide(DB00909)	TAAGCGGTAACGTCTATAAGC	0.363																																						uc010fpl.2																			0				ovary(6)|central_nervous_system(5)|skin(2)	13						c.(5671-5673)CGT>CCT		sodium channel, voltage-gated, type IX, alpha	Lamotrigine(DB00555)|Lidocaine(DB00281)						165.0	171.0	169.0					2																	167055444		2161	4280	6441	SO:0001583	missense	6335					voltage-gated sodium channel complex	voltage-gated sodium channel activity	g.chr2:167055444C>G	X82835	CCDS46441.1	2q24	2014-09-17	2007-01-23		ENSG00000169432	ENSG00000169432		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10597	protein-coding gene	gene with protein product		603415	"""sodium channel, voltage-gated, type IX, alpha polypeptide"""			7720699, 10198179, 16382098	Standard	NM_002977		Approved	Nav1.7, PN1, NE-NA, NENA, ETHA	uc010fpl.3	Q15858	OTTHUMG00000154044	ENST00000409435.1:c.5705G>C	2.37:g.167055444C>G	ENSP00000386330:p.Arg1902Pro					uc002udp.2_Intron	p.R1891P	NM_002977	NP_002968	Q15858	SCN9A_HUMAN			27	6013	-			1902			IQ.		A1BUH5|Q6B4R9|Q6B4S0|Q6B4S1|Q70HX1|Q70HX2|Q8WTU1|Q8WWN4	Missense_Mutation	SNP	ENST00000409435.1	37	c.5672G>C	CCDS46441.1	.	.	.	.	.	.	.	.	.	.	C	13.22	2.172160	0.38315	.	.	ENSG00000169432	ENST00000409672;ENST00000375387;ENST00000303354;ENST00000409435	D;D;D;D	0.96491	-4.0;-4.03;-4.03;-4.03	6.08	3.34	0.38264	.	0.183937	0.39544	N	0.001334	D	0.95872	0.8656	M	0.66939	2.045	0.42059	D	0.991154	P	0.46912	0.886	P	0.49637	0.617	D	0.94942	0.8092	10	0.62326	D	0.03	.	10.3652	0.44019	0.0:0.7962:0.0:0.2038	.	1891	E7EUN6	.	P	1891;1903;1903;1902	ENSP00000386306:R1891P;ENSP00000364536:R1903P;ENSP00000304748:R1903P;ENSP00000386330:R1902P	ENSP00000304748:R1903P	R	-	2	0	SCN9A	166763690	0.000000	0.05858	0.998000	0.56505	0.610000	0.37248	-0.006000	0.12833	0.928000	0.37168	-0.186000	0.12905	CGT		0.363	SCN9A-004	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000333639.1	NM_002977	
COL3A1	1281	broad.mit.edu	37	2	189868848	189868848	+	Silent	SNP	G	G	A	rs113870310	byFrequency	TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr2:189868848G>A	ENST00000304636.3	+	39	2972	c.2802G>A	c.(2800-2802)tcG>tcA	p.S934S	COL3A1_ENST00000317840.5_Intron	NM_000090.3	NP_000081	P02461	CO3A1_HUMAN	collagen, type III, alpha 1	934	Triple-helical region.				aging (GO:0007568)|axon guidance (GO:0007411)|blood vessel development (GO:0001568)|cell-matrix adhesion (GO:0007160)|cellular response to amino acid stimulus (GO:0071230)|cerebral cortex development (GO:0021987)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|digestive tract development (GO:0048565)|extracellular fibril organization (GO:0043206)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|heart development (GO:0007507)|integrin-mediated signaling pathway (GO:0007229)|negative regulation of immune response (GO:0050777)|negative regulation of neuron migration (GO:2001223)|peptide cross-linking (GO:0018149)|platelet activation (GO:0030168)|positive regulation of Rho protein signal transduction (GO:0035025)|response to cytokine (GO:0034097)|response to mechanical stimulus (GO:0009612)|response to radiation (GO:0009314)|skeletal system development (GO:0001501)|skin development (GO:0043588)|transforming growth factor beta receptor signaling pathway (GO:0007179)|wound healing (GO:0042060)	collagen type III trimer (GO:0005586)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)	extracellular matrix structural constituent (GO:0005201)|integrin binding (GO:0005178)|metal ion binding (GO:0046872)|platelet-derived growth factor binding (GO:0048407)	p.S934S(1)		NS(2)|breast(1)|central_nervous_system(7)|cervix(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(60)|ovary(4)|pancreas(1)|prostate(5)|skin(10)|upper_aerodigestive_tract(3)|urinary_tract(3)	126			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		Collagenase(DB00048)	AGAAGGGATCGCCTGGTGCCC	0.488													g|||	2	0.000399361	0.0	0.0	5008	,	,		14549	0.0		0.002	False		,,,				2504	0.0					uc002uqj.1																			1	Substitution - coding silent(1)	p.S934S(1)	central_nervous_system(1)	central_nervous_system(7)|ovary(4)|large_intestine(2)	13						c.(2800-2802)TCG>TCA		collagen type III alpha 1 preproprotein	Collagenase(DB00048)|Palifermin(DB00039)						31.0	36.0	34.0					2																	189868848		2203	4300	6503	SO:0001819	synonymous_variant	1281				axon guidance|cell-matrix adhesion|collagen biosynthetic process|collagen fibril organization|fibril organization|heart development|integrin-mediated signaling pathway|negative regulation of immune response|peptide cross-linking|platelet activation|response to cytokine stimulus|response to radiation|skin development|transforming growth factor beta receptor signaling pathway	collagen type III|extracellular space	extracellular matrix structural constituent|integrin binding|platelet-derived growth factor binding	g.chr2:189868848G>A	X15332	CCDS2297.1	2q32.2	2014-09-17	2008-06-23		ENSG00000168542	ENSG00000168542		"""Collagens"""	2201	protein-coding gene	gene with protein product		120180	"""Ehlers-Danlos syndrome type IV, autosomal dominant"""	EDS4A		2780304, 2834369	Standard	NM_000090		Approved		uc002uqj.1	P02461	OTTHUMG00000132648	ENST00000304636.3:c.2802G>A	2.37:g.189868848G>A							p.S934S	NM_000090	NP_000081	P02461	CO3A1_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.141)		39	2919	+			934			Triple-helical region.		D2JYH5|D3DPH4|P78429|Q15112|Q16403|Q53S91|Q541P8|Q6LDB3|Q6LDJ2|Q6LDJ3|Q7KZ56|Q8N6U4|Q9UC88|Q9UC89|Q9UC90|Q9UC91|R4N3C5|V9GZI1	Silent	SNP	ENST00000304636.3	37	c.2802G>A	CCDS2297.1																																																																																				0.488	COL3A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255899.3	NM_000090	
NBEAL1	65065	broad.mit.edu	37	2	204037528	204037528	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr2:204037528A>G	ENST00000449802.1	+	40	6521	c.6188A>G	c.(6187-6189)aAa>aGa	p.K2063R		NM_001114132.1	NP_001107604.1	Q6ZS30	NBEL1_HUMAN	neurobeachin-like 1	2063	BEACH. {ECO:0000255|PROSITE- ProRule:PRU00026}.									NS(1)|breast(3)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(8)|liver(1)|lung(8)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	37						GATCTTTCCAAACCAATTGGG	0.328																																						uc002uzt.3																			0				ovary(1)|skin(1)	2						c.(6187-6189)AAA>AGA		neurobeachin-like 1 isoform 3							133.0	125.0	127.0					2																	204037528		1800	4070	5870	SO:0001583	missense	65065						binding	g.chr2:204037528A>G	AY172970	CCDS46495.1	2q33	2013-01-10			ENSG00000144426	ENSG00000144426		"""WD repeat domain containing"""	20681	protein-coding gene	gene with protein product		609816	"""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 17"", ""amyotrophic lateral sclerosis 2 (juvenile) chromosome region, candidate 16"""	ALS2CR17, ALS2CR16		15193433	Standard	NM_001114132		Approved	MGC164581	uc002uzt.3	Q6ZS30	OTTHUMG00000154129	ENST00000449802.1:c.6188A>G	2.37:g.204037528A>G	ENSP00000399903:p.Lys2063Arg					NBEAL1_uc002uzs.3_Missense_Mutation_p.K773R	p.K2063R	NM_001114132	NP_001107604	Q6ZS30	NBEL1_HUMAN			40	6521	+			2063			BEACH.		A6NHD5|Q6Y876|Q6ZP36|Q6ZQY5|Q8N8R4|Q96Q30|Q96Q31	Missense_Mutation	SNP	ENST00000449802.1	37	c.6188A>G	CCDS46495.1	.	.	.	.	.	.	.	.	.	.	A	29.4	4.999443	0.93227	.	.	ENSG00000144426	ENST00000449802;ENST00000340268;ENST00000414576	D;D	0.82433	-1.61;-1.61	6.17	6.17	0.99709	BEACH domain (4);	0.000000	0.85682	D	0.000000	D	0.89873	0.6841	M	0.62016	1.91	0.80722	D	1	D;D	0.89917	1.0;0.999	D;D	0.87578	0.998;0.997	D	0.90396	0.4399	10	0.66056	D	0.02	.	15.8048	0.78491	1.0:0.0:0.0:0.0	.	2063;2052	Q6ZS30;C9JGK5	NBEL1_HUMAN;.	R	2063;2063;78	ENSP00000399903:K2063R;ENSP00000388466:K78R	ENSP00000344985:K2063R	K	+	2	0	NBEAL1	203745773	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	9.287000	0.95975	2.371000	0.80710	0.533000	0.62120	AAA		0.328	NBEAL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333982.4		
SIRPA	140885	broad.mit.edu	37	20	1895993	1895993	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr20:1895993A>G	ENST00000358771.4	+	2	480	c.328A>G	c.(328-330)Aac>Gac	p.N110D	SIRPA_ENST00000356025.3_Missense_Mutation_p.N110D|SIRPA_ENST00000400068.3_Missense_Mutation_p.N110D	NM_001040023.1	NP_001035112.1	P78324	SHPS1_HUMAN	signal-regulatory protein alpha	110	Ig-like V-type.				blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|leukocyte migration (GO:0050900)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)				cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(13)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	21				Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)		CCGCATCGGTAACATCACCCC	0.502																																					GBM(155;1668 1920 5945 42733 48121)	uc002wfq.2																			0				ovary(1)	1						c.(328-330)AAC>GAC		signal-regulatory protein alpha precursor							142.0	118.0	126.0					20																	1895993		2203	4294	6497	SO:0001583	missense	140885				blood coagulation|cell adhesion|cell junction assembly|leukocyte migration	integral to membrane|plasma membrane	SH3 domain binding	g.chr20:1895993A>G	D86043	CCDS13022.1	20p13	2013-01-11	2006-03-29	2006-03-29	ENSG00000198053	ENSG00000198053		"""Signal-regulatory proteins"", ""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / C1-set domain containing"""	9662	protein-coding gene	gene with protein product		602461	"""protein tyrosine phosphatase, non-receptor type substrate 1"""	PTPNS1		9070220, 9062191, 16339511	Standard	XM_005260669		Approved	SHPS1, SIRP, MYD-1, BIT, P84, SHPS-1, SIRPalpha, CD172a, SIRPalpha2, MFR, SIRP-ALPHA-1	uc002wfr.3	P78324	OTTHUMG00000031682	ENST00000358771.4:c.328A>G	20.37:g.1895993A>G	ENSP00000351621:p.Asn110Asp					SIRPA_uc010zps.1_Missense_Mutation_p.N90D|SIRPA_uc002wfr.2_Missense_Mutation_p.N110D|SIRPA_uc002wfs.2_Missense_Mutation_p.N110D|SIRPA_uc002wft.2_Missense_Mutation_p.N110D	p.N110D	NM_001040022	NP_001035111	P78324	SHPS1_HUMAN		Colorectal(46;0.018)|READ - Rectum adenocarcinoma(1;0.0556)	3	688	+			110			Ig-like V-type.|Extracellular (Potential).		A2A2E1|A8K411|B2R6C3|O00683|O43799|Q8N517|Q8TAL8|Q9H0Z2|Q9UDX2|Q9UIJ6|Q9Y4U9	Missense_Mutation	SNP	ENST00000358771.4	37	c.328A>G	CCDS13022.1	.	.	.	.	.	.	.	.	.	.	A	12.06	1.825884	0.32237	.	.	ENSG00000198053	ENST00000400068;ENST00000356025;ENST00000358771	T;T;T	0.65916	-0.18;-0.18;-0.18	5.11	1.37	0.22104	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.169933	0.41396	N	0.000894	T	0.49167	0.1541	L	0.49699	1.58	0.38396	D	0.945544	B;B;B	0.10296	0.003;0.002;0.001	B;B;B	0.19946	0.016;0.005;0.027	T	0.42327	-0.9458	10	0.45353	T	0.12	.	3.8036	0.08768	0.5976:0.1867:0.2157:0.0	.	90;110;110	B4DP97;P78324-2;P78324	.;.;SHPS1_HUMAN	D	110	ENSP00000382941:N110D;ENSP00000348307:N110D;ENSP00000351621:N110D	ENSP00000348307:N110D	N	+	1	0	SIRPA	1843993	0.443000	0.25641	0.995000	0.50966	0.705000	0.40729	0.426000	0.21363	0.431000	0.26258	0.454000	0.30748	AAC		0.502	SIRPA-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000077568.2	NM_080792	
