#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	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
TMC7	79905	broad.mit.edu	37	16	19070964	19070964	+	Intron	SNP	C	C	T	rs531463899		TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr16:19070964C>T	ENST00000304381.5	+	15	2236				RP11-626G11.5_ENST00000571934.1_RNA|TMC7_ENST00000421369.3_Intron|TMC7_ENST00000569532.1_Missense_Mutation_p.R752C	NM_024847.3	NP_079123.3	Q7Z402	TMC7_HUMAN	transmembrane channel-like 7						ion transport (GO:0006811)	integral component of membrane (GO:0016021)				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						GGCCCAGCCGCGTCCAGCTTC	0.517													C|||	1	0.000199681	0.0008	0.0	5008	,	,		19847	0.0		0.0	False		,,,				2504	0.0					ENST00000569532.1																			0				breast(2)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(12)|ovary(1)|prostate(1)|skin(4)|urinary_tract(1)	28						c.(2254-2256)Cgt>Tgt		transmembrane channel-like 7																																				SO:0001627	intron_variant	79905					integral to membrane		g.chr16:19070964C>T	AY263165	CCDS10573.1, CCDS53992.1, CCDS73837.1	16p13.11	2008-02-05			ENSG00000170537	ENSG00000170537			23000	protein-coding gene	gene with protein product						12812529, 12906855	Standard	XM_005255597		Approved	FLJ21240	uc002dfq.3	Q7Z402	OTTHUMG00000131456	ENST00000304381.5:c.2106+148C>T	16.37:g.19070964C>T						TMC7_ENST00000304381.5_Intron|TMC7_ENST00000421369.3_Intron	p.R752C			Q7Z402	TMC7_HUMAN			15	2384	+			0					E7ERB6|Q5H9Q8|Q7Z5M4|Q86WX0|Q9H766	Missense_Mutation	SNP	ENST00000304381.5	37	c.2254C>T	CCDS10573.1																																																																																				0.517	TMC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254276.3	NM_024847		6	10	0	0	0	1	0	6	10				
CACNA1B	774	broad.mit.edu	37	9	141016186	141016186	+	Missense_Mutation	SNP	C	C	T			TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr9:141016186C>T	ENST00000371372.1	+	47	6900	c.6755C>T	c.(6754-6756)tCt>tTt	p.S2252F	CACNA1B_ENST00000277551.2_Missense_Mutation_p.L2190F|CACNA1B_ENST00000371355.4_Missense_Mutation_p.S2253F|CACNA1B_ENST00000371363.1_Missense_Mutation_p.S2250F|CACNA1B_ENST00000371357.1_Missense_Mutation_p.S2251F|CACNA1B_ENST00000277549.5_Missense_Mutation_p.S1446F	NM_000718.3|NM_001243812.1	NP_000709.1|NP_001230741.1	Q00975	CAC1B_HUMAN	calcium channel, voltage-dependent, N type, alpha 1B subunit	2252					calcium ion import (GO:0070509)|locomotory behavior (GO:0007626)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|neurotransmitter secretion (GO:0007269)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of heart contraction (GO:0008016)|response to pain (GO:0048265)|synaptic transmission (GO:0007268)|transport (GO:0006810)	dendrite (GO:0030425)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|high voltage-gated calcium channel activity (GO:0008331)|protein C-terminus binding (GO:0008022)|voltage-gated calcium channel activity (GO:0005245)			NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80	all_cancers(76;0.166)			OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	Amlodipine(DB00381)|Gabapentin(DB00996)|Levetiracetam(DB01202)|Spironolactone(DB00421)|Verapamil(DB00661)	GCCCCTGGCTCTCGAATTGGC	0.662																																						ENST00000277549.5																			0				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(1)|endometrium(10)|kidney(2)|large_intestine(17)|lung(31)|ovary(1)|prostate(1)|skin(2)|stomach(2)|urinary_tract(2)	80						c.(4336-4338)tCt>tTt		calcium channel, voltage-dependent, N type, alpha 1B subunit	Amlodipine(DB00381)|Gabapentin(DB00996)						33.0	39.0	37.0					9																	141016186		1985	4160	6145	SO:0001583	missense	774				membrane depolarization|synaptic transmission	voltage-gated calcium channel complex	ATP binding|protein C-terminus binding|voltage-gated calcium channel activity	g.chr9:141016186C>T	AB209467	CCDS59522.1, CCDS59523.1	9q34	2013-01-10	2007-02-16		ENSG00000148408	ENSG00000148408		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"", ""EF-hand domain containing"""	1389	protein-coding gene	gene with protein product		601012		CACNL1A5		8825650, 16382099	Standard	NM_000718		Approved	Cav2.2, CACNN	uc004cog.3	Q00975	OTTHUMG00000021002	ENST00000371372.1:c.6755C>T	9.37:g.141016186C>T	ENSP00000360423:p.Ser2252Phe					CACNA1B_ENST00000277551.2_Missense_Mutation_p.L2190F|CACNA1B_ENST00000371355.4_Missense_Mutation_p.S2253F|CACNA1B_ENST00000371357.1_Missense_Mutation_p.S2251F|CACNA1B_ENST00000371363.1_Missense_Mutation_p.S2250F|CACNA1B_ENST00000371372.1_Missense_Mutation_p.S2252F	p.S1446F			Q00975	CAC1B_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;1.16e-05)|Epithelial(140;0.000476)	47	6906	+	all_cancers(76;0.166)		2252					B1AQK5	Missense_Mutation	SNP	ENST00000371372.1	37	c.4337C>T	CCDS59522.