#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	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_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
AFF3	3899	hgsc.bcm.edu	37	2	100623382	100623382	+	Silent	SNP	G	G	A			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr2:100623382G>A	ENST00000409236.2	-	5	697	c.585C>T	c.(583-585)acC>acT	p.T195T	AFF3_ENST00000317233.4_Silent_p.T195T|AFF3_ENST00000409579.1_Silent_p.T220T|AFF3_ENST00000356421.2_Silent_p.T220T			P51826	AFF3_HUMAN	AF4/FMR2 family, member 3	195					embryonic hindlimb morphogenesis (GO:0035116)|regulation of transcription, DNA-templated (GO:0006355)|response to tumor necrosis factor (GO:0034612)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)			NS(1)|breast(3)|central_nervous_system(1)|cervix(3)|endometrium(9)|kidney(4)|large_intestine(20)|liver(1)|lung(28)|ovary(3)|pancreas(1)|prostate(4)|skin(5)|urinary_tract(3)	86						GCCTCTCCTGGGTCTGAAGGC	0.592																																																	0													65.0	68.0	67.0					2																	100623382		2203	4300	6503	SO:0001819	synonymous_variant	3899			U34360	CCDS33258.1, CCDS42723.1	2q11.2-q12	2008-02-05	2005-06-27	2005-06-27	ENSG00000144218	ENSG00000144218			6473	protein-coding gene	gene with protein product		601464	"""lymphoid nuclear protein related to AF4"""	LAF4		8662235, 8555498	Standard	XM_005263945		Approved	MLLT2-like	uc002taf.3	P51826	OTTHUMG00000153011	ENST00000409236.2:c.585C>T	2.37:g.100623382G>A			B7ZM46|B9EGL9|D3DVI6|Q53RD6|Q53S47|Q53SI6|Q53TB9|Q59F27|Q8IWJ5	Silent	SNP	ENST00000409236.2	37	CCDS42723.1																																																																																				0.592	AFF3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000328982.3		NM_002285	
ALDH4A1	8659	hgsc.bcm.edu;ucsc.edu	37	1	19202926	19202926	+	Silent	SNP	T	T	C	rs2230706	byFrequency	TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr1:19202926T>C	ENST00000375341.3	-	12	1478	c.1221A>G	c.(1219-1221)gcA>gcG	p.A407A	ALDH4A1_ENST00000538309.1_Silent_p.A347A|ALDH4A1_ENST00000290597.5_Silent_p.A407A|RP13-279N23.2_ENST00000494072.3_3'UTR|ALDH4A1_ENST00000538839.1_Intron	NM_003748.3	NP_003739.2	P30038	AL4A1_HUMAN	aldehyde dehydrogenase 4 family, member A1	407					4-hydroxyproline catabolic process (GO:0019470)|cellular nitrogen compound metabolic process (GO:0034641)|glutamate biosynthetic process (GO:0006537)|proline biosynthetic process (GO:0006561)|proline catabolic process (GO:0006562)|proline catabolic process to glutamate (GO:0010133)|proline metabolic process (GO:0006560)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)	1-pyrroline-5-carboxylate dehydrogenase activity (GO:0003842)|aldehyde dehydrogenase (NAD) activity (GO:0004029)|electron carrier activity (GO:0009055)|identical protein binding (GO:0042802)			cervix(2)|endometrium(1)|large_intestine(3)|lung(8)|prostate(1)	15		Colorectal(325;3.46e-05)|all_lung(284;0.000321)|Lung NSC(340;0.000398)|Renal(390;0.000518)|Breast(348;0.000812)|Ovarian(437;0.00764)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.00479)|BRCA - Breast invasive adenocarcinoma(304;3.67e-05)|Kidney(64;0.000182)|KIRC - Kidney renal clear cell carcinoma(64;0.00269)|STAD - Stomach adenocarcinoma(196;0.00644)|READ - Rectum adenocarcinoma(331;0.0649)		GTGAGGAGCGTGCGTGCTCCA	0.642													C|||	3306	0.660144	0.4728	0.768	5008	,	,		17831	0.7044		0.7117	False		,,,				2504	0.7382																0								C	,,	2130,2274		525,1080,597	41.0	28.0	33.0		1041,1221,1221	-4.2	0.6	1	dbSNP_98	33	5950,2650		2065,1820,415	no	coding-synonymous,coding-synonymous,coding-synonymous	ALDH4A1	NM_001161504.1,NM_003748.3,NM_170726.2	,,	2590,2900,1012	CC,CT,TT		30.814,48.3651,37.8653	,,	347/504,407/564,407/564	19202926	8080,4924	2202	4300	6502	SO:0001819	synonymous_variant	8659			U24266	CCDS188.1, CCDS53272.1	1p36	2008-02-05			ENSG00000159423	ENSG00000159423	1.5.1.12	"""Aldehyde dehydrogenases"""	406	protein-coding gene	gene with protein product		606811		ALDH4		8621661	Standard	NM_003748		Approved	P5CDh	uc001bbc.3	P30038	OTTHUMG00000002443	ENST00000375341.3:c.1221A>G	1.37:g.19202926T>C			A8K1Q7|B4DGE4|D2D4A3|Q16882|Q53HU4|Q5JNV6|Q8IZ38|Q96IF0|Q9UDI6	Silent	SNP	ENST00000375341.3	37	CCDS188.1																																																																																				0.642	ALDH4A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006954.1			
AMY1B	277	hgsc.bcm.edu	37	1	104236035	104236035	+	Missense_Mutation	SNP	T	T	G			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr1:104236035T>G	ENST00000330330.5	-	5	925	c.631A>C	c.(631-633)Att>Ctt	p.I211L	AMY1B_ENST00000464691.1_5'UTR|AMY1B_ENST00000370080.3_Missense_Mutation_p.I211L	NM_001008218.1	NP_001008219.1	P04745	AMY1_HUMAN	amylase, alpha 1B (salivary)	211					carbohydrate metabolic process (GO:0005975)|digestion (GO:0007586)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	alpha-amylase activity (GO:0004556)|metal ion binding (GO:0046872)	p.I211L(1)		large_intestine(1)|lung(1)	2		all_epithelial(167;3.05e-05)|all_lung(203;0.000199)|Lung NSC(277;0.000451)		Colorectal(144;0.0654)|all cancers(265;0.0808)|Epithelial(280;0.0921)|Lung(183;0.111)		GAAGCATCAATTCTGAACCCT	0.433																																																	1	Substitution - Missense(1)	large_intestine(1)											1.0	1.0	1.0					1																	104236035		4	10	14	SO:0001583	missense	277				CCDS30783.1	1p21	2012-10-02	2007-05-03		ENSG00000174876	ENSG00000174876	3.2.1.1		475	protein-coding gene	gene with protein product		104701	"""amylase, alpha 1B; salivary"""	AMY1			Standard	XM_005270758		Approved			P04745	OTTHUMG00000011021	ENST00000330330.5:c.631A>C	1.37:g.104236035T>G	ENSP00000330484:p.Ile211Leu		A6NJS5|A8K8H6|Q13763|Q5T083	Missense_Mutation	SNP	ENST00000330330.5	37	CCDS30783.1	.	.	.	.	.	.	.	.	.	.	-	4.573	0.106493	0.08780	.	.	ENSG00000174876	ENST00000416771;ENST00000370080;ENST00000330330;ENST00000446703	D;D;D	0.98164	-4.76;-4.76;-4.76	2.08	0.934	0.19477	.	0.604997	0.17383	N	0.176244	D	0.94145	0.8122	.	.	.	0.24160	N	0.995664	.	.	.	.	.	.	D	0.89483	0.3751	7	0.32370	T	0.25	.	11.1212	0.48291	0.0:0.0:0.5065:0.4935	.	.	.	.	L	211	ENSP00000359097:I211L;ENSP00000330484:I211L;ENSP00000390219:I211L	ENSP00000330484:I211L	I	-	1	0	AMY1B	104037558	0.994000	0.37717	0.993000	0.49108	0.262000	0.26303	0.279000	0.18771	-0.419000	0.07439	-1.122000	0.02009	ATT		0.433	AMY1B-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000030309.1		NM_001008218	
AHCYL1	10768	hgsc.bcm.edu;ucsc.edu	37	1	110553923	110553923	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr1:110553923T>A	ENST00000369799.5	+	3	687	c.320T>A	c.(319-321)gTg>gAg	p.V107E	AHCYL1_ENST00000475081.1_3'UTR|AHCYL1_ENST00000393614.4_Missense_Mutation_p.V60E|AHCYL1_ENST00000359172.3_Missense_Mutation_p.V60E	NM_001242673.1|NM_001242674.1|NM_006621.5	NP_001229602.1|NP_001229603.1|NP_006612.2	O43865	SAHH2_HUMAN	adenosylhomocysteinase-like 1	107					mRNA polyadenylation (GO:0006378)|one-carbon metabolic process (GO:0006730)|positive regulation of sodium ion transport (GO:0010765)|protein export from nucleus (GO:0006611)|regulation of anion transport (GO:0044070)|regulation of ion transmembrane transporter activity (GO:0032412)|regulation of mRNA 3'-end processing (GO:0031440)	endoplasmic reticulum (GO:0005783)|extracellular vesicular exosome (GO:0070062)	adenosylhomocysteinase activity (GO:0004013)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(6)|ovary(1)|prostate(2)	18		all_epithelial(167;3.58e-05)|all_lung(203;0.000116)|Lung NSC(277;0.000233)		Lung(183;0.0259)|Colorectal(144;0.123)|all cancers(265;0.134)|Epithelial(280;0.141)|LUSC - Lung squamous cell carcinoma(189;0.143)		AATTTCTGTGTGAAGAACATC	0.502																																																	0													181.0	116.0	138.0					1																	110553923		2203	4300	6503	SO:0001583	missense	10768			U82761	CCDS818.1, CCDS55620.1	1p13	2014-06-12	2009-06-12		ENSG00000168710	ENSG00000168710			344	protein-coding gene	gene with protein product	"""inositol 1,4,5-trisphosphate receptor-binding protein"", ""protein phosphatase 1, regulatory subunit 78"""	607826	"""S-adenosylhomocysteine hydrolase-like 1"""			11904675, 16754674, 12525476	Standard	NM_006621		Approved	XPVKONA, IRBIT, PPP1R78	uc001dyx.3	O43865	OTTHUMG00000011652	ENST00000369799.5:c.320T>A	1.37:g.110553923T>A	ENSP00000358814:p.Val107Glu		B4E168|Q2TAJ6|Q502W8|Q5VSM0|Q6P171|Q96PK4|Q9UG84	Missense_Mutation	SNP	ENST00000369799.5	37	CCDS818.1	.	.	.	.	.	.	.	.	.	.	T	33	5.236495	0.95240	.	.	ENSG00000168710	ENST00000369799;ENST00000359172;ENST00000393614	D;D;D	0.82167	-1.58;-1.58;-1.58	5.93	5.93	0.95920	.	0.000000	0.85682	D	0.000000	D	0.93324	0.7872	H	0.96080	3.765	0.80722	D	1	D	0.61080	0.989	D	0.72982	0.979	D	0.95248	0.8357	10	0.87932	D	0	-25.3709	16.3756	0.83387	0.0:0.0:0.0:1.0	.	107	O43865	SAHH2_HUMAN	E	107;60;60	ENSP00000358814:V107E;ENSP00000352092:V60E;ENSP00000377238:V60E	ENSP00000352092:V60E	V	+	2	0	AHCYL1	110355446	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.040000	0.89188	2.270000	0.75569	0.460000	0.39030	GTG		0.502	AHCYL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032243.1			
AP3D1	8943	hgsc.bcm.edu;ucsc.edu	37	19	2121803	2121803	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr19:2121803A>G	ENST00000345016.5	-	12	1262	c.1031T>C	c.(1030-1032)cTc>cCc	p.L344P	AP3D1_ENST00000355272.6_Missense_Mutation_p.L344P|AP3D1_ENST00000590683.1_5'UTR|AP3D1_ENST00000356926.4_Missense_Mutation_p.L253P|AP3D1_ENST00000350812.6_Missense_Mutation_p.L175P	NM_003938.6	NP_003929.4	O14617	AP3D1_HUMAN	adaptor-related protein complex 3, delta 1 subunit	344					anterograde axon cargo transport (GO:0008089)|anterograde synaptic vesicle transport (GO:0048490)|antigen processing and presentation, exogenous lipid antigen via MHC class Ib (GO:0048007)|endosome to melanosome transport (GO:0035646)|eye pigment biosynthetic process (GO:0006726)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein localization to membrane (GO:0072657)|protein localization to organelle (GO:0033365)|regulation of sequestering of zinc ion (GO:0061088)|synaptic vesicle membrane organization (GO:0048499)	endosome membrane (GO:0010008)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|membrane coat (GO:0030117)|terminal bouton (GO:0043195)	protein transporter activity (GO:0008565)|transporter activity (GO:0005215)			breast(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(23)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	37		Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTGCAGGATGAGGTCCTTGTG	0.652																																																	0													120.0	137.0	132.0					19																	2121803		2137	4215	6352	SO:0001583	missense	8943			U91930	CCDS42459.1, CCDS58638.1	19p13.3	2014-09-04			ENSG00000065000	ENSG00000065000			568	protein-coding gene	gene with protein product		607246				9151686, 9303295	Standard	NM_003938		Approved	ADTD	uc002lva.4	O14617	OTTHUMG00000180354	ENST00000345016.5:c.1031T>C	19.37:g.2121803A>G	ENSP00000344055:p.Leu344Pro		O00202|O75262|Q59HF5|Q96G11|Q9H3C6	Missense_Mutation	SNP	ENST00000345016.5	37	CCDS42459.1	.	.	.	.	.	.	.	.	.	.	A	24.6	4.547530	0.86022	.	.	ENSG00000065000	ENST00000356926;ENST00000345016;ENST00000355272;ENST00000343722;ENST00000350812	T;T;T;T	0.33654	1.4;1.4;1.4;1.4	4.39	4.39	0.52855	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	D	0.000000	T	0.66458	0.2791	M	0.91459	3.21	0.80722	D	1	D;D;D	0.89917	0.999;1.0;1.0	D;D;D	0.87578	0.986;0.996;0.998	T	0.75199	-0.3402	10	0.87932	D	0	-37.0306	13.0686	0.59048	1.0:0.0:0.0:0.0	.	344;344;253	O14617-5;O14617;G5E988	.;AP3D1_HUMAN;.	P	253;344;344;344;175	ENSP00000349398:L253P;ENSP00000344055:L344P;ENSP00000347416:L344P;ENSP00000342321:L175P	ENSP00000341579:L344P	L	-	2	0	AP3D1	2072803	1.000000	0.71417	1.000000	0.80357	0.989000	0.77384	9.067000	0.93955	1.759000	0.51996	0.379000	0.24179	CTC		0.652	AP3D1-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000450912.1			
B4GALNT2	124872	hgsc.bcm.edu	37	17	47246988	47246988	+	Silent	SNP	C	C	A			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr17:47246988C>A	ENST00000300404.2	+	11	1658	c.1599C>A	c.(1597-1599)gcC>gcA	p.A533A	B4GALNT2_ENST00000393354.2_Silent_p.A473A|RP11-708H21.4_ENST00000575159.1_lincRNA|B4GALNT2_ENST00000504681.1_Silent_p.A447A	NM_153446.2	NP_703147.2	Q8NHY0	B4GN2_HUMAN	beta-1,4-N-acetyl-galactosaminyl transferase 2	533					lipid glycosylation (GO:0030259)|negative regulation of cell-cell adhesion (GO:0022408)|protein glycosylation (GO:0006486)|UDP-N-acetylgalactosamine metabolic process (GO:0019276)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	integral component of Golgi membrane (GO:0030173)|integral component of membrane (GO:0016021)	acetylgalactosaminyltransferase activity (GO:0008376)			endometrium(3)|large_intestine(6)|liver(2)|lung(8)|ovary(1)|prostate(1)|skin(1)|stomach(1)|urinary_tract(1)	24			all cancers(6;0.000316)			AACTGGCTGCCCTAGAGAAGA	0.542																																					GBM(124;244 1635 8663 18097 33175)												0													96.0	87.0	90.0					17																	47246988		2203	4300	6503	SO:0001819	synonymous_variant	124872			AJ517770	CCDS11544.1, CCDS54139.1, CCDS54140.1	17q21.33	2013-02-22	2006-01-08	2006-01-08	ENSG00000167080	ENSG00000167080	2.4.1.-	"""Beta 4-glycosyltransferases"", ""Glycosyltransferase family 2 domain containing"""	24136	protein-coding gene	gene with protein product		111730	"""UDP-GalNAc:Neu5Acalpha2-3Galbeta-R beta1,4-N-acetylgalactosaminyltransferase"""	GALGT2		8782649, 12678917	Standard	NM_153446		Approved	Sda, Cad	uc002ion.2	Q8NHY0	OTTHUMG00000161307	ENST00000300404.2:c.1599C>A	17.37:g.47246988C>A			B4DZE4|Q14CP1|Q86Y40	Silent	SNP	ENST00000300404.2	37	CCDS11544.1																																																																																				0.542	B4GALNT2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000364477.1		NM_153446	
CENPF	1063	hgsc.bcm.edu	37	1	214815523	214815523	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr1:214815523C>T	ENST00000366955.3	+	12	4010	c.3842C>T	c.(3841-3843)aCa>aTa	p.T1281I		NM_016343.3	NP_057427.3	P49454	CENPF_HUMAN	centromere protein F, 350/400kDa	0					cell differentiation (GO:0030154)|cell proliferation (GO:0008283)|chromosome segregation (GO:0007059)|DNA replication (GO:0006260)|G2/M transition of mitotic cell cycle (GO:0000086)|kinetochore assembly (GO:0051382)|metaphase plate congression (GO:0051310)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|muscle organ development (GO:0007517)|negative regulation of transcription, DNA-templated (GO:0045892)|protein transport (GO:0015031)|regulation of cell cycle (GO:0051726)|regulation of G2/M transition of mitotic cell cycle (GO:0010389)|regulation of striated muscle tissue development (GO:0016202)|response to drug (GO:0042493)	chromosome, centromeric region (GO:0000775)|condensed chromosome outer kinetochore (GO:0000940)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|kinetochore (GO:0000776)|midbody (GO:0030496)|nuclear envelope (GO:0005635)|nuclear matrix (GO:0016363)|nucleus (GO:0005634)|pronucleus (GO:0045120)|spindle (GO:0005819)|spindle pole (GO:0000922)	chromatin binding (GO:0003682)|dynein binding (GO:0045502)|protein C-terminus binding (GO:0008022)|protein homodimerization activity (GO:0042803)|transcription factor binding (GO:0008134)			NS(2)|breast(2)|central_nervous_system(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(37)|lung(47)|ovary(7)|prostate(3)|skin(6)|stomach(1)|urinary_tract(1)	126				all cancers(67;0.00836)|OV - Ovarian serous cystadenocarcinoma(81;0.00855)|GBM - Glioblastoma multiforme(131;0.0694)|Epithelial(68;0.0833)		GAGTTGTCAACAAGTCAAAAC	0.398																																					Colon(80;575 1284 11000 14801 43496)												0													66.0	64.0	65.0					1																	214815523		2203	4300	6503	SO:0001583	missense	1063			U30872	CCDS31023.1	1q41	2013-11-05	2013-01-17		ENSG00000117724	ENSG00000117724			1857	protein-coding gene	gene with protein product	"""mitosin"""	600236	"""centromere protein F, 350/400kDa (mitosin)"""			7904902, 7851898	Standard	NM_016343		Approved	hcp-1	uc001hkm.3	P49454	OTTHUMG00000036955	ENST00000366955.3:c.3842C>T	1.37:g.214815523C>T	ENSP00000355922:p.Thr1281Ile		Q13171|Q13246|Q5VVM7	Missense_Mutation	SNP	ENST00000366955.3	37	CCDS31023.1	.	.	.	.	.	.	.	.	.	.	C	18.10	3.549347	0.65311	.	.	ENSG00000117724	ENST00000366955	T	0.22539	1.95	5.06	5.06	0.68205	.	0.410430	0.18039	N	0.153662	T	0.27098	0.0664	.	.	.	0.31221	N	0.697449	P	0.48230	0.907	P	0.46796	0.527	T	0.11397	-1.0589	9	0.42905	T	0.14	.	15.3551	0.74421	0.0:1.0:0.0:0.0	.	1281	P49454	CENPF_HUMAN	I	1281	ENSP00000355922:T1281I	ENSP00000355922:T1281I	T	+	2	0	CENPF	212882146	0.000000	0.05858	0.996000	0.52242	0.850000	0.48378	0.547000	0.23299	2.356000	0.79943	0.511000	0.50034	ACA		0.398	CENPF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089749.1		NM_016343	
