#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_AAChange	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_Codon	i_COSMIC_Gene	i_COSMIC_Gene_Freq	i_COSMIC_Site_Freq	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ChromChange	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_Drug_Target	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Exon	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_Genome_Plus_Minus_10_Bp	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_IGV	i_Mutation_Status	i_NTotCov_SOL	i_NVaf_SOL	i_NVarCov_SOL	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_TTotCov_SOL	i_TVaf_SOL	i_TVarCov_SOL	i_Transcript_Id	i_Ttot_rna	i_Tvaf_rna	i_Tvar_rna	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_dbSNPPopFreq	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_germline-maf-frequency	i_havana_transcript	i_note	i_refseq_mrna_id	i_secondary_variant_classification
FAM43B	163933	broad.mit.edu	37	1	20880268	20880270	+	In_Frame_Del	DEL	GAG	GAG	-			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	GAG	GAG					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr1:20880268_20880270delGAG	ENST00000332947.4	+	1	1337_1339	c.802_804delGAG	c.(802-804)gagdel	p.E272del		NM_207334.2	NP_997217.1	Q6ZT52	FA43B_HUMAN	family with sequence similarity 43, member B	272										large_intestine(1)|lung(2)	3		Colorectal(325;0.000147)|Renal(390;0.000469)|Lung NSC(340;0.00412)|all_lung(284;0.00419)|Breast(348;0.00979)|Myeloproliferative disorder(586;0.0393)|Ovarian(437;0.0427)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0178)|COAD - Colon adenocarcinoma(152;1.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000132)|Kidney(64;0.00016)|GBM - Glioblastoma multiforme(114;0.000399)|KIRC - Kidney renal clear cell carcinoma(64;0.00258)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)|Lung(427;0.195)		ggaggaggacgaggaggaggagg	0.744																																					p.268_268del													.	FAM43B	10		0			c.802_804del									121,39,3262		29,0,63,5,29,1585						-0.4	1.0			5	4,54,6868		0,0,4,2,50,3407	no	codingComplex	FAM43B	NM_207334.2		29,0,67,7,79,4992	A1A1,A1A2,A1R,A2A2,A2R,RR		0.8374,4.6756,2.1067				125,93,10130				SO:0001651	inframe_deletion	163933	exon1			GAGGACGAGGAGG	AK126900	CCDS209.1	1p36.12	2014-08-14			ENSG00000183114	ENSG00000183114			31791	protein-coding gene	gene with protein product						21461611	Standard	NM_207334		Approved	FLJ44952	uc001bdj.3	Q6ZT52	OTTHUMG00000057491	ENST00000332947.4:c.802_804delGAG	1.37:g.20880277_20880279delGAG	ENSP00000331397:p.Glu272del		Somatic	3	0	0		WXS	Illumina HiSeq	Phase_I	7	0.43	3	NM_207334	1	0.00	0	A5PKT8|A5PL01	In_Frame_Del	DEL	ENST00000332947.4	37	CCDS209.1																																																																																					0.744	FAM43B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000127759.1		NM_207334	
SEC22B	9554	broad.mit.edu	37	1	145109290	145109306	+	RNA	DEL	AAAGAAAAAAAAAAACC	AAAGAAAAAAAAAAACC	-	rs7364468|rs367922551|rs373765269|rs143391068|rs7553859|rs372715481|rs6657661|rs9424677|rs7367456		TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	AAAGAAAAAAAAAAACC	AAAGAAAAAAAAAAACC					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr1:145109290_145109306delAAAGAAAAAAAAAAACC	ENST00000453618.1	+	0	512							O75396	SC22B_HUMAN	SEC22 vesicle trafficking protein homolog B (S. cerevisiae) (gene/pseudogene)						ER to Golgi vesicle-mediated transport (GO:0006888)|protein transport (GO:0015031)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum-Golgi intermediate compartment (GO:0005793)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)											tctcaaaaaaaaagaaaaaaaaaaaccaaaaacaaaA	0.438																																					.													.	.			0			.																																											9554	.			AAAAAAAAAGAAA	AF047442		1q21.1	2012-04-20	2010-03-12	2006-04-25	ENSG00000223380				10700	protein-coding gene	gene with protein product		604029	"""SEC22, vesicle trafficking protein (S. cerevisiae)-like 1"", ""SEC22 vesicle trafficking protein-like 1 (S. cerevisiae)"", ""SEC22 vesicle trafficking protein homolog B (S. cerevisiae)"""	SEC22L1		9094723, 16354670	Standard	NM_004892		Approved	sec22b, ERS-24	uc031poa.1	O75396	OTTHUMG00000013745		1.37:g.145109290_145109306delAAAGAAAAAAAAAAACC			Somatic	12	0	0		WXS	Illumina HiSeq	Phase_I	12	0.33	4	.	1	0.00	0	A8K1G0	RNA	DEL	ENST00000453618.1	37																																																																																						0.438	SEC22B-001	KNOWN	basic	processed_transcript	processed_transcript		OTTHUMT00000038523.5		NM_004892	
LOR	4014	broad.mit.edu	37	1	153233515	153233515	+	Silent	SNP	C	C	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr1:153233515C>T	ENST00000368742.3	+	2	147	c.90C>T	c.(88-90)ggC>ggT	p.G30G		NM_000427.2	NP_000418.2	P23490	LORI_HUMAN	loricrin	30					keratinization (GO:0031424)|keratinocyte differentiation (GO:0030216)|peptide cross-linking (GO:0018149)	cornified envelope (GO:0001533)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	protein binding, bridging (GO:0030674)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			lung(2)	2	all_lung(78;3.35e-32)|Lung NSC(65;1.22e-30)|Hepatocellular(266;0.0877)|all_hematologic(923;0.127)|Melanoma(130;0.242)		LUSC - Lung squamous cell carcinoma(543;0.171)			gcggcagcggcggtggtggct	0.697																																					p.G30G													.	LOR	19		0			c.C90T												6.0	8.0	8.0					1																	153233515		1962	3919	5881	SO:0001819	synonymous_variant	4014	exon2			CAGCGGCGGTGGT	M61120	CCDS30870.1	1q21	2008-02-05			ENSG00000203782	ENSG00000203782			6663	protein-coding gene	gene with protein product		152445				2007607, 1355480	Standard	NM_000427		Approved		uc001fbm.3	P23490	OTTHUMG00000013938	ENST00000368742.3:c.90C>T	1.37:g.153233515C>T			Somatic	54	0	0		WXS	Illumina HiSeq	Phase_I	90	0.04	4	NM_000427	0		0	Q5T869|Q5XKF8	Silent	SNP	ENST00000368742.3	37	CCDS30870.1																																																																																					0.697	LOR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000039107.1		NM_000427	
APOA1BP	128240	broad.mit.edu	37	1	156562379	156562379	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr1:156562379A>G	ENST00000368235.3	+	4	476	c.433A>G	c.(433-435)Agg>Ggg	p.R145G	APOA1BP_ENST00000368234.3_Missense_Mutation_p.R145G|APOA1BP_ENST00000368233.3_Missense_Mutation_p.R145G|APOA1BP_ENST00000467374.1_3'UTR	NM_144772.2	NP_658985.2			apolipoprotein A-I binding protein											central_nervous_system(1)|large_intestine(2)|lung(3)|prostate(2)|urinary_tract(1)	9	all_hematologic(923;0.088)|Hepatocellular(266;0.158)					TTACCCCAAAAGGCCTAACAA	0.562																																					p.R145G													.	APOA1BP	16		0			c.A433G												172.0	173.0	173.0					1																	156562379		2203	4300	6503	SO:0001583	missense	128240	exon4			CCCAAAAGGCCTA	AJ315849	CCDS1145.1	1q21	2008-08-14			ENSG00000163382	ENSG00000163382			18453	protein-coding gene	gene with protein product	"""apoA-I binding protein"""	608862				11991719, 17533573	Standard	NM_144772		Approved	AIBP, MGC119143, MGC119144, MGC119145, YJEFN1	uc001fph.3	Q8NCW5	OTTHUMG00000033206	ENST00000368235.3:c.433A>G	1.37:g.156562379A>G	ENSP00000357218:p.Arg145Gly		Somatic	65	0	0		WXS	Illumina HiSeq	Phase_I	114	0.03	3	NM_144772	292	0.00	0		Missense_Mutation	SNP	ENST00000368235.3	37	CCDS1145.1	.	.	.	.	.	.	.	.	.	.	A	18.26	3.584003	0.65992	.	.	ENSG00000163382	ENST00000446584;ENST00000368234;ENST00000368235;ENST00000368233	T;T;T	0.42131	0.98;0.98;0.98	3.8	3.8	0.43715	YjeF-related protein, N-terminal (5);	0.050499	0.64402	D	0.000001	T	0.46151	0.1378	M	0.74467	2.265	0.54753	D	0.999989	D;P;D	0.61697	0.984;0.942;0.99	P;P;P	0.61328	0.887;0.538;0.848	T	0.49872	-0.8893	10	0.51188	T	0.08	.	7.9688	0.30115	0.6495:0.3505:0.0:0.0	.	145;145;145	Q5T3I3;Q8NCW5;Q5T3I4	.;AIBP_HUMAN;.	G	163;145;145;145	ENSP00000357217:R145G;ENSP00000357218:R145G;ENSP00000357216:R145G	ENSP00000357216:R145G	R	+	1	2	APOA1BP	154829003	1.000000	0.71417	1.000000	0.80357	0.774000	0.43823	2.781000	0.47750	1.596000	0.50062	0.533000	0.62120	AGG			0.562	APOA1BP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000081044.1		NM_144772	
DDX59	83479	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	1	200618324	200618324	+	Missense_Mutation	SNP	C	C	G			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr1:200618324C>G	ENST00000331314.6	-	6	1558	c.1345G>C	c.(1345-1347)Gta>Cta	p.V449L	DDX59_ENST00000367348.3_Missense_Mutation_p.V449L|DDX59_ENST00000447706.2_Missense_Mutation_p.V449L	NM_001031725.4	NP_001026895.2	Q5T1V6	DDX59_HUMAN	DEAD (Asp-Glu-Ala-Asp) box polypeptide 59	449	Helicase C-terminal. {ECO:0000255|PROSITE-ProRule:PRU00542}.					cytoplasm (GO:0005737)|intracellular (GO:0005622)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(2)|liver(1)|lung(9)|ovary(3)	21						TCCACAAATACTAACACTGGA	0.318																																					p.V449L													.	.			0			c.G1345C												101.0	99.0	100.0					1																	200618324		2203	4299	6502	SO:0001583	missense	83479	exon6			CAAATACTAACAC	BC041801	CCDS30964.1	1q32.1	2010-07-14			ENSG00000118197	ENSG00000118197		"""Zinc fingers, HIT-type"", ""DEAD-boxes"""	25360	protein-coding gene	gene with protein product		615464					Standard	NM_001031725		Approved	DKFZP564B1023, ZNHIT5	uc009wzk.3	Q5T1V6	OTTHUMG00000035725	ENST00000331314.6:c.1345G>C	1.37:g.200618324C>G	ENSP00000330460:p.Val449Leu		Somatic	156	0	0		WXS	Illumina HiSeq	.	169	0.28	48	NM_001031725	54	0.35	19	Q6PJL2|Q8IVW3|Q9H0W3	Missense_Mutation	SNP	ENST00000331314.6	37	CCDS30964.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	35|35	5.456017|5.456017	0.96223|0.96223	.|.	.|.	ENSG00000118197|ENSG00000118197	ENST00000429498|ENST00000447706;ENST00000413408;ENST00000367348;ENST00000367346;ENST00000331314;ENST00000433235	.|D;T;D;D;T	.|0.94417	.|-3.42;3.25;-3.42;-3.42;3.25	6.06|6.06	6.06|6.06	0.98353|0.98353	.|Helicase, C-terminal (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.97315|0.97315	0.9122|0.9122	M|M	0.85299|0.85299	2.745|2.745	0.80722|0.80722	D|D	1|1	.|D;D	.|0.63046	.|0.96;0.992	.|P;P	.|0.60286	.|0.751;0.872	D|D	0.97168|0.97168	0.9842|0.9842	5|10	.|0.72032	.|D	.|0.01	-13.0665|-13.0665	20.6314|20.6314	0.99525|0.99525	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|449;449	.|B7Z5N6;Q5T1V6	.|.;DDX59_HUMAN	T|L	26|449;87;449;35;449;92	.|ENSP00000394367:V449L;ENSP00000394304:V87L;ENSP00000356317:V449L;ENSP00000330460:V449L;ENSP00000409954:V92L	.|ENSP00000330460:V449L	S|V	-|-	2|1	0|0	DDX59|DDX59	198884947|198884947	1.000000|1.000000	0.71417|0.71417	0.343000|0.343000	0.25615|0.25615	0.977000|0.977000	0.68977|0.68977	7.416000|7.416000	0.80143|0.80143	2.885000|2.885000	0.99019|0.99019	0.579000|0.579000	0.79373|0.79373	AGT|GTA			0.318	DDX59-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000086883.2		NM_001031725.4	
VN1R17P	441931	broad.mit.edu	37	1	247401118	247401118	+	lincRNA	DEL	A	A	-			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr1:247401118delA	ENST00000428687.1	-	0	47																											AAACATTTTTAATGACAATAT	0.328																																					.													.	.			0			.																																											0	.			ATTTTTAATGACA																													1.37:g.247401118delA			Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	.	0		0		RNA	DEL	ENST00000428687.1	37																																																																																						0.328	RP11-488L18.8-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000099306.1			
