#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_Mutation_Status	i_OREGANNO_ID	i_OREGANNO_Values	i_ORegAnno_bin	i_Other_Transcripts	i_Protein_Change	i_Refseq_mRNA_Id	i_Refseq_prot_Id	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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	i_t_alt_count_full	i_t_ref_count_full	isArtifactMode	oxoGCut	pox	pox_cutoff	qox	t_alt_count	t_ref_count	validation_alt_allele	validation_method	validation_status	validation_tumor_sample
RP11-146E13.4	0	broad.mit.edu	37	14	19857036	19857036	+	lincRNA	SNP	A	A	G	rs374719458		TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr14:19857036A>G	ENST00000548109.1	+	0	72																											CTGGATAATAAAGTTCATCTC	0.373																																						ENST00000548109.1																			0																																																			0							g.chr14:19857036A>G																													14.37:g.19857036A>G			Somatic								WXS	Illumina GAIIx	Phase_I					0	72	+									RNA	SNP	ENST00000548109.1	37																																																																																						0.373	RP11-146E13.4-001	KNOWN	basic	lincRNA	lincRNA	OTTHUMT00000409408.1			3	89	0	0	0	1	0	3	89				
APEH	327	broad.mit.edu	37	3	49716365	49716365	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr3:49716365G>A	ENST00000296456.5	+	12	1541	c.1141G>A	c.(1141-1143)Gct>Act	p.A381T	APEH_ENST00000438011.1_Missense_Mutation_p.A381T	NM_001640.3	NP_001631.3	P13798	ACPH_HUMAN	acylaminoacyl-peptide hydrolase	381					beta-amyloid metabolic process (GO:0050435)|proteolysis (GO:0006508)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|nuclear membrane (GO:0031965)	omega peptidase activity (GO:0008242)|poly(A) RNA binding (GO:0044822)|serine-type endopeptidase activity (GO:0004252)			endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15				BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)		CTTTGACTCGGCTCAGCGCAG	0.607																																						ENST00000296456.5																			0				endometrium(3)|large_intestine(1)|lung(6)|ovary(1)|skin(1)|stomach(2)|urinary_tract(1)	15						c.(1141-1143)Gct>Act		acylaminoacyl-peptide hydrolase							77.0	72.0	74.0					3																	49716365		2203	4300	6503	SO:0001583	missense	327				proteolysis	cytoplasm|nuclear membrane	serine-type endopeptidase activity	g.chr3:49716365G>A	D38441	CCDS2801.1	3p21	2013-05-29	2013-05-29		ENSG00000164062	ENSG00000164062	3.4.19.1		586	protein-coding gene	gene with protein product	"""acylaminoacyl-peptidase"""	102645	"""N-acylaminoacyl-peptide hydrolase"""	D3F15S2, DNF15S2, D3S48E		2392324	Standard	NM_001640		Approved		uc003cxf.3	P13798	OTTHUMG00000156882	ENST00000296456.5:c.1141G>A	3.37:g.49716365G>A	ENSP00000296456:p.Ala381Thr		Somatic				APEH_ENST00000438011.1_Missense_Mutation_p.A381T	p.A381T	NM_001640.3	NP_001631.3	WXS	Illumina GAIIx	Phase_I	P13798	ACPH_HUMAN		BRCA - Breast invasive adenocarcinoma(193;4.53e-05)|Kidney(197;0.00218)|KIRC - Kidney renal clear cell carcinoma(197;0.00244)	12	1541	+			381					Q9BQ33|Q9P0Y2	Missense_Mutation	SNP	ENST00000296456.5	37	c.1141G>A	CCDS2801.1	.	.	.	.	.	.	.	.	.	.	G	15.57	2.871281	0.51695	.	.	ENSG00000164062	ENST00000296456;ENST00000442186;ENST00000438011	T;T	0.43294	0.95;0.95	5.62	4.72	0.59763	Six-bladed beta-propeller, TolB-like (1);Peptidase S9A/B/C, oligopeptidase, N-terminal beta-propeller (1);	0.405904	0.28322	N	0.015780	T	0.38427	0.1040	L	0.56280	1.765	0.31060	N	0.714217	B;B	0.18968	0.032;0.014	B;B	0.19946	0.027;0.017	T	0.38650	-0.9651	10	0.12766	T	0.61	-24.1998	15.3547	0.74418	0.0:0.2638:0.7362:0.0	.	381;381	C9JIF9;P13798	.;ACPH_HUMAN	T	381;306;381	ENSP00000296456:A381T;ENSP00000415862:A381T	ENSP00000296456:A381T	A	+	1	0	APEH	49691369	0.220000	0.23631	0.766000	0.31476	0.910000	0.53928	1.111000	0.31159	1.306000	0.44926	0.561000	0.74099	GCT		0.607	APEH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000346415.2			4	66	0	0	0	1	0	4	66				
OTUD4	54726	broad.mit.edu	37	4	146059006	146059006	+	Missense_Mutation	SNP	G	G	A	rs558808115		TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr4:146059006G>A	ENST00000447906.2	-	21	3108	c.2921C>T	c.(2920-2922)aCt>aTt	p.T974I	OTUD4_ENST00000455611.2_Intron|OTUD4_ENST00000454497.2_Missense_Mutation_p.T909I			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	974					protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					AACAGGCACAGTTTCTCTCTC	0.463																																						ENST00000454497.2																			0				breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33						c.(2725-2727)aCt>aTt		OTU domain containing 4							128.0	133.0	131.0					4																	146059006		2203	4300	6503	SO:0001583	missense	54726						protein binding	g.chr4:146059006G>A		CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"""OTU domain containing"""	24949	protein-coding gene	gene with protein product		611744	"""OTU domain containing 4"""			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.2921C>T	4.37:g.146059006G>A	ENSP00000395487:p.Thr974Ile		Somatic				OTUD4_ENST00000455611.2_Intron|OTUD4_ENST00000447906.2_Missense_Mutation_p.T974I	p.T909I	NM_001102653.1	NP_001096123.1	WXS	Illumina GAIIx	Phase_I	Q01804	OTUD4_HUMAN			21	2863	-	all_hematologic(180;0.151)		973					B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Missense_Mutation	SNP	ENST00000447906.2	37	c.2726C>T		.	.	.	.	.	.	.	.	.	.	G	13.28	2.191504	0.38707	.	.	ENSG00000164164	ENST00000454497;ENST00000447906	T;T	0.34275	1.37;1.37	6.17	5.33	0.75918	.	1.059000	0.07258	N	0.867023	T	0.32793	0.0841	N	0.24115	0.695	0.80722	D	1	B;B	0.13145	0.007;0.004	B;B	0.14023	0.01;0.004	T	0.02275	-1.1184	10	0.59425	D	0.04	-0.3286	15.5098	0.75772	0.0658:0.0:0.9342:0.0	.	974;973	G3V0I6;Q01804	.;OTUD4_HUMAN	I	909;974	ENSP00000409279:T909I;ENSP00000395487:T974I	ENSP00000395487:T974I	T	-	2	0	OTUD4	146278456	0.027000	0.19231	0.108000	0.21378	0.880000	0.50808	2.210000	0.42816	1.621000	0.50320	0.655000	0.94253	ACT		0.463	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000365117.2	NM_017493		4	119	0	0	0	1	0	4	119				
