#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_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	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
Unknown	0	genome.wustl.edu	37	Unknown	0	0	+	IGR	SNP	G	G	A			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	G	G	G	A	G	G	Verified	Invalid:failed_liftOver	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chrUnknown:0G>A								None (None upstream) : None (None downstream)																								0.0																																						dbGAP											0			MT																																								14964	SO:0001628	intergenic_variant	0																															Unknown.37:g.0G>A		2685	1.17	32		NA	NA	NA	14964	3977	11.56	523		Missense_Mutation	SNP	HMMPfam_Cytochrom_B_N,HMMPfam_Cytochrom_B_C,superfamily_Cytochrome_b/b6_C,superfamily_Transmembr_di-haem_cytochrome	p.V73M		37	c.217		MT																																																																																			-	HMMPfam_Cytochrom_B_N,superfamily_Transmembr_di-haem_cytochrome	0	0					MT-CYB			G			14964	+1	no_stop_codon:bad_bp_length_for_coding_region	ENST00000361789	ensembl	human	known	54_36p	missense	SNP	NULL	A
SMC1A	8243	genome.wustl.edu	37	X	53423537	53423537	+	Splice_Site	SNP	C	C	A			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chrX:53423537C>A	ENST00000322213.4	-	17	2690	c.2563G>T	c.(2563-2565)Gag>Tag	p.E855*		NM_006306.2	NP_006297.2	Q14683	SMC1A_HUMAN	structural maintenance of chromosomes 1A	855					DNA repair (GO:0006281)|gene expression (GO:0010467)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic cell cycle checkpoint (GO:0007093)|mitotic sister chromatid cohesion (GO:0007064)|mitotic sister chromatid segregation (GO:0000070)|mitotic spindle organization (GO:0007052)|mRNA splicing, via spliceosome (GO:0000398)|negative regulation of DNA endoreduplication (GO:0032876)|response to radiation (GO:0009314)|RNA splicing (GO:0008380)|signal transduction in response to DNA damage (GO:0042770)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin core heterodimer (GO:0008280)|condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|meiotic cohesin complex (GO:0030893)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(3)|central_nervous_system(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(8)|ovary(5)|upper_aerodigestive_tract(2)	49						CTTTGTTCCTCCTGGTCCCAG	0.483																																						dbGAP											0			X											134.0	103.0	113.0					X																	53423537		2203	4300	6503	53440262	SO:0001630	splice_region_variant	0			S78271	CCDS14352.1, CCDS75985.1	Xp11.22-p11.21	2014-09-17	2006-07-06	2006-07-06	ENSG00000072501	ENSG00000072501		"""Structural maintenance of chromosomes proteins"""	11111	protein-coding gene	gene with protein product		300040	"""SMC1 (structural maintenance of chromosomes 1, yeast)-like 1"", ""SMC1 structural maintenance of chromosomes 1-like 1 (yeast)"""	SMC1L1		7757074	Standard	NM_006306		Approved	DXS423E, KIAA0178, SB1.8, Smcb	uc004dsg.3	Q14683	OTTHUMG00000021614	ENST00000322213.4:c.2563-1G>T	X.37:g.53423537C>A		31	18.42	7		0	93.18	41	53440262	14	89.05	122	O14995|Q16351|Q2M228	Nonsense_Mutation	SNP	HMMPfam_SMC_N,HMMPfam_SMC_hinge,superfamily_SMC_hinge,superfamily_SSF52540	p.E855*	ENST00000322213.4	37	c.2563	CCDS14352.1	X	.	.	.	.	.	.	.	.	.	.	C	43	9.867809	0.99284	.	.	ENSG00000072501	ENST00000322213	.	.	.	4.61	4.61	0.57282	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.16420	T	0.52	.	14.5166	0.67824	0.0:1.0:0.0:0.0	.	.	.	.	X	855	.	ENSP00000323421:E855X	E	-	1	0	SMC1A	53440262	1.000000	0.71417	1.000000	0.80357	0.925000	0.55904	7.169000	0.77578	2.225000	0.72522	0.529000	0.55759	GAG	-	HMMPfam_SMC_N,superfamily_SSF52540		0.483	SMC1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SMC1A	protein_coding	OTTHUMT00000056756.2	C	NM_006306	Nonsense_Mutation	53440262	-1	no_errors	NM_006306.2	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	A
SPEN	23013	genome.wustl.edu	37	1	16203089	16203089	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr1:16203089C>G	ENST00000375759.3	+	3	1001	c.797C>G	c.(796-798)aCa>aGa	p.T266R	SPEN_ENST00000471538.1_3'UTR	NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	266	Arg-rich.|Ser-rich.				negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)			NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		TCTAGACCCACAAGGTCCCCT	0.527																																						dbGAP											0			1											44.0	42.0	43.0					1																	16203089		2200	4291	6491	16075676	SO:0001583	missense	0				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.797C>G	1.37:g.16203089C>G	ENSP00000364912:p.Thr266Arg	59	1.67	1		12	65.71	23	16075676	61	44.25	50	Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	HMMPfam_RRM_1,HMMSmart_RRM,HMMPfam_SPOC,superfamily_SPOC-like,superfamily_SSF54928	p.T266R	ENST00000375759.3	37	c.797	CCDS164.1	1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	15.78|15.78	2.935838|2.935838	0.52972|0.52972	.|.	.|.	ENSG00000065526|ENSG00000065526	ENST00000442985|ENST00000375759;ENST00000438066;ENST00000375753	.|T;T	.|0.32988	.|3.11;1.43	5.78|5.78	5.78|5.78	0.91487|0.91487	.|.	.|.	.|.	.|.	.|.	T|T	0.20941|0.20941	0.0504|0.0504	N|N	0.14661|0.14661	0.345|0.345	0.50467|0.50467	D|D	0.999872|0.999872	.|P	.|0.49961	.|0.93	.|P	.|0.44860	.|0.462	T|T	0.03296|0.03296	-1.1051|-1.1051	5|9	.|0.13853	.|T	.|0.58	-12.9867|-12.9867	14.2012|14.2012	0.65705|0.65705	0.0:0.9288:0.0:0.0712|0.0:0.9288:0.0:0.0712	.|.	.|266	.|Q96T58	.|MINT_HUMAN	E|R	7|266;225;225	.|ENSP00000364912:T266R;ENSP00000388021:T225R	.|ENSP00000364906:T225R	Q|T	+|+	1|2	0|0	SPEN|SPEN	16075676|16075676	0.736000|0.736000	0.28164|0.28164	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.547000|5.547000	0.67249|0.67249	2.744000|2.744000	0.94065|0.94065	0.563000|0.563000	0.77884|0.77884	CAA|ACA	-	NULL		0.527	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SPEN	protein_coding	OTTHUMT00000025993.1	C	NM_015001		16075676	+1	no_errors	NM_015001.2	genbank	human	reviewed	54_36p	missense	SNP	0.920	G
KLHDC7A	127707	genome.wustl.edu	37	1	18809481	18809481	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr1:18809481C>T	ENST00000400664.1	+	1	2058	c.2006C>T	c.(2005-2007)aCg>aTg	p.T669M		NM_152375.2	NP_689588.2	Q5VTJ3	KLD7A_HUMAN	kelch domain containing 7A	669						integral component of membrane (GO:0016021)				endometrium(1)|kidney(1)|large_intestine(4)|lung(11)|ovary(2)|skin(1)|upper_aerodigestive_tract(2)	22		Colorectal(325;3.46e-05)|all_lung(284;0.000152)|Lung NSC(340;0.000185)|Breast(348;0.00046)|Renal(390;0.000518)|Ovarian(437;0.0014)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00462)|BRCA - Breast invasive adenocarcinoma(304;1.41e-05)|Kidney(64;0.00017)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		AAGGACCGCACGGCCGAGATG	0.692																																						dbGAP											0			1											38.0	38.0	38.0					1																	18809481		2203	4300	6503	18682068	SO:0001583	missense	0			AK096072	CCDS185.2	1p36.13	2008-02-05			ENSG00000179023	ENSG00000179023			26791	protein-coding gene	gene with protein product							Standard	NM_152375		Approved	FLJ38753	uc001bax.3	Q5VTJ3	OTTHUMG00000002431	ENST00000400664.1:c.2006C>T	1.37:g.18809481C>T	ENSP00000383505:p.Thr669Met	11	0.00	0		NA	NA	NA	18682068	35	28.00	14	Q8N8W6	Missense_Mutation	SNP	HMMPfam_Kelch_1,HMMSmart_Kelch,superfamily_Gal_oxid_central	p.T669M	ENST00000400664.1	37	c.2006	CCDS185.2	1	.	.	.	.	.	.	.	.	.	.	C	22.1	4.238136	0.79800	.	.	ENSG00000179023	ENST00000400664;ENST00000540290	T	0.20069	2.1	4.68	4.68	0.58851	Kelch-type beta propeller (1);	0.063405	0.64402	D	0.000009	T	0.45397	0.1340	M	0.67953	2.075	0.51233	D	0.999912	D;D	0.89917	1.0;1.0	D;D	0.79784	0.993;0.993	T	0.47471	-0.9115	10	0.72032	D	0.01	.	16.1501	0.81611	0.0:1.0:0.0:0.0	.	606;669	A7E2V3;Q5VTJ3	.;KLD7A_HUMAN	M	669;606	ENSP00000383505:T669M	ENSP00000383505:T669M	T	+	2	0	KLHDC7A	18682068	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	5.941000	0.70195	2.123000	0.65237	0.561000	0.74099	ACG	-	superfamily_Gal_oxid_central		0.692	KLHDC7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KLHDC7A	protein_coding	OTTHUMT00000006923.3	C	NM_152375		18682068	+1	no_errors	NM_152375.2	genbank	human	validated	54_36p	missense	SNP	1.000	T
