#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
SMPDL3B	27293	broad.mit.edu	37	1	28285085	28285085	+	Silent	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr1:28285085G>A	ENST00000373894.3	+	8	1295	c.1104G>A	c.(1102-1104)ccG>ccA	p.P368P	RP11-460I13.2_ENST00000448015.1_RNA|SMPDL3B_ENST00000549094.1_Silent_p.P320P|XKR8_ENST00000373884.5_5'Flank	NM_014474.2	NP_055289.2	Q92485	ASM3B_HUMAN	sphingomyelin phosphodiesterase, acid-like 3B	368					sphingomyelin catabolic process (GO:0006685)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	hydrolase activity, acting on glycosyl bonds (GO:0016798)|sphingomyelin phosphodiesterase activity (GO:0004767)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(3)|pancreas(1)|skin(3)|upper_aerodigestive_tract(1)	16		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000431)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;5.68e-24)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00587)|READ - Rectum adenocarcinoma(331;0.055)		ATGGGGTGCCGGACGCCAGCG	0.617																																						uc001bpg.2																			0				ovary(3)	3						c.(1102-1104)CCG>CCA		acid sphingomyelinase-like phosphodiesterase 3B							49.0	50.0	50.0					1																	28285085		2203	4300	6503	SO:0001819	synonymous_variant	27293				sphingomyelin catabolic process	extracellular space	hydrolase activity, acting on glycosyl bonds|sphingomyelin phosphodiesterase activity	g.chr1:28285085G>A	Y08134	CCDS30655.1, CCDS30656.1	1p35.3	2008-02-05			ENSG00000130768	ENSG00000130768			21416	protein-coding gene	gene with protein product							Standard	NM_014474		Approved	ASML3B	uc001bpg.3	Q92485	OTTHUMG00000003910	ENST00000373894.3:c.1104G>A	1.37:g.28285085G>A						SMPDL3B_uc010ofq.1_Silent_p.P162P|SMPDL3B_uc010ofr.1_Silent_p.P320P|XKR8_uc001bph.1_5'Flank	p.P368P	NM_014474	NP_055289	Q92485	ASM3B_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.0419)|OV - Ovarian serous cystadenocarcinoma(117;5.68e-24)|Colorectal(126;1.65e-08)|COAD - Colon adenocarcinoma(152;1.7e-06)|KIRC - Kidney renal clear cell carcinoma(1967;0.00273)|STAD - Stomach adenocarcinoma(196;0.00303)|BRCA - Breast invasive adenocarcinoma(304;0.00587)|READ - Rectum adenocarcinoma(331;0.055)	8	1295	+		Colorectal(325;3.46e-05)|all_lung(284;0.000414)|Lung NSC(340;0.000431)|Renal(390;0.00121)|Breast(348;0.00345)|Ovarian(437;0.00503)|all_neural(195;0.0208)|Myeloproliferative disorder(586;0.0255)	368					B7ZB35|Q5T0Z0|Q96CB7	Silent	SNP	ENST00000373894.3	37	c.1104G>A	CCDS30655.1																																																																																				0.617	SMPDL3B-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000011170.1	NM_014474	
BRDT	676	broad.mit.edu	37	1	92479806	92479806	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr1:92479806C>A	ENST00000362005.3	+	20	3237	c.2819C>A	c.(2818-2820)aCa>aAa	p.T940K	BRDT_ENST00000370389.2_Missense_Mutation_p.T867K|BRDT_ENST00000399546.2_Missense_Mutation_p.T940K|BRDT_ENST00000394530.3_Missense_Mutation_p.T894K|BRDT_ENST00000402388.1_Missense_Mutation_p.T940K	NM_001242805.1	NP_001229734	Q58F21	BRDT_HUMAN	bromodomain, testis-specific	940					cell differentiation (GO:0030154)|chromatin remodeling (GO:0006338)|histone displacement (GO:0001207)|male meiosis (GO:0007140)|male meiosis I (GO:0007141)|mRNA processing (GO:0006397)|positive regulation of transcription during meiosis (GO:0051039)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)|spermatogenesis (GO:0007283)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	histone binding (GO:0042393)|lysine-acetylated histone binding (GO:0070577)|transcription coactivator activity (GO:0003713)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(11)|lung(24)|ovary(1)|prostate(4)|skin(2)|stomach(2)|urinary_tract(2)	56		all_lung(203;0.00531)|Lung NSC(277;0.0194)		all cancers(265;0.0228)|Epithelial(280;0.133)		GACATTATGACAATGTTTGAA	0.269																																						uc001dok.3																			0				stomach(2)|ovary(1)|lung(1)	4						c.(2818-2820)ACA>AAA		testis-specific bromodomain protein							48.0	48.0	48.0					1																	92479806		2202	4273	6475	SO:0001583	missense	676				regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus	protein serine/threonine kinase activity|transcription coactivator activity	g.chr1:92479806C>A	AF019085	CCDS735.1, CCDS55615.1, CCDS55616.1, CCDS72820.1	1p22.1	2010-12-23			ENSG00000137948	ENSG00000137948			1105	protein-coding gene	gene with protein product	"""cancer/testis antigen 9"""	602144				9367677	Standard	NM_001726		Approved	BRD6, CT9	uc010osz.2	Q58F21	OTTHUMG00000010113	ENST00000362005.3:c.2819C>A	1.37:g.92479806C>A	ENSP00000354568:p.Thr940Lys					BRDT_uc001dol.3_Missense_Mutation_p.T940K|BRDT_uc010osz.1_Missense_Mutation_p.T944K|BRDT_uc009wdf.2_Missense_Mutation_p.T867K|BRDT_uc010ota.1_Missense_Mutation_p.T894K|BRDT_uc010otb.1_Missense_Mutation_p.T894K|BRDT_uc001dom.3_Missense_Mutation_p.T940K	p.T940K	NM_207189	NP_997072	Q58F21	BRDT_HUMAN		all cancers(265;0.0228)|Epithelial(280;0.133)	19	3168	+		all_lung(203;0.00531)|Lung NSC(277;0.0194)	940					A6NF68|B7Z811|B7Z890|B7ZAX7|D3DT32|O14789|Q05DQ4|Q6P5T1|Q7Z4A6|Q8IWI6	Missense_Mutation	SNP	ENST00000362005.3	37	c.2819C>A	CCDS735.1	.	.	.	.	.	.	.	.	.	.	C	14.53	2.563148	0.45694	.	.	ENSG00000137948	ENST00000362005;ENST00000370389;ENST00000399546;ENST00000394530;ENST00000402388	T;T;T;T;T	0.07021	3.23;3.24;3.23;3.28;3.23	5.25	4.14	0.48551	.	0.129515	0.34676	N	0.003762	T	0.08133	0.0203	L	0.48362	1.52	0.33625	D	0.605352	D;D;D;D	0.58620	0.983;0.983;0.983;0.983	P;P;P;P	0.51016	0.656;0.656;0.656;0.656	T	0.01899	-1.1251	10	0.72032	D	0.01	-16.049	13.6641	0.62384	0.0:0.9085:0.0:0.0915	.	894;894;944;940	B7ZAX7;B7Z811;B7Z890;Q58F21	.;.;.;BRDT_HUMAN	K	940;867;940;894;940	ENSP00000354568:T940K;ENSP00000359416:T867K;ENSP00000387822:T940K;ENSP00000378038:T894K;ENSP00000384051:T940K	ENSP00000354568:T940K	T	+	2	0	BRDT	92252394	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	3.445000	0.52921	2.457000	0.83068	0.563000	0.77884	ACA		0.269	BRDT-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000027980.2	NM_207189	
COL11A1	1301	broad.mit.edu	37	1	103345386	103345386	+	Silent	SNP	A	A	G			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr1:103345386A>G	ENST00000370096.3	-	66	5439	c.5127T>C	c.(5125-5127)aaT>aaC	p.N1709N	COL11A1_ENST00000512756.1_Silent_p.N1593N|COL11A1_ENST00000358392.2_Silent_p.N1721N|COL11A1_ENST00000353414.4_Silent_p.N1670N	NM_001854.3	NP_001845.3	P12107	COBA1_HUMAN	collagen, type XI, alpha 1	1709	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				cartilage condensation (GO:0001502)|chondrocyte development (GO:0002063)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|embryonic skeletal system morphogenesis (GO:0048704)|endodermal cell differentiation (GO:0035987)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inner ear morphogenesis (GO:0042472)|proteoglycan metabolic process (GO:0006029)|sensory perception of sound (GO:0007605)|tendon development (GO:0035989)|ventricular cardiac muscle tissue morphogenesis (GO:0055010)|visual perception (GO:0007601)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix binding (GO:0050840)|extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)			NS(3)|biliary_tract(1)|breast(5)|central_nervous_system(2)|cervix(1)|endometrium(17)|kidney(8)|large_intestine(28)|lung(157)|ovary(6)|pancreas(2)|prostate(6)|skin(9)|stomach(1)|upper_aerodigestive_tract(11)|urinary_tract(1)	258		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)		GGTAGGTGAAATTTTGCCGAG	0.423																																						uc001dul.2																			0				ovary(6)|breast(3)|upper_aerodigestive_tract(1)|central_nervous_system(1)|pancreas(1)	12						c.(5125-5127)AAT>AAC		alpha 1 type XI collagen isoform A							118.0	105.0	109.0					1																	103345386		2203	4300	6503	SO:0001819	synonymous_variant	1301				collagen fibril organization|detection of mechanical stimulus involved in sensory perception of sound|visual perception	collagen type XI	extracellular matrix binding|extracellular matrix structural constituent|protein binding, bridging	g.chr1:103345386A>G	J04177	CCDS778.1, CCDS780.1, CCDS780.2, CCDS53348.1	1p21	2013-01-16			ENSG00000060718	ENSG00000060718		"""Collagens"""	2186	protein-coding gene	gene with protein product	"""collagen XI, alpha-1 polypeptide"""	120280		COLL6		3182841	Standard	NM_080630		Approved	STL2, CO11A1	uc001dul.3	P12107	OTTHUMG00000010872	ENST00000370096.3:c.5127T>C	1.37:g.103345386A>G						COL11A1_uc001duk.2_Silent_p.N905N|COL11A1_uc001dum.2_Silent_p.N1721N|COL11A1_uc001dun.2_Silent_p.N1670N|COL11A1_uc009weh.2_Silent_p.N1593N	p.N1709N	NM_001854	NP_001845	P12107	COBA1_HUMAN		Lung(183;0.186)|all cancers(265;0.242)|Epithelial(280;0.248)	66	5445	-		all_epithelial(167;2.52e-07)|all_lung(203;3.11e-05)|Lung NSC(277;6.61e-05)|Breast(1374;0.181)	1709			Fibrillar collagen NC1.		B1ASK7|D3DT73|E9PCU0|Q14034|Q149N0|Q9UIT4|Q9UIT5|Q9UIT6	Silent	SNP	ENST00000370096.3	37	c.5127T>C	CCDS778.1																																																																																				0.423	COL11A1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000029997.1	NM_080630	
SLC6A17	388662	broad.mit.edu	37	1	110740739	110740739	+	Silent	SNP	A	A	G			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr1:110740739A>G	ENST00000331565.4	+	12	2342	c.1857A>G	c.(1855-1857)gcA>gcG	p.A619A		NM_001010898.2	NP_001010898.1	Q9H1V8	S6A17_HUMAN	solute carrier family 6 (neutral amino acid transporter), member 17	619					alanine transport (GO:0032328)|glycine transport (GO:0015816)|leucine transport (GO:0015820)|neutral amino acid transport (GO:0015804)|proline transport (GO:0015824)	cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|synaptic vesicle (GO:0008021)	neurotransmitter:sodium symporter activity (GO:0005328)			breast(1)|endometrium(4)|kidney(4)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(2)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	37		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)		GGGCCATGGCACTCCTGATCA	0.657																																						uc009wfq.2																			0				ovary(1)|pancreas(1)	2						c.(1855-1857)GCA>GCG		solute carrier family 6, member 17							88.0	77.0	81.0					1																	110740739		2203	4300	6503	SO:0001819	synonymous_variant	388662				alanine transport|glycine transport|leucine transport|proline transport	cell junction|integral to plasma membrane|synaptic vesicle membrane	neurotransmitter:sodium symporter activity	g.chr1:110740739A>G		CCDS30799.1	1p13.2	2013-07-19	2013-07-19		ENSG00000197106	ENSG00000197106		"""Solute carriers"""	31399	protein-coding gene	gene with protein product		610299	"""solute carrier family 6 (neurotransmitter transporter), member 17"", ""solute carrier family 6, member 17"""				Standard	NM_001010898		Approved		uc009wfq.3	Q9H1V8	OTTHUMG00000011761	ENST00000331565.4:c.1857A>G	1.37:g.110740739A>G							p.A619A	NM_001010898	NP_001010898	Q9H1V8	S6A17_HUMAN		Lung(183;0.0282)|Epithelial(280;0.0372)|all cancers(265;0.0378)|Colorectal(144;0.0438)|LUSC - Lung squamous cell carcinoma(189;0.151)|COAD - Colon adenocarcinoma(174;0.151)	12	2318	+		all_cancers(81;9.9e-06)|all_epithelial(167;3.24e-06)|all_lung(203;0.000116)|Lung NSC(277;0.000233)	619			Helical; Name=12; (Potential).		A6NEA8|A8K1R7|B9EIR5|Q5T5Q9	Silent	SNP	ENST00000331565.4	37	c.1857A>G	CCDS30799.1																																																																																				0.657	SLC6A17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032550.2	XM_371280	
NCF2	4688	broad.mit.edu	37	1	183542320	183542320	+	Splice_Site	SNP	C	C	T	rs147657171		TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr1:183542320C>T	ENST00000367535.3	-	5	860	c.609G>A	c.(607-609)acG>acA	p.T203T	NCF2_ENST00000418089.1_Intron|NCF2_ENST00000367536.1_Splice_Site_p.T203T|NCF2_ENST00000413720.1_Splice_Site_p.T158T	NM_000433.3	NP_000424.2	P19878	NCF2_HUMAN	neutrophil cytosolic factor 2	203					aging (GO:0007568)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular defense response (GO:0006968)|cellular response to hormone stimulus (GO:0032870)|innate immune response (GO:0045087)|interaction with host (GO:0051701)|phagosome maturation (GO:0090382)|positive regulation of blood pressure (GO:0045777)|positive regulation of neuron apoptotic process (GO:0043525)|respiratory burst (GO:0045730)|response to activity (GO:0014823)|response to drug (GO:0042493)|response to glucose (GO:0009749)|response to hyperoxia (GO:0055093)|response to laminar fluid shear stress (GO:0034616)|response to lipopolysaccharide (GO:0032496)|response to progesterone (GO:0032570)|superoxide anion generation (GO:0042554)|superoxide metabolic process (GO:0006801)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|NADPH oxidase complex (GO:0043020)|nucleolus (GO:0005730)|phagolysosome (GO:0032010)	electron carrier activity (GO:0009055)|protein C-terminus binding (GO:0008022)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(10)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	30					Dextromethorphan(DB00514)	TCCCACCTACCGTCGCCTTGC	0.572																																						uc001gqj.3																			0				ovary(3)	3						c.(607-609)ACG>ACA		neutrophil cytosolic factor 2		C	,,,	0,4406		0,0,2203	186.0	173.0	178.0		609,609,,474	4.2	1.0	1	dbSNP_134	178	2,8598	2.2+/-6.3	0,2,4298	no	coding-synonymous-near-splice,coding-synonymous-near-splice,intron,coding-synonymous-near-splice	NCF2	NM_000433.3,NM_001127651.2,NM_001190789.1,NM_001190794.1	,,,	0,2,6501	TT,TC,CC		0.0233,0.0,0.0154	,,,	203/527,203/527,,158/482	183542320	2,13004	2203	4300	6503	SO:0001630	splice_region_variant	4688				cellular defense response|innate immune response|respiratory burst|superoxide anion generation	NADPH oxidase complex|nucleolus	electron carrier activity|protein C-terminus binding	g.chr1:183542320C>T	BC001606	CCDS1356.1, CCDS53446.1, CCDS53447.1	1q25	2014-09-17	2008-07-31		ENSG00000116701	ENSG00000116701		"""Tetratricopeptide (TTC) repeat domain containing"""	7661	protein-coding gene	gene with protein product	"""NADPH oxidase activator 2"", ""chronic granulomatous disease, autosomal 2"""	608515	"""neutrophil cytosolic factor 2 (65kD, chronic granulomatous disease, autosomal 2)"""				Standard	NM_000433		Approved	p67phox, NOXA2	uc001gqk.4	P19878	OTTHUMG00000035329	ENST00000367535.3:c.609+1G>A	1.37:g.183542320C>T						NCF2_uc010pod.1_Silent_p.T158T|NCF2_uc010poe.1_Intron|NCF2_uc001gqk.3_Silent_p.T203T	p.T203T	NM_000433	NP_000424	P19878	NCF2_HUMAN			5	884	-			203					B2R6Q1|B4DKQ7|B4DQA7|E9PHJ2|E9PHX3|Q2PP06|Q8NFC7|Q9BV51	Silent	SNP	ENST00000367535.3	37	c.609G>A	CCDS1356.1																																																																																				0.572	NCF2-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085483.1	NM_000433	Silent
GALNT2	2590	broad.mit.edu	37	1	230314000	230314000	+	Missense_Mutation	SNP	G	G	C			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr1:230314000G>C	ENST00000366672.4	+	2	235	c.163G>C	c.(163-165)Gac>Cac	p.D55H	GALNT2_ENST00000541865.1_Intron|GALNT2_ENST00000543760.1_Missense_Mutation_p.D17H	NM_004481.3	NP_004472.1	Q10471	GALT2_HUMAN	polypeptide N-acetylgalactosaminyltransferase 2	55					cellular protein metabolic process (GO:0044267)|immunoglobulin biosynthetic process (GO:0002378)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein O-linked glycosylation (GO:0006493)|protein O-linked glycosylation via serine (GO:0018242)|protein O-linked glycosylation via threonine (GO:0018243)	extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|Golgi stack (GO:0005795)|integral component of Golgi membrane (GO:0030173)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)	carbohydrate binding (GO:0030246)|manganese ion binding (GO:0030145)|polypeptide N-acetylgalactosaminyltransferase activity (GO:0004653)			breast(2)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|prostate(5)|skin(2)	32	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)				TAAAAAGAAAGACCTTCATCA	0.473																																						uc010pwa.1																			0				ovary(2)	2						c.(163-165)GAC>CAC		polypeptide N-acetylgalactosaminyltransferase 2							99.0	90.0	93.0					1																	230314000		2203	4300	6503	SO:0001583	missense	2590				immunoglobulin biosynthetic process|protein O-linked glycosylation via serine|protein O-linked glycosylation via threonine	extracellular region|Golgi cisterna membrane|integral to Golgi membrane|perinuclear region of cytoplasm	manganese ion binding|polypeptide N-acetylgalactosaminyltransferase activity|sugar binding	g.chr1:230314000G>C	BC041120	CCDS1582.1	1q41-q42	2014-03-13	2014-03-13		ENSG00000143641	ENSG00000143641	2.4.1.41	"""Glycosyltransferase family 2 domain containing"""	4124	protein-coding gene	gene with protein product	"""polypeptide GalNAc transferase 2"""	602274	"""UDP-N-acetyl-alpha-D-galactosamine:polypeptide N-acetylgalactosaminyltransferase 2 (GalNAc-T2)"""			9592121, 7592619	Standard	NM_004481		Approved	GalNAc-T2	uc010pwa.1	Q10471	OTTHUMG00000037771	ENST00000366672.4:c.163G>C	1.37:g.230314000G>C	ENSP00000355632:p.Asp55His					GALNT2_uc010pvy.1_Missense_Mutation_p.D17H|GALNT2_uc010pvz.1_Intron	p.D55H	NM_004481	NP_004472	Q10471	GALT2_HUMAN			2	235	+	Breast(184;0.193)|Ovarian(103;0.249)	all_cancers(173;0.156)|Prostate(94;0.179)	55			Lumenal (Potential).		A8K1Y3|B7Z8V8|C5HU00|Q9NPY4	Missense_Mutation	SNP	ENST00000366672.4	37	c.163G>C	CCDS1582.1	.	.	.	.	.	.	.	.	.	.	G	15.95	2.984287	0.53827	.	.	ENSG00000143641	ENST00000543760;ENST00000366672;ENST00000543291	T;T	0.57273	0.41;0.44	5.71	5.71	0.89125	.	2.346620	0.01102	N	0.005387	T	0.57666	0.2069	L	0.53249	1.67	0.80722	D	1	B;B	0.02656	0.0;0.0	B;B	0.04013	0.001;0.001	T	0.21245	-1.0251	10	0.44086	T	0.13	.	15.3495	0.74370	0.0:0.0:1.0:0.0	.	55;17	Q10471;G3V1S6	GALT2_HUMAN;.	H	17;55;55	ENSP00000445017:D17H;ENSP00000355632:D55H	ENSP00000355632:D55H	D	+	1	0	GALNT2	228380623	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	5.606000	0.67641	2.694000	0.91930	0.591000	0.81541	GAC		0.473	GALNT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000092158.1	NM_004481	
LGALS8	3964	broad.mit.edu	37	1	236704996	236704996	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr1:236704996A>G	ENST00000366584.4	+	6	1074	c.508A>G	c.(508-510)Ata>Gta	p.I170V	LGALS8_ENST00000526589.1_Missense_Mutation_p.I170V|LGALS8_ENST00000450372.2_Missense_Mutation_p.I170V|LGALS8_ENST00000341872.6_Missense_Mutation_p.I170V|RP11-385F5.4_ENST00000433131.1_RNA|LGALS8_ENST00000526634.1_Missense_Mutation_p.I170V|LGALS8_ENST00000416919.2_Intron|LGALS8_ENST00000527974.1_Missense_Mutation_p.I170V|LGALS8_ENST00000525042.1_Intron|LGALS8_ENST00000352231.2_Missense_Mutation_p.I170V|LGALS8_ENST00000323938.6_Missense_Mutation_p.I143V	NM_201544.2	NP_963838.1	O00214	LEG8_HUMAN	lectin, galactoside-binding, soluble, 8	170					plasma cell differentiation (GO:0002317)|T cell costimulation (GO:0031295)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)	carbohydrate binding (GO:0030246)			kidney(1)|large_intestine(5)|lung(6)|ovary(1)|prostate(1)|skin(1)|stomach(5)	20	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	OV - Ovarian serous cystadenocarcinoma(106;0.00117)			ACTGACAGAGATAAGTAGAGA	0.308																																						uc001hxz.1																			0				ovary(1)	1						c.(508-510)ATA>GTA		galectin-8 isoform b							28.0	30.0	29.0					1																	236704996		2198	4296	6494	SO:0001583	missense	3964					cytoplasm|extracellular space	sugar binding	g.chr1:236704996A>G	X91790	CCDS1611.1, CCDS1612.1	1q43	2011-08-04	2008-07-25		ENSG00000116977	ENSG00000116977		"""Lectins, galactoside-binding"""	6569	protein-coding gene	gene with protein product	"""galectin 8"""	606099				7852431, 8692978	Standard	NM_201545		Approved	PCTA-1	uc001hxy.2	O00214	OTTHUMG00000039953	ENST00000366584.4:c.508A>G	1.37:g.236704996A>G	ENSP00000355543:p.Ile170Val					LGALS8_uc001hxw.1_Missense_Mutation_p.I170V|LGALS8_uc001hxy.1_Missense_Mutation_p.I170V|LGALS8_uc009xgg.1_RNA|LGALS8_uc001hya.1_Missense_Mutation_p.I170V|LGALS8_uc001hyb.1_Missense_Mutation_p.I170V|LGALS8_uc001hyc.1_Intron	p.I170V	NM_201543	NP_963837	O00214	LEG8_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.00117)		7	889	+	Ovarian(103;0.0634)|Breast(184;0.221)	all_cancers(173;0.0253)|Prostate(94;0.174)	170					O15215|Q5T3P5|Q5T3Q4|Q8TEV1|Q96B92|Q9BXC8|Q9H584|Q9H585|Q9UEZ6|Q9UP32|Q9UP33|Q9UP34	Missense_Mutation	SNP	ENST00000366584.4	37	c.508A>G	CCDS1612.1	.	.	.	.	.	.	.	.	.	.	A	4.717	0.133381	0.09032	.	.	ENSG00000116977	ENST00000527974;ENST00000352231;ENST00000406509;ENST00000526589;ENST00000341872;ENST00000450372;ENST00000366584;ENST00000356238;ENST00000323938;ENST00000526634	T;T;T;T;T;T;T;T;T	0.06218	3.72;3.72;3.55;3.72;3.7;3.72;3.7;3.33;3.7	5.14	4.0	0.46444	.	0.463835	0.23426	N	0.048312	T	0.03390	0.0098	N	0.08118	0	0.21184	N	0.999762	B;B	0.31274	0.101;0.317	B;B	0.33454	0.034;0.164	T	0.46884	-0.9159	10	0.16896	T	0.51	-6.4298	8.9253	0.35637	0.8119:0.1881:0.0:0.0	.	170;170	O00214;O00214-2	LEG8_HUMAN;.	V	170;170;170;170;170;170;170;170;143;170	ENSP00000431398:I170V;ENSP00000309576:I170V;ENSP00000385999:I170V;ENSP00000435460:I170V;ENSP00000342139:I170V;ENSP00000408657:I170V;ENSP00000355543:I170V;ENSP00000434860:I143V;ENSP00000437040:I170V	ENSP00000434860:I143V	I	+	1	0	LGALS8	234771619	1.000000	0.71417	0.150000	0.22450	0.223000	0.24884	2.544000	0.45761	0.948000	0.37687	0.533000	0.62120	ATA		0.308	LGALS8-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000096365.2	NM_006499	
VN1R5	317705	broad.mit.edu	37	1	247419512	247419512	+	IGR	SNP	A	A	G			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr1:247419512A>G								RP11-488L18.8 (14387 upstream) : Y_RNA (38624 downstream)																							TACCATATAAATCTTCTTTTA	0.353																																						uc010pyu.1																			0					0						c.(139-141)ATC>GTC		vomeronasal 1 receptor 5							148.0	149.0	148.0					1																	247419512		1839	4078	5917	SO:0001628	intergenic_variant	317705				response to pheromone	integral to membrane|plasma membrane	pheromone receptor activity	g.chr1:247419512A>G																													1.37:g.247419512A>G							p.I47V	NM_173858	NP_776257	Q7Z5H4	VN1R5_HUMAN	OV - Ovarian serous cystadenocarcinoma(106;0.00854)		2	139	+	all_cancers(71;5.7e-05)|all_epithelial(71;1.03e-05)|Breast(184;0.0226)|Ovarian(71;0.0377)|all_lung(81;0.0607)|Lung NSC(105;0.0661)	all_cancers(173;0.0314)	47			Cytoplasmic (Potential).			Missense_Mutation	SNP		37	c.139A>G																																																																																				0	0.353								
CALML5	51806	broad.mit.edu	37	10	5541186	5541186	+	Silent	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr10:5541186C>T	ENST00000380332.3	-	1	347	c.216G>A	c.(214-216)gcG>gcA	p.A72A		NM_017422.4	NP_059118.2	Q9NZT1	CALL5_HUMAN	calmodulin-like 5	72	EF-hand 2. {ECO:0000255|PROSITE- ProRule:PRU00448}.				epidermis development (GO:0008544)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)	calcium ion binding (GO:0005509)			biliary_tract(1)|large_intestine(2)|lung(2)|ovary(1)|skin(1)|stomach(1)	8						CCTTCTTCGCCGCCGTCAGGA	0.662																																					GBM(149;1055 3356 43077)	uc001iic.2																			0					0						c.(214-216)GCG>GCA		calmodulin-like 5							44.0	47.0	46.0					10																	5541186		2203	4300	6503	SO:0001819	synonymous_variant	51806				epidermis development|signal transduction		calcium ion binding|protein binding	g.chr10:5541186C>T	AF172852	CCDS7068.1	10p15.1	2013-01-10			ENSG00000178372	ENSG00000178372		"""EF-hand domain containing"""	18180	protein-coding gene	gene with protein product	"""calmodulin-like skin protein"""	605183				10777582	Standard	NM_017422		Approved	CLSP	uc001iic.2	Q9NZT1	OTTHUMG00000017598	ENST00000380332.3:c.216G>A	10.37:g.5541186C>T							p.A72A	NM_017422	NP_059118	Q9NZT1	CALL5_HUMAN			1	348	-			72			EF-hand 2.		Q5SQI3|Q8IXU8	Silent	SNP	ENST00000380332.3	37	c.216G>A	CCDS7068.1																																																																																				0.662	CALML5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046556.1	NM_017422	
SORCS3	22986	broad.mit.edu	37	10	106899184	106899184	+	Silent	SNP	C	C	T	rs531557060	byFrequency	TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr10:106899184C>T	ENST00000369701.3	+	8	1469	c.1242C>T	c.(1240-1242)taC>taT	p.Y414Y		NM_014978.1	NP_055793.1	Q9UPU3	SORC3_HUMAN	sortilin-related VPS10 domain containing receptor 3	414					learning (GO:0007612)|memory (GO:0007613)|neuropeptide signaling pathway (GO:0007218)|regulation of long term synaptic depression (GO:1900452)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|neuronal postsynaptic density (GO:0097481)	neuropeptide receptor activity (GO:0008188)			autonomic_ganglia(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(19)|lung(63)|ovary(6)|pancreas(1)|prostate(6)|skin(8)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	131		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)		CCAGCTACTACGTGTCTTATC	0.488													C|||	2	0.000399361	0.0	0.0	5008	,	,		20845	0.0		0.0	False		,,,				2504	0.002				NSCLC(116;1497 1690 7108 13108 14106)	uc001kyi.1																			0				ovary(6)|skin(3)|central_nervous_system(1)	10						c.(1240-1242)TAC>TAT		VPS10 domain receptor protein SORCS 3 precursor							189.0	172.0	178.0					10																	106899184		2203	4300	6503	SO:0001819	synonymous_variant	22986					integral to membrane	neuropeptide receptor activity	g.chr10:106899184C>T	AB028982	CCDS7558.1	10q23-q25	2006-04-12			ENSG00000156395	ENSG00000156395			16699	protein-coding gene	gene with protein product		606285				11499680	Standard	NM_014978		Approved	KIAA1059, SORCS	uc001kyi.1	Q9UPU3	OTTHUMG00000019011	ENST00000369701.3:c.1242C>T	10.37:g.106899184C>T							p.Y414Y	NM_014978	NP_055793	Q9UPU3	SORC3_HUMAN		Epithelial(162;1.58e-07)|all cancers(201;1.02e-05)|BRCA - Breast invasive adenocarcinoma(275;0.0628)	8	1469	+		Colorectal(252;0.134)|Breast(234;0.142)|Lung NSC(174;0.191)	414			Lumenal (Potential).		Q5VXF9|Q9NQJ2	Silent	SNP	ENST00000369701.3	37	c.1242C>T	CCDS7558.1																																																																																				0.488	SORCS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050221.1	NM_014978	