FGD5	152273	broad.mit.edu	37	3	14960268	14960268	+	Missense_Mutation	SNP	G	G	A	rs536923009		TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr3:14960268G>A	ENST00000285046.5	+	13	3607	c.3497G>A	c.(3496-3498)cGc>cAc	p.R1166H	FGD5_ENST00000476851.1_3'UTR|FGD5-AS1_ENST00000430166.1_RNA|FGD5_ENST00000543601.1_Missense_Mutation_p.R925H	NM_152536.3	NP_689749.3	Q6ZNL6	FGD5_HUMAN	FYVE, RhoGEF and PH domain containing 5	1166	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin cytoskeleton organization (GO:0030036)|cytoskeleton organization (GO:0007010)|filopodium assembly (GO:0046847)|positive regulation of GTPase activity (GO:0043547)|regulation of Cdc42 GTPase activity (GO:0043088)|regulation of cell shape (GO:0008360)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|Golgi apparatus (GO:0005794)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|ruffle (GO:0001726)	guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|small GTPase binding (GO:0031267)			NS(2)|breast(2)|endometrium(3)|kidney(5)|large_intestine(10)|lung(25)|ovary(3)|pancreas(1)|prostate(2)|urinary_tract(1)	54						CAGGTCAGCCGCCCTGTGATG	0.602													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16072	0.0		0.0	False		,,,				2504	0.0					uc003bzc.2																			0				ovary(3)|kidney(1)|pancreas(1)	5						c.(3496-3498)CGC>CAC		FYVE, RhoGEF and PH domain containing 5							87.0	86.0	86.0					3																	14960268		2008	4167	6175	SO:0001583	missense	152273				actin cytoskeleton organization|filopodium assembly|regulation of Cdc42 GTPase activity|regulation of cell shape	cytoskeleton|Golgi apparatus|lamellipodium|ruffle	metal ion binding|Rho guanyl-nucleotide exchange factor activity|small GTPase binding	g.chr3:14960268G>A	AK097276	CCDS46767.1	3p25.1	2013-01-10			ENSG00000154783	ENSG00000154783		"""Zinc fingers, FYVE domain containing"", ""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	19117	protein-coding gene	gene with protein product		614788					Standard	NM_152536		Approved	ZFYVE23, FLJ39957, FLJ00274	uc003bzc.3	Q6ZNL6	OTTHUMG00000155556	ENST00000285046.5:c.3497G>A	3.37:g.14960268G>A	ENSP00000285046:p.Arg1166His					FGD5_uc011avk.1_Missense_Mutation_p.R1166H|FGD5_uc003bzd.2_Missense_Mutation_p.R244H	p.R1166H	NM_152536	NP_689749	Q6ZNL6	FGD5_HUMAN			13	3607	+			1166			PH 1.		B3KVQ3|Q6MZY1|Q7Z303|Q8IYP3|Q8N861|Q8N8G4	Missense_Mutation	SNP	ENST00000285046.5	37	c.3497G>A	CCDS46767.1	.	.	.	.	.	.	.	.	.	.	G	19.55	3.849338	0.71603	.	.	ENSG00000154783	ENST00000285046;ENST00000543601	T;T	0.75821	-0.97;-0.97	3.86	3.86	0.44501	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.281795	0.25436	N	0.030693	T	0.81138	0.4760	L	0.54323	1.7	0.47949	D	0.999552	D;D	0.89917	0.998;1.0	P;D	0.65443	0.876;0.935	T	0.82938	-0.0209	10	0.72032	D	0.01	-24.6711	12.6537	0.56776	0.0:0.0:1.0:0.0	.	925;1166	B7ZM68;Q6ZNL6	.;FGD5_HUMAN	H	1166;925	ENSP00000285046:R1166H;ENSP00000445949:R925H	ENSP00000285046:R1166H	R	+	2	0	FGD5	14935272	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	4.967000	0.63722	1.988000	0.58038	0.591000	0.81541	CGC		0.602	FGD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340628.1	NM_152536	
OR5AC2	81050	broad.mit.edu	37	3	97806681	97806681	+	Missense_Mutation	SNP	G	G	A	rs200290395		TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr3:97806681G>A	ENST00000358642.2	+	1	665	c.665G>A	c.(664-666)cGt>cAt	p.R222H		NM_054106.1	NP_473447.1	Q9NZP5	O5AC2_HUMAN	olfactory receptor, family 5, subfamily AC, member 2	222					detection of chemical stimulus involved in sensory perception of smell (GO:0050911)|sensory perception of smell (GO:0007608)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(4)|large_intestine(3)|lung(13)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	28						TCTTATACTCGTGTGCTCTTT	0.373																																						uc011bgs.1																			0				skin(1)	1						c.(664-666)CGT>CAT		olfactory receptor, family 5, subfamily AC,							37.0	38.0	38.0					3																	97806681		2203	4300	6503	SO:0001583	missense	81050				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr3:97806681G>A	AF179759	CCDS33796.1	3q11.2	2013-09-23			ENSG00000196578	ENSG00000196578		"""GPCR / Class A : Olfactory receptors"""	15431	protein-coding gene	gene with protein product							Standard	NM_054106		Approved	HSA1	uc011bgs.2	Q9NZP5	OTTHUMG00000160083	ENST00000358642.2:c.665G>A	3.37:g.97806681G>A	ENSP00000351466:p.Arg222His						p.R222H	NM_054106	NP_473447	Q9NZP5	O5AC2_HUMAN			1	665	+			222			Cytoplasmic (Potential).			Missense_Mutation	SNP	ENST00000358642.2	37	c.665G>A	CCDS33796.1	.	.	.	.	.	.	.	.	.	.	G	15.18	2.758057	0.49468	.	.	ENSG00000196578	ENST00000358642	T	0.00107	8.72	4.42	-6.27	0.02026	GPCR, rhodopsin-like superfamily (1);	2.231340	0.02412	U	0.081750	T	0.00073	0.0002	N	0.04724	-0.175	0.09310	N	1	B	0.16166	0.016	B	0.15484	0.013	T	0.39482	-0.9612	10	0.66056	D	0.02	1.6995	0.6556	0.00834	0.2262:0.2056:0.1583:0.41	.	222	Q9NZP5	O5AC2_HUMAN	H	222	ENSP00000351466:R222H	ENSP00000351466:R222H	R	+	2	0	OR5AC2	99289371	0.000000	0.05858	0.000000	0.03702	0.956000	0.61745	-5.596000	0.00111	-0.786000	0.04516	0.523000	0.50628	CGT		0.373	OR5AC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359116.1		
DTX3L	151636	broad.mit.edu	37	3	122289489	122289489	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr3:122289489A>G	ENST00000296161.4	+	4	2312	c.2123A>G	c.(2122-2124)cAc>cGc	p.H708R	DTX3L_ENST00000383661.3_Missense_Mutation_p.H196R	NM_138287.3	NP_612144.1	Q8TDB6	DTX3L_HUMAN	deltex 3 like, E3 ubiquitin ligase	708					cellular response to DNA damage stimulus (GO:0006974)|double-strand break repair (GO:0006302)|histone monoubiquitination (GO:0010390)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	histone binding (GO:0042393)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(2)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|ovary(2)|prostate(1)|upper_aerodigestive_tract(1)	24				GBM - Glioblastoma multiforme(114;0.0459)		GATATTCACCACAAAACATCC	0.423																																						uc003efk.2																			0				ovary(2)|lung(1)|breast(1)	4						c.(2122-2124)CAC>CGC		deltex 3-like							108.0	106.0	107.0					3																	122289489		2203	4300	6503	SO:0001583	missense	151636				histone monoubiquitination|response to DNA damage stimulus	cytoplasm|nucleus	histone binding|ubiquitin-protein ligase activity|zinc ion binding	g.chr3:122289489A>G		CCDS3015.1	3q21.1	2014-01-28	2014-01-28		ENSG00000163840	ENSG00000163840		"""RING-type (C3HC4) zinc fingers"""	30323	protein-coding gene	gene with protein product	"""rhysin 2"""	613143	"""deltex 3-like (Drosophila)"""			12670957, 22411408	Standard	NM_138287		Approved	BBAP	uc003efk.3	Q8TDB6	OTTHUMG00000159524	ENST00000296161.4:c.2123A>G	3.37:g.122289489A>G	ENSP00000296161:p.His708Arg					DTX3L_uc010hrj.2_Missense_Mutation_p.H196R	p.H708R	NM_138287	NP_612144	Q8TDB6	DTX3L_HUMAN		GBM - Glioblastoma multiforme(114;0.0459)	4	2212	+			708					B3KWH6|Q53ZZ3|Q5MJP7	Missense_Mutation	SNP	ENST00000296161.4	37	c.2123A>G	CCDS3015.1	.	.	.	.	.	.	.	.	.	.	A	25.5	4.642725	0.87859	.	.	ENSG00000163840	ENST00000296161;ENST00000383661	T;T	0.50277	0.75;0.75	5.07	5.07	0.68467	.	0.000000	0.56097	D	0.000035	T	0.77157	0.4089	H	0.95114	3.625	0.58432	D	0.999994	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.84303	0.0506	10	0.87932	D	0	-12.5689	13.7979	0.63182	1.0:0.0:0.0:0.0	.	196;708	Q8TDB6-2;Q8TDB6	.;DTX3L_HUMAN	R	708;196	ENSP00000296161:H708R;ENSP00000373157:H196R	ENSP00000296161:H708R	H	+	2	0	DTX3L	123772179	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	9.096000	0.94182	2.131000	0.65755	0.459000	0.35465	CAC		0.423	DTX3L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355966.1	NM_138287	
PDGFRA	5156	broad.mit.edu	37	4	55156661	55156661	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr4:55156661C>T	ENST00000257290.5	+	22	3393	c.3062C>T	c.(3061-3063)cCt>cTt	p.P1021L	FIP1L1_ENST00000507166.1_Missense_Mutation_p.P781L	NM_006206.4	NP_006197.1	P16234	PGFRA_HUMAN	platelet-derived growth factor receptor, alpha polypeptide	1021					adrenal gland development (GO:0030325)|cardiac myofibril assembly (GO:0055003)|cell activation (GO:0001775)|cell chemotaxis (GO:0060326)|cellular response to amino acid stimulus (GO:0071230)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic digestive tract morphogenesis (GO:0048557)|embryonic skeletal system morphogenesis (GO:0048704)|epidermal growth factor receptor signaling pathway (GO:0007173)|estrogen metabolic process (GO:0008210)|extracellular matrix organization (GO:0030198)|face morphogenesis (GO:0060325)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hematopoietic progenitor cell differentiation (GO:0002244)|in utero embryonic development (GO:0001701)|innate immune response (GO:0045087)|Leydig cell differentiation (GO:0033327)|lung development (GO:0030324)|luteinization (GO:0001553)|male genitalia development (GO:0030539)|metanephric glomerular capillary formation (GO:0072277)|negative regulation of platelet activation (GO:0010544)|neurotrophin TRK receptor signaling pathway (GO:0048011)|odontogenesis of dentin-containing tooth (GO:0042475)|palate development (GO:0060021)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet aggregation (GO:0070527)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|platelet-derived growth factor receptor-alpha signaling pathway (GO:0035790)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cell proliferation by VEGF-activated platelet derived growth factor receptor signaling pathway (GO:0038091)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of DNA replication (GO:0045740)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of phospholipase C activity (GO:0010863)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of chemotaxis (GO:0050920)|regulation of mesenchymal stem cell differentiation (GO:2000739)|retina vasculature development in camera-type eye (GO:0061298)|signal transduction involved in regulation of gene expression (GO:0023019)|viral process (GO:0016032)|wound healing (GO:0042060)	cytoplasm (GO:0005737)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)|intrinsic component of plasma membrane (GO:0031226)|membrane (GO:0016020)|microvillus (GO:0005902)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|platelet-derived growth factor alpha-receptor activity (GO:0005018)|platelet-derived growth factor binding (GO:0048407)|platelet-derived growth factor receptor binding (GO:0005161)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor binding (GO:0038085)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|autonomic_ganglia(1)|bone(1)|breast(4)|central_nervous_system(17)|cervix(1)|endometrium(4)|eye(1)|gastrointestinal_tract_(site_indeterminate)(1)|haematopoietic_and_lymphoid_tissue(22)|kidney(6)|large_intestine(26)|liver(4)|lung(48)|ovary(4)|prostate(6)|skin(11)|small_intestine(49)|soft_tissue(727)|stomach(32)|urinary_tract(1)	967	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		Becaplermin(DB00102)|Imatinib(DB00619)|Pazopanib(DB06589)|Ponatinib(DB08901)|Regorafenib(DB08896)|Sunitinib(DB01268)	TACATCATTCCTCTGCCTGAC	0.562			"""Mis, O, T"""	FIP1L1	"""GIST, idiopathic hypereosinophilic syndrome, paediatric GBM"""				Gastrointestinal Stromal Tumors, Sporadic Multiple Primary;Familial Intestinal Neurofibromatosis	TSP Lung(21;0.16)																											Pancreas(151;208 1913 7310 23853 37092)	uc003han.3				Dom	yes		4	4q11-q13	5156	Mis|O|T	"""platelet-derived growth factor, alpha-receptor"""			"""L, M, O"""	FIP1L1		GIST|idiopathic hypereosinophilic syndrome		0				soft_tissue(572)|small_intestine(40)|stomach(16)|lung(16)|central_nervous_system(13)|haematopoietic_and_lymphoid_tissue(7)|skin(3)|ovary(3)|gastrointestinal_tract_(site_indeterminate)(1)|autonomic_ganglia(1)|prostate(1)|bone(1)	674						c.