OTUD1	220213	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	10	23729299	23729299	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr10:23729299C>T	ENST00000376495.3	+	1	1102	c.913C>T	c.(913-915)Cgg>Tgg	p.R305W		NM_001145373.2	NP_001138845.1	Q5VV17	OTUD1_HUMAN	OTU deubiquitinase 1	305					protein K63-linked deubiquitination (GO:0070536)		ubiquitin-specific protease activity (GO:0004843)			breast(1)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|lung(2)	5						CAAGTATCTGCGGCAGAGGAA	0.592																																					p.R305W													.	.			0			c.C913T												41.0	45.0	44.0					10																	23729299		692	1591	2283	SO:0001583	missense	220213	exon1			TATCTGCGGCAGA	AK096389	CCDS44366.1	10p12.31	2014-02-24	2014-02-24		ENSG00000165312	ENSG00000165312		"""OTU domain containing"""	27346	protein-coding gene	gene with protein product		612022	"""OTU domain containing 1"""	OTDC1		23827681	Standard	NM_001145373		Approved	DUBA7	uc001irr.2	Q5VV17	OTTHUMG00000017819	ENST00000376495.3:c.913C>T	10.37:g.23729299C>T	ENSP00000365678:p.Arg305Trp		Somatic	59	0	0		WXS	Illumina HiSeq	.	43	0.23	10	NM_001145373	15	0.27	4		Missense_Mutation	SNP	ENST00000376495.3	37	CCDS44366.1	.	.	.	.	.	.	.	.	.	.	C	16.65	3.181584	0.57800	.	.	ENSG00000165312	ENST00000376495	T	0.42900	0.96	4.63	2.69	0.31865	.	0.089667	0.46442	U	0.000287	T	0.25494	0.0620	L	0.32530	0.975	0.42116	D	0.991409	P	0.43607	0.812	B	0.33121	0.158	T	0.04537	-1.0944	10	0.87932	D	0	-18.1823	7.6458	0.28318	0.2971:0.6234:0.0:0.0795	.	305	Q5VV17	OTUD1_HUMAN	W	305	ENSP00000365678:R305W	ENSP00000365678:R305W	R	+	1	2	OTUD1	23769305	1.000000	0.71417	0.978000	0.43139	0.300000	0.27592	2.993000	0.49425	0.323000	0.23307	0.643000	0.83706	CGG			0.592	OTUD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000047215.1		XM_166659	
PPA1	5464	hgsc.bcm.edu	37	10	71969413	71969413	+	Silent	SNP	A	A	G			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr10:71969413A>G	ENST00000373232.3	-	7	639	c.540T>C	c.(538-540)ccT>ccC	p.P180P		NM_021129.3	NP_066952.1	Q15181	IPYR_HUMAN	pyrophosphatase (inorganic) 1	180					diphosphate metabolic process (GO:0071344)|gene expression (GO:0010467)|phosphate-containing compound metabolic process (GO:0006796)|tRNA aminoacylation for protein translation (GO:0006418)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	inorganic diphosphatase activity (GO:0004427)|magnesium ion binding (GO:0000287)			breast(2)|endometrium(1)|large_intestine(2)|lung(3)|skin(2)	10						CTAAGTAGCCAGGTTTCAGCC	0.348																																					p.P180P													PPA1,NS,carcinoma,-1,1	PPA1	-1	1	0			c.T540C												104.0	107.0	106.0					10																	71969413		2203	4300	6503	SO:0001819	synonymous_variant	5464	exon7			GTAGCCAGGTTTC	AF154065	CCDS7299.1	10q11.1-q24	2012-10-02	2005-10-07	2005-10-07	ENSG00000180817	ENSG00000180817	3.6.1.1		9226	protein-coding gene	gene with protein product	"""cytosolic inorganic pyrophosphatase"", ""inorganic pyrophosphatase 1"", ""pyrophosphate phospho-hydrolase"""	179030	"""pyrophosphatase (inorganic)"""	PP		10542310, 975879	Standard	NM_021129		Approved	SID6-8061, Ppase, IOPPP, PP1	uc001jqv.1	Q15181	OTTHUMG00000018399	ENST00000373232.3:c.540T>C	10.37:g.71969413A>G			Somatic	108	0.0185185185	2		WXS	Illumina HiSeq	.	127	0.06	7	NM_021129	543	0.00	1	Q2M348|Q5SQT7|Q6P7P4|Q9UQJ5|Q9Y5B1	Silent	SNP	ENST00000373232.3	37	CCDS7299.1																																																																																					0.348	PPA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000048490.2		NM_021129	
PPRC1	23082	ucsc.edu	37	10	103904028	103904028	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr10:103904028C>T	ENST00000278070.2	+	7	3611	c.3572C>T	c.(3571-3573)cCg>cTg	p.P1191L	PPRC1_ENST00000489648.1_3'UTR|PPRC1_ENST00000413464.2_Missense_Mutation_p.P1191L|PPRC1_ENST00000370012.1_Missense_Mutation_p.P158L	NM_015062.3	NP_055877.3	Q5VV67	PPRC1_HUMAN	peroxisome proliferator-activated receptor gamma, coactivator-related 1	1191					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			central_nervous_system(1)|cervix(1)|endometrium(9)|kidney(5)|large_intestine(10)|lung(19)|ovary(1)|prostate(1)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	56		Colorectal(252;0.122)		Epithelial(162;4.97e-08)|all cancers(201;8.99e-07)		TGTCCTCCTCCGGCTCCTGCT	0.522																																					p.P1191L													.	PPRC1	151		0			c.C3572T												83.0	79.0	80.0					10																	103904028		2203	4300	6503	SO:0001583	missense	23082	exon7			CTCCTCCGGCTCC	AF325193	CCDS7529.1, CCDS73186.1	10q24.32	2013-02-12	2006-10-17		ENSG00000148840	ENSG00000148840		"""RNA binding motif (RRM) containing"""	30025	protein-coding gene	gene with protein product			"""peroxisome proliferative activated receptor, gamma, coactivator-related 1"""			9628581, 11340167	Standard	XM_005269656		Approved	PRC, KIAA0595, MGC74642	uc001kum.3	Q5VV67	OTTHUMG00000018948	ENST00000278070.2:c.3572C>T	10.37:g.103904028C>T	ENSP00000278070:p.Pro1191Leu		Somatic	45	0	0		WXS	Illumina HiSeq		40	0.10	4	NM_015062	109	0.00	0	Q5VV66|Q6P3U5|Q6P3W1|Q76N31|Q9BUJ3|Q9BZE5|Q9Y4E0	Missense_Mutation	SNP	ENST00000278070.2	37	CCDS7529.1	.	.	.	.	.	.	.	.	.	.	C	15.69	2.908500	0.52333	.	.	ENSG00000148840	ENST00000278070;ENST00000413464;ENST00000370012	T;T;T	0.28895	2.01;2.0;1.59	5.25	-0.522	0.11928	.	0.593417	0.17954	N	0.156418	T	0.12390	0.0301	N	0.08118	0	0.52099	D	0.999943	B;B;B	0.06786	0.001;0.001;0.001	B;B;B	0.04013	0.001;0.001;0.001	T	0.06716	-1.0811	10	0.49607	T	0.09	.	4.2134	0.10522	0.2517:0.2442:0.0:0.5041	.	1191;1071;1191	E7EVG6;Q5VV67-2;Q5VV67	.;.;PPRC1_HUMAN	L	1191;1191;158	ENSP00000278070:P1191L;ENSP00000399743:P1191L;ENSP00000359029:P158L	ENSP00000278070:P1191L	P	+	2	0	PPRC1	103894018	0.336000	0.24757	0.995000	0.50966	0.959000	0.62525	-0.523000	0.06230	0.003000	0.14656	-0.339000	0.08088	CCG			0.522	PPRC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000050021.1		NM_015062	
VWA2	340706	broad.mit.edu;bcgsc.ca	37	10	116050067	116050067	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr10:116050067A>G	ENST00000392982.3	+	13	2441	c.2191A>G	c.(2191-2193)Aat>Gat	p.N731D				Q5GFL6	VWA2_HUMAN	von Willebrand factor A domain containing 2	731	EGF-like 2. {ECO:0000255|PROSITE- ProRule:PRU00076}.				calcium-independent cell-matrix adhesion (GO:0007161)|protein homooligomerization (GO:0051260)|regulation of insulin receptor signaling pathway (GO:0046626)	basement membrane (GO:0005604)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	identical protein binding (GO:0042802)			central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(6)|ovary(2)|prostate(1)|skin(1)|stomach(1)	26				Epithelial(162;0.036)|all cancers(201;0.0793)		CGTCCTGCAGAATGGGAGCTA	0.597																																					p.N731D													.	VWA2	64		0			c.A2191G																																									SO:0001583	missense	340706	exon13			CTGCAGAATGGGA	AK127756	CCDS7589.1, CCDS7589.2	10q25.3	2009-11-06			ENSG00000165816	ENSG00000165816			24709	protein-coding gene	gene with protein product						15580307, 14506275	Standard	NM_001272046		Approved	FLJ45857, FLJ16213, CCSP-2, AMACO, NET42	uc001lbl.2	Q5GFL6	OTTHUMG00000019082	ENST00000392982.3:c.2191A>G	10.37:g.116050067A>G	ENSP00000376708:p.Asn731Asp		Somatic	49	0	0		WXS	Illumina HiSeq	Phase_I	45	0.09	4	NM_001272046	4	0.00	0	A1A5D4|B5MDJ8|Q6ZS39|Q6ZWJ7|Q708C5|Q70UZ8	Missense_Mutation	SNP	ENST00000392982.3	37		.	.	.	.	.	.	.	.	.	.	A	3.619	-0.077960	0.07184	.	.	ENSG00000165816	ENST00000392982	D	0.91894	-2.93	5.47	-1.3	0.09259	EGF (1);Epidermal growth factor-like (1);Epidermal growth factor-like, type 3 (1);	0.713915	0.14674	N	0.305157	T	0.76506	0.3997	.	.	.	0.09310	N	1	B	0.10296	0.003	B	0.10450	0.005	T	0.63070	-0.6719	9	0.07325	T	0.83	.	2.5977	0.04858	0.3472:0.3921:0.145:0.1157	.	731	Q5GFL6	VWA2_HUMAN	D	731	ENSP00000376708:N731D	ENSP00000376708:N731D	N	+	1	0	VWA2	116040057	0.001000	0.12720	0.070000	0.20053	0.533000	0.34776	0.293000	0.19029	-0.231000	0.09825	0.528000	0.53228	AAT			0.597	VWA2-001	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000050456.3		NM_198496	
KRTAP5-10	387273	broad.mit.edu	37	11	71276851	71276851	+	Missense_Mutation	SNP	A	A	G	rs201070584	byFrequency	TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr11:71276851A>G	ENST00000398531.1	+	1	243	c.218A>G	c.(217-219)gAc>gGc	p.D73G	KRTAP5-10_ENST00000376536.4_Missense_Mutation_p.D73G	NM_001012710.1	NP_001012728.1	Q6L8G5	KR510_HUMAN	keratin associated protein 5-10	73	7 X 4 AA repeats of C-C-X-P.					keratin filament (GO:0045095)				endometrium(2)|large_intestine(1)|lung(4)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	12						TCCAAGGGGGACTGTGGCTCT	0.672																																					p.D73G													KRTAP5-10,NS,carcinoma,-1,1	KRTAP5-10	37	1	0			c.A218G												62.0	84.0	77.0					11																	71276851		2190	4281	6471	SO:0001583	missense	387273	exon1			AGGGGGACTGTGG	AB126079	CCDS41684.1	11q13.4	2008-02-05			ENSG00000204572	ENSG00000204572		"""Keratin associated proteins"""	23605	protein-coding gene	gene with protein product						15144888	Standard	NM_001012710		Approved	KRTAP5.10	uc001oqt.1	Q6L8G5	OTTHUMG00000057585	ENST00000398531.1:c.218A>G	11.37:g.71276851A>G	ENSP00000381542:p.Asp73Gly		Somatic	46	0.2608695652	12		WXS	Illumina HiSeq	Phase_I	37	0.22	8	NM_001012710	0		0	B9EHA4	Missense_Mutation	SNP	ENST00000398531.1	37	CCDS41684.1	.	.	.	.	.	.	.	.	.	.	g	2.213	-0.380257	0.05000	.	.	ENSG00000204572	ENST00000398531;ENST00000376536	T;T	0.00864	5.6;5.69	1.84	0.898	0.19264	.	.	.	.	.	T	0.00300	0.0009	N	0.00063	-2.32	0.19575	N	0.999969	B	0.02656	0.0	B	0.01281	0.0	T	0.46816	-0.9164	9	0.59425	D	0.04	.	6.0403	0.19730	0.3144:0.0:0.6856:0.0	.	73	Q6L8G5	KR510_HUMAN	G	73	ENSP00000381542:D73G;ENSP00000365719:D73G	ENSP00000365719:D73G	D	+	2	0	KRTAP5-10	70954499	0.827000	0.29292	0.711000	0.30485	0.001000	0.01503	2.306000	0.43673	-0.017000	0.14103	-0.492000	0.04666	GAC			0.672	KRTAP5-10-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000127968.2			
ATN1	1822	hgsc.bcm.edu	37	12	7045915	7045915	+	Missense_Mutation	SNP	G	G	T	rs148885085	byFrequency	TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr12:7045915G>T	ENST00000356654.4	+	5	1722	c.1485G>T	c.(1483-1485)caG>caT	p.Q495H	ATN1_ENST00000396684.2_Missense_Mutation_p.Q495H	NM_001007026.1	NP_001007027.1	P54259	ATN1_HUMAN	atrophin 1	495	Poly-Gln.				cell migration (GO:0016477)|central nervous system development (GO:0007417)|maintenance of cell polarity (GO:0030011)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron apoptotic process (GO:0051402)|toxin metabolic process (GO:0009404)|transcription, DNA-templated (GO:0006351)	cell junction (GO:0030054)|cytoplasm (GO:0005737)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)	protein domain specific binding (GO:0019904)|transcription corepressor activity (GO:0003714)			breast(5)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(15)|ovary(2)|pancreas(1)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(2)	40						agcagcagcagcagcagcagc	0.642																																					p.Q495H													ATN1,colon,carcinoma,0,1	ATN1	0	1	0			c.G1485T												40.0	52.0	48.0					12																	7045915		2181	4270	6451	SO:0001583	missense	1822	exon5			GCAGCAGCAGCAG	U23851	CCDS31734.1	12p	2007-08-01	2005-03-15	2005-03-17		ENSG00000111676			3033	protein-coding gene	gene with protein product		607462	"""dentatorubral-pallidoluysian atrophy (atrophin-1)"""	D12S755E, DRPLA		8136826	Standard	NM_001940		Approved	B37	uc001qrw.1	P54259		ENST00000356654.4:c.1485G>T	12.37:g.7045915G>T	ENSP00000349076:p.Gln495His		Somatic	44	0.0227272727	1		WXS	Illumina HiSeq	.	190	0.05	9	NM_001007026	497	0.00	1	Q99495|Q99621|Q9UEK7	Missense_Mutation	SNP	ENST00000356654.4	37	CCDS31734.1	.	.	.	.	.	.	.	.	.	.	g	0.610	-0.825352	0.02734	.	.	ENSG00000111676	ENST00000356654;ENST00000396684;ENST00000544325;ENST00000229279	T;T;T	0.50277	0.75;0.75;0.75	.	.	.	.	.	.	.	.	T	0.23410	0.0566	N	0.02011	-0.69	0.09310	N	1	P	0.43826	0.818	P	0.46629	0.522	T	0.12837	-1.0532	7	0.33940	T	0.23	.	.	.	.	.	495	P54259	ATN1_HUMAN	H	495;495;495;80	ENSP00000349076:Q495H;ENSP00000379915:Q495H;ENSP00000441744:Q495H	ENSP00000229279:Q80H	Q	+	3	2	ATN1	6916176	0.036000	0.19791	0.514000	0.27761	0.306000	0.27790	0.389000	0.20751	0.000000	0.14550	0.000000	0.15137	CAG			0.642	ATN1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000401948.2		NM_001940	