TRIM51	84767	broad.mit.edu	37	11	55653041	55653041	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr11:55653041C>T	ENST00000449290.2	+	2	229	c.137C>T	c.(136-138)aCg>aTg	p.T46M	TRIM51_ENST00000244891.3_5'Flank	NM_032681.3	NP_116070.2	Q9BSJ1	TRI51_HUMAN	tripartite motif-containing 51	46						intracellular (GO:0005622)	zinc ion binding (GO:0008270)	p.T46M(1)									TGGCAAGACACGGCAGTTCTT	0.493																																						uc010rip.1																			1	Substitution - Missense(1)		endometrium(1)		0						c.(136-138)ACG>ATG		SPRY domain containing 5							40.0	34.0	36.0					11																	55653041		692	1591	2283	SO:0001583	missense	84767					intracellular	zinc ion binding	g.chr11:55653041C>T	BC005014		11p11	2013-01-09	2012-05-18	2012-05-18	ENSG00000124900	ENSG00000124900		"""Tripartite motif containing / Tripartite motif containing"", ""RING-type (C3HC4) zinc fingers"""	19023	protein-coding gene	gene with protein product			"""SPRY domain containing 5"""	SPRYD5			Standard	NM_032681		Approved	TRIM51A	uc010rip.2	Q9BSJ1	OTTHUMG00000156437	ENST00000449290.2:c.137C>T	11.37:g.55653041C>T	ENSP00000395086:p.Thr46Met					SPRYD5_uc010riq.1_5'Flank	p.T46M	NM_032681	NP_116070	Q9BSJ1	SPRY5_HUMAN			2	229	+		all_epithelial(135;0.226)	46			RING-type.		A6NMG2	Missense_Mutation	SNP	ENST00000449290.2	37	c.137C>T		.	.	.	.	.	.	.	.	.	.	.	1.844	-0.466738	0.04476	.	.	ENSG00000124900	ENST00000449290	T	0.08193	3.12	0.803	-0.941	0.10402	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, RING-type (2);Zinc finger, C3HC4 RING-type (1);	.	.	.	.	T	0.08223	0.0205	L	0.60067	1.865	0.09310	N	1	B	0.15930	0.015	B	0.14023	0.01	T	0.36212	-0.9757	9	0.32370	T	0.25	.	5.2197	0.15362	0.0:0.4188:0.0:0.5812	.	46	Q9BSJ1	SPRY5_HUMAN	M	46	ENSP00000395086:T46M	ENSP00000395086:T46M	T	+	2	0	SPRYD5	55409617	0.000000	0.05858	0.000000	0.03702	0.004000	0.04260	-0.055000	0.11807	-1.170000	0.02769	-1.353000	0.01230	ACG		0.493	TRIM51-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000391522.1	NM_032681	
MEN1	4221	broad.mit.edu	37	11	64575418	64575418	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr11:64575418C>T	ENST00000337652.1	-	3	1117	c.614G>A	c.(613-615)gGc>gAc	p.G205D	MEN1_ENST00000478548.1_5'Flank|MEN1_ENST00000394376.1_Missense_Mutation_p.G205D|MEN1_ENST00000377326.3_Missense_Mutation_p.G200D|MEN1_ENST00000394374.2_Missense_Mutation_p.G205D|MEN1_ENST00000312049.6_Missense_Mutation_p.G200D|MEN1_ENST00000377321.1_Intron|MEN1_ENST00000377313.1_Missense_Mutation_p.G205D|MEN1_ENST00000443283.1_Missense_Mutation_p.G205D|MEN1_ENST00000377316.2_Missense_Mutation_p.G200D|MEN1_ENST00000315422.4_Missense_Mutation_p.G200D	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	205					brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)			NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						GTTGCCCTTGCCGTGCCAGGT	0.627			"""D, Mis, N, F, S"""		"""parathyroid tumors, Pancreatic neuroendocrine tumors"""	"""parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"""			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												Esophageal Squamous(1;83 158 15500 18603 18803 29295)	uc001obj.2			yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	D|Mis|N|F|S	multiple endocrine neoplasia type 1 gene			E		parathyroid adenoma|pituitary adenoma|pancreatic islet cell|carcinoid	parathyroid tumors|Pancreatic neuroendocrine tumors		0				parathyroid(105)|pancreas(64)|gastrointestinal_tract_(site_indeterminate)(15)|small_intestine(13)|lung(9)|pituitary(7)|NS(7)|adrenal_gland(5)|soft_tissue(4)|central_nervous_system(4)|thymus(2)|stomach(1)|retroperitoneum(1)|skin(1)	238						c.(613-615)GGC>GAC		menin isoform 1							84.0	66.0	72.0					11																	64575418		2201	4297	6498	SO:0001583	missense	4221	Hyperparathyroidism_Familial_Isolated|Multiple_Endocrine_Neoplasia_type_1	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	DNA repair|histone lysine methylation|MAPKKK cascade|negative regulation of cell proliferation|negative regulation of cyclin-dependent protein kinase activity|negative regulation of JNK cascade|negative regulation of osteoblast differentiation|negative regulation of protein phosphorylation|negative regulation of sequence-specific DNA binding transcription factor activity|negative regulation of telomerase activity|negative regulation of transcription from RNA polymerase II promoter|osteoblast development|positive regulation of protein binding|positive regulation of transforming growth factor beta receptor signaling pathway|response to gamma radiation|response to UV|transcription, DNA-dependent	chromatin|cleavage furrow|cytosol|histone methyltransferase complex|nuclear matrix|soluble fraction	double-stranded DNA binding|four-way junction DNA binding|protein binding, bridging|protein N-terminus binding|R-SMAD binding|transcription regulatory region DNA binding|Y-form DNA binding	g.chr11:64575418C>T	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"""menin"""	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.614G>A	11.37:g.64575418C>T	ENSP00000337088:p.Gly205Asp					MEN1_uc001obk.2_Missense_Mutation_p.G205D|MEN1_uc001obl.2_Intron|MEN1_uc001obm.2_Missense_Mutation_p.G200D|MEN1_uc001obn.2_Missense_Mutation_p.G205D|MEN1_uc001obo.2_Missense_Mutation_p.G205D|MEN1_uc001obp.2_Missense_Mutation_p.G200D|MEN1_uc001obq.2_Missense_Mutation_p.G205D|MEN1_uc001obr.2_Missense_Mutation_p.G205D	p.G205D	NM_130800	NP_570712	O00255	MEN1_HUMAN			3	687	-			205					A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Missense_Mutation	SNP	ENST00000337652.1	37	c.614G>A	CCDS8083.1	.	.	.	.	.	.	.	.	.	.	C	28.3	4.907473	0.92107	.	.	ENSG00000133895	ENST00000377316;ENST00000377326;ENST00000312049;ENST00000315422;ENST00000337652;ENST00000394376;ENST00000394374;ENST00000443283;ENST00000377313;ENST00000440873;ENST00000450708;ENST00000413626	D;D;D;D;D;D;D;D;D;D;D;D	0.99773	-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72;-6.72	4.76	4.76	0.60689	.	0.061993	0.64402	D	0.000004	D	0.99654	0.9872	M	0.67397	2.05	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.97398	0.9994	10	0.87932	D	0	-21.0729	15.7236	0.77736	0.0:1.0:0.0:0.0	.	200;205	O00255-2;O00255	.;MEN1_HUMAN	D	200;200;200;200;205;205;205;205;205;200;200;200	ENSP00000366533:G200D;ENSP00000366543:G200D;ENSP00000308975:G200D;ENSP00000323747:G200D;ENSP00000337088:G205D;ENSP00000377901:G205D;ENSP00000377899:G205D;ENSP00000396940:G205D;ENSP00000366530:G205D;ENSP00000413944:G200D;ENSP00000394933:G200D;ENSP00000411218:G200D	ENSP00000308975:G200D	G	-	2	0	MEN1	64331994	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.890000	0.75633	2.382000	0.81193	0.456000	0.33151	GGC		0.627	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1		
CCDC81	60494	broad.mit.edu	37	11	86123501	86123501	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr11:86123501A>G	ENST00000445632.2	+	11	1563	c.1291A>G	c.(1291-1293)Agt>Ggt	p.S431G	CCDC81_ENST00000278487.3_Missense_Mutation_p.S166G|CCDC81_ENST00000528728.1_Missense_Mutation_p.S166G|CCDC81_ENST00000354755.1_Missense_Mutation_p.S341G	NM_001156474.1	NP_001149946.1	Q6ZN84	CCD81_HUMAN	coiled-coil domain containing 81	431										kidney(3)|large_intestine(8)|lung(6)|skin(2)|upper_aerodigestive_tract(1)	20		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)				ATATTCCCGGAGTCTCCTGAA	0.418																																						uc001pbx.1																			0				skin(1)	1						c.(1291-1293)AGT>GGT		coiled-coil domain containing 81 isoform 1							121.0	117.0	118.0					11																	86123501		2202	4299	6501	SO:0001583	missense	60494							g.chr11:86123501A>G	AK131331	CCDS8276.1, CCDS53691.1	11q14.2	2006-03-09			ENSG00000149201	ENSG00000149201			26281	protein-coding gene	gene with protein product							Standard	NM_001156474		Approved	FLJ16339, FLJ23514	uc001pbx.2	Q6ZN84	OTTHUMG00000167213	ENST00000445632.2:c.1291A>G	11.37:g.86123501A>G	ENSP00000415528:p.Ser431Gly					CCDC81_uc001pbw.1_Missense_Mutation_p.S341G|CCDC81_uc010rtq.1_Missense_Mutation_p.S214G|CCDC81_uc001pby.1_Missense_Mutation_p.S166G	p.S431G	NM_001156474	NP_001149946	Q6ZN84	CCD81_HUMAN			11	1719	+		Acute lymphoblastic leukemia(157;5.51e-06)|all_hematologic(158;0.00535)	431					A0AVL7|Q53FW3|Q9H5E5	Missense_Mutation	SNP	ENST00000445632.2	37	c.1291A>G	CCDS53691.1	.	.	.	.	.	.	.	.	.	.	A	10.82	1.457202	0.26161	.	.	ENSG00000149201	ENST00000354755;ENST00000278487;ENST00000445632;ENST00000528728	T;T;T;T	0.43688	0.94;0.94;0.94;0.94	5.51	0.361	0.16107	.	0.533801	0.20619	N	0.088802	T	0.23370	0.0565	L	0.37561	1.115	0.28286	N	0.923777	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.0	T	0.08806	-1.0704	9	.	.	.	-5.5595	0.8815	0.01235	0.3301:0.1661:0.3234:0.1804	.	166;431;341	Q6ZN84-3;Q6ZN84;Q6ZN84-2	.;CCD81_HUMAN;.	G	341;166;431;166	ENSP00000346800:S341G;ENSP00000278487:S166G;ENSP00000415528:S431G;ENSP00000437165:S166G	.	S	+	1	0	CCDC81	85801149	0.967000	0.33354	0.974000	0.42286	0.936000	0.57629	0.472000	0.22116	0.054000	0.16065	-0.274000	0.10170	AGT		0.418	CCDC81-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393756.1	NM_021827	
GLI1	2735	broad.mit.edu	37	12	57863263	57863263	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr12:57863263C>T	ENST00000228682.2	+	11	1449	c.1358C>T	c.(1357-1359)tCc>tTc	p.S453F	GLI1_ENST00000543426.1_Missense_Mutation_p.S325F|GLI1_ENST00000546141.1_Missense_Mutation_p.S412F	NM_005269.2	NP_005260.1	P08151	GLI1_HUMAN	GLI family zinc finger 1	453					cerebellar cortex morphogenesis (GO:0021696)|digestive tract morphogenesis (GO:0048546)|dorsal/ventral pattern formation (GO:0009953)|epidermal cell differentiation (GO:0009913)|lung development (GO:0030324)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|notochord regression (GO:0060032)|osteoblast differentiation (GO:0001649)|pituitary gland development (GO:0021983)|positive regulation of cell proliferation (GO:0008284)|positive regulation of DNA replication (GO:0045740)|positive regulation of smoothened signaling pathway (GO:0045880)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|proximal/distal pattern formation (GO:0009954)|regulation of smoothened signaling pathway (GO:0008589)|smoothened signaling pathway (GO:0007224)|smoothened signaling pathway involved in regulation of cerebellar granule cell precursor cell proliferation (GO:0021938)|spermatogenesis (GO:0007283)|ventral midline development (GO:0007418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|primary cilium (GO:0072372)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|metal ion binding (GO:0046872)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|transcription regulatory region DNA binding (GO:0044212)			NS(1)|breast(7)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(4)|kidney(2)|large_intestine(8)|lung(22)|ovary(6)|pancreas(2)|prostate(2)|skin(5)|upper_aerodigestive_tract(2)|urinary_tract(1)	69			GBM - Glioblastoma multiforme(3;3.99e-32)			AGTGACCACTCCCCGGCAGGG	0.602																																					Pancreas(157;841 1936 10503 41495 50368)	uc001snx.2																			0				skin(4)|ovary(4)|breast(3)|central_nervous_system(1)|urinary_tract(1)|kidney(1)|pancreas(1)	15						c.(1357-1359)TCC>TTC		GLI family zinc finger 1 isoform 1							73.0	62.0	66.0					12																	57863263		2203	4300	6503	SO:0001583	missense	2735				epidermal cell differentiation|negative regulation of canonical Wnt receptor signaling pathway|osteoblast differentiation|positive regulation of DNA replication|positive regulation of smoothened signaling pathway|positive regulation of transcription from RNA polymerase II promoter	cytosol|nucleus	transcription regulatory region DNA binding|zinc ion binding	g.chr12:57863263C>T		CCDS8940.1, CCDS53806.1, CCDS53807.1	12q13.2-q13.3	2013-01-25	2009-03-05	2005-01-14		ENSG00000111087		"""Zinc fingers, C2H2-type"""	4317	protein-coding gene	gene with protein product		165220	"""glioma-associated oncogene homolog 1 (zinc finger protein)"", ""glioma-associated oncogene family zinc finger 1"""	GLI		2850480	Standard	NM_005269		Approved		uc001snx.3	P08151		ENST00000228682.2:c.1358C>T	12.37:g.57863263C>T	ENSP00000228682:p.Ser453Phe					GLI1_uc009zpq.2_Missense_Mutation_p.S325F	p.S453F	NM_005269	NP_005260	P08151	GLI1_HUMAN	GBM - Glioblastoma multiforme(3;3.99e-32)		11	1436	+			453					D0EUY3|E9PQQ9|F5H6H8|Q8TDN9	Missense_Mutation	SNP	ENST00000228682.2	37	c.1358C>T	CCDS8940.1	.	.	.	.	.	.	.	.	.	.	C	22.9	4.354282	0.82243	.	.	ENSG00000111087	ENST00000543426;ENST00000228682;ENST00000546141;ENST00000528467	T;T;T;T	0.17854	2.37;2.25;2.33;2.33	4.49	4.49	0.54785	.	0.000000	0.50627	D	0.000110	T	0.41026	0.1141	M	0.72118	2.19	0.80722	D	1	D	0.76494	0.999	D	0.81914	0.995	T	0.33033	-0.9884	10	0.87932	D	0	.	15.0811	0.72117	0.0:1.0:0.0:0.0	.	453	P08151	GLI1_HUMAN	F	325;453;412;412	ENSP00000437607:S325F;ENSP00000228682:S453F;ENSP00000441006:S412F;ENSP00000434408:S412F	ENSP00000228682:S453F	S	+	2	0	GLI1	56149530	1.000000	0.71417	1.000000	0.80357	0.912000	0.54170	7.562000	0.82300	2.484000	0.83849	0.563000	0.77884	TCC		0.602	GLI1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394197.1	NM_005269	
CAND1	55832	broad.mit.edu	37	12	67691247	67691247	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr12:67691247G>T	ENST00000545606.1	+	5	989	c.552G>T	c.(550-552)ttG>ttT	p.L184F		NM_018448.3	NP_060918.2	Q86VP6	CAND1_HUMAN	cullin-associated and neddylation-dissociated 1	184					cell differentiation (GO:0030154)|negative regulation of catalytic activity (GO:0043086)|positive regulation of RNA polymerase II transcriptional preinitiation complex assembly (GO:0045899)|protein ubiquitination (GO:0016567)|SCF complex assembly (GO:0010265)	cullin-RING ubiquitin ligase complex (GO:0031461)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nucleus (GO:0005634)|ubiquitin ligase complex (GO:0000151)				NS(1)|central_nervous_system(1)|endometrium(2)|kidney(5)|large_intestine(10)|lung(12)|prostate(1)|skin(2)|stomach(1)	35			GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)		TTCCCCAGTTGACCAGCCCTA	0.368																																						uc001stn.2																			0				central_nervous_system(1)|skin(1)	2						c.(550-552)TTG>TTT		TIP120 protein							137.0	139.0	138.0					12																	67691247		2203	4300	6503	SO:0001583	missense	55832				cell differentiation|negative regulation of catalytic activity|protein ubiquitination|regulation of transcription, DNA-dependent|transcription, DNA-dependent	nucleus|ubiquitin ligase complex	protein binding	g.chr12:67691247G>T		CCDS8977.1	12q14	2008-02-05			ENSG00000111530	ENSG00000111530			30688	protein-coding gene	gene with protein product	"""TBP interacting protein"""	607727				10048485, 8954946	Standard	NM_018448		Approved	TIP120A, DKFZp434M1414, KIAA0829, TIP120	uc001stn.2	Q86VP6	OTTHUMG00000169060	ENST00000545606.1:c.552G>T	12.37:g.67691247G>T	ENSP00000442318:p.Leu184Phe					CAND1_uc001sto.2_5'Flank	p.L184F	NM_018448	NP_060918	Q86VP6	CAND1_HUMAN	GBM - Glioblastoma multiforme(1;1.13e-10)|Lung(24;0.000342)|LUSC - Lung squamous cell carcinoma(43;0.196)	GBM - Glioblastoma multiforme(28;0.0279)	5	989	+			184			HEAT 5.		B2RAU3|O94918|Q6PIY4|Q8NDJ4|Q96JZ9|Q96T19|Q9BTC4|Q9H0G2|Q9P0H7|Q9UF85	Missense_Mutation	SNP	ENST00000545606.1	37	c.552G>T	CCDS8977.1	.	.	.	.	.	.	.	.	.	.	G	20.5	3.999175	0.74818	.	.	ENSG00000111530	ENST00000545606;ENST00000299218;ENST00000540047	T	0.74632	-0.86	5.61	4.71	0.59529	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	D	0.88066	0.6337	M	0.93197	3.39	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.89657	0.3874	9	.	.	.	-5.6672	10.1796	0.42959	0.1474:0.0:0.8526:0.0	.	184	Q86VP6	CAND1_HUMAN	F	184;184;26	ENSP00000442318:L184F	.	L	+	3	2	CAND1	65977514	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	4.464000	0.60134	2.657000	0.90304	0.655000	0.94253	TTG		0.368	CAND1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402105.1	NM_018448	
MGAT4C	25834	broad.mit.edu	37	12	86374059	86374059	+	Missense_Mutation	SNP	G	G	A	rs566418071		TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr12:86374059G>A	ENST00000604798.1	-	8	1649	c.445C>T	c.(445-447)Cgt>Tgt	p.R149C	MGAT4C_ENST00000332156.1_Missense_Mutation_p.R149C|MGAT4C_ENST00000552435.2_Intron|MGAT4C_ENST00000393205.2_Missense_Mutation_p.R178C|MGAT4C_ENST00000549405.2_Missense_Mutation_p.R149C|MGAT4C_ENST00000548651.1_Missense_Mutation_p.R149C|MGAT4C_ENST00000552808.2_Missense_Mutation_p.R149C			Q9UBM8	MGT4C_HUMAN	MGAT4 family, member C	149					cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)	Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity (GO:0008454)|metal ion binding (GO:0046872)			breast(1)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(17)|ovary(4)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	41						ATGGCATCACGCCAGGAAGAA	0.398													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16782	0.0		0.0	False		,,,				2504	0.0					uc001tai.3																			0				ovary(3)	3						c.(445-447)CGT>TGT		alpha-1,3-mannosyl-glycoprotein							81.0	80.0	80.0					12																	86374059		2203	4300	6503	SO:0001583	missense	25834				post-translational protein modification|protein N-linked glycosylation via asparagine	Golgi membrane|integral to membrane	alpha-1,3-mannosylglycoprotein 4-beta-N-acetylglucosaminyltransferase activity|metal ion binding	g.chr12:86374059G>A		CCDS9030.1	12q21	2014-07-14	2014-07-14		ENSG00000182050	ENSG00000182050		"""Mannosyl-glycoprotein beta N-acetylglucosaminyltransferases"""	30871	protein-coding gene	gene with protein product		607385	"""mannosyl (alpha-1,3-)-glycoprotein beta-1,4-N-acetylglucosaminyltransferase, isozyme C (putative)"""			10570912	Standard	NM_013244		Approved	HGNT-IV-H	uc001tal.4	Q9UBM8	OTTHUMG00000169846	ENST00000604798.1:c.445C>T	12.37:g.86374059G>A	ENSP00000474896:p.Arg149Cys					MGAT4C_uc001tal.3_Missense_Mutation_p.R149C|MGAT4C_uc001taj.3_Missense_Mutation_p.R149C|MGAT4C_uc001tak.3_Missense_Mutation_p.R149C|MGAT4C_uc010sum.1_Missense_Mutation_p.R173C|MGAT4C_uc001tah.3_Missense_Mutation_p.R149C	p.R149C	NM_013244	NP_037376	Q9UBM8	MGT4C_HUMAN			8	1695	-			149			Lumenal (Potential).		B4DRH2|Q4G199|Q9UIU5	Missense_Mutation	SNP	ENST00000604798.1	37	c.445C>T	CCDS9030.1	.	.	.	.	.	.	.	.	.	.	G	8.835	0.940816	0.18281	.	.	ENSG00000182050	ENST00000332156;ENST00000393205;ENST00000549405;ENST00000550460;ENST00000552808;ENST00000548651;ENST00000547225	D;D;D;D;D;D	0.85556	-2.0;-2.0;-2.0;-2.0;-2.0;-2.0	5.58	4.59	0.56863	.	0.169518	0.52532	D	0.000061	T	0.62208	0.2409	N	0.02916	-0.46	0.58432	D	0.999999	B;B	0.14012	0.009;0.005	B;B	0.08055	0.003;0.003	T	0.59225	-0.7494	10	0.34782	T	0.22	-17.5819	3.6286	0.08123	0.3462:0.0:0.6538:0.0	.	178;149	B4DRH2;Q9UBM8	.;MGT4C_HUMAN	C	149;178;149;149;149;149;149	ENSP00000331664:R149C;ENSP00000376900:R178C;ENSP00000449022:R149C;ENSP00000446647:R149C;ENSP00000447253:R149C;ENSP00000449172:R149C	ENSP00000331664:R149C	R	-	1	0	MGAT4C	84898190	1.000000	0.71417	1.000000	0.80357	0.022000	0.10575	7.687000	0.84139	2.612000	0.88384	0.655000	0.94253	CGT		0.398	MGAT4C-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000406212.2	NM_013244	
CFAP54	144535	broad.mit.edu	37	12	97087577	97087577	+	Silent	SNP	A	A	G			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr12:97087577A>G	ENST00000524981.4	+	45	6365	c.6342A>G	c.(6340-6342)agA>agG	p.R2114R				Q96N23	CL055_HUMAN		0																	TAGAAGCAAGAATCCTCAAGG	0.308																																						uc001tet.1																			0				skin(6)|ovary(1)	7						c.(1615-1617)AGA>AGG		hypothetical protein LOC374467							100.0	100.0	100.0					12																	97087577		2202	4296	6498	SO:0001819	synonymous_variant	374467							g.chr12:97087577A>G																												ENST00000524981.4:c.6342A>G	12.37:g.97087577A>G							p.R539R	NM_198520	NP_940922	Q6ZTY8	CL063_HUMAN			12	1695	+			539						Silent	SNP	ENST00000524981.4	37	c.1617A>G																																																																																					0.308	C12orf55-003	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000395046.4		
RIMBP2	23504	broad.mit.edu	37	12	130926697	130926697	+	Silent	SNP	C	C	T	rs149109982	byFrequency	TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr12:130926697C>T	ENST00000261655.4	-	8	1312	c.1149G>A	c.(1147-1149)acG>acA	p.T383T	RIMBP2_ENST00000536002.1_Silent_p.T291T|RIMBP2_ENST00000535703.1_Silent_p.T291T	NM_015347.4	NP_056162.4	O15034	RIMB2_HUMAN	RIMS binding protein 2	383	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.				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)		CCACCAGCAGCGTGCACTGCA	0.637													C|||	2	0.000399361	0.0	0.0014	5008	,	,		19882	0.001		0.0	False		,,,				2504	0.0					uc001uil.2																			0				upper_aerodigestive_tract(3)|ovary(3)|large_intestine(2)|central_nervous_system(2)|pancreas(1)	11						c.(1147-1149)ACG>ACA		RIM-binding protein 2				2,4404	4.2+/-10.8	0,2,2201	108.0	96.0	100.0		1149	-3.9	1.0	12	dbSNP_134	100	0,8600		0,0,4300	no	coding-synonymous	RIMBP2	NM_015347.4		0,2,6501	TT,TC,CC		0.0,0.0454,0.0154		383/1053	130926697	2,13004	2203	4300	6503	SO:0001819	synonymous_variant	23504					cell junction|synapse		g.chr12:130926697C>T	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.1149G>A	12.37:g.130926697C>T						RIMBP2_uc001uim.2_Silent_p.T291T|RIMBP2_uc001uin.1_Silent_p.T42T	p.T383T	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)	8	1313	-	all_neural(191;0.101)|Medulloblastoma(191;0.163)	all_epithelial(31;0.213)	383					Q96ID2	Silent	SNP	ENST00000261655.4	37	c.1149G>A	CCDS31925.1																																																																																				0.637	RIMBP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000399520.1	NM_015347	
MTUS2	23281	broad.mit.edu	37	13	29600822	29600822	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr13:29600822G>T	ENST00000431530.3	+	1	2075	c.2017G>T	c.(2017-2019)Gtt>Ttt	p.V673F		NM_001033602.2	NP_001028774.2	Q5JR59	MTUS2_HUMAN	microtubule associated tumor suppressor candidate 2	663	Mediates interaction with MAPRE1.					cytoplasm (GO:0005737)|microtubule (GO:0005874)	microtubule binding (GO:0008017)|protein homodimerization activity (GO:0042803)			NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(3)|prostate(1)|skin(1)	20						CGCCTCGCTGGTTCCAGTGGG	0.587																																						uc001usl.3																			0					0						c.(2017-2019)GTT>TTT		hypothetical protein LOC23281 isoform a							40.0	45.0	44.0					13																	29600822		1972	4133	6105	SO:0001583	missense	23281					cytoplasm|microtubule	microtubule binding|protein homodimerization activity	g.chr13:29600822G>T	AB018317	CCDS41874.1, CCDS45022.1	13q12.3	2013-01-17	2009-10-20	2009-10-20	ENSG00000132938	ENSG00000132938			20595	protein-coding gene	gene with protein product	"""+TIP of 150 kDa"", ""cardiac zipper protein"""		"""KIAA0774"""	KIAA0774		19543227	Standard	NM_001033602		Approved	TIP150, CAZIP, ICIS	uc001usl.4	Q5JR59	OTTHUMG00000016657	ENST00000431530.3:c.2017G>T	13.37:g.29600822G>T	ENSP00000392057:p.Val673Phe						p.V673F	NM_001033602	NP_001028774	Q5JR59	MTUS2_HUMAN			1	2075	+			663			Mediates interaction with MAPRE1.		A7E292|B4DF81|O94872|Q08E97|Q5JQR3|Q8N5E2	Missense_Mutation	SNP	ENST00000431530.3	37	c.2017G>T	CCDS45022.1	.	.	.	.	.	.	.	.	.	.	g	7.973	0.749406	0.15778	.	.	ENSG00000132938	ENST00000431530	T	0.18657	2.2	5.65	3.0	0.34707	.	0.237728	0.29260	N	0.012672	T	0.26557	0.0649	L	0.51422	1.61	0.43841	D	0.996424	B	0.33477	0.413	B	0.43251	0.413	T	0.01570	-1.1322	9	.	.	.	.	12.8045	0.57605	0.0635:0.2216:0.7149:0.0	.	663	Q5JR59	MTUS2_HUMAN	F	673	ENSP00000392057:V673F	.	V	+	1	0	MTUS2	28498822	1.000000	0.71417	0.649000	0.29536	0.012000	0.07955	2.008000	0.40893	0.179000	0.19938	-0.795000	0.03280	GTT		0.587	MTUS2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000044336.3	XM_166270	