CNDP1	84735	hgsc.bcm.edu;ucsc.edu	37	18	72234508	72234508	+	Missense_Mutation	SNP	A	A	G			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr18:72234508A>G	ENST00000358821.3	+	6	824	c.596A>G	c.(595-597)gAa>gGa	p.E199G	CNDP1_ENST00000585136.1_3'UTR|CNDP1_ENST00000582365.1_Missense_Mutation_p.E156G	NM_032649.5	NP_116038	Q96KN2	CNDP1_HUMAN	carnosine dipeptidase 1 (metallopeptidase M20 family)	199						extracellular region (GO:0005576)	carboxypeptidase activity (GO:0004180)|dipeptidase activity (GO:0016805)|metal ion binding (GO:0046872)|metallopeptidase activity (GO:0008237)|tripeptidase activity (GO:0034701)			breast(1)|central_nervous_system(1)|endometrium(2)|kidney(3)|large_intestine(4)|lung(12)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)	27		Esophageal squamous(42;0.129)|Prostate(75;0.157)|Melanoma(33;0.211)		BRCA - Breast invasive adenocarcinoma(31;0.109)		GAGGGGATGGAAGAGGCTGGC	0.433																																					Melanoma(32;1029 1042 25286 38395 44237)												0													104.0	116.0	112.0					18																	72234508		2203	4300	6503	SO:0001583	missense	84735				CCDS12007.1	18q22.3	2014-07-14			ENSG00000150656	ENSG00000150656	3.4.13.20		20675	protein-coding gene	gene with protein product	"""carnosinase 1"", ""glutamate carboxypeptidase-like protein 2"""	609064				12473676	Standard	NM_032649		Approved	MGC10825, CN1, CPGL2, HsT2308	uc002llq.3	Q96KN2	OTTHUMG00000132852	ENST00000358821.3:c.596A>G	18.37:g.72234508A>G	ENSP00000351682:p.Glu199Gly		Q14D40|Q17S05|Q2TBG0|Q6UWK2|Q9BT98	Missense_Mutation	SNP	ENST00000358821.3	37	CCDS12007.1	.	.	.	.	.	.	.	.	.	.	A	26.0	4.699706	0.88830	.	.	ENSG00000150656	ENST00000358821	D	0.98550	-4.99	5.31	5.31	0.75309	ArgE/DapE/ACY1/CPG2/YscS, conserved site (1);	0.000000	0.85682	D	0.000000	D	0.99426	0.9797	H	0.98833	4.345	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.98130	1.0430	10	0.87932	D	0	-37.3488	14.9158	0.70795	1.0:0.0:0.0:0.0	.	199	Q96KN2	CNDP1_HUMAN	G	199	ENSP00000351682:E199G	ENSP00000351682:E199G	E	+	2	0	CNDP1	70385488	1.000000	0.71417	0.936000	0.37596	0.952000	0.60782	8.613000	0.90913	2.005000	0.58758	0.477000	0.44152	GAA		0.433	CNDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256326.1		NM_032649	
CPLX2	10814	hgsc.bcm.edu	37	5	175306957	175306957	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr5:175306957G>A	ENST00000359546.4	+	5	957	c.314G>A	c.(313-315)tGc>tAc	p.C105Y	CPLX2_ENST00000515094.1_Missense_Mutation_p.C105Y|CPLX2_ENST00000393745.3_Missense_Mutation_p.C105Y	NM_001008220.1|NM_006650.3	NP_001008221.1|NP_006641.1	Q6PUV4	CPLX2_HUMAN	complexin 2	105					cell differentiation (GO:0030154)|mast cell degranulation (GO:0043303)|nervous system development (GO:0007399)|positive regulation of synaptic plasticity (GO:0031915)|regulation of exocytosis (GO:0017157)|synaptic vesicle exocytosis (GO:0016079)|vesicle docking involved in exocytosis (GO:0006904)	dendrite (GO:0030425)|mast cell granule (GO:0042629)|neuronal cell body (GO:0043025)|synapse (GO:0045202)|synaptobrevin 2-SNAP-25-syntaxin-1a-complexin II complex (GO:0070033)|synaptobrevin 2-SNAP-25-syntaxin-3-complexin complex (GO:0070554)				endometrium(3)|kidney(2)|lung(3)|ovary(2)	10	all_cancers(89;0.004)|Renal(175;0.000269)|Lung NSC(126;0.00441)|all_lung(126;0.00747)	Medulloblastoma(196;0.0208)|all_neural(177;0.0416)|all_hematologic(541;0.214)	Kidney(164;3.85e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000183)			CCTGCGGGCTGCGGGGACGAG	0.627																																																	0													36.0	39.0	38.0					5																	175306957		2202	4300	6502	SO:0001583	missense	10814			U35100	CCDS4396.1	5q35.2	2008-05-23			ENSG00000145920	ENSG00000145920			2310	protein-coding gene	gene with protein product		605033				7553862, 16162394	Standard	XM_005265798		Approved	CPX-2, DKFZp547D155	uc003mdf.1	Q6PUV4	OTTHUMG00000130665	ENST00000359546.4:c.314G>A	5.37:g.175306957G>A	ENSP00000352544:p.Cys105Tyr		B2RAG2|O09056|Q13329|Q28184|Q52M15|Q64386	Missense_Mutation	SNP	ENST00000359546.4	37	CCDS4396.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	g|g	21.5|21.5	4.152236|4.152236	0.78001|0.78001	.|.	.|.	ENSG00000145920|ENSG00000145920	ENST00000393746|ENST00000359546;ENST00000509837;ENST00000393745;ENST00000514150;ENST00000515094	.|.	.|.	.|.	5.14|5.14	5.14|5.14	0.70334|0.70334	.|.	.|0.000000	.|0.85682	.|U	.|0.000000	.|T	.|0.79667	.|0.4485	M|M	0.79123|0.79123	2.44|2.44	0.80722|0.80722	D|D	1|1	.|D	.|0.55800	.|0.973	.|D	.|0.77557	.|0.99	.|T	.|0.82374	.|-0.0489	.|9	.|0.87932	.|D	.|0	.|-1.5347	16.1282|16.1282	0.81408|0.81408	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	.|105	.|Q6PUV4	.|CPLX2_HUMAN	.|Y	-1|105	.|.	.|ENSP00000352544:C105Y	.|C	+|+	.|2	.|0	CPLX2|CPLX2	175239563|175239563	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.952000|0.952000	0.60782|0.60782	9.720000|9.720000	0.98763|0.98763	2.397000|2.397000	0.81536|0.81536	0.454000|0.454000	0.30748|0.30748	.|TGC		0.627	CPLX2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253157.2			
CR1	1378	hgsc.bcm.edu;ucsc.edu	37	1	207791580	207791580	+	Missense_Mutation	SNP	C	C	G			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr1:207791580C>G	ENST00000367049.4	+	42	7054	c.7054C>G	c.(7054-7056)Cat>Gat	p.H2352D	CR1_ENST00000367053.1_Missense_Mutation_p.H1902D|CR1_ENST00000400960.2_Missense_Mutation_p.H1902D|CR1_ENST00000367051.1_Missense_Mutation_p.H1902D|CR1_ENST00000367052.1_Missense_Mutation_p.H1902D	NM_000651.4	NP_000642.3	P17927	CR1_HUMAN	complement component (3b/4b) receptor 1 (Knops blood group)	1902					complement activation, classical pathway (GO:0006958)|complement receptor mediated signaling pathway (GO:0002430)|innate immune response (GO:0045087)|negative regulation of complement activation, alternative pathway (GO:0045957)|negative regulation of complement activation, classical pathway (GO:0045959)|negative regulation of serine-type endopeptidase activity (GO:1900004)|positive regulation of serine-type endopeptidase activity (GO:1900005)|regulation of complement activation (GO:0030449)	cell surface (GO:0009986)|extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	complement component C3b binding (GO:0001851)|complement component C3b receptor activity (GO:0004877)|complement component C4b binding (GO:0001855)|complement component C4b receptor activity (GO:0001861)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(9)|kidney(11)|large_intestine(13)|lung(33)|ovary(3)|prostate(6)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	82						CCAATTGGATCATTATTGCAA	0.438																																																	0													230.0	218.0	222.0					1																	207791580		1915	4126	6041	SO:0001583	missense	1378			Y00816	CCDS44308.1, CCDS44309.1	1q32	2014-07-19	2006-01-12		ENSG00000203710	ENSG00000203710		"""CD molecules"", ""Blood group antigens"", ""Complement system"""	2334	protein-coding gene	gene with protein product		120620	"""complement component (3b/4b) receptor 1, including Knops blood group system"""			1708809	Standard	XM_005273064		Approved	CD35, KN	uc001hfx.3	P17927	OTTHUMG00000036311	ENST00000367049.4:c.7054C>G	1.37:g.207791580C>G	ENSP00000356016:p.His2352Asp		Q16744|Q16745|Q5SR43|Q5SR45|Q9UQV2	Missense_Mutation	SNP	ENST00000367049.4	37	CCDS44308.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	2.057|2.057	-0.416249|-0.416249	0.04766|0.04766	.|.	.|.	ENSG00000203710|ENSG00000203710	ENST00000367052;ENST00000367051;ENST00000367053;ENST00000400960;ENST00000367049|ENST00000529814	T;T;T;T;T|.	0.76060|.	-0.99;-0.99;-0.99;-0.99;-0.99|.	4.19|4.19	2.3|2.3	0.28687|0.28687	Complement control module (2);Sushi/SCR/CCP (2);|.	.|.	.|.	.|.	.|.	T|T	0.32941|0.32941	0.0846|0.0846	L|L	0.36672|0.36672	1.1|1.1	0.09310|0.09310	N|N	1|1	D;D|.	0.59767|.	0.981;0.986|.	P;P|.	0.62491|.	0.892;0.903|.	T|T	0.20706|0.20706	-1.0267|-1.0267	9|5	0.16896|.	T|.	0.51|.	.|.	5.7883|5.7883	0.18347|0.18347	0.0:0.697:0.1974:0.1057|0.0:0.697:0.1974:0.1057	.|.	1902;2352|.	P17927;E9PDY4|.	CR1_HUMAN;.|.	D|M	1902;1902;1902;1902;2352|524	ENSP00000356019:H1902D;ENSP00000356018:H1902D;ENSP00000356020:H1902D;ENSP00000383744:H1902D;ENSP00000356016:H2352D|.	ENSP00000356016:H2352D|.	H|I	+|+	1|3	0|3	CR1|CR1	205858203|205858203	0.010000|0.010000	0.17322|0.17322	0.002000|0.002000	0.10522|0.10522	0.734000|0.734000	0.41952|0.41952	1.824000|1.824000	0.39072|0.39072	0.718000|0.718000	0.32166|0.32166	-0.302000|-0.302000	0.09304|0.09304	CAT|ATC		0.438	CR1-012	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000382527.1		NM_000573	
DTNA	1837	hgsc.bcm.edu	37	18	32431802	32431802	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr18:32431802C>T	ENST00000399113.3	+	14	1361	c.1361C>T	c.(1360-1362)cCt>cTt	p.P454L	DTNA_ENST00000348997.5_Missense_Mutation_p.P451L|DTNA_ENST00000597599.1_Missense_Mutation_p.P394L|DTNA_ENST00000601125.1_Missense_Mutation_p.P76L|DTNA_ENST00000598774.1_Missense_Mutation_p.P397L|DTNA_ENST00000591182.1_Missense_Mutation_p.P102L|DTNA_ENST00000269190.7_Missense_Mutation_p.P455L|DTNA_ENST00000598334.1_Missense_Mutation_p.P394L|DTNA_ENST00000597674.1_Missense_Mutation_p.P76L|DTNA_ENST00000283365.9_Missense_Mutation_p.P397L|DTNA_ENST00000399121.5_Missense_Mutation_p.P394L|DTNA_ENST00000596745.1_Missense_Mutation_p.P204L|DTNA_ENST00000269191.6_Missense_Mutation_p.P454L|DTNA_ENST00000269192.7_Missense_Mutation_p.P163L|DTNA_ENST00000599844.1_Missense_Mutation_p.P76L|DTNA_ENST00000598142.1_Missense_Mutation_p.P397L|DTNA_ENST00000444659.1_Missense_Mutation_p.P454L|DTNA_ENST00000556414.3_Missense_Mutation_p.P106L|DTNA_ENST00000595022.1_Missense_Mutation_p.P394L|DTNA_ENST00000399097.3_Missense_Mutation_p.P102L			Q9Y4J8	DTNA_HUMAN	dystrobrevin, alpha	454					neuromuscular synaptic transmission (GO:0007274)|signal transduction (GO:0007165)|striated muscle contraction (GO:0006941)|synaptic transmission (GO:0007268)	axon (GO:0030424)|cell junction (GO:0030054)|cytoplasm (GO:0005737)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|synapse (GO:0045202)	calcium ion binding (GO:0005509)|zinc ion binding (GO:0008270)			endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(1)|large_intestine(2)|lung(19)|prostate(1)|upper_aerodigestive_tract(1)	29						CAGCAGCCACCTCAGCAGAGA	0.423																																																	0													70.0	63.0	65.0					18																	32431802		2203	4300	6503	SO:0001583	missense	1837			U84540	CCDS11908.1, CCDS11909.1, CCDS42426.1, CCDS45848.1, CCDS56060.1, CCDS56061.1, CCDS56062.1, CCDS56063.1, CCDS59309.1, CCDS59310.1, CCDS59311.1, CCDS59312.1, CCDS59313.1, CCDS59314.1	18q12	2014-09-17			ENSG00000134769	ENSG00000134769			3057	protein-coding gene	gene with protein product	"""dystrophin-related protein 3"""	601239				8081380, 15834686	Standard	NM_001390		Approved	D18S892E, DTN, DTN-1, DTN-2, DTN-3, DRP3	uc010dmn.1	Q9Y4J8	OTTHUMG00000132309	ENST00000399113.3:c.1361C>T	18.37:g.32431802C>T	ENSP00000382064:p.Pro454Leu		A8K541|A8MSZ0|A8MUY4|B4DGS6|B4DIR0|B4DIU8|M0QYX6|M0R397|O15332|O15333|O75697|Q13197|Q13198|Q13199|Q13498|Q13499|Q13500|Q59GK7|Q9BS59	Missense_Mutation	SNP	ENST00000399113.3	37	CCDS59311.1	.	.	.	.	.	.	.	.	.	.	C	9.024	0.985512	0.18889	.	.	ENSG00000134769	ENST00000399119;ENST00000283365;ENST00000399114;ENST00000269190;ENST00000399097;ENST00000348997;ENST00000399121;ENST00000444659;ENST00000269191;ENST00000399113;ENST00000269192;ENST00000450377;ENST00000556414	T;T;T;T;T;T	0.18338	2.23;2.22;2.24;2.22;2.23;2.22	5.67	4.8	0.61643	.	1.051700	0.07328	N	0.878760	T	0.14098	0.0341	N	0.14661	0.345	0.09310	N	0.999999	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.15719	0.0;0.0;0.002;0.005;0.001;0.0;0.008;0.0;0.0;0.002;0.014;0.0;0.0;0.0;0.004	B;B;B;B;B;B;B;B;B;B;B;B;B;B;B	0.15052	0.003;0.001;0.002;0.007;0.004;0.004;0.012;0.0;0.0;0.007;0.012;0.0;0.0;0.0;0.004	T	0.35724	-0.9777	10	0.14656	T	0.56	0.0019	18.437	0.90650	0.0:0.7787:0.2213:0.0	.	106;163;144;204;76;454;454;394;397;102;451;394;405;397;397	B4DIU8;B4DIR0;B7Z3X3;B4DGS6;Q9Y4J8-8;Q9Y4J8;Q9Y4J8-3;A8K541;F5H5C1;Q9Y4J8-6;Q9Y4J8-4;E9PEH8;Q59GK7;Q9Y4J8-2;Q9Y4J8-5	.;.;.;.;.;DTNA_HUMAN;.;.;.;.;.;.;.;.;.	L	397;397;394;455;102;451;454;454;454;454;163;102;106	ENSP00000283365:P397L;ENSP00000269190:P455L;ENSP00000336682:P451L;ENSP00000405819:P454L;ENSP00000269191:P454L;ENSP00000382064:P454L	ENSP00000269190:P455L	P	+	2	0	DTNA	30685800	0.263000	0.24083	0.098000	0.21074	0.930000	0.56654	1.472000	0.35376	1.386000	0.46466	0.655000	0.94253	CCT		0.423	DTNA-005	PUTATIVE	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255422.2		NM_001390	
ECHS1	1892	hgsc.bcm.edu;ucsc.edu	37	10	135179506	135179506	+	Missense_Mutation	SNP	G	G	T	rs200584793		TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr10:135179506G>T	ENST00000368547.3	-	6	1068	c.713C>A	c.(712-714)gCg>gAg	p.A238E		NM_004092.3	NP_004083.3	P30084	ECHM_HUMAN	enoyl CoA hydratase, short chain, 1, mitochondrial	238					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation (GO:0006635)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	enoyl-CoA hydratase activity (GO:0004300)			NS(1)|central_nervous_system(1)|kidney(1)|large_intestine(2)|lung(1)|ovary(2)|prostate(1)|skin(1)	10		all_cancers(35;1.14e-09)|all_epithelial(44;5.79e-08)|Lung NSC(174;0.00263)|all_lung(145;0.0039)|all_neural(114;0.0299)|Melanoma(40;0.123)|Colorectal(31;0.172)|Glioma(114;0.203)		all cancers(32;1.62e-06)|OV - Ovarian serous cystadenocarcinoma(35;5.75e-06)|Epithelial(32;7.58e-06)		TTTGGCCATCGCTACTACAAT	0.488																																					GBM(132;1720 1771 5373 10277 21402)												0													214.0	178.0	191.0					10																	135179506		2202	4300	6502	SO:0001583	missense	1892				CCDS7681.1	10q26.2-q26.3	2010-05-04	2010-04-30		ENSG00000127884	ENSG00000127884	4.2.1.17		3151	protein-coding gene	gene with protein product		602292	"""enoyl Coenzyme A hydratase, short chain, 1, mitochondrial"""			8012501	Standard	NM_004092		Approved	SCEH	uc001lmu.3	P30084	OTTHUMG00000019320	ENST00000368547.3:c.713C>A	10.37:g.135179506G>T	ENSP00000357535:p.Ala238Glu		O00739|Q5VWY1|Q96H54	Missense_Mutation	SNP	ENST00000368547.3	37	CCDS7681.1	.	.	.	.	.	.	.	.	.	.	G	9.242	1.038560	0.19669	.	.	ENSG00000127884	ENST00000368547	T	0.69561	-0.41	5.39	4.43	0.53597	Crontonase, C-terminal (1);	0.161207	0.53938	D	0.000045	T	0.61553	0.2356	L	0.49640	1.575	0.21915	N	0.999471	B	0.32862	0.387	B	0.36186	0.219	T	0.59521	-0.7439	10	0.51188	T	0.08	.	11.9997	0.53224	0.0:0.0:0.8277:0.1723	.	238	P30084	ECHM_HUMAN	E	238	ENSP00000357535:A238E	ENSP00000357535:A238E	A	-	2	0	ECHS1	135029496	0.980000	0.34600	0.044000	0.18714	0.017000	0.09413	3.820000	0.55693	2.701000	0.92244	0.555000	0.69702	GCG		0.488	ECHS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051156.1			
FAM129A	116496	hgsc.bcm.edu	37	1	184764659	184764659	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr1:184764659C>T	ENST00000367511.3	-	14	2432	c.2239G>A	c.(2239-2241)Gaa>Aaa	p.E747K	FAM129A_ENST00000487074.1_5'UTR	NM_052966.2	NP_443198.1	Q9BZQ8	NIBAN_HUMAN	family with sequence similarity 129, member A	747	Glu-rich.				negative regulation of protein phosphorylation (GO:0001933)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of translation (GO:0045727)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|plasma membrane (GO:0005886)				autonomic_ganglia(1)|breast(1)|cervix(2)|endometrium(4)|large_intestine(6)|liver(1)|lung(22)|ovary(3)|skin(3)|upper_aerodigestive_tract(2)	45						TTTTCCTCTTCTTCTTCATTT	0.547																																																	0													151.0	161.0	157.0					1																	184764659		2203	4300	6503	SO:0001583	missense	116496			AF288391	CCDS1364.1	1q25	2008-10-08	2006-11-23	2006-11-23	ENSG00000135842	ENSG00000135842			16784	protein-coding gene	gene with protein product	"""cell growth inhibiting protein 39"""		"""chromosome 1 open reading frame 24"""	C1orf24		15085203, 16444351	Standard	NM_052966		Approved	NIBAN, GIG39	uc001gra.4	Q9BZQ8	OTTHUMG00000035388	ENST00000367511.3:c.2239G>A	1.37:g.184764659C>T	ENSP00000356481:p.Glu747Lys		Q2TTR2|Q5TEM8|Q8TEI5|Q9H593|Q9H9Y8|Q9HCB9	Missense_Mutation	SNP	ENST00000367511.3	37	CCDS1364.1	.	.	.	.	.	.	.	.	.	.	C	14.85	2.659688	0.47572	.	.	ENSG00000135842	ENST00000367511	T	0.15603	2.41	5.44	3.52	0.40303	.	0.355286	0.23844	N	0.044002	T	0.10551	0.0258	L	0.29908	0.895	0.09310	N	1	B	0.19583	0.037	B	0.17098	0.017	T	0.32851	-0.9891	10	0.10902	T	0.67	-2.4055	8.6959	0.34296	0.156:0.7659:0.0:0.0781	.	747	Q9BZQ8	NIBAN_HUMAN	K	747	ENSP00000356481:E747K	ENSP00000356481:E747K	E	-	1	0	FAM129A	183031282	0.000000	0.05858	0.466000	0.27168	0.471000	0.32888	0.194000	0.17135	1.243000	0.43853	0.491000	0.48974	GAA		0.547	FAM129A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085786.1			