NOTCH2	4853	genome.wustl.edu	37	1	120464979	120464979	+	Missense_Mutation	SNP	A	A	T			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	A	A	A	T	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr1:120464979A>T	ENST00000256646.2	-	28	5312	c.5093T>A	c.(5092-5094)aTc>aAc	p.I1698N	NOTCH2_ENST00000493703.1_5'Flank	NM_024408.3	NP_077719.2	Q04721	NOTC2_HUMAN	notch 2	1698					apoptotic process (GO:0006915)|atrial septum morphogenesis (GO:0060413)|bone remodeling (GO:0046849)|cell cycle arrest (GO:0007050)|cell fate determination (GO:0001709)|cell growth (GO:0016049)|ciliary body morphogenesis (GO:0061073)|determination of left/right symmetry (GO:0007368)|embryonic limb morphogenesis (GO:0030326)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|humoral immune response (GO:0006959)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|intracellular receptor signaling pathway (GO:0030522)|morphogenesis of an epithelial sheet (GO:0002011)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nervous system development (GO:0007399)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|organ morphogenesis (GO:0009887)|placenta blood vessel development (GO:0060674)|positive regulation of apoptotic process (GO:0043065)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cell proliferation (GO:0008284)|positive regulation of Ras protein signal transduction (GO:0046579)|pulmonary valve morphogenesis (GO:0003184)|regulation of transcription, DNA-templated (GO:0006355)|stem cell maintenance (GO:0019827)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cell surface (GO:0009986)|cilium (GO:0005929)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|ligand-activated RNA polymerase II transcription factor binding transcription factor activity (GO:0038049)|receptor activity (GO:0004872)			breast(4)|central_nervous_system(6)|cervix(1)|endometrium(8)|haematopoietic_and_lymphoid_tissue(9)|kidney(9)|large_intestine(19)|liver(1)|lung(57)|ovary(4)|pancreas(1)|prostate(7)|skin(24)|stomach(2)|upper_aerodigestive_tract(5)|urinary_tract(1)	158	all_neural(166;0.153)	all_lung(203;1.96e-06)|Lung NSC(69;1.47e-05)|all_epithelial(167;0.000809)		Lung(183;0.0242)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTTTGCCATGATTACCCCCAG	0.502			"""N, F, Mis"""		"""marginal zone lymphoma, DLBCL"""				Alagille Syndrome																													dbGAP		Dom	yes		1	1p13-p11	4853	Notch homolog 2		L	0			1											68.0	65.0	66.0					1																	120464979		2203	4300	6503	120266502	SO:0001583	missense	0	Familial Cancer Database	ALGS1, ALGS2.Alagille-Watson syndrome	AF315356	CCDS908.1	1p13-p11	2013-01-10	2010-06-24		ENSG00000134250	ENSG00000134250		"""Ankyrin repeat domain containing"""	7882	protein-coding gene	gene with protein product		600275	"""Notch (Drosophila) homolog 2"", ""Notch homolog 2 (Drosophila)"""			7698746	Standard	NM_001200001		Approved		uc001eik.3	Q04721	OTTHUMG00000012177	ENST00000256646.2:c.5093T>A	1.37:g.120464979A>T	ENSP00000256646:p.Ile1698Asn	80	1.20	1		42	48.15	39	120266502	85	54.36	106	Q5T3X7|Q99734|Q9H240	Missense_Mutation	SNP	PatternScan_ASX_HYDROXYL,HMMPfam_Notch,HMMSmart_NL,superfamily_Notch_region,HMMSmart_EGF_CA,HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK,HMMPfam_EGF,HMMSmart_EGF,HMMPfam_NOD,HMMPfam_NODP,PatternScan_EGF_1,PatternScan_EGF_2,HMMPfam_EGF_CA,PatternScan_EGF_CA,superfamily_SSF57196	p.I1698N	ENST00000256646.2	37	c.5093	CCDS908.1	1	.	.	.	.	.	.	.	.	.	.	A	21.3	4.126629	0.77549	.	.	ENSG00000134250	ENST00000256646	D	0.82803	-1.65	5.65	5.65	0.86999	.	0.000000	0.38548	U	0.001658	T	0.80149	0.4570	L	0.59436	1.845	0.46521	D	0.99908	D	0.56521	0.976	P	0.47744	0.556	D	0.83818	0.0245	10	0.87932	D	0	.	15.3506	0.74380	1.0:0.0:0.0:0.0	.	1698	Q04721	NOTC2_HUMAN	N	1698	ENSP00000256646:I1698N	ENSP00000256646:I1698N	I	-	2	0	NOTCH2	120266502	1.000000	0.71417	0.995000	0.50966	0.970000	0.65996	9.287000	0.95975	2.279000	0.76181	0.533000	0.62120	ATC	-	NULL		0.502	NOTCH2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NOTCH2	protein_coding	OTTHUMT00000033679.1	A	NM_024408		120266502	-1	no_errors	NM_024408.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
GREB1	9687	genome.wustl.edu	37	2	11741046	11741046	+	Silent	SNP	C	C	T			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr2:11741046C>T	ENST00000381486.2	+	16	2754	c.2454C>T	c.(2452-2454)ttC>ttT	p.F818F	GREB1_ENST00000234142.5_Silent_p.F818F	NM_014668.3	NP_055483.2	Q4ZG55	GREB1_HUMAN	growth regulation by estrogen in breast cancer 1	818						integral component of membrane (GO:0016021)				breast(3)|central_nervous_system(2)|endometrium(2)|kidney(4)|large_intestine(9)|lung(9)|ovary(1)	30	all_hematologic(175;0.127)|Acute lymphoblastic leukemia(172;0.155)			Epithelial(75;0.115)|OV - Ovarian serous cystadenocarcinoma(76;0.186)		TGACCTCCTTCCCGTATGCAC	0.587																																					Ovarian(39;850 945 2785 23371 33093)	dbGAP											0			2											135.0	143.0	140.0					2																	11741046		2147	4246	6393	11658497	SO:0001819	synonymous_variant	0				CCDS33146.1, CCDS33147.1, CCDS42655.1	2p25.1	2010-02-17	2009-09-10		ENSG00000196208	ENSG00000196208			24885	protein-coding gene	gene with protein product	"""gene regulated by estrogen in breast cancer"""	611736				11103799	Standard	NM_014668		Approved	KIAA0575	uc002rbk.1	Q4ZG55	OTTHUMG00000141276	ENST00000381486.2:c.2454C>T	2.37:g.11741046C>T		67	4.29	3		NA	NA	NA	11658497	88	50.00	90	A6NHD0|A6NKN0|B5MDA9|O60321|Q7Z5S2|Q9H2Q6|Q9H2Q7|Q9H2Q8	Silent	SNP	NULL	p.F818	ENST00000381486.2	37	c.2454	CCDS42655.1	2																																																																																			-	NULL		0.587	GREB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GREB1	protein_coding	OTTHUMT00000280490.1	C	NM_014668		11658497	+1	no_errors	NM_014668.3	genbank	human	reviewed	54_36p	silent	SNP	1.000	T
SCTR	6344	genome.wustl.edu	37	2	120204459	120204459	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr2:120204459C>T	ENST00000019103.5	-	11	1283	c.1016G>A	c.(1015-1017)cGc>cAc	p.R339H		NM_002980.2	NP_002971.2	P47872	SCTR_HUMAN	secretin receptor	339					digestion (GO:0007586)|excretion (GO:0007588)|G-protein coupled receptor signaling pathway (GO:0007186)	cytoplasmic microtubule (GO:0005881)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	secretin receptor activity (GO:0015055)			central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|prostate(1)|skin(3)	19					Secretin(DB00021)	CCTGGCCAGGCGCCTGGGGAC	0.602																																						dbGAP											0			2											58.0	62.0	60.0					2																	120204459		2203	4300	6503	119920929	SO:0001583	missense	0				CCDS2127.1	2q14.1	2012-08-10			ENSG00000080293	ENSG00000080293		"""GPCR / Class B : Glucagon receptors"""	10608	protein-coding gene	gene with protein product		182098				1646711	Standard	NM_002980		Approved		uc002tma.3	P47872	OTTHUMG00000131407	ENST00000019103.5:c.1016G>A	2.37:g.120204459C>T	ENSP00000019103:p.Arg339His	34	5.41	2		NA	NA	NA	119920929	70	46.72	64	Q12961|Q13213|Q53T00	Missense_Mutation	SNP	HMMPfam_7tm_2,HMMPfam_HRM,HMMSmart_SM00008,PatternScan_G_PROTEIN_RECEP_F2_1,PatternScan_G_PROTEIN_RECEP_F2_2,superfamily_Hormone receptor domain (HRM Pfam 02793),superfamily_Family A G protein-coupled receptor-like	p.R339H	ENST00000019103.5	37	c.1016	CCDS2127.1	2	.	.	.	.	.	.	.	.	.	.	C	22.0	4.230987	0.79688	.	.	ENSG00000080293	ENST00000019103	T	0.43688	0.94	5.34	5.34	0.76211	GPCR, family 2-like (1);	0.000000	0.56097	D	0.000028	T	0.75155	0.3811	H	0.94264	3.515	0.58432	D	0.99999	D	0.89917	1.0	D	0.87578	0.998	T	0.82224	-0.0563	10	0.87932	D	0	.	18.2135	0.89878	0.0:1.0:0.0:0.0	.	339	P47872	SCTR_HUMAN	H	339	ENSP00000019103:R339H	ENSP00000019103:R339H	R	-	2	0	SCTR	119920929	0.998000	0.40836	0.968000	0.41197	0.289000	0.27227	3.896000	0.56266	2.776000	0.95493	0.655000	0.94253	CGC	-	HMMPfam_7tm_2,superfamily_Family A G protein-coupled receptor-like		0.602	SCTR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SCTR	protein_coding	OTTHUMT00000254198.2	C			119920929	-1	no_errors	NM_002980.2	genbank	human	reviewed	54_36p	missense	SNP	0.995	T