OR52M1	119772	broad.mit.edu	37	11	4567078	4567078	+	Missense_Mutation	SNP	T	T	C			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr11:4567078T>C	ENST00000360213.1	+	1	658	c.658T>C	c.(658-660)Tcc>Ccc	p.S220P		NM_001004137.1	NP_001004137.1	Q8NGK5	O52M1_HUMAN	olfactory receptor, family 52, subfamily M, member 1	220						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)		TATTGCTGCATCCTATGTGAT	0.522																																						ENST00000360213.1																			0				endometrium(2)|large_intestine(2)|lung(9)|pancreas(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	18						c.(658-660)Tcc>Ccc		olfactory receptor, family 52, subfamily M, member 1							263.0	247.0	252.0					11																	4567078		2201	4298	6499	SO:0001583	missense	119772				sensory perception of smell	integral to membrane|plasma membrane	olfactory receptor activity	g.chr11:4567078T>C	AB065789	CCDS31353.1	11p15.4	2012-08-09	2002-11-13	2002-11-15	ENSG00000197790	ENSG00000197790		"""GPCR / Class A : Olfactory receptors"""	15225	protein-coding gene	gene with protein product			"""olfactory receptor, family 52, subfamily M, member 1 pseudogene"""	OR52M1P			Standard	NM_001004137		Approved		uc010qyf.2	Q8NGK5	OTTHUMG00000165706	ENST00000360213.1:c.658T>C	11.37:g.4567078T>C	ENSP00000353343:p.Ser220Pro		Somatic					p.S220P	NM_001004137.1	NP_001004137.1	WXS	Illumina GAIIx	Phase_I	Q8NGK5	O52M1_HUMAN		Epithelial(150;8.45e-12)|BRCA - Breast invasive adenocarcinoma(625;0.0285)|LUSC - Lung squamous cell carcinoma(625;0.19)	1	658	+		Medulloblastoma(188;0.0075)|Breast(177;0.0461)|all_neural(188;0.0577)	220						Missense_Mutation	SNP	ENST00000360213.1	37	c.658T>C	CCDS31353.1	.	.	.	.	.	.	.	.	.	.	T	15.74	2.922553	0.52653	.	.	ENSG00000197790	ENST00000360213	T	0.46819	0.86	5.01	5.01	0.66863	GPCR, rhodopsin-like superfamily (1);	0.000000	0.47093	D	0.000258	T	0.78130	0.4235	H	0.97516	4.02	0.25075	N	0.990962	D	0.69078	0.997	D	0.67231	0.95	T	0.76713	-0.2858	10	0.87932	D	0	.	13.9773	0.64282	0.0:0.0:0.0:1.0	.	220	Q8NGK5	O52M1_HUMAN	P	220	ENSP00000353343:S220P	ENSP00000353343:S220P	S	+	1	0	OR52M1	4523654	0.957000	0.32711	0.969000	0.41365	0.789000	0.44602	3.065000	0.49994	2.233000	0.73108	0.528000	0.53228	TCC		0.522	OR52M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385847.1	NM_001004137		4	141	0	0	0	1	0	4	141				
RABL6	55684	broad.mit.edu	37	9	139734309	139734309	+	Missense_Mutation	SNP	G	G	C			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr9:139734309G>C	ENST00000311502.7	+	13	2158	c.1922G>C	c.(1921-1923)aGt>aCt	p.S641T	RABL6_ENST00000371663.4_Missense_Mutation_p.S642T|RABL6_ENST00000371675.3_Missense_Mutation_p.S526T|RABL6_ENST00000357466.2_Intron|RABL6_ENST00000432842.2_3'UTR			Q3YEC7	RABL6_HUMAN	RAB, member RAS oncogene family-like 6	641					small GTPase mediated signal transduction (GO:0007264)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTP binding (GO:0005525)										AAGGAGAGCAGTGAGGAAGGT	0.682																																						ENST00000371675.3																			0											c.(1576-1578)aGt>aCt		RAB, member RAS oncogene family-like 6							18.0	23.0	22.0					9																	139734309		1961	4127	6088	SO:0001583	missense	55684							g.chr9:139734309G>C	AK094382	CCDS48058.1, CCDS55352.1, CCDS55353.1	9q34.3	2012-06-28	2012-06-28	2012-06-28	ENSG00000196642	ENSG00000196642			24703	protein-coding gene	gene with protein product	"""Rab-like protein 1"", ""partner of ARF"""	610615	"""chromosome 9 open reading frame 86"""	C9orf86		14702039, 16582619, 17962191, 19433581	Standard	NM_024718		Approved	FLJ10101, FLJ13045, pp8875, bA216L13.9, Parf, RBEL1	uc004cjj.1	Q3YEC7	OTTHUMG00000020947	ENST00000311502.7:c.1922G>C	9.37:g.139734309G>C	ENSP00000311134:p.Ser641Thr		Somatic				RABL6_ENST00000357466.2_Intron|RABL6_ENST00000371663.4_Missense_Mutation_p.S642T|RABL6_ENST00000311502.7_Missense_Mutation_p.S641T|RABL6_ENST00000432842.2_3'UTR	p.S526T			WXS	Illumina GAIIx	Phase_I					13	2462	+								A8QVZ7|A8QVZ8|C6K8I4|C6K8I5|Q4F968|Q5T5R7|Q8IWK1|Q8TCL4|Q8WU94|Q96SR8|Q9BU21|Q9H935	Missense_Mutation	SNP	ENST00000311502.7	37	c.1577G>C	CCDS48058.1	.	.	.	.	.	.	.	.	.	.	.	11.74	1.728562	0.30593	.	.	ENSG00000196642	ENST00000371663;ENST00000311502;ENST00000371675;ENST00000435930	T;T;T;T	0.73152	-0.61;-0.63;-0.62;-0.72	4.72	4.72	0.59763	.	0.338891	0.33127	N	0.005251	T	0.78635	0.4314	M	0.71581	2.175	0.46298	D	0.998971	D;D;P	0.71674	0.998;0.965;0.941	D;P;P	0.63703	0.917;0.655;0.453	T	0.77135	-0.2699	10	0.33940	T	0.23	-14.0842	8.9208	0.35610	0.1028:0.0:0.8972:0.0	.	435;642;641	B1AMX5;Q3YEC7-2;Q3YEC7	.;.;PARF_HUMAN	T	642;641;526;435	ENSP00000360727:S642T;ENSP00000311134:S641T;ENSP00000360740:S526T;ENSP00000408442:S435T	ENSP00000311134:S641T	S	+	2	0	C9orf86	138854130	1.000000	0.71417	0.169000	0.22859	0.034000	0.12701	6.146000	0.71777	2.162000	0.67917	0.561000	0.74099	AGT		0.682	RABL6-009	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000055141.4	NM_024718		10	4	0	0	0	1	0	10	4				
PYROXD2	84795	broad.mit.edu	37	10	100147057	100147057	+	Silent	SNP	A	A	G			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr10:100147057A>G	ENST00000370575.4	-	14	1503	c.1455T>C	c.(1453-1455)gaT>gaC	p.D485D	PYROXD2_ENST00000483923.1_5'UTR	NM_032709.2	NP_116098.2	Q8N2H3	PYRD2_HUMAN	pyridine nucleotide-disulphide oxidoreductase domain 2	485							oxidoreductase activity (GO:0016491)			central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						CCTCGATGCAATCAAACACTG	0.483																																						ENST00000370575.4																			0				central_nervous_system(1)|endometrium(2)|large_intestine(4)|lung(3)|prostate(1)|upper_aerodigestive_tract(1)	12						c.(1453-1455)gaT>gaC		pyridine nucleotide-disulphide oxidoreductase domain 2							91.0	86.0	88.0					10																	100147057		2203	4300	6503	SO:0001819	synonymous_variant	84795						oxidoreductase activity	g.chr10:100147057A>G	AK074429	CCDS7474.1	10q24.2	2009-04-22	2009-04-22	2009-04-22	ENSG00000119943	ENSG00000119943			23517	protein-coding gene	gene with protein product			"""chromosome 10 open reading frame 33"""	C10orf33			Standard	NM_032709		Approved	FLJ23849	uc001kpc.3	Q8N2H3	OTTHUMG00000018877	ENST00000370575.4:c.1455T>C	10.37:g.100147057A>G			Somatic				PYROXD2_ENST00000483923.1_5'UTR	p.D485D	NM_032709.2	NP_116098.2	WXS	Illumina GAIIx	Phase_I	Q8N2H3	PYRD2_HUMAN			14	1503	-			485					D3DR61|Q5TAA9|Q9BRQ1	Silent	SNP	ENST00000370575.4	37	c.1455T>C	CCDS7474.1																																																																																				0.483	PYROXD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000049782.2	NM_032709		16	22	0	0	0	1	0	16	22				
