#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
ANKIB1	54467	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	92027912	92027912	+	Silent	SNP	C	C	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr7:92027912C>A	ENST00000265742.3	+	20	3295	c.2919C>A	c.(2917-2919)atC>atA	p.I973I		NM_019004.1	NP_061877.1	Q9P2G1	AKIB1_HUMAN	ankyrin repeat and IBR domain containing 1	973							zinc ion binding (GO:0008270)	p.I973I(1)		cervix(1)|endometrium(7)|kidney(3)|large_intestine(10)|lung(19)|skin(1)	41	all_cancers(62;2.06e-09)|all_epithelial(64;9.24e-09)|Breast(17;0.0034)|all_lung(186;0.0509)|Lung NSC(181;0.0692)		STAD - Stomach adenocarcinoma(171;6.16e-05)|all cancers(6;0.00183)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TCGGCAACATCATGGCTTGGT	0.488																																																	1	Substitution - coding silent(1)	kidney(1)											136.0	132.0	134.0					7																	92027912		2026	4185	6211	SO:0001819	synonymous_variant	54467			AB037807	CCDS47639.1	7q21.3	2013-01-10			ENSG00000001629	ENSG00000001629		"""Ankyrin repeat domain containing"""	22215	protein-coding gene	gene with protein product							Standard	NM_019004		Approved	DKFZP434A0225, KIAA1386	uc003ulw.2	Q9P2G1	OTTHUMG00000155859	ENST00000265742.3:c.2919C>A	7.37:g.92027912C>A			Q6GMS4|Q6P3S9|Q9NTD7|Q9NW49	Silent	SNP	ENST00000265742.3	37	CCDS47639.1																																																																																				0.488	ANKIB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000342018.1			
AP3B1	8546	hgsc.bcm.edu	37	5	77396836	77396838	+	In_Frame_Del	DEL	TTC	TTC	-	rs199702315	byFrequency	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr5:77396836_77396838delTTC	ENST00000255194.6	-	21	2584_2586	c.2409_2411delGAA	c.(2407-2412)aagaaa>aaa	p.803_804KK>K	AP3B1_ENST00000519295.1_In_Frame_Del_p.754_755KK>K	NM_001271769.1	NP_001258698.1	O00203	AP3B1_HUMAN	adaptor-related protein complex 3, beta 1 subunit	803				Missing (in Ref. 1; AAD03778). {ECO:0000305}.	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)|blood coagulation (GO:0007596)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|positive regulation of NK T cell differentiation (GO:0051138)|protein targeting to lysosome (GO:0006622)	AP-3 adaptor complex (GO:0030123)|cytoplasmic vesicle (GO:0031410)|Golgi apparatus (GO:0005794)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)	GTP-dependent protein binding (GO:0030742)|protein phosphatase binding (GO:0019903)			breast(5)|central_nervous_system(2)|cervix(1)|endometrium(3)|large_intestine(12)|lung(12)|prostate(1)|skin(2)|urinary_tract(1)	39		all_lung(232;0.000397)|Lung NSC(167;0.00106)|Ovarian(174;0.0105)|Prostate(461;0.215)		OV - Ovarian serous cystadenocarcinoma(54;8.23e-47)|Epithelial(54;2.74e-41)|all cancers(79;4.8e-36)		TTGCTTTGTTTTCTTTTCTTTCT	0.266									Hermansky-Pudlak syndrome					32	0.00638978	0.0	0.0115	5008	,	,		16595	0.0		0.0219	False		,,,				2504	0.002																0										16,4220		0,16,2102						4.3	0.1			46	161,8049		4,153,3948	no	coding	AP3B1	NM_003664.3		4,169,6050	A1A1,A1R,RR		1.961,0.3777,1.4221				177,12269				SO:0001651	inframe_deletion	8546	Familial Cancer Database	HPS, HPS1-8	U81504	CCDS4041.1, CCDS64186.1	5q14.1	2014-09-17			ENSG00000132842	ENSG00000132842			566	protein-coding gene	gene with protein product		603401				9182526, 9151686	Standard	NM_003664		Approved	ADTB3A, HPS2	uc003kfj.4	O00203	OTTHUMG00000106919	ENST00000255194.6:c.2409_2411delGAA	5.37:g.77396836_77396838delTTC	ENSP00000255194:p.Lys804del		E5RJ68|O00580|Q7Z393|Q9HD66	In_Frame_Del	DEL	ENST00000255194.6	37	CCDS4041.1																																																																																				0.266	AP3B1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000225548.2			
C14orf39	317761	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	60928115	60928116	+	Missense_Mutation	DNP	CT	CT	TC			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C|T	C|T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr14:60928115_60928116CT>TC	ENST00000321731.3	-	13	1232_1233	c.1073_1074AG>GA	c.(1072-1074)cAG>cGA	p.Q358R		NM_174978.2	NP_777638	Q8N1H7	S6OS1_HUMAN	chromosome 14 open reading frame 39	358					multicellular organismal development (GO:0007275)|regulation of sequence-specific DNA binding transcription factor activity (GO:0051090)			p.Q358R(2)|p.Q358Q(1)		breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(5)|lung(7)|ovary(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	30				OV - Ovarian serous cystadenocarcinoma(108;0.0448)		TTGATTGTTTCTGTGGGGTTAA	0.277																																																	3	Substitution - Missense(2)|Substitution - coding silent(1)	kidney(3)																																								SO:0001583	missense	317761			AK098187	CCDS9746.1	14q23.1	2012-11-05	2012-11-05	2012-11-05	ENSG00000179008	ENSG00000179008			19849	protein-coding gene	gene with protein product							Standard	NM_174978		Approved	SIX6OS1	uc001xez.4	Q8N1H7	OTTHUMG00000140332	ENST00000321731.3:c.1073_1074delinsTC	14.37:g.60928115_60928116delinsTC	ENSP00000324920:p.Gln358Arg		Q08AQ4	Silent|Missense_Mutation	SNP	ENST00000321731.3	37	CCDS9746.1																																																																																				0.277	C14orf39-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276948.1		NM_174978	
C1orf162	128346	broad.mit.edu;ucsc.edu	37	1	112019442	112019442	+	Silent	SNP	A	A	C	rs201845325		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr1:112019442A>C	ENST00000343534.5	+	3	310	c.60A>C	c.(58-60)acA>acC	p.T20T	C1orf162_ENST00000464591.1_3'UTR|C1orf162_ENST00000369718.3_Silent_p.T20T	NM_174896.2	NP_777556.1	Q8NEQ5	CA162_HUMAN	chromosome 1 open reading frame 162	20						integral component of membrane (GO:0016021)		p.T20T(1)		NS(1)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)	5		all_cancers(81;0.00116)|all_epithelial(167;0.000761)|all_lung(203;0.00277)|Lung NSC(277;0.0043)		Lung(183;0.0236)|Colorectal(144;0.0286)|all cancers(265;0.0572)|Epithelial(280;0.0862)|COAD - Colon adenocarcinoma(174;0.112)|LUSC - Lung squamous cell carcinoma(189;0.134)		CTCTCTCCACAGCAGCCCCAA	0.453																																																	1	Substitution - coding silent(1)	kidney(1)											216.0	183.0	194.0					1																	112019442		2203	4300	6503	SO:0001819	synonymous_variant	128346			BC017973	CCDS837.1, CCDS72837.1	1p13.2	2008-02-05			ENSG00000143110	ENSG00000143110			28344	protein-coding gene	gene with protein product						12477932	Standard	XM_005270475		Approved	MGC24133	uc001ebe.3	Q8NEQ5	OTTHUMG00000011750	ENST00000343534.5:c.60A>C	1.37:g.112019442A>C			Q5QNZ1	Silent	SNP	ENST00000343534.5	37	CCDS837.1																																																																																				0.453	C1orf162-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000032471.1		NM_174896	
CCDC3	83643	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	12940511	12940511	+	Missense_Mutation	SNP	G	G	T	rs150259960		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr10:12940511G>T	ENST00000378825.3	-	3	844	c.718C>A	c.(718-720)Ctg>Atg	p.L240M	CCDC3_ENST00000378839.1_Missense_Mutation_p.L115M	NM_031455.3	NP_113643.1	Q9BQI4	CCDC3_HUMAN	coiled-coil domain containing 3	240						endoplasmic reticulum (GO:0005783)|extracellular region (GO:0005576)		p.L240M(1)		central_nervous_system(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)|prostate(2)	11		Ovarian(717;0.0822)	BRCA - Breast invasive adenocarcinoma(52;0.163)			TGGTTCGCCAGCTCCAGGTGG	0.692																																																	1	Substitution - Missense(1)	kidney(1)											49.0	52.0	51.0					10																	12940511		2203	4300	6503	SO:0001583	missense	83643			BC051334	CCDS7093.1, CCDS60484.1	10p14	2004-02-13			ENSG00000151468	ENSG00000151468			23813	protein-coding gene	gene with protein product							Standard	NM_031455		Approved	DKFZp761F241	uc001ilq.1	Q9BQI4	OTTHUMG00000017689	ENST00000378825.3:c.718C>A	10.37:g.12940511G>T	ENSP00000368102:p.Leu240Met		Q5VYV8|Q5VYV9	Missense_Mutation	SNP	ENST00000378825.3	37	CCDS7093.1	.	.	.	.	.	.	.	.	.	.	G	16.73	3.203609	0.58234	.	.	ENSG00000151468	ENST00000378839;ENST00000378825	T	0.17370	2.28	5.42	4.5	0.54988	.	0.401864	0.23088	U	0.052070	T	0.16896	0.0406	L	0.36672	1.1	0.25333	N	0.989015	P	0.42203	0.773	P	0.45071	0.468	T	0.07028	-1.0794	10	0.36615	T	0.2	-4.1071	9.1325	0.36854	0.076:0.2783:0.6457:0.0	.	240	Q9BQI4	CCDC3_HUMAN	M	115;240	ENSP00000368116:L115M	ENSP00000368102:L240M	L	-	1	2	CCDC3	12980517	1.000000	0.71417	0.986000	0.45419	0.942000	0.58702	5.501000	0.66950	1.269000	0.44280	0.561000	0.74099	CTG		0.692	CCDC3-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000046829.1		NM_031455	
CCT8L2	150160	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	17073177	17073177	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr22:17073177C>G	ENST00000359963.3	-	1	523	c.264G>C	c.(262-264)tgG>tgC	p.W88C		NM_014406.4	NP_055221.1	Q96SF2	TCPQM_HUMAN	chaperonin containing TCP1, subunit 8 (theta)-like 2	88					anion transport (GO:0006820)|cellular protein metabolic process (GO:0044267)|potassium ion transmembrane transport (GO:0071805)|transport (GO:0006810)	cytoplasm (GO:0005737)	anion channel activity (GO:0005253)|ATP binding (GO:0005524)|calcium-activated potassium channel activity (GO:0015269)	p.W88C(1)		breast(3)|endometrium(7)|kidney(1)|large_intestine(8)|liver(2)|lung(37)|ovary(3)|prostate(3)|skin(2)|stomach(1)	67	all_hematologic(4;0.00567)|Acute lymphoblastic leukemia(84;0.0977)	all_epithelial(15;0.0157)|Lung NSC(13;0.147)|all_lung(157;0.175)				CCCGGAGGAGCCATGCTGCTG	0.617																																																	1	Substitution - Missense(1)	kidney(1)											71.0	58.0	63.0					22																	17073177		2203	4300	6503	SO:0001583	missense	150160			AP003553	CCDS13738.1	22q11.1	2011-09-01			ENSG00000198445	ENSG00000198445			15553	protein-coding gene	gene with protein product							Standard	NM_014406		Approved	CESK1	uc002zlp.1	Q96SF2	OTTHUMG00000141302	ENST00000359963.3:c.264G>C	22.37:g.17073177C>G	ENSP00000353048:p.Trp88Cys		A4QPH3|Q9UJS3	Missense_Mutation	SNP	ENST00000359963.3	37	CCDS13738.1	.	.	.	.	.	.	.	.	.	.	c	0.458	-0.890444	0.02491	.	.	ENSG00000198445	ENST00000359963	T	0.78246	-1.16	2.0	0.943	0.19531	.	1.327020	0.05804	U	0.612755	T	0.57504	0.2058	N	0.08118	0	0.09310	N	0.999997	B	0.06786	0.001	B	0.06405	0.002	T	0.52548	-0.8561	10	0.87932	D	0	-2.029	3.8843	0.09091	0.0:0.7711:0.0:0.2289	.	88	Q96SF2	TCPQM_HUMAN	C	88	ENSP00000353048:W88C	ENSP00000353048:W88C	W	-	3	0	CCT8L2	15453177	0.001000	0.12720	0.028000	0.17463	0.037000	0.13140	-0.034000	0.12225	1.126000	0.42016	0.393000	0.25936	TGG		0.617	CCT8L2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000280580.1			