BRCA2	675	broad.mit.edu	37	13	32911000	32911000	+	Silent	SNP	T	T	C			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr13:32911000T>C	ENST00000380152.3	+	11	2741	c.2508T>C	c.(2506-2508)ccT>ccC	p.P836P	BRCA2_ENST00000544455.1_Silent_p.P836P			P51587	BRCA2_HUMAN	breast cancer 2, early onset	836	Interaction with NPM1.				brain development (GO:0007420)|cell aging (GO:0007569)|centrosome duplication (GO:0051298)|cytokinesis (GO:0000910)|DNA damage response, signal transduction by p53 class mediator resulting in transcription of p21 class mediator (GO:0006978)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|female gonad development (GO:0008585)|hemopoiesis (GO:0030097)|histone H3 acetylation (GO:0043966)|histone H4 acetylation (GO:0043967)|inner cell mass cell proliferation (GO:0001833)|intrinsic apoptotic signaling pathway in response to DNA damage by p53 class mediator (GO:0042771)|male meiosis I (GO:0007141)|negative regulation of mammary gland epithelial cell proliferation (GO:0033600)|nucleotide-excision repair (GO:0006289)|oocyte maturation (GO:0001556)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokinesis (GO:0032465)|replication fork protection (GO:0048478)|response to gamma radiation (GO:0010332)|response to UV-C (GO:0010225)|response to X-ray (GO:0010165)|spermatogenesis (GO:0007283)	BRCA2-MAGE-D1 complex (GO:0033593)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)|secretory granule (GO:0030141)	gamma-tubulin binding (GO:0043015)|H3 histone acetyltransferase activity (GO:0010484)|H4 histone acetyltransferase activity (GO:0010485)|protease binding (GO:0002020)|single-stranded DNA binding (GO:0003697)			NS(3)|breast(13)|central_nervous_system(5)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(32)|liver(1)|lung(41)|oesophagus(5)|ovary(22)|pancreas(4)|prostate(3)|salivary_gland(1)|skin(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	183		Lung SC(185;0.0262)		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)		TGTTGCCACCTGAAAAATACA	0.308			"""D, Mis, N, F, S"""		"""breast, ovarian, pancreatic"""	"""breast, ovarian, pancreatic, leukemia  (FANCB, FANCD1)"""		Homologous recombination	Pancreatic Cancer, Familial Clustering of;Li-Fraumeni syndrome;Hereditary Prostate Cancer;Hereditary Breast-Ovarian Cancer, BRCA2 type;Fanconi Anemia type D1, bi-allelic BRCA2 mutations;Fanconi Anemia	TCGA Ovarian(8;0.087)																											Esophageal Squamous(138;838 1285 7957 30353 30468 36915 49332)	uc001uub.1			yes	Rec	yes	Hereditary breast/ovarian cancer	13	13q12	675	D|Mis|N|F|S	familial breast/ovarian cancer gene 2			"""L, E"""		breast|ovarian|pancreatic|leukemia  (FANCB|FANCD1)	breast|ovarian|pancreatic		0				ovary(20)|endometrium(8)|lung(7)|breast(7)|oesophagus(5)|large_intestine(4)|central_nervous_system(3)|pancreas(3)|skin(2)|upper_aerodigestive_tract(1)|cervix(1)|salivary_gland(1)|liver(1)|kidney(1)	64						c.(2506-2508)CCT>CCC	Direct_reversal_of_damage|Homologous_recombination	breast cancer 2, early onset							57.0	59.0	58.0					13																	32911000		2202	4299	6501	SO:0001819	synonymous_variant	675	Fanconi_Anemia_type_D1_bi-allelic_BRCA2_mutations|Fanconi_Anemia|Pancreatic_Cancer_Familial_Clustering_of|Hereditary_Breast-Ovarian_Cancer_BRCA2_type|Hereditary_Prostate_Cancer|Li-Fraumeni_syndrome	Familial Cancer Database	incl.: Hereditary Pancreatic Adenocarcinoma, Insulin-Dependent Diabetes Mellitus - Exocrine Insufficiency - Familial Pancreatic Cancer, PNCA1;LFS, SBLA syndrome (Sarcoma Breast Leukemia Adrenal cancer), incl.: Cancer with In Vitro Radioresistence, Familial, Li-Fraumeni-like s.;HPC; ;FANCD1;Pancytopenia Dysmelia, FA (several complementation groups)	cell cycle cytokinesis|centrosome duplication|double-strand break repair via homologous recombination|negative regulation of mammary gland epithelial cell proliferation|nucleotide-excision repair|positive regulation of transcription, DNA-dependent|regulation of S phase of mitotic cell cycle	BRCA2-MAGE-D1 complex|centrosome|nucleoplasm|stored secretory granule	gamma-tubulin binding|H3 histone acetyltransferase activity|H4 histone acetyltransferase activity|protease binding|single-stranded DNA binding	g.chr13:32911000T>C	U43746	CCDS9344.1	13q12-q13	2014-09-17	2003-10-14		ENSG00000139618	ENSG00000139618		"""Fanconi anemia, complementation groups"""	1101	protein-coding gene	gene with protein product	"""BRCA1/BRCA2-containing complex, subunit 2"""	600185	"""Fanconi anemia, complementation group D1"""	FANCD1, FACD, FANCD		8091231, 7581463, 15057823	Standard	NM_000059		Approved	FAD, FAD1, BRCC2	uc001uub.1	P51587	OTTHUMG00000017411	ENST00000380152.3:c.2508T>C	13.37:g.32911000T>C		TCGA Ovarian(8;0.087)					p.P836P	NM_000059	NP_000050	P51587	BRCA2_HUMAN		all cancers(112;7.13e-07)|Epithelial(112;1.59e-05)|OV - Ovarian serous cystadenocarcinoma(117;0.000732)|BRCA - Breast invasive adenocarcinoma(63;0.0291)|GBM - Glioblastoma multiforme(144;0.0704)	11	2735	+		Lung SC(185;0.0262)	836			Interaction with NPM1.		O00183|O15008|Q13879|Q5TBJ7	Silent	SNP	ENST00000380152.3	37	c.2508T>C	CCDS9344.1																																																																																				0.308	BRCA2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046000.2	NM_000059	
ARL11	115761	broad.mit.edu	37	13	50204952	50204952	+	Silent	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr13:50204952G>A	ENST00000282026.1	+	2	704	c.369G>A	c.(367-369)aaG>aaA	p.K123K	ARL11_ENST00000490932.1_Intron	NM_138450.5	NP_612459.1	Q969Q4	ARL11_HUMAN	ADP-ribosylation factor-like 11	123					hematopoietic progenitor cell differentiation (GO:0002244)|small GTPase mediated signal transduction (GO:0007264)	intracellular (GO:0005622)	GTP binding (GO:0005525)			kidney(1)|large_intestine(4)|ovary(1)	6		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	KIRC - Kidney renal clear cell carcinoma(9;0.119)|Kidney(9;0.169)	GBM - Glioblastoma multiforme(99;1.67e-09)		TGGCCAACAAGCAGGAGGCAC	0.602																																						uc001vdf.1																			0					0						c.(367-369)AAG>AAA		ADP-ribosylation factor-like 11							67.0	67.0	67.0					13																	50204952		2203	4300	6503	SO:0001819	synonymous_variant	115761				small GTPase mediated signal transduction	intracellular	GTP binding|protein binding	g.chr13:50204952G>A	AF441378	CCDS9419.1	13q14.12	2014-05-09			ENSG00000152213	ENSG00000152213		"""ADP-ribosylation factors-like"", ""ADP-ribosylation factors"""	24046	protein-coding gene	gene with protein product		609351				12477932	Standard	NM_138450		Approved	ARLTS1, FLJ33930	uc001vdf.2	Q969Q4	OTTHUMG00000016919	ENST00000282026.1:c.369G>A	13.37:g.50204952G>A							p.K123K	NM_138450	NP_612459	Q969Q4	ARL11_HUMAN	KIRC - Kidney renal clear cell carcinoma(9;0.119)|Kidney(9;0.169)	GBM - Glioblastoma multiforme(99;1.67e-09)	2	515	+		Lung NSC(96;2.1e-05)|Breast(56;0.00015)|Prostate(109;0.00174)|Hepatocellular(98;0.0207)|Myeloproliferative disorder(33;0.163)|Lung SC(185;0.187)|all_neural(104;0.19)	123			GTP (By similarity).			Silent	SNP	ENST00000282026.1	37	c.369G>A	CCDS9419.1																																																																																				0.602	ARL11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044929.2	NM_138450	
PROZ	8858	broad.mit.edu	37	13	113812987	113812987	+	Missense_Mutation	SNP	G	G	A	rs200554473	byFrequency	TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr13:113812987G>A	ENST00000375547.2	+	1	20	c.13G>A	c.(13-15)Gtc>Atc	p.V5I	PROZ_ENST00000342783.4_Missense_Mutation_p.V5I	NM_003891.2	NP_003882.1	P22891	PROZ_HUMAN	protein Z, vitamin K-dependent plasma glycoprotein	5					blood coagulation (GO:0007596)|cellular protein metabolic process (GO:0044267)|peptidyl-glutamic acid carboxylation (GO:0017187)|post-translational protein modification (GO:0043687)|proteolysis (GO:0006508)	endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)	calcium ion binding (GO:0005509)|serine-type endopeptidase activity (GO:0004252)			NS(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(4)|prostate(2)|skin(2)	16	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.216)	all cancers(43;0.104)		Menadione(DB00170)	GGCAGGCTGCGTCCCACTGCT	0.657													G|||	5	0.000998403	0.0	0.0	5008	,	,		13757	0.004		0.0	False		,,,				2504	0.001					uc001vta.1																			0					0						c.(13-15)GTC>ATC		protein Z, vitamin K-dependent plasma	Menadione(DB00170)						97.0	61.0	73.0					13																	113812987		2202	4298	6500	SO:0001583	missense	8858				blood coagulation|peptidyl-glutamic acid carboxylation|post-translational protein modification|proteolysis	endoplasmic reticulum lumen|extracellular region|Golgi lumen	calcium ion binding|serine-type endopeptidase activity	g.chr13:113812987G>A	M55670	CCDS9531.1, CCDS58300.1	13q34	2008-07-18			ENSG00000126231	ENSG00000126231			9460	protein-coding gene	gene with protein product		176895				2244898, 2403355	Standard	NM_001256134		Approved	PZ	uc010agr.2	P22891	OTTHUMG00000017376	ENST00000375547.2:c.13G>A	13.37:g.113812987G>A	ENSP00000364697:p.Val5Ile					PROZ_uc010agr.1_Missense_Mutation_p.V5I	p.V5I	NM_003891	NP_003882	P22891	PROZ_HUMAN	all cancers(43;0.104)		1	20	+	all_lung(23;0.000374)|Lung NSC(43;0.0107)|Lung SC(71;0.0753)|all_neural(89;0.0804)|Hepatocellular(20;0.0877)|Medulloblastoma(90;0.163)	all_lung(25;0.216)	5					A6NMB4|Q15213|Q5JVF5|Q5JVF6	Missense_Mutation	SNP	ENST00000375547.2	37	c.13G>A	CCDS9531.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	0.007	-1.995344	0.00435	.	.	ENSG00000126231	ENST00000375547;ENST00000342783	D;D	0.96104	-3.57;-3.91	2.47	-4.95	0.03048	.	1.598140	0.04653	N	0.407509	D	0.85847	0.5792	N	0.03608	-0.345	0.09310	N	1	B;B	0.02656	0.0;0.0	B;B	0.01281	0.0;0.0	T	0.76085	-0.3088	10	0.87932	D	0	.	4.5695	0.12203	0.3024:0.0:0.5015:0.1961	.	5;5	P22891-2;P22891	.;PROZ_HUMAN	I	5	ENSP00000364697:V5I;ENSP00000344458:V5I	ENSP00000344458:V5I	V	+	1	0	PROZ	112860988	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-2.519000	0.00952	-2.101000	0.00846	-1.786000	0.00637	GTC		0.657	PROZ-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000045845.1	NM_003891	
PPP4R4	57718	broad.mit.edu	37	14	94703972	94703972	+	Nonsense_Mutation	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr14:94703972C>T	ENST00000304338.3	+	8	956	c.802C>T	c.(802-804)Cga>Tga	p.R268*		NM_058237.1	NP_478144.1	Q6NUP7	PP4R4_HUMAN	protein phosphatase 4, regulatory subunit 4	268					negative regulation of phosphoprotein phosphatase activity (GO:0032515)|regulation of protein serine/threonine phosphatase activity (GO:0080163)	cytoplasm (GO:0005737)|protein serine/threonine phosphatase complex (GO:0008287)	protein phosphatase regulator activity (GO:0019888)			NS(1)|breast(2)|central_nervous_system(1)|kidney(2)|large_intestine(15)|lung(10)|skin(7)|upper_aerodigestive_tract(2)	40						CAGCAGTGTACGACTTGCAGC	0.358																																						uc001ycs.1																			0				skin(3)|upper_aerodigestive_tract(1)	4						c.(802-804)CGA>TGA		HEAT-like repeat-containing protein isoform 1							160.0	150.0	154.0					14																	94703972		2203	4300	6503	SO:0001587	stop_gained	57718					cytoplasm|protein serine/threonine phosphatase complex	protein binding	g.chr14:94703972C>T	AB046842, BC068491	CCDS9921.1, CCDS9922.1	14q32.2	2014-07-18	2008-09-16	2008-09-16	ENSG00000119698	ENSG00000119698		"""Serine/threonine phosphatases / Protein phosphatase 4, regulatory subunits"""	23788	protein-coding gene	gene with protein product	"""cilia and flagella associated protein 14"""		"""KIAA1622"""	KIAA1622		18715871	Standard	NM_020958		Approved	PP4R4, CFAP14	uc001ycs.1	Q6NUP7		ENST00000304338.3:c.802C>T	14.37:g.94703972C>T	ENSP00000305924:p.Arg268*						p.R268*	NM_058237	NP_478144	Q6NUP7	PP4R4_HUMAN			8	956	+			268			HEAT 2.		Q9BUF8|Q9HCF0	Nonsense_Mutation	SNP	ENST00000304338.3	37	c.802C>T	CCDS9921.1	.	.	.	.	.	.	.	.	.	.	C	38	6.826482	0.97869	.	.	ENSG00000119698	ENST00000304338	.	.	.	5.57	4.69	0.59074	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-10.6348	14.5325	0.67936	0.0:0.9292:0.0:0.0708	.	.	.	.	X	268	.	ENSP00000305924:R268X	R	+	1	2	PPP4R4	93773725	1.000000	0.71417	0.987000	0.45799	0.995000	0.86356	3.746000	0.55127	1.340000	0.45581	0.585000	0.79938	CGA		0.358	PPP4R4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000413056.1	NM_058237	
AQR	9716	broad.mit.edu	37	15	35166951	35166951	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr15:35166951A>G	ENST00000156471.5	-	29	3577	c.3352T>C	c.(3352-3354)Tct>Cct	p.S1118P		NM_014691.2	NP_055506.1	O60306	AQR_HUMAN	aquarius intron-binding spliceosomal factor	1118					mRNA splicing, via spliceosome (GO:0000398)	catalytic step 2 spliceosome (GO:0071013)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)			breast(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(10)|lung(18)|ovary(1)|prostate(6)|skin(4)|upper_aerodigestive_tract(2)	57		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)		GTGAAGAGAGACTGCTCCATG	0.428																																						uc001ziv.2																			0				large_intestine(1)	1						c.(3352-3354)TCT>CCT		aquarius							138.0	132.0	134.0					15																	35166951		1916	4136	6052	SO:0001583	missense	9716					catalytic step 2 spliceosome	RNA binding	g.chr15:35166951A>G	AB011132	CCDS42013.1	15q13	2013-09-12	2013-09-12			ENSG00000021776			29513	protein-coding gene	gene with protein product	"""functional spliceosome-associated protein 164"""	610548	"""aquarius homolog (mouse)"""			9626505, 16949364	Standard	NM_014691		Approved	KIAA0560, fSAP164, IBP160	uc001ziv.3	O60306		ENST00000156471.5:c.3352T>C	15.37:g.35166951A>G	ENSP00000156471:p.Ser1118Pro						p.S1118P	NM_014691	NP_055506	O60306	AQR_HUMAN		all cancers(64;4.34e-18)|GBM - Glioblastoma multiforme(113;4.59e-07)|BRCA - Breast invasive adenocarcinoma(123;0.0283)	29	3533	-		Lung NSC(122;8.7e-10)|all_lung(180;1.47e-08)	1118					A0JP17|A5YKK3|Q2YDX9|Q6IRU8|Q6PIC8	Missense_Mutation	SNP	ENST00000156471.5	37	c.3352T>C	CCDS42013.1	.	.	.	.	.	.	.	.	.	.	A	25.7	4.663021	0.88251	.	.	ENSG00000021776	ENST00000156471;ENST00000543879	D	0.96459	-4.02	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	D	0.98121	0.9380	H	0.94423	3.535	0.58432	D	0.999999	P	0.47409	0.895	P	0.52881	0.712	D	0.99063	1.0831	10	0.72032	D	0.01	-21.112	15.6723	0.77289	1.0:0.0:0.0:0.0	.	1118	O60306	AQR_HUMAN	P	1118	ENSP00000156471:S1118P	ENSP00000156471:S1118P	S	-	1	0	AQR	32954243	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	9.262000	0.95591	2.105000	0.64084	0.528000	0.53228	TCT		0.428	AQR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000417526.2	NM_014691	
KIAA1024	23251	broad.mit.edu	37	15	79750063	79750063	+	Missense_Mutation	SNP	T	T	C			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr15:79750063T>C	ENST00000305428.3	+	2	1649	c.1574T>C	c.(1573-1575)cTt>cCt	p.L525P		NM_015206.2	NP_056021.1	Q9UPX6	K1024_HUMAN	KIAA1024	525						integral component of membrane (GO:0016021)				central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(13)|lung(23)|ovary(2)|pancreas(2)|prostate(1)	49						TTCCGATTTCTTGATGACATG	0.502																																						uc002bew.1																			0				pancreas(2)|ovary(1)|central_nervous_system(1)	4						c.(1573-1575)CTT>CCT		hypothetical protein LOC23251							101.0	81.0	88.0					15																	79750063		2196	4293	6489	SO:0001583	missense	23251					integral to membrane		g.chr15:79750063T>C	AB028947	CCDS32306.1	15q25.1	2007-12-12				ENSG00000169330			29172	protein-coding gene	gene with protein product						10470851	Standard	NM_015206		Approved		uc002bew.1	Q9UPX6		ENST00000305428.3:c.1574T>C	15.37:g.79750063T>C	ENSP00000307461:p.Leu525Pro					KIAA1024_uc010unk.1_Missense_Mutation_p.L525P	p.L525P	NM_015206	NP_056021	Q9UPX6	K1024_HUMAN			2	1649	+			525					A7MD43	Missense_Mutation	SNP	ENST00000305428.3	37	c.1574T>C	CCDS32306.1	.	.	.	.	.	.	.	.	.	.	T	18.36	3.606503	0.66445	.	.	ENSG00000169330	ENST00000305428	T	0.57752	0.38	5.24	5.24	0.73138	.	0.000000	0.85682	D	0.000000	T	0.71005	0.3289	M	0.71581	2.175	0.80722	D	1	D	0.89917	1.0	D	0.87578	0.998	T	0.72551	-0.4259	9	.	.	.	.	15.1171	0.72410	0.0:0.0:0.0:1.0	.	525	Q9UPX6	K1024_HUMAN	P	525	ENSP00000307461:L525P	.	L	+	2	0	KIAA1024	77537118	1.000000	0.71417	0.058000	0.19502	0.967000	0.64934	7.629000	0.83207	1.973000	0.57446	0.402000	0.26972	CTT		0.502	KIAA1024-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416718.1	NM_015206	
SLC7A5	8140	broad.mit.edu	37	16	87873313	87873313	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr16:87873313C>A	ENST00000261622.4	-	5	999	c.934G>T	c.(934-936)Gcc>Tcc	p.A312S	RP4-536B24.2_ENST00000563687.1_RNA|SLC7A5_ENST00000565644.1_Missense_Mutation_p.A46S	NM_003486.5	NP_003477.4	Q01650	LAT1_HUMAN	solute carrier family 7 (amino acid transporter light chain, L system), member 5	312					amino acid transport (GO:0006865)|blood coagulation (GO:0007596)|cell differentiation (GO:0030154)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|leukocyte migration (GO:0050900)|nervous system development (GO:0007399)|neutral amino acid transport (GO:0015804)|transmembrane transport (GO:0055085)|transport (GO:0006810)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	amino acid transmembrane transporter activity (GO:0015171)|L-amino acid transmembrane transporter activity (GO:0015179)|neutral amino acid transmembrane transporter activity (GO:0015175)|peptide antigen binding (GO:0042605)			endometrium(3)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	10				BRCA - Breast invasive adenocarcinoma(80;0.049)	Dextrothyroxine(DB00509)|L-DOPA(DB01235)|Levothyroxine(DB00451)|Liothyronine(DB00279)|Melphalan(DB01042)	CTCACCACGGCCACGGCCTCG	0.652																																						uc002fkm.2																			0					0						c.(934-936)GCC>TCC		solute carrier family 7 (cationic amino acid							87.0	70.0	75.0					16																	87873313		2198	4300	6498	SO:0001583	missense	8140				blood coagulation|cell differentiation|cellular amino acid metabolic process|ion transport|leukocyte migration|nervous system development	apical plasma membrane|cytosol|integral to membrane	neutral amino acid transmembrane transporter activity|peptide antigen binding	g.chr16:87873313C>A	AF077866	CCDS10964.1	16q24.3	2013-05-22	2011-07-12		ENSG00000103257	ENSG00000103257		"""CD molecules"", ""Solute carriers"""	11063	protein-coding gene	gene with protein product		600182				9751058, 7829099	Standard	XM_006721286		Approved	LAT1, E16, D16S469E, MPE16, CD98	uc002fkm.3	Q01650	OTTHUMG00000137658	ENST00000261622.4:c.934G>T	16.37:g.87873313C>A	ENSP00000261622:p.Ala312Ser						p.A312S	NM_003486	NP_003477	Q01650	LAT1_HUMAN		BRCA - Breast invasive adenocarcinoma(80;0.049)	5	1006	-			312					Q8IV97|Q9UBN8|Q9UP15|Q9UQC0	Missense_Mutation	SNP	ENST00000261622.4	37	c.934G>T	CCDS10964.1	.	.	.	.	.	.	.	.	.	.	C	32	5.190326	0.94923	.	.	ENSG00000103257	ENST00000261622	D	0.90504	-2.68	5.41	5.41	0.78517	Amino acid permease domain (1);	0.000000	0.85682	D	0.000000	D	0.96460	0.8845	M	0.91972	3.26	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.97000	0.9728	10	0.87932	D	0	.	18.5445	0.91042	0.0:1.0:0.0:0.0	.	312	Q01650	LAT1_HUMAN	S	312	ENSP00000261622:A312S	ENSP00000261622:A312S	A	-	1	0	SLC7A5	86430814	1.000000	0.71417	1.000000	0.80357	0.828000	0.46876	7.197000	0.77814	2.711000	0.92665	0.563000	0.77884	GCC		0.652	SLC7A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269110.2	NM_003486	
TMEM256-PLSCR3	100529211	broad.mit.edu	37	17	7296587	7296587	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr17:7296587C>T	ENST00000576362.1	-	4	540	c.383G>A	c.(382-384)cGt>cAt	p.R128H	TMEM256-PLSCR3_ENST00000535512.1_Missense_Mutation_p.R128H|TMEM256-PLSCR3_ENST00000324822.11_Missense_Mutation_p.R128H|TMEM256-PLSCR3_ENST00000574401.1_Missense_Mutation_p.R128H|C17orf61-PLSCR3_ENST00000573331.1_3'UTR|TMEM256-PLSCR3_ENST00000576201.1_Missense_Mutation_p.R128H					TMEM256-PLSCR3 readthrough (NMD candidate)																		ACAGCACAGACGGGCGCAGCA	0.716																																						uc002ggm.1																			0					0						c.(382-384)CGT>CAT		phospholipid scramblase 3							9.0	12.0	11.0					17																	7296587		1898	4051	5949	SO:0001583	missense	57048				phospholipid scrambling	integral to membrane|plasma membrane	calcium ion binding|calcium-dependent protein binding|phospholipid scramblase activity|SH3 domain binding	g.chr17:7296587C>T			17p13.1	2013-09-25			ENSG00000187838	ENSG00000187838			49186	other	readthrough							Standard	NR_037719		Approved				OTTHUMG00000178150	ENST00000576362.1:c.383G>A	17.37:g.7296587C>T	ENSP00000460800:p.Arg128His					PLSCR3_uc002ggl.2_Missense_Mutation_p.R128H|PLSCR3_uc002ggq.1_Intron|PLSCR3_uc002ggn.1_Missense_Mutation_p.R128H|PLSCR3_uc002ggo.1_Missense_Mutation_p.R128H|PLSCR3_uc002ggp.1_Intron|PLSCR3_uc002ggr.1_Missense_Mutation_p.R128H|PLSCR3_uc010cmg.1_Missense_Mutation_p.R128H	p.R128H	NM_020360	NP_065093	Q9NRY6	PLS3_HUMAN			5	592	-		Prostate(122;0.173)	128			Cytoplasmic (By similarity).			Missense_Mutation	SNP	ENST00000576362.1	37	c.383G>A		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.562689|5.562689	0.96527|0.96527	.|.	.|.	ENSG00000187838|ENSG00000187838	ENST00000535512;ENST00000324822|ENST00000380658	T;T|.	0.56444|.	0.46;0.46|.	5.64|5.64	5.64|5.64	0.86602|0.86602	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.77718|0.77718	0.4172|0.4172	M|M	0.83852|0.83852	2.665|2.665	0.80722|0.80722	D|D	1|1	D;D|.	0.89917|.	1.0;1.0|.	D;D|.	0.91635|.	0.993;0.999|.	T|T	0.75750|0.75750	-0.3208|-0.3208	10|6	0.87932|0.30854	D|T	0|0.27	-21.0931|-21.0931	17.189|17.189	0.86874|0.86874	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	128;183|.	Q9NRY6;D3DTP7|.	PLS3_HUMAN;.|.	H|I	128|128	ENSP00000438547:R128H;ENSP00000316021:R128H|.	ENSP00000316021:R128H|ENSP00000370033:V128I	R|V	-|-	2|1	0|0	PLSCR3|PLSCR3	7237311|7237311	1.000000|1.000000	0.71417|0.71417	0.157000|0.157000	0.22605|0.22605	0.986000|0.986000	0.74619|0.74619	6.982000|6.982000	0.76173|0.76173	2.675000|2.675000	0.91044|0.91044	0.591000|0.591000	0.81541|0.81541	CGT|GTC		0.716	TMEM256-PLSCR3-008	NOVEL	basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000440808.1		
KRT15	3866	broad.mit.edu	37	17	39673161	39673161	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr17:39673161G>A	ENST00000254043.3	-	3	4222	c.637C>T	c.(637-639)Cgc>Tgc	p.R213C	KRT15_ENST00000393974.3_Missense_Mutation_p.R48C|KRT15_ENST00000393981.3_Missense_Mutation_p.R48C|KRT15_ENST00000393976.2_Missense_Mutation_p.R213C	NM_002275.3	NP_002266	P19012	K1C15_HUMAN	keratin 15	213	Coil 1B.|Rod.				epidermis development (GO:0008544)	extracellular vesicular exosome (GO:0070062)|intermediate filament (GO:0005882)|nucleus (GO:0005634)	scaffold protein binding (GO:0097110)|structural constituent of cytoskeleton (GO:0005200)			NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(3)|lung(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	16		Breast(137;0.000286)				AGGACTCGGCGCAAGCCGTTG	0.592																																						uc002hwy.2																			0					0						c.(637-639)CGC>TGC		keratin 15							65.0	64.0	65.0					17																	39673161		2203	4300	6503	SO:0001583	missense	3866				epidermis development	intermediate filament	protein binding|structural constituent of cytoskeleton	g.chr17:39673161G>A		CCDS11398.1	17q21.2	2013-06-20			ENSG00000171346	ENSG00000171346		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6421	protein-coding gene	gene with protein product	"""keratin-15, basic"", ""keratin-15, beta"", ""type I cytoskeletal 15"", ""cytokeratin 15"""	148030				16831889	Standard	NM_002275		Approved	K15, CK15, K1CO	uc002hwy.3	P19012	OTTHUMG00000133435	ENST00000254043.3:c.637C>T	17.37:g.39673161G>A	ENSP00000254043:p.Arg213Cys					KRT15_uc002hwz.2_Missense_Mutation_p.R115C|KRT15_uc002hxa.2_Missense_Mutation_p.R48C|KRT15_uc002hxb.1_Missense_Mutation_p.R48C	p.R213C	NM_002275	NP_002266	P19012	K1C15_HUMAN			3	828	-		Breast(137;0.000286)	213			Rod.|Coil 1B.		B3KQY1|B3KRA2|E0CX14|Q53XV8|Q9BUG4	Missense_Mutation	SNP	ENST00000254043.3	37	c.637C>T	CCDS11398.1	.	.	.	.	.	.	.	.	.	.	G	13.05	2.122190	0.37436	.	.	ENSG00000171346	ENST00000254043;ENST00000393974;ENST00000393976;ENST00000393981;ENST00000458290	D;D;D;D;D	0.92545	-3.06;-3.06;-3.06;-3.06;-3.06	4.87	4.87	0.63330	Filament (1);	0.000000	0.49916	D	0.000122	D	0.95478	0.8531	M	0.75777	2.31	0.54753	D	0.999985	D;P;P	0.89917	1.0;0.865;0.94	D;P;P	0.79108	0.992;0.479;0.479	D	0.95758	0.8798	10	0.87932	D	0	.	14.7065	0.69194	0.0:0.0:0.8549:0.1451	.	48;213;213	A8MT21;B3KVF5;P19012	.;.;K1C15_HUMAN	C	213;48;213;48;48	ENSP00000254043:R213C;ENSP00000377544:R48C;ENSP00000377546:R213C;ENSP00000377550:R48C;ENSP00000409282:R48C	ENSP00000254043:R213C	R	-	1	0	KRT15	36926687	0.996000	0.38824	1.000000	0.80357	0.171000	0.22731	4.705000	0.61838	2.518000	0.84900	0.655000	0.94253	CGC		0.592	KRT15-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257301.1	NM_002275	
PITPNC1	26207	broad.mit.edu	37	17	65528973	65528973	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr17:65528973G>A	ENST00000581322.1	+	2	104	c.104G>A	c.(103-105)cGg>cAg	p.R35Q	PITPNC1_ENST00000335257.6_Missense_Mutation_p.R35Q|PITPNC1_ENST00000299954.9_Missense_Mutation_p.R35Q|PITPNC1_ENST00000580974.1_Missense_Mutation_p.R35Q			Q9UKF7	PITC1_HUMAN	phosphatidylinositol transfer protein, cytoplasmic 1	35					phospholipid transport (GO:0015914)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)	lipid binding (GO:0008289)|phosphatidylinositol transporter activity (GO:0008526)			breast(1)|kidney(2)|large_intestine(3)|liver(2)|lung(4)|prostate(2)|skin(3)	17	all_cancers(12;3.03e-10)		BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)			CAGAGTGACCGGGGAGAAGGG	0.532																																						uc002jgc.2																			0				skin(1)	1						c.(103-105)CGG>CAG		phosphatidylinositol transfer protein,							51.0	55.0	54.0					17																	65528973		2020	4175	6195	SO:0001583	missense	26207				signal transduction	cytoplasm	lipid binding|phosphatidylinositol transporter activity|protein binding	g.chr17:65528973G>A	AF171102	CCDS58587.1, CCDS58588.1	17q24.3	2008-02-05							21045	protein-coding gene	gene with protein product		605134				10531358	Standard	NM_012417		Approved	RDGBB1, RDGBB, RDGB-BETA	uc002jgc.4	Q9UKF7		ENST00000581322.1:c.104G>A	17.37:g.65528973G>A	ENSP00000464006:p.Arg35Gln					PITPNC1_uc002jgb.2_Missense_Mutation_p.R35Q	p.R35Q	NM_012417	NP_036549	Q9UKF7	PITC1_HUMAN	BRCA - Breast invasive adenocarcinoma(8;2.08e-08)|Colorectal(3;0.198)		2	451	+	all_cancers(12;3.03e-10)		35					A8K473|J3QR20|Q96I07	Missense_Mutation	SNP	ENST00000581322.1	37	c.104G>A	CCDS58588.1	.	.	.	.	.	.	.	.	.	.	G	16.64	3.180406	0.57800	.	.	ENSG00000154217	ENST00000335257;ENST00000299954	T;T	0.41400	1.0;1.0	5.75	5.75	0.90469	START-like domain (1);	0.000000	0.85682	D	0.000000	T	0.47210	0.1433	L	0.46157	1.445	0.58432	D	0.999997	P;P	0.50443	0.935;0.883	P;B	0.46796	0.527;0.206	T	0.35798	-0.9774	10	0.44086	T	0.13	-15.0561	19.942	0.97168	0.0:0.0:1.0:0.0	.	35;35	Q9UKF7;Q9UKF7-2	PITC1_HUMAN;.	Q	35	ENSP00000335618:R35Q;ENSP00000299954:R35Q	ENSP00000299954:R35Q	R	+	2	0	PITPNC1	62959435	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.062000	0.89475	2.714000	0.92807	0.561000	0.74099	CGG		0.532	PITPNC1-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000447194.1	NM_012417	