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	17.63|17.63	3.437351|3.437351	0.62955|0.62955	.|.	.|.	ENSG00000148408|ENSG00000148408	ENST00000277551|ENST00000371372;ENST00000277549;ENST00000371363;ENST00000371357;ENST00000371355	D|D;D;D;D;D	0.96587|0.97016	-4.06|-3.99;-4.21;-3.99;-3.97;-3.97	5.11|5.11	5.11|5.11	0.69529|0.69529	.|.	.|0.906908	.|0.09427	.|N	.|0.803553	D|D	0.97062|0.97062	0.9040|0.9040	L|L	0.40543|0.40543	1.245|1.245	0.51767|0.51767	D|D	0.999938|0.999938	.|D;D	.|0.71674	.|0.995;0.998	.|P;P	.|0.62089	.|0.798;0.898	D|D	0.95097|0.95097	0.8227|0.8227	6|10	.|0.54805	.|T	.|0.06	.|.	18.5267|18.5267	0.90975|0.90975	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|2251;2250	.|B1AQK7;B1AQK6	.|.;.	F|F	2190|2252;1446;2250;2251;2253	ENSP00000277551:L2190F|ENSP00000360423:S2252F;ENSP00000277549:S1446F;ENSP00000360414:S2250F;ENSP00000360408:S2251F;ENSP00000360406:S2253F	.|ENSP00000277549:S1446F	L|S	+|+	1|2	0|0	CACNA1B|CACNA1B	140136007|140136007	1.000000|1.000000	0.71417|0.71417	0.982000|0.982000	0.44146|0.44146	0.068000|0.068000	0.16541|0.16541	5.387000|5.387000	0.66243|0.66243	2.381000|2.381000	0.81170|0.81170	0.555000|0.555000	0.69702|0.69702	CTC|TCT		0.662	CACNA1B-001	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000055380.1	NM_000718		17	25	0	0	0	1	0	17	25				
STON1	11037	broad.mit.edu	37	2	48809422	48809422	+	Silent	SNP	C	C	T	rs149386954	byFrequency	TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr2:48809422C>T	ENST00000406226.1	+	3	1845	c.1650C>T	c.(1648-1650)gcC>gcT	p.A550A	STON1-GTF2A1L_ENST00000309827.2_Silent_p.A550A|STON1-GTF2A1L_ENST00000394751.3_Silent_p.A550A|STON1_ENST00000404752.1_Silent_p.A550A|STON1-GTF2A1L_ENST00000405008.1_Silent_p.A550A|STON1-GTF2A1L_ENST00000394754.1_Silent_p.A550A|STON1-GTF2A1L_ENST00000402114.2_Silent_p.A550A|STON1_ENST00000309835.3_Silent_p.A550A	NM_001198595.1	NP_001185524.1	Q9Y6Q2	STON1_HUMAN	stonin 1	550	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|regulation of endocytosis (GO:0030100)	clathrin adaptor complex (GO:0030131)				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)			TCAACATGGCCTCATTGGCGC	0.468													C|||	28	0.00559105	0.0	0.0014	5008	,	,		20434	0.0		0.002	False		,,,				2504	0.0256					ENST00000309835.3																			0				NS(1)|endometrium(1)|kidney(2)|large_intestine(9)|lung(19)|prostate(3)|skin(2)	37						c.(1648-1650)gcC>gcT		stonin 1		C	,,,,	1,4405		0,1,2202	156.0	152.0	153.0		1650,1650,1650,1650,1650	3.7	0.9	2	dbSNP_134	153	22,8578	16.0+/-53.3	1,20,4279	no	coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous,coding-synonymous	STON1,STON1-GTF2A1L	NM_001198593.1,NM_001198594.1,NM_001198595.1,NM_006873.3,NM_172311.2	,,,,	1,21,6481	TT,TC,CC		0.2558,0.0227,0.1768	,,,,	550/1159,550/1136,550/736,550/736,550/1183	48809422	23,12983	2203	4300	6503	SO:0001819	synonymous_variant	11037							g.chr2:48809422C>T	AF026169	CCDS1841.1	2p16.3	2008-02-05			ENSG00000243244	ENSG00000243244			17003	protein-coding gene	gene with protein product	"""stoned B homolog 1 (Drosophila)"""	605357				14504226, 10364255	Standard	NM_001198595		Approved	SBLF, stoned-b1		Q9Y6Q2	OTTHUMG00000129169	ENST00000406226.1:c.1650C>T	2.37:g.48809422C>T						STON1-GTF2A1L_ENST00000309827.2_Silent_p.A550A|STON1_ENST00000406226.1_Silent_p.A550A|STON1_ENST00000404752.1_Silent_p.A550A|STON1-GTF2A1L_ENST00000402114.2_Silent_p.A550A|STON1-GTF2A1L_ENST00000405008.1_Silent_p.A550A|STON1-GTF2A1L_ENST00000394754.1_Silent_p.A550A|STON1-GTF2A1L_ENST00000394751.3_Silent_p.A550A	p.A550A					Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		1	1660	+		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.175)						A8MXJ1|B5MCF5|B7ZL16|Q96JE3|Q9BYX3	Silent	SNP	ENST00000406226.1	37	c.1650C>T	CCDS1841.1																																																																																				0.468	STON1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323848.2	NM_006873		6	125	0	0	0	1	0	6	125				