CDC16	8881	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	115004884	115004884	+	Missense_Mutation	SNP	T	T	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr13:115004884T>G	ENST00000356221.3	+	5	408	c.300T>G	c.(298-300)aaT>aaG	p.N100K	CDC16_ENST00000252457.5_Missense_Mutation_p.N99K|CDC16_ENST00000375312.3_Missense_Mutation_p.N6K|CDC16_ENST00000375310.1_Missense_Mutation_p.N6K|CDC16_ENST00000252458.6_Missense_Mutation_p.N6K|CDC16_ENST00000360383.3_Missense_Mutation_p.N100K|CDC16_ENST00000375308.1_Missense_Mutation_p.N6K			Q13042	CDC16_HUMAN	cell division cycle 16	100					anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|cell proliferation (GO:0008283)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic spindle assembly checkpoint (GO:0007094)|negative regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051436)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|protein K11-linked ubiquitination (GO:0070979)|regulation of mitosis (GO:0007088)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)	anaphase-promoting complex (GO:0005680)|centrosome (GO:0005813)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleoplasm (GO:0005654)|spindle (GO:0005819)		p.N99K(1)		endometrium(3)|kidney(2)|large_intestine(5)|liver(2)|lung(6)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	22	Lung NSC(43;0.00299)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.0191)|all_epithelial(44;0.00716)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.238)	BRCA - Breast invasive adenocarcinoma(86;0.0886)			AGCCCATCAATAAAAGATTAT	0.443																																																	1	Substitution - Missense(1)	kidney(1)											61.0	65.0	64.0					13																	115004884		2203	4300	6503	SO:0001583	missense	8881			U18291	CCDS9542.2	13q34	2013-01-17	2013-01-17		ENSG00000130177	ENSG00000130177		"""Anaphase promoting complex subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	1720	protein-coding gene	gene with protein product	"""anaphase-promoting complex, subunit 6"""	603461	"""CDC16 (cell division cycle 16, S. cerevisiae, homolog)"", ""CDC16 cell division cycle 16 homolog (S. cerevisiae)"", ""cell division cycle 16 homolog (S. cerevisiae)"""			7736578	Standard	NM_001078645		Approved	APC6, ANAPC6, CUT9	uc001vul.1	Q13042	OTTHUMG00000017402	ENST00000356221.3:c.300T>G	13.37:g.115004884T>G	ENSP00000348554:p.Asn100Lys		A2A365|Q5T8C8|Q96AE6|Q9Y564	Missense_Mutation	SNP	ENST00000356221.3	37	CCDS9542.2	.	.	.	.	.	.	.	.	.	.	t	11.72	1.723561	0.30593	.	.	ENSG00000130177	ENST00000360383;ENST00000375312;ENST00000356221;ENST00000375310;ENST00000252457;ENST00000375308;ENST00000252458	T;T;T	0.39592	1.07;1.07;1.07	5.73	3.1	0.35709	Tetratricopeptide-like helical (1);	0.083787	0.85682	D	0.000000	T	0.24851	0.0603	N	0.19112	0.55	0.42796	D	0.993916	B;B;B;B	0.31054	0.061;0.306;0.226;0.156	B;B;B;B	0.27076	0.045;0.055;0.076;0.016	T	0.03993	-1.0986	9	.	.	.	-20.3028	11.0696	0.47995	0.0:0.7991:0.0:0.2009	.	100;99;99;100	B4DK74;Q13042-3;Q13042-2;Q13042	.;.;.;CDC16_HUMAN	K	100;6;100;6;99;6;6	ENSP00000353549:N100K;ENSP00000348554:N100K;ENSP00000252457:N99K	.	N	+	3	2	CDC16	114022986	1.000000	0.71417	0.991000	0.47740	0.544000	0.35116	1.601000	0.36773	0.364000	0.24374	-0.242000	0.12053	AAT		0.443	CDC16-009	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000276737.1		NM_003903	
CYLD	1540	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	50783997	50783997	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	C	A	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr16:50783997C>A	ENST00000427738.3	+	2	593	c.388C>A	c.(388-390)Cct>Act	p.P130T	CYLD_ENST00000398568.2_Missense_Mutation_p.P130T|CYLD_ENST00000568704.2_Missense_Mutation_p.P130T|CYLD_ENST00000311559.9_Missense_Mutation_p.P130T|CYLD_ENST00000540145.1_Missense_Mutation_p.P130T|CYLD_ENST00000569418.1_Missense_Mutation_p.P130T|CYLD_ENST00000564326.1_Missense_Mutation_p.P130T|CYLD_ENST00000566206.1_Missense_Mutation_p.P130T			Q9NQC7	CYLD_HUMAN	cylindromatosis (turban tumor syndrome)	130	Interaction with TRIP.				cell cycle (GO:0007049)|innate immune response (GO:0045087)|necroptotic process (GO:0070266)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of type I interferon production (GO:0032480)|nucleotide-binding domain, leucine rich repeat containing receptor signaling pathway (GO:0035872)|nucleotide-binding oligomerization domain containing signaling pathway (GO:0070423)|positive regulation of extrinsic apoptotic signaling pathway (GO:2001238)|protein K63-linked deubiquitination (GO:0070536)|regulation of intrinsic apoptotic signaling pathway (GO:2001242)|regulation of microtubule cytoskeleton organization (GO:0070507)|regulation of mitotic cell cycle (GO:0007346)|ubiquitin-dependent protein catabolic process (GO:0006511)|Wnt signaling pathway (GO:0016055)	centrosome (GO:0005813)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|microtubule (GO:0005874)|nucleus (GO:0005634)	Lys63-specific deubiquitinase activity (GO:0061578)|proline-rich region binding (GO:0070064)|protein kinase binding (GO:0019901)|ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.P130T(1)		central_nervous_system(4)|endometrium(1)|haematopoietic_and_lymphoid_tissue(4)|kidney(3)|large_intestine(9)|lung(17)|pancreas(1)|skin(22)|upper_aerodigestive_tract(1)	62		all_cancers(37;0.0156)				CGTGGGCTGTCCTGTGAAAGT	0.448			"""Mis, N, F, S"""		cylindroma	cylindroma			Multiple Trichoepithelioma, Familial;Familial Cylindromatosis																														yes	Rec	yes	Familial cylindromatosis	16	16q12-q13	1540	familial cylindromatosis gene		E	1	Substitution - Missense(1)	kidney(1)											76.0	73.0	74.0					16																	50783997		1845	4096	5941	SO:0001583	missense	1540	Familial Cancer Database	;FADC, Turban Tumor syndrome, Epithelioma Adenoides Cysticum of Brooke, Hereditary Multiple Benign Cystic Epithelioma, Dermal Eccrine Cylindromatosis, Brooke-Spiegler s.	AB020656	CCDS42164.1, CCDS45482.1	16q12-q13	2014-09-17							2584	protein-coding gene	gene with protein product	"""ubiquitin specific peptidase like 2"""	605018		CYLD1		7493027	Standard	NM_015247		Approved	KIAA0849, USPL2	uc002egq.1	Q9NQC7		ENST00000427738.3:c.388C>A	16.37:g.50783997C>A	ENSP00000392025:p.Pro130Thr		O94934|Q7L3N6|Q96EH0|Q9NZX9	Missense_Mutation	SNP	ENST00000427738.3	37	CCDS45482.1	.	.	.	.	.	.	.	.	.	.	C	11.93	1.785117	0.31593	.	.	ENSG00000083799	ENST00000540145;ENST00000311559;ENST00000427738;ENST00000398568	T;T;T;T	0.74002	-0.8;-0.8;-0.8;-0.8	6.17	3.15	0.36227	Cytoskeleton-associated protein, Gly-rich domain (3);	0.416130	0.29066	N	0.013247	T	0.52354	0.1729	N	0.14661	0.345	0.32723	N	0.509998	B;B;B;B	0.20164	0.042;0.034;0.034;0.042	B;B;B;B	0.25506	0.061;0.036;0.036;0.061	T	0.50783	-0.8787	10	0.13470	T	0.59	-3.2756	7.0451	0.25040	0.0:0.5884:0.27:0.1416	.	130;130;130;130	A8KAB0;F5H2R7;Q9NQC7-2;Q9NQC7	.;.;.;CYLD_HUMAN	T	130	ENSP00000445447:P130T;ENSP00000308928:P130T;ENSP00000392025:P130T;ENSP00000381574:P130T	ENSP00000308928:P130T	P	+	1	0	CYLD	49341498	0.981000	0.34729	0.976000	0.42696	0.923000	0.55619	2.494000	0.45329	0.914000	0.36822	0.655000	0.94253	CCT		0.448	CYLD-010	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000422998.2			
DENND4A	10260	broad.mit.edu;hgsc.bcm.edu	37	15	65983198	65983198	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr15:65983198C>G	ENST00000431932.2	-	22	3810	c.3602G>C	c.(3601-3603)aGg>aCg	p.R1201T	DENND4A_ENST00000567323.1_5'Flank|DENND4A_ENST00000443035.3_Missense_Mutation_p.R1244T	NM_005848.3	NP_005839.3	Q7Z401	MYCPP_HUMAN	DENN/MADD domain containing 4A	1201					positive regulation of Rab GTPase activity (GO:0032851)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.R1203T(1)|p.R1244T(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(17)|lung(11)|ovary(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	51						TAAATCACGCCTAGCAGATGG	0.418																																																	2	Substitution - Missense(2)	kidney(2)											79.0	78.0	78.0					15																	65983198		1974	4156	6130	SO:0001583	missense	10260			AF534403	CCDS45285.1, CCDS53949.1	15q22.31	2012-10-03	2006-01-27	2006-01-27				"""DENN/MADD domain containing"""	24321	protein-coding gene	gene with protein product		600382	"""c-myc promoter binding protein"""	MYCPBP		8056341, 12906859	Standard	NM_005848		Approved	IRLB	uc002api.3	Q7Z401		ENST00000431932.2:c.3602G>C	15.37:g.65983198C>G	ENSP00000396830:p.Arg1201Thr		E7EPL3|Q14655|Q86T77|Q8IVX2|Q8NB93	Missense_Mutation	SNP	ENST00000431932.2	37	CCDS45285.1	.	.	.	.	.	.	.	.	.	.	C	10.22	1.288981	0.23478	.	.	ENSG00000174485	ENST00000443035;ENST00000431932	T;T	0.05580	3.42;3.43	5.37	2.44	0.29823	.	0.459602	0.23325	N	0.049405	T	0.06645	0.0170	L	0.47716	1.5	0.42111	D	0.991389	B;B	0.32573	0.376;0.115	B;B	0.32090	0.14;0.105	T	0.33111	-0.9881	10	0.41790	T	0.15	.	9.5083	0.39060	0.0:0.7154:0.0:0.2846	.	1244;1201	E7EPL3;Q7Z401	.;MYCPP_HUMAN	T	1244;1201	ENSP00000391167:R1244T;ENSP00000396830:R1201T	ENSP00000396830:R1201T	R	-	2	0	DENND4A	63770252	0.543000	0.26434	0.835000	0.33067	0.979000	0.70002	1.687000	0.37680	0.769000	0.33313	0.655000	0.94253	AGG		0.418	DENND4A-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419611.1		NM_005848	