(3061-3063)CCT>CTT		platelet-derived growth factor receptor alpha	Becaplermin(DB00102)|Imatinib(DB00619)|Sunitinib(DB01268)						160.0	134.0	143.0					4																	55156661		2203	4300	6503	SO:0001583	missense	5156	Gastrointestinal_Stromal_Tumors_Sporadic_Multiple_Primary|Familial_Intestinal_Neurofibromatosis	Familial Cancer Database	Sporadic Multiple GIST;Familial Intestinal Stromal Tumors, NF3B, subset of Familial GIST,	cardiac myofibril assembly|cell activation|luteinization|metanephric glomerular capillary formation|peptidyl-tyrosine phosphorylation|positive regulation of cell migration|positive regulation of DNA replication|positive regulation of fibroblast proliferation|protein autophosphorylation|retina vasculature development in camera-type eye	cytoplasm|integral to plasma membrane|nucleus	ATP binding|platelet-derived growth factor alpha-receptor activity|platelet-derived growth factor binding|platelet-derived growth factor receptor binding|protein homodimerization activity|vascular endothelial growth factor receptor activity	g.chr4:55156661C>T	D50001	CCDS3495.1	4q12	2014-09-17			ENSG00000134853	ENSG00000134853		"""CD molecules"", ""Immunoglobulin superfamily / I-set domain containing"""	8803	protein-coding gene	gene with protein product		173490					Standard	NM_006206		Approved	CD140a, PDGFR2	uc003han.4	P16234	OTTHUMG00000128699	ENST00000257290.5:c.3062C>T	4.37:g.55156661C>T	ENSP00000257290:p.Pro1021Leu	TSP Lung(21;0.16)				PDGFRA_uc003haa.2_Missense_Mutation_p.P781L	p.P1021L	NM_006206	NP_006197	P16234	PGFRA_HUMAN	GBM - Glioblastoma multiforme(1;4.18e-71)|all cancers(1;4.76e-45)|LUSC - Lung squamous cell carcinoma(32;0.00256)		22	3393	+	all_cancers(7;0.000425)|all_lung(4;0.000343)|Lung NSC(11;0.000467)|all_epithelial(27;0.0131)|all_neural(26;0.0209)|Glioma(25;0.08)		1021			Cytoplasmic (Potential).		B2RE69|E9PBH0|Q6P4H5|Q96KZ7|Q9UD28	Missense_Mutation	SNP	ENST00000257290.5	37	c.3062C>T	CCDS3495.1	.	.	.	.	.	.	.	.	.	.	C	28.5	4.927926	0.92389	.	.	ENSG00000145216;ENSG00000134853	ENST00000507166;ENST00000257290	T;T	0.78246	-1.16;-0.99	5.93	5.93	0.95920	.	0.000000	0.31949	U	0.006811	D	0.88062	0.6336	M	0.68593	2.085	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.87967	0.2734	10	0.87932	D	0	.	20.3363	0.98740	0.0:1.0:0.0:0.0	.	1021	P16234	PGFRA_HUMAN	L	781;1021	ENSP00000423325:P781L;ENSP00000257290:P1021L	ENSP00000423325:P781L	P	+	2	0	FIP1L1;PDGFRA	54851418	1.000000	0.71417	0.970000	0.41538	0.659000	0.38960	7.358000	0.79466	2.814000	0.96858	0.563000	0.77884	CCT		0.562	PDGFRA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250598.2	NM_006206	
FSTL5	56884	broad.mit.edu	37	4	162697175	162697175	+	Missense_Mutation	SNP	T	T	C			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr4:162697175T>C	ENST00000306100.5	-	5	897	c.461A>G	c.(460-462)gAt>gGt	p.D154G	FSTL5_ENST00000536695.1_Missense_Mutation_p.D153G|FSTL5_ENST00000427802.2_Missense_Mutation_p.D153G|FSTL5_ENST00000379164.4_Missense_Mutation_p.D153G	NM_001128427.2|NM_020116.4	NP_001121899.1|NP_064501.2	Q8N475	FSTL5_HUMAN	follistatin-like 5	154						extracellular region (GO:0005576)	calcium ion binding (GO:0005509)			central_nervous_system(1)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(18)|lung(43)|ovary(4)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	91	all_hematologic(180;0.24)			COAD - Colon adenocarcinoma(41;0.179)		ATTTTGTAAATCTAATAGCAT	0.279																																						uc003iqh.2																			0				ovary(2)|pancreas(2)|upper_aerodigestive_tract(1)|large_intestine(1)|central_nervous_system(1)|skin(1)	8						c.(460-462)GAT>GGT		follistatin-like 5 isoform a							53.0	52.0	53.0					4																	162697175		2200	4293	6493	SO:0001583	missense	56884					extracellular region	calcium ion binding	g.chr4:162697175T>C	BC036502	CCDS3802.1, CCDS47157.1, CCDS47158.1	4q32.3	2013-01-11			ENSG00000168843	ENSG00000168843		"""EF-hand domain containing"", ""Immunoglobulin superfamily / I-set domain containing"""	21386	protein-coding gene	gene with protein product						10574462, 15527507	Standard	NM_020116		Approved	DKFZp566D234, KIAA1263	uc003iqh.4	Q8N475	OTTHUMG00000161397	ENST00000306100.5:c.461A>G	4.37:g.162697175T>C	ENSP00000305334:p.Asp154Gly					FSTL5_uc003iqi.2_Missense_Mutation_p.D153G|FSTL5_uc010iqv.2_Missense_Mutation_p.D153G	p.D154G	NM_020116	NP_064501	Q8N475	FSTL5_HUMAN		COAD - Colon adenocarcinoma(41;0.179)	5	897	-	all_hematologic(180;0.24)		154					E9PCP6|Q9NSW7|Q9ULF7	Missense_Mutation	SNP	ENST00000306100.5	37	c.461A>G	CCDS3802.1	.	.	.	.	.	.	.	.	.	.	T	11.77	1.736842	0.30774	.	.	ENSG00000168843	ENST00000306100;ENST00000379164;ENST00000427802;ENST00000536695	T;T;T;T	0.74209	-0.8;-0.78;-0.82;-0.78	5.3	4.12	0.48240	.	0.093823	0.64402	N	0.000001	T	0.79598	0.4473	M	0.71581	2.175	0.58432	D	0.999998	D;D;D	0.67145	0.996;0.979;0.993	P;P;P	0.57620	0.824;0.652;0.628	T	0.76269	-0.3021	10	0.24483	T	0.36	.	10.3219	0.43771	0.0:0.0775:0.0:0.9225	.	153;153;154	E9PCP6;F8VZ90;Q8N475	.;.;FSTL5_HUMAN	G	154;153;153;153	ENSP00000305334:D154G;ENSP00000368462:D153G;ENSP00000389270:D153G;ENSP00000440409:D153G	ENSP00000305334:D154G	D	-	2	0	FSTL5	162916625	1.000000	0.71417	0.999000	0.59377	0.035000	0.12851	6.134000	0.71689	0.959000	0.37980	0.528000	0.53228	GAT		0.279	FSTL5-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000364773.2	NM_020116	
CHSY3	337876	broad.mit.edu	37	5	129243856	129243856	+	Missense_Mutation	SNP	C	C	G			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr5:129243856C>G	ENST00000305031.4	+	2	1247	c.889C>G	c.(889-891)Ctt>Gtt	p.L297V	CTC-575N7.1_ENST00000515569.1_RNA|CTC-575N7.1_ENST00000503616.1_RNA|CHSY3_ENST00000507545.1_3'UTR	NM_175856.4	NP_787052.3	Q70JA7	CHSS3_HUMAN	chondroitin sulfate synthase 3	297					carbohydrate metabolic process (GO:0005975)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate metabolic process (GO:0030204)|glycosaminoglycan metabolic process (GO:0030203)|small molecule metabolic process (GO:0044281)	Golgi cisterna membrane (GO:0032580)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238)|metal ion binding (GO:0046872)|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510)			central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(7)|lung(9)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|urinary_tract(1)	28		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)		TATTGAAGAGCTTGGAAAGCT	0.473																																						uc003kvd.2																			0				ovary(2)|pancreas(1)	3						c.(889-891)CTT>GTT		chondroitin sulfate synthase 3							87.0	88.0	88.0					5																	129243856		2203	4300	6503	SO:0001583	missense	337876					Golgi cisterna membrane|integral to membrane	glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity|metal ion binding|N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity	g.chr5:129243856C>G	AB086062	CCDS34223.1	5q13	2013-02-19			ENSG00000198108	ENSG00000198108	2.4.1.175, 2.4.1.226	"""Beta 3-glycosyltransferases"", ""Beta 4-glycosyltransferases"""	24293	protein-coding gene	gene with protein product		609963				12907687	Standard	XM_005271982		Approved	CSS3, CHSY-2	uc003kvd.3	Q70JA7	OTTHUMG00000163043	ENST00000305031.4:c.889C>G	5.37:g.129243856C>G	ENSP00000302629:p.Leu297Val						p.L297V	NM_175856	NP_787052	Q70JA7	CHSS3_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)	OV - Ovarian serous cystadenocarcinoma(64;0.136)	2	889	+		all_cancers(142;0.0227)|Breast(839;0.198)|Prostate(80;0.215)|Lung NSC(810;0.239)	297			Lumenal (Potential).		B2RP97|Q76L22|Q86Y52	Missense_Mutation	SNP	ENST00000305031.4	37	c.889C>G	CCDS34223.1	.	.	.	.	.	.	.	.	.	.	C	12.98	2.101888	0.37048	.	.	ENSG00000198108	ENST00000305031	D	0.84800	-1.9	4.33	3.46	0.39613	.	0.000000	0.33691	N	0.004648	T	0.73544	0.3600	N	0.17312	0.475	0.46678	D	0.99915	B	0.34161	0.439	B	0.33521	0.165	T	0.70468	-0.4863	9	.	.	.	.	14.6624	0.68882	0.1468:0.8532:0.0:0.0	.	297	Q70JA7	CHSS3_HUMAN	V	297	ENSP00000302629:L297V	.	L	+	1	0	CHSY3	129271755	0.994000	0.37717	0.995000	0.50966	0.986000	0.74619	1.189000	0.32114	1.400000	0.46741	0.591000	0.81541	CTT		0.473	CHSY3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371453.1	NM_175856	
SLIT3	6586	broad.mit.edu	37	5	168175347	168175347	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr5:168175347G>A	ENST00000519560.1	-	20	2649	c.2230C>T	c.(2230-2232)Cgc>Tgc	p.R744C	SLIT3_ENST00000332966.8_Missense_Mutation_p.R744C|SLIT3_ENST00000404867.3_Missense_Mutation_p.R744C	NM_001271946.1|NM_003062.2	NP_001258875.1|NP_003053	O75094	SLIT3_HUMAN	slit homolog 3 (Drosophila)	744	LRRNT 4.				apoptotic process involved in luteolysis (GO:0061364)|axon extension involved in axon guidance (GO:0048846)|axon guidance (GO:0007411)|cellular response to hormone stimulus (GO:0032870)|negative chemotaxis (GO:0050919)|negative regulation of cell growth (GO:0030308)|negative regulation of cell proliferation (GO:0008285)|negative regulation of chemokine-mediated signaling pathway (GO:0070100)|negative regulation of gene expression (GO:0010629)|organ morphogenesis (GO:0009887)|response to cortisol (GO:0051414)|Roundabout signaling pathway (GO:0035385)	extracellular space (GO:0005615)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)|Roundabout binding (GO:0048495)	p.R744S(1)		endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(15)|liver(2)|lung(48)|ovary(4)|prostate(7)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(1)	100	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			GGGAGGGCGCGGAGCCCCTTG	0.632																																					Ovarian(29;311 847 10864 17279 24903)	uc003mab.2																			1	Substitution - Missense(1)		lung(1)	ovary(3)|skin(1)	4						c.(2230-2232)CGC>TGC		slit homolog 3 precursor							86.0	86.0	86.0					5																	168175347		2203	4300	6503	SO:0001583	missense	6586				apoptosis involved in luteolysis|axon extension involved in axon guidance|cellular response to hormone stimulus|negative chemotaxis|negative regulation of cell growth|negative regulation of chemokine-mediated signaling pathway|response to cortisol stimulus|Roundabout signaling pathway	extracellular space|mitochondrion	calcium ion binding|Roundabout binding	g.chr5:168175347G>A	AB011538	CCDS4369.1, CCDS64311.1	5q35	2008-07-18	2001-11-28		ENSG00000184347	ENSG00000184347			11087	protein-coding gene	gene with protein product		603745	"""slit (Drosophila) homolog 3"""	SLIL2		9693030, 9813312	Standard	NM_001271946		Approved	slit2, MEGF5, SLIT1, Slit-3	uc010jjg.4	O75094	OTTHUMG00000130409	ENST00000519560.1:c.2230C>T	5.37:g.168175347G>A	ENSP00000430333:p.Arg744Cys					SLIT3_uc010jjg.2_Missense_Mutation_p.R744C	p.R744C	NM_003062	NP_003053	O75094	SLIT3_HUMAN	Kidney(164;7.53e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)		20	2650	-	Renal(175;0.000159)|Lung NSC(126;0.0174)|all_lung(126;0.0392)	Medulloblastoma(196;0.0399)|all_neural(177;0.0966)	744			LRRNT 4.		A6H8U9|J3KNP3|O95804|Q9UFH5	Missense_Mutation	SNP	ENST00000519560.1	37	c.2230C>T	CCDS4369.1	.	.	.	.	.	.	.	.	.	.	g	18.27	3.586246	0.66105	.	.	ENSG00000184347	ENST00000519560;ENST00000332966;ENST00000404867	D;D;D	0.96459	-4.02;-4.02;-4.02	5.3	5.3	0.74995	Leucine-rich repeat-containing N-terminal (2);	0.439088	0.25851	N	0.027892	D	0.97501	0.9182	M	0.80982	2.52	0.37083	D	0.899081	D	0.65815	0.995	P	0.58970	0.849	D	0.99926	1.1289	10	0.87932	D	0	.	13.9178	0.63911	0.0:0.0:0.848:0.152	.	744	O75094	SLIT3_HUMAN	C	744	ENSP00000430333:R744C;ENSP00000332164:R744C;ENSP00000384890:R744C	ENSP00000332164:R744C	R	-	1	0	SLIT3	168107925	0.011000	0.17503	0.921000	0.36526	0.680000	0.39746	1.456000	0.35201	2.483000	0.83821	0.550000	0.68814	CGC		0.632	SLIT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252792.4	NM_003062	