SUMO3	6612	broad.mit.edu	37	21	46233863	46233863	+	Missense_Mutation	SNP	G	G	C	rs13050872	byFrequency	TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr21:46233863G>C	ENST00000411651.2	-	2	290	c.178C>G	c.(178-180)Ctc>Gtc	p.L60V	SUMO3_ENST00000397893.3_Intron|SUMO3_ENST00000479153.1_Intron|SUMO3_ENST00000332859.6_Intron|SUMO3_ENST00000397898.3_Intron					small ubiquitin-like modifier 3											prostate(1)	1				Colorectal(79;0.058)		CACACGGGGAGGCTCTGCGGG	0.657													G|||	731	0.145966	0.0106	0.1239	5008	,	,		16129	0.1002		0.2992	False		,,,				2504	0.2342					ENST00000411651.2																			0				prostate(1)	1						c.(178-180)Ctc>Gtc		small ubiquitin-like modifier 3		G		257,4149	146.9+/-181.5	7,243,1953	76.0	62.0	67.0			-2.6	0.0	21	dbSNP_121	67	2713,5887	431.6+/-356.9	437,1839,2024	no	intron	SUMO3	NM_006936.2		444,2082,3977	CC,CG,GG		31.5465,5.833,22.8356			46233863	2970,10036	2203	4300	6503	SO:0001583	missense	6612				protein sumoylation	cytoplasm|kinetochore	protein binding	g.chr21:46233863G>C		CCDS33587.1, CCDS68220.1	21q22.3	2013-06-05	2013-06-05	2004-05-19	ENSG00000184900	ENSG00000184900			11124	protein-coding gene	gene with protein product		602231	"""SMT3 (suppressor of mif two 3, yeast) homolog 1"", ""SMT3 suppressor of mif two 3 homolog 3 (yeast)"", ""SMT3 suppressor of mif two 3 homolog 3 (S. cerevisiae)"""	SMT3H1		9119407	Standard	NM_006936		Approved	SMT3A	uc002zfz.1	P55854	OTTHUMG00000090256	ENST00000411651.2:c.178C>G	21.37:g.46233863G>C	ENSP00000409666:p.Leu60Val					SUMO3_ENST00000397893.3_Intron|SUMO3_ENST00000397898.3_Intron|SUMO3_ENST00000479153.1_Intron|SUMO3_ENST00000332859.6_Intron	p.L60V			P55854	SUMO3_HUMAN		Colorectal(79;0.058)	2	290	-			50			Ubiquitin-like.			Missense_Mutation	SNP	ENST00000411651.2	37	c.178C>G		361	0.1652930402930403	5	0.01016260162601626	53	0.1464088397790055	60	0.1048951048951049	243	0.32058047493403696	G	0.443	-0.897461	0.02472	0.05833	0.315465	ENSG00000184900	ENST00000411651	T	0.33216	1.42	1.29	-2.57	0.06248	.	.	.	.	.	T	0.00012	0.0000	.	.	.	0.80722	P	0.0	B	0.09022	0.002	B	0.04013	0.001	T	0.40194	-0.9576	7	0.37606	T	0.19	.	1.8991	0.03264	0.1988:0.1798:0.4429:0.1785	rs13050872;rs17290193;rs13050872	60	B4DUW4	.	V	60	ENSP00000409666:L60V	ENSP00000409666:L60V	L	-	1	0	SUMO3	45058291	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-0.034000	0.12225	-2.112000	0.00835	-0.786000	0.03341	CTC		0.657	SUMO3-201	KNOWN	basic	protein_coding	protein_coding				4	62	0	0	0	1	0	4	62				
KRTAP4-11	653240	broad.mit.edu	37	17	39274291	39274291	+	Missense_Mutation	SNP	T	T	C	rs200214744|rs565505867	byFrequency	TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr17:39274291T>C	ENST00000391413.2	-	1	315	c.277A>G	c.(277-279)Atg>Gtg	p.M93V		NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	keratin associated protein 4-11	93	27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].					keratin filament (GO:0045095)		p.M93V(4)		endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000371)			TGGCAGCACATAGACTGGCAG	0.662																																						ENST00000391413.2																			4	Substitution - Missense(4)	p.M93V(4)	endometrium(3)|kidney(1)	endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|lung(8)|prostate(5)|skin(1)	33						c.(277-279)Atg>Gtg		keratin associated protein 4-11							6.0	10.0	8.0					17																	39274291		651	1556	2207	SO:0001583	missense	653240					keratin filament		g.chr17:39274291T>C	AC025904	CCDS45675.1	17q21.2	2013-06-25			ENSG00000212721	ENSG00000212721		"""Keratin associated proteins"""	18911	protein-coding gene	gene with protein product			"""keratin associated protein 4-14"""	KRTAP4-14			Standard	NM_033059		Approved	KAP4.11, KAP4.14	uc002hvz.3	Q9BYQ6	OTTHUMG00000133586	ENST00000391413.2:c.277A>G	17.37:g.39274291T>C	ENSP00000375232:p.Met93Val						p.M93V	NM_033059.3	NP_149048.2	Q9BYQ6	KR411_HUMAN	STAD - Stomach adenocarcinoma(17;0.000371)		1	315	-		Breast(137;0.000496)	93			27 X 5 AA repeats of C-C-[GIKRQVHEL]- [SPTR]-[STVQRMC].		A0AUY2	Missense_Mutation	SNP	ENST00000391413.2	37	c.277A>G	CCDS45675.1	.	.	.	.	.	.	.	.	.	.	.	0.073	-1.199029	0.01581	.	.	ENSG00000212721	ENST00000391413	T	0.00580	6.43	4.25	-4.9	0.03094	.	.	.	.	.	T	0.00109	0.0003	N	0.00040	-2.49	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.43097	-0.9412	9	0.02654	T	1	.	0.4739	0.00536	0.3479:0.2455:0.1203:0.2863	.	93	Q9BYQ6	KR411_HUMAN	V	93	ENSP00000375232:M93V	ENSP00000375232:M93V	M	-	1	0	KRTAP4-11	36527817	.	.	0.012000	0.15200	0.010000	0.07245	.	.	-1.319000	0.02286	-1.132000	0.01976	ATG		0.662	KRTAP4-11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257690.1			4	46	0	0	0	1	0	4	46				