GNA11	2767	broad.mit.edu	37	19	3118942	3118942	+	Missense_Mutation	SNP	A	A	T			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr19:3118942A>T	ENST00000078429.4	+	5	868	c.626A>T	c.(625-627)cAg>cTg	p.Q209L	GNA11_ENST00000586180.1_3'UTR|AC005262.3_ENST00000587701.1_RNA|AC005262.2_ENST00000585980.1_RNA	NM_002067.2	NP_002058.2	P29992	GNA11_HUMAN	guanine nucleotide binding protein (G protein), alpha 11 (Gq class)	209					action potential (GO:0001508)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|blood coagulation (GO:0007596)|cellular response to pH (GO:0071467)|developmental pigmentation (GO:0048066)|heart development (GO:0007507)|phospholipase C-activating dopamine receptor signaling pathway (GO:0060158)|platelet activation (GO:0030168)|regulation of melanocyte differentiation (GO:0045634)|signal transduction (GO:0007165)|skeletal system development (GO:0001501)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|heterotrimeric G-protein complex (GO:0005834)|lysosomal membrane (GO:0005765)|plasma membrane (GO:0005886)	G-protein beta/gamma-subunit complex binding (GO:0031683)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|metal ion binding (GO:0046872)|signal transducer activity (GO:0004871)|type 2A serotonin receptor binding (GO:0031826)	p.Q209L(80)|p.Q209P(2)		endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)		GTGGGGGGCCAGCGGTCGGAG	0.612			Mis		uveal melanoma																																	ENST00000078429.4				Dom	yes		19	19p13.3	2767	Mis	"""guanine nucleotide binding protein (G protein), alpha 11 (Gq class)"""			E			uveal melanoma		82	Substitution - Missense(82)	p.Q209L(80)|p.Q209P(2)	eye(69)|skin(8)|meninges(5)	endometrium(2)|eye(132)|kidney(1)|large_intestine(2)|lung(1)|meninges(5)|ovary(1)|prostate(1)|skin(16)	161						c.(625-627)cAg>cTg		guanine nucleotide binding protein (G protein), alpha 11 (Gq class)							104.0	89.0	94.0					19																	3118942		2203	4300	6503	SO:0001583	missense	2767				activation of phospholipase C activity by dopamine receptor signaling pathway|G-protein signaling, coupled to cAMP nucleotide second messenger|platelet activation|protein ADP-ribosylation|regulation of action potential	cytoplasm|heterotrimeric G-protein complex	G-protein beta/gamma-subunit complex binding|G-protein-coupled receptor binding|GTP binding|GTPase activity|signal transducer activity	g.chr19:3118942A>T	AF493900	CCDS12103.1	19p13.3	2014-02-04			ENSG00000088256	ENSG00000088256			4379	protein-coding gene	gene with protein product		139313	"""hypocalciuric hypercalcemia 2"""	HHC2		1302014, 23802516	Standard	NM_002067		Approved	FBH, FBH2, FHH2	uc002lxd.3	P29992	OTTHUMG00000180631	ENST00000078429.4:c.626A>T	19.37:g.3118942A>T	ENSP00000078429:p.Gln209Leu		Somatic				AC005262.3_ENST00000587701.1_RNA|GNA11_ENST00000586180.1_3'UTR	p.Q209L	NM_002067.2	NP_002058.2	WXS	Illumina GAIIx	Phase_I	P29992	GNA11_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (162;6.79e-05)|OV - Ovarian serous cystadenocarcinoma(105;2.68e-113)|Epithelial(107;1.22e-111)|all cancers(105;5.78e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00141)|STAD - Stomach adenocarcinoma(1328;0.181)	5	868	+		Hepatocellular(1079;0.137)	209					O15109|Q14350|Q6IB00	Missense_Mutation	SNP	ENST00000078429.4	37	c.626A>T	CCDS12103.1	.	.	.	.	.	.	.	.	.	.	.	15.05	2.718086	0.48622	.	.	ENSG00000088256	ENST00000078429	D	0.91237	-2.81	3.26	3.26	0.37387	.	0.000000	0.64402	U	0.000006	D	0.96950	0.9004	H	0.99357	4.53	0.80722	D	1	D	0.59767	0.986	D	0.68483	0.958	D	0.96823	0.9605	10	0.87932	D	0	.	10.7338	0.46113	1.0:0.0:0.0:0.0	.	209	P29992	GNA11_HUMAN	L	209	ENSP00000078429:Q209L	ENSP00000078429:Q209L	Q	+	2	0	GNA11	3069942	1.000000	0.71417	0.438000	0.26821	0.027000	0.11550	9.104000	0.94239	1.256000	0.44068	0.379000	0.24179	CAG		0.612	GNA11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452261.2	NM_002067		25	33	0	0	0	1	0	25	33				
NDUFA5	4698	broad.mit.edu	37	7	123190629	123190629	+	Silent	SNP	T	T	A	rs371230838		TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr7:123190629T>A	ENST00000355749.2	-	3	537	c.78A>T	c.(76-78)atA>atT	p.I26I	NDUFA5_ENST00000471770.1_Silent_p.I26I|NDUFA5_ENST00000467117.1_5'UTR	NM_001282419.1|NM_005000.2	NP_001269348.1|NP_004991.1	Q16718	NDUA5_HUMAN	NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5	26					cellular metabolic process (GO:0044237)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex I (GO:0005747)	NADH dehydrogenase (ubiquinone) activity (GO:0008137)			large_intestine(1)|urinary_tract(1)	2						TTGTGTACAATATTCTTAGCC	0.318																																						ENST00000471770.1																			0				large_intestine(1)|urinary_tract(1)	2						c.(76-78)atA>atT		NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5	NADH(DB00157)						76.0	83.0	81.0					7																	123190629		2202	4299	6501	SO:0001819	synonymous_variant	4698				mitochondrial electron transport, NADH to ubiquinone|transport	mitochondrial respiratory chain complex I	NADH dehydrogenase (ubiquinone) activity	g.chr7:123190629T>A		CCDS5788.1, CCDS64760.1, CCDS75655.1, CCDS75656.1	7q31.33	2013-06-19	2013-06-19		ENSG00000128609	ENSG00000128609		"""Mitochondrial respiratory chain complex / Complex I"""	7688	protein-coding gene	gene with protein product	"""complex I 13kDa subunit B"", ""ubiquinone reductase"", ""type I dehydrogenase"", ""NADH-ubiquinone oxidoreductase 13 kDa-B subunit"""	601677	"""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5 (13kD, B13)"", ""NADH dehydrogenase (ubiquinone) 1 alpha subcomplex, 5, 13kDa"""			9763677, 9021153	Standard	XM_005250371		Approved	B13, NUFM, CI-13KD-B, UQOR13, CI-13kB	uc003vks.3	Q16718	OTTHUMG00000157348	ENST00000355749.2:c.78A>T	7.37:g.123190629T>A			Somatic				NDUFA5_ENST00000355749.2_Silent_p.I26I|NDUFA5_ENST00000467117.1_5'UTR	p.I26I	NM_001282419.1|NM_001282420.1|NM_001282421.1	NP_001269348.1|NP_001269349.1|NP_001269350.1	WXS	Illumina GAIIx	Phase_I	Q16718	NDUA5_HUMAN			3	212	-			26					B2RD98|Q5H9R2|Q6IRX7	Silent	SNP	ENST00000355749.2	37	c.78A>T	CCDS5788.1	.	