PSORS1C1	170679	broad.mit.edu	37	6	31106528	31106528	+	Missense_Mutation	SNP	T	T	C			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr6:31106528T>C	ENST00000259881.9	+	5	428	c.139T>C	c.(139-141)Tgc>Cgc	p.C47R	PSORS1C1_ENST00000481450.2_Intron|PSORS1C1_ENST00000547221.1_5'UTR|PSORS1C2_ENST00000259845.4_Intron	NM_014068.2	NP_054787.2	Q9UIG5	PS1C1_HUMAN	psoriasis susceptibility 1 candidate 1	47										kidney(1)|ovary(2)|prostate(1)|skin(1)	5						TGACCGACTTTGCCACATGGA	0.557																																						uc003nsl.1																			0				ovary(1)	1						c.(139-141)TGC>CGC		SEEK1 protein							155.0	152.0	153.0					6																	31106528		1511	2709	4220	SO:0001583	missense	170679							g.chr6:31106528T>C	AB031479	CCDS34390.1	6p21.3	2014-01-28	2003-06-12		ENSG00000204540	ENSG00000204540			17202	protein-coding gene	gene with protein product		613525	"""chromosome 6 open reading frame 16"""	C6orf16			Standard	NM_014068		Approved	SEEK1	uc003nsl.2	Q9UIG5	OTTHUMG00000031077	ENST00000259881.9:c.139T>C	6.37:g.31106528T>C	ENSP00000259881:p.Cys47Arg					PSORS1C1_uc010jsj.1_Intron|PSORS1C1_uc003nsn.1_Intron|PSORS1C2_uc003nso.3_Intron	p.C47R	NM_014068	NP_054787	Q9UIG5	PS1C1_HUMAN			5	413	+			47					B0V083|Q5ST21|Q86WJ8|Q86WJ9|Q96QC3	Missense_Mutation	SNP	ENST00000259881.9	37	c.139T>C	CCDS34390.1	.	.	.	.	.	.	.	.	.	.	T	9.787	1.176955	0.21787	.	.	ENSG00000204540	ENST00000259881	T	0.15487	2.42	3.22	-6.45	0.01914	.	.	.	.	.	T	0.01976	0.0062	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.01281	0.0	T	0.48811	-0.9002	9	0.87932	D	0	.	4.2471	0.10677	0.166:0.2818:0.0:0.5522	.	47	Q9UIG5	PS1C1_HUMAN	R	47	ENSP00000259881:C47R	ENSP00000259881:C47R	C	+	1	0	PSORS1C1	31214507	0.000000	0.05858	0.000000	0.03702	0.096000	0.18686	-1.950000	0.01530	-0.758000	0.04690	-0.781000	0.03364	TGC		0.557	PSORS1C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000076110.3	NM_014068	
MRAP2	112609	broad.mit.edu	37	6	84799086	84799086	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr6:84799086C>A	ENST00000257776.4	+	4	639	c.504C>A	c.(502-504)aaC>aaA	p.N168K		NM_138409.2	NP_612418.2	Q96G30	MRAP2_HUMAN	melanocortin 2 receptor accessory protein 2	168					energy homeostasis (GO:0097009)|energy reserve metabolic process (GO:0006112)|feeding behavior (GO:0007631)|positive regulation of cAMP biosynthetic process (GO:0030819)|protein localization to cell surface (GO:0034394)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	corticotropin hormone receptor binding (GO:0031780)|identical protein binding (GO:0042802)|type 1 melanocortin receptor binding (GO:0070996)|type 3 melanocortin receptor binding (GO:0031781)|type 4 melanocortin receptor binding (GO:0031782)|type 5 melanocortin receptor binding (GO:0031783)			NS(1)|breast(1)|endometrium(1)|large_intestine(4)|lung(4)|pancreas(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	19						ACATCCCCAACTTTGTGAACA	0.502																																						uc003pkg.3																			0				skin(2)	2						c.(502-504)AAC>AAA		melanocortin 2 receptor accessory protein 2							121.0	121.0	121.0					6																	84799086		2203	4300	6503	SO:0001583	missense	112609				positive regulation of cAMP biosynthetic process|protein localization at cell surface	endoplasmic reticulum|plasma membrane	corticotropin hormone receptor binding|type 1 melanocortin receptor binding|type 3 melanocortin receptor binding|type 4 melanocortin receptor binding|type 5 melanocortin receptor binding	g.chr6:84799086C>A	AK090775	CCDS5001.1	6q14.3	2009-10-06	2008-07-16	2008-07-16	ENSG00000135324	ENSG00000135324			21232	protein-coding gene	gene with protein product		615410	"""chromosome 6 open reading frame 117"""	C6orf117			Standard	NM_138409		Approved	bA51G5.2	uc003pkg.4	Q96G30	OTTHUMG00000015121	ENST00000257776.4:c.504C>A	6.37:g.84799086C>A	ENSP00000257776:p.Asn168Lys					MRAP2_uc010kbo.2_Missense_Mutation_p.N82K	p.N168K	NM_138409	NP_612418	Q96G30	MRAP2_HUMAN			4	694	+			168					A8K9M1|Q8IXM9|Q8N2D1	Missense_Mutation	SNP	ENST00000257776.4	37	c.504C>A	CCDS5001.1	.	.	.	.	.	.	.	.	.	.	C	25.5	4.640950	0.87859	.	.	ENSG00000135324	ENST00000257776	D	0.88124	-2.34	5.33	5.33	0.75918	.	0.000000	0.85682	D	0.000000	D	0.90621	0.7059	L	0.54323	1.7	0.80722	D	1	D	0.67145	0.996	D	0.64776	0.929	D	0.91135	0.4941	10	0.87932	D	0	-1.4142	19.3838	0.94548	0.0:1.0:0.0:0.0	.	168	Q96G30	MRAP2_HUMAN	K	168	ENSP00000257776:N168K	ENSP00000257776:N168K	N	+	3	2	MRAP2	84855805	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	1.821000	0.39041	2.670000	0.90874	0.655000	0.94253	AAC		0.502	MRAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041367.1	NM_138409	
ULBP1	80329	broad.mit.edu	37	6	150291168	150291168	+	Silent	SNP	C	C	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr6:150291168C>T	ENST00000229708.3	+	4	685	c.642C>T	c.(640-642)gcC>gcT	p.A214A		NM_025218.2	NP_079494.1	Q9BZM6	N2DL1_HUMAN	UL16 binding protein 1	214					antigen processing and presentation (GO:0019882)|natural killer cell activation (GO:0030101)|natural killer cell mediated cytotoxicity (GO:0042267)|regulation of immune response (GO:0050776)	anchored component of plasma membrane (GO:0046658)|endoplasmic reticulum (GO:0005783)|plasma membrane (GO:0005886)	natural killer cell lectin-like receptor binding (GO:0046703)	p.A214A(1)		large_intestine(3)|lung(5)|pancreas(1)|skin(1)	10		Ovarian(120;0.0907)	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.14e-11)		CCTCTCTGGCCCCAGGCACAA	0.562																																						uc003qnp.2																			1	Substitution - coding silent(1)		lung(1)	pancreas(1)	1						c.(640-642)GCC>GCT		UL16 binding protein 1 precursor							122.0	100.0	107.0					6																	150291168		2203	4300	6503	SO:0001819	synonymous_variant	80329				antigen processing and presentation|immune response|natural killer cell activation|regulation of immune response	anchored to membrane|endoplasmic reticulum|MHC class I protein complex	MHC class I receptor activity	g.chr6:150291168C>T	AF304377	CCDS5223.1	6q25	2003-04-29			ENSG00000111981	ENSG00000111981			14893	protein-coding gene	gene with protein product		605697				11239445, 11827464	Standard	XM_005267151		Approved	RAET1I	uc003qnp.3	Q9BZM6	OTTHUMG00000015810	ENST00000229708.3:c.642C>T	6.37:g.150291168C>T							p.A214A	NM_025218	NP_079494	Q9BZM6	N2DL1_HUMAN	BRCA - Breast invasive adenocarcinoma(37;0.193)	OV - Ovarian serous cystadenocarcinoma(155;2.14e-11)	4	685	+		Ovarian(120;0.0907)	214					Q5VY81|Q8IZW3|Q8IZX6	Silent	SNP	ENST00000229708.3	37	c.642C>T	CCDS5223.1																																																																																				0.562	ULBP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042677.2		
PACRG	135138	broad.mit.edu	37	6	163235289	163235289	+	Silent	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr6:163235289G>A	ENST00000337019.3	+	3	491	c.267G>A	c.(265-267)tcG>tcA	p.S89S	PACRG_ENST00000542669.1_3'UTR|PACRG_ENST00000366888.2_Silent_p.S89S|PACRG_ENST00000366889.2_Silent_p.S89S	NM_152410.2	NP_689623.2	Q96M98	PACRG_HUMAN	PARK2 co-regulated	89					spermatid development (GO:0007286)	cell body (GO:0044297)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|sperm midpiece (GO:0097225)				endometrium(2)|large_intestine(6)|lung(8)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	20		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)		AGCATGATTCGAAAGGAAACA	0.517																																						uc003qua.2																			0					0						c.(265-267)TCG>TCA		parkin co-regulated gene protein isoform 1							98.0	98.0	98.0					6																	163235289		2203	4300	6503	SO:0001819	synonymous_variant	135138							g.chr6:163235289G>A	AK057286	CCDS5284.1, CCDS43524.1	6q26	2004-07-01			ENSG00000112530	ENSG00000112530			19152	protein-coding gene	gene with protein product		608427				12547187	Standard	NM_001080378		Approved	PARK2CRG, FLJ32724, Glup, HAK005771	uc003qua.3	Q96M98	OTTHUMG00000016116	ENST00000337019.3:c.267G>A	6.37:g.163235289G>A						PACRG_uc003qub.2_Silent_p.S89S|PACRG_uc003quc.2_Silent_p.S89S	p.S89S	NM_152410	NP_689623	Q96M98	PACRG_HUMAN		OV - Ovarian serous cystadenocarcinoma(33;4.31e-19)|GBM - Glioblastoma multiforme(2;7.42e-11)|BRCA - Breast invasive adenocarcinoma(81;3.19e-05)|KIRC - Kidney renal clear cell carcinoma(3;0.205)|Kidney(3;0.242)	3	491	+		Breast(66;2.41e-05)|Ovarian(120;0.0245)|Prostate(117;0.0273)|all_neural(5;0.0416)|Glioma(2;0.203)	89					E1P5B5|Q6IMB8|Q8IZM1|Q8NHP5|Q9H1V9	Silent	SNP	ENST00000337019.3	37	c.267G>A	CCDS5284.1	.	.	.	.	.	.	.	.	.	.	G	8.734	0.917307	0.17982	.	.	ENSG00000112530	ENST00000534958	.	.	.	5.52	-1.78	0.07957	.	.	.	.	.	T	0.25195	0.0612	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.27502	-1.0072	4	.	.	.	-10.6882	3.038	0.06128	0.3465:0.3351:0.229:0.0893	.	.	.	.	K	5	.	.	E	+	1	0	PACRG	163155279	0.017000	0.18338	1.000000	0.80357	0.995000	0.86356	-0.854000	0.04299	-0.252000	0.09528	-0.222000	0.12452	GAA		0.517	PACRG-003	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000400424.1	NM_152410	