SNRNP48	154007	broad.mit.edu	37	6	7601664	7601664	+	Missense_Mutation	SNP	G	G	C	rs141422613		TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr6:7601664G>C	ENST00000342415.5	+	5	561	c.502G>C	c.(502-504)Gta>Cta	p.V168L		NM_152551.3	NP_689764.3	Q6IEG0	SNR48_HUMAN	small nuclear ribonucleoprotein 48kDa (U11/U12)	168					mRNA processing (GO:0006397)|RNA splicing (GO:0008380)	U12-type spliceosomal complex (GO:0005689)	metal ion binding (GO:0046872)			kidney(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						CTATGATTTCGTAGTTGAGGA	0.378																																						ENST00000342415.5																			0				kidney(2)|lung(5)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)	10						c.(502-504)Gta>Cta		small nuclear ribonucleoprotein 48kDa (U11/U12)							103.0	100.0	101.0					6																	7601664		2203	4300	6503	SO:0001583	missense	154007				mRNA processing	cytoplasm|U12-type spliceosomal complex	metal ion binding	g.chr6:7601664G>C	AK056796	CCDS4502.1	6p24.3	2011-10-11	2008-10-29	2008-10-29	ENSG00000168566	ENSG00000168566			21368	protein-coding gene	gene with protein product	"""U11/U12 snRNP 48K"""		"""chromosome 6 open reading frame 151"""	C6orf151		15146077	Standard	XR_427825		Approved	FLJ32234, dJ512B11.2, dJ336K20B.1	uc003mxr.3	Q6IEG0	OTTHUMG00000014213	ENST00000342415.5:c.502G>C	6.37:g.7601664G>C	ENSP00000339834:p.Val168Leu						p.V168L	NM_152551.3	NP_689764.3	Q6IEG0	SNR48_HUMAN			5	561	+			168					A8K8P4|Q14C91|Q5T339|Q5THM1|Q5THM2|Q96MK1	Missense_Mutation	SNP	ENST00000342415.5	37	c.502G>C	CCDS4502.1	.	.	.	.	.	.	.	.	.	.	G	31	5.083486	0.94050	.	.	ENSG00000168566	ENST00000342415	T	0.39787	1.06	5.95	5.95	0.96441	.	0.000000	0.85682	D	0.000000	T	0.53769	0.1817	L	0.50333	1.59	0.53688	D	0.999979	D	0.69078	0.997	D	0.76575	0.988	T	0.53194	-0.8473	10	0.72032	D	0.01	-15.1815	17.8657	0.88794	0.0:0.0:1.0:0.0	.	168	Q6IEG0	SNR48_HUMAN	L	168	ENSP00000339834:V168L	ENSP00000339834:V168L	V	+	1	0	SNRNP48	7546663	1.000000	0.71417	0.998000	0.56505	0.983000	0.72400	6.457000	0.73505	2.826000	0.97356	0.491000	0.48974	GTA		0.378	SNRNP48-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039787.3	NM_152551		34	60	0	0	0	1	0	34	60				
KIF25	3834	broad.mit.edu	37	6	168443303	168443303	+	Missense_Mutation	SNP	G	G	T			TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr6:168443303G>T	ENST00000443060.2	+	9	1283	c.892G>T	c.(892-894)Gcc>Tcc	p.A298S	KIF25_ENST00000354419.2_Missense_Mutation_p.A298S|KIF25_ENST00000351261.3_Intron			Q9UIL4	KIF25_HUMAN	kinesin family member 25	298	Kinesin motor. {ECO:0000255|PROSITE- ProRule:PRU00283}.				ATP catabolic process (GO:0006200)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|mitotic sister chromatid segregation (GO:0000070)|negative regulation of autophagy (GO:0010507)|organelle organization (GO:0006996)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			NS(2)|breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29		Breast(66;1.07e-05)|Ovarian(120;0.0728)		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)		CAGCCTTGCGGCCCTGGCAGG	0.662																																						ENST00000443060.2																			0				NS(2)|breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(7)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	29						c.(892-894)Gcc>Tcc		kinesin family member 25							104.0	100.0	102.0					6																	168443303		2203	4300	6503	SO:0001583	missense	0				microtubule-based movement|mitotic sister chromatid segregation	cytoplasm|kinesin complex|microtubule	ATP binding|microtubule motor activity	g.chr6:168443303G>T	AB012722	CCDS5305.1, CCDS43530.1	6q27	2008-02-05	2003-01-09	2003-01-10	ENSG00000125337	ENSG00000125337		"""Kinesins"""	6390	protein-coding gene	gene with protein product		603815	"""kinesin-like 3"""	KNSL3		9925910	Standard	NM_030615		Approved		uc003qwk.1	Q9UIL4	OTTHUMG00000016035	ENST00000443060.2:c.892G>T	6.37:g.168443303G>T	ENSP00000388878:p.Ala298Ser					KIF25_ENST00000351261.3_Intron|KIF25_ENST00000354419.2_Missense_Mutation_p.A298S	p.A298S			Q9UIL4	KIF25_HUMAN		Epithelial(4;7.7e-30)|OV - Ovarian serous cystadenocarcinoma(33;5.82e-22)|BRCA - Breast invasive adenocarcinoma(4;1.38e-10)|GBM - Glioblastoma multiforme(31;0.000756)	9	1283	+		Breast(66;1.07e-05)|Ovarian(120;0.0728)	298					O94775|Q5SZU9	Missense_Mutation	SNP	ENST00000443060.2	37	c.892G>T	CCDS5305.1	.	.	.	.	.	.	.	.	.	.	G	16.62	3.174722	0.57692	.	.	ENSG00000125337	ENST00000443060;ENST00000354419	T;T	0.77358	-1.09;-1.09	4.13	4.13	0.48395	Kinesin, motor domain (3);	0.067083	0.64402	D	0.000013	T	0.75191	0.3816	L	0.59967	1.855	0.80722	D	1	D	0.52996	0.957	P	0.52881	0.712	T	0.77236	-0.2662	10	0.48119	T	0.1	-20.7057	13.6293	0.62186	0.0:0.0:1.0:0.0	.	298	Q9UIL4	KIF25_HUMAN	S	298	ENSP00000388878:A298S;ENSP00000346401:A298S	ENSP00000346401:A298S	A	+	1	0	KIF25	168186152	1.000000	0.71417	0.034000	0.17996	0.057000	0.15508	5.351000	0.66022	2.011000	0.59026	0.543000	0.68304	GCC		0.662	KIF25-004	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000362509.1			41	60	1	0	1.04594e-18	1	1.09575e-18	41	60				