GALNS	2588	hgsc.bcm.edu;ucsc.edu	37	16	88908325	88908325	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr16:88908325G>T	ENST00000268695.5	-	3	387	c.299C>A	c.(298-300)aCc>aAc	p.T100N	GALNS_ENST00000542788.1_Intron|GALNS_ENST00000565364.1_5'UTR	NM_000512.4	NP_000503.1	P34059	GALNS_HUMAN	galactosamine (N-acetyl)-6-sulfatase	100	Catalytic domain.				carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate catabolic process (GO:0042340)|keratan sulfate metabolic process (GO:0042339)|small molecule metabolic process (GO:0044281)	extracellular vesicular exosome (GO:0070062)|lysosomal lumen (GO:0043202)	metal ion binding (GO:0046872)|N-acetylgalactosamine-4-sulfatase activity (GO:0003943)|N-acetylgalactosamine-6-sulfatase activity (GO:0043890)|sulfuric ester hydrolase activity (GO:0008484)			breast(1)|endometrium(4)|kidney(2)|large_intestine(7)|lung(8)	22				BRCA - Breast invasive adenocarcinoma(80;0.0496)		ATGGGCGTTGGTGGTGTAGAA	0.627																																					GBM(129;1929 2344 25209 33204)												0													157.0	109.0	125.0					16																	88908325		2194	4300	6494	SO:0001583	missense	2588			D17629	CCDS10970.1	16q24.3	2014-07-03	2014-07-03		ENSG00000141012	ENSG00000141012	3.1.6.4	"""Arylsulfatase family"""	4122	protein-coding gene	gene with protein product	"""Morquio syndrome"", ""mucopolysaccharidosis type IVA"""	612222	"""galactosamine (N-acetyl)-6-sulfate sulfatase"""			1755850	Standard	NM_000512		Approved	GAS, GALNAC6S	uc002fly.4	P34059	OTTHUMG00000137862	ENST00000268695.5:c.299C>A	16.37:g.88908325G>T	ENSP00000268695:p.Thr100Asn		Q86VK3	Missense_Mutation	SNP	ENST00000268695.5	37	CCDS10970.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.72|14.72	2.618854|2.618854	0.46736|0.46736	.|.	.|.	ENSG00000141012|ENSG00000141012	ENST00000439266|ENST00000268695	.|D	.|0.91295	.|-2.82	5.24|5.24	4.28|4.28	0.50868|0.50868	.|Alkaline phosphatase-like, alpha/beta/alpha (1);Sulfatase (1);Alkaline-phosphatase-like, core domain (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.91157|0.91157	0.7215|0.7215	L|L	0.39467|0.39467	1.215|1.215	0.80722|0.80722	D|D	1|1	.|D;D	.|0.71674	.|0.998;0.998	.|P;P	.|0.61275	.|0.886;0.886	D|D	0.88175|0.88175	0.2867|0.2867	6|10	0.87932|0.13108	D|T	0|0.6	.|.	16.2479|16.2479	0.82454|0.82454	0.0:0.1329:0.8671:0.0|0.0:0.1329:0.8671:0.0	.|.	.|100;100	.|B2R6P1;P34059	.|.;GALNS_HUMAN	T|N	59|100	.|ENSP00000268695:T100N	ENSP00000402127:P59T|ENSP00000268695:T100N	P|T	-|-	1|2	0|0	GALNS|GALNS	87435826|87435826	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.957000|0.957000	0.61999|0.61999	7.707000|7.707000	0.84623|0.84623	1.342000|1.342000	0.45619|0.45619	0.561000|0.561000	0.74099|0.74099	CCA|ACC		0.627	GALNS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000269543.1			
GLE1	2733	hgsc.bcm.edu	37	9	131267089	131267089	+	Missense_Mutation	SNP	C	C	G	rs150246404	byFrequency	TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr9:131267089C>G	ENST00000309971.4	+	1	111	c.5C>G	c.(4-6)cCg>cGg	p.P2R	GLE1_ENST00000539582.1_5'UTR|GLE1_ENST00000372770.4_Missense_Mutation_p.P2R	NM_001003722.1	NP_001003722.1	Q53GS7	GLE1_HUMAN	GLE1 RNA export mediator	2	Interaction with NUP155.				mRNA export from nucleus (GO:0006406)|poly(A)+ mRNA export from nucleus (GO:0016973)|protein transport (GO:0015031)	cytoplasm (GO:0005737)|extracellular space (GO:0005615)|membrane (GO:0016020)|nuclear pore (GO:0005643)|plasma membrane (GO:0005886)	identical protein binding (GO:0042802)			breast(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(3)|skin(2)|upper_aerodigestive_tract(1)	16						CCAACCATGCCGTCTGAGGGT	0.637													C|||	2	0.000399361	0.0	0.0	5008	,	,		16096	0.0		0.002	False		,,,				2504	0.0																0								C	ARG/PRO,ARG/PRO	0,4406		0,0,2203	78.0	74.0	75.0		5,5	4.3	1.0	9	dbSNP_134	75	6,8594	5.0+/-18.6	0,6,4294	yes	missense,missense	GLE1	NM_001003722.1,NM_001499.2	103,103	0,6,6497	GG,GC,CC		0.0698,0.0,0.0461	probably-damaging,probably-damaging	2/699,2/660	131267089	6,13000	2203	4300	6503	SO:0001583	missense	2733			AF058922	CCDS6904.1, CCDS35154.1	9q34.13	2014-09-17	2013-06-18	2007-10-04	ENSG00000119392	ENSG00000119392			4315	protein-coding gene	gene with protein product		603371	"""GLE1 (yeast homolog)-like, RNA export mediator"", ""GLE1 RNA export mediator-like (yeast)"", ""GLE1 RNA export mediator (yeast)"", ""lethal congenital contracture syndrome 1"", ""GLE1 RNA export mediator homolog (yeast)"""	GLE1L, LCCS1		9618489, 18204449	Standard	NM_001499		Approved	hGLE1	uc004bvj.3	Q53GS7	OTTHUMG00000020749	ENST00000309971.4:c.5C>G	9.37:g.131267089C>G	ENSP00000308622:p.Pro2Arg		O75458|Q53GT9|Q5VVU1|Q8NCP6|Q9UFL6	Missense_Mutation	SNP	ENST00000309971.4	37	CCDS35154.1	.	.	.	.	.	.	.	.	.	.	C	19.86	3.906407	0.72868	0.0	6.98E-4	ENSG00000119392	ENST00000309971;ENST00000372770	T;T	0.71222	-0.55;-0.14	5.21	4.31	0.51392	.	0.225709	0.44688	D	0.000432	T	0.66703	0.2816	M	0.66939	2.045	0.80722	D	1	B;B	0.24823	0.068;0.112	B;B	0.24974	0.026;0.057	T	0.67385	-0.5684	10	0.72032	D	0.01	-20.6583	8.6968	0.34301	0.1837:0.6617:0.1546:0.0	.	2;2	Q53GS7;Q53GS7-2	GLE1_HUMAN;.	R	2	ENSP00000308622:P2R;ENSP00000361856:P2R	ENSP00000308622:P2R	P	+	2	0	GLE1	130306910	1.000000	0.71417	1.000000	0.80357	0.861000	0.49209	3.679000	0.54634	1.423000	0.47198	0.561000	0.74099	CCG		0.637	GLE1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054456.1		NM_001003722	
GLG1	2734	hgsc.bcm.edu;ucsc.edu	37	16	74506246	74506246	+	Splice_Site	SNP	C	C	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr16:74506246C>T	ENST00000422840.2	-	14	2115		c.e14+1		GLG1_ENST00000447066.2_Splice_Site|GLG1_ENST00000205061.5_Splice_Site	NM_001145667.1	NP_001139139.1	Q92896	GSLG1_HUMAN	golgi glycoprotein 1						blood coagulation (GO:0007596)|bone morphogenesis (GO:0060349)|leukocyte migration (GO:0050900)|negative regulation of protein processing (GO:0010955)|negative regulation of transforming growth factor beta receptor signaling pathway (GO:0030512)|regulation of chondrocyte differentiation (GO:0032330)	extracellular matrix (GO:0031012)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	receptor binding (GO:0005102)			breast(2)|cervix(2)|endometrium(6)|kidney(8)|large_intestine(6)|lung(28)|ovary(3)|prostate(1)|skin(1)	57						ACATCACTTACGTGGCAGAAG	0.408																																																	0													109.0	105.0	106.0					16																	74506246		2198	4300	6498	SO:0001630	splice_region_variant	2734				CCDS32485.1, CCDS45526.1, CCDS45527.1	16q22-q23	2010-02-12	2010-02-12			ENSG00000090863			4316	protein-coding gene	gene with protein product		600753	"""golgi apparatus protein 1"""			8530051, 7531823	Standard	NM_012201		Approved	MG-160, ESL-1, CFR-1	uc002fcx.3	Q92896		ENST00000422840.2:c.2115+1G>A	16.37:g.74506246C>T			B7Z8Y4|D3DUJ7|Q13221|Q6P9D1	Splice_Site	SNP	ENST00000422840.2	37	CCDS45527.1	.	.	.	.	.	.	.	.	.	.	C	17.99	3.522361	0.64747	.	.	ENSG00000090863	ENST00000205061;ENST00000447066;ENST00000422840	.	.	.	5.77	5.77	0.91146	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	19.9946	0.97381	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	GLG1	73063747	1.000000	0.71417	0.998000	0.56505	0.541000	0.35023	7.417000	0.80156	2.728000	0.93425	0.591000	0.81541	.		0.408	GLG1-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000435750.1		NM_012201	Intron
GRB2	2885	hgsc.bcm.edu	37	17	73316550	73316550	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr17:73316550C>T	ENST00000392562.1	-	6	1335	c.553G>A	c.(553-555)Gtc>Atc	p.V185I	GRB2_ENST00000578961.1_Missense_Mutation_p.M128I|GRB2_ENST00000462266.1_5'UTR|GRB2_ENST00000316804.5_Missense_Mutation_p.V185I|GRB2_ENST00000392563.1_Missense_Mutation_p.V144I|GRB2_ENST00000392564.1_Missense_Mutation_p.V185I|GRB2_ENST00000316615.5_Missense_Mutation_p.V144I			P62993	GRB2_HUMAN	growth factor receptor-bound protein 2	185	SH3 2. {ECO:0000255|PROSITE- ProRule:PRU00192}.				aging (GO:0007568)|anatomical structure formation involved in morphogenesis (GO:0048646)|axon guidance (GO:0007411)|blood coagulation (GO:0007596)|branching involved in labyrinthine layer morphogenesis (GO:0060670)|cell-cell signaling (GO:0007267)|cellular response to ionizing radiation (GO:0071479)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|Fc-gamma receptor signaling pathway involved in phagocytosis (GO:0038096)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|leukocyte migration (GO:0050900)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|platelet activation (GO:0030168)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of reactive oxygen species metabolic process (GO:2000379)|protein heterooligomerization (GO:0051291)|Ras protein signal transduction (GO:0007265)|receptor internalization (GO:0031623)|regulation of MAPK cascade (GO:0043408)|signal transduction in response to DNA damage (GO:0042770)|T cell costimulation (GO:0031295)|viral process (GO:0016032)	cell-cell junction (GO:0005911)|COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Grb2-EGFR complex (GO:0070436)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|vesicle membrane (GO:0012506)	ephrin receptor binding (GO:0046875)|epidermal growth factor receptor binding (GO:0005154)|identical protein binding (GO:0042802)|insulin receptor substrate binding (GO:0043560)|neurotrophin TRKA receptor binding (GO:0005168)|poly(A) RNA binding (GO:0044822)|protein kinase binding (GO:0019901)|SH3 domain binding (GO:0017124)|SH3/SH2 adaptor activity (GO:0005070)			breast(2)|kidney(1)|large_intestine(3)|lung(7)|ovary(3)|skin(1)	17	all_cancers(13;5.44e-09)|all_epithelial(9;1.1e-09)|Breast(9;1.85e-09)|all_lung(278;0.222)		all cancers(21;1.09e-07)|Epithelial(20;1.23e-06)|Lung(188;0.185)		Pegademase bovine(DB00061)	TTATCCATGACATGGATAAAA	0.562																																																	0													110.0	116.0	114.0					17																	73316550		2203	4300	6503	SO:0001583	missense	2885				CCDS11721.1, CCDS11722.1	17q24-q25	2013-02-14			ENSG00000177885	ENSG00000177885		"""SH2 domain containing"""	4566	protein-coding gene	gene with protein product		108355					Standard	NM_002086		Approved	NCKAP2	uc002jnx.4	P62993	OTTHUMG00000134332	ENST00000392562.1:c.553G>A	17.37:g.73316550C>T	ENSP00000376345:p.Val185Ile		P29354|Q14450|Q63057|Q63059	Missense_Mutation	SNP	ENST00000392562.1	37	CCDS11721.1	.	.	.	.	.	.	.	.	.	.	C	21.8	4.201225	0.79015	.	.	ENSG00000177885	ENST00000316804;ENST00000392562;ENST00000392564;ENST00000392563;ENST00000316615	T;T;T;T;T	0.57107	0.42;0.42;0.42;0.42;0.42	5.45	5.45	0.79879	Src homology-3 domain (4);	0.000000	0.85682	D	0.000000	T	0.61274	0.2334	L	0.49350	1.555	0.80722	D	1	P;P	0.41475	0.751;0.59	B;P	0.49887	0.426;0.625	T	0.57412	-0.7816	10	0.42905	T	0.14	-34.617	19.4688	0.94954	0.0:1.0:0.0:0.0	.	144;185	P62993-2;P62993	.;GRB2_HUMAN	I	185;185;185;144;144	ENSP00000339007:V185I;ENSP00000376345:V185I;ENSP00000376347:V185I;ENSP00000376346:V144I;ENSP00000317360:V144I	ENSP00000317360:V144I	V	-	1	0	GRB2	70828145	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	5.892000	0.69790	2.838000	0.97847	0.561000	0.74099	GTC		0.562	GRB2-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259476.1			
HAUS1	115106	hgsc.bcm.edu;ucsc.edu	37	18	43708041	43708041	+	Splice_Site	SNP	G	G	A			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr18:43708041G>A	ENST00000282058.6	+	9	867	c.787G>A	c.(787-789)Gat>Aat	p.D263N	HAUS1_ENST00000588704.1_3'UTR|HAUS1_ENST00000585518.1_3'UTR	NM_138443.3	NP_612452.1	Q96CS2	HAUS1_HUMAN	HAUS augmin-like complex, subunit 1	263					centrosome organization (GO:0051297)|mitotic nuclear division (GO:0007067)|spindle assembly (GO:0051225)	centrosome (GO:0005813)|cytoplasm (GO:0005737)|HAUS complex (GO:0070652)|microtubule (GO:0005874)				endometrium(1)|kidney(1)|large_intestine(2)|lung(2)|ovary(1)	7						CTTCCTGTAGGATAGCATTGA	0.318																																					NSCLC(79;183 1423 5813 15597 38427)												0													98.0	84.0	89.0					18																	43708041		2203	4299	6502	SO:0001630	splice_region_variant	115106			AY360137	CCDS11928.1	18q21.1	2013-10-11	2009-04-20	2009-04-20	ENSG00000152240	ENSG00000152240		"""HAUS augmin-like complex subunits"""	25174	protein-coding gene	gene with protein product		608775	"""coiled-coil domain containing 5 (spindle associated)"""	CCDC5		19427217	Standard	NR_026978		Approved	HEI-C, HsT1461, FLJ40084	uc002lbu.3	Q96CS2	OTTHUMG00000132638	ENST00000282058.6:c.787-1G>A	18.37:g.43708041G>A			B2RDM7|Q8N837	Missense_Mutation	SNP	ENST00000282058.6	37	CCDS11928.1	.	.	.	.	.	.	.	.	.	.	G	5.840	0.339276	0.11069	.	.	ENSG00000152240	ENST00000282058	.	.	.	5.06	3.93	0.45458	.	0.257668	0.44097	D	0.000492	T	0.25044	0.0608	N	0.16066	0.365	0.34416	D	0.696915	B	0.09022	0.002	B	0.09377	0.004	T	0.22977	-1.0201	8	.	.	.	-11.8307	6.3736	0.21495	0.1629:0.0:0.8371:0.0	.	263	Q96CS2	HAUS1_HUMAN	N	263	.	.	D	+	1	0	HAUS1	41962039	1.000000	0.71417	0.993000	0.49108	0.336000	0.28762	1.921000	0.40035	2.504000	0.84457	0.585000	0.79938	GAT		0.318	HAUS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255885.1		NM_138443	Missense_Mutation
HELQ	113510	hgsc.bcm.edu	37	4	84350864	84350864	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr4:84350864C>T	ENST00000295488.3	-	12	2493	c.2331G>A	c.(2329-2331)atG>atA	p.M777I	HELQ_ENST00000510985.1_Missense_Mutation_p.M710I	NM_133636.2	NP_598375	Q8TDG4	HELQ_HUMAN	helicase, POLQ-like	777					double-strand break repair via homologous recombination (GO:0000724)	nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|nucleic acid binding (GO:0003676)			breast(1)|cervix(2)|endometrium(2)|kidney(2)|large_intestine(10)|lung(17)|ovary(2)|skin(2)	38						ATGTACCATTCATGAAATGAT	0.338								Other identified genes with known or suspected DNA repair function																																									0													43.0	40.0	41.0					4																	84350864		2199	4297	6496	SO:0001583	missense	113510			AF436845	CCDS3603.1, CCDS75158.1	4q21.23	2009-02-26			ENSG00000163312	ENSG00000163312			18536	protein-coding gene	gene with protein product		606769				11751861	Standard	XM_005262711		Approved	Hel308	uc003hom.3	Q8TDG4	OTTHUMG00000130423	ENST00000295488.3:c.2331G>A	4.37:g.84350864C>T	ENSP00000295488:p.Met777Ile		Q05DF9|Q502W9|Q659B8|Q6ZQX4|Q6ZTS4|Q96EX7	Missense_Mutation	SNP	ENST00000295488.3	37	CCDS3603.1	.	.	.	.	.	.	.	.	.	.	C	13.85	2.359008	0.41801	.	.	ENSG00000163312	ENST00000295488;ENST00000510985	T;T	0.40476	1.03;1.03	5.22	5.22	0.72569	.	0.098933	0.64402	D	0.000002	T	0.34832	0.0911	L	0.52266	1.64	0.53005	D	0.999964	P;B	0.41159	0.74;0.069	B;B	0.35931	0.214;0.032	T	0.11690	-1.0577	10	0.22706	T	0.39	-9.9733	13.7152	0.62691	0.1541:0.8459:0.0:0.0	.	710;777	E3W980;Q8TDG4	.;HELQ_HUMAN	I	777;710	ENSP00000295488:M777I;ENSP00000424539:M710I	ENSP00000295488:M777I	M	-	3	0	HELQ	84569888	0.996000	0.38824	0.996000	0.52242	0.778000	0.44026	3.107000	0.50329	2.420000	0.82092	0.467000	0.42956	ATG		0.338	HELQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252810.1		NM_133636	