EPGN	255324	genome.wustl.edu	37	4	75174834	75174834	+	Missense_Mutation	SNP	C	C	A			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr4:75174834C>A	ENST00000413830.1	+	2	129	c.68C>A	c.(67-69)gCa>gAa	p.A23E	EPGN_ENST00000332112.4_Missense_Mutation_p.A23E|EPGN_ENST00000514968.1_Missense_Mutation_p.A23E|EPGN_ENST00000509145.1_Intron|EPGN_ENST00000505212.1_Missense_Mutation_p.A23E|EPGN_ENST00000503098.1_Missense_Mutation_p.A23E|EPGN_ENST00000502358.1_Missense_Mutation_p.A23E	NM_001270989.1	NP_001257918.1	Q6UW88	EPGN_HUMAN	epithelial mitogen	23					activation of MAPK activity (GO:0000187)|angiogenesis (GO:0001525)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epidermal growth factor-activated receptor activity (GO:0045741)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of mitosis (GO:0045840)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	epidermal growth factor receptor binding (GO:0005154)|growth factor activity (GO:0008083)|MAP kinase kinase activity (GO:0004708)			breast(3)|liver(1)|lung(1)|skin(1)	6			Lung(101;0.196)			ACCGAAGAGGCAGCCGTGACT	0.423																																						dbGAP											0			4											132.0	130.0	131.0					4																	75174834		2203	4300	6503	75393698	SO:0001583	missense	0				CCDS59475.1, CCDS59476.1, CCDS59477.1, CCDS59478.1, CCDS59479.1	4q13.3	2012-12-07	2012-12-07						17470	protein-coding gene	gene with protein product			"""epithelial mitogen homolog (mouse)"""				Standard	NM_001270989		Approved	epigen, EPG, PRO9904, ALGV3072	uc003hic.2	Q6UW88		ENST00000413830.1:c.68C>A	4.37:g.75174834C>A	ENSP00000411898:p.Ala23Glu	82	4.65	4		0	100.00	1	75393698	92	48.63	89	A1BMM3|A1BMM4|A1BMM5|A1BMM6|A1BMM7|A1BMM8|A8K090	Missense_Mutation	SNP	HMMSmart_EGF,PatternScan_EGF_1,PatternScan_EGF_2,superfamily_SSF57196	p.A23E	ENST00000413830.1	37	c.68	CCDS59478.1	4	.	.	.	.	.	.	.	.	.	.	C	17.87	3.494173	0.64186	.	.	ENSG00000182585	ENST00000413830;ENST00000332112;ENST00000514968;ENST00000503098;ENST00000502358;ENST00000505212	T;T	0.23754	1.97;1.89	5.64	3.8	0.43715	.	0.431349	0.22798	N	0.055515	T	0.24547	0.0595	L	0.40543	1.245	0.09310	N	0.999999	B;B;B;P;P;B	0.47762	0.023;0.047;0.008;0.835;0.9;0.047	B;B;B;P;P;B	0.49999	0.016;0.027;0.018;0.628;0.628;0.027	T	0.06752	-1.0809	10	0.11485	T	0.65	-0.0694	8.0347	0.30486	0.0:0.7979:0.0:0.2021	.	23;23;23;23;23;23	Q6UW88;Q6UW88-3;Q6UW88-5;Q6UW88-4;Q6UW88-6;Q6UW88-2	EPGN_HUMAN;.;.;.;.;.	E	23	ENSP00000411898:A23E;ENSP00000330375:A23E	ENSP00000330375:A23E	A	+	2	0	EPGN	75393698	0.388000	0.25197	0.041000	0.18516	0.166000	0.22503	0.667000	0.25112	0.748000	0.32831	0.557000	0.71058	GCA	-	NULL		0.423	EPGN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EPGN	protein_coding	OTTHUMT00000362738.1	C	NM_001013442		75393698	+1	no_errors	NM_001013442.1	genbank	human	provisional	54_36p	missense	SNP	0.236	A
HADH	3033	genome.wustl.edu	37	4	108948853	108948853	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr4:108948853G>T	ENST00000309522.3	+	6	795	c.646G>T	c.(646-648)Ggg>Tgg	p.G216W	HADH_ENST00000603302.1_Missense_Mutation_p.G216W|HADH_ENST00000403312.1_Missense_Mutation_p.G275W|HADH_ENST00000510728.1_3'UTR|HADH_ENST00000454409.2_Missense_Mutation_p.G220W|HADH_ENST00000505878.1_Missense_Mutation_p.G220W	NM_005327.4	NP_005318	P40939	ECHA_HUMAN	hydroxyacyl-CoA dehydrogenase	544					cardiolipin acyl-chain remodeling (GO:0035965)|cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|glycerophospholipid biosynthetic process (GO:0046474)|phospholipid metabolic process (GO:0006644)|response to drug (GO:0042493)|response to insulin (GO:0032868)|small molecule metabolic process (GO:0044281)	mitochondrial fatty acid beta-oxidation multienzyme complex (GO:0016507)|mitochondrial inner membrane (GO:0005743)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	3-hydroxyacyl-CoA dehydrogenase activity (GO:0003857)|acetyl-CoA C-acetyltransferase activity (GO:0003985)|enoyl-CoA hydratase activity (GO:0004300)|fatty-acyl-CoA binding (GO:0000062)|long-chain-3-hydroxyacyl-CoA dehydrogenase activity (GO:0016509)|long-chain-enoyl-CoA hydratase activity (GO:0016508)|NAD binding (GO:0051287)			endometrium(2)|kidney(1)|large_intestine(3)|lung(3)|ovary(1)|skin(2)|upper_aerodigestive_tract(3)	15		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;0.000168)		GGACACTCCTGGGTTTATTGT	0.453																																						dbGAP											0			4											93.0	89.0	91.0					4																	108948853		2203	4300	6503	109168302	SO:0001583	missense	0			X96752	CCDS3678.1, CCDS54790.1	4q22-q26	2012-10-02	2010-04-30		ENSG00000138796	ENSG00000138796	1.1.1.35		4799	protein-coding gene	gene with protein product		601609	"""L-3-hydroxyacyl-Coenzyme A dehydrogenase, short chain"", ""hydroxyacyl-Coenzyme A dehydrogenase"""	HADHSC		975867, 16176262	Standard	NM_001184705		Approved	HADH1, SCHAD	uc010ilx.3	Q16836	OTTHUMG00000131810	ENST00000309522.3:c.646G>T	4.37:g.108948853G>T	ENSP00000312288:p.Gly216Trp	127	7.86	11		42	50.00	42	109168302	218	48.50	210	B2R7L4|B4DYP2|Q16679|Q53T69|Q53TA2|Q96GT7|Q9UQC5	Missense_Mutation	SNP	HMMPfam_3HCDH,HMMPfam_3HCDH_N,PatternScan_3HCDH,superfamily_6-phosphogluconate dehydrogenase C-terminal domain-like,superfamily_NAD(P)-binding Rossmann-fold domains	p.G216W	ENST00000309522.3	37	c.646	CCDS3678.1	4	.	.	.	.	.	.	.	.	.	.	G	26.3	4.722267	0.89298	.	.	ENSG00000138796	ENST00000403312;ENST00000309522;ENST00000505878;ENST00000454409	D;D;D	0.99816	-6.91;-6.91;-6.91	5.52	5.52	0.82312	3-hydroxyacyl-CoA dehydrogenase, C-terminal (1);3-hydroxyacyl-CoA dehydrogenase, conserved site (1);NAD(P)-binding domain (1);6-phosphogluconate dehydrogenase, C-terminal-like (1);	0.052745	0.85682	D	0.000000	D	0.99930	0.9968	H	0.99968	5.105	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;1.0;1.0	D	0.95728	0.8772	10	0.87932	D	0	-21.813	19.0405	0.92997	0.0:0.0:1.0:0.0	.	275;220;216	Q16836-2;E9PF18;Q16836	.;.;HCDH_HUMAN	W	216;216;220;220	ENSP00000312288:G216W;ENSP00000425952:G220W;ENSP00000395167:G220W	ENSP00000312288:G216W	G	+	1	0	HADH	109168302	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	9.683000	0.98657	2.594000	0.87642	0.491000	0.48974	GGG	-	HMMPfam_3HCDH,PatternScan_3HCDH,superfamily_6-phosphogluconate dehydrogenase C-terminal domain-like		0.453	HADH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	HADH	protein_coding	OTTHUMT00000254750.2	G	NM_005327		109168302	+1	no_errors	NM_005327.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