DIXDC1	85458	hgsc.bcm.edu	37	11	111865799	111865800	+	Frame_Shift_Ins	INS	-	-	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr11:111865799_111865800insG	ENST00000440460.2	+	16	1788_1789	c.1491_1492insG	c.(1492-1494)ggafs	p.G498fs	DIXDC1_ENST00000389821.4_3'UTR|DIXDC1_ENST00000315253.5_Frame_Shift_Ins_p.G287fs	NM_001037954.2	NP_001033043.1	Q155Q3	DIXC1_HUMAN	DIX domain containing 1	499					camera-type eye development (GO:0043010)|cell cycle (GO:0007049)|cerebellar cortex development (GO:0021695)|cerebral cortex radially oriented cell migration (GO:0021799)|forebrain development (GO:0030900)|forebrain ventricular zone progenitor cell division (GO:0021869)|negative regulation of neuron differentiation (GO:0045665)|positive regulation of axonogenesis (GO:0050772)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|positive regulation of JNK cascade (GO:0046330)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of JNK cascade (GO:0046328)|regulation of microtubule cytoskeleton organization (GO:0070507)|Wnt signaling pathway (GO:0016055)	axon terminus (GO:0043679)|cell cortex (GO:0005938)|cell junction (GO:0030054)|cytosol (GO:0005829)|neuronal cell body (GO:0043025)|protein complex (GO:0043234)	gamma-tubulin binding (GO:0043015)|mitogen-activated protein kinase kinase kinase binding (GO:0031435)			cervix(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)	17		all_cancers(61;7.58e-15)|all_epithelial(67;5.42e-09)|Melanoma(852;1.91e-06)|all_hematologic(158;0.000405)|Acute lymphoblastic leukemia(157;0.000967)|Breast(348;0.0112)|all_neural(223;0.0281)|Medulloblastoma(222;0.0425)		Epithelial(105;2.99e-07)|BRCA - Breast invasive adenocarcinoma(274;6.72e-07)|all cancers(92;6.25e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.0548)		TTCCAACGGCAGGAAAAGGAGC	0.47																																																	0																																										SO:0001589	frameshift_variant	85458			AB051522	CCDS60957.1, CCDS73381.1, CCDS73382.1	11q23.1	2014-03-20			ENSG00000150764	ENSG00000150764			23695	protein-coding gene	gene with protein product		610493				12792787	Standard	NM_001037954		Approved	KIAA1735, Dixin	uc001pmm.3	Q155Q3	OTTHUMG00000166912	ENST00000440460.2:c.1493dupG	11.37:g.111865801_111865801dupG	ENSP00000394352:p.Gly498fs		A1A5D8|E9PRV4|Q6P2J8|Q6PIK4|Q86SR7|Q8IVY4|Q96N69|Q9C0C8	Frame_Shift_Ins	INS	ENST00000440460.2	37																																																																																					0.470	DIXDC1-202	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_001037954	
DOCK8	81704	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	406989	406989	+	Silent	SNP	T	T	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr9:406989T>A	ENST00000453981.1	+	28	3562	c.3450T>A	c.(3448-3450)acT>acA	p.T1150T	DOCK8_ENST00000382329.1_Silent_p.T617T|DOCK8_ENST00000432829.2_Silent_p.T1082T|DOCK8_ENST00000469391.1_Silent_p.T1050T			Q8NF50	DOCK8_HUMAN	dedicator of cytokinesis 8	1150					blood coagulation (GO:0007596)|dendritic cell migration (GO:0036336)|immunological synapse formation (GO:0001771)|memory T cell proliferation (GO:0061485)|negative regulation of T cell apoptotic process (GO:0070233)|small GTPase mediated signal transduction (GO:0007264)	cell leading edge (GO:0031252)|cytosol (GO:0005829)|membrane (GO:0016020)	guanyl-nucleotide exchange factor activity (GO:0005085)	p.T1150T(1)|p.T1082T(1)		breast(1)|central_nervous_system(5)|endometrium(2)|kidney(6)|large_intestine(13)|lung(22)|ovary(3)|prostate(3)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(6)	65		all_cancers(5;2.13e-17)|all_epithelial(5;2.15e-12)|all_lung(10;6.69e-11)|Lung NSC(10;1.08e-10)|Acute lymphoblastic leukemia(5;0.000242)|all_hematologic(5;0.00317)|Breast(48;0.0151)|Prostate(43;0.128)		all cancers(5;9.3e-07)|GBM - Glioblastoma multiforme(5;2.41e-06)|Epithelial(6;0.00557)|Lung(218;0.00942)		TCGATCTGACTTCCGAGTACC	0.527																																																	2	Substitution - coding silent(2)	kidney(2)											105.0	101.0	102.0					9																	406989		2203	4300	6503	SO:0001819	synonymous_variant	81704			AK090429	CCDS6440.1, CCDS6440.2, CCDS55283.1, CCDS55284.1	9p24.3	2014-09-17			ENSG00000107099	ENSG00000107099			19191	protein-coding gene	gene with protein product		611432				11214971	Standard	NM_203447		Approved	FLJ00026, FLJ00152, ZIR8, FLJ00346	uc003zgf.2	Q8NF50	OTTHUMG00000078789	ENST00000453981.1:c.3450T>A	9.37:g.406989T>A			A2A350|A2BDF2|A4FU78|B7ZLP0|E9PH09|Q3MV16|Q5JPJ1|Q8TEP1|Q8WUY2|Q9BYJ5|Q9H1Q2|Q9H1Q3|Q9H308|Q9H7P2	Silent	SNP	ENST00000453981.1	37	CCDS6440.2																																																																																				0.527	DOCK8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000171792.5		XM_036307	
DOPEY1	23033	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	83823121	83823121	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr6:83823121T>C	ENST00000349129.2	+	7	1021	c.761T>C	c.(760-762)tTt>tCt	p.F254S	DOPEY1_ENST00000536812.1_3'UTR|DOPEY1_ENST00000237163.5_Missense_Mutation_p.F254S|DOPEY1_ENST00000369739.3_Missense_Mutation_p.F254S	NM_015018.3	NP_055833.2	Q5JWR5	DOP1_HUMAN	dopey family member 1	254					protein transport (GO:0015031)			p.F254S(1)		breast(4)|central_nervous_system(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(16)|ovary(5)|pancreas(1)|prostate(1)|skin(5)|upper_aerodigestive_tract(2)	67		all_cancers(76;2.29e-06)|Acute lymphoblastic leukemia(125;3.41e-06)|all_hematologic(105;0.000865)|all_epithelial(107;0.00203)		BRCA - Breast invasive adenocarcinoma(397;0.053)		CTCTTCTGTTTTCCATTCCAC	0.363																																																	1	Substitution - Missense(1)	kidney(1)											156.0	135.0	142.0					6																	83823121		2203	4300	6503	SO:0001583	missense	23033			AK027030	CCDS4996.1, CCDS64467.1	6q15	2013-03-05	2006-02-02	2006-02-02	ENSG00000083097	ENSG00000083097			21194	protein-coding gene	gene with protein product			"""KIAA1117"""	KIAA1117		16301316, 16303751, 10931277	Standard	NM_015018		Approved	dJ202D23.2	uc011dyy.2	Q5JWR5	OTTHUMG00000016365	ENST00000349129.2:c.761T>C	6.37:g.83823121T>C	ENSP00000195654:p.Phe254Ser		Q86XV1|Q9H5J5|Q9NSL4|Q9UPN5|Q9Y414	Missense_Mutation	SNP	ENST00000349129.2	37	CCDS4996.1	.	.	.	.	.	.	.	.	.	.	T	21.3	4.134552	0.77662	.	.	ENSG00000083097	ENST00000349129;ENST00000237163;ENST00000369739	T;T;T	0.27104	1.7;1.7;1.69	5.81	5.81	0.92471	Dopey, N-terminal (1);	0.000000	0.85682	D	0.000000	T	0.51618	0.1685	M	0.89904	3.07	0.80722	D	1	D;D	0.76494	0.999;0.999	D;D	0.83275	0.996;0.996	T	0.60652	-0.7221	10	0.49607	T	0.09	.	16.1592	0.81686	0.0:0.0:0.0:1.0	.	254;254	B2RWN9;Q5JWR5	.;DOP1_HUMAN	S	254	ENSP00000195654:F254S;ENSP00000237163:F254S;ENSP00000358754:F254S	ENSP00000237163:F254S	F	+	2	0	DOPEY1	83879840	1.000000	0.71417	1.000000	0.80357	0.513000	0.34164	7.913000	0.87471	2.210000	0.71456	0.533000	0.62120	TTT		0.363	DOPEY1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043785.2		NM_015018	
DYRK1A	1859	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	38845082	38845082	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr21:38845082A>G	ENST00000398960.2	+	2	182	c.107A>G	c.(106-108)cAt>cGt	p.H36R	DYRK1A_ENST00000321219.8_Missense_Mutation_p.H36R|DYRK1A_ENST00000451934.1_Missense_Mutation_p.H36R|DYRK1A_ENST00000462274.1_3'UTR|DYRK1A_ENST00000339659.4_Missense_Mutation_p.H36R|DYRK1A_ENST00000338785.3_Missense_Mutation_p.H36R|DYRK1A_ENST00000398956.2_Missense_Mutation_p.H36R	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	36					circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)	p.H36R(1)		breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CAGATGCCCCATTCACATCAG	0.488																																					Melanoma(114;464 1602 31203 43785 45765)												1	Substitution - Missense(1)	kidney(1)											142.0	125.0	131.0					21																	38845082		2203	4300	6503	SO:0001583	missense	1859			U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.107A>G	21.37:g.38845082A>G	ENSP00000381932:p.His36Arg		O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	37	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	A	27.6	4.845673	0.91197	.	.	ENSG00000157540	ENST00000338785;ENST00000455097;ENST00000426672;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956	T;T;T;T;T;T;T	0.56103	0.52;0.8;0.48;0.53;0.52;0.48;0.53	6.16	6.16	0.99307	.	0.000000	0.85682	D	0.000000	T	0.61850	0.2380	L	0.46157	1.445	0.80722	D	1	D;D;P;D;D	0.53462	0.96;0.96;0.932;0.96;0.96	D;D;P;D;D	0.64237	0.923;0.923;0.84;0.923;0.923	T	0.55315	-0.8160	10	0.07325	T	0.83	.	16.8061	0.85666	1.0:0.0:0.0:0.0	.	36;36;36;36;36	Q13627-3;Q13627-4;Q13627;Q13627-2;Q13627-5	.;.;DYR1A_HUMAN;.;.	R	36	ENSP00000342690:H36R;ENSP00000412269:H36R;ENSP00000340373:H36R;ENSP00000319032:H36R;ENSP00000416089:H36R;ENSP00000381932:H36R;ENSP00000381929:H36R	ENSP00000319032:H36R	H	+	2	0	DYRK1A	37766952	1.000000	0.71417	1.000000	0.80357	0.981000	0.71138	8.962000	0.93254	2.367000	0.80283	0.528000	0.53228	CAT		0.488	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1		NM_001396	