NPSR1	387129	broad.mit.edu	37	7	34698051	34698051	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr7:34698051C>A	ENST00000360581.1	+	1	155	c.27C>A	c.(25-27)agC>agA	p.S9R	AC005493.1_ENST00000399077.1_Intron|NPSR1_ENST00000359791.1_Missense_Mutation_p.S9R|NPSR1-AS1_ENST00000419766.1_RNA|NPSR1_ENST00000381539.3_Missense_Mutation_p.S9R|NPSR1_ENST00000381542.1_Missense_Mutation_p.S9R|NPSR1_ENST00000531252.1_Missense_Mutation_p.S9R|NPSR1_ENST00000465305.1_Missense_Mutation_p.S9R|NPSR1_ENST00000381553.3_Missense_Mutation_p.S9R	NM_207172.1	NP_997055.1	Q6W5P4	NPSR1_HUMAN	neuropeptide S receptor 1	9						cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	neuropeptide receptor activity (GO:0008188)|vasopressin receptor activity (GO:0005000)			endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|large_intestine(5)|lung(14)|pancreas(1)|skin(7)	31					Halothane(DB01159)	CAGAGGGCAGCTTCGATTCCA	0.572																																						uc003teg.1																			0				skin(3)|pancreas(1)	4						c.(25-27)AGC>AGA		G protein-coupled receptor for asthma	Halothane(DB01159)						104.0	91.0	95.0					7																	34698051		2203	4300	6503	SO:0001583	missense	387129					cytoplasm|integral to membrane|plasma membrane	vasopressin receptor activity	g.chr7:34698051C>A	AY255536	CCDS5443.1, CCDS5444.1, CCDS75579.1, CCDS75580.1, CCDS75581.1	7p14.3	2012-08-08	2006-05-10	2006-05-10	ENSG00000187258	ENSG00000187258		"""GPCR / Class A : Neuropeptide receptors : S"""	23631	protein-coding gene	gene with protein product		608595	"""G protein-coupled receptor 154"""	GPR154		12679517, 15073379	Standard	NM_207173		Approved	PGR14, GPRA	uc003tei.1	Q6W5P4	OTTHUMG00000099383	ENST00000360581.1:c.27C>A	7.37:g.34698051C>A	ENSP00000353788:p.Ser9Arg					AAA1_uc010kwo.1_Intron|AAA1_uc010kwp.1_Intron|AAA1_uc003tdz.2_Intron|AAA1_uc010kwq.1_Intron|AAA1_uc003teb.1_Intron|AAA1_uc011kaq.1_Intron|NPSR1_uc003teh.1_Missense_Mutation_p.S9R|NPSR1_uc010kwt.1_5'UTR|NPSR1_uc010kwu.1_5'UTR|NPSR1_uc010kwv.1_Missense_Mutation_p.S9R|NPSR1_uc003tei.1_Missense_Mutation_p.S9R|NPSR1_uc010kww.1_Missense_Mutation_p.S9R|NPSR1_uc011kar.1_Missense_Mutation_p.S9R	p.S9R	NM_207172	NP_997055	Q6W5P4	NPSR1_HUMAN			1	155	+			9			Extracellular (Potential).		A2RTZ4|Q2XP58|Q56H76|Q56H77|Q56H78|Q6JSL4|Q6JSL5|Q6JSL6|Q6JSL7|Q6JSL8|Q6W5P3|Q6ZMB8	Missense_Mutation	SNP	ENST00000360581.1	37	c.27C>A	CCDS5444.1	.	.	.	.	.	.	.	.	.	.	C	15.33	2.801707	0.50315	.	.	ENSG00000187258	ENST00000381553;ENST00000465305;ENST00000360581;ENST00000381542;ENST00000359791;ENST00000531252;ENST00000381539	T;T;T;T;T;T;T	0.32272	1.46;1.46;1.46;1.46;1.46;1.46;1.46	4.53	4.53	0.55603	.	0.534882	0.18708	N	0.133383	T	0.27313	0.0670	L	0.27053	0.805	0.35490	D	0.798917	P;P;P;P;P;B	0.44429	0.718;0.835;0.703;0.835;0.703;0.392	B;P;B;P;B;B	0.44561	0.298;0.453;0.318;0.453;0.318;0.134	T	0.37572	-0.9700	10	0.72032	D	0.01	-19.9121	12.9527	0.58409	0.0:1.0:0.0:0.0	.	9;9;9;9;9;9	B7ZMA2;Q6W5P4-5;Q6W5P4-2;Q6W5P4-4;Q6W5P4-3;Q6W5P4	.;.;.;.;.;NPSR1_HUMAN	R	9	ENSP00000370965:S9R;ENSP00000434955:S9R;ENSP00000353788:S9R;ENSP00000370953:S9R;ENSP00000352839:S9R;ENSP00000433258:S9R;ENSP00000370950:S9R	ENSP00000352839:S9R	S	+	3	2	NPSR1	34664576	0.801000	0.28930	0.891000	0.34965	0.281000	0.26958	1.833000	0.39161	2.499000	0.84300	0.655000	0.94253	AGC		0.572	NPSR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000216837.1	NM_207173	
WBSCR17	64409	broad.mit.edu	37	7	70597924	70597924	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr7:70597924G>A	ENST00000333538.5	+	1	770	c.136G>A	c.(136-138)Gcc>Acc	p.A46T		NM_022479.1	NP_071924.1	Q6IS24	GLTL3_HUMAN	Williams-Beuren syndrome chromosome region 17	46					protein glycosylation (GO:0006486)	Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			NS(5)|breast(2)|central_nervous_system(1)|endometrium(7)|kidney(7)|large_intestine(22)|lung(45)|ovary(2)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	100		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)				CCGGCCGCGCGCCGAGGTGGC	0.677																																						uc003tvy.2																			0				skin(3)|upper_aerodigestive_tract(1)|ovary(1)|pancreas(1)|central_nervous_system(1)	7						c.(136-138)GCC>ACC		UDP-GalNAc:polypeptide							26.0	27.0	26.0					7																	70597924		2196	4292	6488	SO:0001583	missense	64409					Golgi membrane|integral to membrane	polypeptide N-acetylgalactosaminyltransferase activity|sugar binding	g.chr7:70597924G>A	AF410457	CCDS5540.1	7q11.23	2014-03-13			ENSG00000185274	ENSG00000185274		"""Glycosyltransferase family 2 domain containing"""	16347	protein-coding gene	gene with protein product	"""polypeptide N-acetylgalactosaminyltransferase-like 3"", ""polypeptide GalNAc transferase 3"""	615137				12073013, 15744064, 22787146	Standard	NM_022479		Approved	GALNTL3, GalNAc-T5L	uc003tvy.4	Q6IS24	OTTHUMG00000129783	ENST00000333538.5:c.136G>A	7.37:g.70597924G>A	ENSP00000329654:p.Ala46Thr						p.A46T	NM_022479	NP_071924	Q6IS24	GLTL3_HUMAN			1	136	+		all_cancers(73;0.2)|Lung NSC(55;0.094)|all_lung(88;0.125)	46			Lumenal (Potential).		Q8NFV9|Q9NTA8	Missense_Mutation	SNP	ENST00000333538.5	37	c.136G>A	CCDS5540.1	.	.	.	.	.	.	.	.	.	.	G	19.62	3.860927	0.71834	.	.	ENSG00000185274	ENST00000333538	T	0.55052	0.54	4.72	4.72	0.59763	.	0.560500	0.16105	N	0.229375	T	0.56441	0.1985	N	0.22421	0.69	0.43761	D	0.996272	D	0.76494	0.999	D	0.68621	0.959	T	0.44421	-0.9329	10	0.11182	T	0.66	.	16.8419	0.85971	0.0:0.0:1.0:0.0	.	46	Q6IS24	GLTL3_HUMAN	T	46	ENSP00000329654:A46T	ENSP00000329654:A46T	A	+	1	0	WBSCR17	70235860	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	3.674000	0.54598	2.448000	0.82819	0.467000	0.42956	GCC		0.677	WBSCR17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252006.1	NM_022479	
SSC4D	136853	broad.mit.edu	37	7	76033702	76033702	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr7:76033702C>T	ENST00000275560.3	-	2	402	c.55G>A	c.(55-57)Ggg>Agg	p.G19R	ZP3_ENST00000336517.4_Intron	NM_080744.1	NP_542782.1														autonomic_ganglia(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(2)|lung(9)|pancreas(1)|prostate(1)|skin(2)|urinary_tract(1)	21						AACCTCCACCCCCAGCGCTTC	0.597																																						uc003ufb.2																			0				pancreas(1)	1						c.(55-57)GGG>AGG		scavenger receptor cysteine rich domain							126.0	116.0	119.0					7																	76033702		2203	4300	6503	SO:0001583	missense	136853					extracellular region|membrane	scavenger receptor activity	g.chr7:76033702C>T																												ENST00000275560.3:c.55G>A	7.37:g.76033702C>T	ENSP00000275560:p.Gly19Arg					ZP3_uc003ufc.3_Intron	p.G19R	NM_080744	NP_542782	Q8WTU2	SRB4D_HUMAN			2	403	-			19						Missense_Mutation	SNP	ENST00000275560.3	37	c.55G>A	CCDS5585.1	.	.	.	.	.	.	.	.	.	.	C	11.55	1.672434	0.29693	.	.	ENSG00000146700	ENST00000275560	T	0.01215	5.16	4.99	3.16	0.36331	.	0.714189	0.12756	N	0.441758	T	0.01835	0.0058	L	0.56769	1.78	0.23978	N	0.996286	B	0.29085	0.232	B	0.35607	0.206	T	0.45425	-0.9262	10	0.20519	T	0.43	.	6.506	0.22196	0.1781:0.7301:0.0:0.0918	.	19	Q8WTU2	SRB4D_HUMAN	R	19	ENSP00000275560:G19R	ENSP00000275560:G19R	G	-	1	0	SRCRB4D	75871638	0.103000	0.21917	0.163000	0.22734	0.684000	0.39900	2.056000	0.41355	0.810000	0.34279	-0.328000	0.08392	GGG		0.597	SRCRB4D-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253001.3		
RELN	5649	broad.mit.edu	37	7	103417022	103417022	+	Nonsense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr7:103417022G>A	ENST00000428762.1	-	4	685	c.526C>T	c.(526-528)Cag>Tag	p.Q176*	RELN_ENST00000424685.2_Nonsense_Mutation_p.Q176*|RELN_ENST00000343529.5_Nonsense_Mutation_p.Q176*	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	176	Reelin. {ECO:0000255|PROSITE- ProRule:PRU00363}.				associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		TCACACAACTGCTGGGCTAAA	0.403																																					NSCLC(146;835 1944 15585 22231 52158)	uc003vca.2																			0				ovary(8)|upper_aerodigestive_tract(5)|large_intestine(2)|central_nervous_system(2)|skin(1)|pancreas(1)	19						c.(526-528)CAG>TAG		reelin isoform a							129.0	121.0	124.0					7																	103417022		2203	4300	6503	SO:0001587	stop_gained	5649				axon guidance|cell adhesion|cerebral cortex tangential migration|glial cell differentiation|neuron migration|peptidyl-tyrosine phosphorylation|positive regulation of protein kinase activity|positive regulation of small GTPase mediated signal transduction|response to pain|spinal cord patterning	cytoplasm|dendrite|extracellular space|proteinaceous extracellular matrix	metal ion binding|protein serine/threonine/tyrosine kinase activity|serine-type peptidase activity	g.chr7:103417022G>A		CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.526C>T	7.37:g.103417022G>A	ENSP00000392423:p.Gln176*					RELN_uc010liz.2_Nonsense_Mutation_p.Q176*	p.Q176*	NM_005045	NP_005036	P78509	RELN_HUMAN		COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)	4	686	-			176			Reelin.		A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Nonsense_Mutation	SNP	ENST00000428762.1	37	c.526C>T	CCDS47680.1	.	.	.	.	.	.	.	.	.	.	G	39	7.875216	0.98537	.	.	ENSG00000189056	ENST00000428762;ENST00000343529;ENST00000424685;ENST00000448171	.	.	.	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.49607	T	0.09	.	19.121	0.93364	0.0:0.0:1.0:0.0	.	.	.	.	X	176	.	ENSP00000345694:Q176X	Q	-	1	0	RELN	103204258	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	8.038000	0.88943	2.814000	0.96858	0.591000	0.81541	CAG		0.403	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1	NM_005045	
CTTNBP2	83992	broad.mit.edu	37	7	117432019	117432019	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr7:117432019G>T	ENST00000160373.3	-	4	1322	c.1231C>A	c.(1231-1233)Caa>Aaa	p.Q411K	CTTNBP2_ENST00000487820.1_5'Flank	NM_033427.2	NP_219499.1	Q8WZ74	CTTB2_HUMAN	cortactin binding protein 2	411	Pro-rich.				brain development (GO:0007420)	cell projection (GO:0042995)|synaptic vesicle (GO:0008021)				breast(3)|central_nervous_system(3)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(36)|ovary(4)|prostate(5)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83	Lung NSC(10;0.0018)|all_lung(10;0.002)			LUSC - Lung squamous cell carcinoma(290;0.133)		CCTGGTGTTTGAGCGGTGGGA	0.522																																						uc003vjf.2																			0				ovary(4)|central_nervous_system(1)	5						c.(1231-1233)CAA>AAA		cortactin binding protein 2							199.0	177.0	185.0					7																	117432019		2203	4300	6503	SO:0001583	missense	83992							g.chr7:117432019G>T		CCDS5774.1	7q31	2013-01-10	2004-06-08	2004-06-09	ENSG00000077063	ENSG00000077063		"""Ankyrin repeat domain containing"""	15679	protein-coding gene	gene with protein product		609772	"""cortactin binding protein 2"""	CORTBP2, C7orf8		11707066	Standard	XM_005250635		Approved	KIAA1758, Orf4	uc003vjf.3	Q8WZ74	OTTHUMG00000022880	ENST00000160373.3:c.1231C>A	7.37:g.117432019G>T	ENSP00000160373:p.Gln411Lys						p.Q411K	NM_033427	NP_219499	Q8WZ74	CTTB2_HUMAN		LUSC - Lung squamous cell carcinoma(290;0.133)	4	1323	-	Lung NSC(10;0.0018)|all_lung(10;0.002)		411			Pro-rich.		O43389|Q7LG11|Q9C0A5	Missense_Mutation	SNP	ENST00000160373.3	37	c.1231C>A	CCDS5774.1	.	.	.	.	.	.	.	.	.	.	G	0	-2.770025	0.00081	.	.	ENSG00000077063	ENST00000160373	T	0.63744	-0.06	4.52	4.52	0.55395	.	0.571274	0.16235	N	0.223406	T	0.56645	0.1999	M	0.75447	2.3	0.09310	N	1	B	0.24368	0.102	B	0.21360	0.034	T	0.43261	-0.9402	10	0.19147	T	0.46	-3.2383	7.4765	0.27378	0.0879:0.0:0.7447:0.1674	.	411	Q8WZ74	CTTB2_HUMAN	K	411	ENSP00000160373:Q411K	ENSP00000160373:Q411K	Q	-	1	0	CTTNBP2	117219255	0.991000	0.36638	0.096000	0.21009	0.012000	0.07955	2.855000	0.48333	2.500000	0.84329	0.460000	0.39030	CAA		0.522	CTTNBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059201.4	NM_033427	