HPGDS	27306	hgsc.bcm.edu;ucsc.edu	37	4	95229888	95229888	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr4:95229888G>A	ENST00000295256.5	-	4	323	c.233C>T	c.(232-234)gCt>gTt	p.A78V	HPGDS_ENST00000514774.1_5'UTR	NM_014485.2	NP_055300.1	O60760	HPGDS_HUMAN	hematopoietic prostaglandin D synthase	78	GST N-terminal.				arachidonic acid metabolic process (GO:0019369)|cyclooxygenase pathway (GO:0019371)|glutathione derivative biosynthetic process (GO:1901687)|locomotory behavior (GO:0007626)|prostaglandin metabolic process (GO:0006693)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	cytoplasm (GO:0005737)|cytosol (GO:0005829)	calcium ion binding (GO:0005509)|glutathione transferase activity (GO:0004364)|magnesium ion binding (GO:0000287)|prostaglandin-D synthase activity (GO:0004667)|protein homodimerization activity (GO:0042803)			breast(1)|cervix(1)|lung(3)|ovary(1)|urinary_tract(1)	7					Glutathione(DB00143)	TGTGTTTCCAGCCAAATCTGT	0.343																																					Colon(86;1802 1843 17863 46794)												0													134.0	125.0	128.0					4																	95229888		2203	4300	6503	SO:0001583	missense	27306			D82073	CCDS3640.1	4q22.2	2012-06-21			ENSG00000163106	ENSG00000163106		"""Glutathione S-transferases / Soluble"""	17890	protein-coding gene	gene with protein product	"""glutathione S-transferase sigma"""	602598				9323136, 9353279, 11672424	Standard	XM_005262932		Approved	GSTS, PGDS, H-PGDS, PGD2, GSTS1-1	uc003hte.1	O60760	OTTHUMG00000130974	ENST00000295256.5:c.233C>T	4.37:g.95229888G>A	ENSP00000295256:p.Ala78Val		Q6FHT9	Missense_Mutation	SNP	ENST00000295256.5	37	CCDS3640.1	.	.	.	.	.	.	.	.	.	.	G	6.912	0.537881	0.13188	.	.	ENSG00000163106	ENST00000295256	T	0.02631	4.22	5.43	5.43	0.79202	Glutathione S-transferase, C-terminal-like (1);Glutathione S-transferase, N-terminal (1);Thioredoxin-like fold (1);	0.156225	0.45361	D	0.000380	T	0.03783	0.0107	L	0.48986	1.54	0.45108	D	0.998129	P	0.50943	0.94	B	0.42625	0.393	T	0.57522	-0.7797	10	0.19590	T	0.45	.	10.2053	0.43109	0.0899:0.0:0.9101:0.0	.	78	O60760	HPGDS_HUMAN	V	78	ENSP00000295256:A78V	ENSP00000295256:A78V	A	-	2	0	HPGDS	95448911	1.000000	0.71417	1.000000	0.80357	0.973000	0.67179	4.620000	0.61226	2.538000	0.85594	0.561000	0.74099	GCT		0.343	HPGDS-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253587.1		NM_014485	
ICAM1	3383	hgsc.bcm.edu	37	19	10394734	10394734	+	Silent	SNP	T	T	C			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr19:10394734T>C	ENST00000264832.3	+	4	988	c.663T>C	c.(661-663)ctT>ctC	p.L221L	ICAM4_ENST00000393717.2_5'Flank|ICAM1_ENST00000423829.2_Intron|ICAM4_ENST00000340992.4_5'Flank|CTD-2369P2.8_ENST00000589379.1_RNA|ICAM4_ENST00000380770.3_5'Flank|CTD-2369P2.5_ENST00000592893.1_RNA	NM_000201.2	NP_000192.2	P05362	ICAM1_HUMAN	intercellular adhesion molecule 1	221					adhesion of symbiont to host (GO:0044406)|cell adhesion (GO:0007155)|cell adhesion mediated by integrin (GO:0033627)|cell aging (GO:0007569)|cellular response to alkaloid (GO:0071312)|cellular response to glucose stimulus (GO:0071333)|cellular response to hypoxia (GO:0071456)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to nutrient levels (GO:0031669)|cellular response to tumor necrosis factor (GO:0071356)|cytokine-mediated signaling pathway (GO:0019221)|establishment of endothelial barrier (GO:0061028)|extracellular matrix organization (GO:0030198)|heterophilic cell-cell adhesion (GO:0007157)|interferon-gamma-mediated signaling pathway (GO:0060333)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|membrane to membrane docking (GO:0022614)|negative regulation of calcium ion transport (GO:0051926)|negative regulation of endothelial cell apoptotic process (GO:2000352)|negative regulation of extrinsic apoptotic signaling pathway via death domain receptors (GO:1902042)|ovarian follicle development (GO:0001541)|positive regulation of actin filament polymerization (GO:0030838)|positive regulation of cellular extravasation (GO:0002693)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of Rho GTPase activity (GO:0032321)|positive regulation of vasoconstriction (GO:0045907)|receptor-mediated virion attachment to host cell (GO:0046813)|regulation of cell adhesion (GO:0030155)|regulation of cell shape (GO:0008360)|regulation of immune response (GO:0050776)|regulation of leukocyte mediated cytotoxicity (GO:0001910)|regulation of ruffle assembly (GO:1900027)|response to amino acid (GO:0043200)|response to amphetamine (GO:0001975)|response to copper ion (GO:0046688)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to gonadotropin (GO:0034698)|response to ionizing radiation (GO:0010212)|response to organic cyclic compound (GO:0014070)|response to sulfur dioxide (GO:0010477)|T cell activation via T cell receptor contact with antigen bound to MHC molecule on antigen presenting cell (GO:0002291)|T cell antigen processing and presentation (GO:0002457)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	integrin binding (GO:0005178)|receptor activity (GO:0004872)|transmembrane signaling receptor activity (GO:0004888)|virus receptor activity (GO:0001618)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(4)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14			OV - Ovarian serous cystadenocarcinoma(20;1.39e-09)|Epithelial(33;2.81e-06)|all cancers(31;6.56e-06)		Hyaluronan(DB08818)|Natalizumab(DB00108)	CCCCACAACTTGTCAGCCCCC	0.637																																																	0													77.0	81.0	80.0					19																	10394734		2203	4300	6503	SO:0001819	synonymous_variant	3383				CCDS12231.1	19p13.3-p13.2	2014-01-30	2008-07-18			ENSG00000090339		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Endogenous ligands"""	5344	protein-coding gene	gene with protein product	"""human rhinovirus receptor"""	147840				2453850, 3871395	Standard	NM_000201		Approved	BB2, CD54	uc002mnq.2	P05362		ENST00000264832.3:c.663T>C	19.37:g.10394734T>C			B2R6M3|Q5NKV7|Q96B50	Silent	SNP	ENST00000264832.3	37	CCDS12231.1																																																																																				0.637	ICAM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000451207.1			
LRRC55	219527	hgsc.bcm.edu	37	11	56950122	56950122	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr11:56950122A>C	ENST00000497933.1	+	1	902	c.755A>C	c.(754-756)aAg>aCg	p.K252T		NM_001005210.2	NP_001005210.1	Q6ZSA7	LRC55_HUMAN	leucine rich repeat containing 55	222	LRRCT.				ion transport (GO:0006811)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				endometrium(3)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(2)|lung(13)|ovary(2)|skin(2)	25						CCCCTGCTGAAGTGGCTGCGA	0.617																																																	0													86.0	81.0	83.0					11																	56950122		2201	4296	6497	SO:0001583	missense	219527				CCDS31539.1	11q12.1	2008-02-05			ENSG00000183908	ENSG00000183908			32324	protein-coding gene	gene with protein product		615213					Standard	NM_001005210		Approved	FLJ45686	uc001njl.2	Q6ZSA7	OTTHUMG00000159309	ENST00000497933.1:c.755A>C	11.37:g.56950122A>C	ENSP00000419542:p.Lys252Thr		A7E2U7|B2RN81	Missense_Mutation	SNP	ENST00000497933.1	37	CCDS31539.1	.	.	.	.	.	.	.	.	.	.	A	13.93	2.384572	0.42308	.	.	ENSG00000183908	ENST00000497933	T	0.02323	4.34	5.53	4.37	0.52481	Cysteine-rich flanking region, C-terminal (1);	0.098264	0.45126	N	0.000397	T	0.02156	0.0067	N	0.05351	-0.065	0.33143	D	0.544668	B	0.22003	0.063	B	0.30495	0.116	T	0.39313	-0.9620	10	0.20519	T	0.43	.	11.5956	0.50970	0.8504:0.1496:0.0:0.0	.	222	Q6ZSA7	LRC55_HUMAN	T	252	ENSP00000419542:K252T	ENSP00000419542:K252T	K	+	2	0	LRRC55	56706698	1.000000	0.71417	1.000000	0.80357	0.923000	0.55619	3.243000	0.51392	0.898000	0.36418	0.459000	0.35465	AAG		0.617	LRRC55-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000354503.2		NM_001005210	
MAP4K5	11183	hgsc.bcm.edu;ucsc.edu	37	14	50952347	50952348	+	Frame_Shift_Del	DEL	AT	AT	-			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr14:50952347_50952348delAT	ENST00000013125.4	-	5	588_589	c.270_271delAT	c.(268-273)ctatggfs	p.W91fs	MAP4K5_ENST00000557578.1_5'UTR	NM_006575.4|NM_198794.2	NP_006566.2|NP_942089.1	Q9Y4K4	M4K5_HUMAN	mitogen-activated protein kinase kinase kinase kinase 5	91	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of JUN kinase activity (GO:0007257)|intracellular signal transduction (GO:0035556)|protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|small GTPase regulator activity (GO:0005083)			endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	15	all_epithelial(31;0.000415)|Breast(41;0.0102)					ATACAAATCCATAGTTTTTCCC	0.322																																																	0																																										SO:0001589	frameshift_variant	11183			U77129		14q11.2-q21	2011-06-09				ENSG00000012983		"""Mitogen-activated protein kinase cascade / Kinase kinase kinase kinases"""	6867	protein-coding gene	gene with protein product	"""germinal center kinase-related"""	604923				9038372, 8274451	Standard	NM_198794		Approved	KHS1, GCKR, KHS	uc001wyb.3	Q9Y4K4		ENST00000013125.4:c.270_271delAT	14.37:g.50952347_50952348delAT	ENSP00000013125:p.Trp91fs		Q8IYF6	Frame_Shift_Del	DEL	ENST00000013125.4	37																																																																																					0.322	MAP4K5-001	KNOWN	non_canonical_conserved|basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000410880.1		NM_006575	
MAPK9	5601	hgsc.bcm.edu	37	5	179676014	179676014	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr5:179676014C>T	ENST00000452135.2	-	6	873	c.575G>A	c.(574-576)cGg>cAg	p.R192Q	MAPK9_ENST00000347470.4_Missense_Mutation_p.R192Q|MAPK9_ENST00000455781.1_Missense_Mutation_p.R192Q|MAPK9_ENST00000343111.6_Missense_Mutation_p.R192Q|MAPK9_ENST00000425491.2_Missense_Mutation_p.R192Q|MAPK9_ENST00000393360.3_Missense_Mutation_p.R192Q|MAPK9_ENST00000524170.1_5'UTR|MAPK9_ENST00000397072.3_3'UTR|MAPK9_ENST00000539014.1_Missense_Mutation_p.R192Q			P45984	MK09_HUMAN	mitogen-activated protein kinase 9	192	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cellular response to growth factor stimulus (GO:0071363)|cellular response to interleukin-1 (GO:0071347)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to tumor necrosis factor (GO:0071356)|cellular response to UV (GO:0034644)|central nervous system development (GO:0007417)|Fc-epsilon receptor signaling pathway (GO:0038095)|innate immune response (GO:0045087)|JNK cascade (GO:0007254)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|neuron projection development (GO:0031175)|positive regulation of apoptotic process (GO:0043065)|positive regulation of apoptotic signaling pathway (GO:2001235)|positive regulation of cell morphogenesis involved in differentiation (GO:0010770)|positive regulation of chemokine production (GO:0032722)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of nitric oxide biosynthetic process (GO:0045429)|positive regulation of nitric-oxide synthase biosynthetic process (GO:0051770)|positive regulation of prostaglandin biosynthetic process (GO:0031394)|positive regulation of prostaglandin secretion (GO:0032308)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of transcription, DNA-templated (GO:0045893)|protein targeting to mitochondrion (GO:0006626)|regulation of JNK cascade (GO:0046328)|regulation of protein ubiquitination (GO:0031396)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)|release of cytochrome c from mitochondria (GO:0001836)|response to amine (GO:0014075)|response to cadmium ion (GO:0046686)|response to drug (GO:0042493)|response to mechanical stimulus (GO:0009612)|response to stress (GO:0006950)|response to toxic substance (GO:0009636)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|cysteine-type endopeptidase activator activity involved in apoptotic process (GO:0008656)|JUN kinase activity (GO:0004705)|transcription factor binding (GO:0008134)	p.R192L(4)		central_nervous_system(2)|endometrium(5)|kidney(1)|large_intestine(5)|lung(10)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26	all_cancers(89;6.54e-05)|all_epithelial(37;1.22e-05)|Renal(175;0.000269)|Lung NSC(126;0.00199)|all_lung(126;0.00351)|Breast(19;0.137)	all_cancers(40;0.0236)|Medulloblastoma(196;0.0133)|all_neural(177;0.0199)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			TTCGGGCGCCCGGTAGTACCG	0.552																																																	4	Substitution - Missense(4)	lung(4)											218.0	230.0	226.0					5																	179676014		2203	4300	6503	SO:0001583	missense	5601			U09759	CCDS4453.1, CCDS4454.1, CCDS43409.1, CCDS43410.1, CCDS47356.1	5q35	2011-06-09			ENSG00000050748	ENSG00000050748	2.7.11.1	"""Mitogen-activated protein kinase cascade / Kinases"""	6886	protein-coding gene	gene with protein product	"""Jun kinase"""	602896		PRKM9		8001819	Standard	NM_002752		Approved	JNK2, p54a, SAPK	uc003mls.4	P45984	OTTHUMG00000130934	ENST00000452135.2:c.575G>A	5.37:g.179676014C>T	ENSP00000394560:p.Arg192Gln		A8K0S3|B5BU66|B5M0B4|D3DWQ8|D3DWQ9|Q15708|Q15710|Q15711|Q8N5C5	Missense_Mutation	SNP	ENST00000452135.2	37	CCDS4453.1	.	.	.	.	.	.	.	.	.	.	C	27.9	4.870126	0.91587	.	.	ENSG00000050748	ENST00000452135;ENST00000393360;ENST00000455781;ENST00000343111;ENST00000347470;ENST00000425491;ENST00000539014	D;D;D;D;D;D;D	0.83992	-1.79;-1.79;-1.79;-1.79;-1.79;-1.79;-1.79	5.59	4.73	0.59995	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.070647	0.56097	D	0.000024	D	0.90909	0.7143	M	0.85777	2.775	0.80722	D	1	D;P;D;D;D	0.76494	0.999;0.866;0.993;0.98;0.998	D;B;P;B;P	0.65233	0.933;0.309;0.504;0.4;0.869	D	0.92319	0.5864	10	0.87932	D	0	-8.9828	14.4306	0.67246	0.0:0.9295:0.0:0.0705	.	192;192;192;192;192	P45984-5;P45984-4;P45984-3;P45984-2;P45984	.;.;.;.;MK09_HUMAN	Q	192	ENSP00000394560:R192Q;ENSP00000377028:R192Q;ENSP00000389338:R192Q;ENSP00000345524:R192Q;ENSP00000321410:R192Q;ENSP00000397422:R192Q;ENSP00000443149:R192Q	ENSP00000345524:R192Q	R	-	2	0	MAPK9	179608620	1.000000	0.71417	0.977000	0.42913	0.498000	0.33706	7.711000	0.84669	1.376000	0.46267	0.650000	0.86243	CGG		0.552	MAPK9-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000253530.3			
MMAA	166785	hgsc.bcm.edu;ucsc.edu	37	4	146560425	146560425	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr4:146560425A>C	ENST00000281317.5	+	2	1344	c.134A>C	c.(133-135)aAt>aCt	p.N45T	MMAA_ENST00000541599.1_5'UTR	NM_172250.2	NP_758454.1	Q8IVH4	MMAA_HUMAN	methylmalonic aciduria (cobalamin deficiency) cblA type	45					cellular lipid metabolic process (GO:0044255)|cobalamin biosynthetic process (GO:0009236)|cobalamin metabolic process (GO:0009235)|fatty acid beta-oxidation (GO:0006635)|short-chain fatty acid catabolic process (GO:0019626)|small molecule metabolic process (GO:0044281)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	mitochondrial matrix (GO:0005759)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(6)|lung(8)|ovary(1)	17	all_hematologic(180;0.151)				Cyanocobalamin(DB00115)|Hydroxocobalamin(DB00200)	CAGCCGTTTAATTCTCTTGGA	0.418																																																	0													142.0	138.0	139.0					4																	146560425		2203	4300	6503	SO:0001583	missense	166785			AF524841	CCDS3766.1	4q31.1	2011-05-12	2005-07-11			ENSG00000151611			18871	protein-coding gene	gene with protein product		607481	"""methylmalonic aciduria (cobalamin deficiency) type A"""			12438653	Standard	NM_172250		Approved	cblA	uc003ikh.4	Q8IVH4		ENST00000281317.5:c.134A>C	4.37:g.146560425A>C	ENSP00000281317:p.Asn45Thr		B3KX40|Q495G7	Missense_Mutation	SNP	ENST00000281317.5	37	CCDS3766.1	.	.	.	.	.	.	.	.	.	.	a	16.35	3.098559	0.56183	.	.	ENSG00000151611	ENST00000281317;ENST00000537246	D	0.91686	-2.89	5.42	-0.142	0.13448	.	1.140130	0.06315	N	0.703327	D	0.87136	0.6102	L	0.43152	1.355	0.09310	N	0.999999	B;B	0.06786	0.0;0.001	B;B	0.04013	0.0;0.001	T	0.71636	-0.4533	10	0.39692	T	0.17	-23.2473	5.6152	0.17428	0.5628:0.2467:0.1905:0.0	.	45;45	Q8IVH4;D6RIS5	MMAA_HUMAN;.	T	45	ENSP00000281317:N45T	ENSP00000281317:N45T	N	+	2	0	MMAA	146779875	0.000000	0.05858	0.002000	0.10522	0.860000	0.49131	-0.804000	0.04535	-0.159000	0.11021	0.533000	0.62120	AAT		0.418	MMAA-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000364668.2			