DYRK1A	1859	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	38862648	38862648	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr21:38862648C>G	ENST00000398960.2	+	6	911	c.836C>G	c.(835-837)cCa>cGa	p.P279R	DYRK1A_ENST00000321219.8_Missense_Mutation_p.P279R|DYRK1A_ENST00000451934.1_Missense_Mutation_p.P279R|DYRK1A_ENST00000339659.4_Missense_Mutation_p.P270R|DYRK1A_ENST00000338785.3_Missense_Mutation_p.P279R|DYRK1A_ENST00000398956.2_Missense_Mutation_p.P279R|DYRK1A_ENST00000455387.2_Missense_Mutation_p.P51R	NM_001396.3|NM_130438.2	NP_001387.2|NP_569122.1	Q13627	DYR1A_HUMAN	dual-specificity tyrosine-(Y)-phosphorylation regulated kinase 1A	279	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				circadian rhythm (GO:0007623)|mitotic cell cycle (GO:0000278)|negative regulation of DNA damage response, signal transduction by p53 class mediator (GO:0043518)|nervous system development (GO:0007399)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of protein deacetylation (GO:0090312)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)	nuclear speck (GO:0016607)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	ATP binding (GO:0005524)|non-membrane spanning protein tyrosine kinase activity (GO:0004715)|protein kinase activity (GO:0004672)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|protein tyrosine kinase activity (GO:0004713)|tau protein binding (GO:0048156)	p.P279R(1)		breast(4)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(5)|lung(10)|ovary(3)|pancreas(1)|prostate(3)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	42						CTTGCGACTCCAGAACTTAGT	0.423																																					Melanoma(114;464 1602 31203 43785 45765)												1	Substitution - Missense(1)	kidney(1)											103.0	94.0	97.0					21																	38862648		2203	4300	6503	SO:0001583	missense	1859			U52373	CCDS13653.1, CCDS13654.1, CCDS42925.1, CCDS42926.1	21q22.13	2010-04-21			ENSG00000157540	ENSG00000157540			3091	protein-coding gene	gene with protein product		600855		DYRK1, DYRK, MNBH		9284911	Standard	NM_130436		Approved		uc002ywk.3	Q13627	OTTHUMG00000086657	ENST00000398960.2:c.836C>G	21.37:g.38862648C>G	ENSP00000381932:p.Pro279Arg		O60769|Q92582|Q92810|Q9UNM5	Missense_Mutation	SNP	ENST00000398960.2	37	CCDS42925.1	.	.	.	.	.	.	.	.	.	.	C	28.6	4.931409	0.92389	.	.	ENSG00000157540	ENST00000338785;ENST00000339659;ENST00000321219;ENST00000451934;ENST00000398960;ENST00000398956;ENST00000455387	T;T;T;T;T;T;T	0.18174	2.23;2.23;2.23;2.23;2.23;2.23;2.23	5.91	5.91	0.95273	Serine/threonine-protein kinase-like domain (1);Serine/threonine-protein kinase, catalytic  domain (1);Protein kinase-like domain (1);Protein kinase, catalytic domain (1);	0.048262	0.85682	D	0.000000	T	0.29223	0.0727	N	0.12961	0.28	0.80722	D	1	D;D;D;D;D	0.71674	0.998;0.998;0.995;0.994;0.998	D;D;D;D;D	0.78314	0.991;0.991;0.957;0.928;0.991	T	0.15235	-1.0444	10	0.87932	D	0	.	20.2989	0.98608	0.0:1.0:0.0:0.0	.	279;279;279;270;279	Q13627-3;Q13627-4;Q13627;Q13627-2;Q13627-5	.;.;DYR1A_HUMAN;.;.	R	279;270;279;279;279;279;51	ENSP00000342690:P279R;ENSP00000340373:P270R;ENSP00000319032:P279R;ENSP00000416089:P279R;ENSP00000381932:P279R;ENSP00000381929:P279R;ENSP00000407854:P51R	ENSP00000319032:P279R	P	+	2	0	DYRK1A	37784518	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.741000	0.84997	2.794000	0.96219	0.573000	0.79308	CCA		0.423	DYRK1A-006	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000194804.1		NM_001396	
E2F5	1875	broad.mit.edu	37	8	86119690	86119690	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr8:86119690C>A	ENST00000416274.2	+	5	615	c.581C>A	c.(580-582)tCt>tAt	p.S194Y	E2F5_ENST00000256117.5_Missense_Mutation_p.S195Y|E2F5_ENST00000519128.1_3'UTR|E2F5_ENST00000521429.1_Missense_Mutation_p.S21Y|E2F5_ENST00000418930.2_Missense_Mutation_p.S194Y|E2F5_ENST00000517476.1_Missense_Mutation_p.S33Y	NM_001083588.1|NM_001951.3	NP_001077057.1|NP_001942.2	Q15329	E2F5_HUMAN	E2F transcription factor 5, p130-binding	194	Dimerization. {ECO:0000255}.				gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|organ morphogenesis (GO:0009887)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of cell cycle (GO:0051726)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|transcription factor complex (GO:0005667)	DNA binding (GO:0003677)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription factor binding (GO:0008134)	p.S194Y(1)		NS(1)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)	8						CAGGCACCTTCTGGTACACAA	0.353																																																	1	Substitution - Missense(1)	kidney(1)											48.0	47.0	48.0					8																	86119690		1807	4067	5874	SO:0001583	missense	1875			X86097	CCDS47885.1, CCDS47886.1, CCDS55254.1	8q21.2	2004-01-29			ENSG00000133740	ENSG00000133740			3119	protein-coding gene	gene with protein product		600967				7892279	Standard	NM_001083588		Approved		uc003ycz.4	Q15329	OTTHUMG00000164785	ENST00000416274.2:c.581C>A	8.37:g.86119690C>A	ENSP00000398124:p.Ser194Tyr		E9PBN9|Q16601|Q92756	Missense_Mutation	SNP	ENST00000416274.2	37	CCDS47885.1	.	.	.	.	.	.	.	.	.	.	C	18.81	3.703645	0.68501	.	.	ENSG00000133740	ENST00000418930;ENST00000256117;ENST00000416274;ENST00000517476;ENST00000521429;ENST00000518234	D;D;D;D;D;D	0.86297	-2.1;-2.1;-2.1;-2.1;-2.1;-2.1	5.79	5.79	0.91817	.	0.113314	0.64402	D	0.000009	D	0.90854	0.7127	M	0.69248	2.105	0.45594	D	0.998537	D;P;P	0.63880	0.993;0.948;0.913	D;P;P	0.63113	0.911;0.673;0.474	D	0.87098	0.2177	10	0.10111	T	0.7	-7.6587	16.5119	0.84288	0.0:0.8607:0.1393:0.0	.	21;194;194	E5RHD4;Q15329-2;Q15329	.;.;E2F5_HUMAN	Y	194;195;194;33;21;30	ENSP00000414312:S194Y;ENSP00000256117:S195Y;ENSP00000398124:S194Y;ENSP00000429120:S33Y;ENSP00000428606:S21Y;ENSP00000429669:S30Y	ENSP00000256117:S195Y	S	+	2	0	E2F5	86306942	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	2.527000	0.45615	2.741000	0.93983	0.585000	0.79938	TCT		0.353	E2F5-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380274.1		NM_001951	
EPHA10	284656	broad.mit.edu	37	1	38227126	38227126	+	Silent	SNP	G	G	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina GAIIx	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr1:38227126G>T	ENST00000373048.4	-	3	800	c.801C>A	c.(799-801)ggC>ggA	p.G267G	EPHA10_ENST00000427468.2_Silent_p.G267G|EPHA10_ENST00000319637.6_Silent_p.G267G	NM_001099439.1	NP_001092909.1	Q5JZY3	EPHAA_HUMAN	EPH receptor A10	267					ephrin receptor signaling pathway (GO:0048013)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|transmembrane-ephrin receptor activity (GO:0005005)	p.G267G(1)		NS(2)|breast(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(13)|prostate(3)|skin(8)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	50	Acute lymphoblastic leukemia(166;0.074)|all_hematologic(146;0.197)	Myeloproliferative disorder(586;0.0255)|all_neural(195;0.164)				AGCTGCAGCGGCCCACAGGCA	0.692																																																	1	Substitution - coding silent(1)	kidney(1)											23.0	26.0	25.0					1																	38227126		2166	4211	6377	SO:0001819	synonymous_variant	284656			AK090974	CCDS425.1, CCDS41305.1	1p34.3	2013-02-11			ENSG00000183317	ENSG00000183317		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	19987	protein-coding gene	gene with protein product		611123				12477932	Standard	NM_001099439		Approved	FLJ16103, FLJ33655	uc009vvi.3	Q5JZY3	OTTHUMG00000004325	ENST00000373048.4:c.801C>A	1.37:g.38227126G>T			A4FU89|J3KPB5|Q6NW42	Silent	SNP	ENST00000373048.4	37	CCDS41305.1																																																																																				0.692	EPHA10-003	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000012497.2		NM_173641	
EPHA7	2045	broad.mit.edu;hgsc.bcm.edu	37	6	93969181	93969181	+	Silent	SNP	G	G	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr6:93969181G>C	ENST00000369303.4	-	10	1999	c.1815C>G	c.(1813-1815)acC>acG	p.T605T		NM_004440.3	NP_004431.1	Q15375	EPHA7_HUMAN	EPH receptor A7	605					brain development (GO:0007420)|branching morphogenesis of a nerve (GO:0048755)|ephrin receptor signaling pathway (GO:0048013)|negative chemotaxis (GO:0050919)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphorylation (GO:0016310)|positive regulation of neuron apoptotic process (GO:0043525)|regulation of cell-cell adhesion (GO:0022407)|regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043281)|regulation of ERK1 and ERK2 cascade (GO:0070372)|regulation of peptidyl-tyrosine phosphorylation (GO:0050730)|regulation of protein autophosphorylation (GO:0031952)|retinal ganglion cell axon guidance (GO:0031290)	dendrite (GO:0030425)|integral component of plasma membrane (GO:0005887)|neuromuscular junction (GO:0031594)|neuronal cell body (GO:0043025)|postsynaptic membrane (GO:0045211)	ATP binding (GO:0005524)|axon guidance receptor activity (GO:0008046)|chemorepellent activity (GO:0045499)|GPI-linked ephrin receptor activity (GO:0005004)|protein tyrosine kinase activity (GO:0004713)	p.T605T(1)		NS(1)|breast(1)|central_nervous_system(7)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(16)|lung(43)|ovary(8)|pancreas(1)|prostate(1)|skin(8)|stomach(1)|upper_aerodigestive_tract(13)|urinary_tract(1)	112		all_cancers(76;7.47e-10)|Acute lymphoblastic leukemia(125;1.88e-09)|all_hematologic(75;1.75e-07)|all_epithelial(107;3.6e-05)|Lung NSC(302;0.0368)|all_lung(197;0.0509)|Colorectal(196;0.142)		BRCA - Breast invasive adenocarcinoma(108;0.0847)		TGTAGGTTTTGGTGCCTGGAA	0.428																																																	1	Substitution - coding silent(1)	kidney(1)											191.0	175.0	180.0					6																	93969181		2203	4300	6503	SO:0001819	synonymous_variant	2045			L36642	CCDS5031.1, CCDS75494.1	6q16.3	2013-02-11	2004-10-28		ENSG00000135333	ENSG00000135333		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3390	protein-coding gene	gene with protein product		602190	"""EphA7"""			9267020	Standard	NM_004440		Approved	Hek11	uc003poe.3	Q15375	OTTHUMG00000015228	ENST00000369303.4:c.1815C>G	6.37:g.93969181G>C			A0AUX7|B2R8W1|B7ZLJ9|B7ZLK0|Q59G40|Q5VTU0|Q8N368|Q9H124	Silent	SNP	ENST00000369303.4	37	CCDS5031.1																																																																																				0.428	EPHA7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041545.1			