ELAVL1	1994	broad.mit.edu	37	19	8028639	8028639	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr19:8028639G>A	ENST00000407627.2	-	6	838	c.709C>T	c.(709-711)Cca>Tca	p.P237S	ELAVL1_ENST00000596459.1_Missense_Mutation_p.P237S|ELAVL1_ENST00000593807.1_3'UTR|ELAVL1_ENST00000351593.5_Missense_Mutation_p.P264S	NM_001419.2	NP_001410.2	Q15717	ELAV1_HUMAN	ELAV like RNA binding protein 1	237					3'-UTR-mediated mRNA stabilization (GO:0070935)|gene expression (GO:0010467)|mRNA metabolic process (GO:0016071)|mRNA stabilization (GO:0048255)|multicellular organismal development (GO:0007275)|positive regulation of translation (GO:0045727)|regulation of stem cell maintenance (GO:2000036)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	AU-rich element binding (GO:0017091)|double-stranded RNA binding (GO:0003725)|mRNA 3'-UTR AU-rich region binding (GO:0035925)|mRNA 3'-UTR binding (GO:0003730)|mRNA binding (GO:0003729)|nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	20						GCGTTTCCTGGCACGTTGACG	0.632																																						uc002mjb.2																			0					0						c.(709-711)CCA>TCA		ELAV-like 1							58.0	48.0	51.0					19																	8028639		2203	4300	6503	SO:0001583	missense	1994				3'-UTR-mediated mRNA stabilization|multicellular organismal development	cytoplasm|nucleoplasm	identical protein binding|mRNA binding|nucleotide binding	g.chr19:8028639G>A	U38175	CCDS12193.1	19p13.2	2013-10-03	2013-10-03			ENSG00000066044		"""RNA binding motif (RRM) containing"""	3312	protein-coding gene	gene with protein product	"""embryonic lethal, abnormal vision, drosophila, homolog-like 1"", ""Hu antigen R"""	603466	"""ELAV (embryonic lethal, abnormal vision, Drosophila)-like 1 (Hu antigen R)"""	HUR		8626503, 9003489	Standard	NM_001419		Approved	HuR, Hua, MelG	uc002mjb.3	Q15717		ENST00000407627.2:c.709C>T	19.37:g.8028639G>A	ENSP00000385269:p.Pro237Ser						p.P237S	NM_001419	NP_001410	Q15717	ELAV1_HUMAN			6	876	-			237					B4DVB8|Q53XN6|Q9BTT1	Missense_Mutation	SNP	ENST00000407627.2	37	c.709C>T	CCDS12193.1	.	.	.	.	.	.	.	.	.	.	G	11.97	1.796316	0.31777	.	.	ENSG00000066044	ENST00000407627;ENST00000351593	T;T	0.17054	2.34;2.3	5.85	5.85	0.93711	Nucleotide-binding, alpha-beta plait (1);	0.048756	0.85682	D	0.000000	T	0.13157	0.0319	N	0.25890	0.77	0.51767	D	0.999931	B	0.02656	0.0	B	0.04013	0.001	T	0.07966	-1.0745	10	0.30854	T	0.27	.	13.2643	0.60125	0.0:0.159:0.841:0.0	.	237	Q15717	ELAV1_HUMAN	S	237;264	ENSP00000385269:P237S;ENSP00000264073:P264S	ENSP00000264073:P264S	P	-	1	0	ELAVL1	7934639	1.000000	0.71417	0.997000	0.53966	0.886000	0.51366	6.215000	0.72206	2.767000	0.95098	0.655000	0.94253	CCA		0.632	ELAVL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461494.3	NM_001419	
PDE4A	5141	broad.mit.edu	37	19	10574494	10574494	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr19:10574494C>T	ENST00000352831.6	+	14	1879	c.1769C>T	c.(1768-1770)gCc>gTc	p.A590V	PDE4A_ENST00000380702.2_Missense_Mutation_p.A568V|PDE4A_ENST00000592685.1_Missense_Mutation_p.A568V|PDE4A_ENST00000344979.3_Missense_Mutation_p.A351V|PDE4A_ENST00000293683.5_Missense_Mutation_p.A564V|PDE4A_ENST00000440014.2_Missense_Mutation_p.A529V	NM_001111307.1	NP_001104777.1	P27815	PDE4A_HUMAN	phosphodiesterase 4A, cAMP-specific	590	Catalytic.				cAMP catabolic process (GO:0006198)|cellular response to drug (GO:0035690)|regulation of cAMP-mediated signaling (GO:0043949)|regulation of protein kinase A signaling (GO:0010738)|sensory perception of smell (GO:0007608)|signal transduction (GO:0007165)	cell projection (GO:0042995)|cytosol (GO:0005829)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	3',5'-cyclic-AMP phosphodiesterase activity (GO:0004115)|cAMP binding (GO:0030552)|metal ion binding (GO:0046872)			NS(1)|breast(2)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(4)|large_intestine(3)|lung(4)|ovary(2)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	27			OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		Caffeine(DB00201)|Dipyridamole(DB00975)|Drotaverine(DB06751)|Dyphylline(DB00651)|Enprofylline(DB00824)|Ibudilast(DB05266)|Iloprost(DB01088)|Ketotifen(DB00920)|Oxtriphylline(DB01303)|Pentoxifylline(DB00806)|Roflumilast(DB01656)|Theophylline(DB00277)|Tofisopam(DB08811)	GTGCACTGTGCCGACCTCAGC	0.617																																						uc002moj.2																			0				ovary(1)|breast(1)|central_nervous_system(1)	3						c.(1768-1770)GCC>GTC		phosphodiesterase 4A isoform 1	Cilostazol(DB01166)|Dipyridamole(DB00975)|Dyphylline(DB00651)|Enprofylline(DB00824)|Iloprost(DB01088)|Milrinone(DB00235)|Pentoxifylline(DB00806)|Phentolamine(DB00692)|Tadalafil(DB00820)|Theophylline(DB00277)						96.0	79.0	85.0					19																	10574494		2203	4300	6503	SO:0001583	missense	5141				signal transduction	cytosol|membrane fraction|perinuclear region of cytoplasm|ruffle membrane|soluble fraction	3',5'-cyclic-AMP phosphodiesterase activity|metal ion binding|protein binding	g.chr19:10574494C>T		CCDS12238.1, CCDS45961.1, CCDS45962.1, CCDS45963.1, CCDS58649.1	19p13.2	2010-06-24	2010-06-24			ENSG00000065989	3.1.4.17	"""Phosphodiesterases"""	8780	protein-coding gene	gene with protein product	"""phosphodiesterase E2 dunce homolog (Drosophila)"""	600126	"""phosphodiesterase 4A, cAMP-specific (dunce (Drosophila)-homolog phosphodiesterase E2)"""	DPDE2		8009369	Standard	NM_006202		Approved		uc002moj.2	P27815		ENST00000352831.6:c.1769C>T	19.37:g.10574494C>T	ENSP00000270474:p.Ala590Val					PDE4A_uc002mok.2_Missense_Mutation_p.A564V|PDE4A_uc002mol.2_Missense_Mutation_p.A529V|PDE4A_uc002mom.2_Missense_Mutation_p.A351V|PDE4A_uc002mon.2_Missense_Mutation_p.A45V|PDE4A_uc002moo.2_Missense_Mutation_p.A256V	p.A590V	NM_001111307	NP_001104777	P27815	PDE4A_HUMAN	OV - Ovarian serous cystadenocarcinoma(20;5.8e-10)|Epithelial(33;7.58e-07)|all cancers(31;3.91e-06)		14	1877	+			590			Catalytic.		O75522|O76092|Q16255|Q16691|Q5DM53|Q6PMT2|Q8IVA7|Q8WUQ3|Q9H3H2	Missense_Mutation	SNP	ENST00000352831.6	37	c.1769C>T	CCDS45961.1	.	.	.	.	.	.	.	.	.	.	c	27.4	4.827068	0.90955	.	.	ENSG00000065989	ENST00000419866;ENST00000380702;ENST00000352831;ENST00000293683;ENST00000440014;ENST00000344979;ENST00000380686	T;T;T;T;T	0.80480	-1.38;-1.38;-1.38;-1.38;-1.38	4.37	4.37	0.52481	Metal-dependent phosphohydrolase, HD domain (1);5&apos (2);-cyclic nucleotide phosphodiesterase, catalytic domain (2);3&apos (2);	0.000000	0.85682	D	0.000000	D	0.92815	0.7715	H	0.96576	3.845	0.80722	D	1	D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0	D;D;D;D;D	0.91635	0.994;0.999;0.99;0.998;0.999	D	0.95069	0.8202	10	0.87932	D	0	.	14.3881	0.66961	0.0:1.0:0.0:0.0	.	256;351;529;564;590	P27815-5;P27815-4;P27815-6;P27815-2;P27815	.;.;.;.;PDE4A_HUMAN	V	32;568;590;564;529;351;256	ENSP00000370078:A568V;ENSP00000270474:A590V;ENSP00000293683:A564V;ENSP00000394754:A529V;ENSP00000341007:A351V	ENSP00000293683:A564V	A	+	2	0	PDE4A	10435494	1.000000	0.71417	0.992000	0.48379	0.782000	0.44232	7.767000	0.85331	1.974000	0.57490	0.471000	0.43371	GCC		0.617	PDE4A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000451244.1		
ZNF91	7644	broad.mit.edu	37	19	23542219	23542219	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr19:23542219G>A	ENST00000300619.7	-	4	3767	c.3562C>T	c.(3562-3564)Ccc>Tcc	p.P1188S	ZNF91_ENST00000596528.1_5'Flank|ZNF91_ENST00000397082.2_Missense_Mutation_p.P1156S|ZNF91_ENST00000599743.1_Intron	NM_003430.2	NP_003421.2	Q05481	ZNF91_HUMAN	zinc finger protein 91	1188					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)						all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)				tagagaaggggtttcactgtg	0.537																																						uc002nre.2																			0					0						c.(3562-3564)CCC>TCC		zinc finger protein 91							13.0	13.0	13.0					19																	23542219		1863	4045	5908	SO:0001583	missense	7644					nucleus	DNA binding|sequence-specific DNA binding transcription factor activity|zinc ion binding	g.chr19:23542219G>A	M61871	CCDS42541.1, CCDS74322.1	19p12	2014-02-04	2006-05-12		ENSG00000167232	ENSG00000167232		"""Zinc fingers, C2H2-type"", ""-"""	13166	protein-coding gene	gene with protein product		603971	"""zinc finger protein 91 (HPF7, HTF10)"""			2023909, 2505992	Standard	XR_430154		Approved	HPF7, HTF10	uc002nre.3	Q05481	OTTHUMG00000183268	ENST00000300619.7:c.3562C>T	19.37:g.23542219G>A	ENSP00000300619:p.Pro1188Ser					ZNF91_uc002nrd.2_5'Flank|ZNF91_uc010xrj.1_Missense_Mutation_p.P1156S	p.P1188S	NM_003430	NP_003421	Q05481	ZNF91_HUMAN			4	3675	-		all_lung(12;0.0349)|Lung NSC(12;0.0538)|all_epithelial(12;0.0611)	1188					A8K5E1|B7Z6G6	Missense_Mutation	SNP	ENST00000300619.7	37	c.3562C>T	CCDS42541.1	.	.	.	.	.	.	.	.	.	.	G	2.040	-0.420260	0.04734	.	.	ENSG00000167232	ENST00000300619;ENST00000397082	T;T	0.04970	3.56;3.52	.	.	.	.	.	.	.	.	T	0.05640	0.0148	L	0.38175	1.15	0.23010	N	0.998439	B;B	0.21309	0.054;0.004	B;B	0.21917	0.037;0.001	T	0.38045	-0.9679	8	0.87932	D	0	.	5.5764	0.17225	2.0E-4:0.0:0.9998:0.0	.	1156;1188	Q05481-2;Q05481	.;ZNF91_HUMAN	S	1188;1156	ENSP00000300619:P1188S;ENSP00000380272:P1156S	ENSP00000300619:P1188S	P	-	1	0	ZNF91	23334059	0.001000	0.12720	0.128000	0.21923	0.126000	0.20510	0.042000	0.13949	0.088000	0.17205	0.089000	0.15464	CCC		0.537	ZNF91-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000465891.1	NM_003430	
CYP2A13	1553	broad.mit.edu	37	19	41597726	41597726	+	Silent	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr19:41597726C>T	ENST00000330436.3	+	5	744	c.744C>T	c.(742-744)atC>atT	p.I248I		NM_000766.4	NP_000757.2	Q16696	CP2AD_HUMAN	cytochrome P450, family 2, subfamily A, polypeptide 13	248					small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)	aromatase activity (GO:0070330)|heme binding (GO:0020037)|iron ion binding (GO:0005506)			breast(3)|endometrium(6)|kidney(4)|large_intestine(8)|lung(13)|ovary(3)|prostate(3)|skin(2)	42					Methoxsalen(DB00553)|Nicotine(DB00184)|Testosterone(DB00624)	AGGACTTCATCGCCAAGAAGG	0.557																																						uc002opt.2																			0				ovary(2)|skin(1)	3						c.(742-744)ATC>ATT		cytochrome P450, family 2, subfamily A,	Clomipramine(DB01242)|Nicotine(DB00184)						161.0	122.0	135.0					19																	41597726		2203	4300	6503	SO:0001819	synonymous_variant	1553				xenobiotic metabolic process	endoplasmic reticulum membrane|microsome	aromatase activity|coumarin 7-hydroxylase activity|electron carrier activity|heme binding	g.chr19:41597726C>T	U22028	CCDS12571.1	19q13.2	2013-11-11	2003-01-14		ENSG00000197838	ENSG00000197838		"""Cytochrome P450s"""	2608	protein-coding gene	gene with protein product		608055	"""cytochrome P450, subfamily IIA (phenobarbital-inducible), polypeptide 13"""			7668294, 15128046	Standard	NM_000766		Approved	CPAD, CYP2A	uc002opt.4	Q16696	OTTHUMG00000182762	ENST00000330436.3:c.744C>T	19.37:g.41597726C>T							p.I248I	NM_000766	NP_000757	Q16696	CP2AD_HUMAN			5	753	+			248					Q53YR8|Q6R569|Q6R570|Q9H2X2	Silent	SNP	ENST00000330436.3	37	c.744C>T	CCDS12571.1																																																																																				0.557	CYP2A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000463505.1	NM_000766	
CEACAM3	1084	broad.mit.edu	37	19	42301736	42301736	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr19:42301736G>A	ENST00000357396.3	+	2	521	c.280G>A	c.(280-282)Gca>Aca	p.A94T	CEACAM3_ENST00000344550.4_Missense_Mutation_p.A94T|CEACAM3_ENST00000595255.1_3'UTR|CEACAM3_ENST00000221999.4_Missense_Mutation_p.A94T	NM_001815.2	NP_001806.2	P40198	CEAM3_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 3	94	Ig-like V-type.					integral component of membrane (GO:0016021)		p.A94T(1)		endometrium(2)|kidney(4)|large_intestine(1)|lung(4)|prostate(3)|skin(4)|stomach(1)	19						CCCAGGGGCCGCATACAGCGG	0.463																																						uc002orn.1																			1	Substitution - Missense(1)		lung(1)	skin(1)	1						c.(280-282)GCA>ACA		carcinoembryonic antigen-related cell adhesion							188.0	210.0	202.0					19																	42301736		2181	4300	6481	SO:0001583	missense	1084					integral to membrane		g.chr19:42301736G>A	E03349	CCDS12586.2, CCDS62685.1	19q13.2	2013-01-11			ENSG00000170956	ENSG00000170956		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"""	1815	protein-coding gene	gene with protein product		609142		CGM1			Standard	NM_001815		Approved	CD66d	uc002orn.2	P40198	OTTHUMG00000150142	ENST00000357396.3:c.280G>A	19.37:g.42301736G>A	ENSP00000349971:p.Ala94Thr					CEACAM3_uc010eia.1_Missense_Mutation_p.A94T|CEACAM3_uc002oro.1_RNA	p.A94T	NM_001815	NP_001806	P40198	CEAM3_HUMAN			2	356	+			94			Ig-like V-type.|Extracellular (Potential).		G5E978|Q3KPH9	Missense_Mutation	SNP	ENST00000357396.3	37	c.280G>A	CCDS12586.2	.	.	.	.	.	.	.	.	.	.	G	16.97	3.268890	0.59540	.	.	ENSG00000170956	ENST00000357396;ENST00000389667;ENST00000221999;ENST00000344550	T;T;T	0.66280	-0.2;-0.2;-0.2	3.43	3.43	0.39272	Immunoglobulin subtype (1);Immunoglobulin V-set (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.76955	0.4060	M	0.83483	2.645	0.09310	N	1	D;D	0.89917	1.0;0.975	D;P	0.63192	0.912;0.825	T	0.66031	-0.6024	9	0.62326	D	0.03	.	10.7307	0.46096	0.0:0.0:1.0:0.0	.	94;94	G5E978;P40198	.;CEAM3_HUMAN	T	94	ENSP00000349971:A94T;ENSP00000221999:A94T;ENSP00000341725:A94T	ENSP00000221999:A94T	A	+	1	0	CEACAM3	46993576	0.017000	0.18338	0.003000	0.11579	0.001000	0.01503	3.073000	0.50057	1.639000	0.50556	0.508000	0.49915	GCA		0.463	CEACAM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316509.2	NM_001815	
PPP1R12C	54776	broad.mit.edu	37	19	55624065	55624065	+	Silent	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr19:55624065C>T	ENST00000263433.3	-	2	435	c.420G>A	c.(418-420)gtG>gtA	p.V140V	PPP1R12C_ENST00000376393.2_Silent_p.V140V|PPP1R12C_ENST00000435544.2_Silent_p.V66V	NM_001271618.1|NM_017607.2	NP_001258547.1|NP_060077.1			protein phosphatase 1, regulatory subunit 12C											central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(11)|ovary(1)|prostate(1)|urinary_tract(2)	22			BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)		AGGAGGCGGCCACGTGCAGTG	0.667																																						uc002qix.2																			0				ovary(1)|central_nervous_system(1)	2						c.(418-420)GTG>GTA		protein phosphatase 1, regulatory subunit 12C							61.0	55.0	57.0					19																	55624065		2203	4300	6503	SO:0001819	synonymous_variant	54776					cytoplasm		g.chr19:55624065C>T	AF312028	CCDS12916.1	19q13.42	2013-01-10	2011-10-04		ENSG00000125503	ENSG00000125503		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Ankyrin repeat domain containing"""	14947	protein-coding gene	gene with protein product	"""myosin-binding subunit 85"""	613245	"""leukocyte receptor cluster (LRC) member 3"", ""protein phosphatase 1, regulatory (inhibitor) subunit 12C"""	LENG3		11399775	Standard	NM_017607		Approved	DKFZP434D0412, p84, MBS85, p85	uc002qix.4	Q9BZL4		ENST00000263433.3:c.420G>A	19.37:g.55624065C>T						PPP1R12C_uc010yfs.1_Silent_p.V66V|PPP1R12C_uc002qiy.2_Silent_p.V140V	p.V140V	NM_017607	NP_060077	Q9BZL4	PP12C_HUMAN	BRCA - Breast invasive adenocarcinoma(297;0.209)	GBM - Glioblastoma multiforme(193;0.0449)	2	436	-			140			ANK 2.			Silent	SNP	ENST00000263433.3	37	c.420G>A	CCDS12916.1																																																																																				0.667	PPP1R12C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451814.2	NM_017607	
FAM136A	84908	broad.mit.edu	37	2	70524589	70524589	+	Silent	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr2:70524589G>A	ENST00000037869.3	-	3	327	c.249C>T	c.(247-249)acC>acT	p.T83T	FAM136A_ENST00000430566.1_Silent_p.T190T|FAM136A_ENST00000450256.1_3'UTR	NM_032822.2	NP_116211.2	Q96C01	F136A_HUMAN	family with sequence similarity 136, member A	83						cytoplasm (GO:0005737)|mitochondrion (GO:0005739)				breast(1)|kidney(1)|large_intestine(1)|lung(2)|prostate(1)	6						TGCAATGCATGGTGCACCGGG	0.512																																						uc002sgq.3																			0					0						c.(247-249)ACC>ACT		hypothetical protein LOC84908							86.0	82.0	83.0					2																	70524589		2203	4300	6503	SO:0001819	synonymous_variant	84908					mitochondrion	protein binding	g.chr2:70524589G>A	BC014975	CCDS1904.1	2p14	2014-02-12	2007-07-10		ENSG00000035141	ENSG00000035141			25911	protein-coding gene	gene with protein product	"""hypothetical protein FLJ14668"""					12477932	Standard	NM_032822		Approved	FLJ14668	uc002sgq.4	Q96C01	OTTHUMG00000129668	ENST00000037869.3:c.249C>T	2.37:g.70524589G>A						FAM136A_uc010fdp.2_RNA	p.T83T	NM_032822	NP_116211	Q96C01	F136A_HUMAN			3	326	-			83					Q96SS3	Silent	SNP	ENST00000037869.3	37	c.249C>T	CCDS1904.1																																																																																				0.512	FAM136A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251869.2	NM_032822	
TEKT4	150483	broad.mit.edu	37	2	95537709	95537709	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr2:95537709G>A	ENST00000295201.4	+	1	522	c.385G>A	c.(385-387)Gcc>Acc	p.A129T	TEKT4_ENST00000427593.2_Missense_Mutation_p.A129T|AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4	129					cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						GCTGGAGCGCGCCCTGGACGC	0.657																																						uc002stw.1																			0				ovary(1)|breast(1)|skin(1)	3						c.(385-387)GCC>ACC		tektin 4							17.0	15.0	16.0					2																	95537709		2190	4281	6471	SO:0001583	missense	150483				cell projection organization|microtubule cytoskeleton organization	cilium axoneme|flagellar axoneme|microtubule		g.chr2:95537709G>A	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.385G>A	2.37:g.95537709G>A	ENSP00000295201:p.Ala129Thr					uc002stv.1_Intron|TEKT4_uc010fhr.1_RNA	p.A129T	NM_144705	NP_653306	Q8WW24	TEKT4_HUMAN			1	478	+			129			Potential.			Missense_Mutation	SNP	ENST00000295201.4	37	c.385G>A	CCDS2005.1	.	.	.	.	.	.	.	.	.	.	.	16.94	3.261583	0.59431	.	.	ENSG00000163060	ENST00000295201;ENST00000427593	T;T	0.03301	3.98;3.98	1.84	1.84	0.25277	.	0.000000	0.85682	D	0.000000	T	0.16428	0.0395	M	0.85373	2.75	0.58432	D	0.999999	D	0.89917	1.0	D	0.97110	1.0	T	0.00862	-1.1536	10	0.51188	T	0.08	-1.2637	9.2813	0.37731	0.0:0.0:1.0:0.0	.	129	Q8WW24	TEKT4_HUMAN	T	129	ENSP00000295201:A129T;ENSP00000407596:A129T	ENSP00000295201:A129T	A	+	1	0	TEKT4	94901436	1.000000	0.71417	0.995000	0.50966	0.173000	0.22820	3.661000	0.54503	1.015000	0.39444	0.456000	0.33151	GCC		0.657	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
TEKT4	150483	broad.mit.edu	37	2	95539132	95539132	+	Intron	SNP	A	A	G	rs74376788		TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr2:95539132A>G	ENST00000295201.4	+	2	635				AC097374.2_ENST00000568768.1_RNA	NM_144705.2	NP_653306.1	Q8WW24	TEKT4_HUMAN	tektin 4						cell projection organization (GO:0030030)	cytoplasm (GO:0005737)|microtubule (GO:0005874)|motile cilium (GO:0031514)|nucleus (GO:0005634)				NS(1)|breast(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(15)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	28						AGCAGAACTTACACAGTCAGA	0.567																																						uc002stv.1																			0											c.e9+1		Homo sapiens cDNA FLJ44118 fis, clone TESTI4047069.																																				SO:0001627	intron_variant	0							g.chr2:95539132A>G	AK097438	CCDS2005.1	2q11.2	2008-02-05			ENSG00000163060	ENSG00000163060			31012	protein-coding gene	gene with protein product							Standard	XM_005263876		Approved	MGC27019	uc002stw.1	Q8WW24	OTTHUMG00000130396	ENST00000295201.4:c.499-133A>G	2.37:g.95539132A>G						TEKT4_uc002stw.1_Intron|TEKT4_uc010fhr.1_RNA								9		-									Splice_Site	SNP	ENST00000295201.4	37	c.1317_splice	CCDS2005.1																																																																																				0.567	TEKT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252777.1	NM_144705	
SCN1A	6323	broad.mit.edu	37	2	166847871	166847871	+	Nonsense_Mutation	SNP	T	T	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr2:166847871T>A	ENST00000303395.4	-	26	5913	c.5914A>T	c.(5914-5916)Aaa>Taa	p.K1972*	AC010127.3_ENST00000597623.1_RNA|SCN1A_ENST00000375405.3_Nonsense_Mutation_p.K1961*|SCN1A_ENST00000409050.1_Nonsense_Mutation_p.K1944*|SCN1A_ENST00000423058.2_Nonsense_Mutation_p.K1972*|AC010127.3_ENST00000595647.1_RNA			P35498	SCN1A_HUMAN	sodium channel, voltage-gated, type I, alpha subunit	1972					adult walking behavior (GO:0007628)|membrane depolarization during action potential (GO:0086010)|neuromuscular process controlling posture (GO:0050884)|neuronal action potential (GO:0019228)|neuronal action potential propagation (GO:0019227)|sodium ion transmembrane transport (GO:0035725)|sodium ion transport (GO:0006814)	axon initial segment (GO:0043194)|intercalated disc (GO:0014704)|neuronal cell body (GO:0043025)|node of Ranvier (GO:0033268)|plasma membrane (GO:0005886)|T-tubule (GO:0030315)|voltage-gated sodium channel complex (GO:0001518)|Z disc (GO:0030018)	voltage-gated sodium channel activity (GO:0005248)			NS(4)|breast(5)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(33)|lung(87)|ovary(7)|pancreas(1)|prostate(9)|skin(23)|upper_aerodigestive_tract(2)|urinary_tract(1)	200					Dronedarone(DB04855)|Nitrazepam(DB01595)|Permethrin(DB04930)|Phenacemide(DB01121)|Phenazopyridine(DB01438)|Phenytoin(DB00252)|Topiramate(DB00273)|Valproic Acid(DB00313)|Zonisamide(DB00909)	AGATCAGTTTTTTCTGTAATA	0.363																																						uc010zcz.1																			0				ovary(6)|skin(6)|large_intestine(1)	13						c.(5881-5883)AAA>TAA		sodium channel, voltage-gated, type I, alpha	Lamotrigine(DB00555)|Levetiracetam(DB01202)|Phenacemide(DB01121)|Phenytoin(DB00252)|Topiramate(DB00273)|Zonisamide(DB00909)						92.0	86.0	88.0					2																	166847871		2203	4300	6503	SO:0001587	stop_gained	6323					voltage-gated sodium channel complex	voltage-gated sodium channel activity	g.chr2:166847871T>A	AB093548	CCDS33316.1, CCDS54413.1, CCDS54414.1	2q24.3	2014-09-17	2007-01-23		ENSG00000144285	ENSG00000144285		"""Sodium channels"", ""Voltage-gated ion channels / Sodium channels"""	10585	protein-coding gene	gene with protein product		182389	"""febrile convulsions 3"""	SCN1, FEB3		8062593, 16382098, 11823106	Standard	NM_006920		Approved	Nav1.1, GEFSP2, HBSCI, NAC1, SMEI	uc021vsb.1	P35498	OTTHUMG00000044173	ENST00000303395.4:c.5914A>T	2.37:g.166847871T>A	ENSP00000303540:p.Lys1972*						p.K1961*	NM_006920	NP_008851	P35498	SCN1A_HUMAN			26	5899	-			1972					E9PG49|Q16172|Q585T7|Q8IUJ6|Q96LA3|Q9C008	Nonsense_Mutation	SNP	ENST00000303395.4	37	c.5881A>T	CCDS54413.1	.	.	.	.	.	.	.	.	.	.	T	42	9.375012	0.99151	.	.	ENSG00000144285	ENST00000423058;ENST00000303395;ENST00000375405;ENST00000409050	.	.	.	5.67	5.67	0.87782	.	0.103523	0.42294	D	0.000734	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	15.9152	0.79508	0.0:0.0:0.0:1.0	.	.	.	.	X	1972;1972;1961;1944	.	ENSP00000303540:K1972X	K	-	1	0	SCN1A	166556117	1.000000	0.71417	0.992000	0.48379	0.988000	0.76386	3.773000	0.55333	2.159000	0.67721	0.397000	0.26171	AAA		0.363	SCN1A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000102661.1	NM_006920	