CLSTN2	64084	broad.mit.edu	37	3	140140038	140140038	+	Missense_Mutation	SNP	G	G	A	rs375249688		TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr3:140140038G>A	ENST00000458420.3	+	5	899	c.709G>A	c.(709-711)Gac>Aac	p.D237N		NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN	calsyntenin 2	237	Cadherin 2. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|postsynaptic membrane (GO:0045211)	calcium ion binding (GO:0005509)			NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						GACCGCCTACGACTGTGGACA	0.517										HNSCC(16;0.037)																											GBM(45;858 913 3709 36904 37282)	ENST00000458420.3																			0				NS(1)|breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(13)|liver(1)|lung(42)|pancreas(2)|prostate(1)|skin(6)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(1)	87						c.(709-711)Gac>Aac		calsyntenin 2		G	ASN/ASP	0,4406		0,0,2203	177.0	165.0	169.0		709	5.7	1.0	3		169	1,8599	1.2+/-3.3	0,1,4299	no	missense	CLSTN2	NM_022131.2	23	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	probably-damaging	237/956	140140038	1,13005	2203	4300	6503	SO:0001583	missense	64084				homophilic cell adhesion	endoplasmic reticulum membrane|Golgi membrane|integral to membrane|plasma membrane	calcium ion binding	g.chr3:140140038G>A	AJ278018	CCDS3112.1	3q23	2011-07-01			ENSG00000158258	ENSG00000158258		"""Cadherins / Cadherin-related"""	17448	protein-coding gene	gene with protein product	"""cadherin-related family member 13"""	611323				12498782	Standard	NM_022131		Approved	CSTN2, CS2, FLJ39113, CDHR13	uc003etn.3	Q9H4D0	OTTHUMG00000160139	ENST00000458420.3:c.709G>A	3.37:g.140140038G>A	ENSP00000402460:p.Asp237Asn	HNSCC(16;0.037)					p.D237N	NM_022131.2	NP_071414.2	Q9H4D0	CSTN2_HUMAN			5	899	+			237			Cadherin 2.		B2RCW5|D3DNF4|Q3SX54|Q3ZB76|Q5UE56|Q96HZ2|Q9BSS0	Missense_Mutation	SNP	ENST00000458420.3	37	c.709G>A	CCDS3112.1	.	.	.	.	.	.	.	.	.	.	G	34	5.364454	0.95877	0.0	1.16E-4	ENSG00000158258	ENST00000458420	T	0.79940	-1.32	5.7	5.7	0.88788	Cadherin (5);Cadherin-like (1);	0.000000	0.85682	D	0.000000	D	0.91310	0.7260	H	0.94886	3.595	0.80722	D	1	D	0.65815	0.995	P	0.57468	0.821	D	0.93408	0.6766	10	0.87932	D	0	-7.9719	17.3368	0.87283	0.0:0.0:1.0:0.0	.	237	Q9H4D0	CSTN2_HUMAN	N	237	ENSP00000402460:D237N	ENSP00000402460:D237N	D	+	1	0	CLSTN2	141622728	1.000000	0.71417	0.978000	0.43139	0.954000	0.61252	9.075000	0.94004	2.679000	0.91253	0.655000	0.94253	GAC		0.517	CLSTN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000359393.3	NM_022131		11	157	0	0	0	1	0	11	157				
USP2	9099	broad.mit.edu	37	11	119243580	119243580	+	Missense_Mutation	SNP	C	C	T	rs146005919	byFrequency	TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr11:119243580C>T	ENST00000260187.2	-	2	905	c.611G>A	c.(610-612)cGc>cAc	p.R204H	RP11-334E6.3_ENST00000530918.2_RNA|USP2_ENST00000455332.2_Intron	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	204					cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)			breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		ACTGCCCTTGCGACCATAGTT	0.627																																						ENST00000260187.2																			0				breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24						c.(610-612)cGc>cAc		ubiquitin specific peptidase 2		C	HIS/ARG	0,4398		0,0,2199	66.0	67.0	67.0		611	2.5	1.0	11	dbSNP_134	67	4,8586	3.7+/-12.6	0,4,4291	yes	missense	USP2	NM_004205.4	29	0,4,6490	TT,TC,CC		0.0466,0.0,0.0308	benign	204/606	119243580	4,12984	2199	4295	6494	SO:0001583	missense	9099				cell cycle|muscle organ development|negative regulation of transcription from RNA polymerase II promoter|positive regulation of mitotic cell cycle|protein deubiquitination|protein stabilization|ubiquitin-dependent protein catabolic process	nucleus|perinuclear region of cytoplasm	cyclin binding|cysteine-type endopeptidase activity|metal ion binding|ubiquitin protein ligase binding|ubiquitin thiolesterase activity	g.chr11:119243580C>T	AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"""Ubiquitin-specific peptidases"""	12618	protein-coding gene	gene with protein product		604725	"""ubiquitin specific protease 2"""			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.611G>A	11.37:g.119243580C>T	ENSP00000260187:p.Arg204His					RP11-334E6.3_ENST00000530918.2_RNA|USP2_ENST00000455332.2_Intron	p.R204H	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)	2	905	-		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)	204					B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Missense_Mutation	SNP	ENST00000260187.2	37	c.611G>A	CCDS8422.1	.	