NFKBIB	4793	hgsc.bcm.edu	37	19	39390845	39390845	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr19:39390845G>T	ENST00000313582.5	+	1	207	c.173G>T	c.(172-174)gGg>gTg	p.G58V	SIRT2_ENST00000249396.7_5'Flank|NFKBIB_ENST00000392079.3_Missense_Mutation_p.G45W|SIRT2_ENST00000481381.1_5'Flank|SIRT2_ENST00000358931.5_5'Flank|NFKBIB_ENST00000572515.1_Missense_Mutation_p.G58V|SIRT2_ENST00000392081.2_5'Flank	NM_002503.4	NP_002494.2	Q15653	IKBB_HUMAN	nuclear factor of kappa light polypeptide gene enhancer in B-cells inhibitor, beta	58					innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of NF-kappaB transcription factor activity (GO:0051092)|positive regulation of type I interferon production (GO:0032481)|signal transduction (GO:0007165)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|transcription, DNA-templated (GO:0006351)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|nucleus (GO:0005634)	signal transducer activity (GO:0004871)|transcription coactivator activity (GO:0003713)			endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)	8	all_cancers(60;4.39e-06)|Ovarian(47;0.0454)		Lung(45;0.000419)|LUSC - Lung squamous cell carcinoma(53;0.000554)			ACTGAGGATGGGGACACGTGA	0.637																																					Pancreas(165;1492 2005 6979 7739 34483)												0													15.0	17.0	17.0					19																	39390845		2202	4299	6501	SO:0001583	missense	4793			L40407	CCDS12524.1, CCDS74362.1	19q13.1	2013-01-10				ENSG00000104825		"""Ankyrin repeat domain containing"""	7798	protein-coding gene	gene with protein product		604495				9763672	Standard	NM_002503		Approved	IKBB, TRIP9	uc002ojw.3	Q15653		ENST00000313582.5:c.173G>T	19.37:g.39390845G>T	ENSP00000312988:p.Gly58Val		A8K3F4|Q96BJ7	Missense_Mutation	SNP	ENST00000313582.5	37	CCDS12524.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.24|18.24	3.579196|3.579196	0.65878|0.65878	.|.	.|.	ENSG00000104825|ENSG00000104825	ENST00000509705;ENST00000313582|ENST00000392079	T|T	0.69561|0.52057	-0.41|0.68	5.08|5.08	5.08|5.08	0.68730|0.68730	Ankyrin repeat-containing domain (3);|.	0.000000|0.000000	0.51477|0.51477	D|D	0.000089|0.000089	T|T	0.67915|0.67915	0.2944|0.2944	M|M	0.88377|0.88377	2.95|2.95	0.31050|0.31050	N|N	0.715329|0.715329	D;D|D	0.89917|0.63046	1.0;1.0|0.992	D;D|P	0.97110|0.56960	0.999;1.0|0.81	T|T	0.72906|0.72906	-0.4150|-0.4150	10|10	0.87932|0.37606	D|T	0|0.19	-26.6701|-26.6701	15.4937|15.4937	0.75632|0.75632	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	81;58|45	Q59EM7;Q15653|G5E9C2	.;IKBB_HUMAN|.	V|W	81;58|45	ENSP00000312988:G58V|ENSP00000375929:G45W	ENSP00000312988:G58V|ENSP00000375929:G45W	G|G	+|+	2|1	0|0	NFKBIB|NFKBIB	44082685|44082685	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	5.302000|5.302000	0.65733|0.65733	2.663000|2.663000	0.90544|0.90544	0.609000|0.609000	0.83330|0.83330	GGG|GGG		0.637	NFKBIB-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438155.1		NM_002503	
NOTCH1	4851	hgsc.bcm.edu	37	9	139399349	139399349	+	Silent	SNP	G	G	A	rs558708604		TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr9:139399349G>A	ENST00000277541.6	-	26	4869	c.4794C>T	c.(4792-4794)cgC>cgT	p.R1598R		NM_017617.3	NP_060087.3	P46531	NOTC1_HUMAN	notch 1	1598					anagen (GO:0042640)|aortic valve morphogenesis (GO:0003180)|apoptotic process involved in embryonic digit morphogenesis (GO:1902263)|arterial endothelial cell differentiation (GO:0060842)|atrioventricular node development (GO:0003162)|atrioventricular valve morphogenesis (GO:0003181)|auditory receptor cell fate commitment (GO:0009912)|axonogenesis (GO:0007409)|branching morphogenesis of an epithelial tube (GO:0048754)|cardiac atrium morphogenesis (GO:0003209)|cardiac chamber formation (GO:0003207)|cardiac epithelial to mesenchymal transition (GO:0060317)|cardiac left ventricle morphogenesis (GO:0003214)|cardiac muscle cell proliferation (GO:0060038)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac right atrium morphogenesis (GO:0003213)|cardiac right ventricle formation (GO:0003219)|cardiac septum morphogenesis (GO:0060411)|cardiac vascular smooth muscle cell development (GO:0060948)|cardiac ventricle morphogenesis (GO:0003208)|cell fate specification (GO:0001708)|cell migration involved in endocardial cushion formation (GO:0003273)|cellular response to follicle-stimulating hormone stimulus (GO:0071372)|cellular response to vascular endothelial growth factor stimulus (GO:0035924)|cilium morphogenesis (GO:0060271)|collecting duct development (GO:0072044)|compartment pattern specification (GO:0007386)|coronary artery morphogenesis (GO:0060982)|coronary vein morphogenesis (GO:0003169)|determination of left/right symmetry (GO:0007368)|distal tubule development (GO:0072017)|embryonic hindlimb morphogenesis (GO:0035116)|endocardial cell differentiation (GO:0060956)|endocardial cushion morphogenesis (GO:0003203)|endocardium development (GO:0003157)|endocardium morphogenesis (GO:0003160)|endoderm development (GO:0007492)|epithelial to mesenchymal transition (GO:0001837)|epithelial to mesenchymal transition involved in endocardial cushion formation (GO:0003198)|forebrain development (GO:0030900)|foregut morphogenesis (GO:0007440)|gene expression (GO:0010467)|glial cell differentiation (GO:0010001)|glomerular mesangial cell development (GO:0072144)|growth involved in heart morphogenesis (GO:0003241)|hair follicle morphogenesis (GO:0031069)|heart development (GO:0007507)|heart looping (GO:0001947)|heart trabecula morphogenesis (GO:0061384)|humoral immune response (GO:0006959)|immune response (GO:0006955)|in utero embryonic development (GO:0001701)|inflammatory response to antigenic stimulus (GO:0002437)|interleukin-4 secretion (GO:0072602)|keratinocyte differentiation (GO:0030216)|left/right axis specification (GO:0070986)|liver development (GO:0001889)|lung development (GO:0030324)|mesenchymal cell development (GO:0014031)|mitral valve formation (GO:0003192)|negative regulation of anoikis (GO:2000811)|negative regulation of BMP signaling pathway (GO:0030514)|negative regulation of calcium ion-dependent exocytosis (GO:0045955)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of catalytic activity (GO:0043086)|negative regulation of cell migration involved in sprouting angiogenesis (GO:0090051)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-substrate adhesion (GO:0010812)|negative regulation of endothelial cell chemotaxis (GO:2001027)|negative regulation of glial cell proliferation (GO:0060253)|negative regulation of myoblast differentiation (GO:0045662)|negative regulation of myotube differentiation (GO:0010832)|negative regulation of neurogenesis (GO:0050768)|negative regulation of oligodendrocyte differentiation (GO:0048715)|negative regulation of ossification (GO:0030279)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of photoreceptor cell differentiation (GO:0046533)|negative regulation of pro-B cell differentiation (GO:2000974)|negative regulation of stem cell differentiation (GO:2000737)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neural tube development (GO:0021915)|neuronal stem cell maintenance (GO:0097150)|Notch receptor processing (GO:0007220)|Notch signaling involved in heart development (GO:0061314)|Notch signaling pathway (GO:0007219)|Notch signaling pathway involved in regulation of secondary heart field cardioblast proliferation (GO:0003270)|pericardium morphogenesis (GO:0003344)|positive regulation of apoptotic process (GO:0043065)|positive regulation of astrocyte differentiation (GO:0048711)|positive regulation of BMP signaling pathway (GO:0030513)|positive regulation of cardiac muscle cell proliferation (GO:0060045)|positive regulation of cell migration (GO:0030335)|positive regulation of cell proliferation (GO:0008284)|positive regulation of epithelial cell proliferation (GO:0050679)|positive regulation of epithelial to mesenchymal transition (GO:0010718)|positive regulation of JAK-STAT cascade (GO:0046427)|positive regulation of keratinocyte differentiation (GO:0045618)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061419)|positive regulation of transcription of Notch receptor target (GO:0007221)|positive regulation of transcription, DNA-templated (GO:0045893)|prostate gland epithelium morphogenesis (GO:0060740)|pulmonary valve morphogenesis (GO:0003184)|regulation of epithelial cell proliferation involved in prostate gland development (GO:0060768)|regulation of extracellular matrix assembly (GO:1901201)|regulation of somitogenesis (GO:0014807)|regulation of transcription from RNA polymerase II promoter involved in myocardial precursor cell differentiation (GO:0003256)|regulation of transcription, DNA-templated (GO:0006355)|response to muramyl dipeptide (GO:0032495)|secretory columnal luminar epithelial cell differentiation involved in prostate glandular acinus development (GO:0060528)|skeletal muscle cell differentiation (GO:0035914)|somatic stem cell division (GO:0048103)|sprouting angiogenesis (GO:0002040)|transcription initiation from RNA polymerase II promoter (GO:0006367)|tube formation (GO:0035148)|vasculogenesis involved in coronary vascular morphogenesis (GO:0060979)|venous endothelial cell differentiation (GO:0060843)|ventricular septum morphogenesis (GO:0060412)|ventricular trabecula myocardium morphogenesis (GO:0003222)	cell surface (GO:0009986)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|extracellular region (GO:0005576)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)|MAML1-RBP-Jkappa- ICN1 complex (GO:0002193)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)|chromatin DNA binding (GO:0031490)|core promoter binding (GO:0001047)|enzyme binding (GO:0019899)|enzyme inhibitor activity (GO:0004857)|receptor activity (GO:0004872)|RNA polymerase II transcription factor binding transcription factor activity involved in positive regulation of transcription (GO:0001190)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)			breast(16)|central_nervous_system(17)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1183)|kidney(4)|large_intestine(1)|lung(57)|oesophagus(2)|ovary(3)|pancreas(1)|prostate(3)|skin(21)|upper_aerodigestive_tract(39)|urinary_tract(3)	1359	all_cancers(76;0.223)	Myeloproliferative disorder(178;0.0511)		OV - Ovarian serous cystadenocarcinoma(145;5.34e-06)|Epithelial(140;7.77e-06)		TGTGCAGCACGCGGCTGAGCT	0.662			"""T, Mis, O"""	TRB@	T-ALL					HNSCC(8;0.001)																														Dom	yes		9	9q34.3	4851	"""Notch homolog 1, translocation-associated (Drosophila) (TAN1)"""		L	0													17.0	23.0	21.0					9																	139399349		2158	4262	6420	SO:0001819	synonymous_variant	4851			AF308602	CCDS43905.1	9q34.3	2013-01-10	2010-06-24		ENSG00000148400	ENSG00000148400		"""Ankyrin repeat domain containing"""	7881	protein-coding gene	gene with protein product		190198	"""Notch (Drosophila) homolog 1 (translocation-associated)"", ""Notch homolog 1, translocation-associated (Drosophila)"""	TAN1		1831692	Standard	NM_017617		Approved		uc004chz.3	P46531	OTTHUMG00000020935	ENST00000277541.6:c.4794C>T	9.37:g.139399349G>A			Q59ED8|Q5SXM3	Silent	SNP	ENST00000277541.6	37	CCDS43905.1																																																																																				0.662	NOTCH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000055087.1		NM_017617	
NPR1	4881	hgsc.bcm.edu	37	1	153660245	153660246	+	Frame_Shift_Del	DEL	GT	GT	-			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	GT	GT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr1:153660245_153660246delGT	ENST00000368680.3	+	14	2700_2701	c.2228_2229delGT	c.(2227-2229)ggtfs	p.G743fs		NM_000906.3	NP_000897.3	P16066	ANPRA_HUMAN	natriuretic peptide receptor 1	743	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				body fluid secretion (GO:0007589)|cell surface receptor signaling pathway (GO:0007166)|cGMP biosynthetic process (GO:0006182)|dopamine metabolic process (GO:0042417)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cell growth (GO:0030308)|negative regulation of smooth muscle cell proliferation (GO:0048662)|positive regulation of cGMP biosynthetic process (GO:0030828)|positive regulation of renal sodium excretion (GO:0035815)|positive regulation of urine volume (GO:0035810)|receptor guanylyl cyclase signaling pathway (GO:0007168)|regulation of blood pressure (GO:0008217)|regulation of blood vessel size (GO:0050880)|regulation of vascular permeability (GO:0043114)|regulation of vasodilation (GO:0042312)	integral component of plasma membrane (GO:0005887)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|G-protein coupled peptide receptor activity (GO:0008528)|GTP binding (GO:0005525)|guanylate cyclase activity (GO:0004383)|hormone binding (GO:0042562)|natriuretic peptide receptor activity (GO:0016941)|peptide hormone binding (GO:0017046)|protein kinase activity (GO:0004672)			NS(1)|breast(1)|endometrium(2)|kidney(1)|large_intestine(8)|liver(1)|lung(17)|ovary(4)|prostate(2)|skin(3)|stomach(1)|upper_aerodigestive_tract(1)	42	all_lung(78;3.75e-32)|Lung NSC(65;1.37e-30)|Hepatocellular(266;0.0877)|Melanoma(130;0.199)		LUSC - Lung squamous cell carcinoma(543;0.151)		Amyl Nitrite(DB01612)|Erythrityl Tetranitrate(DB01613)|Isosorbide Dinitrate(DB00883)|Nesiritide(DB04899)|Nitroglycerin(DB00727)|Nitroprusside(DB00325)	CACGTGGAAGGTTTGGACCTGA	0.609																																					Pancreas(141;1349 1870 15144 15830 40702)												0																																										SO:0001589	frameshift_variant	4881			BC063304	CCDS1051.1	1q21-q22	2014-03-03	2014-03-03		ENSG00000169418	ENSG00000169418			7943	protein-coding gene	gene with protein product	"""guanylate cyclase A"""	108960	"""atrionatriuretic peptide receptor A"", ""natriuretic peptide receptor A"""	ANPRA, NPRA		1979052	Standard	NM_000906		Approved	GUCY2A, ANPa	uc001fcs.4	P16066	OTTHUMG00000037085	ENST00000368680.3:c.2228_2229delGT	1.37:g.153660245_153660246delGT	ENSP00000357669:p.Gly743fs		B0ZBF0|Q5SR08|Q6P4Q3	Frame_Shift_Del	DEL	ENST00000368680.3	37	CCDS1051.1																																																																																				0.609	NPR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000090034.1		NM_000906	
OAS3	4940	hgsc.bcm.edu;ucsc.edu	37	12	113405908	113405908	+	Nonsense_Mutation	SNP	C	C	G			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr12:113405908C>G	ENST00000228928.7	+	14	3212	c.3033C>G	c.(3031-3033)taC>taG	p.Y1011*	RP1-71H24.1_ENST00000552784.1_RNA	NM_006187.2	NP_006178.2	Q9Y6K5	OAS3_HUMAN	2'-5'-oligoadenylate synthetase 3, 100kDa	1011	OAS domain 3.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|interferon-gamma-mediated signaling pathway (GO:0060333)|negative regulation of viral genome replication (GO:0045071)|nucleobase-containing compound metabolic process (GO:0006139)|regulation of ribonuclease activity (GO:0060700)|response to virus (GO:0009615)|type I interferon signaling pathway (GO:0060337)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular space (GO:0005615)|intracellular membrane-bounded organelle (GO:0043231)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	2'-5'-oligoadenylate synthetase activity (GO:0001730)|ATP binding (GO:0005524)|double-stranded RNA binding (GO:0003725)|metal ion binding (GO:0046872)			breast(3)|central_nervous_system(2)|endometrium(2)|kidney(3)|large_intestine(8)|lung(6)|ovary(1)|skin(2)	27						TCTGTATCTACTGGACCATCA	0.562																																																	0													58.0	59.0	59.0					12																	113405908		1966	4152	6118	SO:0001587	stop_gained	4940			AF063613	CCDS44981.1	12q24.2	2008-05-02	2002-08-29			ENSG00000111331			8088	protein-coding gene	gene with protein product		603351	"""2'-5'-oligoadenylate synthetase 3 (100 kD)"""			9790745	Standard	NM_006187		Approved		uc001tug.3	Q9Y6K5	OTTHUMG00000169795	ENST00000228928.7:c.3033C>G	12.37:g.113405908C>G	ENSP00000228928:p.Tyr1011*		Q2HJ14|Q9H3P5	Nonsense_Mutation	SNP	ENST00000228928.7	37	CCDS44981.1	.	.	.	.	.	.	.	.	.	.	C	38	6.865408	0.97897	.	.	ENSG00000111331	ENST00000228928;ENST00000323881	.	.	.	4.88	3.99	0.46301	.	0.000000	0.31542	U	0.007475	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	.	8.6102	0.33797	0.0:0.8965:0.0:0.1035	.	.	.	.	X	1011;1010	.	ENSP00000228928:Y1011X	Y	+	3	2	OAS3	111890291	1.000000	0.71417	1.000000	0.80357	0.257000	0.26127	0.877000	0.28106	1.261000	0.44149	0.655000	0.94253	TAC		0.562	OAS3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405920.1			