GALT	2592	broad.mit.edu	37	9	34648454	34648454	+	Splice_Site	SNP	G	G	A	rs193922250		TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr9:34648454G>A	ENST00000378842.3	+	7	729		c.e7+1		GALT_ENST00000556278.1_Splice_Site|IL11RA_ENST00000555003.1_5'Flank|GALT_ENST00000450095.2_Splice_Site	NM_000155.3	NP_000146.2	P07902	GALT_HUMAN	galactose-1-phosphate uridylyltransferase						carbohydrate metabolic process (GO:0005975)|galactose catabolic process (GO:0019388)|galactose metabolic process (GO:0006012)|small molecule metabolic process (GO:0044281)|UDP-glucose catabolic process (GO:0006258)	cytosol (GO:0005829)|Golgi apparatus (GO:0005794)	UDP-glucose:hexose-1-phosphate uridylyltransferase activity (GO:0008108)|zinc ion binding (GO:0008270)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(2)|lung(5)|upper_aerodigestive_tract(1)	16	all_epithelial(49;0.102)		STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)		ACTCAGGAAGGTGGGAGAGAG	0.532									Galactosemia																													uc003zve.2																			0					0						c.e7+1		galactose-1-phosphate uridylyltransferase							64.0	68.0	67.0					9																	34648454		2203	4300	6503	SO:0001630	splice_region_variant	2592	Galactosemia	Familial Cancer Database	Galactose-1-Phosphate Uridyltransferase Deficiency	galactose catabolic process	cytosol	UDP-glucose:hexose-1-phosphate uridylyltransferase activity|zinc ion binding	g.chr9:34648454G>A	M60091	CCDS6565.1, CCDS59122.1	9p13	2013-01-08			ENSG00000213930	ENSG00000213930	2.7.7.12		4135	protein-coding gene	gene with protein product		606999					Standard	NM_000155		Approved		uc003zve.4	P07902	OTTHUMG00000019836	ENST00000378842.3:c.687+1G>A	9.37:g.34648454G>A						GALT_uc003zvf.2_Splice_Site_p.K120_splice|GALT_uc003zvg.2_Splice_Site_p.K101_splice|GALT_uc003zvh.2_Splice_Site_p.K181_splice|GALT_uc011lop.1_Splice_Site_p.K181_splice|IL11RA_uc003zvi.2_5'Flank	p.K229_splice	NM_000155	NP_000146	P07902	GALT_HUMAN	STAD - Stomach adenocarcinoma(86;0.178)	GBM - Glioblastoma multiforme(74;0.173)	7	754	+	all_epithelial(49;0.102)							B4E097|E7ET32|Q14355|Q14356|Q14357|Q14358|Q14359|Q14360|Q14361|Q14363|Q14364|Q14365|Q14369|Q14370|Q14371|Q14372|Q14373|Q14374|Q14375|Q14377|Q14378|Q14380|Q14381|Q14382|Q14383|Q14384|Q14385|Q14386|Q14387|Q14389|Q16766|Q53XK1|Q5VZ81|Q96BY1	Splice_Site	SNP	ENST00000378842.3	37	c.687_splice	CCDS6565.1	.	.	.	.	.	.	.	.	.	.	G	13.33	2.203599	0.38905	.	.	ENSG00000213930;ENSG00000213930;ENSG00000258728	ENST00000450095;ENST00000378842;ENST00000556278	.	.	.	4.41	3.44	0.39384	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	11.9429	0.52911	0.0:0.1761:0.8239:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	RP11-195F19.29;GALT	34638454	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	4.904000	0.63279	2.459000	0.83118	0.655000	0.94253	.		0.532	GALT-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052231.1	NM_000155	Intron
TDRD7	23424	broad.mit.edu	37	9	100245441	100245441	+	Nonsense_Mutation	SNP	C	C	G			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr9:100245441C>G	ENST00000355295.4	+	15	3018	c.2723C>G	c.(2722-2724)tCa>tGa	p.S908*	TDRD7_ENST00000540902.1_Nonsense_Mutation_p.S228*|TDRD7_ENST00000422139.2_Nonsense_Mutation_p.S834*	NM_014290.2	NP_055105.2	Q8NHU6	TDRD7_HUMAN	tudor domain containing 7	908	Interacts with CABLES1. {ECO:0000250}.|Interacts with CDK17. {ECO:0000250}.				germ cell development (GO:0007281)|lens fiber cell differentiation (GO:0070306)|lens morphogenesis in camera-type eye (GO:0002089)|posttranscriptional regulation of gene expression (GO:0010608)|spermatogenesis (GO:0007283)	chromatoid body (GO:0033391)|cytoplasm (GO:0005737)|mitochondrial matrix (GO:0005759)|P granule (GO:0043186)|ribonucleoprotein granule (GO:0035770)	mRNA binding (GO:0003729)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(2)|pancreas(1)|prostate(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	29		Acute lymphoblastic leukemia(62;0.158)				GTCCACTTATCAAAGCCAGGG	0.498																																						uc004axj.2																			0				ovary(2)|pancreas(1)	3						c.(2722-2724)TCA>TGA		tudor domain containing 7							67.0	60.0	62.0					9																	100245441		2203	4300	6503	SO:0001587	stop_gained	23424				lens fiber cell differentiation|lens morphogenesis in camera-type eye|posttranscriptional regulation of gene expression|spermatogenesis	chromatoid body	mRNA binding	g.chr9:100245441C>G	AB025254	CCDS6725.1	9q22.33	2013-01-23			ENSG00000196116	ENSG00000196116		"""Tudor domain containing"""	30831	protein-coding gene	gene with protein product		611258				21436445	Standard	NM_014290		Approved	PCTAIRE2BP	uc004axj.3	Q8NHU6	OTTHUMG00000020326	ENST00000355295.4:c.2723C>G	9.37:g.100245441C>G	ENSP00000347444:p.Ser908*					TDRD7_uc011lux.1_Nonsense_Mutation_p.S834*|TDRD7_uc010msp.1_Nonsense_Mutation_p.S160*|TDRD7_uc011luy.1_Nonsense_Mutation_p.S228*	p.S908*	NM_014290	NP_055105	Q8NHU6	TDRD7_HUMAN			15	2948	+		Acute lymphoblastic leukemia(62;0.158)	908			Interacts with CDK17 (By similarity).|Interacts with CABLES1 (By similarity).		A6NCI6|B2RBX3|B4DG99|B4DXF7|E7EQD4|Q5VV27|Q96JT1|Q9UFF0|Q9Y2M3	Nonsense_Mutation	SNP	ENST00000355295.4	37	c.2723C>G	CCDS6725.1	.	.	.	.	.	.	.	.	.	.	C	37	6.096468	0.97281	.	.	ENSG00000196116	ENST00000355295;ENST00000422139;ENST00000540902	.	.	.	5.52	4.62	0.57501	.	0.119770	0.64402	D	0.000014	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.10902	T	0.67	-10.0685	15.526	0.75905	0.0:0.8613:0.1387:0.0	.	.	.	.	X	908;834;228	.	ENSP00000347444:S908X	S	+	2	0	TDRD7	99285262	0.731000	0.28111	0.185000	0.23176	0.252000	0.25951	4.223000	0.58587	1.466000	0.48025	0.555000	0.69702	TCA		0.498	TDRD7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053322.1	NM_014290	
TNFSF15	9966	broad.mit.edu	37	9	117552981	117552981	+	Silent	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chr9:117552981G>A	ENST00000374045.4	-	4	620	c.507C>T	c.(505-507)ggC>ggT	p.G169G	TNFSF15_ENST00000374044.1_Silent_p.G92G|AL390240.1_ENST00000408807.1_RNA	NM_001204344.1|NM_005118.3	NP_001191273.1|NP_005109.2	O95150	TNF15_HUMAN	tumor necrosis factor (ligand) superfamily, member 15	169					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation of NF-kappaB-inducing kinase activity (GO:0007250)|cytokine metabolic process (GO:0042107)|immune response (GO:0006955)|positive regulation of cytokine secretion (GO:0050715)|signal transduction (GO:0007165)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(4)|skin(1)	11						TGTTTGGTCGGCCTGCTTGTC	0.527																																						uc004bjh.2																			0					0						c.(505-507)GGC>GGT		tumor necrosis factor (ligand) superfamily,							207.0	169.0	182.0					9																	117552981		2203	4300	6503	SO:0001819	synonymous_variant	9966				activation of caspase activity|activation of NF-kappaB-inducing kinase activity|cytokine metabolic process|immune response	extracellular space|integral to plasma membrane	cytokine activity|tumor necrosis factor receptor binding	g.chr9:117552981G>A	AF039390	CCDS6809.1	9q32	2008-07-21			ENSG00000181634	ENSG00000181634		"""Tumor necrosis factor (ligand) superfamily"""	11931	protein-coding gene	gene with protein product	"""vascular endothelial cell growth inhibitor"", ""TNF superfamily ligand TL1A"", ""TNF ligand-related molecule 1"", ""vascular endothelial growth inhibitor-192A"""	604052				9434163	Standard	NM_005118		Approved	TL1, VEGI, TL1A, VEGI192A, MGC129934, MGC129935	uc004bjh.3	O95150	OTTHUMG00000021011	ENST00000374045.4:c.507C>T	9.37:g.117552981G>A						TNFSF15_uc004bjg.2_Silent_p.G110G	p.G169G	NM_005118	NP_005109	O95150	TNF15_HUMAN			4	623	-			169			Extracellular (Potential).		Q3SX69|Q5VJK8|Q5VWH1|Q8NFE9	Silent	SNP	ENST00000374045.4	37	c.507C>T	CCDS6809.1																																																																																				0.527	TNFSF15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055424.2	NM_005118	
CACNA1F	778	broad.mit.edu	37	X	49077514	49077514	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chrX:49077514G>T	ENST00000376265.2	-	18	2408	c.2347C>A	c.(2347-2349)Cca>Aca	p.P783T	CACNA1F_ENST00000323022.5_Missense_Mutation_p.P772T|CACNA1F_ENST00000376251.1_Missense_Mutation_p.P718T|CACNA1F_ENST00000480889.1_5'Flank	NM_005183.2	NP_005174.2	O60840	CAC1F_HUMAN	calcium channel, voltage-dependent, L type, alpha 1F subunit	783					axonogenesis (GO:0007409)|calcium ion import (GO:0070509)|cellular calcium ion homeostasis (GO:0006874)|dendrite morphogenesis (GO:0048813)|detection of light stimulus involved in visual perception (GO:0050908)|membrane depolarization during action potential (GO:0086010)|retina development in camera-type eye (GO:0060041)|visual perception (GO:0007601)	integral component of membrane (GO:0016021)|perikaryon (GO:0043204)|photoreceptor outer segment (GO:0001750)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)			autonomic_ganglia(1)|breast(8)|central_nervous_system(3)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(17)|lung(24)|ovary(5)|prostate(3)|skin(4)|urinary_tract(1)	85					Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Nimodipine(DB00393)|Spironolactone(DB00421)|Verapamil(DB00661)	TTCTCCTGTGGGAGATCCTTC	0.502																																						uc004dnb.2																			0				breast(3)|ovary(1)|kidney(1)|skin(1)	6						c.(2347-2349)CCA>ACA		calcium channel, voltage-dependent, L type,	Verapamil(DB00661)						226.0	142.0	171.0					X																	49077514		2203	4300	6503	SO:0001583	missense	778				axon guidance|detection of light stimulus involved in visual perception	voltage-gated calcium channel complex	protein binding|voltage-gated calcium channel activity	g.chrX:49077514G>T	AA019975	CCDS35253.1, CCDS59166.1, CCDS59167.1	Xp11.23	2013-01-23	2007-02-16		ENSG00000102001	ENSG00000102001		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1393	protein-coding gene	gene with protein product		300110	"""Aland island eye disease (Forsius-Eriksson ocular albinism, ocular albinism type 2)"""	CSNB2, AIED		9344658, 9662400, 16382099, 12111638, 17525176	Standard	NM_005183		Approved	Cav1.4, JM8, JMC8, CSNBX2, CORDX3, CSNB2A, OA2	uc010nip.3	O60840	OTTHUMG00000022703	ENST00000376265.2:c.2347C>A	X.37:g.49077514G>T	ENSP00000365441:p.Pro783Thr					CACNA1F_uc010nip.2_Missense_Mutation_p.P772T	p.P783T	NM_005183	NP_005174	O60840	CAC1F_HUMAN			18	2409	-			783			Cytoplasmic (Potential).		A6NI29|F5CIQ9|O43901|O95226|Q9UHB1	Missense_Mutation	SNP	ENST00000376265.2	37	c.2347C>A	CCDS35253.1	.	.	.	.	.	.	.	.	.	.	.	6.241	0.412602	0.11812	.	.	ENSG00000102001	ENST00000376251;ENST00000323022;ENST00000376265	D;D;D	0.96232	-3.95;-3.87;-3.86	3.14	3.14	0.36123	.	32.793600	0.00166	N	0.000000	D	0.94709	0.8293	L	0.51422	1.61	0.09310	N	1	P;P	0.38167	0.621;0.487	B;B	0.39904	0.313;0.166	D	0.86249	0.1648	10	0.18710	T	0.47	.	8.9455	0.35756	0.0:0.0:1.0:0.0	.	772;783	F5CIQ9;O60840	.;CAC1F_HUMAN	T	718;772;783	ENSP00000365427:P718T;ENSP00000321618:P772T;ENSP00000365441:P783T	ENSP00000321618:P772T	P	-	1	0	CACNA1F	48964458	0.493000	0.26035	0.006000	0.13384	0.095000	0.18619	2.312000	0.43726	1.843000	0.53566	0.179000	0.17066	CCA		0.502	CACNA1F-007	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000358157.1	NM_005183	
