#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_BAM_File	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_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_Chromosome_hg18	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	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_End_position_hg18	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	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_Mutation_Status	i_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
HCFC1	3054	genome.wustl.edu	37	X	153230156	153230156	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chrX:153230156G>A	ENST00000310441.7	-	2	1181	c.215C>T	c.(214-216)cCa>cTa	p.P72L	HCFC1_ENST00000461098.1_5'Flank|HCFC1_ENST00000354233.3_Missense_Mutation_p.P72L|HCFC1_ENST00000369984.4_Missense_Mutation_p.P72L	NM_005334.2	NP_005325.2	P51610	HCFC1_HUMAN	host cell factor C1	72					cell cycle (GO:0007049)|chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of cell cycle (GO:0045787)|positive regulation of gene expression (GO:0010628)|protein stabilization (GO:0050821)|regulation of protein complex assembly (GO:0043254)|regulation of transcription, DNA-templated (GO:0006355)|release from viral latency (GO:0019046)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|histone acetyltransferase complex (GO:0000123)|membrane (GO:0016020)|mitochondrion (GO:0005739)|MLL1 complex (GO:0071339)|MLL5-L complex (GO:0070688)|neuronal cell body (GO:0043025)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|Set1C/COMPASS complex (GO:0048188)	chromatin binding (GO:0003682)|identical protein binding (GO:0042802)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001205)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)			NS(1)|breast(2)|central_nervous_system(2)|endometrium(12)|kidney(3)|large_intestine(3)|lung(18)|ovary(2)|prostate(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	all_cancers(53;6.23e-16)|all_epithelial(53;5.61e-10)|all_lung(58;3.99e-07)|Lung NSC(58;5.02e-07)|all_hematologic(71;4.25e-06)|Acute lymphoblastic leukemia(192;6.56e-05)					CCTCACGGCTGGGATGAACCA	0.592											OREG0003629	type=REGULATORY REGION|Gene=HCFC1|Dataset=Stanford ENCODE Dataset|EvidenceSubtype=Transient transfection luciferase assay																										dbGAP											0			X											63.0	70.0	67.0					X																	153230156		2101	4192	6293	152883350	SO:0001583	missense	0				CCDS44020.1	Xq28	2014-06-12	2014-06-09		ENSG00000172534	ENSG00000172534			4839	protein-coding gene	gene with protein product	"""VP16-accessory protein"", ""protein phosphatase 1, regulatory subunit 89"""	300019	"""mental retardation, X-linked 3"", ""host cell factor C1 (VP16-accessory protein)"""	HFC1, MRX3		8392914, 23000143	Standard	XM_005274664		Approved	HCF-1, HCF1, CFF, VCAF, MGC70925, PPP1R89	uc004fjp.3	P51610	OTTHUMG00000024222	ENST00000310441.7:c.215C>T	X.37:g.153230156G>A	ENSP00000309555:p.Pro72Leu	Somatic	173	1.14	2	1754	25	81.75	112	WXS	Illumina HiSeq	Phase_IV	152883350	133	46.18	115	Q6P4G5	Missense_Mutation	SNP	HMMPfam_fn3,HMMSmart_SM00060,HMMPfam_Kelch_1,superfamily_Fibronectin type III,superfamily_Galactose oxidase central domain,HMMPfam_Kelch_2	p.P72L	ENST00000310441.7	37	c.215	CCDS44020.1	X	.	.	.	.	.	.	.	.	.	.	G	28.9	4.957903	0.92726	.	.	ENSG00000172534	ENST00000310441;ENST00000369984;ENST00000354233	T;T;T	0.61859	0.07;0.07;0.24	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.71134	0.3304	L	0.46614	1.455	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.73145	-0.4075	10	0.62326	D	0.03	.	16.9947	0.86363	0.0:0.0:1.0:0.0	.	72	P51610	HCFC1_HUMAN	L	72	ENSP00000309555:P72L;ENSP00000359001:P72L;ENSP00000346174:P72L	ENSP00000309555:P72L	P	-	2	0	HCFC1	152883350	1.000000	0.71417	0.987000	0.45799	0.853000	0.48598	9.321000	0.96353	2.276000	0.75962	0.468000	0.43344	CCA	-	superfamily_Galactose oxidase central domain		0.592	HCFC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HCFC1	protein_coding	OTTHUMT00000061099.4	G	NM_005334		152883350	-1	no_errors	NM_005334.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
LINC01562	104054213	genome.wustl.edu	37	1	51696933	51696933	+	lincRNA	SNP	C	C	T			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr1:51696933C>T	ENST00000366181.2	-	0	132				snoU13_ENST00000459356.1_RNA														p.0?(2)									catgtcagacccataatgtgc	0.393																																						dbGAP											2	Whole gene deletion(2)	thyroid(1)|central_nervous_system(1)	1																																								51469521			0																															1.37:g.51696933C>T		Somatic	173	0.57	1		3	0.00	0	WXS	Illumina HiSeq	Phase_IV	51469521	164	44.59	132		RNA	SNP	-	NULL	ENST00000366181.2	37	NULL		1																																																																																			-	-		0.393	RP11-296A18.3-001	KNOWN	basic	lincRNA	ENSG00000210557	lincRNA	OTTHUMT00000022441.1	C			51469521	-1	pseudogene	ENST00000387822	ensembl	human	novel	54_36p	rna	SNP	0.000	T
LRRC40	55631	genome.wustl.edu	37	1	70614235	70614235	+	Silent	SNP	C	C	T			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr1:70614235C>T	ENST00000370952.3	-	14	1717	c.1638G>A	c.(1636-1638)acG>acA	p.T546T		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	546						membrane (GO:0016020)		p.T546T(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						GAAGGTCCAACGTGGTCAGAT	0.358																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	1											203.0	201.0	201.0					1																	70614235		2203	4300	6503	70386823	SO:0001819	synonymous_variant	0				CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.1638G>A	1.37:g.70614235C>T		Somatic	538	0.37	2		10	54.55	12	WXS	Illumina HiSeq	Phase_IV	70386823	279	45.21	231	Q9BTR7|Q9NSK1|Q9NXC1	Silent	SNP	HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52058	p.T546	ENST00000370952.3	37	c.1638	CCDS646.1	1																																																																																			-	HMMPfam_LRR_1,HMMSmart_LRR_TYP,superfamily_SSF52058		0.358	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRRC40	protein_coding	OTTHUMT00000025914.1	C	NM_017768		70386823	-1	no_errors	NM_017768.3	genbank	human	provisional	54_36p	silent	SNP	0.095	T
RGS8	85397	genome.wustl.edu	37	1	182616020	182616020	+	Silent	SNP	C	C	T	rs147293552		TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr1:182616020C>T	ENST00000483095.2	-	7	650	c.393G>A	c.(391-393)acG>acA	p.T131T	RGS8_ENST00000367557.4_Silent_p.T131T|RGS8_ENST00000367556.1_Silent_p.T131T|RGS8_ENST00000258302.4_Silent_p.T149T			P57771	RGS8_HUMAN	regulator of G-protein signaling 8	131	RGS. {ECO:0000255|PROSITE- ProRule:PRU00171}.				positive regulation of GTPase activity (GO:0043547)|termination of G-protein coupled receptor signaling pathway (GO:0038032)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	GTPase activator activity (GO:0005096)	p.T149T(1)		haematopoietic_and_lymphoid_tissue(1)|ovary(1)|stomach(2)|upper_aerodigestive_tract(1)	5						GGTTCTTCCTCGTGGCTTCTC	0.527													C|||	1	0.000199681	0.0	0.0	5008	,	,		17602	0.001		0.0	False		,,,				2504	0.0				Ovarian(189;1262 3804 41973)	dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	1						C	,	1,4405	2.1+/-5.4	0,1,2202	159.0	155.0	156.0		393,447	-1.6	1.0	1	dbSNP_134	156	0,8600		0,0,4300	no	coding-synonymous,coding-synonymous	RGS8	NM_001102450.1,NM_033345.2	,	0,1,6502	TT,TC,CC		0.0,0.0227,0.0077	,	131/181,149/199	182616020	1,13005	2203	4300	6503	180882643	SO:0001819	synonymous_variant	0			AF297015	CCDS1349.1, CCDS41443.1	1q25	2008-07-18	2007-08-14		ENSG00000135824	ENSG00000135824		"""Regulators of G-protein signaling"""	16810	protein-coding gene	gene with protein product		607189	"""regulator of G-protein signalling 8"""			11318611	Standard	NM_001102450		Approved	MGC119067, MGC119068, MGC119069	uc001gpm.1	P57771	OTTHUMG00000035219	ENST00000483095.2:c.393G>A	1.37:g.182616020C>T		Somatic	246	3.52	9		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	180882643	232	38.20	144	B4DGL9|Q3SYD2	Silent	SNP	HMMPfam_RGS,HMMSmart_RGS,superfamily_Regulat_G_prot_signal_superfam	p.T149	ENST00000483095.2	37	c.447	CCDS41443.1	1																																																																																			-	HMMPfam_RGS,HMMSmart_RGS,superfamily_Regulat_G_prot_signal_superfam		0.527	RGS8-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	RGS8	protein_coding	OTTHUMT00000358979.1	C	NM_033345		180882643	-1	no_errors	NM_033345.1	genbank	human	reviewed	54_36p	silent	SNP	0.990	T