ANKRD55	79722	genome.wustl.edu	37	5	55455693	55455693	+	Silent	SNP	C	C	T			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr5:55455693C>T	ENST00000341048.4	-	6	601	c.450G>A	c.(448-450)tcG>tcA	p.S150S	ANKRD55_ENST00000504958.2_Silent_p.S150S|ANKRD55_ENST00000505970.2_5'UTR|ANKRD55_ENST00000513241.2_Silent_p.S121S	NM_024669.2	NP_078945.2	Q3KP44	ANR55_HUMAN	ankyrin repeat domain 55	150										breast(1)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(7)|lung(17)|ovary(1)|prostate(1)|skin(2)|stomach(1)	34		Lung NSC(810;8.69e-05)|Prostate(74;0.00634)|Breast(144;0.0334)|Ovarian(174;0.223)				CGCTGATGTTCGACTGTTGCA	0.463																																						dbGAP											0			5											156.0	134.0	142.0					5																	55455693		2203	4300	6503	55491450	SO:0001819	synonymous_variant	0			AK021857	CCDS34161.1	5q11.2	2013-01-10			ENSG00000164512	ENSG00000164512		"""Ankyrin repeat domain containing"""	25681	protein-coding gene	gene with protein product		615189					Standard	XM_005248599		Approved	FLJ11795	uc003jqu.3	Q3KP44	OTTHUMG00000162305	ENST00000341048.4:c.450G>A	5.37:g.55455693C>T		108	6.90	8		1	0.00	0	55491450	173	42.95	131	B3KVT8|Q3KP45|Q9HAD3	Silent	SNP	HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK	p.S150	ENST00000341048.4	37	c.450	CCDS34161.1	5																																																																																			-	HMMPfam_Ank,HMMSmart_ANK,superfamily_ANK		0.463	ANKRD55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ANKRD55	protein_coding	OTTHUMT00000368510.4	C	NM_024669		55491450	-1	no_errors	NM_024669.1	genbank	human	validated	54_36p	silent	SNP	0.807	T
PCDH1	5097	genome.wustl.edu	37	5	141244061	141244061	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr5:141244061A>G	ENST00000394536.3	-	3	1974	c.1835T>C	c.(1834-1836)tTt>tCt	p.F612S	PCDH1_ENST00000536585.1_Missense_Mutation_p.F590S|PCDH1_ENST00000287008.3_Missense_Mutation_p.F612S|PCDH1_ENST00000503492.1_Intron|PCDH1_ENST00000456271.1_Missense_Mutation_p.F600S|PCDH1_ENST00000511044.1_5'UTR	NM_001278613.1|NM_001278615.1	NP_001265542.1|NP_001265544.1	Q08174	PCDH1_HUMAN	protocadherin 1	612	Cadherin 5. {ECO:0000255|PROSITE- ProRule:PRU00043}.				cell-cell signaling (GO:0007267)|homophilic cell adhesion (GO:0007156)|nervous system development (GO:0007399)	cell-cell junction (GO:0005911)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(3)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(4)|lung(20)|ovary(5)|skin(3)|upper_aerodigestive_tract(1)	51		Lung NSC(810;0.027)|all_lung(500;0.0321)|all_hematologic(541;0.0433)|Prostate(461;0.0453)|Breast(839;0.128)|Lung SC(612;0.238)	KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)	GBM - Glioblastoma multiforme(465;1.06e-05)		ACTCAGCATAAATTTGGGGTC	0.542																																					Ovarian(132;1609 1739 4190 14731 45037)	dbGAP											0			5											83.0	76.0	79.0					5																	141244061		2203	4300	6503	141224245	SO:0001583	missense	0			AK075233	CCDS4267.1, CCDS43375.1	5q31.3	2010-01-26	2007-02-12		ENSG00000156453	ENSG00000156453		"""Cadherins / Protocadherins : Non-clustered"""	8655	protein-coding gene	gene with protein product		603626	"""protocadherin 1 (cadherin-like 1)"""			8508762	Standard	NM_032420		Approved	pc42	uc003llp.3	Q08174	OTTHUMG00000129661	ENST00000394536.3:c.1835T>C	5.37:g.141244061A>G	ENSP00000378043:p.Phe612Ser	201	4.67	10		NA	NA	NA	141224245	257	42.58	195	Q8IUP2	Missense_Mutation	SNP	HMMPfam_Cadherin,HMMSmart_CA,PatternScan_CADHERIN_1,HMMPfam_Cadherin_2,HMMPfam_Protocadherin,superfamily_Cadherin,PatternScan_GREAB_2	p.F612S	ENST00000394536.3	37	c.1835	CCDS43375.1	5	.	.	.	.	.	.	.	.	.	.	a	17.25	3.341385	0.60963	.	.	ENSG00000156453	ENST00000287008;ENST00000394536;ENST00000456271;ENST00000357517;ENST00000536585	T;T;T;T;T	0.79454	-1.27;-1.27;-1.27;-1.27;-1.27	5.76	5.76	0.90799	Cadherin (3);Cadherin-like (1);	0.000000	0.52532	D	0.000061	D	0.92886	0.7737	H	0.98901	4.365	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.998;0.999	D	0.95339	0.8436	10	0.87932	D	0	.	14.0375	0.64654	1.0:0.0:0.0:0.0	.	612;612	Q08174;Q08174-2	PCDH1_HUMAN;.	S	612;612;600;623;590	ENSP00000287008:F612S;ENSP00000378043:F612S;ENSP00000403497:F600S;ENSP00000350122:F623S;ENSP00000438825:F590S	ENSP00000287008:F612S	F	-	2	0	PCDH1	141224245	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	9.339000	0.96797	2.212000	0.71576	0.454000	0.30748	TTT	-	superfamily_Cadherin		0.542	PCDH1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	PCDH1	protein_coding	OTTHUMT00000251862.1	A	NM_032420		141224245	-1	no_errors	NM_032420.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	G
GABRG2	2566	genome.wustl.edu	37	5	161576185	161576185	+	Missense_Mutation	SNP	G	G	T			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr5:161576185G>T	ENST00000361925.4	+	8	1214	c.994G>T	c.(994-996)Gtc>Ttc	p.V332F	GABRG2_ENST00000356592.3_Missense_Mutation_p.V332F|GABRG2_ENST00000393933.4_Missense_Mutation_p.V237F|GABRG2_ENST00000414552.2_Missense_Mutation_p.V372F			P18507	GBRG2_HUMAN	gamma-aminobutyric acid (GABA) A receptor, gamma 2	332					adult behavior (GO:0030534)|cellular response to histamine (GO:0071420)|chloride transmembrane transport (GO:1902476)|gamma-aminobutyric acid signaling pathway (GO:0007214)|ion transmembrane transport (GO:0034220)|post-embryonic development (GO:0009791)|synaptic transmission (GO:0007268)|synaptic transmission, GABAergic (GO:0051932)|transmembrane transport (GO:0055085)|transport (GO:0006810)	axon (GO:0030424)|cell junction (GO:0030054)|chloride channel complex (GO:0034707)|cytoplasm (GO:0005737)|dendrite membrane (GO:0032590)|GABA-A receptor complex (GO:1902711)|inhibitory synapse (GO:0060077)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	benzodiazepine receptor activity (GO:0008503)|chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)			NS(1)|breast(1)|cervix(1)|endometrium(6)|kidney(4)|large_intestine(15)|lung(24)|ovary(4)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	62	Renal(175;0.000319)	Medulloblastoma(196;0.0208)|all_neural(177;0.0672)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)	all cancers(165;0.0734)|OV - Ovarian serous cystadenocarcinoma(192;0.135)|Epithelial(171;0.136)	Acamprosate(DB00659)|Adinazolam(DB00546)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Cinolazepam(DB01594)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Clotiazepam(DB01559)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Fludiazepam(DB01567)|Flumazenil(DB01205)|Flurazepam(DB00690)|Ginkgo biloba(DB01381)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GGTCTCCTATGTCACAGCGAT	0.473																																						dbGAP											0			5											260.0	209.0	226.0					5																	161576185		2203	4300	6503	161508763	SO:0001583	missense	0				CCDS4358.1, CCDS4359.1, CCDS47333.1	5q34	2012-06-22			ENSG00000113327	ENSG00000113327		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	4087	protein-coding gene	gene with protein product	"""GABA(A) receptor, gamma 2"""	137164					Standard	NM_198904		Approved		uc010jjc.3	P18507	OTTHUMG00000130350	ENST00000361925.4:c.994G>T	5.37:g.161576185G>T	ENSP00000354651:p.Val332Phe	93	7.00	7		NA	NA	NA	161508763	118	44.08	93	F5HB82|Q6GRL6|Q6PCC3|Q9UDB3|Q9UN15	Missense_Mutation	SNP	HMMPfam_Neur_chan_memb,superfamily_Neurotransmitter-gated ion-channel transmembrane pore,HMMPfam_Neur_chan_LBD,superfamily_Nicotinic receptor ligand binding domain-like,PatternScan_NEUROTR_ION_CHANNEL	p.V332F	ENST00000361925.4	37	c.994	CCDS4358.1	5	.	.	.	.	.	.	.	.	.	.	G	34	5.398771	0.96030	.	.	ENSG00000113327	ENST00000356592;ENST00000414552;ENST00000361925;ENST00000393933	D;D;D;D	0.87029	-2.2;-2.2;-2.2;-2.2	5.88	5.88	0.94601	Neurotransmitter-gated ion-channel transmembrane domain (2);	0.000000	0.85682	D	0.000000	D	0.94729	0.8299	M	0.88241	2.94	0.80722	D	1	D;D;P	0.61080	0.989;0.958;0.949	D;D;D	0.69654	0.965;0.948;0.913	D	0.94781	0.7953	10	0.72032	D	0.01	.	20.2381	0.98363	0.0:0.0:1.0:0.0	.	372;332;332	F5HB82;P18507;P18507-2	.;GBRG2_HUMAN;.	F	332;372;332;237	ENSP00000349000:V332F;ENSP00000410732:V372F;ENSP00000354651:V332F;ENSP00000377510:V237F	ENSP00000349000:V332F	V	+	1	0	GABRG2	161508763	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	6.670000	0.74467	2.779000	0.95612	0.650000	0.86243	GTC	-	HMMPfam_Neur_chan_memb,superfamily_Neurotransmitter-gated ion-channel transmembrane pore		0.473	GABRG2-002	KNOWN	basic|CCDS	protein_coding	GABRG2	protein_coding	OTTHUMT00000252706.1	G			161508763	+1	no_errors	NM_198904.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	T