.	.	.	.	.	.	.	.	.	C	11.44	1.639510	0.29157	0.0	4.66E-4	ENSG00000036672	ENST00000260187;ENST00000530918	T	0.20881	2.04	5.37	2.51	0.30379	.	0.560053	0.17430	N	0.174493	T	0.12689	0.0308	N	0.19112	0.55	0.80722	D	1	B	0.06786	0.001	B	0.01281	0.0	T	0.07558	-1.0766	10	0.51188	T	0.08	-0.8356	7.5622	0.27857	0.0:0.7428:0.0:0.2572	.	204	O75604	UBP2_HUMAN	H	204;174	ENSP00000260187:R204H	ENSP00000260187:R204H	R	-	2	0	USP2	118748790	1.000000	0.71417	0.991000	0.47740	0.994000	0.84299	2.696000	0.47052	0.258000	0.21686	-0.136000	0.14681	CGC		0.627	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2	NM_171997		6	77	0	0	0	1	0	6	77				
OBP2A	29991	broad.mit.edu	37	9	138440527	138440527	+	Intron	SNP	T	T	C	rs2590501	byFrequency	TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr9:138440527T>C	ENST00000539850.1	+	5	414				OBP2A_ENST00000340780.3_Missense_Mutation_p.W143R|OBP2A_ENST00000342114.4_Missense_Mutation_p.L98S|OBP2A_ENST00000371776.1_Intron			Q9NY56	OBP2A_HUMAN	odorant binding protein 2A						response to stimulus (GO:0050896)|sensory perception of chemical stimulus (GO:0007606)|sensory perception of smell (GO:0007608)|transport (GO:0006810)	extracellular region (GO:0005576)	odorant binding (GO:0005549)			endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11				OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)		GTCCCCACCTTGGCTCACCTG	0.597													.|||	2437	0.486621	0.2579	0.5778	5008	,	,		15516	0.6974		0.4274	False		,,,				2504	0.5746					ENST00000340780.3																			0				endometrium(1)|large_intestine(4)|lung(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						c.(427-429)Tgg>Cgg		odorant binding protein 2A		T		922,3484		159,604,1440	53.0	46.0	49.0			-2.5	0.0	9	dbSNP_100	49	3053,5547		799,1455,2046	no	intron	OBP2A	NM_014582.2		958,2059,3486	CC,CT,TT		35.5,20.926,30.5628			138440527	3975,9031	2203	4300	6503	SO:0001627	intron_variant	29991				response to stimulus|sensory perception of smell	extracellular region	odorant binding|transporter activity	g.chr9:138440527T>C	AJ251029	CCDS6992.1	9q34	2014-01-22			ENSG00000122136	ENSG00000122136		"""Lipocalins"""	23380	protein-coding gene	gene with protein product		164320					Standard	NM_014582		Approved	hOBPIIa, OBP, LCN13	uc004cgb.3	Q9NY56	OTTHUMG00000020909	ENST00000539850.1:c.389-27T>C	9.37:g.138440527T>C						OBP2A_ENST00000539850.1_Intron|OBP2A_ENST00000371776.1_Intron|OBP2A_ENST00000342114.4_Missense_Mutation_p.L98S	p.W143R			Q9NY56	OBP2A_HUMAN		OV - Ovarian serous cystadenocarcinoma(145;3.39e-07)|Epithelial(140;1.11e-06)|all cancers(34;2.04e-05)	5	469	+			0					Q5T8A3|Q9NY50|Q9NY53|Q9NY54|Q9NY55	Missense_Mutation	SNP	ENST00000539850.1	37	c.427T>C	CCDS6992.1	967|967	0.44276556776556775|0.44276556776556775	123|123	0.25|0.25	181|181	0.5|0.5	378|378	0.6608391608391608|0.6608391608391608	285|285	0.3759894459102902|0.3759894459102902	t|t	0|0	-2.751831|-2.751831	0.00085|0.00085	0.20926|0.20926	0.355|0.355	ENSG00000122136|ENSG00000122136	ENST00000342114|ENST00000340780	T|T	0.25579|0.33438	1.79|1.41	1.27|1.27	-2.55|-2.55	0.06288|0.06288	.|.	.|.	.|.	.|.	.|.	T|T	0.00012|0.00012	0.0000|0.0000	.|.	.|.	.|.	0.80722|0.80722	P|P	0.0|0.0	B|B	0.02656|0.02656	0.0|0.0	B|B	0.01281|0.01281	0.0|0.0	T|T	0.41324|0.41324	-0.9515|-0.9515	7|7	0.39692|0.41790	T|T	0.17|0.15	.|.	0.5218|0.5218	0.00613|0.00613	0.2448:0.3283:0.242:0.1849|0.2448:0.3283:0.242:0.1849	rs2590501;rs3827834|rs2590501;rs3827834	98|143	Q5T8A4|Q5T8A5	.|.	S|R	98|143	ENSP00000340950:L98S|ENSP00000342097:W143R	ENSP00000340950:L98S|ENSP00000342097:W143R	L|W	+|+	2|1	0|0	OBP2A|OBP2A	137580348|137580348	0.000000|0.000000	0.05858|0.05858	0.000000|0.000000	0.03702|0.03702	0.340000|0.340000	0.28889|0.28889	-2.631000|-2.631000	0.00871|0.00871	-0.799000|-0.799000	0.04439|0.04439	-3.752000|-3.752000	0.00022|0.00022	TTG|TGG		0.597	OBP2A-006	KNOWN	alternative_3_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397904.1	NM_014582		4	46	0	0	0	1	0	4	46				