.	.	.	.	.	.	.	.	.	T	7.828	0.719297	0.15372	.	.	ENSG00000128609	ENST00000378795	.	.	.	5.54	4.35	0.52113	.	.	.	.	.	T	0.64724	0.2624	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.63812	-0.6552	5	0.46703	T	0.11	.	11.0704	0.47999	0.1393:0.0:0.0:0.8607	.	.	.	.	F	22	.	ENSP00000368072:I22F	I	-	1	0	NDUFA5	122977865	1.000000	0.71417	0.262000	0.24481	0.710000	0.40934	1.396000	0.34531	0.972000	0.38314	0.533000	0.62120	ATT		0.318	NDUFA5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348533.1	NM_005000		6	55	0	0	0	1	0	6	55				
BLOC1S6	26258	broad.mit.edu	37	15	45884472	45884472	+	Silent	SNP	C	C	T			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr15:45884472C>T	ENST00000220531.3	+	2	543	c.222C>T	c.(220-222)ctC>ctT	p.L74L	BLOC1S6_ENST00000567461.1_Intron|RP11-96O20.4_ENST00000564080.1_Intron|BLOC1S6_ENST00000567740.1_Intron|BLOC1S6_ENST00000562384.1_Intron|BLOC1S6_ENST00000565216.1_Intron|BLOC1S6_ENST00000565409.1_5'UTR|BLOC1S6_ENST00000564765.1_5'UTR|Y_RNA_ENST00000363549.1_RNA|BLOC1S6_ENST00000566753.1_Silent_p.L74L|BLOC1S6_ENST00000565323.1_Silent_p.L79L|BLOC1S6_ENST00000568816.1_5'UTR	NM_012388.2	NP_036520.1	Q9UL45	BL1S6_HUMAN	biogenesis of lysosomal organelles complex-1, subunit 6, pallidin	74					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|blood coagulation (GO:0007596)|endosome to melanosome transport (GO:0035646)|melanocyte differentiation (GO:0030318)|melanosome organization (GO:0032438)|melanosome transport (GO:0032402)|membrane fusion (GO:0061025)|membrane organization (GO:0061024)|neuron projection development (GO:0031175)|positive regulation of natural killer cell activation (GO:0032816)|positive regulation of pigment cell differentiation (GO:0050942)|post-Golgi vesicle-mediated transport (GO:0006892)|secretion of lysosomal enzymes (GO:0033299)|synaptic vesicle docking involved in exocytosis (GO:0016081)	BLOC-1 complex (GO:0031083)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extrinsic component of membrane (GO:0019898)|transport vesicle (GO:0030133)	actin filament binding (GO:0051015)|identical protein binding (GO:0042802)|protein homodimerization activity (GO:0042803)|syntaxin binding (GO:0019905)										TCCAGGAACTCACGTAAGCTA	0.363																																						ENST00000220531.3																			0											c.(220-222)ctC>ctT		biogenesis of lysosomal organelles complex-1, subunit 6, pallidin							80.0	81.0	80.0					15																	45884472		2198	4298	6496	SO:0001819	synonymous_variant	26258							g.chr15:45884472C>T	AF080470	CCDS10126.1	15q21.1	2013-09-27	2012-08-07	2012-08-01	ENSG00000104164	ENSG00000104164		"""Biogenesis of lysosomal organelles complex-1 subunits"""	8549	protein-coding gene	gene with protein product		604310	"""pallid (mouse) homolog, pallidin"", ""pallidin homolog (mouse)"""	PA, PLDN		10610180	Standard	NM_012388		Approved	HPS9	uc001zvq.3	Q9UL45	OTTHUMG00000131477	ENST00000220531.3:c.222C>T	15.37:g.45884472C>T			Somatic				BLOC1S6_ENST00000568816.1_5'UTR|BLOC1S6_ENST00000565323.1_Silent_p.L79L|BLOC1S6_ENST00000562384.1_Intron|RP11-96O20.4_ENST00000564080.1_Intron|BLOC1S6_ENST00000566753.1_Silent_p.L74L|BLOC1S6_ENST00000567461.1_Intron|BLOC1S6_ENST00000565216.1_Intron|BLOC1S6_ENST00000567740.1_Intron|BLOC1S6_ENST00000565409.1_5'UTR|BLOC1S6_ENST00000564765.1_5'UTR	p.L74L	NM_012388.2	NP_036520.1	WXS	Illumina GAIIx	Phase_I					2	543	+									Silent	SNP	ENST00000220531.3	37	c.222C>T	CCDS10126.1																																																																																				0.363	BLOC1S6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254320.2	NM_012388		21	25	0	0	0	1	0	21	25				
NBPF1	55672	broad.mit.edu	37	1	16918653	16918653	+	Splice_Site	SNP	C	C	T			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr1:16918653C>T	ENST00000430580.2	-	6	853		c.e6+1			NM_017940.3	NP_060410.2	Q3BBV0	NBPF1_HUMAN	neuroblastoma breakpoint family, member 1							cytoplasm (GO:0005737)									UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)		TCTTAACTTACTGTTGTGAAA	0.418																																						ENST00000430580.2																			0											c.e6+1		neuroblastoma breakpoint family, member 1																																				SO:0001630	splice_region_variant	55672					cytoplasm		g.chr1:16918653C>T	AB051480		1p36.13	2013-01-30			ENSG00000219481	ENSG00000219481		"""neuroblastoma breakpoint family"""	26088	protein-coding gene	gene with protein product		610501				11214970, 16079250	Standard	NM_017940		Approved	FLJ20719, KIAA1693	uc001ayw.4	Q3BBV0	OTTHUMG00000002487	ENST00000430580.2:c.34+1G>A	1.37:g.16918653C>T			Somatic						NM_017940.3	NP_060410.2	WXS	Illumina GAIIx	Phase_I	Q3BBV0	NBPF1_HUMAN		UCEC - Uterine corpus endometrioid carcinoma (279;0.00459)|BRCA - Breast invasive adenocarcinoma(304;7.52e-06)|COAD - Colon adenocarcinoma(227;1.05e-05)|Kidney(64;0.00016)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.179)	6	853	-								Q8N4E8|Q9C0H0	Splice_Site	SNP	ENST00000430580.2	37																																																																																						0.418	NBPF1-005	NOVEL	upstream_uORF|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000106436.3	NM_017940	Intron	4	42	0	0	0	1	0	4	42				