CUL3	8452	genome.wustl.edu	37	2	225364617	225364617	+	Intron	SNP	T	T	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	T	T	T	A	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr2:225364617T>A	ENST00000264414.4	-	11	1949				CUL3_ENST00000409096.1_Intron|CUL3_ENST00000344951.4_Intron|CUL3_ENST00000409777.1_Intron	NM_003590.4	NP_003581.1	Q13618	CUL3_HUMAN	cullin 3						cell cycle arrest (GO:0007050)|cell migration (GO:0016477)|COPII vesicle coating (GO:0048208)|cyclin catabolic process (GO:0008054)|embryonic cleavage (GO:0040016)|ER to Golgi vesicle-mediated transport (GO:0006888)|G1/S transition of mitotic cell cycle (GO:0000082)|gastrulation (GO:0007369)|integrin-mediated signaling pathway (GO:0007229)|intrinsic apoptotic signaling pathway (GO:0097193)|mitotic metaphase plate congression (GO:0007080)|negative regulation of Rho protein signal transduction (GO:0035024)|positive regulation of cell proliferation (GO:0008284)|positive regulation of cytokinesis (GO:0032467)|positive regulation of mitotic metaphase/anaphase transition (GO:0045842)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein monoubiquitination (GO:0006513)|protein polyubiquitination (GO:0000209)|protein ubiquitination (GO:0016567)|stem cell division (GO:0017145)|stress fiber assembly (GO:0043149)|trophectodermal cellular morphogenesis (GO:0001831)|Wnt signaling pathway (GO:0016055)	Cul3-RING ubiquitin ligase complex (GO:0031463)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|membrane (GO:0016020)|nucleus (GO:0005634)|polar microtubule (GO:0005827)	POZ domain binding (GO:0031208)			endometrium(6)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(2)|liver(1)|lung(19)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(3)	46		all_lung(227;0.00877)|Lung NSC(271;0.011)|Renal(207;0.0112)|all_hematologic(139;0.138)		Epithelial(121;1.58e-11)|all cancers(144;1.43e-08)|Lung(261;0.00863)|LUSC - Lung squamous cell carcinoma(224;0.00902)		CTTTCTCTGTTTTTTTCTTGC	0.388																																						dbGAP											0			2																																								225072861	SO:0001627	intron_variant	0			U58089	CCDS2462.1, CCDS58751.1	2q36.2	2011-05-24			ENSG00000036257	ENSG00000036257			2553	protein-coding gene	gene with protein product		603136				8681378, 17192413	Standard	NM_003590		Approved		uc002vny.3	Q13618	OTTHUMG00000133167	ENST00000264414.4:c.1610+462A>T	2.37:g.225364617T>A		Somatic	379	0.00	0		7	22.22	2	WXS	Illumina HiSeq	Phase_IV	225072861	336	44.93	275	A8K536|B8ZZC3|O75415|Q569L3|Q9UBI8|Q9UET7	RNA	SNP	-	NULL	ENST00000264414.4	37	NULL	CCDS2462.1	2																																																																																			-	-		0.388	CUL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LOC100131253	protein_coding	OTTHUMT00000256871.2	T			225072861	-1	pseudogene	XR_039607.1	genbank	human	model	54_36p	rna	SNP	0.261	A
VCAN	1462	genome.wustl.edu	37	5	82816697	82816697	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr5:82816697C>A	ENST00000265077.3	+	7	3137	c.2572C>A	c.(2572-2574)Cca>Aca	p.P858T	VCAN_ENST00000502527.2_Intron|VCAN_ENST00000342785.4_Missense_Mutation_p.P858T|VCAN_ENST00000512590.2_Missense_Mutation_p.P810T|VCAN_ENST00000343200.5_Intron	NM_004385.4	NP_004376.2	P13611	CSPG2_HUMAN	versican	858	GAG-alpha (glucosaminoglycan attachment domain).				carbohydrate metabolic process (GO:0005975)|cell adhesion (GO:0007155)|cell recognition (GO:0008037)|chondroitin sulfate biosynthetic process (GO:0030206)|chondroitin sulfate catabolic process (GO:0030207)|chondroitin sulfate metabolic process (GO:0030204)|dermatan sulfate biosynthetic process (GO:0030208)|extracellular matrix organization (GO:0030198)|glial cell migration (GO:0008347)|glycosaminoglycan metabolic process (GO:0030203)|heart development (GO:0007507)|multicellular organismal development (GO:0007275)|osteoblast differentiation (GO:0001649)|small molecule metabolic process (GO:0044281)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|intracellular membrane-bounded organelle (GO:0043231)|lysosomal lumen (GO:0043202)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)|glycosaminoglycan binding (GO:0005539)|hyaluronic acid binding (GO:0005540)	p.P858T(1)		NS(2)|biliary_tract(1)|breast(3)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(52)|lung(64)|ovary(8)|pancreas(3)|prostate(13)|skin(14)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(5)	190		Lung NSC(167;0.0216)|all_lung(232;0.0251)|Ovarian(174;0.142)		OV - Ovarian serous cystadenocarcinoma(54;2.47e-41)|Epithelial(54;2.51e-34)|all cancers(79;5.19e-29)	Hyaluronan(DB08818)	TACTCTTATTCCAGATAGTAC	0.403																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	5											99.0	101.0	101.0					5																	82816697		2203	4300	6503	82852453	SO:0001583	missense	0			X15998	CCDS4060.1, CCDS47242.1, CCDS54875.1, CCDS54876.1	5q14.2-q14.3	2013-05-07	2007-02-15	2007-02-15	ENSG00000038427	ENSG00000038427		"""Immunoglobulin superfamily / V-set domain containing"", ""Proteoglycans / Extracellular Matrix : Hyalectans"""	2464	protein-coding gene	gene with protein product	"""versican proteoglycan"""	118661	"""chondroitin sulfate proteoglycan 2"""	CSPG2		1478664, 21063030	Standard	NM_004385		Approved	PG-M	uc003kii.3	P13611	OTTHUMG00000131321	ENST00000265077.3:c.2572C>A	5.37:g.82816697C>A	ENSP00000265077:p.Pro858Thr	Somatic	808	0.37	3		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	82852453	312	45.09	257	P20754|Q13010|Q13189|Q15123|Q9UCL9|Q9UNW5	Missense_Mutation	SNP	PatternScan_ASX_HYDROXYL,HMMPfam_Sushi,HMMSmart_SM00032,HMMPfam_Xlink,HMMSmart_SM00445,PatternScan_LINK_1,HMMPfam_Lectin_C,HMMSmart_SM00034,HMMSmart_SM00179,HMMSmart_SM00409,HMMPfam_EGF,HMMSmart_SM00181,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_V-set,superfamily_Complement control module/SCR domain,superfamily_C-type lectin-like,PatternScan_EGF_CA,PatternScan_C_TYPE_LECTIN_1,superfamily_Immunoglobulin,superfamily_EGF/Laminin	p.P858T	ENST00000265077.3	37	c.2572	CCDS4060.1	5	.	.	.	.	.	.	.	.	.	.	C	0.920	-0.716119	0.03206	.	.	ENSG00000038427	ENST00000265077;ENST00000342785;ENST00000512590	T;T;T	0.24538	1.85;1.85;1.85	6.07	0.572	0.17357	.	0.932993	0.09061	N	0.854311	T	0.17704	0.0425	L	0.53249	1.67	0.09310	N	1	P;B	0.38597	0.639;0.307	B;B	0.31686	0.134;0.018	T	0.19712	-1.0297	10	0.31617	T	0.26	.	2.5439	0.04732	0.1376:0.5045:0.1215:0.2364	.	858;858	P13611-3;P13611	.;CSPG2_HUMAN	T	858;858;810	ENSP00000265077:P858T;ENSP00000342768:P858T;ENSP00000425959:P810T	ENSP00000265077:P858T	P	+	1	0	VCAN	82852453	0.002000	0.14202	0.004000	0.12327	0.089000	0.18198	-0.209000	0.09358	0.139000	0.18822	-0.150000	0.13652	CCA	-	NULL		0.403	VCAN-001	KNOWN	basic|CCDS	protein_coding	VCAN	protein_coding	OTTHUMT00000254092.3	C	NM_004385		82852453	+1	no_errors	NM_004385.1	genbank	human	validated	54_36p	missense	SNP	0.008	A