ERICH6	131831	hgsc.bcm.edu	37	3	150421527	150421527	+	Silent	SNP	C	C	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr3:150421527C>T	ENST00000295910.6	-	1	211	c.159G>A	c.(157-159)gaG>gaA	p.E53E	FAM194A_ENST00000491361.1_Intron|RP11-103G8.2_ENST00000475393.1_RNA|RP11-103G8.2_ENST00000471093.1_RNA	NM_152394.3	NP_689607.2														NS(1)|autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(1)|large_intestine(10)|lung(14)|ovary(1)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	38						ccaccacctcctcctcctcct	0.602																																																	0																																										SO:0001819	synonymous_variant	131831																														ENST00000295910.6:c.159G>A	3.37:g.150421527C>T				Silent	SNP	ENST00000295910.6	37	CCDS3151.2																																																																																				0.602	FAM194A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257666.1			
FAM96B	51647	broad.mit.edu;hgsc.bcm.edu	37	16	66966160	66966160	+	Silent	SNP	C	C	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr16:66966160C>T	ENST00000422424.2	-	5	473	c.438G>A	c.(436-438)ctG>ctA	p.L146L	CES2_ENST00000417689.1_5'Flank|CES2_ENST00000317091.4_5'Flank	NM_016062.3	NP_057146.1	Q9Y3D0	MIP18_HUMAN	family with sequence similarity 96, member B	146					chromosome segregation (GO:0007059)|small molecule metabolic process (GO:0044281)	CIA complex (GO:0097361)|cytoplasm (GO:0005737)|MMXD complex (GO:0071817)|nucleus (GO:0005634)|spindle (GO:0005819)		p.L146L(2)		kidney(1)	1		Ovarian(137;0.192)		OV - Ovarian serous cystadenocarcinoma(108;0.0862)|Epithelial(162;0.198)		GGGTGTTCTCCAGGGCAGCTG	0.582																																																	2	Substitution - coding silent(2)	kidney(2)											60.0	66.0	64.0					16																	66966160		1989	4175	6164	SO:0001819	synonymous_variant	51647				CCDS45506.1	16q22.1	2014-01-16			ENSG00000166595	ENSG00000166595			24261	protein-coding gene	gene with protein product		614778				11042152, 10810093, 23891004	Standard	NM_016062		Approved	CGI-128	uc021tjy.2	Q9Y3D0	OTTHUMG00000175408	ENST00000422424.2:c.438G>A	16.37:g.66966160C>T				Silent	SNP	ENST00000422424.2	37	CCDS45506.1																																																																																				0.582	FAM96B-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000429890.1		NM_016062	
FREM1	158326	hgsc.bcm.edu	37	9	14808065	14808066	+	Frame_Shift_Ins	INS	-	-	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr9:14808065_14808066insC	ENST00000380880.3	-	17	3743_3744	c.2960_2961insG	c.(2959-2961)ggcfs	p.G987fs	FREM1_ENST00000380881.4_Frame_Shift_Ins_p.G988fs|FREM1_ENST00000422223.2_Frame_Shift_Ins_p.G987fs			Q5H8C1	FREM1_HUMAN	FRAS1 related extracellular matrix 1	987					cell communication (GO:0007154)|cell-matrix adhesion (GO:0007160)|craniofacial suture morphogenesis (GO:0097094)	basement membrane (GO:0005604)|integral component of membrane (GO:0016021)	carbohydrate binding (GO:0030246)|metal ion binding (GO:0046872)			breast(3)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(23)|lung(40)|ovary(4)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	100				GBM - Glioblastoma multiforme(50;3.53e-06)		TCACAAAAGGGCCAGCCTCTCC	0.48																																																	0																																										SO:0001589	frameshift_variant	158326			AK058190	CCDS47952.1, CCDS55293.1	9p22.3	2010-06-04	2004-12-15	2004-12-15	ENSG00000164946	ENSG00000164946			23399	protein-coding gene	gene with protein product		608944	"""chromosome 9 open reading frame 154"""	C9orf154		12838346, 15345741	Standard	NM_144966		Approved	FLJ25461, C9orf145, C9orf143, DKFZp686M16108, TILRR	uc003zlm.3	Q5H8C1	OTTHUMG00000019575	ENST00000380880.3:c.2961dupG	9.37:g.14808067_14808067dupC	ENSP00000370262:p.Gly987fs		B7ZBX4|Q5VV00|Q5VV01|Q6MZI4|Q8NEG9|Q96LI3	Frame_Shift_Ins	INS	ENST00000380880.3	37	CCDS47952.1																																																																																				0.480	FREM1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000339474.2		NM_144966	
HBE1	3046	broad.mit.edu	37	11	5291073	5291073	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr11:5291073C>A	ENST00000380237.1	-	3	392	c.48G>T	c.(46-48)tgG>tgT	p.W16C	HBG2_ENST00000380259.2_Intron|HBE1_ENST00000292896.2_Missense_Mutation_p.W16C|HBG2_ENST00000380252.1_Intron			P02100	HBE_HUMAN	hemoglobin, epsilon 1	16					blood coagulation (GO:0007596)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|protein heterooligomerization (GO:0051291)	blood microparticle (GO:0072562)|cytosol (GO:0005829)|hemoglobin complex (GO:0005833)	heme binding (GO:0020037)|iron ion binding (GO:0005506)|oxygen binding (GO:0019825)|oxygen transporter activity (GO:0005344)	p.W16C(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(12)|skin(1)	20		Medulloblastoma(188;0.00225)|Breast(177;0.0155)|all_neural(188;0.0212)		Epithelial(150;1.34e-09)|BRCA - Breast invasive adenocarcinoma(625;0.135)		TCATCTTGCTCCACAGGCTAG	0.502																																																	1	Substitution - Missense(1)	kidney(1)											107.0	96.0	100.0					11																	5291073		2201	4297	6498	SO:0001583	missense	3046			BC015537	CCDS7756.1	11p15.5	2012-10-02			ENSG00000213931	ENSG00000213931			4830	protein-coding gene	gene with protein product		142100				2649166	Standard	NM_005330		Approved	HBE	uc001mal.1	P02100	OTTHUMG00000066675	ENST00000380237.1:c.48G>T	11.37:g.5291073C>A	ENSP00000369586:p.Trp16Cys		Q6FH44	Missense_Mutation	SNP	ENST00000380237.1	37	CCDS7756.1	.	.	.	.	.	.	.	.	.	.	C	15.97	2.990515	0.54041	.	.	ENSG00000213931	ENST00000380237;ENST00000292896;ENST00000396895	D;D;D	0.95918	-3.85;-3.85;-3.85	5.81	5.81	0.92471	Globin-like (1);Globin, structural domain (1);	0.226724	0.39759	U	0.001274	D	0.98698	0.9563	H	0.97440	4.005	0.80722	D	1	D	0.89917	1.0	D	0.75484	0.986	D	0.99466	1.0944	10	0.87932	D	0	-8.1505	18.6422	0.91399	0.0:1.0:0.0:0.0	.	16	P02100	HBE_HUMAN	C	16	ENSP00000369586:W16C;ENSP00000292896:W16C;ENSP00000380104:W16C	ENSP00000292896:W16C	W	-	3	0	HBE1	5247649	0.999000	0.42202	1.000000	0.80357	0.357000	0.29423	3.201000	0.51059	2.756000	0.94617	0.585000	0.79938	TGG		0.502	HBE1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000142973.2		NM_005330	
HIAT1	64645	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	100546150	100546150	+	Missense_Mutation	SNP	A	A	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr1:100546150A>C	ENST00000370152.3	+	11	1337	c.1201A>C	c.(1201-1203)Aaa>Caa	p.K401Q	SASS6_ENST00000462159.1_5'Flank|RP4-714D9.2_ENST00000432294.1_RNA	NM_033055.2	NP_149044.2	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1	401					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.K401Q(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|skin(1)	16		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)		TGTGGAACTTAAAGAACTGCC	0.413																																																	1	Substitution - Missense(1)	kidney(1)											167.0	163.0	165.0					1																	100546150		2203	4300	6503	SO:0001583	missense	64645			AK096669	CCDS763.1	1p21.3	2008-02-05			ENSG00000156875	ENSG00000156875			23363	protein-coding gene	gene with protein product						9299464	Standard	NM_033055		Approved	DKFZP564L0864	uc001dst.3	Q96MC6	OTTHUMG00000010755	ENST00000370152.3:c.1201A>C	1.37:g.100546150A>C	ENSP00000359171:p.Lys401Gln		Q6P2N7|Q8N8K2|Q8NBV3|Q96NY0|Q9NT25	Missense_Mutation	SNP	ENST00000370152.3	37	CCDS763.1	.	.	.	.	.	.	.	.	.	.	A	14.86	2.662332	0.47572	.	.	ENSG00000156875	ENST00000370152	T	0.80123	-1.34	5.54	5.54	0.83059	Major facilitator superfamily domain, general substrate transporter (1);Major facilitator superfamily domain (1);	0.121832	0.53938	D	0.000052	T	0.44891	0.1315	N	0.03608	-0.345	0.31489	N	0.666234	B	0.16396	0.017	B	0.19148	0.024	T	0.27297	-1.0078	10	0.23302	T	0.38	-26.8999	15.6646	0.77217	1.0:0.0:0.0:0.0	.	401	Q96MC6	HIAT1_HUMAN	Q	401	ENSP00000359171:K401Q	ENSP00000359171:K401Q	K	+	1	0	HIAT1	100318738	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	3.978000	0.56881	2.107000	0.64212	0.533000	0.62120	AAA		0.413	HIAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029657.1		NM_033055	
KIAA0195	9772	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	73488654	73488654	+	Missense_Mutation	SNP	T	T	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr17:73488654T>A	ENST00000314256.7	+	15	2090	c.1696T>A	c.(1696-1698)Tcc>Acc	p.S566T	KIAA0195_ENST00000579208.1_Missense_Mutation_p.S217T|KIAA0195_ENST00000375248.5_Missense_Mutation_p.S576T	NM_014738.4	NP_055553.3	Q12767	K0195_HUMAN	KIAA0195	566						integral component of membrane (GO:0016021)|nucleus (GO:0005634)		p.S566T(1)		breast(2)|endometrium(5)|kidney(2)|large_intestine(7)|lung(17)|ovary(5)|skin(2)|stomach(1)|urinary_tract(1)	42	all_cancers(13;3.15e-09)|all_epithelial(9;5.94e-10)|Breast(9;1.85e-09)|all_lung(278;0.246)		all cancers(21;5.01e-07)|Epithelial(20;5e-06)|Lung(188;0.0809)|LUSC - Lung squamous cell carcinoma(166;0.154)			GCAGAACCCCTCCTGCATCCA	0.592																																																	1	Substitution - Missense(1)	kidney(1)											108.0	95.0	100.0					17																	73488654		2203	4300	6503	SO:0001583	missense	9772				CCDS32732.1	17q25.1	2012-03-01			ENSG00000177728	ENSG00000177728			28983	protein-coding gene	gene with protein product						8724849	Standard	NM_014738		Approved	TMEM94	uc002jnz.4	Q12767		ENST00000314256.7:c.1696T>A	17.37:g.73488654T>A	ENSP00000313885:p.Ser566Thr		O75536|Q86XF1	Missense_Mutation	SNP	ENST00000314256.7	37	CCDS32732.1	.	.	.	.	.	.	.	.	.	.	T	11.37	1.618479	0.28801	.	.	ENSG00000177728	ENST00000314256;ENST00000375248	D;D	0.86562	-2.14;-2.14	5.6	4.53	0.55603	.	0.309061	0.37053	N	0.002264	T	0.74801	0.3764	N	0.17379	0.485	0.35851	D	0.82678	B;B;B	0.06786	0.0;0.001;0.001	B;B;B	0.08055	0.001;0.003;0.001	T	0.69331	-0.5173	10	0.22109	T	0.4	-24.5353	8.7153	0.34408	0.0:0.1466:0.0:0.8534	.	576;576;566	B4DGC6;C9JL75;Q12767	.;.;K0195_HUMAN	T	566;576	ENSP00000313885:S566T;ENSP00000364397:S576T	ENSP00000313885:S566T	S	+	1	0	KIAA0195	71000249	0.995000	0.38212	1.000000	0.80357	0.934000	0.57294	2.345000	0.44018	0.964000	0.38108	0.459000	0.35465	TCC		0.592	KIAA0195-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447303.1		NM_014738	