OSBPL6	114880	broad.mit.edu	37	2	179253861	179253861	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr2:179253861G>A	ENST00000190611.4	+	21	2658	c.2282G>A	c.(2281-2283)tGc>tAc	p.C761Y	OSBPL6_ENST00000409045.3_Missense_Mutation_p.C730Y|OSBPL6_ENST00000409631.1_Missense_Mutation_p.C725Y|OSBPL6_ENST00000392505.2_Missense_Mutation_p.C786Y|OSBPL6_ENST00000359685.3_Missense_Mutation_p.C725Y|OSBPL6_ENST00000315022.2_Missense_Mutation_p.C765Y	NM_032523.3	NP_115912.1	Q9BZF3	OSBL6_HUMAN	oxysterol binding protein-like 6	761					lipid transport (GO:0006869)	cytosol (GO:0005829)|nuclear membrane (GO:0031965)|perinuclear endoplasmic reticulum (GO:0097038)|plasma membrane (GO:0005886)	lipid binding (GO:0008289)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(13)|lung(18)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	46			OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)			GTTTGCATTTGCAAACTCACA	0.333																																						uc002ulx.2																			0				pancreas(1)	1						c.(2281-2283)TGC>TAC		oxysterol-binding protein-like protein 6 isoform							100.0	85.0	90.0					2																	179253861		2203	4300	6503	SO:0001583	missense	114880				lipid transport		lipid binding	g.chr2:179253861G>A	AF392448	CCDS2277.1, CCDS2278.1, CCDS56150.1, CCDS56151.1, CCDS56152.1	2q32.1	2008-05-27			ENSG00000079156	ENSG00000079156		"""Oxysterol binding proteins"""	16388	protein-coding gene	gene with protein product	"""OSBP-related protein 6"""	606734				11483621	Standard	NM_001201480		Approved	ORP6	uc002uly.3	Q9BZF3	OTTHUMG00000132579	ENST00000190611.4:c.2282G>A	2.37:g.179253861G>A	ENSP00000190611:p.Cys761Tyr					OSBPL6_uc002uly.2_Missense_Mutation_p.C786Y|OSBPL6_uc010zfe.1_Missense_Mutation_p.C730Y|OSBPL6_uc002ulz.2_Missense_Mutation_p.C725Y|OSBPL6_uc002uma.2_Missense_Mutation_p.C765Y	p.C761Y	NM_032523	NP_115912	Q9BZF3	OSBL6_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.00578)|Epithelial(96;0.00847)|all cancers(119;0.0335)		21	2660	+			761					B4DTW1|C4AMC0|C4AME4|D3DPF6|D3DPF7|Q4ZG68|Q53T68|Q59H61|Q7Z4Q1|Q86V84|Q8N9T0|Q96SR1	Missense_Mutation	SNP	ENST00000190611.4	37	c.2282G>A	CCDS2277.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.739764	0.89573	.	.	ENSG00000079156	ENST00000392505;ENST00000359685;ENST00000409045;ENST00000190611;ENST00000409631;ENST00000315022	T;T;T;T;T;T	0.34859	1.34;1.34;1.34;1.34;1.34;1.34	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	T	0.74359	0.3706	H	0.96080	3.765	0.80722	D	1	D;D;D;D;D	0.89917	1.0;0.997;0.993;1.0;0.998	D;D;D;D;D	0.91635	0.999;0.993;0.946;0.998;0.988	T	0.82285	-0.0533	10	0.87932	D	0	-13.1457	20.0965	0.97849	0.0:0.0:1.0:0.0	.	730;765;725;786;761	Q9BZF3-4;Q9BZF3-3;Q9BZF3-2;Q9BZF3-5;Q9BZF3	.;.;.;.;OSBL6_HUMAN	Y	786;725;730;761;725;765	ENSP00000376293:C786Y;ENSP00000352713:C725Y;ENSP00000387248:C730Y;ENSP00000190611:C761Y;ENSP00000386885:C725Y;ENSP00000318723:C765Y	ENSP00000190611:C761Y	C	+	2	0	OSBPL6	178962107	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.813000	0.99286	2.824000	0.97209	0.655000	0.94253	TGC		0.333	OSBPL6-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000334393.2	NM_032523	
TTN	7273	broad.mit.edu	37	2	179634524	179634524	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr2:179634524C>A	ENST00000591111.1	-	37	9008	c.8784G>T	c.(8782-8784)aaG>aaT	p.K2928N	TTN_ENST00000359218.5_Missense_Mutation_p.K2882N|TTN-AS1_ENST00000585451.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K2882N|TTN-AS1_ENST00000610005.1_RNA|TTN_ENST00000460472.2_Missense_Mutation_p.K2882N|TTN_ENST00000342992.6_Missense_Mutation_p.K2928N|TTN_ENST00000589042.1_Missense_Mutation_p.K2928N|TTN_ENST00000360870.5_Missense_Mutation_p.K2928N			Q8WZ42	TITIN_HUMAN	titin	13258	Ig-like 16.				adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)			NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			GCACAACTATCTTGAACTTTT	0.458																																						uc010zfg.1																			0				ovary(58)|stomach(19)|large_intestine(17)|lung(16)|skin(16)|breast(10)|pancreas(7)|kidney(4)|central_nervous_system(3)|urinary_tract(2)|upper_aerodigestive_tract(1)	153						c.(8782-8784)AAG>AAT		titin isoform N2-A							210.0	204.0	206.0					2																	179634524		2203	4300	6503	SO:0001583	missense	7273						ATP binding|nucleic acid binding|protein serine/threonine kinase activity|protein tyrosine kinase activity	g.chr2:179634524C>A	X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.8784G>T	2.37:g.179634524C>A	ENSP00000465570:p.Lys2928Asn					TTN_uc010zfh.1_Missense_Mutation_p.K2882N|TTN_uc010zfi.1_Missense_Mutation_p.K2882N|TTN_uc010zfj.1_Missense_Mutation_p.K2882N|TTN_uc002unb.2_Missense_Mutation_p.K2928N	p.K2928N	NM_133378	NP_596869	Q8WZ42	TITIN_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)		37	9008	-			2928					A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37	c.8784G>T		.	.	.	.	.	.	.	.	.	.	C	10.98	1.505239	0.26949	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127;ENST00000360870	T;T;T;T;T	0.67865	-0.29;-0.29;-0.29;-0.29;-0.29	5.93	3.17	0.36434	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Ribonuclease H-like (1);Immunoglobulin-like fold (1);	.	.	.	.	T	0.68081	0.2962	L	0.28504	0.86	0.26188	N	0.979622	D;D;D;D;D	0.76494	0.994;0.994;0.994;0.98;0.999	P;P;P;P;D	0.69479	0.819;0.819;0.819;0.833;0.964	T	0.56080	-0.8038	9	0.87932	D	0	.	6.0225	0.19636	0.0:0.5481:0.0:0.4519	.	2882;2882;2882;2928;2928	D3DPF9;E7EQE6;E7ET18;Q8WZ42;Q8WZ42-6	.;.;.;TITIN_HUMAN;.	N	2928;2882;2882;2882;2882;2928	ENSP00000343764:K2928N;ENSP00000434586:K2882N;ENSP00000340554:K2882N;ENSP00000352154:K2882N;ENSP00000354117:K2928N	ENSP00000340554:K2882N	K	-	3	2	TTN	179342769	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	1.038000	0.30254	0.847000	0.35167	0.563000	0.77884	AAG		0.458	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1	NM_133378	
ZSWIM2	151112	broad.mit.edu	37	2	187692829	187692829	+	Missense_Mutation	SNP	C	C	G			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr2:187692829C>G	ENST00000295131.2	-	9	1823	c.1784G>C	c.(1783-1785)aGt>aCt	p.S595T		NM_182521.2	NP_872327.2	Q8NEG5	ZSWM2_HUMAN	zinc finger, SWIM-type containing 2	595					apoptotic process (GO:0006915)|positive regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902043)|protein polyubiquitination (GO:0000209)		ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(28)|ovary(2)|prostate(4)|skin(6)|urinary_tract(1)	52			OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)			CATACAGTTACTATACCTTTT	0.338																																						uc002upu.1																			0				ovary(2)|skin(1)	3						c.(1783-1785)AGT>ACT		zinc finger, SWIM domain containing 2							96.0	95.0	95.0					2																	187692829		2202	4300	6502	SO:0001583	missense	151112				apoptosis		zinc ion binding	g.chr2:187692829C>G	AK128006	CCDS33348.1	2q32.2	2008-02-05			ENSG00000163012	ENSG00000163012		"""Zinc fingers, SWIM-type"", ""Zinc fingers, ZZ-type"""	30990	protein-coding gene	gene with protein product						12477932	Standard	NM_182521		Approved	MGC33890, ZZZ2	uc002upu.1	Q8NEG5	OTTHUMG00000154259	ENST00000295131.2:c.1784G>C	2.37:g.187692829C>G	ENSP00000295131:p.Ser595Thr						p.S595T	NM_182521	NP_872327	Q8NEG5	ZSWM2_HUMAN	OV - Ovarian serous cystadenocarcinoma(117;0.0274)|Epithelial(96;0.164)		9	1824	-			595					B3KXV6|Q53SI3|Q57ZY3	Missense_Mutation	SNP	ENST00000295131.2	37	c.1784G>C	CCDS33348.1	.	.	.	.	.	.	.	.	.	.	c	3.911	-0.020036	0.07634	.	.	ENSG00000163012	ENST00000295131	T	0.21361	2.01	5.45	0.0641	0.14351	.	0.597661	0.15919	N	0.238200	T	0.08891	0.0220	N	0.08118	0	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.22695	-1.0209	10	0.72032	D	0.01	-3.0957	4.361	0.11203	0.0:0.2647:0.1634:0.5719	.	595	Q8NEG5	ZSWM2_HUMAN	T	595	ENSP00000295131:S595T	ENSP00000295131:S595T	S	-	2	0	ZSWIM2	187401074	0.000000	0.05858	0.000000	0.03702	0.059000	0.15707	-0.328000	0.07945	0.061000	0.16311	-0.578000	0.04140	AGT		0.338	ZSWIM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334565.1	NM_182521	
FAM126B	285172	broad.mit.edu	37	2	201846441	201846441	+	Missense_Mutation	SNP	C	C	T	rs138872845		TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr2:201846441C>T	ENST00000418596.3	-	12	1332	c.1145G>A	c.(1144-1146)cGt>cAt	p.R382H	AC005037.3_ENST00000413848.1_RNA|AC005037.3_ENST00000332935.6_RNA	NM_173822.3	NP_776183.1	Q8IXS8	F126B_HUMAN	family with sequence similarity 126, member B	382						intracellular (GO:0005622)				endometrium(2)|kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)	16						CTTGGCTGAACGCCCAGTTGC	0.493																																						uc002uws.3																			0				ovary(1)	1						c.(1144-1146)CGT>CAT		hypothetical protein LOC285172		C	HIS/ARG	0,4406		0,0,2203	102.0	100.0	101.0		1145	5.8	1.0	2	dbSNP_134	101	1,8599	1.2+/-3.3	0,1,4299	no	missense	FAM126B	NM_173822.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	probably-damaging	382/531	201846441	1,13005	2203	4300	6503	SO:0001583	missense	285172					intracellular		g.chr2:201846441C>T	BC039295	CCDS2335.1	2q33.1	2008-10-02			ENSG00000155744	ENSG00000155744			28593	protein-coding gene	gene with protein product						12477932	Standard	NM_173822		Approved	MGC39518, HYCC2	uc002uws.4	Q8IXS8	OTTHUMG00000132823	ENST00000418596.3:c.1145G>A	2.37:g.201846441C>T	ENSP00000393667:p.Arg382His					FAM126B_uc002uwu.2_Missense_Mutation_p.R356H|FAM126B_uc002uwv.2_Missense_Mutation_p.R382H	p.R382H	NM_173822	NP_776183	Q8IXS8	F126B_HUMAN			12	1333	-			382					B2RCG7|Q4ZG87|Q53TX6	Missense_Mutation	SNP	ENST00000418596.3	37	c.1145G>A	CCDS2335.1	.	.	.	.	.	.	.	.	.	.	C	15.76	2.927537	0.52759	0.0	1.16E-4	ENSG00000155744	ENST00000418596	T	0.80393	-1.37	5.76	5.76	0.90799	.	0.052330	0.85682	D	0.000000	D	0.85969	0.5821	L	0.36672	1.1	0.58432	D	0.999998	D;D	0.76494	0.999;0.999	D;D	0.76071	0.987;0.987	D	0.84551	0.0644	10	0.40728	T	0.16	-9.4248	19.9664	0.97271	0.0:1.0:0.0:0.0	.	188;382	B3KUG1;Q8IXS8	.;F126B_HUMAN	H	382	ENSP00000393667:R382H	ENSP00000393667:R382H	R	-	2	0	FAM126B	201554686	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	4.411000	0.59781	2.718000	0.92993	0.655000	0.94253	CGT		0.493	FAM126B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256285.3	NM_173822	
CHRNG	1146	broad.mit.edu	37	2	233405386	233405386	+	Silent	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr2:233405386C>T	ENST00000389494.3	+	4	336	c.315C>T	c.(313-315)acC>acT	p.T105T	CHRNG_ENST00000389492.3_Silent_p.T105T	NM_005199.4	NP_005190.4	P07510	ACHG_HUMAN	cholinergic receptor, nicotinic, gamma (muscle)	105					muscle contraction (GO:0006936)|regulation of membrane potential (GO:0042391)|signal transduction (GO:0007165)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|transport (GO:0006810)	acetylcholine-gated channel complex (GO:0005892)|cell junction (GO:0030054)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	acetylcholine receptor activity (GO:0015464)|acetylcholine-activated cation-selective channel activity (GO:0004889)|channel activity (GO:0015267)			breast(2)|endometrium(3)|large_intestine(4)|lung(12)|upper_aerodigestive_tract(1)	22		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)		Epithelial(121;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)	Galantamine(DB00674)	TGCCGTCCACCATGGTGTGGC	0.652																																						uc002vsx.1																			0					0						c.(313-315)ACC>ACT		cholinergic receptor, nicotinic, gamma							44.0	35.0	38.0					2																	233405386		2203	4300	6503	SO:0001819	synonymous_variant	1146				muscle contraction	cell junction|postsynaptic membrane	acetylcholine receptor activity	g.chr2:233405386C>T	X01715	CCDS33400.1	2q37.1	2012-10-02	2012-02-07		ENSG00000196811	ENSG00000196811		"""Cholinergic receptors"", ""Ligand-gated ion channels / Acetylcholine receptors, nicotinic"""	1967	protein-coding gene	gene with protein product	"""acetylcholine receptor, nicotinic, gamma (muscle)"""	100730	"""cholinergic receptor, nicotinic, gamma"""	ACHRG			Standard	NM_005199		Approved		uc002vsx.1	P07510	OTTHUMG00000153327	ENST00000389494.3:c.315C>T	2.37:g.233405386C>T						CHRNG_uc010fyd.2_Silent_p.T105T|CHRNG_uc010fye.1_Silent_p.T105T	p.T105T	NM_005199	NP_005190	P07510	ACHG_HUMAN		Epithelial(121;6.39e-16)|BRCA - Breast invasive adenocarcinoma(100;0.00079)|LUSC - Lung squamous cell carcinoma(224;0.00757)|Lung(119;0.0086)	4	336	+		all_hematologic(139;0.00793)|Renal(207;0.0112)|Acute lymphoblastic leukemia(138;0.0182)|all_lung(227;0.0449)|Lung NSC(271;0.132)	105			Extracellular (Potential).		B3KWM8|Q14DU4|Q53RG2	Silent	SNP	ENST00000389494.3	37	c.315C>T	CCDS33400.1																																																																																				0.652	CHRNG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000330743.1	NM_005199	
PREX1	57580	broad.mit.edu	37	20	47309262	47309262	+	Silent	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr20:47309262C>T	ENST00000371941.3	-	8	1006	c.984G>A	c.(982-984)agG>agA	p.R328R	PREX1_ENST00000396220.1_Silent_p.R328R	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	328	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			TGATTCGACCCCTGAAGATGT	0.572																																						uc002xtw.1																			0				lung(3)|ovary(2)|pancreas(1)	6						c.(982-984)AGG>AGA		phosphatidylinositol-3,4,							236.0	187.0	204.0					20																	47309262		2203	4300	6503	SO:0001819	synonymous_variant	57580				actin filament polymerization|apoptosis|induction of apoptosis by extracellular signals|nerve growth factor receptor signaling pathway|neutrophil activation|small GTPase mediated signal transduction|superoxide metabolic process	cytosol|plasma membrane	enzyme binding|phospholipid binding|Rho GTPase activator activity|Rho guanyl-nucleotide exchange factor activity	g.chr20:47309262C>T	AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.984G>A	20.37:g.47309262C>T							p.R328R	NM_020820	NP_065871	Q8TCU6	PREX1_HUMAN	BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)		8	1007	-			328			PH.		E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Silent	SNP	ENST00000371941.3	37	c.984G>A	CCDS13410.1																																																																																				0.572	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1	NM_020820	
TPTE	7179	broad.mit.edu	37	21	10906987	10906987	+	Missense_Mutation	SNP	C	C	A	rs376317057	byFrequency	TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr21:10906987C>A	ENST00000361285.4	-	24	1903	c.1574G>T	c.(1573-1575)aGa>aTa	p.R525I	TPTE_ENST00000415664.2_5'UTR|TPTE_ENST00000342420.5_Missense_Mutation_p.R487I|TPTE_ENST00000298232.7_Missense_Mutation_p.R507I	NM_199261.2	NP_954870	P56180	TPTE_HUMAN	transmembrane phosphatase with tensin homology	525	C2 tensin-type. {ECO:0000255|PROSITE- ProRule:PRU00589}.				peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)|signal transduction (GO:0007165)	integral component of membrane (GO:0016021)	ion channel activity (GO:0005216)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)			NS(1)|breast(1)|central_nervous_system(2)|cervix(2)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(19)|lung(76)|ovary(2)|prostate(2)|skin(8)|urinary_tract(1)	130			Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)		TGGATAAATTCTCCGTGCTTT	0.358													.|||	2	0.000399361	0.0015	0.0	5008	,	,		36204	0.0		0.0	False		,,,				2504	0.0					uc002yip.1																			0				ovary(2)|lung(1)|breast(1)|skin(1)	5						c.(1573-1575)AGA>ATA		transmembrane phosphatase with tensin homology		T	ILE/ARG,ILE/ARG,ILE/ARG	1,4405		0,1,2202	124.0	111.0	116.0		1520,1460,1574	2.4	0.2	21		116	0,8600		0,0,4300	no	missense,missense,missense	TPTE	NM_199259.2,NM_199260.2,NM_199261.2	97,97,97	0,1,6502	AA,AC,CC		0.0,0.0227,0.0077	benign,benign,benign	507/534,487/514,525/552	10906987	1,13005	2203	4300	6503	SO:0001583	missense	7179				signal transduction	integral to membrane	ion channel activity|protein tyrosine phosphatase activity|protein tyrosine/serine/threonine phosphatase activity	g.chr21:10906987C>A	AF007118	CCDS74771.1, CCDS74772.1, CCDS74773.1	21p11	2011-06-09			ENSG00000166157	ENSG00000274391		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"""	12023	protein-coding gene	gene with protein product	"""PTEN-related tyrosine phosphatase"", ""cancer/testis antigen 44"""	604336				10830953, 14659893	Standard	NM_001290224		Approved	PTEN2, CT44	uc002yip.1	P56180	OTTHUMG00000074127	ENST00000361285.4:c.1574G>T	21.37:g.10906987C>A	ENSP00000355208:p.Arg525Ile					TPTE_uc002yis.1_RNA|TPTE_uc002yiq.1_Missense_Mutation_p.R507I|TPTE_uc002yir.1_Missense_Mutation_p.R487I|TPTE_uc010gkv.1_Missense_Mutation_p.R387I	p.R525I	NM_199261	NP_954870	P56180	TPTE_HUMAN	Colorectal(6;3.44e-05)|COAD - Colon adenocarcinoma(6;0.00727)|READ - Rectum adenocarcinoma(6;0.0723)	UCEC - Uterine corpus endometrioid carcinoma (6;0.0974)|all cancers(6;2.54e-22)|Epithelial(6;4.21e-19)|OV - Ovarian serous cystadenocarcinoma(6;1.16e-09)|BRCA - Breast invasive adenocarcinoma(6;7.72e-05)|Lung(8;0.000189)|LUSC - Lung squamous cell carcinoma(6;0.00379)|GBM - Glioblastoma multiforme(6;0.00391)|Kidney(17;0.0773)|LUAD - Lung adenocarcinoma(8;0.247)	24	1942	-			525			C2 tensin-type.		B2RAP7|C9J6D6|C9JKK8|Q6XPS4|Q6XPS5|Q71JA8|Q8NCS8	Missense_Mutation	SNP	ENST00000361285.4	37	c.1574G>T	CCDS13560.2	.	.	.	.	.	.	.	.	.	.	.	8.035	0.762650	0.15914	2.27E-4	0.0	ENSG00000166157	ENST00000298232;ENST00000361285;ENST00000342420	D;D;D	0.85556	-2.0;-2.0;-2.0	2.39	2.39	0.29439	Tensin phosphatase, C2 domain (2);C2 calcium/lipid-binding domain, CaLB (1);	0.246048	0.40302	U	0.001128	T	0.79257	0.4415	L	0.29908	0.895	0.26512	N	0.974585	B;B;P	0.34757	0.439;0.268;0.467	B;B;B	0.43838	0.306;0.225;0.433	T	0.71484	-0.4579	10	0.87932	D	0	-6.0425	6.033	0.19690	0.0:0.1407:0.0:0.8593	.	487;507;525	P56180-3;P56180-2;P56180	.;.;TPTE_HUMAN	I	507;525;487	ENSP00000298232:R507I;ENSP00000355208:R525I;ENSP00000344441:R487I	ENSP00000298232:R507I	R	-	2	0	TPTE	9928858	1.000000	0.71417	0.167000	0.22817	0.003000	0.03518	2.119000	0.41958	0.341000	0.23771	-1.461000	0.01025	AGA		0.358	TPTE-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000157413.1		
B3GALT5	10317	broad.mit.edu	37	21	41033203	41033203	+	Missense_Mutation	SNP	T	T	G			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr21:41033203T>G	ENST00000380620.4	+	5	1309	c.717T>G	c.(715-717)atT>atG	p.I239M	B3GALT5_ENST00000343118.4_Missense_Mutation_p.I239M|AF064860.5_ENST00000416555.1_RNA|B3GALT5_ENST00000380618.1_Missense_Mutation_p.I239M|B3GALT5_ENST00000398714.2_Missense_Mutation_p.I239M			Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	239					protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	16		Prostate(19;2.55e-06)				TCCCATACATTAAACTGGAAG	0.562																																						uc002yyb.1																			0				skin(1)	1						c.(715-717)ATT>ATG		UDP-Gal:betaGlcNAc beta							94.0	94.0	94.0					21																	41033203		2203	4300	6503	SO:0001583	missense	10317				protein glycosylation	endoplasmic reticulum|Golgi membrane|integral to membrane	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity	g.chr21:41033203T>G	AB020337	CCDS13667.1, CCDS74795.1	21q22.3	2013-02-19			ENSG00000183778	ENSG00000183778		"""Beta 3-glycosyltransferases"""	920	protein-coding gene	gene with protein product	"""homolog of C. elegans Bt toxin resistance gene bre-5"", ""GlcNAc-beta-1,3-galactosyltransferase 5"""	604066				10212226	Standard	NM_006057		Approved	beta3Gal-T5, B3GalT-V, GLCT5, B3T5	uc002yyj.1	Q9Y2C3	OTTHUMG00000086725	ENST00000380620.4:c.717T>G	21.37:g.41033203T>G	ENSP00000369994:p.Ile239Met					B3GALT5_uc002yye.2_Missense_Mutation_p.I239M|B3GALT5_uc002yyi.1_Missense_Mutation_p.I239M|B3GALT5_uc002yyj.1_Missense_Mutation_p.I239M|B3GALT5_uc002yyk.1_Missense_Mutation_p.I239M|B3GALT5_uc002yyl.1_Missense_Mutation_p.I239M|B3GALT5_uc002yym.1_Missense_Mutation_p.I239M	p.I239M	NM_033173	NP_149363	Q9Y2C3	B3GT5_HUMAN			5	1309	+		Prostate(19;2.55e-06)	239			Lumenal (Potential).		A8KA86|D3DSI3|Q2M3L5|Q53Z19|Q9NY96|Q9P1X6|Q9P1X7	Missense_Mutation	SNP	ENST00000380620.4	37	c.717T>G	CCDS13667.1	.	.	.	.	.	.	.	.	.	.	T	13.39	2.223069	0.39300	.	.	ENSG00000183778	ENST00000380620;ENST00000380618;ENST00000343118;ENST00000398714	T;T;T;T	0.46819	0.86;0.86;0.86;0.86	5.64	-0.467	0.12150	.	0.343009	0.24001	N	0.042474	T	0.49609	0.1567	L	0.52364	1.645	0.36050	D	0.84069	P	0.51653	0.947	P	0.56042	0.79	T	0.55042	-0.8202	10	0.62326	D	0.03	.	7.3554	0.26717	0.0:0.4211:0.1198:0.4591	.	239	Q9Y2C3	B3GT5_HUMAN	M	239	ENSP00000369994:I239M;ENSP00000369992:I239M;ENSP00000343318:I239M;ENSP00000381699:I239M	ENSP00000343318:I239M	I	+	3	3	B3GALT5	39955073	0.916000	0.31088	0.137000	0.22149	0.049000	0.14656	-0.055000	0.11807	-0.308000	0.08792	-0.242000	0.12053	ATT		0.562	B3GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000195008.2	NM_033170	
SLC35E4	339665	broad.mit.edu	37	22	31032455	31032455	+	Frame_Shift_Del	DEL	G	G	-			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr22:31032455delG	ENST00000343605.4	+	1	817	c.18delG	c.(16-18)ccgfs	p.P6fs	SLC35E4_ENST00000300385.8_Frame_Shift_Del_p.P6fs|SLC35E4_ENST00000406566.1_Frame_Shift_Del_p.P6fs	NM_001001479.2	NP_001001479.1	Q6ICL7	S35E4_HUMAN	solute carrier family 35, member E4	6						integral component of membrane (GO:0016021)				autonomic_ganglia(1)|endometrium(1)|large_intestine(2)|lung(3)|ovary(1)|pancreas(1)|skin(1)	10						GCTGCCCGCCGGAGCACCATG	0.701																																						uc003ais.1																			0					0						c.(16-18)CCGfs		solute carrier family 35, member E4							5.0	6.0	5.0					22																	31032455		2046	4033	6079	SO:0001589	frameshift_variant	339665					integral to membrane		g.chr22:31032455delG		CCDS13882.1	22q12.2	2013-05-22			ENSG00000100036	ENSG00000100036		"""Solute carriers"""	17058	protein-coding gene	gene with protein product							Standard	NM_001001479		Approved		uc003ais.1	Q6ICL7	OTTHUMG00000151110	ENST00000343605.4:c.18delG	22.37:g.31032455delG	ENSP00000339626:p.Pro6fs					SLC35E4_uc003ait.2_5'UTR	p.P6fs	NM_001001479	NP_001001479	Q6ICL7	S35E4_HUMAN			1	663	+			6					Q567P0	Frame_Shift_Del	DEL	ENST00000343605.4	37	c.18delG	CCDS13882.1																																																																																				0.701	SLC35E4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321382.1	XM_290973	
GTSE1	51512	broad.mit.edu	37	22	46708130	46708130	+	Silent	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr22:46708130G>A	ENST00000454366.1	+	5	1067	c.855G>A	c.(853-855)ccG>ccA	p.P285P		NM_016426.6	NP_057510	Q9NYZ3	GTSE1_HUMAN	G-2 and S-phase expressed 1	266					DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|microtubule-based process (GO:0007017)	cytoplasmic microtubule (GO:0005881)|membrane (GO:0016020)				NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|ovary(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	27		Ovarian(80;0.00965)|all_neural(38;0.0416)		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)		AACCTGCCCCGGGTGCTGTCA	0.577																																					GBM(153;542 1915 12487 29016 50495)	uc011aqy.1																			0				ovary(1)	1						c.(853-855)CCG>CCA		G-2 and S-phase expressed 1							37.0	42.0	40.0					22																	46708130		2203	4300	6503	SO:0001819	synonymous_variant	51512				DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest|G2 phase of mitotic cell cycle|microtubule-based process	cytoplasmic microtubule		g.chr22:46708130G>A	AF223408	CCDS14074.2	22q13.2-q13.3	2008-06-10			ENSG00000075218	ENSG00000075218			13698	protein-coding gene	gene with protein product		607477				10974554, 10984615, 12750368	Standard	NM_016426		Approved	GTSE-1, B99	uc011aqy.2	Q9NYZ3	OTTHUMG00000150486	ENST00000454366.1:c.855G>A	22.37:g.46708130G>A						GTSE1_uc011aqz.1_Silent_p.P132P	p.P285P	NM_016426	NP_057510	Q9NYZ3	GTSE1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (28;0.00462)	5	1067	+		Ovarian(80;0.00965)|all_neural(38;0.0416)	266					B0QYM3|Q20WK2|Q53GX5|Q5R3I6|Q6DHX4|Q9BRE0|Q9UGZ9|Q9Y557	Silent	SNP	ENST00000454366.1	37	c.855G>A	CCDS14074.2																																																																																				0.577	GTSE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318360.2	NM_016426	
ITPR1	3708	broad.mit.edu	37	3	4716846	4716846	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr3:4716846G>A	ENST00000443694.2	+	20	2648	c.2648G>A	c.(2647-2649)tGt>tAt	p.C883Y	ITPR1_ENST00000423119.2_Missense_Mutation_p.C898Y|ITPR1_ENST00000544951.1_Intron|ITPR1_ENST00000354582.6_Missense_Mutation_p.C898Y|ITPR1_ENST00000302640.8_Missense_Mutation_p.C883Y|ITPR1_ENST00000456211.2_Missense_Mutation_p.C883Y|ITPR1_ENST00000357086.4_Missense_Mutation_p.C898Y			Q14643	ITPR1_HUMAN	inositol 1,4,5-trisphosphate receptor, type 1	898					activation of phospholipase C activity (GO:0007202)|blood coagulation (GO:0007596)|calcium ion transport (GO:0006816)|endoplasmic reticulum calcium ion homeostasis (GO:0032469)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|inositol phosphate-mediated signaling (GO:0048016)|intrinsic apoptotic signaling pathway in response to endoplasmic reticulum stress (GO:0070059)|negative regulation of calcium-mediated signaling (GO:0050849)|neurotrophin TRK receptor signaling pathway (GO:0048011)|platelet activation (GO:0030168)|post-embryonic development (GO:0009791)|regulation of insulin secretion (GO:0050796)|release of sequestered calcium ion into cytosol (GO:0051209)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|voluntary musculoskeletal movement (GO:0050882)	calcineurin complex (GO:0005955)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear inner membrane (GO:0005637)|nucleolus (GO:0005730)|platelet dense granule membrane (GO:0031088)|platelet dense tubular network (GO:0031094)|platelet dense tubular network membrane (GO:0031095)|postsynaptic density (GO:0014069)|sarcoplasmic reticulum (GO:0016529)	calcium channel inhibitor activity (GO:0019855)|calcium ion transmembrane transporter activity (GO:0015085)|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0005220)|intracellular ligand-gated calcium channel activity (GO:0005218)|phosphatidylinositol binding (GO:0035091)			NS(1)|autonomic_ganglia(1)|breast(10)|endometrium(15)|kidney(6)|large_intestine(27)|liver(1)|lung(27)|ovary(6)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(2)	106				Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	Caffeine(DB00201)	ATATTGGACTGTGTACATGTG	0.393																																						uc003bqa.2																			0				lung(7)|breast(5)|ovary(4)|large_intestine(1)|liver(1)|skin(1)|kidney(1)|pancreas(1)	21						c.(2692-2694)TGT>TAT		inositol 1,4,5-triphosphate receptor, type 1							146.0	133.0	137.0					3																	4716846		1911	4121	6032	SO:0001583	missense	3708				activation of phospholipase C activity|cell death|energy reserve metabolic process|nerve growth factor receptor signaling pathway|platelet activation|regulation of insulin secretion|response to hypoxia	endoplasmic reticulum membrane|integral to membrane|platelet dense granule membrane|platelet dense tubular network membrane	calcium ion transmembrane transporter activity|inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity|intracellular ligand-gated calcium channel activity|phosphatidylinositol binding|protein binding	g.chr3:4716846G>A	D26070	CCDS46740.1, CCDS46740.2, CCDS54550.1, CCDS54551.1	3p26.1	2014-06-12	2011-04-28			ENSG00000150995		"""Ion channels / Inositol triphosphate receptors"""	6180	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 94"""	147265	"""spinocerebellar ataxia 15"", ""spinocerebellar ataxia 16"", ""spinocerebellar ataxia 29"""	SCA15, SCA16, SCA29		7945203, 7500840, 17590087, 17932120, 22986007	Standard	NM_001099952		Approved	Insp3r1, IP3R1, ACV, PPP1R94	uc003bqc.3	Q14643		ENST00000443694.2:c.2648G>A	3.37:g.4716846G>A	ENSP00000401671:p.Cys883Tyr					ITPR1_uc010hca.1_Missense_Mutation_p.C883Y|ITPR1_uc011asu.1_Intron|ITPR1_uc010hcb.1_Missense_Mutation_p.C883Y	p.C898Y	NM_001099952	NP_001093422	Q14643	ITPR1_HUMAN		Epithelial(13;0.0199)|OV - Ovarian serous cystadenocarcinoma(96;0.0361)|all cancers(10;0.0982)	23	3041	+			898			Cytoplasmic (Potential).		E7EPX7|E9PDE9|Q14660|Q99897	Missense_Mutation	SNP	ENST00000443694.2	37	c.2693G>A	CCDS54551.1	.	.	.	.	.	.	.	.	.	.	G	23.4	4.407544	0.83340	.	.	ENSG00000150995	ENST00000356617;ENST00000302640;ENST00000354582;ENST00000423119;ENST00000357086;ENST00000456211;ENST00000443694	D;D;D;D;D;D	0.91792	-2.9;-2.9;-2.9;-2.9;-2.91;-2.9	5.06	5.06	0.68205	.	0.000000	0.85682	D	0.000000	D	0.93083	0.7798	M	0.75615	2.305	0.80722	D	1	B;B;P	0.47762	0.175;0.124;0.9	B;B;P	0.51657	0.077;0.063;0.676	D	0.90483	0.4461	10	0.02654	T	1	.	18.6234	0.91328	0.0:0.0:1.0:0.0	.	883;898;898	E7EPX7;Q14643;G5E9P1	.;ITPR1_HUMAN;.	Y	898;883;898;898;898;883;883	ENSP00000306253:C883Y;ENSP00000346595:C898Y;ENSP00000405934:C898Y;ENSP00000349597:C898Y;ENSP00000397885:C883Y;ENSP00000401671:C883Y	ENSP00000306253:C883Y	C	+	2	0	ITPR1	4691846	1.000000	0.71417	1.000000	0.80357	0.924000	0.55760	7.242000	0.78210	2.641000	0.89580	0.591000	0.81541	TGT		0.393	ITPR1-004	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000337982.3	NM_002222	