RAB3GAP2	25782	broad.mit.edu	37	1	220364491	220364491	+	Missense_Mutation	SNP	G	G	A	rs151225064	byFrequency	TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr1:220364491G>A	ENST00000358951.2	-	14	1522	c.1406C>T	c.(1405-1407)gCg>gTg	p.A469V		NM_012414.3	NP_036546.2	Q9H2M9	RBGPR_HUMAN	RAB3 GTPase activating protein subunit 2 (non-catalytic)	469					establishment of protein localization to endoplasmic reticulum membrane (GO:0097051)|intracellular protein transport (GO:0006886)|positive regulation of catalytic activity (GO:0043085)|positive regulation of endoplasmic reticulum tubular network organization (GO:1903373)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rab GTPase activity (GO:0032851)|regulation of GTPase activity (GO:0043087)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)|protein complex (GO:0043234)	enzyme activator activity (GO:0008047)|enzyme regulator activity (GO:0030234)|GTPase activator activity (GO:0005096)|protein heterodimerization activity (GO:0046982)|Rab GTPase binding (GO:0017137)	p.A469V(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39				GBM - Glioblastoma multiforme(131;0.0443)		CCTTCTTGGCGCATAGATCAC	0.493																																						ENST00000358951.2																			1	Substitution - Missense(1)	p.A469V(1)	prostate(1)	breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(8)|lung(13)|ovary(1)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(1)	39						c.(1405-1407)gCg>gTg		RAB3 GTPase activating protein subunit 2 (non-catalytic)		G	VAL/ALA	0,4406		0,0,2203	137.0	134.0	135.0		1406	5.7	0.9	1	dbSNP_134	135	2,8598	2.2+/-6.3	0,2,4298	no	missense	RAB3GAP2	NM_012414.3	64	0,2,6501	AA,AG,GG		0.0233,0.0,0.0154	probably-damaging	469/1394	220364491	2,13004	2203	4300	6503	SO:0001583	missense	25782				intracellular protein transport	cytoplasm|soluble fraction	GTPase activator activity|protein heterodimerization activity	g.chr1:220364491G>A	AB020646	CCDS31028.1	1q41	2014-03-03			ENSG00000118873	ENSG00000118873			17168	protein-coding gene	gene with protein product		609275				15696165, 16532399, 24482476	Standard	NM_012414		Approved	RAB3-GAP150, KIAA0839, DKFZP434D245, SPG69	uc010puk.1	Q9H2M9	OTTHUMG00000037139	ENST00000358951.2:c.1406C>T	1.37:g.220364491G>A	ENSP00000351832:p.Ala469Val		Somatic					p.A469V	NM_012414.3	NP_036546.2	WXS	Illumina GAIIx	Phase_I	Q9H2M9	RBGPR_HUMAN		GBM - Glioblastoma multiforme(131;0.0443)	14	1522	-			469					A6H8V0|O75872|Q9HAB0|Q9UFJ7|Q9UQ15	Missense_Mutation	SNP	ENST00000358951.2	37	c.1406C>T	CCDS31028.1	.	.	.	.	.	.	.	.	.	.	G	35	5.508939	0.96386	0.0	2.33E-4	ENSG00000118873	ENST00000358951	D	0.90444	-2.67	5.65	5.65	0.86999	.	0.000000	0.85682	D	0.000000	D	0.94925	0.8359	M	0.65975	2.015	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.94568	0.7768	10	0.56958	D	0.05	.	19.7176	0.96129	0.0:0.0:1.0:0.0	.	469	Q9H2M9	RBGPR_HUMAN	V	469	ENSP00000351832:A469V	ENSP00000351832:A469V	A	-	2	0	RAB3GAP2	218431114	1.000000	0.71417	0.907000	0.35723	0.936000	0.57629	9.090000	0.94144	2.670000	0.90874	0.563000	0.77884	GCG		0.493	RAB3GAP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090205.2	NM_012414		5	129	0	0	0	1	0	5	129				
PCDHB7	56129	broad.mit.edu	37	5	140554267	140554267	+	Silent	SNP	G	G	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr5:140554267G>A	ENST00000231137.3	+	1	2025	c.1851G>A	c.(1849-1851)gtG>gtA	p.V617V		NM_018940.2	NP_061763.1	Q9Y5E2	PCDB7_HUMAN	protocadherin beta 7	617	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			TATTCGGCGTGTGGGCGCACA	0.677																																						ENST00000231137.3																			0				NS(2)|breast(2)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(20)|lung(54)|ovary(5)|prostate(7)|skin(7)|upper_aerodigestive_tract(4)|urinary_tract(1)	119						c.(1849-1851)gtG>gtA									33.0	50.0	44.0					5																	140554267		2163	4261	6424	SO:0001819	synonymous_variant	0				calcium-dependent cell-cell adhesion|homophilic cell adhesion	integral to membrane|plasma membrane	calcium ion binding	g.chr5:140554267G>A	AF152500	CCDS4249.1	5q31	2010-01-26			ENSG00000113212	ENSG00000113212		"""Cadherins / Protocadherins : Clustered"""	8692	other	protocadherin		606333				10380929	Standard	NM_018940		Approved	PCDH-BETA7	uc003lit.3	Q9Y5E2	OTTHUMG00000129608	ENST00000231137.3:c.1851G>A	5.37:g.140554267G>A			Somatic					p.V617V	NM_018940.2	NP_061763.1	WXS	Illumina GAIIx	Phase_I	Q9Y5E2	PCDB7_HUMAN	KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)		1	2025	+			617			Cadherin 6.		A1L3Y8	Silent	SNP	ENST00000231137.3	37	c.1851G>A	CCDS4249.1																																																																																				0.677	PCDHB7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251803.2	NM_018940		23	105	0	0	0	1	0	23	105				
CSMD3	114788	broad.mit.edu	37	8	113694820	113694820	+	Missense_Mutation	SNP	G	G	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr8:113694820G>A	ENST00000297405.5	-	16	2772	c.2528C>T	c.(2527-2529)gCa>gTa	p.A843V	CSMD3_ENST00000455883.2_Missense_Mutation_p.A739V|CSMD3_ENST00000352409.3_Missense_Mutation_p.A843V|CSMD3_ENST00000343508.3_Missense_Mutation_p.A803V	NM_198123.1	NP_937756.1	Q7Z407	CSMD3_HUMAN	CUB and Sushi multiple domains 3	843	Sushi 4. {ECO:0000255|PROSITE- ProRule:PRU00302}.					integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						AAACCGCCGTGCATTGATTGG	0.348										HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)																												ENST00000297405.5																			0				breast(7)|central_nervous_system(6)|endometrium(44)|haematopoietic_and_lymphoid_tissue(8)|kidney(36)|large_intestine(72)|liver(5)|lung(389)|ovary(24)|prostate(6)|skin(23)|upper_aerodigestive_tract(19)|urinary_tract(7)	646						c.(2527-2529)gCa>gTa		CUB and Sushi multiple domains 3							99.0	99.0	99.0					8																	113694820		2203	4300	6503	SO:0001583	missense	114788					integral to membrane|plasma membrane		g.chr8:113694820G>A	AY210419	CCDS6315.1, CCDS6316.2, CCDS6317.1	8q23.3	2007-01-06			ENSG00000164796	ENSG00000164796			19291	protein-coding gene	gene with protein product		608399					Standard	NM_052900		Approved		uc003ynu.3	Q7Z407	OTTHUMG00000157027	ENST00000297405.5:c.2528C>T	8.37:g.113694820G>A	ENSP00000297405:p.Ala843Val	HNSCC(6;0.00088)|TCGA Ovarian(7;0.080)	Somatic				CSMD3_ENST00000455883.2_Missense_Mutation_p.A739V|CSMD3_ENST00000343508.3_Missense_Mutation_p.A803V|CSMD3_ENST00000352409.3_Missense_Mutation_p.A843V	p.A843V	NM_198123.1	NP_937756.1	WXS	Illumina GAIIx	Phase_I	Q7Z407	CSMD3_HUMAN			16	2772	-			843			Sushi 4.		