KLF10	7071	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	103663602	103663602	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr8:103663602C>T	ENST00000285407.6	-	3	1258	c.958G>A	c.(958-960)Gtg>Atg	p.V320M	KLF10_ENST00000395884.3_Missense_Mutation_p.V309M	NM_005655.2	NP_005646.1	Q13118	KLF10_HUMAN	Kruppel-like factor 10	320					bone mineralization (GO:0030282)|cell proliferation (GO:0008283)|cell-cell signaling (GO:0007267)|cellular response to peptide (GO:1901653)|cellular response to starvation (GO:0009267)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of osteoclast differentiation (GO:0045672)|regulation of circadian rhythm (GO:0042752)|skeletal system development (GO:0001501)|somatic stem cell maintenance (GO:0035019)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	nucleus (GO:0005634)	core promoter sequence-specific DNA binding (GO:0001046)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.V320M(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(3)	18	all_epithelial(15;5.63e-07)|Lung NSC(17;8.18e-05)|all_lung(17;0.000169)		OV - Ovarian serous cystadenocarcinoma(57;0.000112)|STAD - Stomach adenocarcinoma(118;0.0826)			TGGGGTACCACAAACATGACA	0.602																																					Esophageal Squamous(16;495 519 2144 16528 44005)												1	Substitution - Missense(1)	kidney(1)											93.0	97.0	96.0					8																	103663602		2203	4300	6503	SO:0001583	missense	7071			U21847	CCDS6294.1, CCDS47905.1	8q22.3	2014-09-17	2004-11-29	2004-12-01	ENSG00000155090	ENSG00000155090		"""Kruppel-like transcription factors"", ""Zinc fingers, C2H2-type"""	11810	protein-coding gene	gene with protein product		601878	"""TGFB inducible early growth response"""	TIEG		8584037, 9721211	Standard	NM_001032282		Approved	EGRA, TIEG1	uc011lhk.1	Q13118	OTTHUMG00000164735	ENST00000285407.6:c.958G>A	8.37:g.103663602C>T	ENSP00000285407:p.Val320Met		A8MVH0|B2R794|L0R4P6|L0R679|O75411|Q503B2	Missense_Mutation	SNP	ENST00000285407.6	37	CCDS6294.1	.	.	.	.	.	.	.	.	.	.	C	26.4	4.732655	0.89482	.	.	ENSG00000155090	ENST00000285407;ENST00000395884	T;T	0.15603	2.41;2.47	5.5	5.5	0.81552	.	0.076118	0.53938	D	0.000044	T	0.39145	0.1067	M	0.63843	1.955	0.80722	D	1	D;D	0.65815	0.995;0.966	P;P	0.61397	0.888;0.618	T	0.03268	-1.1054	10	0.51188	T	0.08	.	19.7664	0.96346	0.0:1.0:0.0:0.0	.	320;309	Q13118;O75411	KLF10_HUMAN;.	M	320;309	ENSP00000285407:V320M;ENSP00000379222:V309M	ENSP00000285407:V320M	V	-	1	0	KLF10	103732778	1.000000	0.71417	0.997000	0.53966	0.982000	0.71751	4.884000	0.63135	2.735000	0.93741	0.655000	0.94253	GTG		0.602	KLF10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379967.1			
LEPREL1	55214	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	189689771	189689771	+	Silent	SNP	G	G	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr3:189689771G>T	ENST00000319332.5	-	12	1922	c.1725C>A	c.(1723-1725)ctC>ctA	p.L575L	LEPREL1_ENST00000427335.2_Silent_p.L394L	NM_018192.3	NP_060662.2	Q8IVL5	P3H2_HUMAN	leprecan-like 1	575	Fe2OG dioxygenase. {ECO:0000255|PROSITE- ProRule:PRU00805}.				collagen metabolic process (GO:0032963)|extracellular matrix organization (GO:0030198)|negative regulation of cell proliferation (GO:0008285)|peptidyl-proline hydroxylation (GO:0019511)	basement membrane (GO:0005604)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|Golgi apparatus (GO:0005794)	iron ion binding (GO:0005506)|L-ascorbic acid binding (GO:0031418)|procollagen-proline 3-dioxygenase activity (GO:0019797)	p.L575L(1)		NS(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|kidney(1)|large_intestine(10)|liver(1)|lung(8)|ovary(2)|prostate(2)|skin(5)	41	all_cancers(143;4.01e-10)|Ovarian(172;0.0925)		Lung(62;4.35e-05)	GBM - Glioblastoma multiforme(93;0.02)	L-Proline(DB00172)|Succinic acid(DB00139)|Vitamin C(DB00126)	TGGGATGACTGAGGTCATTTC	0.463																																																	1	Substitution - coding silent(1)	kidney(1)											77.0	65.0	69.0					3																	189689771		2203	4300	6503	SO:0001819	synonymous_variant	55214				CCDS3294.1, CCDS46981.1	3q29	2014-01-28			ENSG00000090530	ENSG00000090530	1.14.11.7		19317	protein-coding gene	gene with protein product	"""prolyl 3-hydroxylase 2"""	610341				15063763, 21885030	Standard	NM_018192		Approved	FLJ10718, MLAT4, P3H2	uc011bsk.2	Q8IVL5	OTTHUMG00000156312	ENST00000319332.5:c.1725C>A	3.37:g.189689771G>T			B3KPK0|B3KWI9|D3DNV8|Q9NVI2	Silent	SNP	ENST00000319332.5	37	CCDS3294.1																																																																																				0.463	LEPREL1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000343855.1		NM_018192	
LMTK2	22853	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	97822827	97822827	+	Missense_Mutation	SNP	C	C	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	C	G	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr7:97822827C>G	ENST00000297293.5	+	11	3343	c.3050C>G	c.(3049-3051)aCt>aGt	p.T1017S		NM_014916.3	NP_055731.2	Q8IWU2	LMTK2_HUMAN	lemur tyrosine kinase 2	1017					early endosome to late endosome transport (GO:0045022)|endocytic recycling (GO:0032456)|negative regulation of catalytic activity (GO:0043086)|peptidyl-serine phosphorylation (GO:0018105)|peptidyl-threonine phosphorylation (GO:0018107)|protein autophosphorylation (GO:0046777)|protein phosphorylation (GO:0006468)|receptor recycling (GO:0001881)|transferrin transport (GO:0033572)	early endosome (GO:0005769)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)|recycling endosome (GO:0055037)	ATP binding (GO:0005524)|myosin VI binding (GO:0070853)|protein phosphatase inhibitor activity (GO:0004864)|protein serine/threonine kinase activity (GO:0004674)	p.T1017S(2)		NS(2)|breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(13)|lung(25)|ovary(1)|pancreas(2)|skin(2)|stomach(3)	59	all_cancers(62;3.23e-09)|all_epithelial(64;7.65e-10)|Lung NSC(181;0.00902)|all_lung(186;0.0104)|Esophageal squamous(72;0.0125)					GGATCTCACACTCCCCAGAAA	0.597																																																	2	Substitution - Missense(2)	kidney(2)											88.0	96.0	93.0					7																	97822827		2203	4300	6503	SO:0001583	missense	22853			AB029002	CCDS5654.1	7q22.1	2014-06-12			ENSG00000164715	ENSG00000164715			17880	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 100"""	610989				15005709	Standard	NM_014916		Approved	KIAA1079, KPI2, KPI-2, cprk, LMR2, BREK, AATYK2, PPP1R100	uc003upd.2	Q8IWU2	OTTHUMG00000154256	ENST00000297293.5:c.3050C>G	7.37:g.97822827C>G	ENSP00000297293:p.Thr1017Ser		A4D272|Q75MG7|Q9UPS3	Missense_Mutation	SNP	ENST00000297293.5	37	CCDS5654.1	.	.	.	.	.	.	.	.	.	.	C	0.005	-2.188027	0.00305	.	.	ENSG00000164715	ENST00000297293	T	0.74315	-0.83	5.27	2.12	0.27331	.	0.707592	0.15183	N	0.276018	T	0.49304	0.1549	N	0.19112	0.55	0.09310	N	1	B	0.02656	0.0	B	0.04013	0.001	T	0.35674	-0.9779	10	0.02654	T	1	.	4.5894	0.12299	0.1232:0.3909:0.3975:0.0884	.	1017	Q8IWU2	LMTK2_HUMAN	S	1017	ENSP00000297293:T1017S	ENSP00000297293:T1017S	T	+	2	0	LMTK2	97660763	0.000000	0.05858	0.001000	0.08648	0.062000	0.15995	1.019000	0.30014	0.694000	0.31654	0.650000	0.86243	ACT		0.597	LMTK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000334560.1		NM_014916	
LSM1	27257	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	38029515	38029515	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr8:38029515A>G	ENST00000311351.4	-	2	478	c.83T>C	c.(82-84)cTt>cCt	p.L28P	LSM1_ENST00000522515.1_5'UTR|LSM1_ENST00000520755.1_Missense_Mutation_p.L28P	NM_014462.2	NP_055277.1	O15116	LSM1_HUMAN	LSM1, U6 small nuclear RNA associated	28					exonucleolytic nuclear-transcribed mRNA catabolic process involved in deadenylation-dependent decay (GO:0043928)|gene expression (GO:0010467)|histone mRNA catabolic process (GO:0071044)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|RNA splicing, via transesterification reactions (GO:0000375)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|nucleus (GO:0005634)|ribonucleoprotein complex (GO:0030529)	poly(A) RNA binding (GO:0044822)	p.L28P(1)		kidney(2)|large_intestine(3)|lung(2)	7	Colorectal(12;0.000442)					AAAGCCTATAAGTGTCCTTCC	0.343											OREG0018720	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											98.0	103.0	101.0					8																	38029515		2203	4300	6503	SO:0001583	missense	27257			AF000177	CCDS6103.1	8p11.2	2014-02-14	2014-02-14		ENSG00000175324	ENSG00000175324			20472	protein-coding gene	gene with protein product		607281	"""LSM1 homolog, U6 small nuclear RNA associated (S. cerevisiae)"""			12515382, 11953827	Standard	NM_014462		Approved	CASM, YJL124C	uc003xkw.3	O15116	OTTHUMG00000164051	ENST00000311351.4:c.83T>C	8.37:g.38029515A>G	ENSP00000310596:p.Leu28Pro	875	B2R5E6	Missense_Mutation	SNP	ENST00000311351.4	37	CCDS6103.1	.	.	.	.	.	.	.	.	.	.	A	24.8	4.575747	0.86645	.	.	ENSG00000175324	ENST00000311351;ENST00000520755	T;T	0.53423	0.62;0.62	5.93	5.93	0.95920	Like-Sm ribonucleoprotein (LSM) domain, eukaryotic/archaea-type (1);Like-Sm ribonucleoprotein (LSM) domain (1);Like-Sm ribonucleoprotein (LSM)-related domain (1);	0.123185	0.53938	D	0.000047	T	0.79329	0.4427	H	0.96916	3.905	0.80722	D	1	D	0.89917	1.0	D	0.77004	0.989	D	0.86356	0.1714	10	0.87932	D	0	-13.8514	15.3562	0.74428	1.0:0.0:0.0:0.0	.	28	O15116	LSM1_HUMAN	P	28	ENSP00000310596:L28P;ENSP00000430021:L28P	ENSP00000310596:L28P	L	-	2	0	LSM1	38148672	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	8.661000	0.91125	2.273000	0.75805	0.482000	0.46254	CTT		0.343	LSM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376965.1		NM_014462	