CYP4Z2P	163720	broad.mit.edu	37	1	47325354	47325354	+	RNA	SNP	G	G	A	rs4660360		TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr1:47325354G>A	ENST00000505841.1	-	0	1175					NR_002788.2		Q8N1L4	CP4Z2_HUMAN	cytochrome P450, family 4, subfamily Z, polypeptide 2, pseudogene							integral component of membrane (GO:0016021)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen (GO:0016705)										CATCTGGAAAGGTAATGGGTT	0.438																																						ENST00000505841.1																			0																																																			0							g.chr1:47325354G>A	AY262057		1p33	2013-07-25	2013-05-03		ENSG00000154198	ENSG00000154198		"""Cytochrome P450s"""	24426	pseudogene	pseudogene						15059886	Standard	NR_002788		Approved	FLJ40054	uc031pmm.1	Q8N1L4	OTTHUMG00000008024		1.37:g.47325354G>A								NR_002788.2						0	1175	-								Q66ZJ5	RNA	SNP	ENST00000505841.1	37																																																																																						0.438	CYP4Z2P-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000361094.1	NR_002788		9	79	0	0	0	1	0	9	79				
WDR16	146845	broad.mit.edu	37	17	9497560	9497560	+	Missense_Mutation	SNP	C	C	T	rs77839011	byFrequency	TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr17:9497560C>T	ENST00000352665.5	+	4	527	c.458C>T	c.(457-459)gCa>gTa	p.A153V	WDR16_ENST00000299764.5_Missense_Mutation_p.A163V|WDR16_ENST00000396219.3_Missense_Mutation_p.A85V|WDR16_ENST00000576499.1_3'UTR	NM_145054.4	NP_659491.4			WD repeat domain 16											NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31						GGCAGCCCTGCAGCCGGCCTC	0.493													C|||	12	0.00239617	0.0008	0.0	5008	,	,		15040	0.0		0.0109	False		,,,				2504	0.0					ENST00000352665.5																			0				NS(1)|breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(1)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	31						c.(457-459)gCa>gTa		WD repeat domain 16		C	VAL/ALA,VAL/ALA	4,4402	8.1+/-20.4	0,4,2199	105.0	108.0	107.0		254,458	5.3	0.1	17	dbSNP_131	107	66,8534	41.2+/-98.3	2,62,4236	yes	missense,missense	WDR16	NM_001080556.1,NM_145054.4	64,64	2,66,6435	TT,TC,CC		0.7674,0.0908,0.5382	probably-damaging,probably-damaging	85/553,153/621	9497560	70,12936	2203	4300	6503	SO:0001583	missense	146845					cytoplasm|intracellular membrane-bounded organelle	protein binding	g.chr17:9497560C>T	AB065281	CCDS11149.2, CCDS42262.1	17p13.1	2014-08-01			ENSG00000166596	ENSG00000166596		"""WD repeat domain containing"""	16053	protein-coding gene	gene with protein product	"""WD40-repeat protein upregulated in HCC"""	609804				15967112	Standard	NM_001080556		Approved	WDRPUH, FLJ37528	uc002gly.3	Q8N1V2	OTTHUMG00000150149	ENST00000352665.5:c.458C>T	17.37:g.9497560C>T	ENSP00000339449:p.Ala153Val					WDR16_ENST00000396219.3_Missense_Mutation_p.A85V|WDR16_ENST00000299764.5_Missense_Mutation_p.A163V	p.A153V	NM_145054.4	NP_659491.4	Q8N1V2	WDR16_HUMAN			4	527	+			153						Missense_Mutation	SNP	ENST00000352665.5	37	c.458C>T	CCDS11149.2	7	0.003205128205128205	1	0.0020325203252032522	0	0.0	0	0.0	6	0.0079155672823219	C	19.68	3.873242	0.72180	9.08E-4	0.007674	ENSG00000166596	ENST00000352665;ENST00000396219;ENST00000299764	T;D;T	0.89196	2.68;-2.48;5.01	5.3	5.3	0.74995	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	0.000000	0.85682	D	0.000000	D	0.90338	0.6977	M	0.77103	2.36	0.80722	D	1	P;P;D	0.54601	0.935;0.934;0.967	P;P;P	0.53649	0.731;0.623;0.728	D	0.90701	0.4620	10	0.46703	T	0.11	-22.6198	18.0915	0.89477	0.0:1.0:0.0:0.0	.	163;85;153	Q8N1V2-2;Q8N1V2-3;Q8N1V2	.;.;WDR16_HUMAN	V	153;85;163	ENSP00000339449:A153V;ENSP00000379521:A85V;ENSP00000299764:A163V	ENSP00000299764:A163V	A	+	2	0	WDR16	9438285	1.000000	0.71417	0.141000	0.22245	0.431000	0.31685	5.092000	0.64511	2.645000	0.89757	0.591000	0.81541	GCA		0.493	WDR16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000316569.2	NM_145054		5	105	0	0	0	1	0	5	105				
ZNF814	730051	broad.mit.edu	37	19	58385546	58385546	+	Missense_Mutation	SNP	G	G	T	rs201682072		TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr19:58385546G>T	ENST00000435989.2	-	3	1446	c.1212C>A	c.(1210-1212)gaC>gaA	p.D404E	ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN	zinc finger protein 814	404					regulation of transcription, DNA-templated (GO:0006355)	intracellular (GO:0005622)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.D404E(10)		NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						AATGTTTTTTGTCAGTGTGAA	0.393																																						ENST00000435989.2																			10	Substitution - Missense(10)	p.D404E(10)	urinary_tract(3)|kidney(3)|prostate(2)|NS(1)|skin(1)	NS(1)|central_nervous_system(2)|endometrium(3)|kidney(9)|lung(2)|prostate(4)|skin(1)|urinary_tract(3)	25						c.