LMO3	55885	hgsc.bcm.edu;broad.mit.edu;bcgsc.ca	37	12	16713458	16713458	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr12:16713458G>T	ENST00000320122.6	-	3	743	c.221C>A	c.(220-222)aCg>aAg	p.T74K	LMO3_ENST00000441439.2_Missense_Mutation_p.T74K|LMO3_ENST00000541295.1_Missense_Mutation_p.T92K|LMO3_ENST00000354662.1_Missense_Mutation_p.T74K|LMO3_ENST00000540445.1_Missense_Mutation_p.T96K|LMO3_ENST00000534946.1_Missense_Mutation_p.T74K|LMO3_ENST00000541846.1_Missense_Mutation_p.T74K|LMO3_ENST00000447609.1_Missense_Mutation_p.T74K|LMO3_ENST00000540848.1_Missense_Mutation_p.T74K|LMO3_ENST00000537304.1_Missense_Mutation_p.T74K|LMO3_ENST00000535535.1_Missense_Mutation_p.T74K|LMO3_ENST00000261169.6_Missense_Mutation_p.T85K	NM_001243611.1	NP_001230540.1	Q8TAP4	LMO3_HUMAN	LIM domain only 3 (rhombotin-like 2)	74					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)		zinc ion binding (GO:0008270)			endometrium(2)|large_intestine(2)|skin(1)	5		Hepatocellular(102;0.244)				GCAGTTTCCCGTTACACCAAA	0.413																																					p.T96K													.	.			0			c.C287A												105.0	84.0	91.0					12																	16713458		2203	4300	6503	SO:0001583	missense	55885	exon5			TTTCCCGTTACAC	BC026311	CCDS8678.1, CCDS58210.1, CCDS58211.1, CCDS58212.1	12p13	2004-05-19			ENSG00000048540	ENSG00000048540			6643	protein-coding gene	gene with protein product		180386		RBTNL2		11489251	Standard	NM_018640		Approved	Rhom-3, DAT1	uc010shy.2	Q8TAP4	OTTHUMG00000168837	ENST00000320122.6:c.221C>A	12.37:g.16713458G>T	ENSP00000312856:p.Thr74Lys		Somatic	83	0	0		WXS	Illumina HiSeq	.	247	0.06	14	NM_001243613	4	0.25	1	B4DG90|B4DH35|Q58A66|Q58A67|Q8N974|Q9UDD5	Missense_Mutation	SNP	ENST00000320122.6	37	CCDS8678.1	.	.	.	.	.	.	.	.	.	.	G	17.59	3.427564	0.62733	.	.	ENSG00000048540	ENST00000354662;ENST00000441439;ENST00000447609;ENST00000320122;ENST00000261169;ENST00000542544;ENST00000540848;ENST00000535535;ENST00000537304;ENST00000541295;ENST00000534946;ENST00000540445;ENST00000541846;ENST00000539534;ENST00000546281;ENST00000537757;ENST00000546279;ENST00000538051;ENST00000545436;ENST00000540590	T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T;T	0.60040	0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.94;0.22;0.54	4.58	4.58	0.56647	Zinc finger, LIM-type (1);	0.000000	0.85682	D	0.000000	T	0.54615	0.1869	L	0.31578	0.945	0.80722	D	1	P;P;P;P	0.50710	0.938;0.854;0.719;0.767	P;B;B;B	0.48982	0.597;0.414;0.302;0.273	T	0.59311	-0.7478	10	0.54805	T	0.06	.	15.7204	0.77705	0.0:0.0:1.0:0.0	.	96;92;74;85	B4DH35;B4DG90;Q8TAP4;Q58A67	.;.;LMO3_HUMAN;.	K	74;74;74;74;85;54;74;74;74;92;74;96;74;74;74;74;74;74;74;74	ENSP00000346689:T74K;ENSP00000412479:T74K;ENSP00000413703:T74K;ENSP00000312856:T74K;ENSP00000261169:T85K;ENSP00000445751:T74K;ENSP00000446115:T74K;ENSP00000440099:T74K;ENSP00000446463:T92K;ENSP00000439275:T74K;ENSP00000442786:T96K;ENSP00000444393:T74K;ENSP00000443807:T74K;ENSP00000442713:T74K;ENSP00000445193:T74K;ENSP00000441360:T74K;ENSP00000445504:T74K;ENSP00000444269:T74K;ENSP00000439989:T74K	ENSP00000261169:T85K	T	-	2	0	LMO3	16604725	1.000000	0.71417	0.630000	0.29268	0.802000	0.45316	8.883000	0.92426	2.363000	0.80096	0.591000	0.81541	ACG			0.413	LMO3-014	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000401279.1		NM_018640	
DDX11	1663	broad.mit.edu	37	12	31238044	31238044	+	Frame_Shift_Del	DEL	A	A	-			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr12:31238044delA	ENST00000407793.2	+	5	873	c.622delA	c.(622-624)aaafs	p.K209fs	DDX11_ENST00000545668.1_Frame_Shift_Del_p.K209fs|DDX11_ENST00000350437.4_Frame_Shift_Del_p.K209fs|DDX11_ENST00000251758.5_Frame_Shift_Del_p.K209fs|DDX11_ENST00000542838.1_Frame_Shift_Del_p.K209fs|DDX11_ENST00000228264.6_Frame_Shift_Del_p.K183fs	NM_030653.3|NM_152438.1	NP_085911.2|NP_689651.1	Q96FC9	DDX11_HUMAN	DEAD/H (Asp-Glu-Ala-Asp/His) box helicase 11	209	Glu-rich.|Helicase ATP-binding. {ECO:0000255|PROSITE-ProRule:PRU00541}.				activation of signaling protein activity involved in unfolded protein response (GO:0006987)|ATP catabolic process (GO:0006200)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)|sister chromatid cohesion (GO:0007062)|viral process (GO:0016032)	midbody (GO:0030496)|nuclear chromatin (GO:0000790)|nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	4 iron, 4 sulfur cluster binding (GO:0051539)|ATP binding (GO:0005524)|ATP-dependent DNA helicase activity (GO:0004003)|DNA-dependent ATPase activity (GO:0008094)|double-stranded DNA binding (GO:0003690)|helicase activity (GO:0004386)|metal ion binding (GO:0046872)|RNA binding (GO:0003723)|single-stranded DNA binding (GO:0003697)			breast(4)|central_nervous_system(1)|cervix(1)|endometrium(4)|kidney(11)|large_intestine(5)|lung(23)|prostate(3)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)	57	all_cancers(9;1.77e-11)|all_lung(12;6.21e-11)|all_epithelial(9;6.49e-11)|Lung NSC(12;1.06e-08)|Acute lymphoblastic leukemia(23;0.0122)|all_hematologic(23;0.0429)|Lung SC(12;0.0592)|Esophageal squamous(101;0.233)					TGATGAGGAGAAAAAGGTGGC	0.617										Multiple Myeloma(12;0.14)																											p.K208fs													.	DDX11	188		0			c.622delA												31.0	31.0	31.0					12																	31238044		2194	4282	6476	SO:0001589	frameshift_variant	1663	exon5			GAGGAGAAAAAGG	U75969	CCDS8721.1, CCDS41767.1, CCDS44856.1, CCDS58224.1	12p11.21	2012-02-23	2012-02-23		ENSG00000013573	ENSG00000013573		"""DEAD-boxes"""	2736	protein-coding gene	gene with protein product	"""CHL1-like helicase homolog (S. cerevisiae)"""	601150	"""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11 (S.cerevisiae CHL1-like helicase)"", ""DEAD/H (Asp-Glu-Ala-Asp/His) box polypeptide 11"""				Standard	NM_030653		Approved	CHLR1, KRG2, CHL1, ChlR1, WABS	uc001rjv.2	Q96FC9	OTTHUMG00000168435	ENST00000407793.2:c.622delA	12.37:g.31238044delA	ENSP00000384703:p.Lys209fs		Somatic	178	0	0		WXS	Illumina HiSeq	Phase_I	805	0.01	8	NM_030653	268	0.00	0	Q13333|Q86VQ4|Q86W62|Q92498|Q92770|Q92998|Q92999	Frame_Shift_Del	DEL	ENST00000407793.2	37	CCDS44856.1																																																																																					0.617	DDX11-202	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000399728.1		NM_030653	
KRT72	140807	broad.mit.edu;bcgsc.ca	37	12	52985290	52985290	+	Silent	SNP	G	G	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr12:52985290G>T	ENST00000537672.2	-	5	931	c.921C>A	c.(919-921)gcC>gcA	p.A307A	KRT72_ENST00000354310.4_Silent_p.A307A|KRT72_ENST00000398066.3_Silent_p.A119A|KRT72_ENST00000293745.2_Silent_p.A307A	NM_001146225.1	NP_001139697.1	Q14CN4	K2C72_HUMAN	keratin 72	307	Coil 2.|Rod.					extracellular vesicular exosome (GO:0070062)|keratin filament (GO:0045095)	structural molecule activity (GO:0005198)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(14)|ovary(5)|pancreas(1)|prostate(3)|skin(3)|upper_aerodigestive_tract(2)	36				BRCA - Breast invasive adenocarcinoma(357;0.195)		TGCTCTTTAGGGCAATCTCCT	0.582																																					p.A307A													.	KRT72	70		0			c.C921A												153.0	114.0	127.0					12																	52985290		2203	4300	6503	SO:0001819	synonymous_variant	140807	exon5			CTTTAGGGCAATC	AY033495	CCDS8833.1, CCDS53795.1	12q13.13	2013-06-25			ENSG00000170486	ENSG00000170486		"""-"", ""Intermediate filaments type II, keratins (basic)"""	28932	protein-coding gene	gene with protein product		608246				12648212, 11703281, 16831889	Standard	NM_080747		Approved	K6IRS2, KRT6IRS2, KRT6, K6irs	uc001saq.2	Q14CN4	OTTHUMG00000169744	ENST00000537672.2:c.921C>A	12.37:g.52985290G>T			Somatic	74	0	0		WXS	Illumina HiSeq	Phase_I	110	0.29	32	NM_001146225	1	1.00	1	B4DEI8|H9KV51|Q8NA87|Q8WWY9|Q8WWZ0	Silent	SNP	ENST00000537672.2	37	CCDS8833.1																																																																																					0.582	KRT72-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000405693.1		NM_080747	
ANAPC5	51433	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	12	121775139	121775139	+	Silent	SNP	C	C	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr12:121775139C>T	ENST00000261819.3	-	6	835	c.714G>A	c.(712-714)aaG>aaA	p.K238K	ANAPC5_ENST00000544314.1_5'Flank|ANAPC5_ENST00000536366.1_Silent_p.K117K|ANAPC5_ENST00000344395.4_Silent_p.K139K|ANAPC5_ENST00000441917.2_Silent_p.K139K|ANAPC5_ENST00000541887.1_Silent_p.K238K	NM_016237.4	NP_057321.2	Q9UJX4	APC5_HUMAN	anaphase promoting complex subunit 5	238					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	protein phosphatase binding (GO:0019903)			breast(6)|endometrium(3)|kidney(3)|large_intestine(5)|lung(10)|prostate(1)|skin(3)	31	all_neural(191;0.0684)|Medulloblastoma(191;0.0922)					TGTTTAATTCCTTCTGCAAGG	0.373																																					p.K238K													.	.			0			c.G714A												97.0	100.0	99.0					12																	121775139		2203	4300	6503	SO:0001819	synonymous_variant	51433	exon6			TAATTCCTTCTGC	AF191339	CCDS9220.1, CCDS45000.1	12q24.31	2014-08-12			ENSG00000089053	ENSG00000089053		"""Anaphase promoting complex subunits"""	15713	protein-coding gene	gene with protein product		606948				9469815	Standard	NM_016237		Approved	APC5	uc001uag.3	Q9UJX4	OTTHUMG00000169157	ENST00000261819.3:c.714G>A	12.37:g.121775139C>T			Somatic	62	0	0		WXS	Illumina HiSeq	.	53	0.57	30	NM_016237	154	0.66	102	E9PFB2|Q8N4H7|Q9BQD4	Silent	SNP	ENST00000261819.3	37	CCDS9220.1																																																																																					0.373	ANAPC5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000402582.1			
IRS2	8660	hgsc.bcm.edu;broad.mit.edu	37	13	110435932	110435932	+	Nonsense_Mutation	SNP	G	G	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr13:110435932G>T	ENST00000375856.3	-	1	2983	c.2469C>A	c.(2467-2469)taC>taA	p.Y823*		NM_003749.2	NP_003740.2	Q9Y4H2	IRS2_HUMAN	insulin receptor substrate 2	823					brain development (GO:0007420)|cell proliferation (GO:0008283)|cellular response to glucose stimulus (GO:0071333)|cellular response to insulin stimulus (GO:0032869)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|glucose metabolic process (GO:0006006)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|JAK-STAT cascade involved in growth hormone signaling pathway (GO:0060397)|lipid homeostasis (GO:0055088)|mammary gland development (GO:0030879)|negative regulation of B cell apoptotic process (GO:0002903)|negative regulation of kinase activity (GO:0033673)|negative regulation of plasma membrane long-chain fatty acid transport (GO:0010748)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of B cell proliferation (GO:0030890)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fatty acid beta-oxidation (GO:0032000)|positive regulation of glucose import (GO:0046326)|positive regulation of glucose metabolic process (GO:0010907)|positive regulation of glycogen biosynthetic process (GO:0045725)|positive regulation of insulin secretion (GO:0032024)|positive regulation of mesenchymal cell proliferation (GO:0002053)|regulation of lipid metabolic process (GO:0019216)|response to glucose (GO:0009749)|signal transduction (GO:0007165)	cytosol (GO:0005829)|plasma membrane (GO:0005886)	signal transducer activity (GO:0004871)			kidney(2)|large_intestine(2)|lung(8)|ovary(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)	19	all_cancers(4;7.57e-15)|all_epithelial(4;5.91e-09)|all_lung(23;7.64e-07)|Lung NSC(43;0.000183)|Colorectal(4;0.00159)|all_neural(89;0.00294)|Medulloblastoma(90;0.00596)|Lung SC(71;0.0155)	Breast(118;0.159)	all cancers(43;0.00815)|BRCA - Breast invasive adenocarcinoma(86;0.11)|Epithelial(84;0.127)|GBM - Glioblastoma multiforme(44;0.147)			TCATGAGCACGTACTGGTCGC	0.731																																					p.Y823X	Melanoma(100;613 2409 40847)												.	.			0			c.C2469A												5.0	7.0	6.0					13																	110435932		2038	4065	6103	SO:0001587	stop_gained	8660	exon1			GAGCACGTACTGG	AB000732	CCDS9510.1	13q34	2013-01-10			ENSG00000185950	ENSG00000185950		"""Pleckstrin homology (PH) domain containing"""	6126	protein-coding gene	gene with protein product		600797				9312143	Standard	NM_003749		Approved		uc001vqv.3	Q9Y4H2	OTTHUMG00000017338	ENST00000375856.3:c.2469C>A	13.37:g.110435932G>T	ENSP00000365016:p.Tyr823*		Somatic	64	0	0		WXS	Illumina HiSeq	.	57	0.28	16	NM_003749	11	0.73	8	Q96RR2|Q9BZG0|Q9Y6I5	Nonsense_Mutation	SNP	ENST00000375856.3	37	CCDS9510.1	.	.	.	.	.	.	.	.	.	.	G	42	9.511810	0.99192	.	.	ENSG00000185950	ENST00000375856	.	.	.	5.14	-4.65	0.03339	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-15.5849	15.1825	0.72972	0.6893:0.0:0.3107:0.0	.	.	.	.	X	823	.	ENSP00000365016:Y823X	Y	-	3	2	IRS2	109233933	0.782000	0.28689	0.960000	0.40013	0.944000	0.59088	-0.145000	0.10265	-0.883000	0.03982	-0.390000	0.06520	TAC			0.731	IRS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000045755.1		NM_003749	