SRGAP3	9901	broad.mit.edu	37	3	9034619	9034619	+	Silent	SNP	C	C	T	rs552319348		TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr3:9034619C>T	ENST00000383836.3	-	20	2956	c.2529G>A	c.(2527-2529)tcG>tcA	p.S843S	SRGAP3_ENST00000360413.3_Silent_p.S819S	NM_014850.3	NP_055665.1	O43295	SRGP3_HUMAN	SLIT-ROBO Rho GTPase activating protein 3	843					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)		SRGAP3/RAF1(6)	breast(1)|endometrium(2)|kidney(21)|large_intestine(7)|lung(13)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	54				OV - Ovarian serous cystadenocarcinoma(96;0.0563)		AGCCGTAATCCGAGATGTGCT	0.557			T	RAF1	pilocytic astrocytoma								C|||	1	0.000199681	0.0	0.0	5008	,	,		18959	0.0		0.0	False		,,,				2504	0.001					uc003brf.1				Dom	yes		3	3p25.3	9901	T	SLIT-ROBO Rho GTPase activating protein 3			M	RAF1		pilocytic astrocytoma	SRGAP3/RAF1(4)	0				central_nervous_system(4)|skin(3)|urinary_tract(1)|breast(1)	9						c.(2527-2529)TCG>TCA		SLIT-ROBO Rho GTPase activating protein 3							82.0	77.0	79.0					3																	9034619		2203	4300	6503	SO:0001819	synonymous_variant	9901				regulation of small GTPase mediated signal transduction|small GTPase mediated signal transduction	cytosol	GTPase activator activity|protein binding	g.chr3:9034619C>T	AB007871	CCDS2572.1, CCDS33689.1	3p25.3	2011-07-04	2004-11-12	2004-11-12	ENSG00000196220	ENSG00000196220		"""Rho GTPase activating proteins"""	19744	protein-coding gene	gene with protein product		606525	"""SLIT-ROBO Rho GTPase activating protein 2"""	SRGAP2		12195014	Standard	NM_014850		Approved	KIAA0411, MEGAP, WRP, ARHGAP14	uc003brf.2	O43295	OTTHUMG00000090589	ENST00000383836.3:c.2529G>A	3.37:g.9034619C>T						SRGAP3_uc003brg.1_Silent_p.S819S	p.S843S	NM_014850	NP_055665	O43295	SRGP2_HUMAN		OV - Ovarian serous cystadenocarcinoma(96;0.0563)	20	3205	-			843					Q8IX13|Q8IZV8	Silent	SNP	ENST00000383836.3	37	c.2529G>A	CCDS2572.1																																																																																				0.557	SRGAP3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207137.3		
SLC6A6	6533	broad.mit.edu	37	3	14509599	14509599	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr3:14509599C>A	ENST00000454876.2	+	9	1304	c.975C>A	c.(973-975)gaC>gaA	p.D325E	SLC6A6_ENST00000360861.3_Missense_Mutation_p.D325E			P31641	SC6A6_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 6	325					amino acid transport (GO:0006865)|cellular amino acid metabolic process (GO:0006520)|ion transport (GO:0006811)|taurine transport (GO:0015734)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	neurotransmitter:sodium symporter activity (GO:0005328)|taurine binding (GO:0030977)|taurine:sodium symporter activity (GO:0005369)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(1)|prostate(1)|skin(2)	28						AACTTAGGGACTGTATGCTGC	0.453											OREG0015421	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										uc010heg.2																			0				ovary(1)	1						c.(973-975)GAC>GAA		solute carrier family 6 (neurotransmitter							199.0	196.0	197.0					3																	14509599		2203	4300	6503	SO:0001583	missense	6533				cellular amino acid metabolic process	integral to plasma membrane	amino acid transmembrane transporter activity|neurotransmitter:sodium symporter activity|taurine:sodium symporter activity	g.chr3:14509599C>A		CCDS33705.1, CCDS46765.1	3p25.1	2013-07-19	2013-07-19		ENSG00000131389	ENSG00000131389		"""Solute carriers"""	11052	protein-coding gene	gene with protein product	"""taurine transporter"""	186854	"""solute carrier family 6 (neurotransmitter transporter, taurine), member 6"""			8010975, 8382624	Standard	XM_006713307		Approved	TAUT	uc010heg.4	P31641	OTTHUMG00000155525	ENST00000454876.2:c.975C>A	3.37:g.14509599C>A	ENSP00000398063:p.Asp325Glu		OREG0015421	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)	695	SLC6A6_uc003byq.2_Missense_Mutation_p.D325E|SLC6A6_uc003byr.2_Intron	p.D325E	NM_001134367	NP_001127839	P31641	SC6A6_HUMAN			16	1266	+			325					B2RNU7|Q9BRI2|Q9BXB0	Missense_Mutation	SNP	ENST00000454876.2	37	c.975C>A	CCDS33705.1	.	.	.	.	.	.	.	.	.	.	C	32	5.105755	0.94292	.	.	ENSG00000131389	ENST00000454876;ENST00000360861	T;T	0.79454	-1.27;-1.27	5.35	5.35	0.76521	.	0.136806	0.64402	D	0.000005	D	0.93465	0.7915	H	0.99143	4.445	0.80722	D	1	D	0.76494	0.999	D	0.68765	0.96	D	0.96252	0.9184	10	0.87932	D	0	.	19.0628	0.93100	0.0:1.0:0.0:0.0	.	325	P31641	SC6A6_HUMAN	E	325	ENSP00000398063:D325E;ENSP00000354107:D325E	ENSP00000354107:D325E	D	+	3	2	SLC6A6	14484603	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.792000	0.85828	2.499000	0.84300	0.467000	0.42956	GAC		0.453	SLC6A6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340507.1	NM_003043	
ADCY5	111	broad.mit.edu	37	3	123003491	123003491	+	Missense_Mutation	SNP	C	C	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr3:123003491C>A	ENST00000462833.1	-	21	4962	c.3750G>T	c.(3748-3750)atG>atT	p.M1250I	RP11-797D24.4_ENST00000608436.1_RNA|ADCY5_ENST00000309879.5_Missense_Mutation_p.M900I|ADCY5_ENST00000491190.1_Missense_Mutation_p.M908I	NM_183357.2	NP_899200.1	O95622	ADCY5_HUMAN	adenylate cyclase 5	1250					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenosine receptor signaling pathway (GO:0001973)|adenylate cyclase-activating dopamine receptor signaling pathway (GO:0007191)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting dopamine receptor signaling pathway (GO:0007195)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|cellular response to glucagon stimulus (GO:0071377)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|locomotory behavior (GO:0007626)|neuromuscular process controlling balance (GO:0050885)|neurotrophin TRK receptor signaling pathway (GO:0048011)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|primary cilium (GO:0072372)	adenylate cyclase activity (GO:0004016)|adenylate cyclase binding (GO:0008179)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein heterodimerization activity (GO:0046982)			breast(2)|endometrium(4)|kidney(3)|large_intestine(12)|lung(22)|ovary(5)|prostate(2)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(2)	60				GBM - Glioblastoma multiforme(114;0.0342)		GGAAGTAGGTCATCATCTCGC	0.607																																						uc003egh.1																			0				ovary(4)	4						c.(3748-3750)ATG>ATT		adenylate cyclase 5							180.0	160.0	166.0					3																	123003491		2203	4300	6503	SO:0001583	missense	111				activation of phospholipase C activity|activation of protein kinase A activity|cellular response to glucagon stimulus|energy reserve metabolic process|nerve growth factor receptor signaling pathway|synaptic transmission|transmembrane transport|water transport	integral to membrane|plasma membrane	adenylate cyclase activity|ATP binding|metal ion binding	g.chr3:123003491C>A	U65473	CCDS3022.1, CCDS56274.1	3q21.1	2013-02-04			ENSG00000173175	ENSG00000173175	4.6.1.1	"""Adenylate cyclases"""	236	protein-coding gene	gene with protein product		600293				10481931	Standard	NM_183357		Approved	AC5	uc003egh.2	O95622	OTTHUMG00000159517	ENST00000462833.1:c.3750G>T	3.37:g.123003491C>A	ENSP00000419361:p.Met1250Ile					ADCY5_uc003egg.1_Missense_Mutation_p.M908I	p.M1250I	NM_183357	NP_899200	O95622	ADCY5_HUMAN		GBM - Glioblastoma multiforme(114;0.0342)	21	3750	-			1250			Cytoplasmic (Potential).		B7Z8A6|Q7RTV7|Q8NFM3	Missense_Mutation	SNP	ENST00000462833.1	37	c.3750G>T	CCDS3022.1	.	.	.	.	.	.	.	.	.	.	C	9.859	1.195765	0.22037	.	.	ENSG00000173175	ENST00000462833;ENST00000491190;ENST00000309879	T;T;T	0.26957	1.7;1.7;1.7	5.0	5.0	0.66597	Adenylyl cyclase class-3/4/guanylyl cyclase (3);	0.056505	0.64402	D	0.000002	T	0.14399	0.0348	N	0.13003	0.285	0.47065	D	0.999305	B;B	0.09022	0.002;0.0	B;B	0.14023	0.01;0.004	T	0.08006	-1.0743	10	0.33141	T	0.24	.	8.9264	0.35643	0.1407:0.5909:0.2684:0.0	.	1250;908	O95622;B3KWA8	ADCY5_HUMAN;.	I	1250;908;900	ENSP00000419361:M1250I;ENSP00000418537:M908I;ENSP00000308685:M900I	ENSP00000308685:M900I	M	-	3	0	ADCY5	124486181	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.133000	0.42093	2.595000	0.87683	0.655000	0.94253	ATG		0.607	ADCY5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355889.4	XM_171048	
ATP2C1	27032	broad.mit.edu	37	3	130672707	130672707	+	Missense_Mutation	SNP	A	A	G			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr3:130672707A>G	ENST00000510168.1	+	9	1124	c.574A>G	c.(574-576)Aca>Gca	p.T192A	ATP2C1_ENST00000328560.8_Missense_Mutation_p.T192A|ATP2C1_ENST00000533801.2_Missense_Mutation_p.T187A|ATP2C1_ENST00000359644.3_Missense_Mutation_p.T192A|ATP2C1_ENST00000508532.1_Missense_Mutation_p.T192A|ATP2C1_ENST00000504948.1_Missense_Mutation_p.T176A|ATP2C1_ENST00000507488.2_Missense_Mutation_p.T176A|ATP2C1_ENST00000422190.2_Missense_Mutation_p.T192A|ATP2C1_ENST00000513801.1_Missense_Mutation_p.T176A|ATP2C1_ENST00000393221.4_Missense_Mutation_p.T226A|ATP2C1_ENST00000504381.1_Missense_Mutation_p.T137A|ATP2C1_ENST00000428331.2_Missense_Mutation_p.T192A|ATP2C1_ENST00000505330.1_Missense_Mutation_p.T176A			P98194	AT2C1_HUMAN	ATPase, Ca++ transporting, type 2C, member 1	192					actin cytoskeleton reorganization (GO:0031532)|calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|calcium-dependent cell-cell adhesion (GO:0016339)|cellular calcium ion homeostasis (GO:0006874)|cellular manganese ion homeostasis (GO:0030026)|epidermis development (GO:0008544)|Golgi calcium ion homeostasis (GO:0032468)|Golgi calcium ion transport (GO:0032472)|ion transmembrane transport (GO:0034220)|manganese ion transmembrane transport (GO:0071421)|manganese ion transport (GO:0006828)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|signal transduction (GO:0007165)|transmembrane transport (GO:0055085)	Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|trans-Golgi network (GO:0005802)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calcium-transporting ATPase activity (GO:0005388)|manganese ion binding (GO:0030145)|manganese-transporting ATPase activity (GO:0015410)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)			breast(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(15)|prostate(2)|skin(2)|urinary_tract(1)	39					Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Sevoflurane(DB01236)	GACAGGTGAGACAACGCCTTG	0.438									Hailey-Hailey disease																												Esophageal Squamous(99;456 1443 27647 34099 42636)	uc003enl.2																			0				skin(1)	1						c.(574-576)ACA>GCA		calcium-transporting ATPase 2C1 isoform 1a	Arsenic trioxide(DB01169)|Desflurane(DB01189)|Enflurane(DB00228)|Halothane(DB01159)|Isoflurane(DB00753)|Methoxyflurane(DB01028)|Miconazole(DB01110)|Sevoflurane(DB01236)						141.0	134.0	137.0					3																	130672707		2203	4300	6503	SO:0001583	missense	27032	Hailey-Hailey_disease	Familial Cancer Database	HHD, Familial Benign Chronic Pemphigus, Benign Familial Pemphigus	actin cytoskeleton reorganization|ATP biosynthetic process|calcium-dependent cell-cell adhesion|cellular calcium ion homeostasis|cellular manganese ion homeostasis|epidermis development|Golgi calcium ion homeostasis|Golgi calcium ion transport|positive regulation of I-kappaB kinase/NF-kappaB cascade	Golgi apparatus|Golgi membrane|integral to membrane|trans-Golgi network	ATP binding|ATP binding|calcium ion binding|calcium-transporting ATPase activity|manganese ion binding|manganese-transporting ATPase activity|metal ion binding|signal transducer activity	g.chr3:130672707A>G	AF181120	CCDS33856.1, CCDS46912.1, CCDS46913.1, CCDS46914.1, CCDS56278.1, CCDS56279.1, CCDS56280.1, CCDS56281.1, CCDS75006.1	3q21.3	2012-10-22			ENSG00000017260	ENSG00000017260	3.6.3.8	"""ATPases / P-type"""	13211	protein-coding gene	gene with protein product	"""secretory pathway Ca2+/Mn2+ ATPase 1"", ""calcium-transporting ATPase type 2C member 1"""	604384	"""benign chronic pemphigus (Hailey-Hailey disease)"""	BCPM		10615129, 10767338	Standard	NM_001001485		Approved	KIAA1347, ATP2C1A, PMR1, SPCA1	uc011bli.2	P98194	OTTHUMG00000136802	ENST00000510168.1:c.574A>G	3.37:g.130672707A>G	ENSP00000427461:p.Thr192Ala					ATP2C1_uc011blg.1_Missense_Mutation_p.T226A|ATP2C1_uc011blh.1_Missense_Mutation_p.T187A|ATP2C1_uc011bli.1_Missense_Mutation_p.T226A|ATP2C1_uc003enk.2_Missense_Mutation_p.T176A|ATP2C1_uc003enm.2_Missense_Mutation_p.T192A|ATP2C1_uc003enn.2_Missense_Mutation_p.T176A|ATP2C1_uc003eno.2_Missense_Mutation_p.T192A|ATP2C1_uc003enp.2_Missense_Mutation_p.T192A|ATP2C1_uc003enq.2_Missense_Mutation_p.T192A|ATP2C1_uc003enr.2_Missense_Mutation_p.T192A|ATP2C1_uc003ens.2_Missense_Mutation_p.T192A|ATP2C1_uc003ent.2_Missense_Mutation_p.T192A	p.T192A	NM_014382	NP_055197	P98194	AT2C1_HUMAN			9	796	+			192			Cytoplasmic (By similarity).		B2RAT7|B4DSW3|B7Z3X9|G3XAH8|G8JLN9|O76005|Q86V72|Q86V73|Q8N6V1|Q8NCJ7	Missense_Mutation	SNP	ENST00000510168.1	37	c.574A>G	CCDS46914.1	.	.	.	.	.	.	.	.	.	.	A	16.97	3.267973	0.59540	.	.	ENSG00000017260	ENST00000505330;ENST00000504381;ENST00000507488;ENST00000393221;ENST00000533801;ENST00000510168;ENST00000508532;ENST00000504948;ENST00000513801;ENST00000328560;ENST00000428331;ENST00000359644;ENST00000422190;ENST00000347421	D;D;D;D;D;D;D;D;D;D;D;D;D	0.90069	-2.61;-2.61;-2.61;-2.61;-2.61;-2.61;-2.61;-2.61;-2.61;-2.61;-2.61;-2.61;-2.61	5.42	5.42	0.78866	ATPase, P-type, ATPase-associated domain (1);ATPase,  P-type, cytoplasmic transduction domain A (1);	0.000000	0.85682	D	0.000000	D	0.83198	0.5202	N	0.24115	0.695	0.80722	D	1	B;B;B;B;B;B;B	0.28026	0.165;0.198;0.106;0.165;0.106;0.016;0.02	B;B;B;B;B;B;B	0.31751	0.075;0.123;0.135;0.075;0.135;0.044;0.074	T	0.80386	-0.1404	10	0.33940	T	0.23	.	15.4614	0.75359	1.0:0.0:0.0:0.0	.	226;187;226;192;226;192;192	G3XAH8;B4DSW3;B4E2Q0;P98194-5;B7Z3X9;P98194-2;P98194	.;.;.;.;.;.;AT2C1_HUMAN	A	176;137;176;226;187;192;192;176;176;192;192;192;192;191	ENSP00000423774:T176A;ENSP00000425320:T137A;ENSP00000421326:T176A;ENSP00000376914:T226A;ENSP00000432956:T187A;ENSP00000427461:T192A;ENSP00000424783:T192A;ENSP00000423330:T176A;ENSP00000422872:T176A;ENSP00000329664:T192A;ENSP00000395809:T192A;ENSP00000352665:T192A;ENSP00000402677:T192A	ENSP00000329664:T192A	T	+	1	0	ATP2C1	132155397	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.962000	0.93254	2.062000	0.61559	0.528000	0.53228	ACA		0.438	ATP2C1-008	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356648.2	NM_001001486	
AADACL2	344752	broad.mit.edu	37	3	151475174	151475174	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr3:151475174C>T	ENST00000356517.3	+	5	1107	c.998C>T	c.(997-999)aCc>aTc	p.T333I	RP11-454C18.2_ENST00000483843.2_RNA|RP11-454C18.2_ENST00000475855.1_RNA	NM_207365.3	NP_997248.2	Q6P093	ADCL2_HUMAN	arylacetamide deacetylase-like 2	333						extracellular region (GO:0005576)|integral component of membrane (GO:0016021)	carboxylic ester hydrolase activity (GO:0052689)			NS(1)|breast(1)|endometrium(2)|large_intestine(4)|liver(1)|lung(13)|skin(2)	24			LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)			TTGCCACTAACCTATATTCTT	0.378																																						uc003ezc.2																			0					0						c.(997-999)ACC>ATC		arylacetamide deacetylase-like 2 precursor							144.0	136.0	139.0					3																	151475174		2203	4299	6502	SO:0001583	missense	344752					extracellular region|integral to membrane	carboxylesterase activity	g.chr3:151475174C>T	BC065724	CCDS3161.2	3q25.1	2010-12-14			ENSG00000197953	ENSG00000197953			24427	protein-coding gene	gene with protein product							Standard	NM_207365		Approved	MGC72001	uc003ezc.3	Q6P093	OTTHUMG00000155914	ENST00000356517.3:c.998C>T	3.37:g.151475174C>T	ENSP00000348911:p.Thr333Ile					AADACL2_uc010hvn.2_Missense_Mutation_p.T120I	p.T333I	NM_207365	NP_997248	Q6P093	ADCL2_HUMAN	LUSC - Lung squamous cell carcinoma(72;0.0394)|Lung(72;0.0813)		5	1118	+			333					Q5HYJ4	Missense_Mutation	SNP	ENST00000356517.3	37	c.998C>T	CCDS3161.2	.	.	.	.	.	.	.	.	.	.	C	35	5.596848	0.96602	.	.	ENSG00000197953	ENST00000356517	T	0.13901	2.55	5.01	5.01	0.66863	Alpha/beta hydrolase fold-3 (1);	0.057542	0.64402	D	0.000001	T	0.48040	0.1478	M	0.91972	3.26	0.47819	D	0.999528	D	0.89917	1.0	D	0.87578	0.998	T	0.59836	-0.7379	10	0.87932	D	0	-3.7693	18.0851	0.89455	0.0:1.0:0.0:0.0	.	333	Q6P093	ADCL2_HUMAN	I	333	ENSP00000348911:T333I	ENSP00000348911:T333I	T	+	2	0	AADACL2	152957864	1.000000	0.71417	0.023000	0.16930	0.978000	0.69477	6.423000	0.73361	2.613000	0.88420	0.591000	0.81541	ACC		0.378	AADACL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342288.3	NM_207365	
PIK3CA	5290	broad.mit.edu	37	3	178928081	178928081	+	Missense_Mutation	SNP	A	A	C	rs397517200		TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr3:178928081A>C	ENST00000263967.3	+	8	1516	c.1359A>C	c.(1357-1359)gaA>gaC	p.E453D		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	453	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.		E -> Q (in CRC; likely involved in disease pathogenesis; shows an increase in lipid kinase activity; may disrupt the interaction of the C2 PI3K-type domain with the iSH2 region of the p85 regulatory subunit).|Missing (in MCAP). {ECO:0000269|PubMed:22729224}.		angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|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)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H450fs*9(1)|p.G451_L456>V(1)|p.P449_L455del(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	ATGGATTAGAAGATTTGCTGA	0.348		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	uc003fjk.2		57		Dom	yes		3	3q26.3	5290	Mis	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			"""E, O"""			colorectal|gastric|gliobastoma|breast		3	Complex - frameshift(1)|Complex - deletion inframe(1)|Deletion - In frame(1)	p.E453K(5)|p.E453A(1)|p.P449_L455del(1)|p.G451_L456>V(1)|p.E453del(1)|p.E453Q(1)	endometrium(2)|breast(1)	breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553						c.(1357-1359)GAA>GAC		phosphoinositide-3-kinase, catalytic, alpha							136.0	129.0	131.0					3																	178928081		1828	4091	5919	SO:0001583	missense	5290				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	g.chr3:178928081A>C		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1359A>C	3.37:g.178928081A>C	ENSP00000263967:p.Glu453Asp	HNSCC(19;0.045)|TSP Lung(28;0.18)					p.E453D	NM_006218	NP_006209	P42336	PK3CA_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		8	1516	+	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		453		E -> Q (in cancer; shows an increase in lipid kinase activity; may disrupt the interaction of the C2 PI3K-type domain with the iSH2 region of the p85 regulatory subunit).	C2 PI3K-type.		Q14CW1|Q99762	Missense_Mutation	SNP	ENST00000263967.3	37	c.1359A>C	CCDS43171.1	.	.	.	.	.	.	.	.	.	.	A	10.95	1.495300	0.26774	.	.	ENSG00000121879	ENST00000263967	T	0.69926	-0.44	5.64	4.49	0.54785	C2 calcium/lipid-binding domain, CaLB (1);Phosphoinositide 3-kinase, C2 (1);	0.000000	0.85682	D	0.000000	T	0.41073	0.1143	N	0.05383	-0.06	0.58432	D	0.999999	B	0.12630	0.006	B	0.17098	0.017	T	0.15607	-1.0431	10	0.13108	T	0.6	-22.2286	7.7372	0.28821	0.763:0.0:0.237:0.0	.	453	P42336	PK3CA_HUMAN	D	453	ENSP00000263967:E453D	ENSP00000263967:E453D	E	+	3	2	PIK3CA	180410775	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.017000	0.40981	0.989000	0.38761	0.533000	0.62120	GAA		0.348	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
PIK3CA	5290	broad.mit.edu	37	3	178928087	178928101	+	In_Frame_Del	DEL	GCTGAACCCTATTGG	GCTGAACCCTATTGG	-	rs397517200		TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr3:178928087_178928101delGCTGAACCCTATTGG	ENST00000263967.3	+	8	1522_1536	c.1365_1379delGCTGAACCCTATTGG	c.(1363-1380)ttgctgaaccctattggt>ttt	p.455_460LLNPIG>F		NM_006218.2	NP_006209.2	P42336	PK3CA_HUMAN	phosphatidylinositol-4,5-bisphosphate 3-kinase, catalytic subunit alpha	455	C2 PI3K-type. {ECO:0000255|PROSITE- ProRule:PRU00880}.				angiogenesis (GO:0001525)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|endothelial cell migration (GO:0043542)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|hypomethylation of CpG island (GO:0044029)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin receptor signaling pathway via phosphatidylinositol 3-kinase (GO:0038028)|leukocyte migration (GO:0050900)|negative regulation of anoikis (GO:2000811)|negative regulation of fibroblast apoptotic process (GO:2000270)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of peptidyl-serine phosphorylation (GO:0033138)|protein kinase B signaling (GO:0043491)|regulation of genetic imprinting (GO:2000653)|regulation of multicellular organism growth (GO:0040014)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|vasculature development (GO:0001944)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cytosol (GO:0005829)|lamellipodium (GO:0030027)|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)|kinase activity (GO:0016301)|phosphatidylinositol 3-kinase activity (GO:0035004)|phosphatidylinositol-4,5-bisphosphate 3-kinase activity (GO:0046934)|protein kinase activator activity (GO:0030295)|protein serine/threonine kinase activity (GO:0004674)	p.H450fs*9(1)|p.N457K(1)|p.G451_L456>V(1)		NS(16)|autonomic_ganglia(4)|biliary_tract(22)|bone(1)|breast(2150)|central_nervous_system(110)|cervix(33)|endometrium(473)|eye(1)|haematopoietic_and_lymphoid_tissue(35)|kidney(14)|large_intestine(1202)|liver(42)|lung(202)|meninges(1)|oesophagus(28)|ovary(235)|pancreas(17)|penis(8)|pituitary(12)|prostate(10)|skin(155)|small_intestine(1)|soft_tissue(18)|stomach(121)|thyroid(80)|upper_aerodigestive_tract(70)|urinary_tract(208)	5269	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		Caffeine(DB00201)	TAGAAGATTTGCTGAACCCTATTGGTGTTACTGGA	0.33		57	Mis		"""colorectal, gastric, gliobastoma, breast"""					HNSCC(19;0.045)|TSP Lung(28;0.18)																											Colon(199;1504 1750 3362 26421 31210 32040)	uc003fjk.2		57		Dom	yes		3	3q26.3	5290	Mis	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			"""E, O"""			colorectal|gastric|gliobastoma|breast		3	Substitution - Missense(1)|Complex - frameshift(1)|Complex - deletion inframe(1)	p.N457K(1)|p.G451_L456>V(1)|p.P449_L455del(1)	breast(2)|endometrium(1)	breast(1564)|large_intestine(776)|endometrium(246)|urinary_tract(195)|ovary(141)|skin(112)|stomach(98)|thyroid(77)|central_nervous_system(69)|lung(65)|upper_aerodigestive_tract(58)|haematopoietic_and_lymphoid_tissue(27)|cervix(25)|biliary_tract(22)|liver(20)|oesophagus(17)|pancreas(11)|penis(8)|pituitary(8)|autonomic_ganglia(4)|prostate(3)|kidney(2)|meninges(1)|eye(1)|NS(1)|soft_tissue(1)|bone(1)	3553						c.(1363-1380)TTGCTGAACCCTATTGGT>TTT		phosphoinositide-3-kinase, catalytic, alpha																																				SO:0001651	inframe_deletion	5290				epidermal growth factor receptor signaling pathway|fibroblast growth factor receptor signaling pathway|insulin receptor signaling pathway|leukocyte migration|nerve growth factor receptor signaling pathway|phosphatidylinositol-mediated signaling|platelet activation|T cell costimulation|T cell receptor signaling pathway		1-phosphatidylinositol-3-kinase activity|ATP binding|phosphatidylinositol-4,5-bisphosphate 3-kinase activity	g.chr3:178928087_178928101delGCTGAACCCTATTGG		CCDS43171.1	3q26.3	2014-09-17	2012-07-13		ENSG00000121879	ENSG00000121879	2.7.1.153		8975	protein-coding gene	gene with protein product		171834	"""phosphoinositide-3-kinase, catalytic, alpha polypeptide"""			1322797	Standard	NM_006218		Approved	PI3K	uc003fjk.3	P42336	OTTHUMG00000157311	ENST00000263967.3:c.1365_1379delGCTGAACCCTATTGG	3.37:g.178928087_178928101delGCTGAACCCTATTGG	ENSP00000263967:p.Leu455_Gly460delinsPhe	HNSCC(19;0.045)|TSP Lung(28;0.18)					p.455_460LLNPIG>F	NM_006218	NP_006209	P42336	PK3CA_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;9.59e-28)|GBM - Glioblastoma multiforme(14;0.003)|BRCA - Breast invasive adenocarcinoma(182;0.0282)		8	1522_1536	+	all_cancers(143;1.19e-17)|Ovarian(172;0.00769)|Breast(254;0.155)		455_460			C2 PI3K-type.		Q14CW1|Q99762	In_Frame_Del	DEL	ENST00000263967.3	37	c.1365_1379delGCTGAACCCTATTGG	CCDS43171.1																																																																																				0.330	PIK3CA-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000348409.2		