(1210-1212)gaC>gaA		zinc finger protein 814							117.0	93.0	100.0					19																	58385546		692	1591	2283	SO:0001583	missense	730051				regulation of transcription, DNA-dependent	intracellular	nucleic acid binding|zinc ion binding	g.chr19:58385546G>T		CCDS46212.1	19q13.43	2013-01-08			ENSG00000204514	ENSG00000204514		"""Zinc fingers, C2H2-type"", ""-"""	33258	protein-coding gene	gene with protein product							Standard	NM_001144989		Approved		uc002qqo.2	B7Z6K7		ENST00000435989.2:c.1212C>A	19.37:g.58385546G>T	ENSP00000410545:p.Asp404Glu					ZNF814_ENST00000595295.1_Intron|ZNF814_ENST00000597342.1_Intron|ZNF814_ENST00000597832.1_Intron|ZNF814_ENST00000596604.1_Intron|ZNF814_ENST00000600634.1_Intron	p.D404E	NM_001144989.1	NP_001138461.1	B7Z6K7	ZN814_HUMAN			3	1446	-			404					A6NF35	Missense_Mutation	SNP	ENST00000435989.2	37	c.1212C>A	CCDS46212.1	.	.	.	.	.	.	.	.	.	.	.	11.12	1.545823	0.27652	.	.	ENSG00000204514	ENST00000435989;ENST00000376205	T	0.14640	2.49	2.33	-4.66	0.03329	Zinc finger, C2H2 (1);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04363	0.0120	N	0.03177	-0.4	0.09310	N	1	B	0.13145	0.007	B	0.10450	0.005	T	0.33574	-0.9863	9	0.54805	T	0.06	.	1.2175	0.01917	0.3897:0.3041:0.1331:0.1731	.	404	B7Z6K7	ZN814_HUMAN	E	404;266	ENSP00000410545:D404E	ENSP00000365378:D266E	D	-	3	2	ZNF814	63077358	0.000000	0.05858	0.000000	0.03702	0.038000	0.13279	-1.489000	0.02306	-2.531000	0.00491	-1.292000	0.01352	GAC		0.393	ZNF814-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466976.1	XM_001725708		3	12	1	0	1	1	1	3	12				
MUC5B	727897	broad.mit.edu	37	11	1264418	1264418	+	Missense_Mutation	SNP	C	C	G	rs201556927		TCGA-EM-A4FR-01A-11D-A257-08	TCGA-EM-A4FR-10A-01D-A25A-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cea715a5-b042-482e-9a2a-aa2781a086e2	b6b2661b-4529-47d8-84aa-cf750080d78b	g.chr11:1264418C>G	ENST00000529681.1	+	31	6366	c.6308C>G	c.(6307-6309)aCa>aGa	p.T2103R	MUC5B_ENST00000447027.1_Missense_Mutation_p.T2106R|RP11-532E4.2_ENST00000532061.2_RNA	NM_002458.2	NP_002449.2	Q9HC84	MUC5B_HUMAN	mucin 5B, oligomeric mucus/gel-forming	2103	11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.				cellular protein metabolic process (GO:0044267)|cellular response to epidermal growth factor stimulus (GO:0071364)|cellular response to glucocorticoid stimulus (GO:0071385)|cellular response to retinoic acid (GO:0071300)|epithelial cell differentiation (GO:0030855)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|response to lipopolysaccharide (GO:0032496)|response to ozone (GO:0010193)|response to sulfur dioxide (GO:0010477)|response to vitamin A (GO:0033189)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)		CACACCGCCACAGTGCTGACC	0.622																																						ENST00000447027.1																			0				cervix(2)|endometrium(36)|kidney(9)|lung(89)|urinary_tract(1)	137						c.(6316-6318)aCa>aGa		mucin 5B, oligomeric mucus/gel-forming							20.0	26.0	24.0					11																	1264418		1678	3752	5430	SO:0001583	missense	727897				cell adhesion	extracellular region	extracellular matrix structural constituent|protein binding	g.chr11:1264418C>G	U95031, AF086604	CCDS44515.1, CCDS44515.2	11p15.5	2007-01-19	2006-03-14			ENSG00000117983		"""Mucins"""	7516	protein-coding gene	gene with protein product		600770	"""mucin 5, subtype B, tracheobronchial"""	MUC5		9804771	Standard	NM_002458		Approved	MG1	uc001lta.3	Q9HC84		ENST00000529681.1:c.6308C>G	11.37:g.1264418C>G	ENSP00000436812:p.Thr2103Arg					RP11-532E4.2_ENST00000532061.2_RNA|MUC5B_ENST00000529681.1_Missense_Mutation_p.T2103R	p.T2106R			Q9HC84	MUC5B_HUMAN		BRCA - Breast invasive adenocarcinoma(625;0.00141)|Lung(200;0.0853)|LUSC - Lung squamous cell carcinoma(625;0.1)	31	6375	+		all_cancers(49;6.97e-08)|all_epithelial(84;3.45e-05)|Breast(177;0.000307)|Ovarian(85;0.000953)|Medulloblastoma(188;0.0109)|all_neural(188;0.0299)|Lung NSC(207;0.229)	2103			11 X approximate tandem repeats, Ser/Thr- rich.|7 X Cys-rich subdomain repeats.|Thr-rich.		O00447|O00573|O14985|O15494|O95291|O95451|Q14881|Q7M4S5|Q99552|Q9UE28	Missense_Mutation	SNP	ENST00000529681.1	37	c.6317C>G	CCDS44515.2	.	.	.	.	.	.	.	.	.	.	c	3.402	-0.122015	0.06795	.	.	ENSG00000117983	ENST00000529681;ENST00000447027;ENST00000349637;ENST00000406844	T;T	0.21543	2.0;2.15	1.15	1.15	0.20763	.	.	.	.	.	T	0.29321	0.0730	L	0.46157	1.445	0.09310	N	1	D;D	0.59357	0.985;0.985	P;P	0.59115	0.852;0.852	T	0.08513	-1.0718	9	0.87932	D	0	.	5.4799	0.16717	0.0:0.7913:0.0:0.2087	rs3021160	2796;2106	A7Y9J9;E9PBJ0	.;.	R	2103;2106;2104;2173	ENSP00000436812:T2103R;ENSP00000415793:T2106R	ENSP00000343037:T2104R	T	+	2	0	MUC5B	1220994	0.001000	0.12720	0.011000	0.14972	0.125000	0.20455	-0.020000	0.12525	0.927000	0.37143	0.195000	0.17529	ACA		0.622	MUC5B-002	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000390041.2	XM_001126093		3	12	0	0	0	1	0	3	12				