WAC	51322	genome.wustl.edu	37	10	28824556	28824556	+	Silent	SNP	C	C	T			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr10:28824556C>T	ENST00000354911.4	+	3	305	c.144C>T	c.(142-144)gaC>gaT	p.D48D	WAC_ENST00000375664.4_Silent_p.D3D|WAC-AS1_ENST00000527986.1_RNA|WAC_ENST00000347934.4_Silent_p.D48D|WAC_ENST00000375646.1_Silent_p.D3D|WAC_ENST00000428935.1_Silent_p.D3D|WAC_ENST00000532233.1_3'UTR	NM_016628.4	NP_057712.2	Q9BTA9	WAC_HUMAN	WW domain containing adaptor with coiled-coil	48					cellular response to DNA damage stimulus (GO:0006974)|G1 DNA damage checkpoint (GO:0044783)|histone H2B conserved C-terminal lysine ubiquitination (GO:0071894)|histone monoubiquitination (GO:0010390)|negative regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032435)|positive regulation of macroautophagy (GO:0016239)|positive regulation of transcription, DNA-templated (GO:0045893)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)|spliceosomal complex (GO:0005681)	chromatin binding (GO:0003682)|RNA polymerase II core binding (GO:0000993)	p.D48D(1)		NS(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(5)|kidney(3)|large_intestine(7)|lung(11)|ovary(1)|urinary_tract(1)	32						AGATGCGAGACGCCGGAGATC	0.448																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	10											102.0	102.0	102.0					10																	28824556		2203	4300	6503	28864562	SO:0001819	synonymous_variant	0			AK055852	CCDS7159.1, CCDS7160.1, CCDS7161.1	10p12.1	2007-05-17	2003-03-19		ENSG00000095787	ENSG00000095787			17327	protein-coding gene	gene with protein product		615049	"""WW domain-containing adaptor with coiled coil"""			11827461	Standard	NR_024557		Approved	Wwp4, FLJ31290, PRO1741, BM-016, MGC10753	uc001iuf.3	Q9BTA9	OTTHUMG00000017872	ENST00000354911.4:c.144C>T	10.37:g.28824556C>T		Somatic	358	2.45	9		102	52.11	111	WXS	Illumina HiSeq	Phase_IV	28864562	343	46.42	298	A8K2A9|C9JBT9|D3DRW5|D3DRW6|D3DRW7|Q53EN9|Q5JU75|Q5JU77|Q5VXK0|Q5VXK2|Q8TCK1|Q96DP3|Q96FW6|Q96JI3	Silent	SNP	HMMPfam_WW,HMMSmart_SM00456,PatternScan_WW_DOMAIN_1,superfamily_WW domain	p.D48	ENST00000354911.4	37	c.144	CCDS7159.1	10																																																																																			-	NULL		0.448	WAC-017	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	WAC	protein_coding	OTTHUMT00000047371.1	C	NM_100264		28864562	+1	no_errors	NM_016628.3	genbank	human	reviewed	54_36p	silent	SNP	1.000	T
PLCE1	51196	genome.wustl.edu	37	10	95993941	95993941	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr10:95993941C>A	ENST00000371380.3	+	5	2321	c.2086C>A	c.(2086-2088)Cac>Aac	p.H696N	PLCE1_ENST00000371385.3_Missense_Mutation_p.H388N|PLCE1_ENST00000371375.1_Missense_Mutation_p.H388N|PLCE1_ENST00000260766.3_Missense_Mutation_p.H696N			Q9P212	PLCE1_HUMAN	phospholipase C, epsilon 1	696	Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00168}.				activation of MAPK activity (GO:0000187)|calcium-mediated signaling (GO:0019722)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|diacylglycerol biosynthetic process (GO:0006651)|epidermal growth factor receptor signaling pathway (GO:0007173)|glomerulus development (GO:0032835)|heart development (GO:0007507)|inositol phosphate metabolic process (GO:0043647)|inositol phosphate-mediated signaling (GO:0048016)|lipid catabolic process (GO:0016042)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|phospholipid metabolic process (GO:0006644)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|positive regulation of GTPase activity (GO:0043547)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|Ras protein signal transduction (GO:0007265)|regulation of cell growth (GO:0001558)|regulation of G-protein coupled receptor protein signaling pathway (GO:0008277)|regulation of protein kinase activity (GO:0045859)|regulation of Ras protein signal transduction (GO:0046578)|regulation of smooth muscle contraction (GO:0006940)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)|enzyme binding (GO:0019899)|guanyl-nucleotide exchange factor activity (GO:0005085)|phosphatidylinositol phospholipase C activity (GO:0004435)|phospholipase C activity (GO:0004629)|Ras GTPase binding (GO:0017016)|receptor signaling protein activity (GO:0005057)	p.H696N(1)		liver(1)|ovary(2)|skin(4)|upper_aerodigestive_tract(1)	8		Colorectal(252;0.0458)				ACGTGCCCTGCACATCCCTGG	0.552																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	10											150.0	157.0	155.0					10																	95993941		2073	4201	6274	95983931	SO:0001583	missense	0				CCDS41552.1, CCDS53555.1	10q23	2010-02-22			ENSG00000138193	ENSG00000138193	3.1.4.11		17175	protein-coding gene	gene with protein product	"""nephrosis type 3"""	608414				11022047, 11022048	Standard	NM_016341		Approved	KIAA1516, PLCE, NPHS3	uc001kjk.3	Q9P212	OTTHUMG00000018789	ENST00000371380.3:c.2086C>A	10.37:g.95993941C>A	ENSP00000360431:p.His696Asn	Somatic	317	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	95983931	329	42.58	244	A6NGW0|A6NLA1|A7MBN7|A8K1D7|B9EIJ6|Q1X6H8|Q5VWL4|Q5VWL5|Q9H9X8|Q9HBX6|Q9HC53|Q9UHV3	Missense_Mutation	SNP	HMMPfam_C2,HMMSmart_SM00239,HMMPfam_RA,HMMSmart_SM00314,HMMPfam_PI-PLC-X,HMMSmart_SM00148,HMMPfam_PI-PLC-Y,HMMSmart_SM00149,HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF,superfamily_C2 domain (Calcium/lipid-binding domain CaLB),HMMPfam_efhand_like,superfamily_PLC-like phosphodiesterases,superfamily_EF-hand	p.H696N	ENST00000371380.3	37	c.2086	CCDS41552.1	10	.	.	.	.	.	.	.	.	.	.	C	11.83	1.756883	0.31137	.	.	ENSG00000138193	ENST00000260766;ENST00000371380;ENST00000371385;ENST00000371375	T;T;T;T	0.27557	1.66;1.66;1.66;1.66	5.78	4.77	0.60923	Guanine-nucleotide dissociation stimulator CDC25 (4);Ras guanine nucleotide exchange factor, domain (1);	0.055371	0.64402	D	0.000002	T	0.06917	0.0176	N	0.00289	-1.7	0.40213	D	0.977642	B;B;B	0.09022	0.001;0.001;0.002	B;B;B	0.12156	0.007;0.003;0.002	T	0.37314	-0.9711	10	0.02654	T	1	.	11.7894	0.52061	0.363:0.637:0.0:0.0	.	696;388;696	B7ZM61;Q9P212-2;Q9P212	.;.;PLCE1_HUMAN	N	696;696;388;388	ENSP00000260766:H696N;ENSP00000360431:H696N;ENSP00000360438:H388N;ENSP00000360426:H388N	ENSP00000260766:H696N	H	+	1	0	PLCE1	95983931	1.000000	0.71417	1.000000	0.80357	0.980000	0.70556	6.458000	0.73509	2.894000	0.99253	0.655000	0.94253	CAC	-	HMMPfam_RasGEF,HMMSmart_SM00147,superfamily_Ras GEF		0.552	PLCE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	PLCE1	protein_coding	OTTHUMT00000049469.3	C	NM_016341		95983931	+1	no_errors	NM_016341.3	genbank	human	validated	54_36p	missense	SNP	1.000	A