NAP1L5	266812	broad.mit.edu	37	4	89618484	89618486	+	In_Frame_Del	DEL	TCC	TCC	-	rs201095744|rs147461195	byFrequency	TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr4:89618484_89618486delTCC	ENST00000323061.5	-	1	900_902	c.420_422delGGA	c.(418-423)gaggaa>gaa	p.140_141EE>E	HERC3_ENST00000543130.1_Intron|HERC3_ENST00000402738.1_Intron|HERC3_ENST00000264345.3_Intron	NM_153757.2	NP_715638.1	Q96NT1	NP1L5_HUMAN	nucleosome assembly protein 1-like 5	140	Glu-rich.				nucleosome assembly (GO:0006334)	nucleus (GO:0005634)				endometrium(2)|lung(3)|skin(1)|upper_aerodigestive_tract(1)	7				OV - Ovarian serous cystadenocarcinoma(123;0.000181)		gtactcctcttcctcctcctcct	0.606														5	0.000998403	0.0008	0.0058	5008	,	,		14727	0.0		0.0	False		,,,				2504	0.0					uc003hrx.2																			0				skin(1)	1						c.(418-423)GAGGAA>GAA		nucleosome assembly protein 1-like 5																																				SO:0001651	inframe_deletion	266812				nucleosome assembly	nucleus	protein binding	g.chr4:89618484_89618486delTCC	NM_153757	CCDS3632.1	4q21-q22	2006-04-12			ENSG00000177432	ENSG00000177432			19968	protein-coding gene	gene with protein product		612203				12383514	Standard	NM_153757		Approved	DRLM	uc003hrx.3	Q96NT1	OTTHUMG00000130950	ENST00000323061.5:c.420_422delGGA	4.37:g.89618493_89618495delTCC	ENSP00000320488:p.Glu143del					HERC3_uc003hrw.1_Intron|HERC3_uc011cdn.1_Intron|HERC3_uc011cdo.1_Intron	p.140_141EE>E	NM_153757	NP_715638	Q96NT1	NP1L5_HUMAN		OV - Ovarian serous cystadenocarcinoma(123;0.000181)	1	538_540	-			140_141			Glu-rich.			In_Frame_Del	DEL	ENST00000323061.5	37	c.420_422delGGA	CCDS3632.1																																																																																				0.606	NAP1L5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253551.1	NM_153757	
FBN2	2201	broad.mit.edu	37	5	127728897	127728897	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr5:127728897C>T	ENST00000508053.1	-	16	2370	c.1396G>A	c.(1396-1398)Ggc>Agc	p.G466S	FBN2_ENST00000262464.4_Missense_Mutation_p.G466S|FBN2_ENST00000508989.1_Missense_Mutation_p.G433S			P35556	FBN2_HUMAN	fibrillin 2	466					anatomical structure morphogenesis (GO:0009653)|bone trabecula formation (GO:0060346)|embryonic limb morphogenesis (GO:0030326)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of bone mineralization (GO:0030501)|positive regulation of osteoblast differentiation (GO:0045669)|sequestering of TGFbeta in extracellular matrix (GO:0035583)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)			NS(1)|autonomic_ganglia(1)|biliary_tract(1)|breast(1)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(37)|liver(1)|lung(89)|ovary(9)|pancreas(2)|prostate(6)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(1)	197		all_cancers(142;0.0216)|Prostate(80;0.0551)	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)		GGAGAAAAGCCATTGCCTCCA	0.587																																						uc003kuu.2																			0				ovary(8)|large_intestine(4)|pancreas(1)|kidney(1)|skin(1)	15						c.(1396-1398)GGC>AGC		fibrillin 2 precursor							85.0	87.0	86.0					5																	127728897		2203	4300	6503	SO:0001583	missense	2201				bone trabecula formation|negative regulation of transforming growth factor beta receptor signaling pathway by extracellular sequestering of TGFbeta|positive regulation of bone mineralization|positive regulation of osteoblast differentiation	microfibril	calcium ion binding|extracellular matrix structural constituent	g.chr5:127728897C>T	U03272	CCDS34222.1	5q23-q31	2008-08-01	2008-08-01			ENSG00000138829			3604	protein-coding gene	gene with protein product	"""fibrillin 5"""	612570	"""congenital contractural arachnodactyly"""	CCA		1852206, 8120105	Standard	NM_001999		Approved	DA9	uc003kuu.3	P35556		ENST00000508053.1:c.1396G>A	5.37:g.127728897C>T	ENSP00000424571:p.Gly466Ser					FBN2_uc003kuv.2_Missense_Mutation_p.G433S	p.G466S	NM_001999	NP_001990	P35556	FBN2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.0268)|Kidney(363;0.0488)	OV - Ovarian serous cystadenocarcinoma(64;0.0821)|Epithelial(69;0.146)	10	1835	-		all_cancers(142;0.0216)|Prostate(80;0.0551)	466					B4DU01|Q59ES6	Missense_Mutation	SNP	ENST00000508053.1	37	c.1396G>A	CCDS34222.1	.	.	.	.	.	.	.	.	.	.	C	15.62	2.886326	0.51908	.	.	ENSG00000138829	ENST00000262464;ENST00000508053;ENST00000508989	D;D;D	0.85484	-1.79;-1.79;-1.99	3.98	3.98	0.46160	.	0.179046	0.38959	N	0.001516	D	0.86732	0.6003	M	0.87381	2.88	0.47037	D	0.999297	P;P	0.52842	0.956;0.956	B;B	0.42653	0.394;0.394	D	0.86746	0.1957	10	0.21540	T	0.41	.	17.3754	0.87391	0.0:1.0:0.0:0.0	.	433;466	D6RJI3;P35556	.;FBN2_HUMAN	S	466;466;433	ENSP00000262464:G466S;ENSP00000424571:G466S;ENSP00000425596:G433S	ENSP00000262464:G466S	G	-	1	0	FBN2	127756796	1.000000	0.71417	0.989000	0.46669	0.947000	0.59692	5.498000	0.66931	2.505000	0.84491	0.563000	0.77884	GGC		0.587	FBN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000371618.2	NM_001999	
PCDHB3	56132	broad.mit.edu	37	5	140481943	140481943	+	Silent	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr5:140481943G>A	ENST00000231130.2	+	1	1710	c.1710G>A	c.(1708-1710)gcG>gcA	p.A570A	AC005754.7_ENST00000607216.1_RNA	NM_018937.2	NP_061760.1	Q9Y5E6	PCDB3_HUMAN	protocadherin beta 3	570	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|cell adhesion (GO:0007155)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|endometrium(8)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(19)|lung(24)|ovary(1)|pancreas(1)|prostate(3)|skin(4)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	72			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			ACGGCTCCGCGCCCTGCACCG	0.711																																						uc003lio.2																			0				ovary(1)|pancreas(1)	2						c.(1708-1710)GCG>GCA		protocadherin beta 3 precursor							12.0	16.0	15.0					5																	140481943		2135	4184	6319	SO:0001819	synonymous_variant	56132				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to plasma membrane	calcium ion binding	g.chr5:140481943G>A	AF152496	CCDS4245.1	5q31	2010-01-26			ENSG00000113205	ENSG00000113205		"""Cadherins / Protocadherins : Clustered"""	8688	other	protocadherin		606329				10380929	Standard	NM_018937		Approved	PCDH-BETA3	uc003lio.3	Q9Y5E6	OTTHUMG00000129622	ENST00000231130.2:c.1710G>A	5.37:g.140481943G>A						uc003lin.2_5'Flank	p.A570A	NM_018937	NP_061760	Q9Y5E6	PCDB3_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		1	1710	+			570			Extracellular (Potential).|Cadherin 6.		B2R8P2	Silent	SNP	ENST00000231130.2	37	c.1710G>A	CCDS4245.1																																																																																				0.711	PCDHB3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251817.2	NM_018937	
PCDHB8	56128	broad.mit.edu	37	5	140558277	140558277	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr5:140558277C>T	ENST00000239444.2	+	1	907	c.662C>T	c.(661-663)cCg>cTg	p.P221L	PCDHB16_ENST00000361016.2_5'Flank	NM_019120.3	NP_061993.2	Q9UN66	PCDB8_HUMAN	protocadherin beta 8	221	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P221L(1)		NS(2)|breast(1)|cervix(2)|endometrium(5)|kidney(6)|large_intestine(14)|liver(1)|lung(38)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	83			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGTGGCTCTCCGCCCAGATCT	0.522																																						uc011dai.1																			1	Substitution - Missense(1)		large_intestine(1)	skin(4)	4						c.(661-663)CCG>CTG		protocadherin beta 8 precursor							104.0	135.0	125.0					5																	140558277		2203	4297	6500	SO:0001583	missense	56128				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:140558277C>T	AF152501	CCDS4250.1	5q31	2010-01-26			ENSG00000120322	ENSG00000120322		"""Cadherins / Protocadherins : Clustered"""	8693	other	protocadherin		606334				10380929	Standard	NM_019120		Approved	PCDH-BETA8, PCDH3I	uc011dai.2	Q9UN66	OTTHUMG00000129621	ENST00000239444.2:c.662C>T	5.37:g.140558277C>T	ENSP00000239444:p.Pro221Leu					PCDHB16_uc003liv.2_5'Flank	p.P221L	NM_019120	NP_061993	Q9UN66	PCDB8_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		1	848	+			221			Cadherin 2.|Extracellular (Potential).		B9EGV1	Missense_Mutation	SNP	ENST00000239444.2	37	c.662C>T	CCDS4250.1	.	.	.	.	.	.	.	.	.	.	c	13.10	2.136943	0.37728	.	.	ENSG00000120322	ENST00000239444	T	0.57436	0.4	4.25	3.36	0.38483	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.75722	0.3888	H	0.97240	3.965	0.43678	D	0.996112	D	0.60160	0.987	P	0.54401	0.751	T	0.82784	-0.0286	9	0.66056	D	0.02	.	12.0568	0.53540	0.0:0.9123:0.0:0.0877	.	221	Q9UN66	PCDB8_HUMAN	L	221	ENSP00000239444:P221L	ENSP00000239444:P221L	P	+	2	0	PCDHB8	140538461	1.000000	0.71417	0.789000	0.31954	0.150000	0.21749	4.629000	0.61290	0.740000	0.32651	0.585000	0.79938	CCG		0.522	PCDHB8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251816.2	NM_019120	
PCDHB13	56123	broad.mit.edu	37	5	140594357	140594357	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr5:140594357C>T	ENST00000341948.4	+	1	849	c.662C>T	c.(661-663)cCg>cTg	p.P221L		NM_018933.2	NP_061756.1	Q9Y5F0	PCDBD_HUMAN	protocadherin beta 13	221	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.P221L(1)		NS(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(14)|liver(4)|lung(24)|ovary(5)|pancreas(1)|skin(4)|upper_aerodigestive_tract(1)	66			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			GGTGGCTCTCCGCCCAGATCT	0.532																																						uc003lja.1																			1	Substitution - Missense(1)	p.P221L(1)	ovary(1)	skin(2)|ovary(1)	3						c.(661-663)CCG>CTG		protocadherin beta 13 precursor							97.0	104.0	102.0					5																	140594357		2203	4300	6503	SO:0001583	missense	56123				calcium-dependent cell-cell adhesion|homophilic cell adhesion|synapse assembly|synaptic transmission	integral to membrane|plasma membrane	calcium ion binding	g.chr5:140594357C>T	AF152492	CCDS4255.1	5q31	2010-01-26			ENSG00000187372	ENSG00000187372		"""Cadherins / Protocadherins : Clustered"""	8684	other	protocadherin		606339				10380929	Standard	NM_018933		Approved	PCDH-BETA13	uc003lja.1	Q9Y5F0	OTTHUMG00000129615	ENST00000341948.4:c.662C>T	5.37:g.140594357C>T	ENSP00000345491:p.Pro221Leu						p.P221L	NM_018933	NP_061756	Q9Y5F0	PCDBD_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		1	849	+			221			Cadherin 2.|Extracellular (Potential).		A8K9V6	Missense_Mutation	SNP	ENST00000341948.4	37	c.662C>T	CCDS4255.1	.	.	.	.	.	.	.	.	.	.	c	29.3	4.992937	0.93167	.	.	ENSG00000187372	ENST00000341948;ENST00000430318;ENST00000419217	T	0.00792	5.69	3.51	2.6	0.31112	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.06554	0.0168	H	0.95982	3.75	0.46478	D	0.999069	D	0.65815	0.995	D	0.71870	0.975	T	0.01162	-1.1432	9	0.66056	D	0.02	.	11.0844	0.48078	0.0:0.9018:0.0:0.0982	.	221	Q9Y5F0	PCDBD_HUMAN	L	221	ENSP00000345491:P221L	ENSP00000345491:P221L	P	+	2	0	PCDHB13	140574541	0.999000	0.42202	0.006000	0.13384	0.808000	0.45660	4.915000	0.63355	0.548000	0.28955	0.306000	0.20318	CCG		0.532	PCDHB13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251810.1	NM_018933	
PCDHGA9	56107	broad.mit.edu	37	5	140782948	140782948	+	Silent	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr5:140782948C>T	ENST00000573521.1	+	1	429	c.429C>T	c.(427-429)aaC>aaT	p.N143N	PCDHGB4_ENST00000519479.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGA5_ENST00000518069.1_Intron|PCDHGA6_ENST00000517434.1_Intron|PCDHGA8_ENST00000398604.2_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron	NM_018921.2|NM_032089.1	NP_061744.1|NP_114478.1	Q9Y5G4	PCDG9_HUMAN	protocadherin gamma subfamily A, 9	143	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|poly(A) RNA binding (GO:0044822)			endometrium(1)|kidney(1)|lung(3)	5			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			TAAAAATTAACGAAATCGCGG	0.473																																						uc003lkh.1																			0					0						c.(427-429)AAC>AAT		protocadherin gamma subfamily A, 9 isoform 1							78.0	81.0	80.0					5																	140782948		1924	4137	6061	SO:0001819	synonymous_variant	56107				homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:140782948C>T	AF152516	CCDS58981.1, CCDS75341.1	5q31	2010-01-26						"""Cadherins / Protocadherins : Clustered"""	8707	other	protocadherin		606296				10380929	Standard	NM_018921		Approved	PCDH-GAMMA-A9		Q9Y5G4		ENST00000573521.1:c.429C>T	5.37:g.140782948C>T						PCDHGA1_uc003lji.1_Intron|PCDHGA2_uc003ljk.1_Intron|PCDHGA3_uc003ljm.1_Intron|PCDHGA3_uc010jfx.1_Intron|PCDHGB1_uc003ljo.1_Intron|PCDHGA4_uc003ljq.1_Intron|PCDHGB2_uc003ljs.1_Intron|PCDHGA5_uc003lju.1_Intron|PCDHGB3_uc003ljw.1_Intron|PCDHGA6_uc003ljy.1_Intron|PCDHGA7_uc003lka.1_Intron|PCDHGB4_uc003lkc.1_Intron|PCDHGA8_uc003lkd.1_Intron|PCDHGB5_uc003lkf.1_Intron|PCDHGA9_uc011dax.1_Silent_p.N143N	p.N143N	NM_018921	NP_061744	Q9Y5G4	PCDG9_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		1	429	+			143			Extracellular (Potential).|Cadherin 2.		A2RU65|Q9Y5C9	Silent	SNP	ENST00000573521.1	37	c.429C>T	CCDS58981.1																																																																																				0.473	PCDHGA9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000437105.1	NM_018921	
AFAP1L1	134265	broad.mit.edu	37	5	148687124	148687124	+	Missense_Mutation	SNP	G	G	A	rs370079883		TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr5:148687124G>A	ENST00000296721.4	+	7	793	c.695G>A	c.(694-696)cGt>cAt	p.R232H	AFAP1L1_ENST00000522492.1_3'UTR|AFAP1L1_ENST00000515000.1_Missense_Mutation_p.R232H	NM_001146337.1|NM_152406.2	NP_001139809.1|NP_689619.1	Q8TED9	AF1L1_HUMAN	actin filament associated protein 1-like 1	232	PH 1. {ECO:0000255|PROSITE- ProRule:PRU00145}.					cell junction (GO:0030054)|cell projection (GO:0042995)|cytoplasm (GO:0005737)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|endometrium(3)|kidney(1)|large_intestine(6)|liver(1)|lung(10)|ovary(1)|pancreas(1)|skin(2)	26			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			CGGAAAAAGCGTTTCGGGCAG	0.627													G|||	1	0.000199681	0.0	0.0	5008	,	,		18661	0.0		0.0	False		,,,				2504	0.001					uc003lqh.2																			0				breast(1)|pancreas(1)	2						c.(694-696)CGT>CAT		actin filament associated protein 1-like 1		G	HIS/ARG,HIS/ARG	0,4406		0,0,2203	71.0	57.0	62.0		695,695	4.9	1.0	5		62	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	AFAP1L1	NM_001146337.1,NM_152406.2	29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging,probably-damaging	232/726,232/769	148687124	1,13005	2203	4300	6503	SO:0001583	missense	134265						protein binding	g.chr5:148687124G>A	AK094067	CCDS34274.1, CCDS54932.1	5q33.1	2013-01-10			ENSG00000157510	ENSG00000157510		"""Pleckstrin homology (PH) domain containing"""	26714	protein-coding gene	gene with protein product		614410					Standard	NM_152406		Approved	FLJ36748	uc003lqh.3	Q8TED9	OTTHUMG00000163441	ENST00000296721.4:c.695G>A	5.37:g.148687124G>A	ENSP00000296721:p.Arg232His					AFAP1L1_uc003lqg.3_Missense_Mutation_p.R232H|AFAP1L1_uc010jgy.2_Missense_Mutation_p.R232H	p.R232H	NM_152406	NP_689619	Q8TED9	AF1L1_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)		7	826	+			232			PH 1.		Q08AN4|Q08AN5|Q8IW82|Q8N8Z5|Q8N9Q4	Missense_Mutation	SNP	ENST00000296721.4	37	c.695G>A	CCDS34274.1	.	.	.	.	.	.	.	.	.	.	G	34	5.297806	0.95574	0.0	1.16E-4	ENSG00000157510	ENST00000296721;ENST00000515000	T;T	0.76060	-0.99;-0.99	4.89	4.89	0.63831	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.099859	0.64402	D	0.000001	D	0.86818	0.6024	M	0.81802	2.56	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;0.996	D	0.87103	0.2180	10	0.46703	T	0.11	-24.1694	18.243	0.89974	0.0:0.0:1.0:0.0	.	232;232;232	Q8TED9-2;Q8TED9;Q8TED9-3	.;AF1L1_HUMAN;.	H	232	ENSP00000296721:R232H;ENSP00000424427:R232H	ENSP00000296721:R232H	R	+	2	0	AFAP1L1	148667317	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	9.657000	0.98554	2.543000	0.85770	0.561000	0.74099	CGT		0.627	AFAP1L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000373443.1	NM_152406	
FAT2	2196	broad.mit.edu	37	5	150901299	150901299	+	Missense_Mutation	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr5:150901299C>T	ENST00000261800.5	-	18	10867	c.10855G>A	c.(10855-10857)Gtg>Atg	p.V3619M		NM_001447.2	NP_001438.1	Q9NYQ8	FAT2_HUMAN	FAT atypical cadherin 2	3619	Cadherin 32. {ECO:0000255|PROSITE- ProRule:PRU00043}.				epithelial cell migration (GO:0010631)|homophilic cell adhesion (GO:0007156)	cell-cell adherens junction (GO:0005913)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(6)|breast(3)|central_nervous_system(3)|cervix(5)|endometrium(15)|haematopoietic_and_lymphoid_tissue(4)|kidney(8)|large_intestine(61)|liver(1)|lung(60)|ovary(6)|prostate(5)|skin(5)|stomach(2)|upper_aerodigestive_tract(11)|urinary_tract(1)	196		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)			ACATGCCACACGTACACATGG	0.627																																						uc003lue.3																			0				ovary(4)|upper_aerodigestive_tract(1)|skin(1)	6						c.(10855-10857)GTG>ATG		FAT tumor suppressor 2 precursor							47.0	36.0	40.0					5																	150901299		2203	4300	6503	SO:0001583	missense	2196				epithelial cell migration|homophilic cell adhesion	cell-cell adherens junction|integral to membrane|nucleus	calcium ion binding	g.chr5:150901299C>T	AF231022	CCDS4317.1	5q33.1	2014-07-21	2013-05-31		ENSG00000086570	ENSG00000086570		"""Cadherins / Cadherin-related"""	3596	protein-coding gene	gene with protein product	"""cadherin-related family member 9"""	604269	"""FAT tumor suppressor (Drosophila) homolog 2"", ""FAT tumor suppressor homolog 2 (Drosophila)"""			9693030	Standard	NM_001447		Approved	MEGF1, CDHF8, HFAT2, CDHR9	uc003lue.4	Q9NYQ8	OTTHUMG00000130126	ENST00000261800.5:c.10855G>A	5.37:g.150901299C>T	ENSP00000261800:p.Val3619Met					GM2A_uc011dcs.1_Intron|FAT2_uc003lud.3_Missense_Mutation_p.V312M	p.V3619M	NM_001447	NP_001438	Q9NYQ8	FAT2_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.000785)|Kidney(363;0.00101)		18	10868	-		Medulloblastoma(196;0.0912)|all_hematologic(541;0.104)	3619			Cadherin 32.|Extracellular (Potential).		O75091|Q9NSR7	Missense_Mutation	SNP	ENST00000261800.5	37	c.10855G>A	CCDS4317.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.12|19.12	3.765010|3.765010	0.69878|0.69878	.|.	.|.	ENSG00000086570|ENSG00000086570	ENST00000520200|ENST00000261800	.|T	.|0.60171	.|0.21	5.95|5.95	5.95|5.95	0.96441|0.96441	.|Cadherin (3);Cadherin-like (1);	.|0.000000	.|0.56097	.|D	.|0.000035	T|T	0.69762|0.69762	0.3147|0.3147	M|M	0.86502|0.86502	2.82|2.82	0.54753|0.54753	D|D	0.999985|0.999985	.|D;D	.|0.69078	.|0.994;0.997	.|P;P	.|0.51453	.|0.67;0.646	T|T	0.75249|0.75249	-0.3384|-0.3384	5|10	.|0.66056	.|D	.|0.02	.|.	10.6917|10.6917	0.45875|0.45875	0.0:0.8589:0.0:0.1411|0.0:0.8589:0.0:0.1411	.|.	.|3619;810	.|Q9NYQ8;E9PDJ8	.|FAT2_HUMAN;.	H|M	477|3619	.|ENSP00000261800:V3619M	.|ENSP00000261800:V3619M	R|V	-|-	2|1	0|0	FAT2|FAT2	150881492|150881492	0.954000|0.954000	0.32549|0.32549	0.982000|0.982000	0.44146|0.44146	0.639000|0.639000	0.38242|0.38242	2.144000|2.144000	0.42197|0.42197	2.826000|2.826000	0.97356|0.97356	0.563000|0.563000	0.77884|0.77884	CGT|GTG		0.627	FAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252434.1	NM_001447	
MDN1	23195	broad.mit.edu	37	6	90387330	90387330	+	Silent	SNP	G	G	A	rs116003199		TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr6:90387330G>A	ENST00000369393.3	-	76	12613	c.12498C>T	c.(12496-12498)agC>agT	p.S4166S	MDN1_ENST00000428876.1_Silent_p.S4166S|RP1-122O8.7_ENST00000438877.1_RNA			Q9NU22	MDN1_HUMAN	MDN1, midasin homolog (yeast)	4166					ATP catabolic process (GO:0006200)|protein complex assembly (GO:0006461)	cytoplasm (GO:0005737)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|unfolded protein binding (GO:0051082)			NS(1)|breast(13)|central_nervous_system(2)|cervix(3)|endometrium(22)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(52)|liver(1)|lung(83)|ovary(10)|pancreas(1)|prostate(10)|skin(6)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(2)	218		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)		BRCA - Breast invasive adenocarcinoma(108;0.0193)		TGGACAATGCGCTCTGGAGAT	0.423													G|||	1	0.000199681	0.0008	0.0	5008	,	,		20697	0.0		0.0	False		,,,				2504	0.0					uc003pnn.1																			0				ovary(8)|skin(2)	10						c.(12496-12498)AGC>AGT		MDN1, midasin homolog		G		0,4406		0,0,2203	148.0	144.0	145.0		12498	-3.0	0.4	6	dbSNP_132	145	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous	MDN1	NM_014611.1		0,1,6502	AA,AG,GG		0.0116,0.0,0.0077		4166/5597	90387330	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	23195				protein complex assembly|regulation of protein complex assembly	nucleus	ATP binding|ATPase activity|unfolded protein binding	g.chr6:90387330G>A	AF503925	CCDS5024.1	6q15	2014-01-28			ENSG00000112159	ENSG00000112159			18302	protein-coding gene	gene with protein product						9205841, 12102729	Standard	XM_005248699		Approved	KIAA0301	uc003pnn.1	Q9NU22	OTTHUMG00000015213	ENST00000369393.3:c.12498C>T	6.37:g.90387330G>A							p.S4166S	NM_014611	NP_055426	Q9NU22	MDN1_HUMAN		BRCA - Breast invasive adenocarcinoma(108;0.0193)	76	12614	-		all_cancers(76;1.47e-06)|Acute lymphoblastic leukemia(125;2.23e-10)|Prostate(29;5.55e-10)|all_hematologic(105;2.42e-06)|all_epithelial(107;0.00246)	4166					O15019|Q5T794	Silent	SNP	ENST00000369393.3	37	c.12498C>T	CCDS5024.1																																																																																				0.423	MDN1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041514.2		
ASCC3	10973	broad.mit.edu	37	6	101248186	101248186	+	Missense_Mutation	SNP	G	G	A	rs371905084		TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr6:101248186G>A	ENST00000369162.2	-	6	1461	c.1117C>T	c.(1117-1119)Cgg>Tgg	p.R373W	ASCC3_ENST00000522650.1_Missense_Mutation_p.R373W	NM_006828.2	NP_006819.2	Q8N3C0	ASCC3_HUMAN	activating signal cointegrator 1 complex subunit 3	373					cell proliferation (GO:0008283)|DNA dealkylation involved in DNA repair (GO:0006307)|DNA duplex unwinding (GO:0032508)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)	ATP binding (GO:0005524)|ATP-dependent 3'-5' DNA helicase activity (GO:0043140)|poly(A) RNA binding (GO:0044822)	p.R373W(1)		breast(4)|central_nervous_system(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(20)|liver(1)|lung(36)|ovary(6)|prostate(4)|skin(3)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	92		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)		CTTTGTATCCGCAATTCCTTA	0.348																																						uc003pqk.2																			1	Substitution - Missense(1)		kidney(1)	ovary(5)|skin(1)	6						c.(1117-1119)CGG>TGG		activating signal cointegrator 1 complex subunit		G	TRP/ARG	1,4405	2.1+/-5.4	0,1,2202	119.0	117.0	118.0		1117	-2.6	0.5	6		118	0,8600		0,0,4300	no	missense	ASCC3	NM_006828.2	101	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	373/2203	101248186	1,13005	2203	4300	6503	SO:0001583	missense	10973				regulation of transcription, DNA-dependent|transcription, DNA-dependent	cytoplasm|microtubule cytoskeleton	ATP binding|ATP-dependent helicase activity|nucleic acid binding	g.chr6:101248186G>A	AJ223948	CCDS5046.1, CCDS5047.1, CCDS75497.1	6q16	2008-02-05		2004-07-28	ENSG00000112249	ENSG00000112249			18697	protein-coding gene	gene with protein product	"""RNA helicase family"""	614217	"""helicase, ATP binding 1"""	HELIC1		10218103	Standard	NM_006828		Approved	RNAH, ASC1p200, dJ121G13.4, dJ467N11.1	uc003pqk.3	Q8N3C0	OTTHUMG00000015279	ENST00000369162.2:c.1117C>T	6.37:g.101248186G>A	ENSP00000358159:p.Arg373Trp					ASCC3_uc011eai.1_Missense_Mutation_p.R275W|ASCC3_uc003pql.2_Missense_Mutation_p.R373W	p.R373W	NM_006828	NP_006819	Q8N3C0	HELC1_HUMAN		BRCA - Breast invasive adenocarcinoma(108;0.0539)|all cancers(137;0.103)|GBM - Glioblastoma multiforme(226;0.199)	6	1446	-		all_cancers(76;1.45e-07)|Acute lymphoblastic leukemia(125;4.99e-11)|all_hematologic(75;5.82e-08)|all_epithelial(87;0.00149)|Hepatocellular(1;0.0893)|Colorectal(196;0.13)	373					E7EW23|O43738|Q4G1A0|Q5VTN2|Q9H1I9|Q9H5A2|Q9NTR0	Missense_Mutation	SNP	ENST00000369162.2	37	c.1117C>T	CCDS5046.1	.	.	.	.	.	.	.	.	.	.	G	16.15	3.041379	0.55003	2.27E-4	0.0	ENSG00000112249	ENST00000369162;ENST00000522650	T;T	0.61627	0.29;0.09	5.51	-2.59	0.06209	.	0.066271	0.64402	D	0.000020	T	0.64170	0.2574	M	0.69823	2.125	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.71414	0.973;0.958	T	0.73075	-0.4097	10	0.49607	T	0.09	.	18.3564	0.90358	0.0:0.0:0.3701:0.6299	.	373;373	E7EW23;Q8N3C0	.;HELC1_HUMAN	W	373	ENSP00000358159:R373W;ENSP00000430769:R373W	ENSP00000358159:R373W	R	-	1	2	ASCC3	101354907	0.988000	0.35896	0.515000	0.27774	0.665000	0.39181	0.223000	0.17719	-0.294000	0.08973	-0.310000	0.09108	CGG		0.348	ASCC3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041632.2	NM_006828	