TAF1	6872	broad.mit.edu	37	X	70587386	70587386	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chrX:70587386G>A	ENST00000373790.4	+	2	269	c.218G>A	c.(217-219)gGg>gAg	p.G73E	TAF1_ENST00000449580.1_Missense_Mutation_p.G73E|TAF1_ENST00000423759.1_Missense_Mutation_p.G73E|TAF1_ENST00000276072.3_Missense_Mutation_p.G73E	NM_004606.3|NM_138923.2	NP_004597.2|NP_620278.1	P21675	TAF1_HUMAN	TAF1 RNA polymerase II, TATA box binding protein (TBP)-associated factor, 250kDa	73	Protein kinase 1.				cellular response to DNA damage stimulus (GO:0006974)|DNA-templated transcription, initiation (GO:0006352)|gene expression (GO:0010467)|histone acetylation (GO:0016573)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription initiation from RNA polymerase II promoter (GO:0060261)|protein autophosphorylation (GO:0046777)|regulation of transcription involved in G2/M transition of mitotic cell cycle (GO:0000117)|RNA polymerase II transcriptional preinitiation complex assembly (GO:0051123)|transcription elongation from RNA polymerase II promoter (GO:0006368)|transcription from RNA polymerase II promoter (GO:0006366)|transcription initiation from RNA polymerase II promoter (GO:0006367)|viral process (GO:0016032)	MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|transcription factor TFIID complex (GO:0005669)	ATP binding (GO:0005524)|histone acetyltransferase activity (GO:0004402)|lysine-acetylated histone binding (GO:0070577)|p53 binding (GO:0002039)|protein serine/threonine kinase activity (GO:0004674)|sequence-specific DNA binding (GO:0043565)|TBP-class protein binding (GO:0017025)|transcription coactivator activity (GO:0003713)|transcription factor binding (GO:0008134)	p.G73E(1)		breast(13)|central_nervous_system(6)|cervix(1)|endometrium(25)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(16)|lung(34)|ovary(9)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(3)	124	Renal(35;0.156)	all_lung(315;0.000321)				GGGGCTTTGGGGCTGGGCAGC	0.522																																						uc004dzu.3																			1	Substitution - Missense(1)	p.G73E(1)	central_nervous_system(1)	ovary(7)|breast(4)|large_intestine(2)|central_nervous_system(2)|lung(1)|skin(1)	17						c.(217-219)GGG>GAG		TBP-associated factor 1 isoform 2							90.0	72.0	78.0					X																	70587386		2203	4300	6503	SO:0001583	missense	6872				G1 phase of mitotic cell cycle|interspecies interaction between organisms|peptidyl-serine phosphorylation|peptidyl-threonine phosphorylation|positive regulation of proteasomal ubiquitin-dependent protein catabolic process|positive regulation of transcription from RNA polymerase II promoter|positive regulation of transcription initiation from RNA polymerase II promoter|protein autophosphorylation|regulation of transcription involved in G2/M-phase of mitotic cell cycle|RNA polymerase II transcriptional preinitiation complex assembly|transcription elongation from RNA polymerase II promoter|viral reproduction	MLL1 complex|transcription factor TFIID complex	ATP binding|histone acetyl-lysine binding|histone acetyltransferase activity|p53 binding|protein binding|protein serine/threonine kinase activity|sequence-specific DNA binding|TBP-class protein binding|transcription coactivator activity	g.chrX:70587386G>A		CCDS14412.1, CCDS35325.1, CCDS69783.1	Xq13.1	2011-07-01	2002-08-29	2001-12-07	ENSG00000147133	ENSG00000147133		"""Chromatin-modifying enzymes / K-acetyltransferases"""	11535	protein-coding gene	gene with protein product		313650	"""TATA box binding protein (TBP)-associated factor, RNA polymerase II, A, 250kD"", ""dystonia 3 (with Parkinsonism)"""	TAF2A, BA2R, CCG1, CCGS, DYT3		3556424, 12928496, 17952504	Standard	XM_005262295		Approved	NSCL2, TAFII250, KAT4, DYT3/TAF1	uc004dzt.4	P21675	OTTHUMG00000022723	ENST00000373790.4:c.218G>A	X.37:g.70587386G>A	ENSP00000362895:p.Gly73Glu					BCYRN1_uc011mpt.1_Intron|TAF1_uc004dzt.3_Missense_Mutation_p.G73E	p.G73E	NM_138923	NP_620278	P21675	TAF1_HUMAN			2	269	+	Renal(35;0.156)	all_lung(315;0.000321)	73			Protein kinase 1.		A5CVC8|A5CVC9|A5CVD0|A5CVD1|B1Q2X3|Q59FZ3|Q6IUZ1|Q70Q86|Q70Q87|Q70T00|Q70T01|Q70T02|Q70T03	Missense_Mutation	SNP	ENST00000373790.4	37	c.218G>A	CCDS35325.1	.	.	.	.	.	.	.	.	.	.	.	23.5	4.429577	0.83776	.	.	ENSG00000147133	ENST00000373790;ENST00000449580;ENST00000423759;ENST00000276072	T;T;T;T	0.16073	2.5;2.55;2.42;2.37	4.51	3.61	0.41365	TAFII-230 TBP-binding (2);	0.000000	0.85682	D	0.000000	T	0.42426	0.1202	M	0.78049	2.395	0.80722	D	1	D;D	0.89917	0.959;1.0	P;D	0.87578	0.777;0.998	T	0.45411	-0.9263	10	0.87932	D	0	.	13.7815	0.63085	0.0:0.1509:0.8491:0.0	.	73;73	P21675;P21675-2	TAF1_HUMAN;.	E	73	ENSP00000362895:G73E;ENSP00000389000:G73E;ENSP00000406549:G73E;ENSP00000276072:G73E	ENSP00000276072:G73E	G	+	2	0	TAF1	70504111	1.000000	0.71417	0.955000	0.39395	0.992000	0.81027	8.606000	0.90888	0.995000	0.38917	0.513000	0.50165	GGG		0.522	TAF1-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058995.2	NM_004606	
ATRX	546	broad.mit.edu	37	X	76872167	76872167	+	Frame_Shift_Del	DEL	A	A	-			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chrX:76872167delA	ENST00000373344.5	-	22	5694	c.5480delT	c.(5479-5481)ttgfs	p.L1827fs	ATRX_ENST00000395603.3_Frame_Shift_Del_p.L1789fs|ATRX_ENST00000480283.1_5'UTR	NM_000489.3	NP_000480.3	P46100	ATRX_HUMAN	alpha thalassemia/mental retardation syndrome X-linked	1827					ATP catabolic process (GO:0006200)|cellular response to hydroxyurea (GO:0072711)|chromatin remodeling (GO:0006338)|DNA damage response, signal transduction by p53 class mediator (GO:0030330)|DNA duplex unwinding (GO:0032508)|DNA methylation (GO:0006306)|DNA recombination (GO:0006310)|DNA repair (GO:0006281)|DNA replication-independent nucleosome assembly (GO:0006336)|forebrain development (GO:0030900)|negative regulation of telomeric RNA transcription from RNA pol II promoter (GO:1901581)|nucleosome assembly (GO:0006334)|positive regulation of nuclear cell cycle DNA replication (GO:0010571)|positive regulation of telomere maintenance (GO:0032206)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of transcription, DNA-templated (GO:0006355)|replication fork processing (GO:0031297)|seminiferous tubule development (GO:0072520)|Sertoli cell development (GO:0060009)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nuclear heterochromatin (GO:0005720)|nucleolus (GO:0005730)|nucleus (GO:0005634)|SWI/SNF superfamily-type complex (GO:0070603)|telomeric heterochromatin (GO:0031933)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|chromo shadow domain binding (GO:0070087)|DNA binding (GO:0003677)|DNA helicase activity (GO:0003678)|DNA translocase activity (GO:0015616)|helicase activity (GO:0004386)|histone binding (GO:0042393)|methylated histone binding (GO:0035064)|zinc ion binding (GO:0008270)	p.?(1)		bone(1)|breast(6)|central_nervous_system(31)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(15)|kidney(14)|large_intestine(1)|liver(1)|lung(40)|ovary(2)|pancreas(13)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(2)	145						TTTTGGAGGCAAGAATTTTGT	0.318			"""Mis, F, N"""		"""Pancreatic neuroendocrine tumors, paediatric GBM"""		ATR-X (alpha thalassemia/mental retardation) syndrome																															uc004ecp.3				Rec	yes		X	Xq21.1	546	Mis|F|N	alpha thalassemia/mental retardation syndrome X-linked	yes	ATR-X (alpha thalassemia/mental retardation) syndrome	E			Pancreatic neuroendocrine tumors		1	Unknown(1)		bone(1)	haematopoietic_and_lymphoid_tissue(14)|pancreas(12)|lung(1)|breast(1)|skin(1)|kidney(1)	30						c.(5479-5481)TTGfs		transcriptional regulator ATRX isoform 1	Phosphatidylserine(DB00144)						123.0	109.0	114.0					X																	76872167		2202	4291	6493	SO:0001589	frameshift_variant	546				DNA methylation|DNA recombination|DNA repair|regulation of transcription, DNA-dependent	nuclear heterochromatin	ATP binding|chromo shadow domain binding|DNA binding|DNA helicase activity|zinc ion binding	g.chrX:76872167delA	U72937	CCDS14434.1, CCDS14435.1	Xq21.1	2014-06-17	2010-06-24		ENSG00000085224	ENSG00000085224			886	protein-coding gene	gene with protein product	"""RAD54 homolog (S. cerevisiae)"""	300032	"""alpha thalassemia/mental retardation syndrome X-linked (RAD54 (S. cerevisiae) homolog)"", ""Juberg-Marsidi syndrome"""	RAD54, JMS		7874112, 1415255, 8503439, 8630485	Standard	NM_000489		Approved	XH2, XNP	uc004ecp.4	P46100	OTTHUMG00000022686	ENST00000373344.5:c.5480delT	X.37:g.76872167delA	ENSP00000362441:p.Leu1827fs					ATRX_uc004ecq.3_Frame_Shift_Del_p.L1789fs|ATRX_uc004eco.3_Frame_Shift_Del_p.L1612fs	p.L1827fs	NM_000489	NP_000480	P46100	ATRX_HUMAN			22	5712	-			1827					D3DTE2|P51068|Q15886|Q59FB5|Q59H31|Q5H9A2|Q5JWI4|Q7Z2J1|Q9H0Z1|Q9NTS3	Frame_Shift_Del	DEL	ENST00000373344.5	37	c.5480delT	CCDS14434.1																																																																																				0.318	ATRX-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058860.2	NM_000489	
ARMCX2	9823	broad.mit.edu	37	X	100910782	100910782	+	Missense_Mutation	SNP	T	T	G			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chrX:100910782T>G	ENST00000328766.5	-	5	2246	c.1793A>C	c.(1792-1794)tAc>tCc	p.Y598S	ARMCX2_ENST00000330154.2_Missense_Mutation_p.Y598S|ARMCX2_ENST00000356824.4_Missense_Mutation_p.Y598S|ARMCX2_ENST00000467416.1_5'Flank	NM_014782.5	NP_055597.1	Q7L311	ARMX2_HUMAN	armadillo repeat containing, X-linked 2	598						integral component of membrane (GO:0016021)				NS(1)|breast(4)|endometrium(3)|kidney(1)|large_intestine(2)|lung(10)|ovary(6)|prostate(1)|skin(1)	29						AGTGCATAAGTAAAAAAGGGA	0.328																																						uc004eid.2																			0				ovary(6)	6						c.(1792-1794)TAC>TCC		ALEX2 protein							77.0	79.0	78.0					X																	100910782		2203	4299	6502	SO:0001583	missense	9823					integral to membrane	binding	g.chrX:100910782T>G	AB011084	CCDS14490.1	Xq21.33-q22.2	2014-03-21			ENSG00000184867	ENSG00000184867		"""Armadillo repeat containing"""	16869	protein-coding gene	gene with protein product		300363				9628581, 11162520, 16221301, 22569362	Standard	XM_005278109		Approved	ALEX2, KIAA0512, GASP9	uc004eif.3	Q7L311	OTTHUMG00000022038	ENST00000328766.5:c.1793A>C	X.37:g.100910782T>G	ENSP00000331662:p.Tyr598Ser					ARMCX2_uc004eie.3_Missense_Mutation_p.Y598S|ARMCX2_uc004eif.3_Missense_Mutation_p.Y598S|ARMCX2_uc004eig.3_Missense_Mutation_p.Y598S|ARMCX2_uc010nnt.2_Missense_Mutation_p.Y598S	p.Y598S	NM_177949	NP_808818	Q7L311	ARMX2_HUMAN			3	2148	-			598					O60267|Q5H9D9	Missense_Mutation	SNP	ENST00000328766.5	37	c.1793A>C	CCDS14490.1	.	.	.	.	.	.	.	.	.	.	T	5.411	0.261042	0.10239	.	.	ENSG00000184867	ENST00000328766;ENST00000330154;ENST00000356824	T;T;T	0.27720	1.65;1.65;1.65	4.1	2.91	0.33838	Armadillo-like helical (1);	0.588535	0.18577	N	0.137163	T	0.10121	0.0248	N	0.02011	-0.69	0.30225	N	0.796401	B	0.14438	0.01	B	0.17979	0.02	T	0.21895	-1.0232	10	0.18276	T	0.48	-0.9532	5.5418	0.17041	0.3136:0.0:0.0:0.6864	.	598	Q7L311	ARMX2_HUMAN	S	598	ENSP00000331662:Y598S;ENSP00000328631:Y598S;ENSP00000349281:Y598S	ENSP00000331662:Y598S	Y	-	2	0	ARMCX2	100797438	1.000000	0.71417	1.000000	0.80357	0.831000	0.47069	0.421000	0.21280	0.691000	0.31592	0.345000	0.21793	TAC		0.328	ARMCX2-011	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057586.1	NM_014782	