KMT2E	55904	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	104749515	104749515	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr7:104749515T>C	ENST00000311117.3	+	23	4140	c.3595T>C	c.(3595-3597)Tgt>Cgt	p.C1199R	KMT2E_ENST00000334914.7_Missense_Mutation_p.C254R|SRPK2_ENST00000493638.1_5'Flank|KMT2E_ENST00000334877.4_Missense_Mutation_p.C1199R|KMT2E_ENST00000257745.4_Missense_Mutation_p.C1199R	NM_182931.2	NP_891847.1	Q8IZD2	KMT2E_HUMAN	lysine (K)-specific methyltransferase 2E	1199					cell cycle arrest (GO:0007050)|cellular response to retinoic acid (GO:0071300)|DNA methylation (GO:0006306)|erythrocyte differentiation (GO:0030218)|histone H3-K4 methylation (GO:0051568)|neutrophil activation (GO:0042119)|neutrophil mediated immunity (GO:0002446)|positive regulation of granulocyte differentiation (GO:0030854)|positive regulation of transcription, DNA-templated (GO:0045893)|retinoic acid receptor signaling pathway (GO:0048384)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|MLL5-L complex (GO:0070688)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|transcription coactivator activity (GO:0003713)|zinc ion binding (GO:0008270)	p.C1199R(1)									TGGTGATGGCTGTGCCAGCAG	0.468																																																	1	Substitution - Missense(1)	kidney(1)											111.0	95.0	101.0					7																	104749515		2203	4300	6503	SO:0001583	missense	55904			AF067804	CCDS34723.1	7q22.1	2013-05-09	2013-05-09	2013-05-09	ENSG00000005483	ENSG00000005483		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	18541	protein-coding gene	gene with protein product		608444	"""myeloid/lymphoid or mixed-lineage leukemia 5 (trithorax homolog, Drosophila)"""	MLL5		9218106, 7672722	Standard	XM_005250493		Approved	HDCMC04P		Q8IZD2	OTTHUMG00000157403	ENST00000311117.3:c.3595T>C	7.37:g.104749515T>C	ENSP00000312379:p.Cys1199Arg		B6ZDE4|B6ZDM3|M4K8J3|Q6P5Y2|Q6PKG4|Q6T316|Q86TI3|Q86W12|Q86WG0|Q86WL2|Q8IV78|Q8IWR5|Q8NFF8|Q9NWE7	Missense_Mutation	SNP	ENST00000311117.3	37	CCDS34723.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	7.060|7.060	0.566128|0.566128	0.13560|0.13560	.|.	.|.	ENSG00000005483|ENSG00000005483	ENST00000311117;ENST00000393656;ENST00000334877;ENST00000351043;ENST00000257745;ENST00000334914|ENST00000473063	D;D;D;T|.	0.91295|.	-2.82;-2.45;-2.82;0.92|.	5.65|5.65	1.6|1.6	0.23607|0.23607	.|.	0.189305|.	0.38326|.	N|.	0.001734|.	T|T	0.24314|0.24314	0.0589|0.0589	N|N	0.24115|0.24115	0.695|0.695	0.24838|0.24838	N|N	0.992484|0.992484	B|.	0.17465|.	0.022|.	B|.	0.17979|.	0.02|.	T|T	0.24404|0.24404	-1.0161|-1.0161	10|5	0.41790|.	T|.	0.15|.	.|.	7.3226|7.3226	0.26536|0.26536	0.1366:0.0:0.2851:0.5783|0.1366:0.0:0.2851:0.5783	.|.	1199|.	Q8IZD2|.	MLL5_HUMAN|.	R|P	1199;1199;1199;1119;1199;254|10	ENSP00000312379:C1199R;ENSP00000335599:C1199R;ENSP00000257745:C1199R;ENSP00000333986:C254R|.	ENSP00000257745:C1199R|.	C|L	+|+	1|2	0|0	MLL5|MLL5	104536751|104536751	0.985000|0.985000	0.35326|0.35326	0.119000|0.119000	0.21687|0.21687	0.568000|0.568000	0.35870|0.35870	2.887000|2.887000	0.48586|0.48586	0.371000|0.371000	0.24564|0.24564	0.383000|0.383000	0.25322|0.25322	TGT|CTG		0.468	KMT2E-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000348697.1			
KMT2C	58508	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	151873357	151873357	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr7:151873357G>T	ENST00000262189.6	-	38	9399	c.9181C>A	c.(9181-9183)Caa>Aaa	p.Q3061K	KMT2C_ENST00000355193.2_Missense_Mutation_p.Q3061K	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	3061	Gln-rich.				histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.Q3061K(2)									TGCCTTTCTTGATCCAAAAGA	0.448																																																	2	Substitution - Missense(2)	kidney(2)											152.0	144.0	147.0					7																	151873357		2203	4300	6503	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.9181C>A	7.37:g.151873357G>T	ENSP00000262189:p.Gln3061Lys		Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.84|18.84	3.709514|3.709514	0.68730|0.68730	.|.	.|.	ENSG00000055609|ENSG00000055609	ENST00000262189;ENST00000355193|ENST00000360104	D;D|.	0.84944|.	-1.91;-1.92|.	5.95|5.95	5.95|5.95	0.96441|0.96441	.|.	0.000000|.	0.42548|.	D|.	0.000700|.	T|.	0.77212|.	0.4097|.	M|M	0.71581|0.71581	2.175|2.175	0.80722|0.80722	D|D	1|1	D;D;D|.	0.71674|.	0.997;0.998;0.998|.	D;D;D|.	0.78314|.	0.98;0.991;0.991|.	T|.	0.74160|.	-0.3755|.	10|.	0.62326|.	D|.	0.03|.	.|.	20.3931|20.3931	0.98965|0.98965	0.0:0.0:1.0:0.0|0.0:0.0:1.0:0.0	.|.	3061;2122;3061|.	Q8NEZ4;Q8NEZ4-2;Q8NEZ4-3|.	MLL3_HUMAN;.;.|.	K|X	3061|566	ENSP00000262189:Q3061K;ENSP00000347325:Q3061K|.	ENSP00000262189:Q3061K|.	Q|S	-|-	1|2	0|0	MLL3|MLL3	151504290|151504290	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	9.869000|9.869000	0.99810|0.99810	2.824000|2.824000	0.97209|0.97209	0.655000|0.655000	0.94253|0.94253	CAA|TCA		0.448	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			
NEGR1	257194	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	72400804	72400804	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr1:72400804G>T	ENST00000357731.5	-	2	606	c.367C>A	c.(367-369)Caa>Aaa	p.Q123K	NEGR1_ENST00000467479.1_5'UTR|NEGR1_ENST00000306821.3_5'UTR|NEGR1_ENST00000434200.1_Missense_Mutation_p.Q121K	NM_173808.2	NP_776169.2	Q7Z3B1	NEGR1_HUMAN	neuronal growth regulator 1	123	Ig-like C2-type 1.				feeding behavior (GO:0007631)|locomotory behavior (GO:0007626)|positive regulation of neuron projection development (GO:0010976)|single organismal cell-cell adhesion (GO:0016337)	anchored component of membrane (GO:0031225)|extracellular vesicular exosome (GO:0070062)|plasma membrane (GO:0005886)		p.Q123K(1)		endometrium(1)|kidney(4)|large_intestine(7)|lung(16)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	32		all_cancers(4;1.26e-06)|Renal(4;1.32e-08)|all_epithelial(4;5.39e-07)|Hepatocellular(141;0.117)		KIRC - Kidney renal clear cell carcinoma(4;0.00529)|Kidney(4;0.00609)|all cancers(265;0.022)|GBM - Glioblastoma multiforme(62;0.0382)|Epithelial(280;0.242)		GGTGTATGTTGAGTCTGAACA	0.378																																																	1	Substitution - Missense(1)	kidney(1)											122.0	110.0	114.0					1																	72400804		2203	4300	6503	SO:0001583	missense	257194			AK092307	CCDS661.1	1p31.1	2013-01-11			ENSG00000172260	ENSG00000172260		"""Immunoglobulin superfamily / I-set domain containing"""	17302	protein-coding gene	gene with protein product	"""a kindred of IgLON"", ""neurotractin"", ""IgLON family member 4"""	613173				10075727	Standard	NM_173808		Approved	KILON, MGC46680, Ntra, IGLON4	uc001dfw.3	Q7Z3B1	OTTHUMG00000009698	ENST00000357731.5:c.367C>A	1.37:g.72400804G>T	ENSP00000350364:p.Gln123Lys		Q5VT21|Q6UY06|Q8N440|Q8NAQ3	Missense_Mutation	SNP	ENST00000357731.5	37	CCDS661.1	.	.	.	.	.	.	.	.	.	.	G	11.65	1.702181	0.30232	.	.	ENSG00000172260	ENST00000357731;ENST00000434200	T;T	0.65364	-0.15;-0.15	5.71	5.71	0.89125	Immunoglobulin subtype (1);Immunoglobulin I-set (1);Immunoglobulin-like (1);Immunoglobulin-like fold (1);	0.057607	0.64402	D	0.000002	T	0.33469	0.0864	N	0.13235	0.315	0.40685	D	0.982344	B;B	0.15719	0.007;0.014	B;B	0.19666	0.026;0.026	T	0.19257	-1.0311	10	0.45353	T	0.12	-6.0013	15.3379	0.74273	0.0:0.1392:0.8608:0.0	.	121;123	B4DI94;Q7Z3B1	.;NEGR1_HUMAN	K	123;121	ENSP00000350364:Q123K;ENSP00000413294:Q121K	ENSP00000350364:Q123K	Q	-	1	0	NEGR1	72173392	1.000000	0.71417	1.000000	0.80357	0.770000	0.43624	4.241000	0.58707	2.699000	0.92147	0.655000	0.94253	CAA		0.378	NEGR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026722.4		NM_173808	
NUP85	79902	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	73204674	73204674	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr17:73204674C>T	ENST00000245544.4	+	2	157	c.86C>T	c.(85-87)cCa>cTa	p.P29L	NUP85_ENST00000449421.2_Intron|NUP85_ENST00000579298.1_Missense_Mutation_p.P29L|NUP85_ENST00000447371.2_5'UTR|NUP85_ENST00000579324.1_Intron|NUP85_ENST00000541827.1_Intron	NM_024844.3	NP_079120.1	Q9BW27	NUP85_HUMAN	nucleoporin 85kDa	29					carbohydrate metabolic process (GO:0005975)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|lamellipodium assembly (GO:0030032)|macrophage chemotaxis (GO:0048246)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoskeleton (GO:0005856)|cytosol (GO:0005829)|kinetochore (GO:0000776)|membrane (GO:0016020)|nuclear envelope (GO:0005635)|nuclear pore outer ring (GO:0031080)		p.P29L(1)		endometrium(1)|kidney(1)|large_intestine(4)|lung(4)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	16	all_lung(278;0.14)|Lung NSC(278;0.168)		all cancers(21;3.45e-06)			GACTGGGGTCCAGGGGAGATG	0.358																																																	1	Substitution - Missense(1)	kidney(1)											170.0	186.0	180.0					17																	73204674		2203	4300	6503	SO:0001583	missense	79902			AF514995	CCDS32730.1	17q25	2006-11-29	2005-11-03	2005-11-03		ENSG00000125450			8734	protein-coding gene	gene with protein product		170285				8124707	Standard	XM_005257690		Approved	NUP75, FLJ12549	uc002jng.1	Q9BW27		ENST00000245544.4:c.86C>T	17.37:g.73204674C>T	ENSP00000245544:p.Pro29Leu		B4DMQ3|B4DPW1|Q8NDI4|Q9H9U1	Missense_Mutation	SNP	ENST00000245544.4	37	CCDS32730.1	.	.	.	.	.	.	.	.	.	.	C	15.43	2.831158	0.50845	.	.	ENSG00000125450	ENST00000245544	.	.	.	4.78	4.78	0.61160	.	0.051862	0.85682	D	0.000000	T	0.73799	0.3633	M	0.63843	1.955	0.80722	D	1	D	0.76494	0.999	D	0.64144	0.922	T	0.71938	-0.4441	9	0.31617	T	0.26	-13.1383	15.9648	0.79961	0.0:1.0:0.0:0.0	.	29	Q9BW27	NUP85_HUMAN	L	29	.	ENSP00000245544:P29L	P	+	2	0	NUP85	70716269	0.991000	0.36638	0.960000	0.40013	0.156000	0.22039	4.012000	0.57131	2.356000	0.79943	0.563000	0.77884	CCA		0.358	NUP85-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000446619.1		NM_024844	