SFXN2	118980	genome.wustl.edu	37	10	104489530	104489530	+	Silent	SNP	G	G	A	rs201849917		TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr10:104489530G>A	ENST00000369893.5	+	6	725	c.558G>A	c.(556-558)gcG>gcA	p.A186A		NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	186				QMALSYFTATTTAVATAVGMNMLTKKAPPLVGRWVPFAAVA AANCVNIPMMRQQELIKGI -> KRRPWWAAGCPLPLWLRL TVSISP (in Ref. 4). {ECO:0000305}.	iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)	p.A186A(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		CTGTGGCTGCGGCTAACTGTG	0.542											OREG0020485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																										dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	10						G		1,4405	2.1+/-5.4	0,1,2202	75.0	81.0	79.0		558	-11.4	0.1	10		79	0,8600		0,0,4300	no	coding-synonymous	SFXN2	NM_178858.4		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		186/323	104489530	1,13005	2203	4300	6503	104479520	SO:0001819	synonymous_variant	0			AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"""Sideroflexins"""	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.558G>A	10.37:g.104489530G>A		Somatic	207	0.00	0	1382	4	33.33	2	WXS	Illumina HiSeq	Phase_IV	104479520	179	47.41	165	Q5JSM6	Silent	SNP	HMMPfam_Mtc	p.A186	ENST00000369893.5	37	c.558	CCDS7539.1	10																																																																																			-	HMMPfam_Mtc		0.542	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SFXN2	protein_coding	OTTHUMT00000050096.2	G	XM_058359		104479520	+1	no_errors	NM_178858.4	genbank	human	validated	54_36p	silent	SNP	0.885	A
USP2	9099	genome.wustl.edu	37	11	119246614	119246614	+	Intron	SNP	G	G	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr11:119246614G>A	ENST00000260187.2	-	2	254				RP11-334E6.3_ENST00000530918.2_RNA|USP2_ENST00000455332.2_Intron	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2						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)		CTTTGGAGCCGGAGGTGGGGC	0.622																																						dbGAP											0			11																																								118751824	SO:0001627	intron_variant	0			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.41-2383C>T	11.37:g.119246614G>A		Somatic	92	1.08	1		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	118751824	84	40.85	58	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Missense_Mutation	SNP	NULL	p.R76Q	ENST00000260187.2	37	c.227	CCDS8422.1	11																																																																																			-	NULL		0.622	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LOC100130353	protein_coding	OTTHUMT00000388361.2	G	NM_171997		118751824	+1	no_errors	XM_001719137.1	genbank	human	model	54_36p	missense	SNP	0.001	A
RNU6-837P	106479936	genome.wustl.edu	37	12	17224377	17224377	+	RNA	SNP	G	G	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr12:17224377G>A	ENST00000391056.1	-	0	62									RNA, U6 small nuclear 837, pseudogene																		tccttgaggaggagccgaact	0.308																																						dbGAP											0			12																																								17115644			0					12p12.3	2013-05-01			ENSG00000212358	ENSG00000212358			47800	pseudogene	RNA, pseudogene							Standard			Approved						12.37:g.17224377G>A		Somatic	805	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	17115644	464	37.80	282		RNA	SNP	-	NULL	ENST00000391056.1	37	NULL		12																																																																																			-	-		0.308	RNU6-837P-201	KNOWN	basic	snRNA	ENSG00000212358	snRNA		G			17115644	-1	no_errors	ENST00000391056	ensembl	human	novel	54_36p	rna	SNP	0.001	A
KRAS	3845	genome.wustl.edu	37	12	25378562	25378562	+	Missense_Mutation	SNP	C	C	T	rs121913527		TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr12:25378562C>T	ENST00000256078.4	-	4	499	c.436G>A	c.(436-438)Gca>Aca	p.A146T	AC087239.1_ENST00000594112.1_5'Flank|KRAS_ENST00000311936.3_Missense_Mutation_p.A146T|KRAS_ENST00000557334.1_Intron	NM_033360.2	NP_203524.1	P01116	RASK_HUMAN	Kirsten rat sarcoma viral oncogene homolog	146			A -> T (in a colorectal cancer sample; somatic mutation). {ECO:0000269|PubMed:16959974}.		actin cytoskeleton organization (GO:0030036)|activation of MAPKK activity (GO:0000186)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|epidermal growth factor receptor signaling pathway (GO:0007173)|epithelial tube branching involved in lung morphogenesis (GO:0060441)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|GTP catabolic process (GO:0006184)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|MAPK cascade (GO:0000165)|negative regulation of cell differentiation (GO:0045596)|negative regulation of neuron apoptotic process (GO:0043524)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of cell proliferation (GO:0008284)|positive regulation of gene expression (GO:0010628)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric-oxide synthase activity (GO:0051000)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of Rac protein signal transduction (GO:0035022)|Ras protein signal transduction (GO:0007265)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of synaptic transmission, GABAergic (GO:0032228)|response to glucocorticoid (GO:0051384)|response to mineralocorticoid (GO:0051385)|small GTPase mediated signal transduction (GO:0007264)|social behavior (GO:0035176)|striated muscle cell differentiation (GO:0051146)|visual learning (GO:0008542)	focal adhesion (GO:0005925)|membrane (GO:0016020)|membrane raft (GO:0045121)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)	GDP binding (GO:0019003)|GMP binding (GO:0019002)|GTP binding (GO:0005525)|protein complex binding (GO:0032403)	p.A146T(75)|p.A146P(7)	UBE2L3/KRAS(2)	NS(6)|adrenal_gland(1)|autonomic_ganglia(3)|biliary_tract(532)|bone(2)|breast(32)|central_nervous_system(14)|cervix(50)|endometrium(411)|eye(4)|gastrointestinal_tract_(site_indeterminate)(7)|genital_tract(1)|haematopoietic_and_lymphoid_tissue(385)|kidney(8)|large_intestine(15267)|liver(29)|lung(3407)|oesophagus(16)|ovary(612)|pancreas(3739)|penis(1)|peritoneum(6)|prostate(96)|salivary_gland(6)|skin(45)|small_intestine(68)|soft_tissue(88)|stomach(207)|testis(17)|thymus(5)|thyroid(159)|upper_aerodigestive_tract(68)|urinary_tract(57)	25349	all_cancers(2;1e-35)|all_epithelial(2;1.97e-38)|all_lung(3;2.1e-23)|Lung NSC(3;1.16e-22)|Acute lymphoblastic leukemia(6;0.00231)|all_hematologic(7;0.00259)|Melanoma(3;0.0301)|Colorectal(261;0.11)|Ovarian(17;0.12)		OV - Ovarian serous cystadenocarcinoma(3;1.23e-21)|Epithelial(3;1.31e-20)|all cancers(3;5.45e-18)|STAD - Stomach adenocarcinoma(2;2.68e-05)			CTTGTCTTTGCTGATGTTTCA	0.323	A146T(AMO1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)|A146T(LS1034_LARGE_INTESTINE)|A146T(NUDHL1_HAEMATOPOIETIC_AND_LYMPHOID_TISSUE)	119	Mis		"""pancreatic, colorectal, lung, thyroid, AML, others"""				Noonan syndrome;Cardiofaciocutaneous syndrome	TSP Lung(1;<1E-08)|Multiple Myeloma(2;<1E-6)																											Pancreas(8;6 143 191 305 2070 2426 4376 10944 11745 26467 38091 50869)	dbGAP		Dom	yes		12	12p12.1	3845	v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog		"""L, E, M, O"""	82	Substitution - Missense(82)	large_intestine(69)|haematopoietic_and_lymphoid_tissue(11)|lung(2)	12											207.0	188.0	195.0					12																	25378562		2203	4300	6503	25269829	SO:0001583	missense	0	Familial Cancer Database	Male Turner syndrome, Pterygium Colli syndrome, incl. Noonan-like/Multiple Giant Cell Lesion syndrome; Noonan s. with multiple lentigines/LEOPARD syndrome;CFC, CFCS	BC010502	CCDS8702.1, CCDS8703.1	12p12.1	2014-09-17	2013-07-08	2005-01-24	ENSG00000133703	ENSG00000133703			6407	protein-coding gene	gene with protein product		190070	"""v-Ki-ras2 Kirsten rat sarcoma 2 viral oncogene homolog"", ""v-Ki-ras2 Kirsten rat sarcoma viral oncogene homolog"""	KRAS2			Standard	NM_004985		Approved	KRAS1	uc001rgp.1	P01116		ENST00000256078.4:c.436G>A	12.37:g.25378562C>T	ENSP00000256078:p.Ala146Thr	Somatic	197	1.01	2		26	27.78	10	WXS	Illumina HiSeq	Phase_IV	25269829	289	39.08	186	A8K8Z5|B0LPF9|P01118|Q96D10	Missense_Mutation	SNP	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.A146T	ENST00000256078.4	37	c.436	CCDS8703.1	12	.	