Q96PZ3	Missense_Mutation	SNP	ENST00000297405.5	37	c.2528C>T	CCDS6315.1	.	.	.	.	.	.	.	.	.	.	G	26.8	4.769141	0.90020	.	.	ENSG00000164796	ENST00000343508;ENST00000297405;ENST00000339701;ENST00000455883;ENST00000352409	T;T;T;T;T	0.25912	1.77;1.77;1.77;1.77;1.77	5.58	5.58	0.84498	Complement control module (2);Sushi/SCR/CCP (3);	0.075478	0.52532	D	0.000071	T	0.50446	0.1616	L	0.60904	1.88	0.40393	D	0.979562	D;D;D	0.76494	0.999;0.999;0.989	D;D;D	0.91635	0.998;0.999;0.921	T	0.48387	-0.9040	10	0.59425	D	0.04	.	19.557	0.95354	0.0:0.0:1.0:0.0	.	739;843;803	Q7Z407-3;Q7Z407;Q7Z407-2	.;CSMD3_HUMAN;.	V	803;843;183;739;843	ENSP00000345799:A803V;ENSP00000297405:A843V;ENSP00000341558:A183V;ENSP00000412263:A739V;ENSP00000343124:A843V	ENSP00000297405:A843V	A	-	2	0	CSMD3	113763996	1.000000	0.71417	0.999000	0.59377	0.996000	0.88848	4.687000	0.61708	2.623000	0.88846	0.650000	0.86243	GCA		0.348	CSMD3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347141.1	NM_052900		28	118	0	0	0	1	0	28	118				
MUC3A	4584	broad.mit.edu	37	7	100609626	100609626	+	Silent	SNP	C	C	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr7:100609626C>A	ENST00000319509.7	+	8	2358	c.2358C>A	c.(2356-2358)gcC>gcA	p.A786A	RP11-395B7.2_ENST00000420080.1_RNA|RP11-395B7.2_ENST00000434775.1_RNA			Q02505	MUC3A_HUMAN	mucin 3A, cell surface associated	2451	Ser-rich.|Thr-rich.				cellular protein metabolic process (GO:0044267)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular region (GO:0005576)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	extracellular matrix constituent, lubricant activity (GO:0030197)|extracellular matrix structural constituent (GO:0005201)			breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(32)|prostate(3)	44						GCCTGACGGCCGGCGCCGCGC	0.766																																						ENST00000319509.7																			0				breast(3)|central_nervous_system(3)|endometrium(1)|kidney(1)|large_intestine(1)|lung(32)|prostate(3)	44						c.(2356-2358)gcC>gcA		mucin 3A, cell surface associated							7.0	7.0	7.0					7																	100609626		860	1954	2814	SO:0001819	synonymous_variant	4584							g.chr7:100609626C>A	AF113616		7q22.1	2012-04-20	2006-03-14		ENSG00000169894	ENSG00000169894		"""Mucins"""	7513	protein-coding gene	gene with protein product		158371	"""mucin 3A, intestinal"""	MUC3		2393399, 10973822	Standard	XM_006710192		Approved		uc003uxl.1	Q02505	OTTHUMG00000157038	ENST00000319509.7:c.2358C>A	7.37:g.100609626C>A			Somatic				RP11-395B7.2_ENST00000420080.1_RNA	p.A786A			WXS	Illumina GAIIx	Phase_I					8	2358	+								O14650|O14651|O43418|O43421|Q02506|Q6W763|Q9H3Q7|Q9UKW9|Q9UN93|Q9UN94|Q9UN95	Silent	SNP	ENST00000319509.7	37	c.2358C>A																																																																																					0.766	MUC3A-001	KNOWN	mRNA_start_NF|cds_start_NF|basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000347215.1	XM_001725354		3	11	1	0	1	1	1	3	11				
ALG1L	200810	broad.mit.edu	37	3	125651539	125651539	+	Silent	SNP	A	A	C			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr3:125651539A>C	ENST00000340333.3	-	3	277	c.114T>G	c.(112-114)ctT>ctG	p.L38L	FAM86JP_ENST00000485843.1_RNA	NM_001015050.2|NM_001195223.1	NP_001015050.2|NP_001182152.1	Q6GMV1	ALG1L_HUMAN	ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like	38							transferase activity, transferring glycosyl groups (GO:0016757)			large_intestine(2)|lung(2)	4						CATCAAGAGTAAGTTGTTCAA	0.423																																						ENST00000340333.3																			0				large_intestine(2)|lung(2)	4						c.(112-114)ctT>ctG		ALG1, chitobiosyldiphosphodolichol beta-mannosyltransferase-like							89.0	82.0	85.0					3																	125651539		2203	4300	6503	SO:0001819	synonymous_variant	200810						transferase activity, transferring glycosyl groups	g.chr3:125651539A>C	BC073816	CCDS33840.1, CCDS74998.1	3q21.2	2013-02-22	2013-02-22		ENSG00000189366	ENSG00000189366		"""Glycosyltransferase group 1 domain containing"""	33721	protein-coding gene	gene with protein product	"""asparagine-linked glycosylation 1-like 1"""		"""asparagine-linked glycosylation 1-like"""				Standard	NM_001015050		Approved	ALG1L1	uc003eig.2	Q6GMV1	OTTHUMG00000159588	ENST00000340333.3:c.114T>G	3.37:g.125651539A>C			Somatic					p.L38L	NM_001015050.2|NM_001195223.1	NP_001015050.2|NP_001182152.1	WXS	Illumina GAIIx	Phase_I	Q6GMV1	ALG1L_HUMAN			3	277	-			38					D3DNA5	Silent	SNP	ENST00000340333.3	37	c.114T>G	CCDS33840.1																																																																																				0.423	ALG1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356347.1	NM_001015050		4	74	0	0	0	1	0	4	74				
LRRTM3	347731	broad.mit.edu	37	10	68687631	68687631	+	Missense_Mutation	SNP	T	T	A			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr10:68687631T>A	ENST00000361320.4	+	2	1535	c.957T>A	c.(955-957)aaT>aaA	p.N319K	CTNNA3_ENST00000373744.4_Intron|CTNNA3_ENST00000433211.2_Intron	NM_178011.3	NP_821079.3	Q86VH5	LRRT3_HUMAN	leucine rich repeat transmembrane neuronal 3	319	LRRCT.				positive regulation of beta-amyloid formation (GO:1902004)	cell junction (GO:0030054)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						GCAGCAGAAATATTTGCTCCC	0.398																																						ENST00000361320.4																			0				breast(1)|cervix(1)|endometrium(3)|kidney(4)|large_intestine(6)|lung(20)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(3)	41						c.(955-957)aaT>aaA		leucine rich repeat transmembrane neuronal 3							77.0	84.0	82.0					10																	68687631		2203	4300	6503	SO:0001583	missense	347731					integral to membrane		g.chr10:68687631T>A	BX640611	CCDS7270.1	10q22.1	2007-01-22				ENSG00000198739			19410	protein-coding gene	gene with protein product		610869				12676565	Standard	XR_247527		Approved		uc001jmz.1	Q86VH5		ENST00000361320.4:c.957T>A	10.37:g.68687631T>A	ENSP00000355187:p.Asn319Lys		Somatic				CTNNA3_ENST00000373744.4_Intron|CTNNA3_ENST00000433211.2_Intron	p.N319K	NM_178011.3	NP_821079.3	WXS	Illumina GAIIx	Phase_I	Q86VH5	LRRT3_HUMAN			2	1535	+			319			LRRCT.		A8K2A3|Q2NKX7|Q6N0A3	Missense_Mutation	SNP	ENST00000361320.4	37	c.957T>A	CCDS7270.1	.	.	.	.	.	.	.	.	.	.	T	2.049	-0.418154	0.04766	.	.	ENSG00000198739	ENST00000361320;ENST00000373722	T	0.04317	3.65	5.8	0.496	0.16896	.	0.000000	0.85682	D	0.000000	T	0.02610	0.0079	N	0.13043	0.29	0.42989	D	0.994482	B;B	0.20459	0.007;0.045	B;B	0.21360	0.009;0.034	T	0.50048	-0.8873	10	0.10636	T	0.68	.	9.5846	0.39508	0.0:0.3875:0.0:0.6125	.	319;319	Q86VH5;Q86VH5-2	LRRT3_HUMAN;.	K	319	ENSP00000355187:N319K	ENSP00000355187:N319K	N	+	3	2	LRRTM3	68357637	1.000000	0.71417	0.999000	0.59377	0.983000	0.72400	1.623000	0.37008	0.058000	0.16222	-0.280000	0.10049	AAT		0.398	LRRTM3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048277.2	NM_178011		14	58	0	0	0	1	0	14	58				