GRIK2	2898	genome.wustl.edu	37	6	102069829	102069829	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr6:102069829A>G	ENST00000421544.1	+	2	611	c.121A>G	c.(121-123)Att>Gtt	p.I41V	GRIK2_ENST00000369137.3_Missense_Mutation_p.I41V|GRIK2_ENST00000369138.1_Missense_Mutation_p.I41V|GRIK2_ENST00000369134.4_5'UTR|GRIK2_ENST00000413795.1_Missense_Mutation_p.I41V|GRIK2_ENST00000358361.3_Missense_Mutation_p.I41V|GRIK2_ENST00000318991.6_Missense_Mutation_p.I41V	NM_021956.4	NP_068775.1	Q13002	GRIK2_HUMAN	glutamate receptor, ionotropic, kainate 2	41					behavioral fear response (GO:0001662)|cellular calcium ion homeostasis (GO:0006874)|glutamate receptor signaling pathway (GO:0007215)|intracellular protein transport (GO:0006886)|ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of synaptic transmission, glutamatergic (GO:0051967)|neuronal action potential (GO:0019228)|positive regulation of synaptic transmission (GO:0050806)|regulation of excitatory postsynaptic membrane potential (GO:0060079)|regulation of inhibitory postsynaptic membrane potential (GO:0060080)|regulation of long-term neuronal synaptic plasticity (GO:0048169)|regulation of short-term neuronal synaptic plasticity (GO:0048172)|regulation of synaptic transmission (GO:0050804)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)	cell junction (GO:0030054)|dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|kainate selective glutamate receptor complex (GO:0032983)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|postsynaptic membrane (GO:0045211)|presynaptic membrane (GO:0042734)	extracellular-glutamate-gated ion channel activity (GO:0005234)|kainate selective glutamate receptor activity (GO:0015277)			NS(1)|breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(37)|ovary(2)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	83		all_cancers(76;1.19e-07)|Acute lymphoblastic leukemia(125;6.17e-11)|all_hematologic(75;6.01e-08)|all_epithelial(87;0.0121)|Colorectal(196;0.14)		all cancers(137;0.112)|BRCA - Breast invasive adenocarcinoma(108;0.124)|GBM - Glioblastoma multiforme(226;0.206)	Amobarbital(DB01351)|Aprobarbital(DB01352)|Butabarbital(DB00237)|Butalbital(DB00241)|Butethal(DB01353)|Heptabarbital(DB01354)|Hexobarbital(DB01355)|Methylphenobarbital(DB00849)|Pentobarbital(DB00312)|Phenobarbital(DB01174)|Primidone(DB00794)|Secobarbital(DB00418)|Talbutal(DB00306)|Thiopental(DB00599)	GCCAGGTGGTATTTTTGAATA	0.318																																						dbGAP											0			6											53.0	51.0	52.0					6																	102069829		2203	4300	6503	102176522	SO:0001583	missense	0				CCDS5048.1, CCDS5049.1, CCDS55045.1	6q16.3	2012-08-29			ENSG00000164418	ENSG00000164418		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4580	protein-coding gene	gene with protein product		138244		GLUR6		8034316	Standard	NM_021956		Approved	GluK2, MRT6	uc003pqp.4	Q13002	OTTHUMG00000016328	ENST00000421544.1:c.121A>G	6.37:g.102069829A>G	ENSP00000397026:p.Ile41Val	87	2.22	2		NA	NA	NA	102176522	139	40.91	99	A6NMY9|B5MCV0|D7RWZ3|D7RWZ4|D7RWZ5|D7RWZ6|D7RWZ7|Q8WWS1|Q96KS6|Q96KS7|Q96KS8	Missense_Mutation	SNP	HMMPfam_Lig_chan,HMMSmart_SM00079,HMMPfam_ANF_receptor,HMMPfam_Lig_chan-Glu_bd,superfamily_Periplasmic binding protein-like I,superfamily_Periplasmic binding protein-like II	p.I41V	ENST00000421544.1	37	c.121	CCDS5048.1	6	.	.	.	.	.	.	.	.	.	.	A	21.9	4.220456	0.79464	.	.	ENSG00000164418	ENST00000421544;ENST00000413795;ENST00000369138;ENST00000358361;ENST00000369137;ENST00000318991;ENST00000403289;ENST00000540076	T;T;T;T;T;T	0.21543	2.0;2.0;2.0;2.0;2.0;2.0	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.23133	0.0559	N	0.19112	0.55	0.80722	D	1	D;D;D	0.62365	0.991;0.984;0.991	D;D;D	0.81914	0.995;0.989;0.995	T	0.13629	-1.0502	10	0.87932	D	0	.	15.9069	0.79436	1.0:0.0:0.0:0.0	.	41;41;41	Q13002-5;Q13002;Q13002-2	.;GRIK2_HUMAN;.	V	41;41;41;41;41;41;41;3	ENSP00000397026:I41V;ENSP00000405596:I41V;ENSP00000358134:I41V;ENSP00000351128:I41V;ENSP00000358133:I41V;ENSP00000313276:I41V	ENSP00000313276:I41V	I	+	1	0	GRIK2	102176522	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.339000	0.96797	2.147000	0.66899	0.533000	0.62120	ATT	-	superfamily_Periplasmic binding protein-like I		0.318	GRIK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GRIK2	protein_coding	OTTHUMT00000043718.1	A			102176522	+1	no_errors	NM_021956.3	genbank	human	reviewed	54_36p	missense	SNP	1.000	G
KCNT1	57582	genome.wustl.edu	37	9	138642020	138642020	+	Missense_Mutation	SNP	T	T	A			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	T	T	T	A	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr9:138642020T>A	ENST00000263604.3	+	3	274	c.274T>A	c.(274-276)Tcg>Acg	p.S92T	KCNT1_ENST00000487664.1_Missense_Mutation_p.S63T|KCNT1_ENST00000298480.5_Missense_Mutation_p.S111T|KCNT1_ENST00000371757.2_Missense_Mutation_p.S111T|KCNT1_ENST00000488444.2_Missense_Mutation_p.S92T|KCNT1_ENST00000486577.2_Missense_Mutation_p.S72T|KCNT1_ENST00000490355.2_Missense_Mutation_p.S92T|KCNT1_ENST00000491806.2_Missense_Mutation_p.S78T			Q5JUK3	KCNT1_HUMAN	potassium channel, subfamily T, member 1	92					potassium ion transmembrane transport (GO:0071805)	voltage-gated potassium channel complex (GO:0008076)	calcium-activated potassium channel activity (GO:0015269)|voltage-gated potassium channel activity (GO:0005249)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(8)|lung(18)|ovary(1)|pancreas(3)|prostate(5)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50		Myeloproliferative disorder(178;0.0821)		OV - Ovarian serous cystadenocarcinoma(145;2.11e-07)|Epithelial(140;1.57e-06)|all cancers(34;9.22e-05)		AAACCAAAGATCGAGTGAGTG	0.602																																						dbGAP											0			9											63.0	54.0	57.0					9																	138642020		2203	4300	6503	137781841	SO:0001583	missense	0			AB037843	CCDS35175.1, CCDS35175.2, CCDS65188.1	9q34.3	2012-07-05			ENSG00000107147	ENSG00000107147		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, calcium-activated"""	18865	protein-coding gene	gene with protein product		608167				10718198, 16382103	Standard	NM_020822		Approved	KCa4.1, KIAA1422	uc011mdq.2	Q5JUK3	OTTHUMG00000020917	ENST00000263604.3:c.274T>A	9.37:g.138642020T>A	ENSP00000263604:p.Ser92Thr	49	3.85	2		NA	NA	NA	137781841	49	30.56	22	B3KXF7|B7ZVY4|B9EGP2|G5E9V0|Q9P2C5	Missense_Mutation	SNP	HMMPfam_BK_channel_a,HMMPfam_Ion_trans_2,superfamily_NAD(P)-bd,superfamily_SSF81324	p.S111T	ENST00000263604.3	37	c.331		9	.	.	.	.	.	.	.	.	.	.	.	14.82	2.649289	0.47362	.	.	ENSG00000107147	ENST00000487664;ENST00000298480;ENST00000371757;ENST00000473941;ENST00000486577;ENST00000491806;ENST00000488444;ENST00000490355;ENST00000263604	T;T;T;T;T	0.48522	1.8;1.72;1.72;0.81;1.78	4.05	4.05	0.47172	.	0.000000	0.64402	U	0.000002	T	0.41119	0.1145	L	0.52364	1.645	0.80722	D	1	B;B	0.28082	0.148;0.2	B;B	0.28385	0.051;0.089	T	0.27123	-1.0083	10	0.26408	T	0.33	0.0214	12.4763	0.55817	0.0:0.0:0.0:1.0	.	111;63	B9EGP2;G5E9V0	.;.	T	63;111;111;58;72;78;92;92;92	ENSP00000417851:S63T;ENSP00000298480:S111T;ENSP00000360822:S111T;ENSP00000420764:S58T;ENSP00000263604:S92T	ENSP00000263604:S92T	S	+	1	0	KCNT1	137781841	1.000000	0.71417	1.000000	0.80357	0.901000	0.52897	7.713000	0.84693	1.613000	0.50231	0.379000	0.24179	TCG	-	NULL		0.602	KCNT1-201	KNOWN	basic|appris_candidate	protein_coding	KCNT1	protein_coding		T	NM_020822		137781841	+1	no_errors	NM_020822.1	genbank	human	provisional	54_36p	missense	SNP	1.000	A