PARP1P1	144	bcgsc.ca	37	13	111591851	111591851	+	IGR	SNP	C	C	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr13:111591851C>T								ANKRD10 (24435 upstream) : LINC00431 (43802 downstream)																							AGGGTTAATCCTGTCGGAAGA	0.463																																					.													.	.			0			.																																									SO:0001628	intergenic_variant	144	.			TTAATCCTGTCGG																													13.37:g.111591851C>T			Somatic	27	0	0		WXS	Illumina HiSeq	Phase_1	16	0.25	4	.	0		0		RNA	SNP		37																																																																																					0	0.463										
MAPK1IP1L	93487	broad.mit.edu;ucsc.edu;bcgsc.ca	37	14	55529374	55529374	+	Silent	SNP	C	C	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr14:55529374C>T	ENST00000395468.4	+	3	234	c.57C>T	c.(55-57)acC>acT	p.T19T	MAPK1IP1L_ENST00000554364.1_3'UTR	NM_144578.3	NP_653179.1	Q8NDC0	MISSL_HUMAN	mitogen-activated protein kinase 1 interacting protein 1-like	19										endometrium(2)|large_intestine(1)|lung(3)	6						CTGCCAAAACCTCTGCTGTGA	0.488																																					p.T19T													.	MAPK1IP1L	14		0			c.C57T												45.0	47.0	46.0					14																	55529374		2203	4300	6503	SO:0001819	synonymous_variant	93487	exon3			CAAAACCTCTGCT	AK025580	CCDS32085.1	14q22.1	2008-01-30	2008-01-30	2008-01-16		ENSG00000168175			19840	protein-coding gene	gene with protein product			"""chromosome 14 open reading frame 32"", ""mitogen activated protein kinase 1 interacting protein 1-like"""	C14orf32		12011110	Standard	NM_144578		Approved		uc001xbq.1	Q8NDC0		ENST00000395468.4:c.57C>T	14.37:g.55529374C>T			Somatic	70	0.0142857143	1		WXS	Illumina HiSeq	Phase_I	72	0.39	28	NM_144578	227	0.44	100	B2RDD8|Q96BG5	Silent	SNP	ENST00000395468.4	37	CCDS32085.1																																																																																					0.488	MAPK1IP1L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000411302.2		NM_144578	
DYNC1H1	1778	broad.mit.edu	37	14	102496591	102496591	+	Silent	SNP	G	G	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr14:102496591G>T	ENST00000360184.4	+	51	10019	c.9855G>T	c.(9853-9855)gtG>gtT	p.V3285V		NM_001376.4	NP_001367.2	Q14204	DYHC1_HUMAN	dynein, cytoplasmic 1, heavy chain 1	3285	Stalk. {ECO:0000250}.				antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|cell death (GO:0008219)|cytoplasmic mRNA processing body assembly (GO:0033962)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based movement (GO:0007018)|mitotic cell cycle (GO:0000278)|mitotic spindle organization (GO:0007052)|stress granule assembly (GO:0034063)|transport (GO:0006810)	centrosome (GO:0005813)|cytoplasmic dynein complex (GO:0005868)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium (GO:0030175)|membrane (GO:0016020)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|poly(A) RNA binding (GO:0044822)			NS(1)|biliary_tract(1)|breast(4)|central_nervous_system(5)|cervix(1)|endometrium(21)|haematopoietic_and_lymphoid_tissue(3)|kidney(10)|large_intestine(28)|lung(60)|ovary(9)|pancreas(1)|prostate(6)|skin(7)|stomach(3)|upper_aerodigestive_tract(4)|urinary_tract(2)	166						TTGATAAGGTGGAACCTGCCG	0.458																																					p.V3285V													.	DYNC1H1	395		0			c.G9855T												121.0	101.0	108.0					14																	102496591		2203	4300	6503	SO:0001819	synonymous_variant	1778	exon51			TAAGGTGGAACCT	AB002323	CCDS9966.1	14q32.31	2006-12-21	2005-11-24	2005-11-24		ENSG00000197102		"""Cytoplasmic dyneins"""	2961	protein-coding gene	gene with protein product		600112	"""dynein, cytoplasmic, heavy polypeptide 1"""	DNECL, DNCL, DNCH1		16260502, 8666668	Standard	NM_001376		Approved	Dnchc1, HL-3, p22, DHC1	uc001yks.2	Q14204		ENST00000360184.4:c.9855G>T	14.37:g.102496591G>T			Somatic	78	0	0		WXS	Illumina HiSeq	Phase_I	54	0.06	3	NM_001376	187	0.00	0	B0I1R0|Q6DKQ7|Q8WU28|Q92814|Q9Y4G5	Silent	SNP	ENST00000360184.4	37	CCDS9966.1																																																																																					0.458	DYNC1H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000414574.1		NM_001376	
CCDC78	124093	ucsc.edu	37	16	772996	772996	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr16:772996C>T	ENST00000293889.6	-	13	1328	c.1223G>A	c.(1222-1224)aGc>aAc	p.S408N		NM_001031737.2	NP_001026907.2	A2IDD5	CCD78_HUMAN	coiled-coil domain containing 78	408					cell projection organization (GO:0030030)|de novo centriole assembly (GO:0098535)|skeletal muscle contraction (GO:0003009)	centriole (GO:0005814)|deuterosome (GO:0098536)|perinuclear region of cytoplasm (GO:0048471)|sarcolemma (GO:0042383)|sarcoplasmic reticulum (GO:0016529)				central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|lung(2)|skin(3)	9		Hepatocellular(780;0.0218)				GGACCAGCAGCTGTGCCCGCT	0.647																																					p.S408N													.	CCDC78	26		0			c.G1223A												57.0	50.0	53.0					16																	772996		2197	4296	6493	SO:0001583	missense	124093	exon13			CAGCAGCTGTGCC	BC042110	CCDS32353.1	16p13.3	2014-07-15		2006-02-20	ENSG00000162004	ENSG00000162004			14153	protein-coding gene	gene with protein product		614666		C16orf25		24075808	Standard	NM_001031737		Approved	FLJ34512	uc002cjg.3	A2IDD5	OTTHUMG00000121176	ENST00000293889.6:c.1223G>A	16.37:g.772996C>T	ENSP00000293889:p.Ser408Asn		Somatic	32	0	0		WXS	Illumina HiSeq		41	0.10	4	NM_001031737	25	0.00	0	B4DNY4|B4E1U6|Q05BY7|Q05CA0|Q6T2V5|Q6ZR33|Q8IUR3|Q8NAY7|Q96S12	Missense_Mutation	SNP	ENST00000293889.6	37	CCDS32353.1	.	.	.	.	.	.	.	.	.	.	C	13.59	2.281358	0.40394	.	.	ENSG00000162004	ENST00000345165;ENST00000293889	T	0.47177	0.85	4.55	3.49	0.39957	.	0.604741	0.14355	N	0.324825	T	0.38054	0.1026	L	0.36672	1.1	0.23519	N	0.997509	P	0.37101	0.582	B	0.38803	0.282	T	0.32824	-0.9892	10	0.87932	D	0	-1.8728	7.9227	0.29857	0.1732:0.7307:0.0:0.0961	.	408	A2IDD5	CCD78_HUMAN	N	258;408	ENSP00000293889:S408N	ENSP00000293889:S408N	S	-	2	0	CCDC78	712997	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	1.129000	0.31381	2.067000	0.61834	0.462000	0.41574	AGC			0.647	CCDC78-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000241665.3		NM_173476	
SMG1	23049	broad.mit.edu	37	16	18844328	18844328	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr16:18844328G>T	ENST00000446231.2	-	51	9138	c.8726C>A	c.(8725-8727)gCc>gAc	p.A2909D	SMG1_ENST00000389467.3_Missense_Mutation_p.A2909D			Q96Q15	SMG1_HUMAN	SMG1 phosphatidylinositol 3-kinase-related kinase	2909					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)			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						TCTTAAGTAGGCCTGAAGAGA	0.488																																					p.A2909D													.	SMG1	401		0			c.C8726A												262.0	250.0	254.0					16																	18844328		1941	4146	6087	SO:0001583	missense	23049	exon51			AAGTAGGCCTGAA	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.8726C>A	16.37:g.18844328G>T	ENSP00000402515:p.Ala2909Asp		Somatic	126	0	0		WXS	Illumina HiSeq	Phase_I	172	0.02	4	NM_015092	28	0.00	0	O43305|Q13284|Q8NFX2|Q96QV0|Q96RW3	Missense_Mutation	SNP	ENST00000446231.2	37	CCDS45430.1	.	.	.	.	.	.	.	.	.	.	G	21.3	4.121616	0.77436	.	.	ENSG00000157106	ENST00000446231;ENST00000389467	T;T	0.01092	5.35;5.35	5.91	5.91	0.95273	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.64402	D	0.000002	T	0.01558	0.0050	N	0.19112	0.55	0.43122	D	0.994844	B	0.27498	0.18	B	0.27796	0.083	T	0.68599	-0.5366	10	0.66056	D	0.02	.	20.3018	0.98617	0.0:0.0:1.0:0.0	.	2909	Q96Q15	SMG1_HUMAN	D	2909	ENSP00000402515:A2909D;ENSP00000374118:A2909D	ENSP00000374118:A2909D	A	-	2	0	SMG1	18751829	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	9.107000	0.94261	2.799000	0.96334	0.650000	0.86243	GCC			0.488	SMG1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000391817.1		NM_015092	
CCDC102A	92922	ucsc.edu	37	16	57552624	57552624	+	Silent	SNP	G	G	A	rs141241860	byFrequency	TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr16:57552624G>A	ENST00000258214.2	-	5	1197	c.951C>T	c.(949-951)gaC>gaT	p.D317D		NM_033212.3	NP_149989.2	Q96A19	C102A_HUMAN	coiled-coil domain containing 102A	317										endometrium(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)	8						GGCCCAGCTCGTCCTGGTGCG	0.632													g|||	2	0.000399361	0.0	0.0	5008	,	,		20491	0.0		0.002	False		,,,				2504	0.0				p.D317D													.	CCDC102A	22		0			c.C951T									0,4396		0,0,2198	44.0	32.0	36.0		951	-8.2	0.8	16	dbSNP_134	36	12,8588	9.1+/-34.3	0,12,4288	no	coding-synonymous	CCDC102A	NM_033212.3		0,12,6486	AA,AG,GG		0.1395,0.0,0.0923		317/551	57552624	12,12984	2198	4300	6498	SO:0001819	synonymous_variant	92922	exon5			CAGCTCGTCCTGG	BC008285	CCDS10784.1	16q13	2008-02-05			ENSG00000135736	ENSG00000135736			28097	protein-coding gene	gene with protein product						12477932	Standard	NM_033212		Approved	MGC10992	uc002elw.3	Q96A19	OTTHUMG00000133472	ENST00000258214.2:c.951C>T	16.37:g.57552624G>A			Somatic	30	0	0		WXS	Illumina HiSeq		33	0.12	4	NM_033212	35	0.00	0	Q9BT74	Silent	SNP	ENST00000258214.2	37	CCDS10784.1																																																																																					0.632	CCDC102A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000257348.1		NM_033212	
BAHCC1	57597	ucsc.edu	37	17	79410887	79410887	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr17:79410887G>T	ENST00000307745.7	+	10	2268	c.2268G>T	c.(2266-2268)gaG>gaT	p.E756D	RP11-1055B8.7_ENST00000570375.1_3'UTR																							CTGAGGAGGAGAGGACGAGGC	0.697																																					.													.	BAHCC1	110		0			.												29.0	37.0	34.0					17																	79410887		1977	3931	5908	SO:0001583	missense	57597	.			GGAGGAGAGGACG																												ENST00000307745.7:c.2268G>T	17.37:g.79410887G>T	ENSP00000303486:p.Glu756Asp		Somatic	11	0	0		WXS	Illumina HiSeq		22	0.18	4	.	0		0		Missense_Mutation	SNP	ENST00000307745.7	37		.	.	.	.	.	.	.	.	.	.	G	11.67	1.706431	0.30232	.	.	ENSG00000171282	ENST00000307745	T	0.14640	2.49	4.06	-3.87	0.04218	.	0.138120	0.29668	N	0.011518	T	0.08802	0.0218	L	0.41632	1.29	0.33817	D	0.628584	P	0.38020	0.615	B	0.37091	0.241	T	0.08785	-1.0705	10	0.72032	D	0.01	.	5.7771	0.18285	0.4838:0.2576:0.2587:0.0	.	756	Q9P281	BAHC1_HUMAN	D	756	ENSP00000303486:E756D	ENSP00000303486:E756D	E	+	3	2	AC110285.1	77025482	0.017000	0.18338	0.024000	0.17045	0.393000	0.30537	-1.322000	0.02695	-0.990000	0.03481	0.650000	0.86243	GAG			0.697	RP11-1055B8.7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding					