OGT	8473	hgsc.bcm.edu;ucsc.edu	37	X	70776831	70776831	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chrX:70776831C>T	ENST00000373719.3	+	10	1413	c.1196C>T	c.(1195-1197)tCt>tTt	p.S399F	OGT_ENST00000373701.3_Missense_Mutation_p.S389F	NM_181672.2|NM_181673.2	NP_858058.1|NP_858059.1	O15294	OGT1_HUMAN	O-linked N-acetylglucosamine (GlcNAc) transferase	399					apoptotic process (GO:0006915)|cellular response to retinoic acid (GO:0071300)|chromatin organization (GO:0006325)|circadian regulation of gene expression (GO:0032922)|histone H3-K4 trimethylation (GO:0080182)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)|negative regulation of protein ubiquitination (GO:0031397)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of catalytic activity (GO:0043085)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of histone H3-K27 methylation (GO:0061087)|positive regulation of histone H3-K4 methylation (GO:0051571)|positive regulation of proteolysis (GO:0045862)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein O-linked glycosylation (GO:0006493)|regulation of gluconeogenesis involved in cellular glucose homeostasis (GO:0090526)|regulation of glycolytic process (GO:0006110)|regulation of insulin receptor signaling pathway (GO:0046626)|regulation of Rac protein signal transduction (GO:0035020)|response to insulin (GO:0032868)|response to nutrient (GO:0007584)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone acetyltransferase complex (GO:0000123)|microtubule organizing center (GO:0005815)|mitochondrion (GO:0005739)|MLL5-L complex (GO:0070688)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	acetylglucosaminyltransferase activity (GO:0008375)|enzyme activator activity (GO:0008047)|phosphatidylinositol-3,4,5-trisphosphate binding (GO:0005547)|protein N-acetylglucosaminyltransferase activity (GO:0016262)|protein O-GlcNAc transferase activity (GO:0097363)			breast(6)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(4)|large_intestine(5)|liver(3)|lung(9)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	43	Renal(35;0.156)					GATGCCTACTCTAATATGGGA	0.398																																																	0													83.0	70.0	75.0					X																	70776831		2203	4299	6502	SO:0001583	missense	8473			U77413	CCDS14414.1, CCDS35502.1	Xq13	2013-07-24	2012-05-04		ENSG00000147162	ENSG00000147162	2.4.1.255	"""Tetratricopeptide (TTC) repeat domain containing"""	8127	protein-coding gene	gene with protein product	"""UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase"""	300255	"""O-linked N-acetylglucosamine (GlcNAc) transferase (UDP-N-acetylglucosamine:polypeptide-N-acetylglucosaminyl transferase)"""			9083068	Standard	NM_181672		Approved	O-GLCNAC, HRNT1, MGC22921, FLJ23071	uc004eaa.2	O15294	OTTHUMG00000033316	ENST00000373719.3:c.1196C>T	X.37:g.70776831C>T	ENSP00000362824:p.Ser399Phe		Q7Z3K0|Q8WWM8|Q96CC1|Q9UG57	Missense_Mutation	SNP	ENST00000373719.3	37	CCDS14414.1	.	.	.	.	.	.	.	.	.	.	C	24.5	4.542218	0.85917	.	.	ENSG00000147162	ENST00000373719;ENST00000373701	T;T	0.16743	2.32;2.32	5.3	5.3	0.74995	Tetratricopeptide-like helical (1);Tetratricopeptide repeat-containing (1);	0.000000	0.85682	D	0.000000	T	0.26412	0.0645	N	0.19112	0.55	0.80722	D	1	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	1.0;0.999;1.0	T	0.06789	-1.0807	10	0.13108	T	0.6	.	18.0148	0.89236	0.0:1.0:0.0:0.0	.	273;389;399	Q548W1;O15294-3;O15294	.;.;OGT1_HUMAN	F	399;389	ENSP00000362824:S399F;ENSP00000362805:S389F	ENSP00000362805:S389F	S	+	2	0	OGT	70693556	1.000000	0.71417	0.995000	0.50966	0.995000	0.86356	7.594000	0.82698	2.445000	0.82738	0.594000	0.82650	TCT		0.398	OGT-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000081829.3		NM_003605, NM_181672	
PBRM1	55193	hgsc.bcm.edu;ucsc.edu	37	3	52712580	52712580	+	Nonsense_Mutation	SNP	G	G	A			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr3:52712580G>A	ENST00000296302.7	-	2	173	c.172C>T	c.(172-174)Cga>Tga	p.R58*	PBRM1_ENST00000409057.1_Nonsense_Mutation_p.R58*|PBRM1_ENST00000337303.4_Nonsense_Mutation_p.R58*|PBRM1_ENST00000394830.3_Nonsense_Mutation_p.R58*|PBRM1_ENST00000409114.3_Nonsense_Mutation_p.R58*|PBRM1_ENST00000410007.1_Nonsense_Mutation_p.R58*|PBRM1_ENST00000409767.1_Nonsense_Mutation_p.R58*|PBRM1_ENST00000356770.4_Nonsense_Mutation_p.R58*			Q86U86	PB1_HUMAN	polybromo 1	58					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.R58*(7)		breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TTATAGTCTCGGATGGTATTA	0.433			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	7	Substitution - Nonsense(7)	kidney(6)|large_intestine(1)											130.0	118.0	122.0					3																	52712580		2203	4300	6503	SO:0001587	stop_gained	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.172C>T	3.37:g.52712580G>A	ENSP00000296302:p.Arg58*		A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Nonsense_Mutation	SNP	ENST00000296302.7	37		.	.	.	.	.	.	.	.	.	.	G	36	5.705422	0.96812	.	.	ENSG00000163939	ENST00000356770;ENST00000394830;ENST00000296302;ENST00000337303;ENST00000409057;ENST00000410007;ENST00000409114;ENST00000409767;ENST00000423351;ENST00000446103;ENST00000431678;ENST00000420148;ENST00000449505;ENST00000450271	.	.	.	5.2	3.17	0.36434	.	0.056365	0.64402	D	0.000002	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	2.9834	8.9802	0.35961	0.0:0.1109:0.6405:0.2486	.	.	.	.	X	58;58;58;58;58;58;58;58;58;2;58;58;58;58	.	ENSP00000296302:R58X	R	-	1	2	PBRM1	52687620	1.000000	0.71417	0.999000	0.59377	0.979000	0.70002	3.452000	0.52971	1.160000	0.42584	0.460000	0.39030	CGA		0.433	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PDZRN4	29951	hgsc.bcm.edu	37	12	41966392	41966392	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr12:41966392A>T	ENST00000402685.2	+	10	1819	c.1811A>T	c.(1810-1812)gAg>gTg	p.E604V	PDZRN4_ENST00000539469.2_Missense_Mutation_p.E346V|PDZRN4_ENST00000298919.7_Missense_Mutation_p.E344V	NM_001164595.1	NP_001158067.1	Q6ZMN7	PZRN4_HUMAN	PDZ domain containing ring finger 4	604							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)			breast(3)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(23)|lung(29)|ovary(3)|pancreas(1)|prostate(2)|skin(4)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	77	all_cancers(12;0.000673)	Lung NSC(34;0.0205)|all_lung(34;0.0264)				CAGTACAATGAGAGCCTCGTA	0.488																																																	0													83.0	82.0	83.0					12																	41966392		2203	4300	6503	SO:0001583	missense	29951			AK094690	CCDS8739.1, CCDS53777.1	12q12	2008-08-14	2008-08-14			ENSG00000165966		"""RING-type (C3HC4) zinc fingers"""	30552	protein-coding gene	gene with protein product	"""similar to semaF cytoplasmic domain associated protein 3"""	609730				11230166, 15010864	Standard	NM_013377		Approved	DKFZp434B0417, LNX4, FLJ33777, IMAGE5767589	uc010skn.2	Q6ZMN7		ENST00000402685.2:c.1811A>T	12.37:g.41966392A>T	ENSP00000384197:p.Glu604Val		Q52LY3|Q52LY4|Q6N052|Q8IUU1|Q9NTP7	Missense_Mutation	SNP	ENST00000402685.2	37	CCDS53777.1	.	.	.	.	.	.	.	.	.	.	A	15.39	2.820571	0.50633	.	.	ENSG00000165966	ENST00000402685;ENST00000539469;ENST00000298919	T;T;T	0.74842	-0.88;3.62;3.62	4.64	4.64	0.57946	.	0.155766	0.43416	D	0.000576	T	0.74989	0.3789	L	0.50333	1.59	0.51767	D	0.999937	D;P;P	0.56521	0.976;0.921;0.507	P;P;B	0.49140	0.601;0.543;0.444	T	0.78628	-0.2130	10	0.62326	D	0.03	-18.7853	14.7814	0.69769	1.0:0.0:0.0:0.0	.	604;344;346	Q6ZMN7;Q6ZMN7-4;Q6ZMN7-2	PZRN4_HUMAN;.;.	V	604;346;344	ENSP00000384197:E604V;ENSP00000439990:E346V;ENSP00000298919:E344V	ENSP00000298919:E344V	E	+	2	0	PDZRN4	40252659	1.000000	0.71417	0.518000	0.27811	0.752000	0.42762	3.834000	0.55798	2.049000	0.60858	0.528000	0.53228	GAG		0.488	PDZRN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403701.1		NM_013377	
PKD1L2	114780	hgsc.bcm.edu;ucsc.edu	37	16	81232574	81232574	+	RNA	SNP	T	T	C			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr16:81232574T>C	ENST00000525539.1	-	0	1235				PKD1L2_ENST00000337114.4_RNA	NM_052892.3	NP_443124.3	Q7Z442	PK1L2_HUMAN	polycystic kidney disease 1-like 2						ion transport (GO:0006811)|neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)	calcium ion binding (GO:0005509)|carbohydrate binding (GO:0030246)			breast(2)|central_nervous_system(2)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(9)|lung(20)|ovary(2)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	44						TCTGGGTTTCTCTGTCCAGGA	0.542																																																	0													127.0	129.0	128.0					16																	81232574		1966	4151	6117			114780			AY164483	CCDS61998.1, CCDS61999.1	16q23.2	2014-09-11			ENSG00000166473	ENSG00000166473			21715	protein-coding gene	gene with protein product		607894				12782129	Standard	NM_052892		Approved	KIAA1879	uc002fgf.1	Q7Z442	OTTHUMG00000166126		16.37:g.81232574T>C			Q6UEE1|Q6ZN46|Q6ZSP2|Q8N1H9|Q96CL2|Q96Q08	Silent	SNP	ENST00000525539.1	37																																																																																					0.542	PKD1L2-001	KNOWN	non_canonical_polymorphism|basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000387972.2			
PUM1	9698	hgsc.bcm.edu;ucsc.edu	37	1	31479895	31479895	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr1:31479895G>T	ENST00000257075.5	-	4	580	c.487C>A	c.(487-489)Cca>Aca	p.P163T	PUM1_ENST00000440538.2_Missense_Mutation_p.P163T|PUM1_ENST00000373741.4_Missense_Mutation_p.P199T|PUM1_ENST00000373742.2_Intron|PUM1_ENST00000373747.3_Missense_Mutation_p.P163T|PUM1_ENST00000426105.2_Missense_Mutation_p.P163T|PUM1_ENST00000423018.2_Intron|PUM1_ENST00000424085.2_Intron	NM_014676.2	NP_055491.1	Q14671	PUM1_HUMAN	pumilio RNA-binding family member 1	163					membrane organization (GO:0061024)|post-Golgi vesicle-mediated transport (GO:0006892)|regulation of translation (GO:0006417)	cytosol (GO:0005829)	poly(A) RNA binding (GO:0044822)			breast(1)|central_nervous_system(2)|endometrium(8)|kidney(4)|large_intestine(8)|lung(17)|ovary(2)|pancreas(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	48		Colorectal(325;0.0211)|Myeloproliferative disorder(586;0.0255)|Ovarian(437;0.0308)|all_neural(195;0.0381)|Breast(348;0.0848)|Medulloblastoma(700;0.123)		STAD - Stomach adenocarcinoma(196;0.0232)|READ - Rectum adenocarcinoma(331;0.0681)		ATTCCTTTTGGTCCATCTTTG	0.388																																																	0													296.0	284.0	288.0					1																	31479895		2203	4300	6503	SO:0001583	missense	9698			AF315592	CCDS338.1, CCDS44099.1	1p35.2	2013-09-02	2013-09-02		ENSG00000134644	ENSG00000134644			14957	protein-coding gene	gene with protein product		607204	"""pumilio (Drosophila) homolog 1"", ""pumilio homolog 1 (Drosophila)"""				Standard	NM_001020658		Approved	PUMH1, KIAA0099	uc001bsh.1	Q14671	OTTHUMG00000003795	ENST00000257075.5:c.487C>A	1.37:g.31479895G>T	ENSP00000257075:p.Pro163Thr		A8K6W4|B4DG92|D3DPN3|E9PCJ0|Q53HH5|Q5VXY7|Q9HAN1	Missense_Mutation	SNP	ENST00000257075.5	37	CCDS338.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	14.26|14.26	2.482844|2.482844	0.44147|0.44147	.|.	.|.	ENSG00000134644|ENSG00000134644	ENST00000257075;ENST00000373747;ENST00000426105;ENST00000440538;ENST00000373741;ENST00000543952|ENST00000525843	T;T;T;T;T|.	0.15952|.	2.38;2.64;2.64;2.61;2.63|.	5.26|5.26	5.26|5.26	0.73747|0.73747	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72669|0.72669	0.3489|0.3489	L|L	0.58101|0.58101	1.795|1.795	0.80722|0.80722	D|D	1|1	P;P;P;B|.	0.50819|.	0.757;0.939;0.488;0.349|.	B;P;B;B|.	0.44394|.	0.225;0.448;0.142;0.142|.	T|T	0.69250|0.69250	-0.5194|-0.5194	10|5	0.25751|.	T|.	0.34|.	-6.1938|-6.1938	19.0513|19.0513	0.93046|0.93046	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	199;163;163;163|.	Q5T1Z8;Q14671-2;Q14671;E9PCJ0|.	.;.;PUM1_HUMAN;.|.	T|N	163;163;163;163;199;163|179	ENSP00000257075:P163T;ENSP00000362852:P163T;ENSP00000391723:P163T;ENSP00000401777:P163T;ENSP00000362846:P199T|.	ENSP00000257075:P163T|.	P|T	-|-	1|2	0|0	PUM1|PUM1	31252482|31252482	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	7.776000|7.776000	0.85560|0.85560	2.736000|2.736000	0.93811|0.93811	0.557000|0.557000	0.71058|0.71058	CCA|ACC		0.388	PUM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000010671.1			
R3HDM1	23518	hgsc.bcm.edu	37	2	136409444	136409444	+	Missense_Mutation	SNP	C	C	T	rs112729561	byFrequency	TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr2:136409444C>T	ENST00000264160.4	+	17	2135	c.1765C>T	c.(1765-1767)Cct>Tct	p.P589S	R3HDM1_ENST00000409478.1_Missense_Mutation_p.P461S|R3HDM1_ENST00000410054.1_Missense_Mutation_p.P534S|R3HDM1_ENST00000329971.3_Missense_Mutation_p.P460S|R3HDM1_ENST00000409606.1_Missense_Mutation_p.P590S	NM_001282798.1|NM_015361.2	NP_001269727.1|NP_056176.2	Q15032	R3HD1_HUMAN	R3H domain containing 1	589	Poly-Pro.						poly(A) RNA binding (GO:0044822)			breast(2)|endometrium(6)|kidney(5)|large_intestine(3)|lung(14)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|urinary_tract(3)	38				BRCA - Breast invasive adenocarcinoma(221;0.127)		GACAGCAGCCcctccaccaca	0.592																																																	0													130.0	108.0	116.0					2																	136409444		2203	4300	6503	SO:0001583	missense	23518			D21852	CCDS2177.1, CCDS63024.1, CCDS63025.1, CCDS63026.1	2q21.3	2012-09-20	2005-09-02	2005-09-02	ENSG00000048991	ENSG00000048991			9757	protein-coding gene	gene with protein product			"""R3H domain (binds single-stranded nucleic acids) containing"""	R3HDM		7584026	Standard	NM_001282798		Approved	KIAA0029	uc002tuo.3	Q15032	OTTHUMG00000131740	ENST00000264160.4:c.1765C>T	2.37:g.136409444C>T	ENSP00000264160:p.Pro589Ser		A8K1V0|B3KXQ9|E9PBB4|E9PG42|G5E9G8|Q8IW32	Missense_Mutation	SNP	ENST00000264160.4	37	CCDS2177.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	18.06|18.06	3.539918|3.539918	0.65085|0.65085	.|.	.|.	ENSG00000048991|ENSG00000048991	ENST00000429703;ENST00000425804|ENST00000409478;ENST00000264160;ENST00000329971;ENST00000410054;ENST00000409606	.|T;T;T;T;T	.|0.45668	.|0.89;0.89;0.89;0.89;0.89	4.92|4.92	4.92|4.92	0.64577|0.64577	.|.	0.316472|0.316472	0.34986|0.34986	N|N	0.003525|0.003525	T|T	0.59252|0.59252	0.2180|0.2180	L|L	0.60455|0.60455	1.87|1.87	0.42720|0.42720	D|D	0.993671|0.993671	.|D;D;D;D	.|0.89917	.|1.0;1.0;0.993;1.0	.|D;D;D;D	.|0.87578	.|0.998;0.992;0.968;0.992	T|T	0.53885|0.53885	-0.8375|-0.8375	6|10	.|0.22109	.|T	.|0.4	-7.9857|-7.9857	16.2572|16.2572	0.82524|0.82524	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|461;590;534;589	.|G5E9G8;E9PBB4;E9PG42;Q15032	.|.;.;.;R3HD1_HUMAN	L|S	312;172|461;589;460;534;590	.|ENSP00000386457:P461S;ENSP00000264160:P589S;ENSP00000331396:P460S;ENSP00000386877:P534S;ENSP00000387010:P590S	.|ENSP00000264160:P589S	P|P	+|+	2|1	0|0	R3HDM1|R3HDM1	136125914|136125914	0.989000|0.989000	0.36119|0.36119	0.998000|0.998000	0.56505|0.56505	0.991000|0.991000	0.79684|0.79684	3.466000|3.466000	0.53071|0.53071	2.414000|2.414000	0.81942|0.81942	0.561000|0.561000	0.74099|0.74099	CCC|CCT		0.592	R3HDM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000254659.1		NM_015361	
RASGRF1	5923	hgsc.bcm.edu;ucsc.edu	37	15	79317727	79317727	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr15:79317727G>C	ENST00000419573.3	-	10	1745	c.1471C>G	c.(1471-1473)Cag>Gag	p.Q491E	RASGRF1_ENST00000558480.2_Missense_Mutation_p.Q491E|RASGRF1_ENST00000560334.1_5'UTR	NM_002891.4	NP_002882.3	Q13972	RGRF1_HUMAN	Ras protein-specific guanine nucleotide-releasing factor 1	491	PH 2. {ECO:0000255|PROSITE- ProRule:PRU00145}.				activation of Rac GTPase activity (GO:0032863)|cell proliferation (GO:0008283)|long-term memory (GO:0007616)|neuron projection development (GO:0031175)|positive regulation of Ras GTPase activity (GO:0032320)|positive regulation of Ras protein signal transduction (GO:0046579)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of neuronal synaptic plasticity (GO:0048168)|regulation of Rac protein signal transduction (GO:0035020)|regulation of Ras protein signal transduction (GO:0046578)|regulation of synaptic plasticity (GO:0048167)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|synaptic transmission (GO:0007268)	cytosol (GO:0005829)|growth cone (GO:0030426)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)	guanyl-nucleotide exchange factor activity (GO:0005085)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			breast(2)|central_nervous_system(2)|endometrium(7)|kidney(4)|large_intestine(18)|lung(23)|ovary(2)|prostate(6)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	71						AGGAAGCACTGTCGCTCGCCC	0.562																																																	0													79.0	78.0	78.0					15																	79317727		2196	4293	6489	SO:0001583	missense	5923			M91815	CCDS10309.1, CCDS42065.1, CCDS45320.1	15q24	2013-01-10			ENSG00000058335	ENSG00000058335		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	9875	protein-coding gene	gene with protein product		606600		GRF1		7684828, 1379731	Standard	NM_153815		Approved	CDC25L, CDC25, GRF55, H-GRF55, GNRP, PP13187	uc002beq.3	Q13972	OTTHUMG00000144172	ENST00000419573.3:c.1471C>G	15.37:g.79317727G>C	ENSP00000405963:p.Gln491Glu		F8VPA5|H0YKF2|J3KQP9|Q16027	Missense_Mutation	SNP	ENST00000419573.3	37	CCDS10309.1	.	.	.	.	.	.	.	.	.	.	G	21.7	4.186738	0.78789	.	.	ENSG00000058335	ENST00000419573;ENST00000394741	T	0.29397	1.57	4.36	4.36	0.52297	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.000000	0.64402	D	0.000001	T	0.55893	0.1949	M	0.81497	2.545	0.80722	D	1	D;D;D;D	0.69078	0.997;0.993;0.993;0.992	D;P;P;D	0.69307	0.963;0.9;0.9;0.932	T	0.62613	-0.6817	10	0.66056	D	0.02	.	14.4585	0.67433	0.0:0.0:1.0:0.0	.	491;491;491;491	A8K270;Q8IUU5;Q13972;F8VPA5	.;.;RGRF1_HUMAN;.	E	491	ENSP00000405963:Q491E	ENSP00000378224:Q491E	Q	-	1	0	RASGRF1	77104782	1.000000	0.71417	0.966000	0.40874	0.927000	0.56198	9.378000	0.97191	2.241000	0.73720	0.585000	0.79938	CAG		0.562	RASGRF1-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000291371.3		NM_002891	