LRP5	4041	genome.wustl.edu	37	11	68115417	68115417	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr11:68115417C>T	ENST00000294304.7	+	2	300	c.194C>T	c.(193-195)gCg>gTg	p.A65V		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	65	Beta-propeller 1.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.A65V(1)		autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						CTGGAGGATGCGGCCGCAGTG	0.652																																						dbGAP											1	Substitution - Missense(1)	haematopoietic_and_lymphoid_tissue(1)	11											52.0	53.0	53.0					11																	68115417		2200	4294	6494	67871993	SO:0001583	missense	0			AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.194C>T	11.37:g.68115417C>T	ENSP00000294304:p.Ala65Val	62	1.59	1		2	0.00	0	67871993	46	48.91	45	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	HMMPfam_Ldl_recept_b,HMMSmart_SM00135,HMMPfam_Ldl_recept_a,HMMSmart_SM00192,PatternScan_LDLRA_1,superfamily_LDL receptor-like module,HMMPfam_EGF,HMMSmart_SM00181,superfamily_EGF/Laminin,superfamily_YWTD domain	p.A65V	ENST00000294304.7	37	c.194	CCDS8181.1	11	.	.	.	.	.	.	.	.	.	.	C	25.6	4.657910	0.88154	.	.	ENSG00000162337	ENST00000294304	D	0.90563	-2.69	4.58	4.58	0.56647	Six-bladed beta-propeller, TolB-like (1);	0.000000	0.41938	U	0.000799	D	0.94042	0.8091	L	0.60957	1.885	0.80722	D	1	D	0.89917	1.0	D	0.72625	0.978	D	0.94494	0.7704	10	0.59425	D	0.04	.	17.3942	0.87440	0.0:1.0:0.0:0.0	.	65	O75197	LRP5_HUMAN	V	65	ENSP00000294304:A65V	ENSP00000294304:A65V	A	+	2	0	LRP5	67871993	1.000000	0.71417	0.765000	0.31456	0.541000	0.35023	7.723000	0.84788	2.245000	0.73994	0.561000	0.74099	GCG	-	HMMSmart_SM00135,superfamily_YWTD domain		0.652	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LRP5	protein_coding	OTTHUMT00000395088.1	C	NM_002335		67871993	+1	no_errors	NM_002335.2	genbank	human	validated	54_36p	missense	SNP	1.000	T
FLT3	2322	genome.wustl.edu	37	13	28592642	28592642	+	Missense_Mutation	SNP	C	C	A	rs121913486|rs121913488		TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr13:28592642C>A	ENST00000241453.7	-	20	2584	c.2503G>T	c.(2503-2505)Gat>Tat	p.D835Y	FLT3_ENST00000380982.4_Missense_Mutation_p.D835Y|FLT3_ENST00000537084.1_Intron	NM_004119.2	NP_004110.2	P36888	FLT3_HUMAN	fms-related tyrosine kinase 3	835	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.		D -> E (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608, ECO:0000269|PubMed:14504097}.|D -> H (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608, ECO:0000269|PubMed:11442493, ECO:0000269|PubMed:14504097}.|D -> N (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608}.|D -> V (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608}.|D -> Y (in acute lymphoblastic leukemia patients and in acute myelogenous leukemia patients; somatic mutation; constitutively activated). {ECO:0000269|PubMed:11290608, ECO:0000269|PubMed:11442493, ECO:0000269|PubMed:14504097}.		B cell differentiation (GO:0030183)|cellular response to cytokine stimulus (GO:0071345)|common myeloid progenitor cell proliferation (GO:0035726)|cytokine-mediated signaling pathway (GO:0019221)|dendritic cell differentiation (GO:0097028)|hemopoiesis (GO:0030097)|leukocyte homeostasis (GO:0001776)|lymphocyte proliferation (GO:0046651)|myeloid progenitor cell differentiation (GO:0002318)|negative regulation of B cell differentiation (GO:0045578)|negative regulation of cell proliferation (GO:0008285)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of MAP kinase activity (GO:0043406)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of phosphatidylinositol 3-kinase activity (GO:0043552)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of tyrosine phosphorylation of STAT protein (GO:0042531)|pro-B cell differentiation (GO:0002328)|pro-T cell differentiation (GO:0002572)|protein autophosphorylation (GO:0046777)|regulation of apoptotic process (GO:0042981)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor signaling pathway (GO:0038084)	endoplasmic reticulum (GO:0005783)|external side of plasma membrane (GO:0009897)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|cytokine receptor activity (GO:0004896)|protein homodimerization activity (GO:0042803)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)	p.D835Y(190)|p.D835H(30)|p.?(23)|p.D835N(6)|p.D835del(1)|p.R834_D835del(1)|p.D835F(1)		NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|haematopoietic_and_lymphoid_tissue(12329)|kidney(2)|large_intestine(8)|lung(30)|ovary(4)|prostate(1)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	12390	Acute lymphoblastic leukemia(6;0.04)	Lung SC(185;0.0156)|Ovarian(182;0.0392)	Colorectal(13;0.000157)|READ - Rectum adenocarcinoma(15;0.105)	OV - Ovarian serous cystadenocarcinoma(117;0.00154)|all cancers(112;0.00459)|GBM - Glioblastoma multiforme(144;0.00562)|Epithelial(112;0.0959)|Lung(94;0.212)	Ponatinib(DB08901)|Sorafenib(DB00398)|Sunitinib(DB01268)	CTCATGATATCTCGAGCCAAT	0.453			"""Mis, O"""		"""AML, ALL"""																																	dbGAP		Dom	yes		13	13q12	2322	fms-related tyrosine kinase 3		L	252	Substitution - Missense(227)|Unknown(23)|Deletion - In frame(2)	haematopoietic_and_lymphoid_tissue(252)	13											187.0	141.0	156.0					13																	28592642		2203	4300	6503	27490642	SO:0001583	missense	0			U02687	CCDS31953.1	13q12	2014-09-17			ENSG00000122025	ENSG00000122025	2.7.10.1	"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3765	protein-coding gene	gene with protein product		136351				8394751	Standard	NM_004119		Approved	STK1, FLK2, CD135	uc001urw.3	P36888	OTTHUMG00000016646	ENST00000241453.7:c.2503G>T	13.37:g.28592642C>A	ENSP00000241453:p.Asp835Tyr	87	5.43	5		300	45.57	252	27490642	94	37.50	57	A0AVG9|B7ZLT7|B7ZLT8|F5H0A0|Q13414	Missense_Mutation	SNP	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,PatternScan_RECEPTOR_TYR_KIN_III,PatternScan_PROTEIN_KINASE_TYR,superfamily_Kinase_like,HMMPfam_ig,PatternScan_PROTEIN_KINASE_ATP,superfamily_SSF48726	p.D835Y	ENST00000241453.7	37	c.2503	CCDS31953.1	13	.	.	.	.	.	.	.	.	.	.	C	28.8	4.949190	0.92660	.	.	ENSG00000122025	ENST00000241453;ENST00000380982	D;D	0.83755	-1.76;-1.76	5.84	5.84	0.93424	Serine-threonine/tyrosine-protein kinase (1);Protein kinase-like domain (1);Tyrosine-protein kinase, catalytic domain (1);Protein kinase, catalytic domain (1);	0.074843	0.56097	D	0.000030	D	0.87981	0.6315	L	0.34521	1.04	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.88564	0.3125	10	0.87932	D	0	.	20.221	0.98325	0.0:1.0:0.0:0.0	.	835	P36888	FLT3_HUMAN	Y	835	ENSP00000241453:D835Y;ENSP00000370369:D835Y	ENSP00000241453:D835Y	D	-	1	0	FLT3	27490642	1.000000	0.71417	0.960000	0.40013	0.940000	0.58332	7.815000	0.86186	2.792000	0.96026	0.556000	0.70494	GAT	-	HMMPfam_Pkinase_Tyr,HMMSmart_TyrKc,superfamily_Kinase_like		0.453	FLT3-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	FLT3	protein_coding	OTTHUMT00000044319.2	C			27490642	-1	no_errors	NM_004119.2	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