.	.	.	.	.	.	.	.	.	C	33	5.234460	0.95207	.	.	ENSG00000133703	ENST00000311936;ENST00000256078	D;D	0.88741	-2.42;-2.42	5.52	5.52	0.82312	Small GTP-binding protein domain (1);	0.045975	0.85682	D	0.000000	D	0.96639	0.8903	H	0.97131	3.945	0.80722	D	1	D;D	0.89917	1.0;0.963	D;P	0.76071	0.987;0.876	D	0.97524	1.0075	10	0.72032	D	0.01	.	18.7849	0.91951	0.0:1.0:0.0:0.0	.	146;146	P01116-2;P01116	.;RASK_HUMAN	T	146	ENSP00000308495:A146T;ENSP00000256078:A146T	ENSP00000256078:A146T	A	-	1	0	KRAS	25269829	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.762000	0.85270	2.757000	0.94681	0.585000	0.79938	GCA	-	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.323	KRAS-004	KNOWN	not_organism_supported|basic|appris_candidate_longest|CCDS	protein_coding	KRAS	protein_coding	OTTHUMT00000412232.1	C	NM_033360		25269829	-1	no_errors	NM_033360.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
AMER2	219287	genome.wustl.edu	37	13	25743843	25743843	+	Missense_Mutation	SNP	T	T	G			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	T	T	T	G	T	T	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr13:25743843T>G	ENST00000515384.1	-	1	2582	c.1915A>C	c.(1915-1917)Atc>Ctc	p.I639L	AMER2_ENST00000357816.2_Missense_Mutation_p.I520L|AMER2_ENST00000381853.3_Missense_Mutation_p.I520L			Q8N7J2	AMER2_HUMAN	APC membrane recruitment protein 2	639					ectoderm development (GO:0007398)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|Wnt signaling pathway (GO:0016055)	plasma membrane (GO:0005886)	phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)	p.I520L(1)									GAAACCGGGATTTTTGTTCTG	0.557																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	13											95.0	95.0	95.0					13																	25743843		2203	4300	6503	24641843	SO:0001583	missense	0			AK055049	CCDS9312.1, CCDS53859.1	13q12.13	2013-10-11	2012-12-03	2012-12-03	ENSG00000165566	ENSG00000165566		"""-"""	26360	protein-coding gene	gene with protein product		614659	"""family with sequence similarity 123A"""	FAM123A		20843316	Standard	XM_005266279		Approved	FLJ25477	uc001uqb.3	Q8N7J2	OTTHUMG00000016602	ENST00000515384.1:c.1915A>C	13.37:g.25743843T>G	ENSP00000426528:p.Ile639Leu	Somatic	222	0.89	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	24641843	250	45.30	207	Q5RL80|Q5VX56|Q8N593|Q96NN5	Missense_Mutation	SNP	HMMPfam_WTX	p.I639L	ENST00000515384.1	37	c.1915	CCDS53859.1	13	.	.	.	.	.	.	.	.	.	.	T	23.4	4.416191	0.83449	.	.	ENSG00000165566	ENST00000357816;ENST00000381853;ENST00000515384	T;T;T	0.43688	1.0;1.0;0.94	5.97	4.78	0.61160	.	0.000000	0.85682	D	0.000000	T	0.42086	0.1187	L	0.27053	0.805	0.48975	D	0.999734	P;P	0.50272	0.89;0.933	P;P	0.52454	0.503;0.699	T	0.37009	-0.9724	10	0.72032	D	0.01	-8.7412	11.8905	0.52626	0.1306:0.0:0.0:0.8694	.	639;520	Q8N7J2;Q8N7J2-2	F123A_HUMAN;.	L	520;520;639	ENSP00000350469:I520L;ENSP00000371277:I520L;ENSP00000426528:I639L	ENSP00000350469:I520L	I	-	1	0	FAM123A	24641843	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.688000	0.68227	1.055000	0.40461	0.533000	0.62120	ATC	-	NULL		0.557	AMER2-002	KNOWN	basic|CCDS	protein_coding	FAM123A	protein_coding	OTTHUMT00000370229.1	T	NM_152704		24641843	-1	no_errors	NM_152704.2	genbank	human	validated	54_36p	missense	SNP	1.000	G
IGHE	3497	genome.wustl.edu	37	14	106067344	106067344	+	lincRNA	SNP	G	G	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr14:106067344G>A	ENST00000390540.2	-	0	1154				IGHE_ENST00000577108.1_RNA|IGHE_ENST00000576077.1_RNA|AL928742.12_ENST00000412518.1_lincRNA																							TTGTGTGGAGGCCAGCTCACC	0.607																																						dbGAP											0			14											46.0	45.0	45.0					14																	106067344		2097	4213	6310	105138389			0																															14.37:g.106067344G>A		Somatic	157	0.00	0		0	0.00	0	WXS	Illumina HiSeq	Phase_IV	105138389	96	45.65	84		Missense_Mutation	SNP	PatternScan_IG_MHC,HMMPfam_C1-set,HMMSmart_SM00407,superfamily_Immunoglobulin	p.P172S	ENST00000390540.2	37	c.514		14																																																																																			-	HMMPfam_C1-set,HMMSmart_SM00407,superfamily_Immunoglobulin		0.607	RP11-731F5.1-001	KNOWN	basic	lincRNA	IGHE	lincRNA	OTTHUMT00000380286.1	G			105138389	-1	no_start_codon:pseudogene:no_stop_codon:bad_bp_length_for_coding_region	ENST00000390541	ensembl	human	known	54_36p	missense	SNP	0.106	A
IDH2	3418	genome.wustl.edu	37	15	90631934	90631934	+	Missense_Mutation	SNP	C	C	T	rs121913502		TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr15:90631934C>T	ENST00000330062.3	-	4	532	c.419G>A	c.(418-420)cGg>cAg	p.R140Q	IDH2_ENST00000559482.1_Intron|IDH2_ENST00000539790.1_Missense_Mutation_p.R10Q|IDH2_ENST00000540499.2_Missense_Mutation_p.R88Q	NM_002168.2	NP_002159.2	P48735	IDHP_HUMAN	isocitrate dehydrogenase 2 (NADP+), mitochondrial	140	Substrate binding. {ECO:0000250}.		R -> G (in D2HGA2). {ECO:0000269|PubMed:20847235}.|R -> Q (in D2HGA2). {ECO:0000269|PubMed:20847235}.		2-oxoglutarate metabolic process (GO:0006103)|carbohydrate metabolic process (GO:0005975)|cellular metabolic process (GO:0044237)|glyoxylate cycle (GO:0006097)|isocitrate metabolic process (GO:0006102)|small molecule metabolic process (GO:0044281)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	isocitrate dehydrogenase (NADP+) activity (GO:0004450)|magnesium ion binding (GO:0000287)|NAD binding (GO:0051287)	p.R140Q(292)|p.R140L(8)		biliary_tract(11)|bone(19)|central_nervous_system(107)|endometrium(1)|haematopoietic_and_lymphoid_tissue(953)|large_intestine(8)|lung(5)|skin(5)	1109	Melanoma(11;0.00551)|Lung NSC(78;0.0196)|all_lung(78;0.04)		BRCA - Breast invasive adenocarcinoma(143;0.0146)|KIRC - Kidney renal clear cell carcinoma(17;0.0286)|Kidney(142;0.0514)|STAD - Stomach adenocarcinoma(125;0.106)			CAGGATGTTCCGGATAGTTCC	0.537			M		GBM																																	dbGAP		Dom	yes		15	15q26.1	3418	"""socitrate dehydrogenase 2 (NADP+), mitochondrial """		M	300	Substitution - Missense(300)	haematopoietic_and_lymphoid_tissue(300)	15											103.0	103.0	103.0					15																	90631934		2200	4298	6498	88432938	SO:0001583	missense	0				CCDS10359.1	15q26.1	2014-09-17			ENSG00000182054	ENSG00000182054	1.1.1.42		5383	protein-coding gene	gene with protein product		147650					Standard	NM_001289910		Approved		uc002box.3	P48735	OTTHUMG00000149815	ENST00000330062.3:c.419G>A	15.37:g.90631934C>T	ENSP00000331897:p.Arg140Gln	Somatic	121	0.00	0		181	45.15	149	WXS	Illumina HiSeq	Phase_IV	88432938	103	42.13	75	B2R6L6|B4DFL2|Q96GT3	Missense_Mutation	SNP	HMMPfam_Iso_dh,PatternScan_IDH_IMDH,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like	p.R140Q	ENST00000330062.3	37	c.419	CCDS10359.1	15	.	.	.	.	.	.	.	.	.	.	C	18.35	3.604397	0.66445	.	.	ENSG00000182054	ENST00000330062;ENST00000539790;ENST00000540499	D;D;D	0.87179	-2.22;-2.22;-2.22	5.67	4.75	0.60458	Isopropylmalate dehydrogenase-like domain (2);	0.000000	0.85682	D	0.000000	D	0.95449	0.8522	H	0.96833	3.89	0.48185	D	0.999601	D	0.89917	1.0	D	0.87578	0.998	D	0.96254	0.9185	10	0.87932	D	0	.	12.4459	0.55651	0.0:0.9189:0.0:0.0811	.	140	P48735	IDHP_HUMAN	Q	140;10;88	ENSP00000331897:R140Q;ENSP00000438457:R10Q;ENSP00000446147:R88Q	ENSP00000331897:R140Q	R	-	2	0	IDH2	88432938	1.000000	0.71417	1.000000	0.80357	0.051000	0.14879	7.797000	0.85911	1.397000	0.46682	-0.258000	0.10820	CGG	-	HMMPfam_Iso_dh,superfamily_Isocitrate/Isopropylmalate dehydrogenase-like		0.537	IDH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	IDH2	protein_coding	OTTHUMT00000313426.1	C			88432938	-1	no_errors	NM_002168.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