RGPD5	84220	hgsc.bcm.edu	37	2	110602778	110602778	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr2:110602778G>A	ENST00000016946.3	+	21	5178	c.5020G>A	c.(5020-5022)Gaa>Aaa	p.E1674K		NM_005054.2	NP_005045.2	Q99666	RGPD5_HUMAN	RANBP2-like and GRIP domain containing 5	1674					protein targeting to Golgi (GO:0000042)	cytoplasm (GO:0005737)				central_nervous_system(1)	1						CCTGCTTCGGGAAATAGAGGC	0.468																																																	0													1.0	1.0	1.0					2																	110602778		1	5	6	SO:0001583	missense	84220			U64675	CCDS2082.1, CCDS2083.1	2q13	2013-01-10			ENSG00000015568	ENSG00000015568		"""Tetratricopeptide (TTC) repeat domain containing"""	32418	protein-coding gene	gene with protein product		612708				15710750, 15815621	Standard	NM_032260		Approved	RGP5, BS-63, DKFZp686I1842		Q99666	OTTHUMG00000130985	ENST00000016946.3:c.5020G>A	2.37:g.110602778G>A	ENSP00000016946:p.Glu1674Lys		Q53QN2|Q53T03|Q59GM7|Q9H0B2	Missense_Mutation	SNP	ENST00000016946.3	37	CCDS2082.1	.	.	.	.	.	.	.	.	.	.	g	8.489	0.861476	0.17178	.	.	ENSG00000015568	ENST00000016946	T	0.54675	0.56	0.702	0.702	0.18110	.	.	.	.	.	T	0.41190	0.1148	M	0.62723	1.935	0.80722	D	1	P	0.48911	0.917	B	0.36134	0.218	T	0.41875	-0.9484	9	0.49607	T	0.09	-35.2953	7.3764	0.26831	0.0:0.0:1.0:0.0	.	1674	Q99666	RGPD5_HUMAN	K	1674	ENSP00000016946:E1674K	ENSP00000016946:E1674K	E	+	1	0	RGPD5	109960067	1.000000	0.71417	0.997000	0.53966	0.036000	0.12997	6.477000	0.73591	0.700000	0.31782	0.109000	0.15622	GAA		0.468	RGPD5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253599.3		NM_005054	
RIOK1	83732	hgsc.bcm.edu;ucsc.edu	37	6	7405162	7405162	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr6:7405162G>T	ENST00000379834.2	+	11	1511	c.1004G>T	c.(1003-1005)gGa>gTa	p.G335V		NM_031480.2|NM_153005.1	NP_113668.2|NP_694550.1	Q9BRS2	RIOK1_HUMAN	RIO kinase 1	335	Protein kinase.						ATP binding (GO:0005524)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(2)|lung(6)|ovary(2)|pancreas(1)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	19	Ovarian(93;0.0418)					TACCACGGTGGAGGCGTGTAT	0.458																																																	0													86.0	71.0	76.0					6																	7405162		2203	4300	6503	SO:0001583	missense	83732			BC006104	CCDS4500.1	6p24.3	2012-12-10	2012-12-10		ENSG00000124784	ENSG00000124784			18656	protein-coding gene	gene with protein product			"""RIO kinase 1 (yeast)"""				Standard	NM_031480		Approved	AD034, FLJ30006, bA288G3.1, RRP10	uc003mxn.3	Q9BRS2	OTTHUMG00000014207	ENST00000379834.2:c.1004G>T	6.37:g.7405162G>T	ENSP00000369162:p.Gly335Val		B2RB28|Q8NDC8|Q96NV9	Missense_Mutation	SNP	ENST00000379834.2	37	CCDS4500.1	.	.	.	.	.	.	.	.	.	.	G	25.5	4.647757	0.87958	.	.	ENSG00000124784	ENST00000379834	T	0.08896	3.04	5.7	5.7	0.88788	RIO kinase (1);Protein kinase-like domain (1);RIO-like kinase (1);	0.000000	0.85682	D	0.000000	T	0.33089	0.0851	M	0.92784	3.345	0.80722	D	1	D	0.67145	0.996	D	0.74348	0.983	T	0.41342	-0.9514	10	0.87932	D	0	-27.0129	18.8353	0.92159	0.0:0.0:1.0:0.0	.	335	Q9BRS2	RIOK1_HUMAN	V	335	ENSP00000369162:G335V	ENSP00000369162:G335V	G	+	2	0	RIOK1	7350161	1.000000	0.71417	0.146000	0.22360	0.062000	0.15995	9.595000	0.98260	2.688000	0.91661	0.655000	0.94253	GGA		0.458	RIOK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000039780.2		NM_031480	
RORB	6096	hgsc.bcm.edu;ucsc.edu	37	9	77282715	77282715	+	Missense_Mutation	SNP	G	G	A			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr9:77282715G>A	ENST00000396204.2	+	8	1042	c.1042G>A	c.(1042-1044)Gac>Aac	p.D348N	RORB_ENST00000376896.3_Missense_Mutation_p.D337N			Q92753	RORB_HUMAN	RAR-related orphan receptor B	348	Ligand-binding. {ECO:0000255}.				amacrine cell differentiation (GO:0035881)|cellular response to retinoic acid (GO:0071300)|eye photoreceptor cell development (GO:0042462)|gene expression (GO:0010467)|intracellular receptor signaling pathway (GO:0030522)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of circadian rhythm (GO:0042752)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|retinal cone cell development (GO:0046549)|retinal rod cell development (GO:0046548)|rhythmic process (GO:0048511)|transcription initiation from RNA polymerase II promoter (GO:0006367)|visual perception (GO:0007601)	nucleoplasm (GO:0005654)|nucleus (GO:0005634)	ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|zinc ion binding (GO:0008270)	p.D337Y(1)		breast(2)|large_intestine(4)|lung(1)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)	12					Melatonin(DB01065)	AGGTTCTGATGACCTAGTGAA	0.378																																																	1	Substitution - Missense(1)	lung(1)											152.0	136.0	142.0					9																	77282715		2203	4300	6503	SO:0001583	missense	6096			Y08639	CCDS6646.1	9q22	2013-01-16			ENSG00000198963	ENSG00000198963		"""Nuclear hormone receptors"""	10259	protein-coding gene	gene with protein product		601972				7926749	Standard	NM_006914		Approved	RZRB, NR1F2, ROR-BETA	uc004ajh.3	Q92753	OTTHUMG00000020026	ENST00000396204.2:c.1042G>A	9.37:g.77282715G>A	ENSP00000379507:p.Asp348Asn		Q8WX73	Missense_Mutation	SNP	ENST00000396204.2	37		.	.	.	.	.	.	.	.	.	.	G	36	5.702952	0.96812	.	.	ENSG00000198963	ENST00000376896;ENST00000396204	D;D	0.96967	-4.19;-4.19	6.17	6.17	0.99709	Nuclear hormone receptor, ligand-binding (2);Nuclear hormone receptor, ligand-binding, core (2);	0.043116	0.85682	D	0.000000	D	0.98049	0.9357	M	0.82433	2.59	0.80722	D	1	D;B	0.62365	0.991;0.053	P;B	0.62014	0.897;0.105	D	0.97000	0.9728	10	0.37606	T	0.19	.	20.8794	0.99867	0.0:0.0:1.0:0.0	.	348;337	Q92753;Q58EY0	RORB_HUMAN;.	N	337;348	ENSP00000366093:D337N;ENSP00000379507:D348N	ENSP00000366093:D337N	D	+	1	0	RORB	76472535	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	9.775000	0.98995	2.941000	0.99782	0.655000	0.94253	GAC		0.378	RORB-201	KNOWN	basic	protein_coding	protein_coding				
RPL22L1	200916	hgsc.bcm.edu;ucsc.edu	37	3	170584200	170584200	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr3:170584200T>A	ENST00000295830.8	-	4	653	c.338A>T	c.(337-339)cAa>cTa	p.Q113L	RPL22L1_ENST00000463836.1_Missense_Mutation_p.Q112L	NM_001099645.1	NP_001093115.1	Q6P5R6	RL22L_HUMAN	ribosomal protein L22-like 1	113					translation (GO:0006412)	ribosome (GO:0005840)	structural constituent of ribosome (GO:0003735)			kidney(2)|large_intestine(1)|upper_aerodigestive_tract(1)	4	all_cancers(22;1.96e-19)|all_lung(20;1.59e-15)|Lung NSC(18;7.08e-15)|Ovarian(172;0.00197)|Breast(254;0.137)		LUSC - Lung squamous cell carcinoma(14;1.1e-14)|Lung(28;2.99e-14)			ATCTTCATCTTGACTAATCTG	0.398																																																	0													49.0	45.0	46.0					3																	170584200		1839	4095	5934	SO:0001583	missense	200916			BC062731	CCDS46955.1	3q26.2	2005-08-09			ENSG00000163584	ENSG00000163584			27610	protein-coding gene	gene with protein product							Standard	NM_001099645		Approved		uc003fhc.4	Q6P5R6	OTTHUMG00000158957	ENST00000295830.8:c.338A>T	3.37:g.170584200T>A	ENSP00000346080:p.Gln113Leu		Q32Q77	Missense_Mutation	SNP	ENST00000295830.8	37	CCDS46955.1	.	.	.	.	.	.	.	.	.	.	T	19.76	3.886643	0.72410	.	.	ENSG00000163584	ENST00000295830;ENST00000466674;ENST00000463836	T;T;T	0.43688	0.94;0.94;0.94	5.37	5.37	0.77165	.	0.000000	0.85682	D	0.000000	T	0.53481	0.1799	M	0.87900	2.915	0.80722	D	1	B	0.31413	0.322	B	0.34931	0.192	T	0.59705	-0.7404	10	0.56958	D	0.05	.	15.3775	0.74621	0.0:0.0:0.0:1.0	.	113	Q6P5R6	RL22L_HUMAN	L	113;133;112	ENSP00000346080:Q113L;ENSP00000419713:Q133L;ENSP00000419041:Q112L	ENSP00000346080:Q113L	Q	-	2	0	RPL22L1	172066894	1.000000	0.71417	1.000000	0.80357	0.972000	0.66771	6.283000	0.72646	2.042000	0.60477	0.260000	0.18958	CAA		0.398	RPL22L1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000352586.2		XM_114317	
SEC14L4	284904	hgsc.bcm.edu;ucsc.edu	37	22	30888522	30888522	+	Silent	SNP	G	G	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr22:30888522G>T	ENST00000255858.7	-	8	686	c.603C>A	c.(601-603)gcC>gcA	p.A201A	SEC14L4_ENST00000381982.3_Silent_p.A201A|SEC14L4_ENST00000540456.1_Silent_p.A186A|SEC14L4_ENST00000392772.2_Silent_p.A147A|RP4-539M6.14_ENST00000610156.1_RNA|RP4-539M6.14_ENST00000442126.1_RNA	NM_001161368.1|NM_174977.3	NP_001154840.1|NP_777637.1	Q9UDX3	S14L4_HUMAN	SEC14-like 4 (S. cerevisiae)	201	CRAL-TRIO. {ECO:0000255|PROSITE- ProRule:PRU00056}.					integral component of membrane (GO:0016021)|intracellular (GO:0005622)	lipid binding (GO:0008289)|transporter activity (GO:0005215)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(5)|pancreas(1)|skin(1)	21					Vitamin E(DB00163)	CCAAGTTGAAGGCCACGGGGA	0.547																																																	0													122.0	89.0	101.0					22																	30888522		2203	4300	6503	SO:0001819	synonymous_variant	284904			AY158085	CCDS13878.1, CCDS54517.1	22q12.1	2003-03-10			ENSG00000133488	ENSG00000133488			20627	protein-coding gene	gene with protein product		612825					Standard	NM_174977		Approved	TAP3, dJ130H16.5	uc003aid.2	Q9UDX3	OTTHUMG00000151258	ENST00000255858.7:c.603C>A	22.37:g.30888522G>T			A5D6W7|A6NCV4	Silent	SNP	ENST00000255858.7	37	CCDS13878.1																																																																																				0.547	SEC14L4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321946.1		NM_174977	
SETD2	29072	hgsc.bcm.edu	37	3	47155365	47155365	+	Splice_Site	SNP	C	C	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	PGM			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr3:47155365C>T	ENST00000409792.3	-	5	4758		c.e5+1			NM_014159.6	NP_054878.5	Q9BYW2	SETD2_HUMAN	SET domain containing 2						angiogenesis (GO:0001525)|cell migration involved in vasculogenesis (GO:0035441)|coronary vasculature morphogenesis (GO:0060977)|embryonic cranial skeleton morphogenesis (GO:0048701)|embryonic placenta morphogenesis (GO:0060669)|forebrain development (GO:0030900)|histone H3-K36 trimethylation (GO:0097198)|mesoderm morphogenesis (GO:0048332)|mismatch repair (GO:0006298)|morphogenesis of a branching structure (GO:0001763)|neural tube closure (GO:0001843)|nucleosome organization (GO:0034728)|pericardium development (GO:0060039)|regulation of mRNA export from nucleus (GO:0010793)|regulation of transcription, DNA-templated (GO:0006355)|stem cell development (GO:0048864)|transcription elongation from RNA polymerase II promoter (GO:0006368)	chromosome (GO:0005694)|nucleus (GO:0005634)	histone-lysine N-methyltransferase activity (GO:0018024)			breast(6)|central_nervous_system(5)|endometrium(4)|kidney(63)|large_intestine(18)|lung(26)|ovary(6)|prostate(2)|skin(3)|soft_tissue(1)|stomach(2)|urinary_tract(5)	141		Acute lymphoblastic leukemia(5;0.0169)		BRCA - Breast invasive adenocarcinoma(193;0.000302)|KIRC - Kidney renal clear cell carcinoma(197;0.00732)|Kidney(197;0.00844)		AAAGAACTTACGAAGGAAGGT	0.453			"""N, F, S, Mis"""		clear cell renal carcinoma																																			Rec	yes		3	3p21.31	29072	SET domain containing 2		E	0													106.0	107.0	106.0					3																	47155365		2203	4300	6503	SO:0001630	splice_region_variant	29072			AJ238403	CCDS2749.2	3p21.31	2014-09-17			ENSG00000181555	ENSG00000181555		"""Chromatin-modifying enzymes / K-methyltransferases"""	18420	protein-coding gene	gene with protein product		612778				16118227, 11461154	Standard	NM_014159		Approved	HYPB, HIF-1, KIAA1732, FLJ23184, KMT3A	uc003cqs.3	Q9BYW2	OTTHUMG00000133514	ENST00000409792.3:c.4715+1G>A	3.37:g.47155365C>T			O75397|O75405|Q17RW8|Q5BKS9|Q5QGN2|Q69YI5|Q6IN64|Q6ZN53|Q6ZS25|Q8N3R0|Q8TCN0|Q9C0D1|Q9H696|Q9NZW9	Splice_Site	SNP	ENST00000409792.3	37	CCDS2749.2	.	.	.	.	.	.	.	.	.	.	C	23.1	4.377351	0.82682	.	.	ENSG00000181555	ENST00000451092;ENST00000543224;ENST00000409792	.	.	.	4.53	4.53	0.55603	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	17.8075	0.88606	0.0:1.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	SETD2	47130369	1.000000	0.71417	1.000000	0.80357	0.966000	0.64601	7.256000	0.78350	2.518000	0.84900	0.585000	0.79938	.		0.453	SETD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257479.2		NM_014159	Intron
SFXN4	119559	hgsc.bcm.edu;ucsc.edu	37	10	120900791	120900791	+	Missense_Mutation	SNP	G	G	C			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr10:120900791G>C	ENST00000355697.2	-	14	996	c.977C>G	c.(976-978)aCa>aGa	p.T326R	SFXN4_ENST00000461438.1_5'UTR|SFXN4_ENST00000330036.6_Missense_Mutation_p.T317R	NM_213649.1	NP_998814.1	Q6P4A7	SFXN4_HUMAN	sideroflexin 4	326					iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)			central_nervous_system(1)|cervix(1)|kidney(3)|large_intestine(1)|lung(3)|ovary(1)|skin(1)	11		Lung NSC(174;0.094)|all_lung(145;0.123)		all cancers(201;0.0261)		TGTTTCTTCTGTTGGAGACTG	0.368																																																	0													153.0	159.0	157.0					10																	120900791		2203	4300	6503	SO:0001583	missense	119559				CCDS7610.1	10q26.11	2006-03-13			ENSG00000183605	ENSG00000183605		"""Sideroflexins"""	16088	protein-coding gene	gene with protein product		615564				14756423	Standard	NM_213649		Approved		uc001leb.3	Q6P4A7	OTTHUMG00000019147	ENST00000355697.2:c.977C>G	10.37:g.120900791G>C	ENSP00000347924:p.Thr326Arg		Q6WSU4|Q86TD9	Missense_Mutation	SNP	ENST00000355697.2	37	CCDS7610.1	.	.	.	.	.	.	.	.	.	.	G	19.77	3.889978	0.72524	.	.	ENSG00000183605	ENST00000355697;ENST00000330036;ENST00000392875	T;T	0.29142	1.58;1.58	4.95	4.95	0.65309	.	0.141721	0.46758	D	0.000272	T	0.41673	0.1169	M	0.71581	2.175	0.53005	D	0.999968	P	0.48503	0.911	P	0.49752	0.621	T	0.26503	-1.0101	10	0.11182	T	0.66	-21.8686	16.7538	0.85494	0.0:0.0:1.0:0.0	.	326	Q6P4A7	SFXN4_HUMAN	R	326;317;209	ENSP00000347924:T326R;ENSP00000333200:T317R	ENSP00000333200:T317R	T	-	2	0	SFXN4	120890781	1.000000	0.71417	0.109000	0.21407	0.060000	0.15804	5.979000	0.70508	2.469000	0.83416	0.650000	0.86243	ACA		0.368	SFXN4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050642.3		XM_058406	
PEAK1	79834	hgsc.bcm.edu;ucsc.edu	37	15	77407312	77407312	+	Missense_Mutation	SNP	C	C	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr15:77407312C>T	ENST00000560626.2	-	7	4902	c.4427G>A	c.(4426-4428)cGa>cAa	p.R1476Q	PEAK1_ENST00000312493.4_Missense_Mutation_p.R1476Q			Q9H792	PEAK1_HUMAN	pseudopodium-enriched atypical kinase 1	1476	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell migration (GO:0016477)|peptidyl-tyrosine phosphorylation (GO:0018108)|protein autophosphorylation (GO:0046777)|substrate adhesion-dependent cell spreading (GO:0034446)	actin cytoskeleton (GO:0015629)|cytoplasm (GO:0005737)|focal adhesion (GO:0005925)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)										CAGAGAGTCTCGCACAAAATC	0.522																																																	0													103.0	103.0	103.0					15																	77407312		2124	4224	6348	SO:0001583	missense	0				CCDS42062.1	15q24.3	2013-09-27			ENSG00000173517	ENSG00000173517			29431	protein-coding gene	gene with protein product		614248				16879967, 20534451	Standard	NM_024776		Approved	KIAA2002, sgk269		Q9H792	OTTHUMG00000172618	ENST00000560626.2:c.4427G>A	15.37:g.77407312C>T	ENSP00000452796:p.Arg1476Gln		Q6ZS78|Q8NAZ4|Q8NCM3|Q8TEG7	Missense_Mutation	SNP	ENST00000560626.2	37	CCDS42062.1	.	.	.	.	.	.	.	.	.	.	C	13.91	2.378750	0.42207	.	.	ENSG00000173517	ENST00000312493	T	0.73681	-0.77	5.14	2.07	0.26955	Serine/threonine-protein kinase-like domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.209842	0.27971	N	0.017106	T	0.68284	0.2984	M	0.62723	1.935	0.38848	D	0.95621	B	0.16603	0.018	B	0.17098	0.017	T	0.62756	-0.6787	10	0.51188	T	0.08	-5.9836	9.0784	0.36536	0.0:0.6898:0.0:0.3102	.	1476	Q9H792	PEAK1_HUMAN	Q	1476	ENSP00000309230:R1476Q	ENSP00000309230:R1476Q	R	-	2	0	AC087465.1	75194367	0.257000	0.24022	0.949000	0.38748	0.863000	0.49368	0.889000	0.28282	0.145000	0.18977	0.561000	0.74099	CGA		0.522	PEAK1-001	KNOWN	not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419483.3			