SPTB	6710	genome.wustl.edu	37	14	65237713	65237713	+	Silent	SNP	C	C	A			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	C	C	C	A	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr14:65237713C>A	ENST00000389721.5	-	26	5720	c.5688G>T	c.(5686-5688)cgG>cgT	p.R1896R	SPTB_ENST00000556626.1_Silent_p.R1896R|SPTB_ENST00000542895.1_Silent_p.R1896R|SPTB_ENST00000389720.3_Silent_p.R1896R|SPTB_ENST00000389722.3_Silent_p.R1896R	NM_000347.5	NP_000338.3	P11277	SPTB1_HUMAN	spectrin, beta, erythrocytic	1896					actin filament capping (GO:0051693)|axon guidance (GO:0007411)|hemopoiesis (GO:0030097)|plasma membrane organization (GO:0007009)|porphyrin-containing compound biosynthetic process (GO:0006779)	actin cytoskeleton (GO:0015629)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)|protein complex (GO:0043234)|spectrin (GO:0008091)|spectrin-associated cytoskeleton (GO:0014731)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|ankyrin binding (GO:0030506)|structural constituent of cytoskeleton (GO:0005200)			breast(5)|central_nervous_system(4)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(18)|lung(36)|ovary(8)|pancreas(1)|prostate(4)|skin(10)|urinary_tract(3)	106		all_lung(585;4.15e-09)		all cancers(60;4.33e-34)|OV - Ovarian serous cystadenocarcinoma(108;8.32e-20)|BRCA - Breast invasive adenocarcinoma(234;0.0628)		CTAGCTGGGTCCGGCGCCCGG	0.627																																						dbGAP											0			14											57.0	58.0	58.0					14																	65237713		2203	4300	6503	64307466	SO:0001819	synonymous_variant	0				CCDS32099.1, CCDS32100.1	14q24.1-q24.2	2013-01-10	2008-07-29			ENSG00000070182		"""Pleckstrin homology (PH) domain containing"""	11274	protein-coding gene	gene with protein product	"""spherocytosis, clinical type I"""	182870				2209094	Standard	NM_001024858		Approved		uc001xhr.3	P11277		ENST00000389721.5:c.5688G>T	14.37:g.65237713C>A		26	0.00	0		0	100.00	1	64307466	95	36.24	54	Q15510|Q15519	Silent	SNP	PatternScan_ACTININ_1,PatternScan_ACTININ_2,HMMPfam_CH,HMMSmart_CH,HMMPfam_PH,HMMSmart_PH,HMMPfam_Spectrin,superfamily_Calponin-homology,HMMSmart_SPEC,superfamily_Spectrin,superfamily_SSF50729	p.R1896	ENST00000389721.5	37	c.5688	CCDS32100.1	14																																																																																			-	HMMPfam_Spectrin,HMMSmart_SPEC,superfamily_Spectrin		0.627	SPTB-004	KNOWN	basic|CCDS	protein_coding	SPTB	protein_coding	OTTHUMT00000414080.1	C			64307466	-1	no_errors	NM_001024858.4	genbank	human	validated	54_36p	silent	SNP	1.000	A
AOC4P	90586	genome.wustl.edu	37	17	41020862	41020862	+	RNA	SNP	G	G	A			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr17:41020862G>A	ENST00000585538.1	+	0	1701					NR_002773.1				amine oxidase, copper containing 4, pseudogene																		CACCCACAGCGCCCACTTCAA	0.557																																						dbGAP											0			17																																								38274388			0					17q21.31	2013-06-19			ENSG00000260105	ENSG00000260105			48869	pseudogene	pseudogene						20013028	Standard	NR_002773		Approved				OTTHUMG00000176596		17.37:g.41020862G>A		36	2.70	1		NA	NA	NA	38274388	44	37.84	28		RNA	SNP	-	NULL	ENST00000585538.1	37	NULL		17																																																																																			-	-		0.557	AOC4P-006	KNOWN	basic	processed_transcript	LOC90586	pseudogene	OTTHUMT00000452449.1	G			38274388	+1	pseudogene	NR_002773.1	genbank	human	provisional	54_36p	rna	SNP	0.961	A
ANKRD12	23253	genome.wustl.edu	37	18	9256666	9256666	+	Missense_Mutation	SNP	A	A	G			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	A	A	A	G	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr18:9256666A>G	ENST00000262126.4	+	9	3641	c.3401A>G	c.(3400-3402)aAa>aGa	p.K1134R	ANKRD12_ENST00000383440.2_Missense_Mutation_p.K1111R|ANKRD12_ENST00000400020.3_Missense_Mutation_p.K1111R|RP11-888D10.4_ENST00000609701.1_RNA	NM_015208.4	NP_056023.3	Q6UB98	ANR12_HUMAN	ankyrin repeat domain 12	1134						cytoplasm (GO:0005737)|nucleus (GO:0005634)				NS(1)|breast(3)|central_nervous_system(2)|endometrium(8)|kidney(2)|large_intestine(20)|lung(18)|ovary(3)|pancreas(1)|prostate(4)|skin(1)|urinary_tract(2)	65						ACTGAATCCAAAAATAAAGAA	0.318																																						dbGAP											0			18											54.0	55.0	55.0					18																	9256666		2200	4298	6498	9246666	SO:0001583	missense	0			AY373757	CCDS11843.1, CCDS42411.1	18p11.22	2013-01-10			ENSG00000101745	ENSG00000101745		"""Ankyrin repeat domain containing"""	29135	protein-coding gene	gene with protein product		610616				10048485	Standard	NM_001204056		Approved	KIAA0874, FLJ20053, GAC-1	uc002knv.3	Q6UB98	OTTHUMG00000131595	ENST00000262126.4:c.3401A>G	18.37:g.9256666A>G	ENSP00000262126:p.Lys1134Arg	69	4.11	3		16	38.46	10	9246666	143	47.64	131	O94951|Q658K1|Q6QMF7|Q9H231|Q9H784	Missense_Mutation	SNP	HMMPfam_Ank,HMMSmart_SM00248,superfamily_Ankyrin repeat	p.K1134R	ENST00000262126.4	37	c.3401	CCDS11843.1	18	.	.	.	.	.	.	.	.	.	.	A	15.44	2.833734	0.50951	.	.	ENSG00000101745	ENST00000383440;ENST00000262126	T;T	0.67865	-0.29;-0.29	5.47	4.32	0.51571	.	0.357240	0.32002	N	0.006738	T	0.70395	0.3219	L	0.31207	0.915	0.36326	D	0.858562	D;D	0.71674	0.998;0.997	D;D	0.80764	0.994;0.985	T	0.74562	-0.3624	10	0.45353	T	0.12	-20.2648	11.1632	0.48528	0.9278:0.0:0.0722:0.0	.	1111;1134	Q6UB98-2;Q6UB98	.;ANR12_HUMAN	R	1111;1134	ENSP00000372932:K1111R;ENSP00000262126:K1134R	ENSP00000262126:K1134R	K	+	2	0	ANKRD12	9246666	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	4.846000	0.62860	0.917000	0.36895	0.528000	0.53228	AAA	-	superfamily_Ankyrin repeat		0.318	ANKRD12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	ANKRD12	protein_coding	OTTHUMT00000254478.2	A	NM_015208		9246666	+1	no_errors	NM_015208.1	genbank	human	validated	54_36p	missense	SNP	0.977	G
CECR2	27443	genome.wustl.edu	37	22	17990917	17990917	+	Missense_Mutation	SNP	G	G	A			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr22:17990917G>A	ENST00000400585.2	+	8	892	c.454G>A	c.(454-456)Gtc>Atc	p.V152I	CECR2_ENST00000262608.8_Missense_Mutation_p.V274I|CECR2_ENST00000342247.5_Intron|CECR2_ENST00000400573.5_Missense_Mutation_p.V293I			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	315					apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)				NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		CATCAAACCCGTCAAGCAAGA	0.473																																						dbGAP											0			22											126.0	123.0	124.0					22																	17990917		2044	4187	6231	16370917	SO:0001583	missense	0			AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400585.2:c.454G>A	22.37:g.17990917G>A	ENSP00000383428:p.Val152Ile	161	4.09	7		NA	NA	NA	16370917	113	44.66	92	A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Missense_Mutation	SNP	HMMPfam_Bromodomain,HMMSmart_BROMO,superfamily_Bromodomain,PatternScan_BROMODOMAIN_1	p.V293I	ENST00000400585.2	37	c.877		22	.	.	.	.	.	.	.	.	.	.	G	0.057	-1.233327	0.01505	.	.	ENSG00000099954	ENST00000400585;ENST00000400573;ENST00000262608	T;T;T	0.34859	1.34;1.34;1.34	3.77	1.43	0.22495	.	0.601499	0.13322	N	0.396579	T	0.09247	0.0228	N	0.00707	-1.245	0.09310	N	1	B;B;B	0.02656	0.0;0.0;0.0	B;B;B	0.01281	0.0;0.0;0.0	T	0.34129	-0.9841	10	0.15066	T	0.55	-1.4868	4.7254	0.12938	0.615:0.1804:0.2046:0.0	.	315;152;293	Q9BXF3;B7WPH3;E2QRE6	CECR2_HUMAN;.;.	I	152;293;274	ENSP00000383428:V152I;ENSP00000383417:V293I;ENSP00000262608:V274I	ENSP00000262608:V274I	V	+	1	0	CECR2	16370917	0.997000	0.39634	0.878000	0.34440	0.678000	0.39670	0.709000	0.25734	0.527000	0.28560	-0.324000	0.08512	GTC	-	NULL		0.473	CECR2-002	NOVEL	basic|appris_candidate|exp_conf	protein_coding	CECR2	protein_coding	OTTHUMT00000316226.2	G	NM_031413		16370917	+1	no_errors	ENST00000400585	ensembl	human	known	54_36p	missense	SNP	0.987	A