DNAJA3	9093	genome.wustl.edu	37	16	4500470	4500470	+	Silent	SNP	G	G	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr16:4500470G>A	ENST00000262375.6	+	10	1388	c.1311G>A	c.(1309-1311)acG>acA	p.T437T	DNAJA3_ENST00000355296.4_Silent_p.T437T|DNAJA3_ENST00000431375.2_Silent_p.T284T	NM_005147.5	NP_005138.3	Q96EY1	DNJA3_HUMAN	DnaJ (Hsp40) homolog, subfamily A, member 3	437					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|activation-induced cell death of T cells (GO:0006924)|cell aging (GO:0007569)|mitochondrial DNA replication (GO:0006264)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043154)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of interferon-gamma-mediated signaling pathway (GO:0060336)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of programmed cell death (GO:0043069)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuromuscular junction development (GO:0007528)|positive regulation of apoptotic process (GO:0043065)|positive regulation of protein ubiquitination (GO:0031398)|positive regulation of T cell proliferation (GO:0042102)|protein folding (GO:0006457)|protein stabilization (GO:0050821)|response to heat (GO:0009408)|response to interferon-gamma (GO:0034341)|skeletal muscle acetylcholine-gated channel clustering (GO:0071340)|small GTPase mediated signal transduction (GO:0007264)|T cell differentiation in thymus (GO:0033077)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of plasma membrane (GO:0019897)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)|neuromuscular junction (GO:0031594)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|interferon-gamma receptor binding (GO:0005133)|metal ion binding (GO:0046872)|NF-kappaB binding (GO:0051059)|protein kinase binding (GO:0019901)|small GTPase regulator activity (GO:0005083)|transcription factor binding (GO:0008134)	p.T437T(1)		NS(1)|breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(5)|ovary(2)|upper_aerodigestive_tract(2)	15						TGGAGGGGACGGTGAACGGCG	0.622																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	16											46.0	37.0	40.0					16																	4500470		2197	4298	6495	4440471	SO:0001819	synonymous_variant	0			AF061749	CCDS10515.1, CCDS45400.1, CCDS66930.1	16p13.3	2011-09-02			ENSG00000103423	ENSG00000103423		"""Heat shock proteins / DNAJ (HSP40)"""	11808	protein-coding gene	gene with protein product		608382		TID1		9683573	Standard	NM_005147		Approved	hTid-1	uc002cwk.3	Q96EY1	OTTHUMG00000129470	ENST00000262375.6:c.1311G>A	16.37:g.4500470G>A		Somatic	142	2.74	4		23	42.50	17	WXS	Illumina HiSeq	Phase_IV	4440471	103	46.63	90	B2RAJ5|B4DI33|E7ES32|O75472|Q8WUJ6|Q8WXJ3|Q96D76|Q96IV1|Q9NYH8	Silent	SNP	HMMPfam_DnaJ_CXXCXGXG,superfamily_HSP_DnaJ_cys-rich,HMMPfam_DnaJ,HMMSmart_DnaJ,superfamily_DnaJ_N,HMMPfam_DnaJ_C,superfamily_HSP40_DnaJ_pep,PatternScan_DNAJ_1	p.T437	ENST00000262375.6	37	c.1311	CCDS10515.1	16																																																																																			-	NULL		0.622	DNAJA3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	DNAJA3	protein_coding	OTTHUMT00000251633.1	G			4440471	+1	no_errors	NM_005147.1	genbank	human	validated	54_36p	silent	SNP	0.515	A
SMG1	23049	genome.wustl.edu	37	16	18852979	18852979	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr16:18852979A>T	ENST00000446231.2	-	41	7016	c.6604T>A	c.(6604-6606)Tca>Aca	p.S2202T	SMG1_ENST00000389467.3_Missense_Mutation_p.S2202T			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2202	PI3K/PI4K. {ECO:0000255|PROSITE- ProRule:PRU00269}.				DNA repair (GO:0006281)|gene expression (GO:0010467)|mRNA export from nucleus (GO:0006406)|mRNA metabolic process (GO:0016071)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine phosphorylation (GO:0018105)|phosphatidylinositol phosphorylation (GO:0046854)|protein autophosphorylation (GO:0046777)|response to stress (GO:0006950)|RNA metabolic process (GO:0016070)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	ATP binding (GO:0005524)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)	p.S2198T(1)		NS(2)|breast(8)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(16)|lung(37)|ovary(1)|skin(1)|stomach(4)|urinary_tract(1)	92						ATTAGTCCTGATCTTGTTCCT	0.438																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	16											238.0	225.0	229.0					16																	18852979		1952	4142	6094	18760480	SO:0001583	missense	0			AB061371	CCDS45430.1	16p12.3	2013-07-02	2013-07-02		ENSG00000157106	ENSG00000157106			30045	protein-coding gene	gene with protein product	"""phosphatidylinositol 3-kinase-related kinase"""	607032	"""smg-1 homolog, phosphatidylinositol 3-kinase-related kinase (C. elegans)"""			9455477, 11331269, 17229728	Standard	NM_015092		Approved	LIP, KIAA0421, ATX	uc002dfm.3	Q96Q15	OTTHUMG00000166900	ENST00000446231.2:c.6604T>A	16.37:g.18852979A>T	ENSP00000402515:p.Ser2202Thr	Somatic	1003	1.47	15		38	43.28	29	WXS	Illumina HiSeq	Phase_IV	18760480	265	51.09	281	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	HMMPfam_HEAT,HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,HMMPfam_FATC,superfamily_Protein kinase-like (PK-like),superfamily_ARM repeat,PatternScan_PI3_4_KINASE_2	p.S2202T	ENST00000446231.2	37	c.6604	CCDS45430.1	16	.	.	.	.	.	.	.	.	.	.	A	24.2	4.502896	0.85176	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	D;D	0.81579	-1.51;-1.51	5.48	5.48	0.80851	Protein kinase-like domain (1);Armadillo-type fold (1);Phosphatidylinositol 3-/4-kinase, catalytic (3);	0.000000	0.56097	D	0.000036	D	0.88800	0.6535	M	0.72479	2.2	0.45837	D	0.9987	D;D	0.57257	0.974;0.979	D;D	0.74023	0.953;0.982	D	0.89783	0.3962	10	0.66056	D	0.02	.	15.8631	0.79040	1.0:0.0:0.0:0.0	.	2062;2202	Q96Q15-2;Q96Q15	.;SMG1_HUMAN	T	2202	ENSP00000402515:S2202T;ENSP00000374118:S2202T	ENSP00000374118:S2202T	S	-	1	0	SMG1	18760480	1.000000	0.71417	0.977000	0.42913	0.998000	0.95712	9.212000	0.95126	2.198000	0.70561	0.533000	0.62120	TCA	-	HMMPfam_PI3_PI4_kinase,HMMSmart_SM00146,superfamily_Protein kinase-like (PK-like)		0.438	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	SMG1	protein_coding	OTTHUMT00000391817.1	A	NM_015092		18760480	-1	no_errors	NM_015092.4	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