SLC41A3	54946	hgsc.bcm.edu;ucsc.edu	37	3	125725333	125725333	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr3:125725333G>T	ENST00000315891.6	-	12	1679	c.1441C>A	c.(1441-1443)Ccc>Acc	p.P481T	SLC41A3_ENST00000360370.4_3'UTR|SLC41A3_ENST00000383598.2_3'UTR|SLC41A3_ENST00000346785.5_Missense_Mutation_p.P445T	NM_001008485.1|NM_017836.3	NP_001008485|NP_060306.3	Q96GZ6	S41A3_HUMAN	solute carrier family 41, member 3	481						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	cation transmembrane transporter activity (GO:0008324)			breast(1)|endometrium(4)|large_intestine(6)|lung(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	18				GBM - Glioblastoma multiforme(114;0.167)		CAGATGAAGGGTTGTATGAGG	0.448																																																	0													62.0	60.0	61.0					3																	125725333		2203	4300	6503	SO:0001583	missense	54946				CCDS33842.1, CCDS33843.1, CCDS33844.1, CCDS43144.1, CCDS54635.1	3q21.2	2013-09-02			ENSG00000114544	ENSG00000114544		"""Solute carriers"""	31046	protein-coding gene	gene with protein product		610803					Standard	NM_001164475		Approved	FLJ20473	uc003eij.3	Q96GZ6	OTTHUMG00000162678	ENST00000315891.6:c.1441C>A	3.37:g.125725333G>T	ENSP00000326070:p.Pro481Thr		A6ND60|B3KSD9|B7Z4Y2|C9JE96|E7ENY4|Q8N342|Q8NB27|Q9H9I6|Q9HAB1|Q9NX30	Missense_Mutation	SNP	ENST00000315891.6	37	CCDS33843.1	.	.	.	.	.	.	.	.	.	.	G	3.489	-0.104356	0.06967	.	.	ENSG00000114544	ENST00000346785;ENST00000315891	T;T	0.28454	1.61;1.62	2.64	-0.361	0.12564	.	0.885835	0.09647	N	0.774106	T	0.13543	0.0328	N	0.08118	0	0.09310	N	1	B;B	0.12630	0.006;0.003	B;B	0.12156	0.007;0.003	T	0.26121	-1.0112	10	0.87932	D	0	.	2.3271	0.04225	0.2954:0.0:0.4632:0.2414	.	445;481	Q96GZ6-3;Q96GZ6	.;S41A3_HUMAN	T	445;481	ENSP00000264471:P445T;ENSP00000326070:P481T	ENSP00000326070:P481T	P	-	1	0	SLC41A3	127208023	0.000000	0.05858	0.000000	0.03702	0.022000	0.10575	0.169000	0.16641	-0.099000	0.12263	0.491000	0.48974	CCC		0.448	SLC41A3-024	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000370886.1		NM_017836	
SLC46A1	113235	hgsc.bcm.edu;ucsc.edu	37	17	26727778	26727778	+	Missense_Mutation	SNP	G	G	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr17:26727778G>T	ENST00000440501.1	-	4	1266	c.1171C>A	c.(1171-1173)Ctc>Atc	p.L391I	SARM1_ENST00000457710.3_3'UTR|CTD-2350C19.1_ENST00000583956.1_RNA|SLC46A1_ENST00000584729.1_5'UTR|SLC46A1_ENST00000321666.5_Missense_Mutation_p.L363I	NM_080669.4	NP_542400.2	Q96NT5	PCFT_HUMAN	solute carrier family 46 (folate transporter), member 1	391					cellular iron ion homeostasis (GO:0006879)|folic acid metabolic process (GO:0046655)|folic acid transport (GO:0015884)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|vitamin metabolic process (GO:0006766)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|cell surface (GO:0009986)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	folic acid binding (GO:0005542)|folic acid transporter activity (GO:0008517)|heme transporter activity (GO:0015232)|methotrexate transporter activity (GO:0015350)			lung(5)	5	all_lung(13;0.000533)|Lung NSC(42;0.00171)			UCEC - Uterine corpus endometrioid carcinoma (53;0.153)	Folic Acid(DB00158)|Methotrexate(DB00563)|Sulfasalazine(DB00795)	GCAGAAAAGAGAGCACCTGTG	0.522																																																	0													33.0	39.0	37.0					17																	26727778		2063	4197	6260	SO:0001583	missense	113235			AK054669	CCDS74019.1, CCDS74020.1	17q11.2	2014-09-17	2007-09-24			ENSG00000076351		"""Solute carriers"""	30521	protein-coding gene	gene with protein product	"""heme carrier protein 1"", ""proton-coupled folate transporter"""	611672	"""solute carrier family 46, member 1"""			16143108, 17129779	Standard	XM_005277786		Approved	HCP1, MGC9564, PCFT	uc002hbf.2	Q96NT5		ENST00000440501.1:c.1171C>A	17.37:g.26727778G>T	ENSP00000395653:p.Leu391Ile		Q1HE20|Q86T92|Q8TEG3|Q96FL0	Missense_Mutation	SNP	ENST00000440501.1	37		.	.	.	.	.	.	.	.	.	.	G	19.05	3.751470	0.69533	.	.	ENSG00000076351	ENST00000440501;ENST00000321666	T;D	0.81739	0.42;-1.53	5.55	5.55	0.83447	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.123066	0.53938	D	0.000059	D	0.83330	0.5231	.	.	.	0.58432	D	0.999997	P;D	0.69078	0.89;0.997	P;D	0.63957	0.503;0.92	T	0.78259	-0.2273	9	0.11485	T	0.65	-25.1598	12.7867	0.57510	0.0747:0.0:0.9253:0.0	.	363;391	Q96NT5-2;Q96NT5	.;PCFT_HUMAN	I	391;363	ENSP00000395653:L391I;ENSP00000318828:L363I	ENSP00000318828:L363I	L	-	1	0	SLC46A1	23751905	1.000000	0.71417	1.000000	0.80357	0.847000	0.48162	3.779000	0.55379	2.623000	0.88846	0.563000	0.77884	CTC		0.522	SLC46A1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_080669	
SMYD2	56950	hgsc.bcm.edu;ucsc.edu	37	1	214488133	214488133	+	Missense_Mutation	SNP	A	A	C			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr1:214488133A>C	ENST00000366957.5	+	3	288	c.266A>C	c.(265-267)gAa>gCa	p.E89A	SMYD2_ENST00000415093.2_Missense_Mutation_p.E89A|SMYD2_ENST00000491455.1_3'UTR	NM_020197.2	NP_064582.2	Q9NRG4	SMYD2_HUMAN	SET and MYND domain containing 2	89	SET. {ECO:0000255|PROSITE- ProRule:PRU00190}.				negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|peptidyl-lysine dimethylation (GO:0018027)|peptidyl-lysine monomethylation (GO:0018026)|regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043516)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)	histone methyltransferase activity (H3-K36 specific) (GO:0046975)|metal ion binding (GO:0046872)|p53 binding (GO:0002039)|protein-lysine N-methyltransferase activity (GO:0016279)|RNA polymerase II core binding (GO:0000993)			breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(5)|ovary(1)|upper_aerodigestive_tract(1)	14				OV - Ovarian serous cystadenocarcinoma(81;0.0122)|all cancers(67;0.0209)|GBM - Glioblastoma multiforme(131;0.106)|Epithelial(68;0.144)		CACAAGCTGGAATGTTCTCCC	0.423																																																	0													100.0	98.0	99.0					1																	214488133		2203	4300	6503	SO:0001583	missense	56950			AF226053	CCDS31022.1	1q32.3	2011-07-01			ENSG00000143499	ENSG00000143499		"""Zinc fingers, MYND-type"", ""Chromatin-modifying enzymes / K-methyltransferases"""	20982	protein-coding gene	gene with protein product		610663					Standard	NM_020197		Approved	HSKM-B, ZMYND14, KMT3C	uc021pix.1	Q9NRG4	OTTHUMG00000037066	ENST00000366957.5:c.266A>C	1.37:g.214488133A>C	ENSP00000355924:p.Glu89Ala		B2R9P9|I6L9H7|Q4V765|Q5VSH9|Q96AI4	Missense_Mutation	SNP	ENST00000366957.5	37	CCDS31022.1	.	.	.	.	.	.	.	.	.	.	A	27.8	4.861845	0.91433	.	.	ENSG00000143499	ENST00000366957;ENST00000415093	T;T	0.12984	2.63;2.63	5.57	5.57	0.84162	SET domain (2);Zinc finger, MYND-type (2);	0.044496	0.85682	D	0.000000	T	0.31167	0.0788	L	0.42487	1.325	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.01639	-1.1306	10	0.72032	D	0.01	-3.7688	16.0129	0.80417	1.0:0.0:0.0:0.0	.	89	Q9NRG4	SMYD2_HUMAN	A	89	ENSP00000355924:E89A;ENSP00000388682:E89A	ENSP00000355924:E89A	E	+	2	0	SMYD2	212554756	1.000000	0.71417	0.996000	0.52242	0.997000	0.91878	8.910000	0.92685	2.243000	0.73865	0.459000	0.35465	GAA		0.423	SMYD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000089998.1		NM_020197	
STAP1	26228	hgsc.bcm.edu;ucsc.edu	37	4	68436805	68436805	+	Missense_Mutation	SNP	T	T	A			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr4:68436805T>A	ENST00000265404.2	+	2	206	c.124T>A	c.(124-126)Tat>Aat	p.Y42N	STAP1_ENST00000396225.1_Missense_Mutation_p.Y42N	NM_012108.2	NP_036240.1	Q9ULZ2	STAP1_HUMAN	signal transducing adaptor family member 1	42	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				intracellular protein transport (GO:0006886)|membrane fusion (GO:0061025)|positive regulation of signal transduction (GO:0009967)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein complex (GO:0043234)				NS(1)|large_intestine(1)|liver(1)|lung(7)|skin(1)|urinary_tract(1)	12						CCCACAGGAGTATGAGCATTA	0.299																																																	0													149.0	169.0	162.0					4																	68436805		2203	4299	6502	SO:0001583	missense	26228			AB023483	CCDS3515.1	4q13.2	2013-02-14	2007-08-09		ENSG00000035720	ENSG00000035720		"""SH2 domain containing"""	24133	protein-coding gene	gene with protein product	"""BCR downstream signaling 1"""	604298				10518561, 10679268	Standard	NM_012108		Approved	STAP-1, BRDG1	uc003hde.4	Q9ULZ2	OTTHUMG00000129304	ENST00000265404.2:c.124T>A	4.37:g.68436805T>A	ENSP00000265404:p.Tyr42Asn		B2R980	Missense_Mutation	SNP	ENST00000265404.2	37	CCDS3515.1	.	.	.	.	.	.	.	.	.	.	T	12.16	1.853536	0.32791	.	.	ENSG00000035720	ENST00000265404;ENST00000396225	T;T	0.33438	1.41;1.41	4.36	4.36	0.52297	Pleckstrin homology-type (1);Pleckstrin homology domain (2);	0.158215	0.45126	D	0.000396	T	0.31575	0.0801	L	0.59436	1.845	0.38448	D	0.946899	P	0.40553	0.721	B	0.40982	0.345	T	0.30995	-0.9959	10	0.62326	D	0.03	-2.0261	10.097	0.42482	0.0:0.0:0.0:1.0	.	42	Q9ULZ2	STAP1_HUMAN	N	42	ENSP00000265404:Y42N;ENSP00000379527:Y42N	ENSP00000265404:Y42N	Y	+	1	0	STAP1	68119400	0.996000	0.38824	0.984000	0.44739	0.179000	0.23085	3.748000	0.55142	1.957000	0.56846	0.352000	0.21897	TAT		0.299	STAP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251434.1		NM_012108	
TNS1	7145	hgsc.bcm.edu;ucsc.edu	37	2	218673368	218673368	+	Missense_Mutation	SNP	A	A	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr2:218673368A>T	ENST00000171887.4	-	31	5440	c.4988T>A	c.(4987-4989)cTc>cAc	p.L1663H	TNS1_ENST00000430930.1_Missense_Mutation_p.L1642H|TNS1_ENST00000419504.1_Missense_Mutation_p.L1649H	NM_022648.4	NP_072174.3	Q9HBL0	TENS1_HUMAN	tensin 1	1663					cell-substrate junction assembly (GO:0007044)|fibroblast migration (GO:0010761)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|focal adhesion (GO:0005925)	poly(A) RNA binding (GO:0044822)			breast(2)|cervix(1)|endometrium(6)|kidney(3)|large_intestine(23)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|stomach(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	79		Renal(207;0.0483)|Lung NSC(271;0.213)		Epithelial(149;4.43e-06)|all cancers(144;0.000653)|LUSC - Lung squamous cell carcinoma(224;0.0091)|Lung(261;0.013)		GACAGTGTTGAGAGGGTAGTG	0.498																																																	0													299.0	275.0	283.0					2																	218673368		2203	4300	6503	SO:0001583	missense	7145			AB209238	CCDS2407.1	2q35-q36	2014-06-13	2005-05-13	2005-05-13	ENSG00000079308	ENSG00000079308		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : PTENs"", ""SH2 domain containing"""	11973	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 155"""	600076	"""tensin"", ""matrix-remodelling associated 6"""	TNS, MXRA6			Standard	NM_022648		Approved	DKFZp586K0617, PPP1R155	uc002vgt.2	Q9HBL0	OTTHUMG00000133056	ENST00000171887.4:c.4988T>A	2.37:g.218673368A>T	ENSP00000171887:p.Leu1663His		Q4ZG71|Q6IPI5	Missense_Mutation	SNP	ENST00000171887.4	37	CCDS2407.1	.	.	.	.	.	.	.	.	.	.	A	17.77	3.471229	0.63625	.	.	ENSG00000079308	ENST00000171887;ENST00000446688;ENST00000419504;ENST00000430930	T;T;T;T	0.40756	1.02;1.02;1.02;1.02	4.02	4.02	0.46733	Phosphotyrosine interaction domain (1);Pleckstrin homology-type (1);Tensin phosphotyrosine-binding domain (1);	0.372440	0.27236	N	0.020297	T	0.59088	0.2168	L	0.58810	1.83	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.997	D;D;D	0.77004	0.989;0.989;0.965	T	0.63418	-0.6642	10	0.87932	D	0	.	13.1543	0.59508	1.0:0.0:0.0:0.0	.	1663;1642;1649	Q9HBL0;E9PGF5;E9PF55	TENS1_HUMAN;.;.	H	1663;801;1649;1642	ENSP00000171887:L1663H;ENSP00000394171:L801H;ENSP00000408724:L1649H;ENSP00000406016:L1642H	ENSP00000171887:L1663H	L	-	2	0	TNS1	218381613	1.000000	0.71417	1.000000	0.80357	0.946000	0.59487	3.320000	0.51991	1.679000	0.50963	0.374000	0.22700	CTC		0.498	TNS1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256672.2		NM_022648	
UBAP2	55833	hgsc.bcm.edu	37	9	33986810	33986810	+	De_novo_Start_OutOfFrame	SNP	A	A	T			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr9:33986810A>T	ENST00000379239.4	-	0	431				UBAP2_ENST00000379238.1_Missense_Mutation_p.D156E|UBAP2_ENST00000539807.1_Intron|UBAP2_ENST00000418786.2_Missense_Mutation_p.D156E|UBAP2_ENST00000360802.1_Missense_Mutation_p.D156E|UBAP2_ENST00000449054.1_Missense_Mutation_p.D156E	NM_001282529.1	NP_001269458.1			ubiquitin associated protein 2											endometrium(4)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(7)|lung(13)|ovary(3)|stomach(1)	32			LUSC - Lung squamous cell carcinoma(29;0.00575)	GBM - Glioblastoma multiforme(74;0.168)		CTTGATTGCAATCAATTCCAT	0.413																																																	0													240.0	243.0	242.0					9																	33986810		2203	4300	6503			55833			AB040924	CCDS6547.1, CCDS75828.1	9p11.2	2008-02-05			ENSG00000137073	ENSG00000137073			14185	protein-coding gene	gene with protein product						8871400	Standard	NM_018449		Approved	KIAA1491, bA176F3.5, FLJ22435	uc003ztq.1	Q5T6F2	OTTHUMG00000000427	ENST00000379239.4:c.-107T>A	9.37:g.33986810A>T				Missense_Mutation	SNP	ENST00000379239.4	37		.	.	.	.	.	.	.	.	.	.	A	17.81	3.481065	0.63849	.	.	ENSG00000137073	ENST00000379238;ENST00000449054;ENST00000360802;ENST00000431417;ENST00000379260;ENST00000418786;ENST00000412543;ENST00000421278	T;T;T;T;T	0.26373	1.74;1.74;1.74;1.74;1.74	5.45	0.162	0.14981	.	0.097410	0.64402	D	0.000002	T	0.33265	0.0857	L	0.46947	1.48	0.45378	D	0.998364	P;D;P;D;P	0.63046	0.911;0.992;0.911;0.986;0.714	P;P;B;P;B	0.60415	0.553;0.874;0.355;0.751;0.406	T	0.02450	-1.1157	10	0.41790	T	0.15	-15.4385	9.2541	0.37573	0.4751:0.0:0.5249:0.0	.	156;81;118;81;156	E7EWG4;F5H4D5;F5H2C8;B4DH66;Q5T6F2	.;.;.;.;UBAP2_HUMAN	E	156;156;156;118;96;156;156;32	ENSP00000368540:D156E;ENSP00000416932:D156E;ENSP00000354039:D156E;ENSP00000404436:D156E;ENSP00000414800:D156E	ENSP00000354039:D156E	D	-	3	2	UBAP2	33976810	0.985000	0.35326	0.997000	0.53966	0.885000	0.51271	0.835000	0.27531	0.036000	0.15547	0.459000	0.35465	GAT		0.413	UBAP2-202	KNOWN	basic	protein_coding	protein_coding			NM_018449	
VHL	7428	hgsc.bcm.edu;ucsc.edu	37	3	10188243	10188243	+	Missense_Mutation	SNP	T	T	C			TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr3:10188243T>C	ENST00000256474.2	+	2	1226	c.386T>C	c.(385-387)cTg>cCg	p.L129P	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	129	Involved in binding to CCT complex.		L -> LE (in VHLD).		cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.H125fs*27(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GATGGGCTTCTGGTTAACCAA	0.473		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	1	Deletion - Frameshift(1)	kidney(1)	GRCh37	CI024081	VHL	I							202.0	186.0	192.0					3																	10188243		2203	4300	6503	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.386T>C	3.37:g.10188243T>C	ENSP00000256474:p.Leu129Pro		B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	T	13.35	2.212082	0.39102	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99848	-7.14	5.07	3.89	0.44902	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.332531	0.28977	N	0.013530	D	0.99591	0.9852	L	0.52573	1.65	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	D	0.98141	1.0436	10	0.51188	T	0.08	-18.8889	10.4626	0.44590	0.0:0.0:0.1639:0.8361	.	129	P40337	VHL_HUMAN	P	129;47	ENSP00000256474:L129P	ENSP00000256474:L129P	L	+	2	0	VHL	10163243	1.000000	0.71417	0.998000	0.56505	0.189000	0.23516	3.266000	0.51569	0.869000	0.35703	-0.460000	0.05396	CTG		0.473	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
ZDHHC11	79844	hgsc.bcm.edu;ucsc.edu	37	5	819652	819653	+	Frame_Shift_Ins	INS	-	-	C	rs572001257		TCGA-BP-4329-01A-02D-1366-10	TCGA-BP-4329-11A-01D-1366-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			SOLID	755f62a8-13ea-4def-b5b6-14b536c56ec2	bf401206-d93e-41a9-9daf-42e565f5307d	g.chr5:819652_819653insC	ENST00000283441.8	-	10	1516_1517	c.1133_1134insG	c.(1132-1134)ggcfs	p.G378fs	ZDHHC11_ENST00000503758.2_5'UTR|ZDHHC11_ENST00000424784.2_Frame_Shift_Ins_p.G378fs	NM_024786.2	NP_079062.1	Q9H8X9	ZDH11_HUMAN	zinc finger, DHHC-type containing 11	378						endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	protein-cysteine S-palmitoyltransferase activity (GO:0019706)|zinc ion binding (GO:0008270)			haematopoietic_and_lymphoid_tissue(1)|liver(1)|lung(10)|pancreas(1)|prostate(5)|skin(2)|urinary_tract(1)	21			Epithelial(17;0.000445)|all cancers(22;0.00176)|OV - Ovarian serous cystadenocarcinoma(19;0.00227)|Lung(60;0.0863)			GTGCCATCGAGCCCCCGTCTGG	0.584																																																	0																																										SO:0001589	frameshift_variant	79844			AK023215	CCDS3857.1	5p15.2	2011-02-09			ENSG00000188818	ENSG00000188818		"""Zinc fingers, DHHC-type"""	19158	protein-coding gene	gene with protein product							Standard	NM_024786		Approved	ZNF399, FLJ13153	uc011cma.1	Q9H8X9	OTTHUMG00000090319	ENST00000283441.8:c.1134dupG	5.37:g.819657_819657dupC	ENSP00000283441:p.Gly378fs		Q6UWR9	Frame_Shift_Ins	INS	ENST00000283441.8	37	CCDS3857.1																																																																																				0.584	ZDHHC11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206681.3		NM_024786	