APBB1	322	broad.mit.edu	37	11	6432092	6432092	+	Missense_Mutation	SNP	C	C	A	rs145320037		TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr11:6432092C>A	ENST00000609360.1	-	2	585	c.486G>T	c.(484-486)gaG>gaT	p.E162D	APBB1_ENST00000389906.2_Missense_Mutation_p.E162D|APBB1_ENST00000311051.3_Missense_Mutation_p.E162D|APBB1_ENST00000299402.6_Missense_Mutation_p.E162D	NM_001164.3	NP_001155.1	O00213	APBB1_HUMAN	amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)	162	Glu-rich.				apoptotic process (GO:0006915)|axonogenesis (GO:0007409)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|histone H4 acetylation (GO:0043967)|negative regulation of cell growth (GO:0030308)|negative regulation of thymidylate synthase biosynthetic process (GO:0050760)|positive regulation of apoptotic process (GO:0043065)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|signal transduction (GO:0007165)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|growth cone (GO:0030426)|lamellipodium (GO:0030027)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|synapse (GO:0045202)	beta-amyloid binding (GO:0001540)|chromatin binding (GO:0003682)|histone binding (GO:0042393)|proline-rich region binding (GO:0070064)|transcription factor binding (GO:0008134)	p.E162D(1)		breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)		catcatcatcctcctcctcct	0.637																																					GBM(147;1810 2556 5672 39622)	ENST00000389906.2																			1	Substitution - Missense(1)	p.E162D(1)	prostate(1)	breast(4)|endometrium(3)|kidney(1)|large_intestine(7)|lung(5)|prostate(2)|skin(1)|urinary_tract(1)	24						c.(484-486)gaG>gaT		amyloid beta (A4) precursor protein-binding, family B, member 1 (Fe65)							35.0	35.0	35.0					11																	6432092		2201	4296	6497	SO:0001583	missense	322				apoptosis|axonogenesis|cell cycle arrest|histone H4 acetylation|negative regulation of cell growth|negative regulation of S phase of mitotic cell cycle|negative regulation of thymidylate synthase biosynthetic process|positive regulation of apoptosis|positive regulation of transcription, DNA-dependent|response to DNA damage stimulus|signal transduction|transcription, DNA-dependent	cytoplasm|growth cone|lamellipodium|nucleus|plasma membrane|synapse	beta-amyloid binding|chromatin binding|histone binding|proline-rich region binding|transcription factor binding	g.chr11:6432092C>A	L77864	CCDS31410.1, CCDS58114.1, CCDS66015.1, CCDS66016.1, CCDS66017.1, CCDS66018.1	11p15	2008-02-01				ENSG00000166313			581	protein-coding gene	gene with protein product		602709		RIR		8955346, 8894693	Standard	NM_001164		Approved	Fe65	uc001mcy.1	O00213		ENST00000609360.1:c.486G>T	11.37:g.6432092C>A	ENSP00000477213:p.Glu162Asp		Somatic				APBB1_ENST00000609360.1_Missense_Mutation_p.E162D|APBB1_ENST00000299402.6_Missense_Mutation_p.E162D|APBB1_ENST00000311051.3_Missense_Mutation_p.E162D	p.E162D			WXS	Illumina GAIIx	Phase_I	O00213	APBB1_HUMAN		Epithelial(150;6.49e-08)|BRCA - Breast invasive adenocarcinoma(625;0.194)	2	585	-		Medulloblastoma(188;0.00263)|all_neural(188;0.026)|Breast(177;0.029)	162			Glu-rich.		A1E379|A6NH82|A6NL69|B7Z1J5|B7Z1J6|B7Z2Y0|D3DQT2|Q7Z324|Q96A93|V9GYK0|V9GYT4	Missense_Mutation	SNP	ENST00000609360.1	37	c.486G>T		.	.	.	.	.	.	.	.	.	.	C	0.439	-0.899741	0.02472	.	.	ENSG00000166313	ENST00000299402;ENST00000311051;ENST00000389906	T;T;T	0.14893	2.47;2.47;2.47	4.85	-4.93	0.03066	.	0.650451	0.13993	N	0.348689	T	0.05318	0.0141	N	0.08118	0	0.27333	N	0.956714	B	0.10296	0.003	B	0.10450	0.005	T	0.38134	-0.9675	10	0.12766	T	0.61	-7.4359	4.4462	0.11598	0.2593:0.2348:0.0:0.5059	.	162	O00213-2	.	D	162	ENSP00000299402:E162D;ENSP00000311912:E162D;ENSP00000374556:E162D	ENSP00000299402:E162D	E	-	3	2	APBB1	6388668	0.040000	0.19996	0.894000	0.35097	0.055000	0.15305	-0.394000	0.07296	-1.017000	0.03367	-0.556000	0.04195	GAG		0.637	APBB1-023	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000471831.1	NM_001164		3	30	1	0	0.004672	1	0.00484504	3	30				
MGME1	92667	broad.mit.edu	37	20	17968940	17968940	+	Splice_Site	SNP	A	A	T			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr20:17968940A>T	ENST00000377710.5	+	4	1151	c.863A>T	c.(862-864)cAg>cTg	p.Q288L	MGME1_ENST00000377704.4_Intron|MGME1_ENST00000467391.1_3'UTR|MGME1_ENST00000377709.1_Splice_Site_p.Q208L	NM_052865.2	NP_443097.1			mitochondrial genome maintenance exonuclease 1																		TACAGCTTTCAGGTCAGGACA	0.453																																						ENST00000377710.5																			0											c.(862-864)cAg>cTg		mitochondrial genome maintenance exonuclease 1							96.0	87.0	90.0					20																	17968940		2203	4300	6503	SO:0001630	splice_region_variant	92667							g.chr20:17968940A>T		CCDS13131.1	20p11.23	2013-08-29	2013-01-11	2013-01-11	ENSG00000125871	ENSG00000125871			16205	protein-coding gene	gene with protein product		615076	"""chromosome 20 open reading frame 72"""	C20orf72		23313956, 23358826, 23434322	Standard	NM_052865		Approved	bA504H3.4, DDK1	uc002wqh.3	Q9BQP7	OTTHUMG00000031955	ENST00000377710.5:c.864+1A>T	20.37:g.17968940A>T			Somatic				MGME1_ENST00000377709.1_Splice_Site_p.Q208L|MGME1_ENST00000377704.4_Intron|MGME1_ENST00000467391.1_3'UTR	p.Q288L	NM_052865.2	NP_443097.1	WXS	Illumina GAIIx	Phase_I					4	1151	+									Splice_Site	SNP	ENST00000377710.5	37	c.863A>T	CCDS13131.1	.	.	.	.	.	.	.	.	.	.	A	23.4	4.413106	0.83449	.	.	ENSG00000125871	ENST00000377710;ENST00000377709	T;T	0.49720	0.77;0.83	5.62	5.62	0.85841	.	0.102324	0.64402	D	0.000001	T	0.66197	0.2765	M	0.70903	2.155	0.80722	D	1	D	0.76494	0.999	D	0.65874	0.939	T	0.67205	-0.5729	10	0.45353	T	0.12	-12.6793	15.4826	0.75539	1.0:0.0:0.0:0.0	.	288	Q9BQP7	CT072_HUMAN	L	288;208	ENSP00000366939:Q288L;ENSP00000366938:Q208L	ENSP00000366938:Q208L	Q	+	2	0	C20orf72	17916940	1.000000	0.71417	1.000000	0.80357	0.593000	0.36681	8.721000	0.91446	2.137000	0.66172	0.379000	0.24179	CAG		0.453	MGME1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078139.1	NM_052865	Missense_Mutation	3	69	0	0	0	1	0	3	69				