AP1M1	8907	genome.wustl.edu	37	19	16337261	16337261	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr19:16337261C>G	ENST00000291439.3	+	6	1025	c.576C>G	c.(574-576)agC>agG	p.S192R	AP1M1_ENST00000590756.1_Missense_Mutation_p.S120R|AP1M1_ENST00000541844.1_Missense_Mutation_p.S120R|AP1M1_ENST00000444449.2_Missense_Mutation_p.S204R|AP1M1_ENST00000429941.2_Missense_Mutation_p.S192R	NM_032493.3	NP_115882.1	Q9BXS5	AP1M1_HUMAN	adaptor-related protein complex 1, mu 1 subunit	192	MHD. {ECO:0000255|PROSITE- ProRule:PRU00404}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|endosome to melanosome transport (GO:0035646)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of defense response to virus by virus (GO:0050690)|viral process (GO:0016032)	clathrin adaptor complex (GO:0030131)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|Golgi membrane (GO:0000139)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|trans-Golgi network membrane (GO:0032588)		p.S192R(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(3)|lung(7)|ovary(3)|prostate(2)	21						TCCTGCGCAGCGAGATCGTGG	0.642																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	19											53.0	34.0	41.0					19																	16337261		2198	4298	6496	16198261	SO:0001583	missense	0				CCDS12342.1, CCDS46008.1	19p13.12	2008-05-23							13667	protein-coding gene	gene with protein product		603535				9653655, 17988225	Standard	NM_032493		Approved	AP47, CLAPM2	uc002ndv.2	Q9BXS5		ENST00000291439.3:c.576C>G	19.37:g.16337261C>G	ENSP00000291439:p.Ser192Arg	Somatic	35	0.00	0		24	41.46	17	WXS	Illumina HiSeq	Phase_IV	16198261	77	47.62	70	Q4TTY5	Missense_Mutation	SNP	HMMPfam_Adap_comp_sub,superfamily_Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor,superfamily_SNARE-like,PatternScan_CLAT_ADAPTOR_M_1,PatternScan_CLAT_ADAPTOR_M_2	p.S192R	ENST00000291439.3	37	c.576	CCDS12342.1	19	.	.	.	.	.	.	.	.	.	.	C	13.33	2.203875	0.38905	.	.	ENSG00000072958	ENST00000444449;ENST00000291439;ENST00000541844;ENST00000429941	T;T;T;T	0.21361	2.01;2.01;2.01;2.01	3.97	-7.26	0.01466	Clathrin adaptor, mu subunit, C-terminal (3);	0.040832	0.85682	D	0.000000	T	0.53481	0.1799	H	0.97587	4.035	0.54753	D	0.99998	D;D;D	0.63880	0.993;0.993;0.993	D;D;D	0.72982	0.966;0.967;0.979	T	0.72763	-0.4195	10	0.87932	D	0	-22.6341	15.0647	0.71983	0.0:0.2077:0.0:0.7923	.	192;204;192	E7ENJ6;Q4TTY5;Q9BXS5	.;.;AP1M1_HUMAN	R	204;192;120;192	ENSP00000388996:S204R;ENSP00000291439:S192R;ENSP00000445682:S120R;ENSP00000411498:S192R	ENSP00000291439:S192R	S	+	3	2	AP1M1	16198261	0.011000	0.17503	0.883000	0.34634	0.017000	0.09413	-1.157000	0.03157	-1.313000	0.02303	-1.010000	0.02471	AGC	-	HMMPfam_Adap_comp_sub,superfamily_Second domain of Mu2 adaptin subunit (ap50) of ap2 adaptor		0.642	AP1M1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	AP1M1	protein_coding	OTTHUMT00000460492.1	C	NM_032493		16198261	+1	no_errors	NM_032493.1	genbank	human	reviewed	54_36p	missense	SNP	0.996	G
SIGLEC1	6614	genome.wustl.edu	37	20	3684541	3684541	+	Missense_Mutation	SNP	C	C	T	rs201660736		TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr20:3684541C>T	ENST00000344754.4	-	4	903	c.904G>A	c.(904-906)Gtc>Atc	p.V302I	SIGLEC1_ENST00000202578.4_Missense_Mutation_p.V302I	NM_023068.3	NP_075556.1	Q9BZZ2	SN_HUMAN	sialic acid binding Ig-like lectin 1, sialoadhesin	302	Ig-like C2-type 2.				cell-matrix adhesion (GO:0007160)|endocytosis (GO:0006897)|inflammatory response (GO:0006954)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|positive regulation of T cell apoptotic process (GO:0070234)|single organismal cell-cell adhesion (GO:0016337)	extracellular region (GO:0005576)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	carbohydrate binding (GO:0030246)	p.V302I(1)		NS(1)|autonomic_ganglia(1)|breast(1)|central_nervous_system(4)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(3)|large_intestine(5)|liver(2)|lung(24)|ovary(3)|pancreas(4)|prostate(3)|skin(8)|upper_aerodigestive_tract(1)	70						CAGGTGTAGACGCCAGCATCG	0.587													C|||	1	0.000199681	0.0008	0.0	5008	,	,		20399	0.0		0.0	False		,,,				2504	0.0					dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	20						C	ILE/VAL	0,4406		0,0,2203	75.0	57.0	63.0		904	-1.9	0.2	20		63	1,8599	1.2+/-3.3	0,1,4299	no	missense	SIGLEC1	NM_023068.3	29	0,1,6502	TT,TC,CC		0.0116,0.0,0.0077	benign	302/1710	3684541	1,13005	2203	4300	6503	3632541	SO:0001583	missense	0			AF230073	CCDS13060.1	20p13	2013-01-29	2006-01-19	2006-01-19	ENSG00000088827	ENSG00000088827		"""CD molecules"", ""Sialic acid binding Ig-like lectins"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / C2-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	11127	protein-coding gene	gene with protein product		600751	"""sialoadhesin"""	SN		8530048	Standard	XM_006723610		Approved	SIGLEC-1, CD169, FLJ00051, FLJ00055, FLJ00073, FLJ32150, dJ1009E24.1, sialoadhesin	uc002wja.3	Q9BZZ2	OTTHUMG00000031757	ENST00000344754.4:c.904G>A	20.37:g.3684541C>T	ENSP00000341141:p.Val302Ile	Somatic	143	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	3632541	160	37.07	96	Q96DL4|Q9GZS5|Q9H1H6|Q9H1H7|Q9H7L7	Missense_Mutation	SNP	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_I-set,HMMPfam_V-set,HMMPfam_ig,HMMPfam_C2-set_2,superfamily_Immunoglobulin	p.V302I	ENST00000344754.4	37	c.904	CCDS13060.1	20	.	.	.	.	.	.	.	.	.	.	C	14.20	2.465813	0.43839	0.0	1.16E-4	ENSG00000088827	ENST00000344754;ENST00000202578	T;T	0.12361	2.69;2.69	5.26	-1.91	0.07641	Immunoglobulin subtype 2 (1);Immunoglobulin-like (1);Immunoglobulin (1);Immunoglobulin-like fold (1);	0.528227	0.14257	N	0.331089	T	0.07593	0.0191	N	0.24115	0.695	0.09310	N	1	B;B;B	0.19817	0.039;0.026;0.039	B;B;B	0.18263	0.012;0.021;0.012	T	0.30416	-0.9979	10	0.37606	T	0.19	.	6.774	0.23609	0.0:0.4362:0.1452:0.4186	.	302;302;302	Q9BZZ2-2;Q9BZZ2;Q9BZZ2-3	.;SN_HUMAN;.	I	302	ENSP00000341141:V302I;ENSP00000202578:V302I	ENSP00000202578:V302I	V	-	1	0	SIGLEC1	3632541	0.000000	0.05858	0.167000	0.22817	0.654000	0.38779	-0.380000	0.07427	-0.226000	0.09899	0.655000	0.94253	GTC	-	HMMSmart_SM00408,HMMSmart_SM00409,HMMPfam_ig,superfamily_Immunoglobulin		0.587	SIGLEC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SIGLEC1	protein_coding	OTTHUMT00000077761.2	C	NM_023068		3632541	-1	no_errors	NM_023068.3	genbank	human	reviewed	54_36p	missense	SNP	0.657	T
RNU6-113P	106479616	genome.wustl.edu	37	21	18803946	18803946	+	RNA	SNP	G	G	A			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr21:18803946G>A	ENST00000516653.1	+	0	82									RNA, U6 small nuclear 113, pseudogene																		acacaaatttgtgatgtgttc	0.363																																						dbGAP											0			21																																								17725817			0					21q21.1	2013-05-01			ENSG00000252462	ENSG00000252462			47076	pseudogene	RNA, pseudogene							Standard			Approved						21.37:g.18803946G>A		Somatic	303	0.00	0		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	17725817	155	47.81	142		RNA	SNP	-	NULL	ENST00000516653.1	37	NULL		21																																																																																			-	-		0.363	RNU6-113P-201	KNOWN	basic	snRNA	ENSG00000209722	snRNA		G			17725817	+1	pseudogene	ENST00000386987	ensembl	human	novel	54_36p	rna	SNP	0.000	A