LIG1	3978	bcgsc.ca	37	19	48634358	48634358	+	Missense_Mutation	SNP	G	G	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr19:48634358G>T	ENST00000263274.7	-	19	2215	c.1796C>A	c.(1795-1797)cCg>cAg	p.P599Q	LIG1_ENST00000536218.1_Missense_Mutation_p.P531Q|LIG1_ENST00000427526.2_Missense_Mutation_p.P568Q	NM_000234.1	NP_000225.1	P18858	DNLI1_HUMAN	ligase I, DNA, ATP-dependent	599					anatomical structure morphogenesis (GO:0009653)|base-excision repair (GO:0006284)|cell division (GO:0051301)|DNA biosynthetic process (GO:0071897)|DNA ligation involved in DNA repair (GO:0051103)|DNA metabolic process (GO:0006259)|DNA repair (GO:0006281)|DNA strand elongation involved in DNA replication (GO:0006271)|double-strand break repair (GO:0006302)|double-strand break repair via homologous recombination (GO:0000724)|double-strand break repair via nonhomologous end joining (GO:0006303)|lagging strand elongation (GO:0006273)|mitotic cell cycle (GO:0000278)|nucleotide-excision repair (GO:0006289)|nucleotide-excision repair, DNA gap filling (GO:0006297)|response to hydrogen peroxide (GO:0042542)|telomere maintenance (GO:0000723)|telomere maintenance via recombination (GO:0000722)|telomere maintenance via semi-conservative replication (GO:0032201)|transcription-coupled nucleotide-excision repair (GO:0006283)	chromosome (GO:0005694)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|DNA ligase (ATP) activity (GO:0003910)|DNA ligase activity (GO:0003909)|metal ion binding (GO:0046872)			breast(1)|cervix(1)|endometrium(7)|kidney(1)|large_intestine(9)|lung(22)|prostate(2)|skin(1)	44		all_epithelial(76;3.1e-06)|all_lung(116;4.39e-06)|Lung NSC(112;8.96e-06)|all_neural(266;0.0189)|Ovarian(192;0.0261)|Breast(70;0.203)		OV - Ovarian serous cystadenocarcinoma(262;8.45e-05)|all cancers(93;0.000423)|Epithelial(262;0.0177)|GBM - Glioblastoma multiforme(486;0.0329)	Bleomycin(DB00290)	GATGATGTCCGGGTACTTCCC	0.597								Nucleotide excision repair (NER)																													p.P599Q													.	LIG1	151		0			c.C1796A												224.0	145.0	172.0					19																	48634358		2203	4300	6503	SO:0001583	missense	3978	exon19			ATGTCCGGGTACT		CCDS12711.1, CCDS74409.1, CCDS74410.1	19q13.2-q13.3	2014-09-17				ENSG00000105486	6.5.1.1		6598	protein-coding gene	gene with protein product		126391					Standard	XM_005258934		Approved		uc002pia.1	P18858		ENST00000263274.7:c.1796C>A	19.37:g.48634358G>T	ENSP00000263274:p.Pro599Gln		Somatic	51	0	0		WXS	Illumina HiSeq	Phase_1	45	0.09	4	NM_000234	305	0.00	0	B2RAI8|Q2TB12|Q32P23	Missense_Mutation	SNP	ENST00000263274.7	37	CCDS12711.1	.	.	.	.	.	.	.	.	.	.	G	27.4	4.823751	0.90873	.	.	ENSG00000105486	ENST00000263274;ENST00000544761;ENST00000427526;ENST00000536218	T;T;T	0.58652	0.32;0.32;0.32	5.29	5.29	0.74685	DNA ligase, ATP-dependent, central (1);	0.000000	0.85682	D	0.000000	D	0.85155	0.5632	H	0.97896	4.1	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	0.90485	0.4463	10	0.87932	D	0	-20.2209	16.8022	0.85617	0.0:0.0:1.0:0.0	.	568;531;599	B4DTU4;F5GZ28;P18858	.;.;DNLI1_HUMAN	Q	599;630;568;531	ENSP00000263274:P599Q;ENSP00000442841:P568Q;ENSP00000441531:P531Q	ENSP00000263274:P599Q	P	-	2	0	LIG1	53326170	1.000000	0.71417	0.961000	0.40146	0.990000	0.78478	9.061000	0.93913	2.647000	0.89833	0.650000	0.86243	CCG			0.597	LIG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000465575.1		NM_000234	
MYH14	79784	ucsc.edu	37	19	50764815	50764815	+	Silent	SNP	G	G	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr19:50764815G>T	ENST00000596571.1	+	18	2385	c.2385G>T	c.(2383-2385)ctG>ctT	p.L795L	MYH14_ENST00000440075.2_Silent_p.L836L|MYH14_ENST00000262269.8_Silent_p.L836L|MYH14_ENST00000425460.1_Silent_p.L803L|MYH14_ENST00000376970.2_Silent_p.L828L|MYH14_ENST00000601313.1_Silent_p.L836L|MYH14_ENST00000598205.1_Silent_p.L803L			Q7Z406	MYH14_HUMAN	myosin, heavy chain 14, non-muscle	795	Myosin motor.				actin filament-based movement (GO:0030048)|actomyosin structure organization (GO:0031032)|ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|mitochondrion morphogenesis (GO:0070584)|neuronal action potential (GO:0019228)|regulation of cell shape (GO:0008360)|sensory perception of sound (GO:0007605)|skeletal muscle atrophy (GO:0014732)|skeletal muscle contraction (GO:0003009)|skeletal muscle tissue development (GO:0007519)|vocalization behavior (GO:0071625)	actomyosin (GO:0042641)|axon (GO:0030424)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|growth cone (GO:0030426)|membrane (GO:0016020)|myosin II complex (GO:0016460)|myosin II filament (GO:0097513)|stress fiber (GO:0001725)	actin-dependent ATPase activity (GO:0030898)|ATP binding (GO:0005524)|microfilament motor activity (GO:0000146)			central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(10)|ovary(1)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	46		all_neural(266;0.0571)|Ovarian(192;0.0728)		OV - Ovarian serous cystadenocarcinoma(262;0.00389)|GBM - Glioblastoma multiforme(134;0.0195)		TGGCCCAGCTGGAAGAGGAGC	0.647																																					p.L836L													.	MYH14	261		0			c.G2508T												37.0	42.0	40.0					19																	50764815		2096	4239	6335	SO:0001819	synonymous_variant	79784	exon21			CCAGCTGGAAGAG	AY165122	CCDS46151.1, CCDS54295.1, CCDS59411.1	19q13.33	2011-09-27	2009-11-19			ENSG00000105357		"""Myosins / Myosin superfamily : Class II"""	23212	protein-coding gene	gene with protein product		608568	"""myosin, heavy polypeptide 14"", ""myosin, heavy chain 14"""	DFNA4		12909352, 15015131, 17940200	Standard	NM_024729		Approved	FLJ13881, KIAA2034, MHC16, MYH17	uc010enu.1	Q7Z406		ENST00000596571.1:c.2385G>T	19.37:g.50764815G>T			Somatic	25	0	0		WXS	Illumina HiSeq		39	0.10	4	NM_001145809	35	0.00	0	B0I1S2|C3TTN4|Q5CZ75|Q6XYE4|Q76B62|Q8WV23|Q96I22|Q9BT27|Q9BW35|Q9H882	Silent	SNP	ENST00000596571.1	37	CCDS59411.1																																																																																					0.647	MYH14-008	NOVEL	basic|appris_candidate|CCDS	protein_coding	protein_coding		OTTHUMT00000464710.2		NM_024729	
CEACAM18	729767	bcgsc.ca	37	19	51983738	51983738	+	Silent	SNP	C	C	T	rs61746204	byFrequency	TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr19:51983738C>T	ENST00000396477.4	+	2	225	c.204C>T	c.(202-204)agC>agT	p.S68S	CEACAM18_ENST00000451626.1_Silent_p.S129S	NM_001278392.1	NP_001265321.1	A8MTB9	CEA18_HUMAN	carcinoembryonic antigen-related cell adhesion molecule 18	68										breast(1)|endometrium(4)|large_intestine(3)|lung(8)|skin(1)	17		all_neural(266;0.0529)		GBM - Glioblastoma multiforme(134;0.00148)|OV - Ovarian serous cystadenocarcinoma(262;0.00979)		CAAACGACAGCGCAGGAAACA	0.567													c|||	8	0.00159744	0.0045	0.0029	5008	,	,		18758	0.0		0.0	False		,,,				2504	0.0				p.S129S													.	CEACAM18	96		0			c.C387T							C		31,4045		0,31,2007	63.0	63.0	63.0		387	-4.8	0.0	19	dbSNP_129	63	0,8382		0,0,4191	no	coding-synonymous	CEACAM18	NM_001080405.1		0,31,6198	TT,TC,CC		0.0,0.7605,0.2488		129/399	51983738	31,12427	2038	4191	6229	SO:0001819	synonymous_variant	729767	exon3			CGACAGCGCAGGA			19q13.41	2013-01-29				ENSG00000213822		"""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	31949	protein-coding gene	gene with protein product							Standard	NM_001278392		Approved		uc002pwv.1	A8MTB9		ENST00000396477.4:c.204C>T	19.37:g.51983738C>T			Somatic	80	0	0		WXS	Illumina HiSeq	Phase_1	90	0.06	5	NM_001080405	0		0	C9JN24	Silent	SNP	ENST00000396477.4	37																																																																																						0.567	CEACAM18-001	PUTATIVE	not_organism_supported|basic|appris_candidate	protein_coding	protein_coding		OTTHUMT00000323114.2			
GCKR	2646	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	2	27730108	27730108	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr2:27730108G>A	ENST00000264717.2	+	13	1136	c.1073G>A	c.(1072-1074)cGa>cAa	p.R358Q	GCKR_ENST00000424318.2_Missense_Mutation_p.R168Q	NM_001486.3	NP_001477.2	Q14397	GCKR_HUMAN	glucokinase (hexokinase 4) regulator	358	SIS 2. {ECO:0000255|PROSITE- ProRule:PRU00797}.				carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|negative regulation of glucokinase activity (GO:0033132)|positive regulation of glucokinase activity (GO:0033133)|protein import into nucleus, translocation (GO:0000060)|regulation of glucose transport (GO:0010827)|response to fructose (GO:0009750)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|triglyceride homeostasis (GO:0070328)|urate metabolic process (GO:0046415)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	carbohydrate binding (GO:0030246)|enzyme inhibitor activity (GO:0004857)|fructose-6-phosphate binding (GO:0070095)			breast(2)|endometrium(4)|kidney(2)|large_intestine(4)|liver(2)|lung(13)|ovary(2)	29	Acute lymphoblastic leukemia(172;0.155)					CCAGATTTCCGAGATGTCCGT	0.488																																					p.R358Q													GCKR,rectum,carcinoma,0,1	GCKR	0	1	0			c.G1073A												242.0	252.0	249.0					2																	27730108		2203	4300	6503	SO:0001583	missense	2646	exon13			ATTTCCGAGATGT	Z48475	CCDS1757.1	2p23	2008-05-21	2004-05-20		ENSG00000084734	ENSG00000084734			4196	protein-coding gene	gene with protein product		600842	"""glucokinase (hexokinase 4) regulatory protein"""			9570959, 8662230	Standard	NM_001486		Approved		uc002rky.3	Q14397	OTTHUMG00000128426	ENST00000264717.2:c.1073G>A	2.37:g.27730108G>A	ENSP00000264717:p.Arg358Gln		Somatic	49	0	0		WXS	Illumina HiSeq	.	66	0.27	18	NM_001486	0		0	A1L4C2|B4DPQ2|Q53RY6|Q99522	Missense_Mutation	SNP	ENST00000264717.2	37	CCDS1757.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	7.018|7.018	0.558087|0.558087	0.13436|0.13436	.|.	.|.	ENSG00000084734|ENSG00000084734	ENST00000411584|ENST00000264717;ENST00000424318	.|D;D	.|0.83419	.|-1.72;-1.72	4.8|4.8	-4.02|-4.02	0.04034|0.04034	.|Sugar isomerase (SIS) (1);	.|1.347880	.|0.04756	.|N	.|0.425533	T|T	0.63593|0.63593	0.2524|0.2524	N|N	0.08118|0.08118	0|0	0.24037|0.24037	N|N	0.996097|0.996097	.|B;B;B	.|0.06786	.|0.001;0.001;0.001	.|B;B;B	.|0.08055	.|0.002;0.003;0.003	T|T	0.55373|0.55373	-0.8151|-0.8151	5|10	.|0.08179	.|T	.|0.78	3.6618|3.6618	10.9419|10.9419	0.47278|0.47278	0.6396:0.0:0.3604:0.0|0.6396:0.0:0.3604:0.0	.|.	.|168;356;358	.|F5H1P6;A8K731;Q14397	.|.;.;GCKR_HUMAN	K|Q	59|358;168	.|ENSP00000264717:R358Q;ENSP00000409109:R168Q	.|ENSP00000264717:R358Q	E|R	+|+	1|2	0|0	GCKR|GCKR	27583612|27583612	0.000000|0.000000	0.05858|0.05858	0.317000|0.317000	0.25265|0.25265	0.659000|0.659000	0.38960|0.38960	-1.682000|-1.682000	0.01935|0.01935	-0.701000|-0.701000	0.05063|0.05063	-0.137000|-0.137000	0.14449|0.14449	GAG|CGA			0.488	GCKR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000250214.1		NM_001486	
ZAK	51776	broad.mit.edu	37	2	174130916	174130916	+	Missense_Mutation	SNP	C	C	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr2:174130916C>T	ENST00000375213.3	+	20	1919	c.1841C>T	c.(1840-1842)gCt>gTt	p.A614V	MLK7-AS1_ENST00000422703.1_RNA|MLTK_ENST00000409176.2_Missense_Mutation_p.A614V|MLK7-AS1_ENST00000423106.2_RNA	NM_016653.2	NP_057737.2	Q9NYL2	MLTK_HUMAN		614					activation of JUN kinase activity (GO:0007257)|activation of MAPKK activity (GO:0000186)|cell cycle arrest (GO:0007050)|cell cycle checkpoint (GO:0000075)|cell death (GO:0008219)|cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|cytoskeleton organization (GO:0007010)|DNA damage checkpoint (GO:0000077)|intracellular signal transduction (GO:0035556)|positive regulation of apoptotic process (GO:0043065)|protein phosphorylation (GO:0006468)|response to radiation (GO:0009314)|response to stress (GO:0006950)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|MAP kinase kinase kinase activity (GO:0004709)|poly(A) RNA binding (GO:0044822)|protein serine/threonine kinase activity (GO:0004674)										TACGCTGCTGCTGTGAGACGG	0.498																																					p.A614V													.	ZAK	62		0			c.C1841T												59.0	57.0	57.0					2																	174130916		2011	4188	6199	SO:0001583	missense	0	exon20			CTGCTGCTGTGAG																												ENST00000375213.3:c.1841C>T	2.37:g.174130916C>T	ENSP00000364361:p.Ala614Val		Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	114	0.04	5	NM_016653	7	0.00	0	B3KPG2|Q53SX1|Q580W8|Q59GY5|Q86YW8|Q9HCC4|Q9HCC5|Q9HDD2|Q9NYE9	Missense_Mutation	SNP	ENST00000375213.3	37	CCDS42777.1	.	.	.	.	.	.	.	.	.	.	C	32	5.146025	0.94603	.	.	ENSG00000091436	ENST00000409176;ENST00000375213	D;D	0.81659	-1.52;-1.52	5.87	5.87	0.94306	.	0.000000	0.85682	D	0.000000	D	0.86472	0.5941	L	0.36672	1.1	0.80722	D	1	D	0.76494	0.999	D	0.80764	0.994	D	0.87015	0.2125	10	0.87932	D	0	.	20.2119	0.98289	0.0:1.0:0.0:0.0	.	614	Q9NYL2	MLTK_HUMAN	V	614	ENSP00000387259:A614V;ENSP00000364361:A614V	ENSP00000364361:A614V	A	+	2	0	AC013461.1	173839162	1.000000	0.71417	0.949000	0.38748	0.801000	0.45260	6.769000	0.74985	2.784000	0.95788	0.585000	0.79938	GCT			0.498	MLTK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000255401.1			