RNF128	79589	broad.mit.edu	37	X	106038858	106038858	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chrX:106038858A>G	ENST00000255499.2	+	7	1452	c.1202A>G	c.(1201-1203)gAt>gGt	p.D401G	RNF128_ENST00000324342.3_Missense_Mutation_p.D375G	NM_194463.1	NP_919445.1	Q8TEB7	RN128_HUMAN	ring finger protein 128, E3 ubiquitin protein ligase	401					negative regulation of cytokine biosynthetic process (GO:0042036)	cytoskeleton (GO:0005856)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)	ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(2)|large_intestine(1)|lung(6)|ovary(1)	11						GTGGCAGTGGATGTTATTCCT	0.358																																						uc004eml.2																			0				ovary(1)|central_nervous_system(1)	2						c.(1201-1203)GAT>GGT		ring finger protein 128 isoform 1							177.0	176.0	176.0					X																	106038858		2203	4300	6503	SO:0001583	missense	79589					endomembrane system|integral to membrane|perinuclear region of cytoplasm	zinc ion binding	g.chrX:106038858A>G	AK027169	CCDS14520.1, CCDS14521.1	Xq22.3	2013-01-09	2012-02-23		ENSG00000133135	ENSG00000133135		"""RING-type (C3HC4) zinc fingers"""	21153	protein-coding gene	gene with protein product		300439	"""ring finger protein 128"""				Standard	NM_024539		Approved	FLJ23516, GRAIL	uc004eml.3	Q8TEB7	OTTHUMG00000022151	ENST00000255499.2:c.1202A>G	X.37:g.106038858A>G	ENSP00000255499:p.Asp401Gly					RNF128_uc004emk.2_Missense_Mutation_p.D375G	p.D401G	NM_194463	NP_919445	Q8TEB7	RN128_HUMAN			7	1452	+			401					A0PJI4|Q6PH80|Q6ZTJ8|Q96RF3|Q9H5E4	Missense_Mutation	SNP	ENST00000255499.2	37	c.1202A>G	CCDS14521.1	.	.	.	.	.	.	.	.	.	.	A	11.34	1.610252	0.28712	.	.	ENSG00000133135	ENST00000324342;ENST00000255499	T;T	0.13778	2.75;2.56	5.71	5.71	0.89125	.	0.218778	0.38111	N	0.001807	T	0.09069	0.0224	L	0.29908	0.895	0.29031	N	0.885716	B;P	0.38370	0.118;0.628	B;B	0.30855	0.026;0.121	T	0.16305	-1.0407	10	0.45353	T	0.12	.	9.0324	0.36267	0.8171:0.1829:0.0:0.0	.	401;375	Q8TEB7;Q8TEB7-2	RN128_HUMAN;.	G	375;401	ENSP00000316127:D375G;ENSP00000255499:D401G	ENSP00000255499:D401G	D	+	2	0	RNF128	105925514	1.000000	0.71417	1.000000	0.80357	0.837000	0.47467	2.745000	0.47459	1.900000	0.55004	0.481000	0.45027	GAT		0.358	RNF128-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057804.1	NM_024539	
LAMP2	3920	broad.mit.edu	37	X	119580241	119580241	+	Silent	SNP	G	G	T			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chrX:119580241G>T	ENST00000200639.4	-	6	919	c.783C>A	c.(781-783)tcC>tcA	p.S261S	LAMP2_ENST00000434600.2_Silent_p.S261S|LAMP2_ENST00000540603.1_Silent_p.S214S|LAMP2_ENST00000538785.1_Silent_p.S150S|LAMP2_ENST00000371335.4_Silent_p.S261S			P13473	LAMP2_HUMAN	lysosomal-associated membrane protein 2	261	Second lumenal domain.				blood coagulation (GO:0007596)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|protein stabilization (GO:0050821)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|late endosome membrane (GO:0031902)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|membrane (GO:0016020)|phagocytic vesicle membrane (GO:0030670)|plasma membrane (GO:0005886)|platelet dense granule membrane (GO:0031088)	enzyme binding (GO:0019899)			endometrium(4)|large_intestine(2)|lung(5)|ovary(2)|urinary_tract(2)	15						AGCTGCCTGTGGAGTGAGTTG	0.423																																						uc004est.3																			0				ovary(1)	1						c.(781-783)TCC>TCA		lysosomal-associated membrane protein 2 isoform							108.0	92.0	97.0					X																	119580241		2203	4300	6503	SO:0001819	synonymous_variant	3920				platelet activation|platelet degranulation	endosome membrane|integral to membrane|late endosome|lysosomal membrane|membrane fraction|plasma membrane|platelet dense granule membrane		g.chrX:119580241G>T	X77196	CCDS14599.1, CCDS14600.1, CCDS48159.1	Xq24-q25	2014-09-17			ENSG00000005893	ENSG00000005893		"""CD molecules"""	6501	protein-coding gene	gene with protein product		309060					Standard	NM_002294		Approved	CD107b	uc004ess.4	P13473	OTTHUMG00000022301	ENST00000200639.4:c.783C>A	X.37:g.119580241G>T						LAMP2_uc004ess.3_Silent_p.S261S|LAMP2_uc011mtz.1_Silent_p.S150S|LAMP2_uc011mua.1_Silent_p.S214S|LAMP2_uc010nqp.1_Silent_p.S261S	p.S261S	NM_002294	NP_002285	P13473	LAMP2_HUMAN			6	963	-			261			Lumenal (Potential).|Second lumenal domain.		A8K4X5|D3DTF0|Q16641|Q6Q3G8|Q96J30|Q99534|Q9UD93	Silent	SNP	ENST00000200639.4	37	c.783C>A	CCDS14599.1																																																																																				0.423	LAMP2-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000058099.1		
GRIA3	2892	broad.mit.edu	37	X	122528885	122528885	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chrX:122528885G>A	ENST00000371251.1	+	6	869	c.817G>A	c.(817-819)Gtc>Atc	p.V273I	GRIA3_ENST00000542149.1_Missense_Mutation_p.V273I|GRIA3_ENST00000264357.5_Missense_Mutation_p.V273I|GRIA3_ENST00000371256.5_Missense_Mutation_p.V273I|GRIA3_ENST00000541091.1_Missense_Mutation_p.V257I			P42263	GRIA3_HUMAN	glutamate receptor, ionotropic, AMPA 3	273					glutamate receptor signaling pathway (GO:0007215)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|cell junction (GO:0030054)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:0004971)|extracellular-glutamate-gated ion channel activity (GO:0005234)			breast(2)|central_nervous_system(1)|endometrium(8)|kidney(3)|large_intestine(8)|lung(25)|ovary(3)|pancreas(2)|skin(2)|soft_tissue(1)|stomach(1)|upper_aerodigestive_tract(1)	57					Lithium(DB01356)	TTTCCAGATTGTCAACAATGA	0.438																																						uc004etq.3																			0				ovary(3)|central_nervous_system(1)|pancreas(1)	5						c.(817-819)GTC>ATC		glutamate receptor, ionotrophic, AMPA 3 isoform	L-Glutamic Acid(DB00142)						133.0	121.0	125.0					X																	122528885		2203	4300	6503	SO:0001583	missense	2892				glutamate signaling pathway|synaptic transmission	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex|cell junction|endocytic vesicle membrane|postsynaptic membrane	alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity|extracellular-glutamate-gated ion channel activity	g.chrX:122528885G>A	U10301	CCDS14604.1, CCDS14605.1, CCDS76017.1	Xq25	2012-08-29	2012-02-03		ENSG00000125675	ENSG00000125675		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4573	protein-coding gene	gene with protein product		305915	"""glutamate receptor, ionotrophic, AMPA 3"""	GLUR3		1319477, 10644433	Standard	NM_007325		Approved	GluA3, GLURC, MRX94	uc004etr.4	P42263	OTTHUMG00000022685	ENST00000371251.1:c.817G>A	X.37:g.122528885G>A	ENSP00000360297:p.Val273Ile					GRIA3_uc004etr.3_Missense_Mutation_p.V273I|GRIA3_uc004ets.3_RNA|GRIA3_uc011muf.1_Missense_Mutation_p.V257I	p.V273I	NM_007325	NP_015564	P42263	GRIA3_HUMAN			7	1110	+			273			Extracellular (Potential).		D3DTF1|Q4VXD5|Q4VXD6|Q9HDA0|Q9HDA1|Q9HDA2|Q9P0H1	Missense_Mutation	SNP	ENST00000371251.1	37	c.817G>A	CCDS14604.1	.	.	.	.	.	.	.	.	.	.	G	9.977	1.227122	0.22542	.	.	ENSG00000125675	ENST00000264357;ENST00000542149;ENST00000371256;ENST00000371251;ENST00000541091	D;D;D;D;D	0.83914	-1.78;-1.78;-1.78;-1.78;-1.78	5.52	5.52	0.82312	Extracellular ligand-binding receptor (1);	0.224000	0.46442	N	0.000298	T	0.80644	0.4662	L	0.49778	1.585	0.58432	D	0.999996	B;B;B	0.20550	0.046;0.001;0.001	B;B;B	0.23275	0.045;0.008;0.005	T	0.75986	-0.3124	10	0.39692	T	0.17	.	17.5067	0.87748	0.0:0.0:1.0:0.0	.	257;273;273	B7Z4C0;P42263;P42263-2	.;GRIA3_HUMAN;.	I	273;273;273;273;257	ENSP00000264357:V273I;ENSP00000446146:V273I;ENSP00000360302:V273I;ENSP00000360297:V273I;ENSP00000446440:V257I	ENSP00000264357:V273I	V	+	1	0	GRIA3	122356566	1.000000	0.71417	1.000000	0.80357	0.031000	0.12232	6.061000	0.71148	2.436000	0.82500	0.594000	0.82650	GTC		0.438	GRIA3-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058854.1	NM_000828	
THOC2	57187	broad.mit.edu	37	X	122761607	122761607	+	Silent	SNP	G	G	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chrX:122761607G>A	ENST00000245838.8	-	23	2725	c.2694C>T	c.(2692-2694)agC>agT	p.S898S	THOC2_ENST00000491737.1_Silent_p.S783S|THOC2_ENST00000355725.4_Silent_p.S898S	NM_001081550.1	NP_001075019.1	Q8NI27	THOC2_HUMAN	THO complex 2	898					mRNA export from nucleus (GO:0006406)|mRNA processing (GO:0006397)|poly(A)+ mRNA export from nucleus (GO:0016973)|RNA splicing (GO:0008380)|viral mRNA export from host cell nucleus (GO:0046784)	THO complex (GO:0000347)|THO complex part of transcription export complex (GO:0000445)|transcription export complex (GO:0000346)	RNA binding (GO:0003723)			breast(2)|endometrium(13)|kidney(4)|large_intestine(11)|lung(26)|ovary(3)|skin(1)|upper_aerodigestive_tract(3)	63						CTCGTTCATAGCTGGTGTGTG	0.388																																						uc004etu.2																			0				ovary(3)	3						c.(2692-2694)AGC>AGT		THO complex 2							178.0	150.0	159.0					X																	122761607		1946	4152	6098	SO:0001819	synonymous_variant	57187				intronless viral mRNA export from host nucleus|mRNA processing|RNA splicing	THO complex part of transcription export complex	protein binding|RNA binding	g.chrX:122761607G>A	AF441770	CCDS43988.1	Xq25-q26.3	2013-02-11	2004-08-09		ENSG00000125676	ENSG00000125676		"""THO complex subunits"""	19073	protein-coding gene	gene with protein product		300395	"""chromosome X open reading frame 3"""	CXorf3		11979277	Standard	NM_001081550		Approved	THO2, dJ506G2.1	uc004etu.3	Q8NI27	OTTHUMG00000022334	ENST00000245838.8:c.2694C>T	X.37:g.122761607G>A						THOC2_uc011muh.1_Silent_p.S823S	p.S898S	NM_001081550	NP_001075019	Q8NI27	THOC2_HUMAN			23	2726	-			898			Potential.		A6NM50|Q5JZ12|Q6IN92|Q9H8I6	Silent	SNP	ENST00000245838.8	37	c.2694C>T	CCDS43988.1																																																																																				0.388	THOC2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058153.3		
WASH6P	653440	broad.mit.edu	37	X	155252868	155252868	+	RNA	SNP	T	T	A			TCGA-06-0213-01A-01D-1491-08	TCGA-06-0213-10A-01D-1491-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	885f9df7-fc27-43c2-9acc-833c410b2db1	0206ce3d-4c48-4f58-8eeb-07a34adc9fcd	g.chrX:155252868T>A	ENST00000461007.1	+	0	1876				AJ271736.10_ENST00000285718.7_RNA			Q9NQA3	WASH6_HUMAN	WAS protein family homolog 6 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)	p.P304P(5)									TAGCCGAGCCTCTCAAGGCAG	0.632																																						uc004fnw.1																			5	Substitution - coding silent(5)		kidney(3)|endometrium(2)								c.(910-912)CCT>CCA		WAS protein family homolog 1																																						0							g.chrX:155252868T>A	AI042587		Xq28 and Yq12	2014-08-28	2008-01-16	2008-01-16	ENSG00000182484	ENSG00000182484		"""Pseudoautosomal regions / PAR2"", ""WAS protein homologs"""	31685	pseudogene	pseudogene			"""family with sequence similarity 39, member A"", ""chromosomes X and Y open reading frame 1"""	FAM39A, CXYorf1		10655549, 12566406, 18159949	Standard	NG_008380		Approved			Q9NQA3	OTTHUMG00000022677		X.37:g.155252868T>A						uc004fnx.3_Silent_p.P90P	p.P304P	NM_182905	NP_878908					6	1571	+								A6NGF1|Q8N305	Silent	SNP	ENST00000461007.1	37	c.912T>A																																																																																					0.632	WASH6P-016	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000058840.1	NG_008380	