TOP3B	8940	genome.wustl.edu	37	22	22328852	22328852	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr22:22328852A>G	ENST00000398793.2	-	3	513	c.79T>C	c.(79-81)Tcc>Ccc	p.S27P	TOP3B_ENST00000413067.2_5'UTR|TOP3B_ENST00000357179.5_Missense_Mutation_p.S27P	NM_003935.3	NP_003926.1	O95985	TOP3B_HUMAN	topoisomerase (DNA) III beta	27	Toprim. {ECO:0000255|PROSITE- ProRule:PRU00995}.				chromosome segregation (GO:0007059)|DNA topological change (GO:0006265)	condensed chromosome (GO:0000793)|nucleus (GO:0005634)	DNA binding (GO:0003677)|DNA topoisomerase activity (GO:0003916)|DNA topoisomerase type I activity (GO:0003917)|poly(A) RNA binding (GO:0044822)	p.S27P(2)		breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(4)|lung(9)|ovary(1)	26	Colorectal(54;0.105)			READ - Rectum adenocarcinoma(21;0.145)		TTGTGTGAGGACAGGCTCCCT	0.612																																						dbGAP											2	Substitution - Missense(2)	haematopoietic_and_lymphoid_tissue(2)	22											77.0	56.0	63.0					22																	22328852		2203	4300	6503	20658852	SO:0001583	missense	0			AF017146	CCDS13797.1	22q11.22	2011-05-24			ENSG00000100038	ENSG00000100038			11993	protein-coding gene	gene with protein product		603582				9786842, 9074928	Standard	XM_005261811		Approved		uc002zvs.3	O95985	OTTHUMG00000167438	ENST00000398793.2:c.79T>C	22.37:g.22328852A>G	ENSP00000381773:p.Ser27Pro	Somatic	123	3.15	4		7	72.00	18	WXS	Illumina HiSeq	Phase_IV	20658852	100	42.86	75	A0M8Q3|Q9BUP5	Missense_Mutation	SNP	PatternScan_TOPOISOMERASE_I_PROK,superfamily_Prokaryotic type I DNA topoisomerase,HMMSmart_SM00436,HMMSmart_SM00437,HMMSmart_SM00493,HMMPfam_Toprim,HMMPfam_Topoisom_bac	p.S27P	ENST00000398793.2	37	c.79	CCDS13797.1	22	.	.	.	.	.	.	.	.	.	.	A	22.7	4.321816	0.81580	.	.	ENSG00000100038	ENST00000357179;ENST00000398793;ENST00000449517;ENST00000424393;ENST00000437929;ENST00000430142;ENST00000456075;ENST00000449704;ENST00000442653;ENST00000437103	T;T;T;T;T	0.22945	1.93;1.93;1.93;1.93;1.93	6.07	4.98	0.66077	DNA topoisomerase, type IA, core domain (1);Toprim domain (2);	0.062069	0.64402	D	0.000002	T	0.43722	0.1260	M	0.79258	2.445	0.80722	D	1	P	0.48834	0.916	P	0.54026	0.74	T	0.42207	-0.9465	10	0.56958	D	0.05	0.0519	12.2963	0.54849	0.8732:0.0:0.0:0.1268	.	27	O95985	TOP3B_HUMAN	P	27	ENSP00000349705:S27P;ENSP00000381773:S27P;ENSP00000390977:S27P;ENSP00000402622:S27P;ENSP00000414538:S27P	ENSP00000349705:S27P	S	-	1	0	TOP3B	20658852	1.000000	0.71417	1.000000	0.80357	0.813000	0.45954	1.310000	0.33551	2.326000	0.78906	0.533000	0.62120	TCC	-	superfamily_Prokaryotic type I DNA topoisomerase,HMMSmart_SM00493,HMMPfam_Toprim		0.612	TOP3B-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	TOP3B	protein_coding	OTTHUMT00000320251.1	A	NM_003935		20658852	-1	no_errors	NM_003935.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	G
RAB36	9609	genome.wustl.edu	37	22	23492294	23492294	+	Silent	SNP	C	C	T			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr22:23492294C>T	ENST00000263116.2	+	3	352	c.312C>T	c.(310-312)caC>caT	p.H104H	RAB36_ENST00000341989.4_Silent_p.H104H	NM_004914.2	NP_004905.2	O95755	RAB36_HUMAN	RAB36, member RAS oncogene family	104					protein transport (GO:0015031)|small GTPase mediated signal transduction (GO:0007264)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)	GTP binding (GO:0005525)	p.H104H(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|ovary(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	15	all_hematologic(9;0.0197)|Acute lymphoblastic leukemia(84;0.181)			READ - Rectum adenocarcinoma(21;0.155)		AGCACTTCCACGGGCAGGTCA	0.622																																						dbGAP											1	Substitution - coding silent(1)	haematopoietic_and_lymphoid_tissue(1)	22											71.0	58.0	62.0					22																	23492294		2203	4300	6503	21822294	SO:0001819	synonymous_variant	0			AB023061	CCDS13805.1	22q11.22	2008-06-11			ENSG00000100228	ENSG00000100228		"""RAB, member RAS oncogene"""	9775	protein-coding gene	gene with protein product		605662				9920784, 10591208	Standard	NM_004914		Approved		uc002zwv.1	O95755	OTTHUMG00000150601	ENST00000263116.2:c.312C>T	22.37:g.23492294C>T		Somatic	170	1.16	2		NA	NA	NA	WXS	Illumina HiSeq	Phase_IV	21822294	139	44.75	115	Q2M390|Q7Z4A9|Q9UHP5	Silent	SNP	HMMSmart_SM00176,HMMSmart_SM00173,HMMSmart_SM00174,HMMSmart_SM00175,HMMSmart_SM00177,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.H104	ENST00000263116.2	37	c.312	CCDS13805.1	22																																																																																			-	NULL		0.622	RAB36-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RAB36	protein_coding	OTTHUMT00000319046.1	C	NM_004914		21822294	+1	no_errors	NM_004914.2	genbank	human	validated	54_36p	silent	SNP	0.967	T
DNMT3A	1788	genome.wustl.edu	37	2	25467106	25467106	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AB-2966-03A-01D-0739-09	TCGA-AB-2966-11A-01D-0739-09	C	C	C	-	C	C	Verified	Valid	Somatic	Phase_I	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina GAIIx	ea13b395-dade-4e11-bedf-a1f36bccfab7	8b0f12c9-65dd-4a1e-9bba-ace290edfddc	g.chr2:25467106delC	ENST00000264709.3	-	15	2106	c.1769delG	c.(1768-1770)ggtfs	p.G590fs	DNMT3A_ENST00000380746.4_Frame_Shift_Del_p.G401fs|DNMT3A_ENST00000402667.1_Frame_Shift_Del_p.G367fs|DNMT3A_ENST00000474887.1_5'UTR|DNMT3A_ENST00000321117.5_Frame_Shift_Del_p.G590fs	NM_175629.2	NP_783328.1	Q9Y6K1	DNM3A_HUMAN	DNA (cytosine-5-)-methyltransferase 3 alpha	590	ADD. {ECO:0000255|PROSITE- ProRule:PRU00865}.				C-5 methylation of cytosine (GO:0090116)|cellular response to amino acid stimulus (GO:0071230)|DNA methylation (GO:0006306)|DNA methylation involved in embryo development (GO:0043045)|DNA methylation involved in gamete generation (GO:0043046)|DNA methylation on cytosine within a CG sequence (GO:0010424)|hypermethylation of CpG island (GO:0044027)|methylation-dependent chromatin silencing (GO:0006346)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of gene expression by genetic imprinting (GO:0006349)|S-adenosylhomocysteine metabolic process (GO:0046498)|S-adenosylmethioninamine metabolic process (GO:0046499)|spermatogenesis (GO:0007283)	chromosome, centromeric region (GO:0000775)|cytoplasm (GO:0005737)|euchromatin (GO:0000791)|nuclear heterochromatin (GO:0005720)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	chromatin binding (GO:0003682)|DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA (cytosine-5-)-methyltransferase activity, acting on CpG substrates (GO:0051718)|DNA binding (GO:0003677)|identical protein binding (GO:0042802)|metal ion binding (GO:0046872)|unmethylated CpG binding (GO:0045322)	p.G590fs*61(1)		breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(964)|kidney(3)|large_intestine(10)|lung(29)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)	1021	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					CCCGTAGGTACCCTTGTGCCC	0.622			"""Mis, F, N, S"""		AML																																	dbGAP		Rec	yes		2	2p23	1788	DNA (cytosine-5-)-methyltransferase 3 alpha		L	1	Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(1)	2											29.0	34.0	33.0					2																	25467106		2203	4300	6503	25320610	SO:0001589	frameshift_variant	0				CCDS1718.2, CCDS33157.1, CCDS46232.1	2p23	2014-09-17			ENSG00000119772	ENSG00000119772			2978	protein-coding gene	gene with protein product		602769				9662389, 10433969	Standard	NM_175630		Approved		uc002rgc.4	Q9Y6K1	OTTHUMG00000094777	ENST00000264709.3:c.1769delG	2.37:g.25467106delC	ENSP00000264709:p.Gly590fs	Somatic	0	0.00	0		0	100.00	2	WXS	Illumina HiSeq	Phase_IV	25320610	0	0.00	0	E9PEB8|Q86TE8|Q86XF5|Q8IZV0|Q8WXU9	Frame_Shift_Del	DEL	HMMPfam_PWWP,HMMSmart_SM00293,HMMPfam_DNA_methylase,superfamily_FYVE/PHD zinc finger,PatternScan_C5_MTASE_1,superfamily_S-adenosyl-L-methionine-dependent methyltransferases,superfamily_Tudor/PWWP/MBT	p.G590fs	ENST00000264709.3	37	c.1769	CCDS33157.1	2																																																																																			-	superfamily_FYVE/PHD zinc finger		0.622	DNMT3A-001	KNOWN	basic|CCDS	protein_coding	DNMT3A	protein_coding	OTTHUMT00000211587.1	C	NM_022552		25320610	-1	no_errors	NM_022552.3	genbank	human	reviewed	54_36p	frame_shift_del	DEL	1.000	-