WNT6	7475	broad.mit.edu	37	2	219724790	219724792	+	In_Frame_Del	DEL	GCT	GCT	-			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	GCT	GCT					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr2:219724790_219724792delGCT	ENST00000233948.3	+	1	247_249	c.30_32delGCT	c.(28-33)gggctg>ggg	p.L17del	WNT6_ENST00000486233.1_3'UTR	NM_006522.3	NP_006513.1	Q9Y6F9	WNT6_HUMAN	wingless-type MMTV integration site family, member 6	17					axis specification (GO:0009798)|branching involved in ureteric bud morphogenesis (GO:0001658)|cell fate commitment (GO:0045165)|cellular response to retinoic acid (GO:0071300)|cornea development in camera-type eye (GO:0061303)|epithelial-mesenchymal cell signaling (GO:0060684)|nephron tubule formation (GO:0072079)|neuron differentiation (GO:0030182)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of gene expression (GO:0010628)|positive regulation of tooth mineralization (GO:0070172)|positive regulation of transcription, DNA-templated (GO:0045893)|Wnt signaling pathway (GO:0016055)	cell surface (GO:0009986)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)	p.L17delL(1)		large_intestine(1)|ovary(2)|skin(1)	4		Renal(207;0.0474)		Epithelial(149;4.53e-07)|all cancers(144;9.3e-05)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00942)		CCCGCCTCGGGCTGCTGCTGCTG	0.773																																					p.10_11del													.	WNT6	21		1	Deletion - In frame(1)	central_nervous_system(1)	c.30_32del									68,3608		1,66,1771						1.6	0.4			5	195,7107		11,173,3467	no	coding	WNT6	NM_006522.3		12,239,5238	A1A1,A1R,RR		2.6705,1.8498,2.3957				263,10715				SO:0001651	inframe_deletion	7475	exon1			CCTCGGGCTGCTG	AF079522	CCDS2425.1	2q35	2008-05-23			ENSG00000115596	ENSG00000115596		"""Wingless-type MMTV integration sites"""	12785	protein-coding gene	gene with protein product		604663				10343101, 11350055	Standard	NM_006522		Approved		uc002vjc.1	Q9Y6F9	OTTHUMG00000133082	ENST00000233948.3:c.30_32delGCT	2.37:g.219724799_219724801delGCT	ENSP00000233948:p.Leu17del		Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	11	0.36	4	NM_006522	4	0.00	0	Q9H1J6|Q9H238	In_Frame_Del	DEL	ENST00000233948.3	37	CCDS2425.1																																																																																					0.773	WNT6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000256727.2		NM_006522	
TPTEP1	387590	broad.mit.edu	37	22	17127506	17127507	+	lincRNA	INS	-	-	A	rs546582747|rs190702005	byFrequency	TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr22:17127506_17127507insA	ENST00000426585.1	+	0	442									transmembrane phosphatase with tensin homology pseudogene 1																		AGGGCCTAGAGAAAAAAAAAAT	0.421													|||unknown(NO_COVERAGE)	11	0.00219649	0.0023	0.0014	5008	,	,		23257	0.001		0.001	False		,,,				2504	0.0051				.													.	.			0			.																																											0	.			CCTAGAGAAAAAA			22q11.1	2013-10-15			ENSG00000100181	ENSG00000100181			43648	pseudogene	pseudogene						14659893	Standard	NR_001591		Approved	psiTPTE22	uc002zlr.3		OTTHUMG00000141300		22.37:g.17127516_17127516dupA			Somatic	4	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	.	0		0		RNA	INS	ENST00000426585.1	37																																																																																						0.421	TPTEP1-002	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000280575.1		NR_001591	
GGT3P	2679	broad.mit.edu	37	22	18775534	18775535	+	RNA	INS	-	-	T	rs200142078		TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	-	-					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr22:18775534_18775535insT	ENST00000412448.1	-	0	834							A6NGU5	GGT3_HUMAN	gamma-glutamyltransferase 3 pseudogene						glutathione biosynthetic process (GO:0006750)|glutathione metabolic process (GO:0006749)|leukotriene biosynthetic process (GO:0019370)	anchored component of external side of plasma membrane (GO:0031362)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	gamma-glutamyltransferase activity (GO:0003840)|glutathione hydrolase activity (GO:0036374)										gtttctttctcttttttttgag	0.52																																					.													.	.			0			.																																											0	.			CTTTCTCTTTTTT			22q11.21	2008-08-05	2008-03-10	2008-03-10	ENSG00000197421	ENSG00000197421		"""Gamma-glutamyltransferases"""	4252	pseudogene	pseudogene			"""gamma-glutamyltransferase 3"""	GGT3		8104871, 18357469	Standard	NR_003267		Approved		uc002zob.1	A6NGU5	OTTHUMG00000150161		22.37:g.18775542_18775542dupT			Somatic	40	0.075	3		WXS	Illumina HiSeq	Phase_I	39	0.00	0	.	0		0		RNA	INS	ENST00000412448.1	37																																																																																						0.520	GGT3P-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000341281.1		NR_003267	
TANGO2	128989	ucsc.edu;bcgsc.ca	37	22	20043537	20043537	+	Splice_Site	SNP	G	G	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr22:20043537G>T	ENST00000327374.4	+	6	629		c.e6+1		TANGO2_ENST00000398042.2_Intron|TANGO2_ENST00000401833.1_Splice_Site|TANGO2_ENST00000434570.2_Splice_Site|TANGO2_ENST00000456048.1_Splice_Site|TANGO2_ENST00000432883.1_Intron|TANGO2_ENST00000401886.1_Intron|TANGO2_ENST00000447208.2_Splice_Site|TANGO2_ENST00000420290.2_Splice_Site	NM_001283106.1|NM_001283116.1|NM_001283148.1|NM_001283154.1|NM_152906.4	NP_001270035.1|NP_001270045.1|NP_001270077.1|NP_001270083.1|NP_690870.3	Q6ICL3	TNG2_HUMAN	transport and golgi organization 2 homolog (Drosophila)																		TTGACGCCAGGTGAGCCTGCC	0.542																																					.													.	TANGO2	4		0			c.451+1G>T												122.0	105.0	111.0					22																	20043537		2203	4300	6503	SO:0001630	splice_region_variant	0	exon6			CGCCAGGTGAGCC		CCDS13772.1, CCDS63404.1, CCDS63405.1, CCDS63406.1, CCDS63407.1, CCDS74821.1, CCDS74822.1	22q11.21	2012-12-13	2012-12-13	2012-12-13	ENSG00000183597	ENSG00000183597			25439	protein-coding gene	gene with protein product			"""chromosome 22 open reading frame 25"""	C22orf25		12477932	Standard	XM_005261222		Approved	DKFZp761P1121	uc002zrc.1	Q6ICL3	OTTHUMG00000150510	ENST00000327374.4:c.451+1G>T	22.37:g.20043537G>T			Somatic	35	0	0		WXS	Illumina HiSeq		36	0.11	4	NM_152906	0		0	A8MUE9|B7WNV6|B7Z583|B7Z730|D3DX23|Q8IW05|Q8NAL0|Q8TCS0|Q96M16	Splice_Site	SNP	ENST00000327374.4	37	CCDS13772.1	.	.	.	.	.	.	.	.	.	.	G	10.94	1.493863	0.26774	.	.	ENSG00000183597	ENST00000447208;ENST00000450664;ENST00000327374;ENST00000401833;ENST00000434168;ENST00000434570;ENST00000420290;ENST00000456048	.	.	.	4.52	4.52	0.55395	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	12.9432	0.58357	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	C22orf25	18423537	1.000000	0.71417	1.000000	0.80357	0.129000	0.20672	7.458000	0.80787	2.499000	0.84300	0.563000	0.77884	.			0.542	TANGO2-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000318689.2		NM_152906	Intron
RAD54L2	23132	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	3	51694124	51694124	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr3:51694124G>A	ENST00000409535.2	+	21	3524	c.3399G>A	c.(3397-3399)atG>atA	p.M1133I	RAD54L2_ENST00000296477.3_Missense_Mutation_p.M827I	NM_015106.2	NP_055921.2	Q9Y4B4	ARIP4_HUMAN	RAD54-like 2 (S. cerevisiae)	1133						nucleus (GO:0005634)	ATP binding (GO:0005524)|DNA binding (GO:0003677)|helicase activity (GO:0004386)|transcription cofactor activity (GO:0003712)			NS(2)|breast(1)|cervix(2)|endometrium(4)|large_intestine(5)|liver(2)|lung(9)|ovary(4)|skin(2)	31				BRCA - Breast invasive adenocarcinoma(193;0.000102)|Kidney(197;0.000758)|KIRC - Kidney renal clear cell carcinoma(197;0.000896)		ATGGTCGGATGGCTGCCTCAG	0.418																																					p.M1133I													.	.			0			c.G3399A												110.0	86.0	94.0					3																	51694124		2203	4300	6503	SO:0001583	missense	23132	exon21			TCGGATGGCTGCC	AB018352	CCDS33765.2	3p21.2	2006-01-17			ENSG00000164080	ENSG00000164080			29123	protein-coding gene	gene with protein product						9872452	Standard	NM_015106		Approved	KIAA0809, SRISNF2L	uc011bdt.2	Q9Y4B4	OTTHUMG00000152936	ENST00000409535.2:c.3399G>A	3.37:g.51694124G>A	ENSP00000386520:p.Met1133Ile		Somatic	108	0	0		WXS	Illumina HiSeq	.	156	0.23	36	NM_015106	17	0.47	8	Q8TB57|Q9BV54	Missense_Mutation	SNP	ENST00000409535.2	37	CCDS33765.2	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	13.67|13.67	2.307296|2.307296	0.40795|0.40795	.|.	.|.	ENSG00000164080|ENSG00000164080	ENST00000432863|ENST00000409535;ENST00000296477	.|D;D	.|0.92965	.|-3.04;-3.14	6.17|6.17	-2.4|-2.4	0.06583|0.06583	.|.	.|0.402448	.|0.31461	.|N	.|0.007619	T|T	0.76097|0.76097	0.3940|0.3940	N|N	0.08118|0.08118	0|0	0.26852|0.26852	N|N	0.968133|0.968133	.|B;B	.|0.09022	.|0.002;0.002	.|B;B	.|0.08055	.|0.003;0.003	T|T	0.63795|0.63795	-0.6556|-0.6556	5|10	.|0.36615	.|T	.|0.2	-0.0449|-0.0449	2.4994|2.4994	0.04630|0.04630	0.4594:0.1196:0.3004:0.1206|0.4594:0.1196:0.3004:0.1206	.|.	.|1133;722	.|Q9Y4B4;B3KV54	.|ARIP4_HUMAN;.	S|I	962|1133;827	.|ENSP00000386520:M1133I;ENSP00000296477:M827I	.|ENSP00000296477:M827I	G|M	+|+	1|3	0|0	RAD54L2|RAD54L2	51669164|51669164	0.992000|0.992000	0.36948|0.36948	0.981000|0.981000	0.43875|0.43875	0.975000|0.975000	0.68041|0.68041	0.220000|0.220000	0.17660|0.17660	-0.303000|-0.303000	0.08856|0.08856	-0.150000|-0.150000	0.13652|0.13652	GGC|ATG			0.418	RAD54L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000328700.2		NM_015106	
IL12A-AS1	101928376	broad.mit.edu	37	3	159818946	159818946	+	RNA	SNP	A	A	G			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr3:159818946A>G	ENST00000497452.1	-	0	517									IL12A antisense RNA 1																		AGGCAGAAAAAGACCTCCAGT	0.493																																					.													.	.			0			.																																											0	.			AGAAAAAGACCTC	AK097161		3q25.33	2013-09-02			ENSG00000244040	ENSG00000244040		"""Long non-coding RNAs"""	49094	non-coding RNA	RNA, long non-coding							Standard	NR_108088		Approved				OTTHUMG00000158951		3.37:g.159818946A>G			Somatic	101	0	0		WXS	Illumina HiSeq	Phase_I	125	0.03	4	.	10	0.00	0		RNA	SNP	ENST00000497452.1	37																																																																																						0.493	IL12A-AS1-001	KNOWN	basic	antisense	antisense		OTTHUMT00000352647.1			
IL12A-AS1	101928376	broad.mit.edu	37	3	159820488	159820488	+	RNA	SNP	C	C	T	rs6778335	byFrequency	TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr3:159820488C>T	ENST00000497452.1	-	0	517									IL12A antisense RNA 1																		TTCCTTCCCCCGTCATGGAAA	0.443													C|||	473	0.0944489	0.1074	0.0375	5008	,	,		19046	0.1002		0.0318	False		,,,				2504	0.1759				.													.	.			0			.																																											0	.			TTCCCCCGTCATG	AK097161		3q25.33	2013-09-02			ENSG00000244040	ENSG00000244040		"""Long non-coding RNAs"""	49094	non-coding RNA	RNA, long non-coding							Standard	NR_108088		Approved				OTTHUMG00000158951		3.37:g.159820488C>T			Somatic	72	0	0		WXS	Illumina HiSeq	Phase_I	77	0.05	4	.	21	0.00	0		RNA	SNP	ENST00000497452.1	37																																																																																						0.443	IL12A-AS1-001	KNOWN	basic	antisense	antisense		OTTHUMT00000352647.1			
OTUD4	54726	hgsc.bcm.edu	37	4	146059041	146059041	+	Silent	SNP	A	A	G			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr4:146059041A>G	ENST00000447906.2	-	21	3073	c.2886T>C	c.(2884-2886)caT>caC	p.H962H	OTUD4_ENST00000455611.2_Intron|OTUD4_ENST00000454497.2_Silent_p.H897H			Q01804	OTUD4_HUMAN	OTU deubiquitinase 4	962					protein K48-linked deubiquitination (GO:0071108)		poly(A) RNA binding (GO:0044822)|ubiquitin-specific protease activity (GO:0004843)			breast(1)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(9)|lung(10)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	33	all_hematologic(180;0.151)					GAGTGGGAGGATGAGCCTTTC	0.478																																					p.H897H													OTUD4,bladder,carcinoma,0,2	OTUD4	0	2	0			c.T2691C												118.0	118.0	118.0					4																	146059041		2203	4300	6503	SO:0001819	synonymous_variant	54726	exon21			GGGAGGATGAGCC		CCDS3764.1, CCDS47139.1	4q31.21	2014-02-24	2014-02-24		ENSG00000164164	ENSG00000164164		"""OTU domain containing"""	24949	protein-coding gene	gene with protein product		611744	"""OTU domain containing 4"""			1475186, 12727813, 19996094	Standard	NM_001102653		Approved	HSHIN1, KIAA1046, DUBA6	uc003ika.4	Q01804	OTTHUMG00000161480	ENST00000447906.2:c.2886T>C	4.37:g.146059041A>G			Somatic	80	0.0125	1		WXS	Illumina HiSeq	.	77	0.05	4	NM_001102653	32	0.00	0	B4DYS4|Q147U2|Q1ZYK1|Q6PG39|Q96MQ5|Q9NT94|Q9UPV6	Silent	SNP	ENST00000447906.2	37																																																																																						0.478	OTUD4-004	KNOWN	basic|appris_principal	protein_coding	protein_coding		OTTHUMT00000365117.2		NM_017493	