NPM1	4869	genome.wustl.edu	37	5	170837547	170837548	+	Frame_Shift_Ins	INS	-	-	CGCG			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	-	-	-	CGCG	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr5:170837547_170837548insCGCG	ENST00000296930.5	+	11	1164_1165	c.863_864insCGCG	c.(862-867)tggcagfs	p.WQ288fs	NPM1_ENST00000517671.1_Frame_Shift_Ins_p.WQ288fs|NPM1_ENST00000351986.6_Frame_Shift_Ins_p.WQ259fs	NM_002520.6	NP_002511.1	P06748	NPM_HUMAN	nucleophosmin (nucleolar phosphoprotein B23, numatrin)	288	Required for nucleolar localization.			WQWRKSL -> CLAVEEVSLRK (in Ref. 6; AAW67752/AAW67755). {ECO:0000305}.|WQWRKSL -> CMAVEEVSLRK (in Ref. 6; AAW67753 and 7; ABC40399). {ECO:0000305}.|WQWRKSL -> CVAVEEVSLRK (in Ref. 6; AAW67754). {ECO:0000305}.	cell aging (GO:0007569)|CENP-A containing nucleosome assembly (GO:0034080)|centrosome cycle (GO:0007098)|DNA repair (GO:0006281)|intracellular protein transport (GO:0006886)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of centrosome duplication (GO:0010826)|negative regulation of protein kinase activity by regulation of protein phosphorylation (GO:0044387)|nucleocytoplasmic transport (GO:0006913)|nucleosome assembly (GO:0006334)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of translation (GO:0045727)|protein localization (GO:0008104)|protein oligomerization (GO:0051259)|regulation of centriole replication (GO:0046599)|regulation of eIF2 alpha phosphorylation by dsRNA (GO:0060735)|regulation of endodeoxyribonuclease activity (GO:0032071)|regulation of endoribonuclease activity (GO:0060699)|response to stress (GO:0006950)|ribosome assembly (GO:0042255)|signal transduction (GO:0007165)|viral process (GO:0016032)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|focal adhesion (GO:0005925)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)|spindle pole centrosome (GO:0031616)	histone binding (GO:0042393)|NF-kappaB binding (GO:0051059)|poly(A) RNA binding (GO:0044822)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)|protein kinase binding (GO:0019901)|protein kinase inhibitor activity (GO:0004860)|ribosomal large subunit binding (GO:0043023)|ribosomal small subunit binding (GO:0043024)|RNA binding (GO:0003723)|Tat protein binding (GO:0030957)|transcription coactivator activity (GO:0003713)|unfolded protein binding (GO:0051082)	p.W288fs*12(2114)|p.W288fs*10(9)|p.Q289fs*11(3)|p.W288*(1)	NPM1/ALK(632)	central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(4261)|kidney(1)|large_intestine(1)|lung(4)|skin(1)	4269	Renal(175;0.000159)|Lung NSC(126;0.00576)|all_lung(126;0.00963)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)	Kidney(164;7.24e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000516)			CAAGATCTCTGGCAGTGGAGGA	0.312			"""T, F """	"""ALK, RARA, MLF1"""	"""NHL, APL, AML"""																																	dbGAP		Dom	yes		5	5q35	4869	"""nucleophosmin (nucleolar phosphoprotein B23, numatrin)"""		L	2127	Insertion - Frameshift(2118)|Complex - frameshift(8)|Substitution - Nonsense(1)	haematopoietic_and_lymphoid_tissue(2127)	5																																								170770153	SO:0001589	frameshift_variant	0			M26697	CCDS4376.1, CCDS4377.1, CCDS43399.1	5q35.1	2014-09-17			ENSG00000181163	ENSG00000181163			7910	protein-coding gene	gene with protein product	"""nucleolar phosphoprotein B23"", ""numatrin"", ""nucleophosmin/nucleoplasmin family, member 1"""	164040				8471164, 8122112	Standard	NM_002520		Approved	B23, NPM	uc003mbi.3	P06748	OTTHUMG00000130465	Exception_encountered	5.37:g.170837547_170837548insCGCG	ENSP00000296930:p.Trp288fs	NA	NA	NA		NA	NA	NA	170770152	NA	NA	NA	A8K3N7|B5BU00|D3DQL6|P08693|Q12826|Q13440|Q13441|Q14115|Q5EU94|Q5EU95|Q5EU96|Q5EU97|Q5EU98|Q5EU99|Q6V962|Q8WTW5|Q96AT6|Q96DC4|Q96EA5|Q9BYG9|Q9UDJ7	Frame_Shift_Ins	INS	HMMPfam_Nucleoplasmin,superfamily_Nucleoplasmin-like core domain	p.W288fs	ENST00000296930.5	37	c.863_864	CCDS4376.1	5																																																																																			-	NULL		0.312	NPM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NPM1	protein_coding	OTTHUMT00000252858.2	-	NM_002520		170770153	+1	no_errors	NM_002520.1	genbank	human	validated	54_36p	frame_shift_ins	INS	1.000:1.000	CGCG
CEBPA	1050	genome.wustl.edu	37	19	33792464	33792465	+	Frame_Shift_Ins	INS	-	-	G			TCGA-AB-2900-03A-01W-0733-08	TCGA-AB-2900-11A-01W-0732-08	-	-	-	G	-	-	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	70e697ae-f265-4598-b261-92c92622bf2d	e553d484-56f9-4c88-b500-f4e4e295b394	g.chr19:33792464_33792465insG	ENST00000498907.2	-	1	1005_1006	c.856_857insC	c.(856-858)cggfs	p.R286fs	CEBPA-AS1_ENST00000592982.2_RNA|CTD-2540B15.11_ENST00000589932.1_RNA|CTD-2540B15.7_ENST00000587312.1_RNA	NM_004364.3	NP_004355.2	P49715	CEBPA_HUMAN	CCAAT/enhancer binding protein (C/EBP), alpha	286	Basic motif. {ECO:0000255|PROSITE- ProRule:PRU00978}.|bZIP. {ECO:0000255|PROSITE- ProRule:PRU00978}.				acute-phase response (GO:0006953)|brown fat cell differentiation (GO:0050873)|cell maturation (GO:0048469)|cellular response to lithium ion (GO:0071285)|cellular response to organic cyclic compound (GO:0071407)|cholesterol metabolic process (GO:0008203)|cytokine-mediated signaling pathway (GO:0019221)|embryonic placenta development (GO:0001892)|generation of precursor metabolites and energy (GO:0006091)|inner ear development (GO:0048839)|liver development (GO:0001889)|lung development (GO:0030324)|macrophage differentiation (GO:0030225)|mitochondrion organization (GO:0007005)|myeloid cell differentiation (GO:0030099)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|organ regeneration (GO:0031100)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of transcription from RNA polymerase III promoter (GO:0045945)|response to glucocorticoid (GO:0051384)|response to vitamin B2 (GO:0033274)|transcription from RNA polymerase II promoter (GO:0006366)|transcription, DNA-templated (GO:0006351)|urea cycle (GO:0000050)|viral process (GO:0016032)|white fat cell differentiation (GO:0050872)	nuclear matrix (GO:0016363)|nucleus (GO:0005634)|Rb-E2F complex (GO:0035189)	DNA binding (GO:0003677)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)|transcription regulatory region DNA binding (GO:0044212)	p.H200_K352>Q(1)|p.R286fs*32(1)|p.?(1)|p.R286fs*38(1)		cervix(1)|haematopoietic_and_lymphoid_tissue(912)|lung(5)|prostate(1)|stomach(1)	920	Esophageal squamous(110;0.137)					GCGCCGCACCCGGTACTCGTTG	0.688			"""Mis, N, F"""		"""AML, MDS"""				Acute Myeloid Leukemia, Familial, associated with CEBPA germline mutation																													dbGAP		Dom	yes		19	19q13.1	1050	"""CCAAT/enhancer binding protein (C/EBP), alpha"""		L	4	Unknown(1)|Complex - deletion inframe(1)|Insertion - Frameshift(1)|Deletion - Frameshift(1)	haematopoietic_and_lymphoid_tissue(4)	19																																								38484305	SO:0001589	frameshift_variant	0	Familial Cancer Database	Familial AML	M37197	CCDS54243.1	19q13.1	2014-09-17				ENSG00000245848		"""basic leucine zipper proteins"""	1833	protein-coding gene	gene with protein product		116897		CEBP		1535333, 1840554	Standard	NM_004364		Approved	C/EBP-alpha	uc002nun.3	P49715		ENST00000498907.2:c.857dupC	19.37:g.33792466_33792466dupG	ENSP00000427514:p.Arg286fs	9	0.00	0		44	32.31	21	38484304	31	32.61	15	A7LNP2|P78319|Q05CA4	Frame_Shift_Ins	INS	HMMSmart_BRLZ,PatternScan_BZIP_BASIC,HMMPfam_bZIP_2	p.R286fs	ENST00000498907.2	37	c.857_856	CCDS54243.1	19																																																																																			-	HMMSmart_BRLZ,HMMPfam_bZIP_2		0.688	CEBPA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CEBPA	protein_coding	OTTHUMT00000365012.1	-	NM_004364		38484305	-1	no_errors	NM_004364.3	genbank	human	reviewed	54_36p	frame_shift_ins	INS	1.000:1.000	G