TMEM200A	114801	broad.mit.edu	37	6	130762663	130762663	+	Missense_Mutation	SNP	G	G	A	rs140251464		TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr6:130762663G>A	ENST00000296978.3	+	3	1967	c.1096G>A	c.(1096-1098)Gga>Aga	p.G366R	TMEM200A_ENST00000392429.1_Missense_Mutation_p.G366R|TMEM200A_ENST00000545622.1_Missense_Mutation_p.G366R	NM_001258276.1|NM_001258277.1|NM_001258278.1	NP_001245205.1|NP_001245206.1|NP_001245207.1	Q86VY9	T200A_HUMAN	transmembrane protein 200A	366						integral component of membrane (GO:0016021)				NS(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(30)|ovary(1)|prostate(4)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52				GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)		TATGGCTCTCGGACCTGGGGC	0.522													G|||	1	0.000199681	0.0	0.0	5008	,	,		19445	0.0		0.0	False		,,,				2504	0.001					uc003qca.2																			0				ovary(1)	1						c.(1096-1098)GGA>AGA		transmembrane protein 200A		G	ARG/GLY	1,4405		0,1,2202	76.0	77.0	77.0		1096	5.0	0.8	6	dbSNP_134	77	0,8600		0,0,4300	no	missense	TMEM200A	NM_052913.2	125	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	probably-damaging	366/492	130762663	1,13005	2203	4300	6503	SO:0001583	missense	114801					integral to membrane		g.chr6:130762663G>A	AB067500	CCDS5140.1	6q23.1	2009-09-04	2007-12-18	2007-12-18	ENSG00000164484	ENSG00000164484			21075	protein-coding gene	gene with protein product			"""KIAA1913"""	KIAA1913		15722956	Standard	NM_001258276		Approved	TTMC	uc010kfh.4	Q86VY9	OTTHUMG00000015557	ENST00000296978.3:c.1096G>A	6.37:g.130762663G>A	ENSP00000296978:p.Gly366Arg					TMEM200A_uc010kfh.2_Missense_Mutation_p.G366R|TMEM200A_uc010kfi.2_Missense_Mutation_p.G366R|TMEM200A_uc003qcb.2_Missense_Mutation_p.G366R	p.G366R	NM_052913	NP_443145	Q86VY9	T200A_HUMAN		GBM - Glioblastoma multiforme(226;0.0139)|OV - Ovarian serous cystadenocarcinoma(155;0.12)	3	1967	+			366			Cytoplasmic (Potential).		Q96PX5	Missense_Mutation	SNP	ENST00000296978.3	37	c.1096G>A	CCDS5140.1	.	.	.	.	.	.	.	.	.	.	G	9.325	1.059107	0.19987	2.27E-4	0.0	ENSG00000164484	ENST00000296978;ENST00000545622;ENST00000392429	.	.	.	5.84	4.97	0.65823	.	0.142252	0.45606	N	0.000343	T	0.37156	0.0993	L	0.32530	0.975	0.41890	D	0.99036	D	0.62365	0.991	P	0.50270	0.636	T	0.14200	-1.0481	9	0.25106	T	0.35	-9.1951	15.2363	0.73432	0.0675:0.0:0.9325:0.0	.	366	Q86VY9	T200A_HUMAN	R	366	.	ENSP00000296978:G366R	G	+	1	0	TMEM200A	130804356	1.000000	0.71417	0.751000	0.31187	0.068000	0.16541	5.485000	0.66850	1.481000	0.48307	-0.122000	0.15005	GGA		0.522	TMEM200A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042201.1	NM_052913	
EGFR	1956	broad.mit.edu	37	7	55249010	55249011	+	In_Frame_Ins	INS	-	-	ACAACCCCC			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr7:55249010_55249011insACAACCCCC	ENST00000275493.2	+	20	2485_2486	c.2308_2309insACAACCCCC	c.(2308-2310)gac>gACAACCCCCac	p.773_774insNPH	EGFR_ENST00000454757.2_In_Frame_Ins_p.720_721insNPH|EGFR_ENST00000455089.1_In_Frame_Ins_p.728_729insNPH|EGFR-AS1_ENST00000442411.1_RNA|EGFR_ENST00000442591.1_Intron	NM_005228.3	NP_005219.2	P00533	EGFR_HUMAN	epidermal growth factor receptor	773	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of phospholipase A2 activity by calcium-mediated signaling (GO:0043006)|activation of phospholipase C activity (GO:0007202)|alkanesulfonate metabolic process (GO:0019694)|astrocyte activation (GO:0048143)|axon guidance (GO:0007411)|cell proliferation (GO:0008283)|cell surface receptor signaling pathway (GO:0007166)|cellular response to amino acid stimulus (GO:0071230)|cellular response to dexamethasone stimulus (GO:0071549)|cellular response to drug (GO:0035690)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to estradiol stimulus (GO:0071392)|cellular response to mechanical stimulus (GO:0071260)|cerebral cortex cell migration (GO:0021795)|circadian rhythm (GO:0007623)|digestive tract morphogenesis (GO:0048546)|diterpenoid metabolic process (GO:0016101)|embryonic placenta development (GO:0001892)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|hair follicle development (GO:0001942)|hydrogen peroxide metabolic process (GO:0042743)|innate immune response (GO:0045087)|learning or memory (GO:0007611)|liver development (GO:0001889)|lung development (GO:0030324)|magnesium ion homeostasis (GO:0010960)|MAPK cascade (GO:0000165)|morphogenesis of an epithelial fold (GO:0060571)|negative regulation of apoptotic process (GO:0043066)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of mitotic cell cycle (GO:0045930)|negative regulation of protein catabolic process (GO:0042177)|neurotrophin TRK receptor signaling pathway (GO:0048011)|ossification (GO:0001503)|ovulation cycle (GO:0042698)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol-mediated signaling (GO:0048015)|polysaccharide metabolic process (GO:0005976)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cyclin-dependent protein serine/threonine kinase activity involved in G1/S transition of mitotic cell cycle (GO:0031659)|positive regulation of DNA repair (GO:0045739)|positive regulation of DNA replication (GO:0045740)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of fibroblast proliferation (GO:0048146)|positive regulation of inflammatory response (GO:0050729)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of phosphorylation (GO:0042327)|positive regulation of protein kinase B signaling (GO:0051897)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of smooth muscle cell proliferation (GO:0048661)|positive regulation of superoxide anion generation (GO:0032930)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of vasoconstriction (GO:0045907)|positive regulation of vasodilation (GO:0045909)|protein autophosphorylation (GO:0046777)|protein insertion into membrane (GO:0051205)|regulation of nitric-oxide synthase activity (GO:0050999)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|response to calcium ion (GO:0051592)|response to cobalamin (GO:0033590)|response to hydroxyisoflavone (GO:0033594)|response to osmotic stress (GO:0006970)|response to oxidative stress (GO:0006979)|response to stress (GO:0006950)|response to UV-A (GO:0070141)|salivary gland morphogenesis (GO:0007435)|signal transduction (GO:0007165)|single organismal cell-cell adhesion (GO:0016337)|tongue development (GO:0043586)|translation (GO:0006412)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|endosome membrane (GO:0010008)|extracellular space (GO:0005615)|focal adhesion (GO:0005925)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|membrane raft (GO:0045121)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|Shc-EGFR complex (GO:0070435)	actin filament binding (GO:0051015)|ATP binding (GO:0005524)|chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|enzyme binding (GO:0019899)|epidermal growth factor-activated receptor activity (GO:0005006)|identical protein binding (GO:0042802)|MAP kinase kinase kinase activity (GO:0004709)|protein heterodimerization activity (GO:0046982)|protein phosphatase binding (GO:0019903)|protein tyrosine kinase activity (GO:0004713)|receptor signaling protein tyrosine kinase activity (GO:0004716)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|transmembrane signaling receptor activity (GO:0004888)|ubiquitin protein ligase binding (GO:0031625)	p.V769_D770insASV(14)|p.D770>GY(3)|p.V769_D770insGVV(3)|p.D770N(2)|p.V769_D770insMASVD(2)|p.D770_N771>AGG(1)|p.V769_D770insCV(1)|p.V769_D770insGSV(1)|p.D770_N771insDG(1)|p.V769_D770insDNV(1)|p.D770fs*61(1)|p.D770_P772>ASVDNR(1)		NS(2)|adrenal_gland(5)|biliary_tract(8)|bone(3)|breast(18)|central_nervous_system(106)|endometrium(26)|eye(3)|haematopoietic_and_lymphoid_tissue(9)|kidney(11)|large_intestine(85)|liver(2)|lung(13575)|oesophagus(21)|ovary(38)|pancreas(3)|peritoneum(11)|pleura(2)|prostate(35)|salivary_gland(11)|skin(9)|small_intestine(1)|soft_tissue(4)|stomach(41)|thymus(2)|thyroid(14)|upper_aerodigestive_tract(59)|urinary_tract(6)	14110	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		Afatinib(DB08916)|Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)|Vandetanib(DB05294)	GGCCAGCGTGGACAACCCCCAC	0.649		8	"""A, O, Mis"""		"""glioma, NSCLC"""	NSCLC			Lung Cancer, Familial Clustering of	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)																												uc003tqk.2		8	yes	Dom	yes	Familial lung cancer	7	7p12.3-p12.1	1956	A|O|Mis	"""epidermal growth factor receptor (erythroblastic leukemia viral (v-erb-b) oncogene homolog, avian)"""			"""E, O"""		NSCLC	glioma|NSCLC		31	Insertion - In frame(23)|Complex - insertion inframe(5)|Substitution - Missense(2)|Insertion - Frameshift(1)	p.H773_V774insNPH(12)|p.V769_D770insASV(12)|p.P772_H773insPR(11)|p.H773R(9)|p.H773_V774insPH(3)|p.H773_V774insH(3)|p.P772_H773insYNP(2)|p.P772_H773insX(2)|p.D770>GY(2)|p.H773Y(2)|p.V769_D770insMASVD(2)|p.V769_D770insGVV(2)|p.H773_V774insGH(1)|p.V769_D770insCV(1)|p.H773_V774insG(1)|p.D770N(1)|p.H773_V774insGNPH(1)|p.D770fs*61(1)|p.D770_P772>ASVDNR(1)|p.H773L(1)|p.V769_D770insGSV(1)|p.V769_D770insDNV(1)|p.P772_H773insDHP(1)|p.P772_H773insTHP(1)|p.P772_H773insDNP(1)|p.H773>NPY(1)|p.P772_H773insQV(1)|p.D770_N771insDG(1)|p.H773_V774>LM(1)|p.D770_N771>AGG(1)	lung(31)	lung(9213)|central_nervous_system(103)|stomach(41)|upper_aerodigestive_tract(39)|prostate(32)|ovary(31)|thyroid(24)|breast(11)|peritoneum(9)|oesophagus(9)|salivary_gland(9)|large_intestine(8)|kidney(8)|urinary_tract(6)|skin(5)|adrenal_gland(5)|soft_tissue(4)|bone(3)|NS(2)|pancreas(2)|haematopoietic_and_lymphoid_tissue(2)|thymus(2)|liver(2)|eye(1)	9571						c.(2308-2310)GAC>GACAACCCCCAC		epidermal growth factor receptor isoform a	Cetuximab(DB00002)|Erlotinib(DB00530)|Gefitinib(DB00317)|Lapatinib(DB01259)|Lidocaine(DB00281)|Panitumumab(DB01269)|Trastuzumab(DB00072)																																			SO:0001652	inframe_insertion	1956	Lung_Cancer_Familial_Clustering_of	Familial Cancer Database	incl. Hereditary Lung cancer, Hereditary Non-Small Cell Lung cancer	activation of phospholipase A2 activity by calcium-mediated signaling|activation of phospholipase C activity|axon guidance|cell proliferation|cell-cell adhesion|negative regulation of apoptosis|negative regulation of epidermal growth factor receptor signaling pathway|ossification|positive regulation of catenin import into nucleus|positive regulation of cell migration|positive regulation of cyclin-dependent protein kinase activity involved in G1/S|positive regulation of epithelial cell proliferation|positive regulation of MAP kinase activity|positive regulation of nitric oxide biosynthetic process|positive regulation of phosphorylation|positive regulation of protein kinase B signaling cascade|protein autophosphorylation|protein insertion into membrane|regulation of nitric-oxide synthase activity|regulation of peptidyl-tyrosine phosphorylation|response to stress|response to UV-A	basolateral plasma membrane|endoplasmic reticulum membrane|endosome|extracellular space|Golgi membrane|integral to membrane|nuclear membrane|Shc-EGFR complex	actin filament binding|ATP binding|double-stranded DNA binding|epidermal growth factor receptor activity|identical protein binding|MAP/ERK kinase kinase activity|protein heterodimerization activity|protein phosphatase binding|receptor signaling protein tyrosine kinase activity	g.chr7:55249010_55249011insACAACCCCC		CCDS5514.1, CCDS5515.1, CCDS5516.1, CCDS47587.1	7p12	2014-09-17	2010-06-25		ENSG00000146648	ENSG00000146648			3236	protein-coding gene	gene with protein product	"""erythroblastic leukemia viral (v-erb-b) oncogene homolog (avian)"""	131550	"""epidermal growth factor receptor (avian erythroblastic leukemia viral (v-erb-b) oncogene homolog)"""	ERBB		1505215	Standard	NM_201282		Approved	ERBB1	uc003tqk.3	P00533	OTTHUMG00000023661	ENST00000275493.2:c.2309_2317dupACAACCCCC	7.37:g.55249011_55249019dupACAACCCCC	ENSP00000275493:p.Asn771_His773dup	TCGA GBM(3;<1E-08)|TSP Lung(4;<1E-08)				EGFR_uc010kzg.1_In_Frame_Ins_p.728_729insNPH|EGFR_uc011kco.1_In_Frame_Ins_p.720_721insNPH|uc003tqo.2_RNA	p.773_774insNPH	NM_005228	NP_005219	P00533	EGFR_HUMAN	GBM - Glioblastoma multiforme(1;0)|all cancers(1;2.19e-314)|Lung(13;4.65e-05)|LUSC - Lung squamous cell carcinoma(13;0.000168)|STAD - Stomach adenocarcinoma(5;0.00164)|Epithelial(13;0.0607)		20	2554_2555	+	all_cancers(1;1.57e-46)|all_epithelial(1;5.62e-37)|Lung NSC(1;9.29e-25)|all_lung(1;4.39e-23)|Esophageal squamous(2;7.55e-08)|Breast(14;0.0318)		773_774			Cytoplasmic (Potential).|Protein kinase.		O00688|O00732|P06268|Q14225|Q68GS5|Q92795|Q9BZS2|Q9GZX1|Q9H2C9|Q9H3C9|Q9UMD7|Q9UMD8|Q9UMG5	In_Frame_Ins	INS	ENST00000275493.2	37	c.2308_2309insACAACCCCC	CCDS5514.1																																																																																				0.649	EGFR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251456.2	NM_005228	
KEL	3792	broad.mit.edu	37	7	142649600	142649600	+	Missense_Mutation	SNP	G	G	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr7:142649600G>T	ENST00000355265.2	-	10	1673	c.1199C>A	c.(1198-1200)cCc>cAc	p.P400H	KEL_ENST00000479768.2_5'UTR	NM_000420.2	NP_000411.1	P23276	KELL_HUMAN	Kell blood group, metallo-endopeptidase	400					vasoconstriction (GO:0042310)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	metal ion binding (GO:0046872)|metalloendopeptidase activity (GO:0004222)			central_nervous_system(1)|endometrium(3)|kidney(5)|large_intestine(11)|lung(34)|ovary(3)|prostate(2)|skin(1)	60	Melanoma(164;0.059)					CCTCACCATGGGTGGTTGCTC	0.552																																						uc003wcb.2																			0				ovary(3)|central_nervous_system(1)	4						c.(1198-1200)CCC>CAC		Kell blood group, metallo-endopeptidase							136.0	117.0	123.0					7																	142649600		2203	4300	6503	SO:0001583	missense	3792				proteolysis|vasoconstriction	integral to membrane|plasma membrane	metal ion binding|metalloendopeptidase activity|protein binding	g.chr7:142649600G>T	BC003135	CCDS34766.1	7q33	2014-07-19	2006-10-10		ENSG00000197993	ENSG00000197993		"""CD molecules"", ""Blood group antigens"""	6308	protein-coding gene	gene with protein product		613883	"""Kell blood group"", ""Kell blood group, metalloendopeptidase"""			1712490, 7683930	Standard	NM_000420		Approved	ECE3, CD238	uc003wcb.3	P23276	OTTHUMG00000157159	ENST00000355265.2:c.1199C>A	7.37:g.142649600G>T	ENSP00000347409:p.Pro400His						p.P400H	NM_000420	NP_000411	P23276	KELL_HUMAN			10	1409	-	Melanoma(164;0.059)		400			Extracellular (Potential).		B2RBV4|Q96RS8|Q99885	Missense_Mutation	SNP	ENST00000355265.2	37	c.1199C>A	CCDS34766.1	.	.	.	.	.	.	.	.	.	.	G	15.49	2.847855	0.51164	.	.	ENSG00000197993	ENST00000355265	T	0.76316	-1.01	5.28	3.49	0.39957	Peptidase M13 (1);	0.421699	0.20516	N	0.090787	D	0.83050	0.5170	M	0.65975	2.015	0.18873	N	0.999984	D	0.69078	0.997	D	0.63113	0.911	T	0.73206	-0.4056	10	0.87932	D	0	0.0028	7.7676	0.28988	0.1849:0.0:0.8151:0.0	.	400	P23276	KELL_HUMAN	H	400	ENSP00000347409:P400H	ENSP00000347409:P400H	P	-	2	0	KEL	142359722	0.058000	0.20735	0.272000	0.24630	0.912000	0.54170	1.067000	0.30616	0.813000	0.34350	-0.140000	0.14226	CCC		0.552	KEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347671.2	NM_000420	
AOC1	26	broad.mit.edu	37	7	150558187	150558187	+	Missense_Mutation	SNP	G	G	A	rs199683372		TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr7:150558187G>A	ENST00000493429.1	+	7	2730	c.2146G>A	c.(2146-2148)Gtg>Atg	p.V716M	AOC1_ENST00000416793.2_Missense_Mutation_p.V735M|AOC1_ENST00000467291.1_Missense_Mutation_p.V716M|AOC1_ENST00000480582.1_3'UTR|AOC1_ENST00000360937.4_Missense_Mutation_p.V716M			P19801	AOC1_HUMAN	amine oxidase, copper containing 1	716					amine metabolic process (GO:0009308)|cellular response to azide (GO:0097185)|cellular response to copper ion (GO:0071280)|cellular response to copper ion starvation (GO:0035874)|cellular response to heparin (GO:0071504)|cellular response to histamine (GO:0071420)|oxidation-reduction process (GO:0055114)|response to antibiotic (GO:0046677)|response to drug (GO:0042493)|sodium ion transmembrane transport (GO:0035725)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|peroxisome (GO:0005777)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	calcium ion binding (GO:0005509)|cation channel activity (GO:0005261)|copper ion binding (GO:0005507)|diamine oxidase activity (GO:0052597)|drug binding (GO:0008144)|heparin binding (GO:0008201)|histamine oxidase activity (GO:0052598)|methylputrescine oxidase activity (GO:0052599)|primary amine oxidase activity (GO:0008131)|propane-1,3-diamine oxidase activity (GO:0052600)|protein complex binding (GO:0032403)|protein homodimerization activity (GO:0042803)|quinone binding (GO:0048038)|receptor activity (GO:0004872)|sodium channel activity (GO:0005272)|zinc ion binding (GO:0008270)									Amiloride(DB00594)	CACTGTGATCGTGTGGCCTCG	0.602																																						uc003why.1																			0				ovary(2)|breast(2)|skin(2)	6						c.(2146-2148)GTG>ATG		amiloride binding protein 1 precursor	Amiloride(DB00594)|Spermine(DB00127)	G	MET/VAL	1,4093		0,1,2046	62.0	71.0	68.0		2146	4.0	1.0	7		68	2,8380		0,2,4189	yes	missense	ABP1	NM_001091.2	21	0,3,6235	AA,AG,GG		0.0239,0.0244,0.024	probably-damaging	716/752	150558187	3,12473	2047	4191	6238	SO:0001583	missense	26				amine metabolic process	extracellular space|peroxisome	copper ion binding|diamine oxidase activity|heparin binding|histamine oxidase activity|methylputrescine oxidase activity|primary amine oxidase activity|propane-1,3-diamine oxidase activity|quinone binding	g.chr7:150558187G>A	AK092514	CCDS43679.1, CCDS64797.1	7q36.1	2013-06-19	2013-06-19	2013-06-19	ENSG00000002726	ENSG00000002726	1.4.3.22		80	protein-coding gene	gene with protein product	"""diamine oxidase"""	104610	"""amiloride binding protein 1 (amine oxidase (copper-containing))"""	ABP1		8182053	Standard	NM_001091		Approved	DAO	uc003wia.2	P19801	OTTHUMG00000158306	ENST00000493429.1:c.2146G>A	7.37:g.150558187G>A	ENSP00000418614:p.Val716Met					ABP1_uc003whz.1_Missense_Mutation_p.V716M|ABP1_uc003wia.1_Missense_Mutation_p.V735M	p.V716M	NM_001091	NP_001082	P19801	ABP1_HUMAN	OV - Ovarian serous cystadenocarcinoma(82;0.0121)	UCEC - Uterine corpus endometrioid carcinoma (81;0.168)	6	6364	+	all_neural(206;0.219)		716					C9J690|Q16683|Q16684|Q56II4|Q6GU42	Missense_Mutation	SNP	ENST00000493429.1	37	c.2146G>A	CCDS43679.1	.	.	.	.	.	.	.	.	.	.	G	19.28	3.797451	0.70567	2.44E-4	2.39E-4	ENSG00000002726	ENST00000493429;ENST00000467291;ENST00000360937;ENST00000416793;ENST00000437714	T;T;T;T	0.03860	3.78;3.78;3.78;3.78	4.84	3.96	0.45880	Copper amine oxidase, C-terminal (1);	0.000000	0.64402	D	0.000001	T	0.07999	0.0200	N	0.08118	0	0.46499	D	0.999075	D;D	0.89917	1.0;1.0	D;D	0.83275	0.97;0.996	T	0.43032	-0.9416	10	0.62326	D	0.03	-8.12	10.8758	0.46911	0.093:0.0:0.907:0.0	.	735;716	C9J690;P19801	.;ABP1_HUMAN	M	716;716;716;735;592	ENSP00000418614:V716M;ENSP00000418328:V716M;ENSP00000354193:V716M;ENSP00000411613:V735M	ENSP00000354193:V716M	V	+	1	0	ABP1	150189120	1.000000	0.71417	0.979000	0.43373	0.895000	0.52256	5.017000	0.64047	1.038000	0.40049	0.305000	0.20034	GTG		0.602	AOC1-009	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350628.1	NM_001091	
DOCK5	80005	broad.mit.edu	37	8	25225732	25225732	+	Silent	SNP	C	C	T			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chr8:25225732C>T	ENST00000276440.7	+	32	3293	c.3249C>T	c.(3247-3249)atC>atT	p.I1083I		NM_024940.6	NP_079216.4	Q9H7D0	DOCK5_HUMAN	dedicator of cytokinesis 5	1083					positive regulation of GTPase activity (GO:0043547)|small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)	guanyl-nucleotide exchange factor activity (GO:0005085)			NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|kidney(9)|large_intestine(13)|lung(20)|ovary(3)|prostate(1)|skin(4)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	72		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)		GAAAGGAAATCGGCTTTAGAA	0.413																																					Pancreas(145;34 1887 3271 10937 30165)	uc003xeg.2																			0				ovary(3)	3						c.(3247-3249)ATC>ATT		dedicator of cytokinesis 5							97.0	84.0	88.0					8																	25225732		2203	4300	6503	SO:0001819	synonymous_variant	80005					cytoplasm	GTP binding|GTPase binding|guanyl-nucleotide exchange factor activity	g.chr8:25225732C>T		CCDS6047.1	8p21.2	2009-04-17			ENSG00000147459	ENSG00000147459			23476	protein-coding gene	gene with protein product						12432077	Standard	NM_024940		Approved	FLJ21034	uc003xeg.3	Q9H7D0	OTTHUMG00000131991	ENST00000276440.7:c.3249C>T	8.37:g.25225732C>T						DOCK5_uc010luf.1_RNA|DOCK5_uc003xeh.1_Silent_p.I797I|DOCK5_uc003xei.2_Silent_p.I653I|DOCK5_uc003xej.2_RNA	p.I1083I	NM_024940	NP_079216	Q9H7D0	DOCK5_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (27;0.0267)|Epithelial(17;1.07e-11)|Colorectal(74;0.0276)|COAD - Colon adenocarcinoma(73;0.0828)	32	3386	+		all_cancers(63;0.0361)|Ovarian(32;0.000711)|all_epithelial(46;0.0153)|Hepatocellular(4;0.115)|Prostate(55;0.13)|Breast(100;0.143)	1083					B2RNY0|Q5XKD5|Q6AI11|Q6PJS6|Q6ZTS6	Silent	SNP	ENST00000276440.7	37	c.3249C>T	CCDS6047.1	.	.	.	.	.	.	.	.	.	.	C	10.08	1.251147	0.22880	.	.	ENSG00000147459	ENST00000444569	.	.	.	5.75	0.769	0.18492	.	.	.	.	.	T	0.58836	0.2150	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.53056	-0.8492	4	.	.	.	.	10.8677	0.46864	0.0:0.5468:0.0:0.4532	.	.	.	.	W	855	.	.	R	+	1	2	DOCK5	25281649	0.206000	0.23470	0.998000	0.56505	0.920000	0.55202	-0.427000	0.06999	0.075000	0.16796	-0.140000	0.14226	CGG		0.413	DOCK5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254955.2	NM_024940	
AFF2	2334	broad.mit.edu	37	X	148072810	148072810	+	Missense_Mutation	SNP	G	G	A			TCGA-06-0879-01A-01W-0424-08	TCGA-06-0879-10A-01W-0424-08								Untested	Somatic	Phase_I	Capture	none			Illumina GAIIx	f96b8966-e0c2-4fb6-b3f6-e76d7953d537	d7f78904-a226-488c-aff8-cbbd2d13882d	g.chrX:148072810G>A	ENST00000370460.2	+	21	4363	c.3884G>A	c.(3883-3885)cGc>cAc	p.R1295H	AFF2_ENST00000286437.5_Missense_Mutation_p.R936H|AFF2_ENST00000342251.3_Missense_Mutation_p.R1262H|AFF2_ENST00000370457.5_Missense_Mutation_p.R1260H	NM_001169123.1|NM_002025.3	NP_001162594.1|NP_002016.2	P51816	AFF2_HUMAN	AF4/FMR2 family, member 2	1295					brain development (GO:0007420)|learning or memory (GO:0007611)|mRNA processing (GO:0006397)|regulation of RNA splicing (GO:0043484)|RNA splicing (GO:0008380)	nuclear speck (GO:0016607)	G-quadruplex RNA binding (GO:0002151)			breast(5)|central_nervous_system(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(29)|liver(2)|lung(39)|ovary(4)|pancreas(5)|prostate(1)|skin(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	109	Acute lymphoblastic leukemia(192;6.56e-05)					AATCTTGTCCGCTACGTTCGC	0.527																																						uc004fcp.2																			0				ovary(3)|pancreas(2)	5						c.(3883-3885)CGC>CAC		fragile X mental retardation 2							244.0	167.0	193.0					X																	148072810		2203	4300	6503	SO:0001583	missense	2334				brain development|mRNA processing|regulation of RNA splicing|RNA splicing	nuclear speck	G-quadruplex RNA binding|protein binding	g.chrX:148072810G>A	U48436	CCDS14684.1, CCDS55521.1, CCDS76040.1	Xq28	2008-02-05	2005-06-27	2005-06-27	ENSG00000155966	ENSG00000155966			3776	protein-coding gene	gene with protein product		300806	"""fragile X mental retardation 2"""	FMR2			Standard	NM_002025		Approved	FRAXE	uc004fcp.3	P51816	OTTHUMG00000022613	ENST00000370460.2:c.3884G>A	X.37:g.148072810G>A	ENSP00000359489:p.Arg1295His					AFF2_uc004fcq.2_Missense_Mutation_p.R1285H|AFF2_uc004fcr.2_Missense_Mutation_p.R1256H|AFF2_uc011mxb.1_Missense_Mutation_p.R1260H|AFF2_uc004fcs.2_Missense_Mutation_p.R1260H|AFF2_uc011mxc.1_Missense_Mutation_p.R936H	p.R1295H	NM_002025	NP_002016	P51816	AFF2_HUMAN			21	4363	+	Acute lymphoblastic leukemia(192;6.56e-05)		1295					A2RTY4|B4DXD5|B7WNQ1|B7ZLD6|B7ZLD9|O43786|O60215|P78407|Q13521|Q14323|Q7Z2F7|Q7Z400|Q9UNA5	Missense_Mutation	SNP	ENST00000370460.2	37	c.3884G>A	CCDS14684.1	.	.	.	.	.	.	.	.	.	.	G	24.0	4.486606	0.84854	.	.	ENSG00000155966	ENST00000370460;ENST00000370457;ENST00000342251;ENST00000286437	T;T;T;T	0.64438	-0.1;-0.1;-0.1;-0.1	5.47	5.47	0.80525	.	0.000000	0.64402	D	0.000001	T	0.71685	0.3369	L	0.41356	1.27	0.80722	D	1	B;D;D;D;D;D	0.89917	0.195;1.0;0.999;1.0;1.0;1.0	B;D;D;D;D;D	0.91635	0.2;0.997;0.995;0.998;0.998;0.999	T	0.66184	-0.5987	10	0.18710	T	0.47	.	18.3933	0.90490	0.0:0.0:1.0:0.0	.	936;1260;1260;1256;1285;1295	B4DXD5;P51816-6;P51816-3;P51816-2;P51816-5;P51816	.;.;.;.;.;AFF2_HUMAN	H	1295;1260;1262;936	ENSP00000359489:R1295H;ENSP00000359486:R1260H;ENSP00000345459:R1262H;ENSP00000286437:R936H	ENSP00000286437:R936H	R	+	2	0	AFF2	147880516	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	6.629000	0.74267	2.283000	0.76528	0.600000	0.82982	CGC		0.527	AFF2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000058673.2	NM_002025	