FLT4	2324	broad.mit.edu;ucsc.edu	37	5	180052904	180052904	+	Silent	SNP	G	G	T			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr5:180052904G>T	ENST00000261937.6	-	10	1464	c.1386C>A	c.(1384-1386)ccC>ccA	p.P462P	FLT4_ENST00000424276.2_5'UTR|FLT4_ENST00000502649.1_Silent_p.P462P|FLT4_ENST00000393347.3_Silent_p.P462P	NM_182925.4	NP_891555.2	P35916	VGFR3_HUMAN	fms-related tyrosine kinase 4	462	Ig-like C2-type 5.				blood vessel morphogenesis (GO:0048514)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|lymph vessel development (GO:0001945)|lymphangiogenesis (GO:0001946)|negative regulation of apoptotic process (GO:0043066)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of cell proliferation (GO:0008284)|positive regulation of endothelial cell migration (GO:0010595)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of JNK cascade (GO:0046330)|positive regulation of MAPK cascade (GO:0043410)|positive regulation of protein kinase C signaling (GO:0090037)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation vascular endothelial growth factor production (GO:0010575)|protein autophosphorylation (GO:0046777)|regulation of blood vessel remodeling (GO:0060312)|sprouting angiogenesis (GO:0002040)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)|vascular endothelial growth factor receptor signaling pathway (GO:0048010)|vascular endothelial growth factor signaling pathway (GO:0038084)|vasculature development (GO:0001944)	cytoplasm (GO:0005737)|extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|growth factor binding (GO:0019838)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase activity (GO:0004714)|vascular endothelial growth factor-activated receptor activity (GO:0005021)			NS(1)|breast(3)|central_nervous_system(2)|endometrium(1)|kidney(6)|large_intestine(5)|liver(2)|lung(37)|ovary(6)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	71	all_cancers(89;2.21e-05)|all_epithelial(37;5.29e-06)|Renal(175;0.000159)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.114)	all_cancers(40;0.00245)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)|all_hematologic(541;0.163)|Ovarian(839;0.238)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)	all cancers(165;0.134)	Axitinib(DB06626)|Pazopanib(DB06589)|Regorafenib(DB08896)|Sorafenib(DB00398)|Sunitinib(DB01268)	AGGGTGTCCAGGGCCGCCAGT	0.662																																					p.P462P	Colon(97;1075 1466 27033 27547 35871)												.	FLT4	356		0			c.C1386A												38.0	44.0	42.0					5																	180052904		2200	4296	6496	SO:0001819	synonymous_variant	2324	exon10			TGTCCAGGGCCGC	X68203	CCDS4457.1, CCDS43412.1	5q34-q35	2013-01-29			ENSG00000037280	ENSG00000037280	2.7.10.1	"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	3767	protein-coding gene	gene with protein product		136352				1319394	Standard	NM_002020		Approved	VEGFR3, PCL	uc003mlz.4	P35916	OTTHUMG00000130931	ENST00000261937.6:c.1386C>A	5.37:g.180052904G>T			Somatic	55	0	0		WXS	Illumina HiSeq	Phase_I	44	0.09	4	NM_182925	2	0.00	0	A8K6L4|B5A926|Q16067|Q86W07|Q86W08	Silent	SNP	ENST00000261937.6	37	CCDS4457.1																																																																																					0.662	FLT4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000253527.4			
MUC21	394263	hgsc.bcm.edu	37	6	30955043	30955043	+	Missense_Mutation	SNP	G	G	A	rs9262385	byFrequency	TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr6:30955043G>A	ENST00000376296.3	+	2	1332	c.1091G>A	c.(1090-1092)gGg>gAg	p.G364E	MUC21_ENST00000486149.2_5'UTR	NM_001010909.2	NP_001010909.2	Q5SSG8	MUC21_HUMAN	mucin 21, cell surface associated	364	28 X 15 AA approximate tandem repeats.|Ser-rich.			G -> E (in Ref. 3; AAQ88781 and 4; CAQ08321). {ECO:0000305}.	cellular protein metabolic process (GO:0044267)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-substrate adhesion (GO:0010812)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(4)|breast(1)|central_nervous_system(2)|endometrium(1)|kidney(1)|large_intestine(7)|lung(11)|ovary(3)|prostate(4)|skin(4)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						ACCAACTCTGGGTCCAGCACG	0.632													a|||	106	0.0211661	0.0197	0.0576	5008	,	,		18768	0.0079		0.0179	False		,,,				2504	0.0143				p.G364E													MUC21,NS,neuroblastoma,0,1	MUC21	0	1	0			c.G1091A							A	GLU/GLY	25,4361		2,21,2170	143.0	141.0	141.0		1091	-6.6	0.0	6	dbSNP_118	141	46,8528		4,38,4245	no	missense	MUC21	NM_001010909.2	98	6,59,6415	AA,AG,GG		0.5365,0.57,0.5478	benign	364/567	30955043	71,12889	2193	4287	6480	SO:0001583	missense	394263	exon2			ACTCTGGGTCCAG	AK056612	CCDS34388.1	6p21.33	2008-05-14	2008-05-14	2008-05-14	ENSG00000204544	ENSG00000204544		"""Mucins"""	21661	protein-coding gene	gene with protein product	"""epiglycanin"""		"""chromosome 6 open reading frame 205"""	C6orf205		17977904	Standard	NM_001010909		Approved	bCX31G15.2	uc003nsh.2	Q5SSG8	OTTHUMG00000031216	ENST00000376296.3:c.1091G>A	6.37:g.30955043G>A	ENSP00000365473:p.Gly364Glu		Somatic	20	0.1	2		WXS	Illumina HiSeq	.	22	0.09	2	NM_001010909	0		0	B0UZT7|B4DQ55|C9JMK2|D9N007|Q0VGF1|Q3B7T2|Q5SS94|Q6UXC5	Missense_Mutation	SNP	ENST00000376296.3	37	CCDS34388.1	.	.	.	.	.	.	.	.	.	.	a	0.072	-1.201075	0.01581	0.0057	0.005365	ENSG00000204544	ENST00000450707;ENST00000376296	T	0.02323	4.34	4.44	-6.61	0.01818	.	.	.	.	.	T	0.00300	0.0009	N	0.08118	0	0.09310	N	1	B	0.12013	0.005	B	0.11329	0.006	T	0.46830	-0.9163	9	0.02654	T	1	0.4928	3.9243	0.09257	0.1415:0.3445:0.3555:0.1585	rs9262385	364	Q5SSG8	MUC21_HUMAN	E	214;364	ENSP00000365473:G364E	ENSP00000365473:G364E	G	+	2	0	MUC21	31063022	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-1.474000	0.02337	-1.580000	0.01644	-2.305000	0.00258	GGG	0.008		0.632	MUC21-001	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000128579.3		NM_001010909	
PKHD1	5314	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	6	51612794	51612794	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr6:51612794G>A	ENST00000371117.3	-	58	9895	c.9620C>T	c.(9619-9621)gCc>gTc	p.A3207V	PKHD1_ENST00000340994.4_Missense_Mutation_p.A3207V	NM_138694.3	NP_619639.3	P08F94	PKHD1_HUMAN	polycystic kidney and hepatic disease 1 (autosomal recessive)	3207			A -> T (in ARPKD). {ECO:0000269|PubMed:19914852}.		cellular calcium ion homeostasis (GO:0006874)|cilium assembly (GO:0042384)|homeostatic process (GO:0042592)|kidney development (GO:0001822)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cellular component movement (GO:0051271)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of protein kinase B signaling (GO:0051898)|positive regulation of cell proliferation (GO:0008284)|regulation of centrosome duplication (GO:0010824)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of TOR signaling (GO:0032006)|single organismal cell-cell adhesion (GO:0016337)	anchored component of external side of plasma membrane (GO:0031362)|apical plasma membrane (GO:0016324)|centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|mitotic spindle (GO:0072686)|perinuclear region of cytoplasm (GO:0048471)|primary cilium (GO:0072372)	receptor activity (GO:0004872)			NS(1)|autonomic_ganglia(1)|breast(8)|central_nervous_system(5)|cervix(1)|endometrium(16)|haematopoietic_and_lymphoid_tissue(4)|kidney(11)|large_intestine(59)|lung(139)|ovary(16)|prostate(8)|skin(20)|soft_tissue(1)|stomach(2)|upper_aerodigestive_tract(7)|urinary_tract(5)	304	Lung NSC(77;0.0605)					AGAGCTGGTGGCCACAATGAC	0.443																																					p.A3207V													.	.			0			c.C9620T												112.0	115.0	114.0					6																	51612794		2203	4300	6503	SO:0001583	missense	5314	exon58			CTGGTGGCCACAA	AF480064	CCDS4935.1, CCDS4936.1	6p21.2-p12	2012-11-26	2003-04-16		ENSG00000170927	ENSG00000170927			9016	protein-coding gene	gene with protein product	"""tigmin"", ""polyductin"", ""fibrocystin"""	606702	"""TIG multiple domains 1"""	TIGM1		9503014	Standard	NM_138694		Approved	ARPKD, FCYT	uc003pah.1	P08F94	OTTHUMG00000014841	ENST00000371117.3:c.9620C>T	6.37:g.51612794G>A	ENSP00000360158:p.Ala3207Val		Somatic	110	0	0		WXS	Illumina HiSeq	.	180	0.29	52	NM_170724	0		0	Q5VUA2|Q5VUA3|Q5VWV1|Q86Z26|Q8TCZ9	Missense_Mutation	SNP	ENST00000371117.3	37	CCDS4935.1	.	.	.	.	.	.	.	.	.	.	G	24.8	4.569101	0.86439	.	.	ENSG00000170927	ENST00000371117;ENST00000340994;ENST00000393616	D;D	0.88201	-2.15;-2.35	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	D	0.93592	0.7954	M	0.72118	2.19	0.42572	D	0.993183	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.83275	0.994;0.996;0.996	D	0.93538	0.6875	10	0.66056	D	0.02	.	18.9315	0.92568	0.0:0.0:1.0:0.0	.	3207;3207;3207	A8MVM9;P08F94-2;P08F94	.;.;PKHD1_HUMAN	V	3207	ENSP00000360158:A3207V;ENSP00000341097:A3207V	ENSP00000341097:A3207V	A	-	2	0	PKHD1	51720753	1.000000	0.71417	1.000000	0.80357	0.913000	0.54294	3.709000	0.54853	2.716000	0.92895	0.655000	0.94253	GCC			0.443	PKHD1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding		OTTHUMT00000040893.1		NM_138694	
ARMC2	84071	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	6	109274550	109274550	+	Silent	SNP	G	G	A	rs552011948		TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr6:109274550G>A	ENST00000392644.4	+	13	2079	c.1911G>A	c.(1909-1911)acG>acA	p.T637T	ARMC2_ENST00000368972.3_Silent_p.T472T	NM_032131.4	NP_115507.4	Q8NEN0	ARMC2_HUMAN	armadillo repeat containing 2	637										endometrium(3)|large_intestine(8)|lung(10)|ovary(1)|prostate(1)|skin(1)	24		all_cancers(87;1.14e-07)|Acute lymphoblastic leukemia(125;2.3e-10)|all_hematologic(75;3.3e-08)|all_epithelial(87;0.000111)|Colorectal(196;0.03)|all_lung(197;0.11)		Epithelial(106;0.000197)|BRCA - Breast invasive adenocarcinoma(108;0.000236)|all cancers(137;0.000279)|OV - Ovarian serous cystadenocarcinoma(136;0.00434)		TCCTGACCACGCTGGGTGAGA	0.602													G|||	1	0.000199681	0.0008	0.0	5008	,	,		14981	0.0		0.0	False		,,,				2504	0.0				p.T637T													.	.			0			c.G1911A												14.0	16.0	16.0					6																	109274550		2194	4292	6486	SO:0001819	synonymous_variant	84071	exon13			GACCACGCTGGGT	BC030603	CCDS5069.2, CCDS69168.1	6q21	2013-02-14			ENSG00000118690	ENSG00000118690		"""Armadillo repeat containing"""	23045	protein-coding gene	gene with protein product							Standard	XM_005267154		Approved	DKFZp434P0714, bA787I22.1	uc003pss.4	Q8NEN0	OTTHUMG00000015335	ENST00000392644.4:c.1911G>A	6.37:g.109274550G>A			Somatic	11	0	0		WXS	Illumina HiSeq	.	17	0.41	7	NM_032131	2	0.00	0	A8K8Y4|B4DGF5|G5E993|Q5VVY8|Q9H0K9	Silent	SNP	ENST00000392644.4	37	CCDS5069.2																																																																																					0.602	ARMC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000041732.2		NM_032131	
INHBA-AS1	285954	broad.mit.edu	37	7	41797976	41797976	+	RNA	DEL	T	T	-	rs571717276		TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	T	T					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr7:41797976delT	ENST00000415848.2	+	0	358					NR_027118.1				INHBA antisense RNA 1																		taaacactgattttttttttc	0.378																																					.													.	.			0			.																																											0	.			CACTGATTTTTTT			7p14.1	2012-10-12	2012-08-15		ENSG00000224116	ENSG00000224116		"""Long non-coding RNAs"""	40303	non-coding RNA	RNA, long non-coding			"""INHBA antisense RNA 1 (non-protein coding)"""				Standard	NR_027118		Approved		uc003tht.4		OTTHUMG00000155114		7.37:g.41797976delT			Somatic	8	0	0		WXS	Illumina HiSeq	Phase_I	6	0.33	2	.	0		0		RNA	DEL	ENST00000415848.2	37																																																																																						0.378	INHBA-AS1-001	KNOWN	basic	antisense	antisense		OTTHUMT00000338451.2		NR_027118	