USP13	8975	broad.mit.edu	37	3	179448030	179448030	+	Missense_Mutation	SNP	A	A	T			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr3:179448030A>T	ENST00000263966.3	+	9	1613	c.1142A>T	c.(1141-1143)cAa>cTa	p.Q381L	USP13_ENST00000496897.1_Missense_Mutation_p.Q316L|USP13_ENST00000482333.1_3'UTR	NM_003940.2	NP_003931.2	Q92995	UBP13_HUMAN	ubiquitin specific peptidase 13 (isopeptidase T-3)	381	USP.				autophagy (GO:0006914)|cell proliferation (GO:0008283)|melanocyte differentiation (GO:0030318)|protein K63-linked deubiquitination (GO:0070536)|protein stabilization (GO:0050821)|regulation of autophagy (GO:0010506)|regulation of transcription, DNA-templated (GO:0006355)|ubiquitin-dependent protein catabolic process (GO:0006511)		cysteine-type endopeptidase activity (GO:0004197)|omega peptidase activity (GO:0008242)|ubiquitin binding (GO:0043130)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)			central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)			GATCCAACACAAGATTTCAAC	0.343																																						ENST00000263966.3																			0				central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(8)|lung(20)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(3)	46						c.(1141-1143)cAa>cTa		ubiquitin specific peptidase 13 (isopeptidase T-3)							124.0	122.0	122.0					3																	179448030		2203	4300	6503	SO:0001583	missense	8975				ubiquitin-dependent protein catabolic process		cysteine-type endopeptidase activity|omega peptidase activity|protein binding|ubiquitin thiolesterase activity|ubiquitin-specific protease activity|zinc ion binding	g.chr3:179448030A>T	U75362	CCDS3235.1	3q26.2-q26.3	2008-04-11	2005-08-08		ENSG00000058056	ENSG00000058056		"""Ubiquitin-specific peptidases"""	12611	protein-coding gene	gene with protein product		603591	"""ubiquitin specific protease 13 (isopeptidase T-3)"""			12838346	Standard	NM_003940		Approved	IsoT-3	uc003fkh.3	Q92995	OTTHUMG00000157783	ENST00000263966.3:c.1142A>T	3.37:g.179448030A>T	ENSP00000263966:p.Gln381Leu		Somatic				USP13_ENST00000496897.1_Missense_Mutation_p.Q316L|USP13_ENST00000482333.1_3'UTR	p.Q381L	NM_003940.2	NP_003931.2	WXS	Illumina GAIIx	Phase_I	Q92995	UBP13_HUMAN	OV - Ovarian serous cystadenocarcinoma(80;1e-25)|GBM - Glioblastoma multiforme(14;0.0169)		9	1613	+	all_cancers(143;7.79e-15)|Ovarian(172;0.0338)|Breast(254;0.148)		381					A8K2S3|B4DYF3|D3DNS2|Q96B25	Missense_Mutation	SNP	ENST00000263966.3	37	c.1142A>T	CCDS3235.1	.	.	.	.	.	.	.	.	.	.	A	15.20	2.763128	0.49574	.	.	ENSG00000058056	ENST00000263966;ENST00000496897;ENST00000497155	T;T;T	0.33438	1.41;1.41;1.41	5.69	5.69	0.88448	Peptidase C19, ubiquitin carboxyl-terminal hydrolase 2 (2);	0.000000	0.85682	D	0.000000	T	0.48077	0.1480	L	0.61036	1.89	0.80722	D	1	D;B	0.56035	0.974;0.03	P;B	0.57960	0.83;0.036	T	0.36138	-0.9760	10	0.33940	T	0.23	-16.1905	15.9458	0.79792	1.0:0.0:0.0:0.0	.	381;381	Q92995;A8K2S3	UBP13_HUMAN;.	L	381;316;27	ENSP00000263966:Q381L;ENSP00000417146:Q316L;ENSP00000420057:Q27L	ENSP00000263966:Q381L	Q	+	2	0	USP13	180930724	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.339000	0.96797	2.162000	0.67917	0.459000	0.35465	CAA		0.343	USP13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000349617.1			29	40	0	0	0	1	0	29	40				
SLC23A3	151295	broad.mit.edu	37	2	220033409	220033409	+	Silent	SNP	G	G	C			TCGA-V4-A9ET-01A-11D-A39W-08	TCGA-V4-A9ET-10A-01D-A39Z-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	bac54523-301a-4579-9f9a-bda77fe3b899	d4ed9f84-a58c-41fd-bd48-8d9fcff1ea71	g.chr2:220033409G>C	ENST00000409878.3	-	5	671	c.639C>G	c.(637-639)gcC>gcG	p.A213A	SLC23A3_ENST00000455516.2_Silent_p.A221A|SLC23A3_ENST00000396775.3_Intron|SLC23A3_ENST00000295738.7_Silent_p.A213A	NM_001144889.1	NP_001138361.1	Q6PIS1	S23A3_HUMAN	solute carrier family 23, member 3	213					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)	transporter activity (GO:0005215)			endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	11		Renal(207;0.0474)		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		AGCAGAACTGGGCTACCTCCC	0.672																																						ENST00000455516.2																			0				endometrium(3)|kidney(1)|large_intestine(2)|lung(4)|urinary_tract(1)	11						c.(661-663)gcC>gcG		solute carrier family 23, member 3							29.0	34.0	32.0					2																	220033409		1993	4161	6154	SO:0001819	synonymous_variant	151295				transmembrane transport	integral to membrane	protein binding|transporter activity	g.chr2:220033409G>C	BC030243	CCDS42819.1, CCDS46517.1, CCDS46518.1	2q35	2013-07-18	2013-07-18		ENSG00000213901	ENSG00000213901		"""Solute carriers"""	20601	protein-coding gene	gene with protein product							Standard	NM_144712		Approved	SVCT3, FLJ31168, Yspl1	uc010zkr.2	Q6PIS1	OTTHUMG00000154616	ENST00000409878.3:c.639C>G	2.37:g.220033409G>C			Somatic				SLC23A3_ENST00000396775.3_Intron|SLC23A3_ENST00000295738.7_Silent_p.A213A|SLC23A3_ENST00000409878.3_Silent_p.A213A	p.A221A	NM_001144890.1	NP_001138362.1	WXS	Illumina GAIIx	Phase_I	Q6PIS1	S23A3_HUMAN		Epithelial(149;9.27e-07)|all cancers(144;0.000156)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)	5	710	-		Renal(207;0.0474)	213					B7Z512|Q2PYN6|Q96NA6	Silent	SNP	ENST00000409878.3	37	c.663C>G	CCDS46518.1																																																																																				0.672	SLC23A3-010	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000336331.2	NM_144712		8	15	0	0	0	1	0	8	15				