MTERF1	7978	broad.mit.edu	37	7	91503609	91503609	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr7:91503609A>G	ENST00000351870.3	-	3	592	c.499T>C	c.(499-501)Ttt>Ctt	p.F167L	MTERF_ENST00000481516.1_5'Flank|MTERF_ENST00000419292.1_Missense_Mutation_p.F147L|MTERF_ENST00000406735.2_Missense_Mutation_p.F147L	NM_006980.3	NP_008911.1	Q99551	MTEF1_HUMAN		167					DNA geometric change (GO:0032392)|DNA-templated transcription, termination (GO:0006353)|gene expression (GO:0010467)|regulation of transcription, DNA-templated (GO:0006355)|termination of mitochondrial transcription (GO:0006393)|transcription from mitochondrial promoter (GO:0006390)	mitochondrial matrix (GO:0005759)|mitochondrial nucleoid (GO:0042645)|mitochondrion (GO:0005739)	double-stranded DNA binding (GO:0003690)|poly(A) RNA binding (GO:0044822)			breast(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(4)|liver(1)|lung(2)|skin(1)	14	all_cancers(62;2.28e-09)|all_epithelial(64;1.07e-07)|Breast(17;0.00371)|all_hematologic(106;0.091)|all_lung(186;0.178)|Lung NSC(181;0.235)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.0993)|Kidney(17;0.118)|Epithelial(20;0.136)|LUSC - Lung squamous cell carcinoma(200;0.176)			GACCGAAAAAAGGATTCAGGA	0.388																																					p.F167L													.	MTERF	32		0			c.T499C												84.0	86.0	85.0					7																	91503609		2203	4300	6503	SO:0001583	missense	7978	exon3			GAAAAAAGGATTC																												ENST00000351870.3:c.499T>C	7.37:g.91503609A>G	ENSP00000248643:p.Phe167Leu		Somatic	76	0	0		WXS	Illumina HiSeq	Phase_I	106	0.04	4	NM_006980	39	0.00	0	A4D1E3|Q32NF8|Q53H51|Q9BVR7	Missense_Mutation	SNP	ENST00000351870.3	37	CCDS5621.1	.	.	.	.	.	.	.	.	.	.	A	27.2	4.809066	0.90707	.	.	ENSG00000127989	ENST00000419292;ENST00000351870;ENST00000406735	T;T;T	0.05786	3.39;3.39;3.39	4.62	4.62	0.57501	.	0.000000	0.85682	D	0.000000	T	0.18964	0.0455	M	0.70275	2.135	0.53688	D	0.999972	D	0.89917	1.0	D	0.87578	0.998	T	0.13953	-1.0490	10	0.06365	T	0.9	-14.5204	13.692	0.62550	1.0:0.0:0.0:0.0	.	167	Q99551	MTERF_HUMAN	L	147;167;147	ENSP00000414116:F147L;ENSP00000248643:F167L;ENSP00000384986:F147L	ENSP00000248643:F167L	F	-	1	0	MTERF	91341545	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.969000	0.87988	2.025000	0.59659	0.482000	0.46254	TTT			0.388	MTERF-003	KNOWN	basic|CCDS	protein_coding	protein_coding		OTTHUMT00000342896.1			
GIGYF1	64599	ucsc.edu	37	7	100282144	100282144	+	Missense_Mutation	SNP	G	G	A			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr7:100282144G>A	ENST00000275732.5	-	13	2767	c.1558C>T	c.(1558-1560)Ccg>Tcg	p.P520S	GIGYF1_ENST00000471340.2_5'Flank	NM_022574.4	NP_072096.2	O75420	PERQ1_HUMAN	GRB10 interacting GYF protein 1	520	GYF. {ECO:0000255|PROSITE- ProRule:PRU00101}.				insulin-like growth factor receptor signaling pathway (GO:0048009)					central_nervous_system(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(6)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	23	Lung NSC(181;0.035)|all_lung(186;0.0509)|Esophageal squamous(72;0.0817)					TCGCCCAGCGGCTGGAAGCCC	0.652																																					p.P520S													.	GIGYF1	113		0			c.C1558T												52.0	60.0	57.0					7																	100282144		2203	4300	6503	SO:0001583	missense	64599	exon13			CCAGCGGCTGGAA	AF053356	CCDS34708.1	7q22	2008-02-11	2008-02-11	2008-02-11	ENSG00000146830	ENSG00000146830			9126	protein-coding gene	gene with protein product	"""GYF domain containing 1"""	612064	"""PERQ amino acid rich, with GYF domain 1"""	PERQ1		9799793, 12771153	Standard	NM_022574		Approved	GYF1	uc003uwg.1	O75420	OTTHUMG00000157036	ENST00000275732.5:c.1558C>T	7.37:g.100282144G>A	ENSP00000275732:p.Pro520Ser		Somatic	35	0	0		WXS	Illumina HiSeq		42	0.10	4	NM_022574	172	0.00	0	Q6Y7W7|Q8WZ38	Missense_Mutation	SNP	ENST00000275732.5	37	CCDS34708.1	.	.	.	.	.	.	.	.	.	.	.	17.63	3.437184	0.62955	.	.	ENSG00000146830	ENST00000539430;ENST00000275732	D	0.85411	-1.98	4.9	4.9	0.64082	GYF (4);	0.000000	0.85682	D	0.000000	D	0.90164	0.6926	M	0.64567	1.98	0.80722	D	1	P	0.38048	0.616	P	0.56788	0.806	D	0.88661	0.3189	10	0.38643	T	0.18	-10.4821	15.6139	0.76750	0.0:0.0:1.0:0.0	.	520	O75420	PERQ1_HUMAN	S	239;520	ENSP00000275732:P520S	ENSP00000275732:P520S	P	-	1	0	GIGYF1	100120080	1.000000	0.71417	0.995000	0.50966	0.008000	0.06430	9.657000	0.98554	2.558000	0.86282	0.491000	0.48974	CCG			0.652	GIGYF1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000347205.2		NM_022574	
ZNF398	57541	hgsc.bcm.edu;broad.mit.edu;ucsc.edu;bcgsc.ca	37	7	148863275	148863275	+	Missense_Mutation	SNP	C	C	G			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr7:148863275C>G	ENST00000475153.1	+	3	713	c.446C>G	c.(445-447)tCc>tGc	p.S149C	ZNF398_ENST00000485111.1_3'UTR|ZNF398_ENST00000335901.4_5'UTR|ZNF398_ENST00000483892.1_5'UTR|ZNF398_ENST00000540950.1_Missense_Mutation_p.S154C|ZNF398_ENST00000491174.1_5'UTR|ZNF398_ENST00000420008.2_5'UTR|ZNF398_ENST00000426851.2_5'UTR			Q8TD17	ZN398_HUMAN	zinc finger protein 398	149	KRAB. {ECO:0000255|PROSITE- ProRule:PRU00119}.				positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)			NS(1)|breast(3)|central_nervous_system(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(14)|ovary(1)	25	Melanoma(164;0.15)		OV - Ovarian serous cystadenocarcinoma(82;0.00143)			GATGATGTCTCCATCTACTTT	0.378																																					p.S149C													.	.			0			c.C446G												109.0	108.0	108.0					7																	148863275		2203	4300	6503	SO:0001583	missense	57541	exon3			ATGTCTCCATCTA	AB037760	CCDS5894.1, CCDS47739.1	7q35	2013-01-08			ENSG00000197024	ENSG00000197024		"""Zinc fingers, C2H2-type"", ""-"""	18373	protein-coding gene	gene with protein product						11779858	Standard	NM_170686		Approved	ZER6, KIAA1339, P51, P71	uc003wfl.3	Q8TD17	OTTHUMG00000158970	ENST00000475153.1:c.446C>G	7.37:g.148863275C>G	ENSP00000420418:p.Ser149Cys		Somatic	123	0	0		WXS	Illumina HiSeq	.	144	0.28	41	NM_170686	106	0.25	26	A8K384|B4E377|Q8TD18|Q9P2K7|Q9UDV8	Missense_Mutation	SNP	ENST00000475153.1	37	CCDS5894.1	.	.	.	.	.	.	.	.	.	.	C	18.68	3.676510	0.67928	.	.	ENSG00000197024	ENST00000475153;ENST00000540950	T;T	0.01838	4.61;4.61	4.91	4.91	0.64330	Krueppel-associated box (4);	0.000000	0.42682	D	0.000675	T	0.06645	0.0170	L	0.36672	1.1	0.80722	D	1	D;D	0.89917	0.999;1.0	D;D	0.85130	0.997;0.983	T	0.19192	-1.0313	10	0.87932	D	0	-21.8821	9.2569	0.37588	0.0:0.9014:0.0:0.0986	.	154;149	B4DXA9;Q8TD17	.;ZN398_HUMAN	C	149;154	ENSP00000420418:S149C;ENSP00000439340:S154C	ENSP00000420418:S149C	S	+	2	0	ZNF398	148494208	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.097000	0.50251	2.268000	0.75426	0.467000	0.42956	TCC			0.378	ZNF398-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000352722.2			
ST18	9705	broad.mit.edu	37	8	53062411	53062411	+	Missense_Mutation	SNP	A	A	G			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr8:53062411A>G	ENST00000276480.7	-	16	2616	c.1933T>C	c.(1933-1935)Ttc>Ctc	p.F645L	RP11-26M5.3_ENST00000520496.1_RNA	NM_014682.2	NP_055497.1	O60284	ST18_HUMAN	suppression of tumorigenicity 18, zinc finger	645					transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|zinc ion binding (GO:0008270)			NS(1)|breast(2)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(14)|lung(38)|ovary(4)|prostate(2)|skin(11)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	85		Lung NSC(129;0.131)|all_epithelial(80;0.217)|all_lung(136;0.229)				CTTGTTTTGAATGGGGAAGAG	0.448																																					p.F645L													.	ST18	212		0			c.T1933C												167.0	154.0	158.0					8																	53062411		2203	4300	6503	SO:0001583	missense	9705	exon16			TTTTGAATGGGGA	AB011107	CCDS6149.1	8q11.23	2014-03-24	2014-03-24	2002-12-13	ENSG00000147488	ENSG00000147488		"""Zinc fingers, C2HC-type containing"""	18695	protein-coding gene	gene with protein product	"""neural zinc finger transcription factor 3"""		"""zinc finger protein 387"", ""suppression of tumorigenicity 18 (breast carcinoma) (zinc finger protein)"""	ZNF387		15489893	Standard	NM_014682		Approved	KIAA0535, ZC2HC10, NZF3	uc003xra.2	O60284	OTTHUMG00000164233	ENST00000276480.7:c.1933T>C	8.37:g.53062411A>G	ENSP00000276480:p.Phe645Leu		Somatic	73	0	0		WXS	Illumina HiSeq	Phase_I	140	0.02	3	NM_014682	0		0	Q17RY1	Missense_Mutation	SNP	ENST00000276480.7	37	CCDS6149.1	.	.	.	.	.	.	.	.	.	.	A	11.54	1.669467	0.29693	.	.	ENSG00000147488	ENST00000276480	T	0.43294	0.95	5.53	5.53	0.82687	Myelin transcription factor 1 (1);	0.100028	0.64402	D	0.000001	T	0.32436	0.0829	L	0.35288	1.05	0.45883	D	0.998735	B	0.12013	0.005	B	0.18871	0.023	T	0.12630	-1.0540	10	0.10902	T	0.67	-13.5352	15.6592	0.77169	1.0:0.0:0.0:0.0	.	645	O60284	ST18_HUMAN	L	645	ENSP00000276480:F645L	ENSP00000276480:F645L	F	-	1	0	ST18	53224964	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.754000	0.55189	2.110000	0.64415	0.377000	0.23210	TTC			0.448	ST18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding		OTTHUMT00000377867.1			
PTENP1	11191	broad.mit.edu;bcgsc.ca	37	9	33675590	33675590	+	RNA	SNP	G	G	C			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr9:33675590G>C	ENST00000532280.1	-	0	1907					NR_023917.1				phosphatase and tensin homolog pseudogene 1 (functional)																		GGATTTGACGGCTCCTCTACT	0.383																																					.													.	.			0			.																																											0	.			TTGACGGCTCCTC	AF023139, BC038293, BY797336		9p13.3	2014-09-11	2014-01-16		ENSG00000237984	ENSG00000237984		"""-"""	9589	pseudogene	pseudogene		613531	"""phosphatase and tensin homolog pseudogene 1"""			9393738, 9620558	Standard	NR_023917		Approved	PTEN2, psiPTEN, PTH2, PTEN-rs, PTENpg1	uc003zth.4		OTTHUMG00000000410		9.37:g.33675590G>C			Somatic	233	0	0		WXS	Illumina HiSeq	Phase_I	247	0.03	8	.	52	0.00	0		RNA	SNP	ENST00000532280.1	37																																																																																						0.383	PTENP1-002	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000395145.1		NR_023917	
FAM205B	389715	broad.mit.edu	37	9	34832997	34832997	+	RNA	SNP	C	C	T	rs200474633		TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	C	C					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr9:34832997C>T	ENST00000455647.2	-	0	3396							Q63HN1	F205B_HUMAN	family with sequence similarity 205, member B																		ATGAAAGCTACGGCTCCATCG	0.587																																					.													.	FAM205B	10		0			.																																											0	.			AAGCTACGGCTCC			9p13.3	2013-05-22	2011-08-15	2011-08-15	ENSG00000257198	ENSG00000257198			24504	other	unknown			"""chromosome 9 open reading frame 144"""	C9orf144			Standard	NR_024481		Approved	DKFZp434J193, C9orf144A	uc003zvp.4	Q63HN1	OTTHUMG00000019839		9.37:g.34832997C>T			Somatic	57	0.0175438596	1		WXS	Illumina HiSeq	Phase_I	51	0.10	5	.	0		0	Q6ZRJ7	RNA	SNP	ENST00000455647.2	37																																																																																						0.587	FAM205B-001	KNOWN	basic	processed_transcript	pseudogene		OTTHUMT00000052246.5		NR_024481	
PGM5P2	595135	broad.mit.edu	37	9	69082095	69082095	+	lincRNA	DEL	A	A	-	rs373416560		TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	A	A					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chr9:69082095delA	ENST00000412376.1	-	0	4066				PGM5P2_ENST00000591037.1_RNA																							TTGAAATATCAATTTTATTTT	0.299																																					.													.	.			0			.																																											0	.			AATATCAATTTTA																													9.37:g.69082095delA			Somatic	36	0.0833333333	3		WXS	Illumina HiSeq	Phase_I	25	0.24	6	.	0		0		RNA	DEL	ENST00000412376.1	37																																																																																						0.299	RP11-87H9.3-001	KNOWN	basic	lincRNA	lincRNA		OTTHUMT00000143173.1			
FRMPD3	84443	bcgsc.ca	37	X	106846480	106846480	+	Silent	SNP	G	G	A			TCGA-2G-AAM2-01A-11D-A435-10	TCGA-2G-AAM2-10A-01D-A438-10	G	G					Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	41feee46-1a42-47e4-9136-5346983071dc	7ec717b0-6a59-4bee-b5f7-b9b0ba2313bb	g.chrX:106846480G>A	ENST00000276185.4	+	16	5310	c.5310G>A	c.(5308-5310)caG>caA	p.Q1770Q				Q5JV73	FRPD3_HUMAN	FERM and PDZ domain containing 3	1770	Gln-rich.					cytoskeleton (GO:0005856)				breast(3)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(16)|ovary(2)|urinary_tract(1)	28						aacaacaacagcagcagcagc	0.582																																					.													.	.			0			.												3.0	2.0	2.0					X																	106846480		690	1560	2250	SO:0001819	synonymous_variant	84443	.			ACAACAGCAGCAG	AB058720	CCDS76006.1	Xq22	2008-02-05			ENSG00000147234	ENSG00000147234			29382	protein-coding gene	gene with protein product						11347906	Standard	NM_032428		Approved	RP5-1070B1.1, KIAA1817		Q5JV73	OTTHUMG00000022165	ENST00000276185.4:c.5310G>A	X.37:g.106846480G>A			Somatic	81	0	0		WXS	Illumina HiSeq	Phase_1	126	0.06	7	.	16	0.00	0	Q96JK8	Silent	SNP	ENST00000276185.4	37																																																																																						0.582	FRMPD3-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				XM_042978	