PIK3R1	5295	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	67590479	67590479	+	Missense_Mutation	SNP	G	G	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr5:67590479G>T	ENST00000521381.1	+	12	2157	c.1541G>T	c.(1540-1542)cGt>cTt	p.R514L	PIK3R1_ENST00000320694.8_Missense_Mutation_p.R214L|PIK3R1_ENST00000274335.5_Missense_Mutation_p.R514L|PIK3R1_ENST00000336483.5_Missense_Mutation_p.R244L|PIK3R1_ENST00000523872.1_Missense_Mutation_p.R151L|PIK3R1_ENST00000521657.1_Missense_Mutation_p.R514L|PIK3R1_ENST00000396611.1_Missense_Mutation_p.R514L	NM_181523.2	NP_852664.1	P27986	P85A_HUMAN	phosphoinositide-3-kinase, regulatory subunit 1 (alpha)	514					B cell differentiation (GO:0030183)|blood coagulation (GO:0007596)|cellular response to UV (GO:0034644)|epidermal growth factor receptor signaling pathway (GO:0007173)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|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)|growth hormone receptor signaling pathway (GO:0060396)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|insulin-like growth factor receptor signaling pathway (GO:0048009)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|leukocyte migration (GO:0050900)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of osteoclast differentiation (GO:0045671)|neurotrophin TRK receptor signaling pathway (GO:0048011)|NFAT protein import into nucleus (GO:0051531)|phosphatidylinositol 3-kinase signaling (GO:0014065)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol phosphorylation (GO:0046854)|phosphatidylinositol-mediated signaling (GO:0048015)|phospholipid metabolic process (GO:0006644)|platelet activation (GO:0030168)|positive regulation of cell migration (GO:0030335)|positive regulation of establishment of protein localization to plasma membrane (GO:0090004)|positive regulation of glucose import (GO:0046326)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|protein phosphorylation (GO:0006468)|regulation of phosphatidylinositol 3-kinase activity (GO:0043551)|small molecule metabolic process (GO:0044281)|T cell costimulation (GO:0031295)|T cell receptor signaling pathway (GO:0050852)|viral process (GO:0016032)	1-phosphatidylinositol-4-phosphate 3-kinase, class IA complex (GO:0005943)|cell-cell junction (GO:0005911)|cytosol (GO:0005829)|membrane (GO:0016020)|phosphatidylinositol 3-kinase complex (GO:0005942)|plasma membrane (GO:0005886)	ErbB-3 class receptor binding (GO:0043125)|insulin binding (GO:0043559)|insulin receptor binding (GO:0005158)|insulin receptor substrate binding (GO:0043560)|insulin-like growth factor receptor binding (GO:0005159)|neurotrophin TRKA receptor binding (GO:0005168)|phosphatidylinositol 3-kinase binding (GO:0043548)|phosphatidylinositol 3-kinase regulator activity (GO:0035014)|protein phosphatase binding (GO:0019903)|transmembrane receptor protein tyrosine kinase adaptor activity (GO:0005068)	p.R214L(1)|p.R514L(1)|p.0?(1)|p.?(1)|p.R244L(1)		breast(12)|central_nervous_system(31)|cervix(1)|endometrium(68)|haematopoietic_and_lymphoid_tissue(5)|kidney(1)|large_intestine(32)|lung(10)|ovary(9)|pancreas(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(3)|urinary_tract(2)	178		Lung NSC(167;1.99e-05)|Prostate(74;0.00308)|Ovarian(174;0.00473)|Colorectal(97;0.0176)		OV - Ovarian serous cystadenocarcinoma(47;3.76e-51)|Lung(70;0.0211)	Isoprenaline(DB01064)	AAGTTTAAACGTGAAGGCAAT	0.358			"""Mis, F, O"""		"""gliobastoma, ovarian, colorectal"""					TCGA GBM(4;<1E-08)																														Rec	yes		5	5q13.1	5295	"""phosphoinositide-3-kinase, regulatory subunit 1 (alpha)"""		"""E, O"""	5	Substitution - Missense(3)|Whole gene deletion(1)|Unknown(1)	kidney(3)|large_intestine(1)|lung(1)											69.0	72.0	71.0					5																	67590479		2203	4300	6503	SO:0001583	missense	5295			M61906	CCDS3993.1, CCDS3994.1, CCDS3995.1, CCDS56374.1	5q13.1	2014-09-17	2008-02-04		ENSG00000145675	ENSG00000145675		"""SH2 domain containing"""	8979	protein-coding gene	gene with protein product		171833				1314371, 18387942	Standard	NM_181524		Approved	GRB1, p85-ALPHA, p85	uc003jva.3	P27986	OTTHUMG00000131251	ENST00000521381.1:c.1541G>T	5.37:g.67590479G>T	ENSP00000428056:p.Arg514Leu		B3KT19|D3DWA0|E7EX19|Q15747|Q4VBZ7|Q53EM6|Q8IXA2|Q8N1C5	Missense_Mutation	SNP	ENST00000521381.1	37	CCDS3993.1	.	.	.	.	.	.	.	.	.	.	G	29.3	4.992955	0.93167	.	.	ENSG00000145675	ENST00000521381;ENST00000521657;ENST00000396611;ENST00000274335;ENST00000320694;ENST00000336483;ENST00000519025;ENST00000523872	T;T;T;T;D;D;T;D	0.82344	-0.51;-0.51;-0.39;-0.51;-1.51;-1.52;0.16;-1.6	5.18	5.18	0.71444	.	0.000000	0.85682	D	0.000000	D	0.90926	0.7148	M	0.81239	2.535	0.80722	D	1	B;B;B;D	0.67145	0.006;0.004;0.004;0.996	B;B;B;P	0.62885	0.004;0.009;0.021;0.908	D	0.91422	0.5159	10	0.66056	D	0.02	-11.8187	19.2559	0.93945	0.0:0.0:1.0:0.0	.	184;244;214;514	B7Z2N8;P27986-2;P27986-3;P27986	.;.;.;P85A_HUMAN	L	514;514;514;514;214;244;187;151	ENSP00000428056:R514L;ENSP00000429277:R514L;ENSP00000379855:R514L;ENSP00000274335:R514L;ENSP00000323512:R214L;ENSP00000338554:R244L;ENSP00000429156:R187L;ENSP00000430098:R151L	ENSP00000274335:R514L	R	+	2	0	PIK3R1	67626235	1.000000	0.71417	0.998000	0.56505	0.992000	0.81027	7.728000	0.84847	2.861000	0.98227	0.650000	0.86243	CGT		0.358	PIK3R1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254013.2		NM_181504	
PPP2R5B	5526	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	64695788	64695788	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr11:64695788G>A	ENST00000164133.2	+	6	1235	c.613G>A	c.(613-615)Gag>Aag	p.E205K		NM_006244.3	NP_006235.1	Q15173	2A5B_HUMAN	protein phosphatase 2, regulatory subunit B', beta	205					activation of signaling protein activity involved in unfolded protein response (GO:0006987)|cellular protein metabolic process (GO:0044267)|endoplasmic reticulum unfolded protein response (GO:0030968)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|protein phosphatase type 2A complex (GO:0000159)	protein phosphatase type 2A regulator activity (GO:0008601)	p.E205K(1)		central_nervous_system(2)|endometrium(4)|kidney(1)|large_intestine(3)|lung(9)|ovary(2)	21						ATTTGATAGTGAGGATCCCCG	0.587																																																	1	Substitution - Missense(1)	kidney(1)											64.0	56.0	59.0					11																	64695788		2201	4297	6498	SO:0001583	missense	5526			L42374	CCDS8085.1	11q12	2010-06-18	2010-04-14		ENSG00000068971	ENSG00000068971		"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9310	protein-coding gene	gene with protein product	"""PP2A, B subunit, B' beta isoform"", ""PP2A, B subunit, B56 beta isoform"", ""PP2A, B subunit, PR61 beta isoform"", ""PP2A, B subunit, R5 beta isoform"", ""serine/threonine protein phosphatase 2A, 56 kDa regulatory subunit, beta isoform"""	601644	"""protein phosphatase 2, regulatory subunit B (B56), beta isoform"", ""protein phosphatase 2, regulatory subunit B', beta isoform"""			7592815	Standard	NM_006244		Approved	FLJ35411, B56B, PR61B	uc001oby.3	Q15173	OTTHUMG00000150043	ENST00000164133.2:c.613G>A	11.37:g.64695788G>A	ENSP00000164133:p.Glu205Lys		Q13853	Missense_Mutation	SNP	ENST00000164133.2	37	CCDS8085.1	.	.	.	.	.	.	.	.	.	.	G	20.9	4.072787	0.76415	.	.	ENSG00000068971	ENST00000164133;ENST00000359279;ENST00000527441	.	.	.	3.56	3.56	0.40772	Armadillo-type fold (1);	0.058338	0.64402	D	0.000003	D	0.83436	0.5254	M	0.90650	3.135	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	D	0.87072	0.2160	9	0.87932	D	0	-22.757	13.5415	0.61676	0.0:0.0:1.0:0.0	.	205	Q15173	2A5B_HUMAN	K	205;232;205	.	ENSP00000164133:E205K	E	+	1	0	PPP2R5B	64452364	1.000000	0.71417	0.980000	0.43619	0.310000	0.27922	9.137000	0.94496	2.322000	0.78497	0.549000	0.68633	GAG		0.587	PPP2R5B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000385465.1		NM_006244	
PRG4	10216	broad.mit.edu	37	1	186276075	186276075	+	Silent	SNP	T	T	C	rs540749159	byFrequency	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr1:186276075T>C	ENST00000445192.2	+	7	1269	c.1224T>C	c.(1222-1224)acT>acC	p.T408T	PRG4_ENST00000367484.3_Intron|PRG4_ENST00000367486.3_Silent_p.T365T|PRG4_ENST00000367483.4_Silent_p.T367T|PRG4_ENST00000367485.4_Silent_p.T315T	NM_005807.3	NP_005798.2	Q92954	PRG4_HUMAN	proteoglycan 4	408	59 X 8 AA repeats of K-X-P-X-P-T-T-X.				cell proliferation (GO:0008283)|hematopoietic stem cell proliferation (GO:0071425)|immune response (GO:0006955)|negative regulation of interleukin-6 biosynthetic process (GO:0045409)|regulation of cell proliferation (GO:0042127)	extracellular space (GO:0005615)	polysaccharide binding (GO:0030247)|scavenger receptor activity (GO:0005044)	p.T408T(1)		NS(2)|breast(1)|central_nervous_system(1)|endometrium(26)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(12)|lung(33)|prostate(7)|skin(9)|upper_aerodigestive_tract(2)|urinary_tract(1)	102						CACCCACCACTCCCAAGGAGC	0.662													-|||	16	0.00319489	0.0053	0.0014	5008	,	,		9339	0.001		0.003	False		,,,				2504	0.0041																1	Substitution - coding silent(1)	kidney(1)																																								SO:0001819	synonymous_variant	23572			U70136	CCDS1369.1, CCDS44287.1, CCDS44288.1	1q25-q31	2008-07-18	2004-11-15		ENSG00000116690	ENSG00000116690			9364	protein-coding gene	gene with protein product	"""lubricin"", ""megakaryocyte stimulating factor"", ""articular superficial zone protein"", ""Jacobs camptodactyly-arthropathy-pericarditis syndrome"", ""camptodactyly, arthropathy, coxa vara, pericarditis syndrome"", ""bG174L6.2 (MSF: megakaryocyte stimulating factor )"""	604283	"""proteoglycan 4, (megakaryocyte stimulating factor, articular superficial zone protein, camptodactyly, arthropathy, coxa vara, pericarditis syndrome)"""	CACP		10545950, 9920774	Standard	NM_005807		Approved	JCAP, SZP, MSF, HAPO, bG174L6.2, FLJ32635	uc001gru.4	Q92954	OTTHUMG00000035574	ENST00000445192.2:c.1224T>C	1.37:g.186276075T>C			Q6DNC4|Q6DNC5|Q6ZMZ5|Q9BX49	Silent	SNP	ENST00000445192.2	37	CCDS1369.1																																																																																				0.662	PRG4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086346.1		NM_005807	
PRRC2A	7916	broad.mit.edu;hgsc.bcm.edu	37	6	31595623	31595623	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr6:31595623T>C	ENST00000376033.2	+	12	1606	c.1372T>C	c.(1372-1374)Tct>Cct	p.S458P	PRRC2A_ENST00000376007.4_Missense_Mutation_p.S458P	NM_004638.3	NP_004629.3	P48634	PRC2A_HUMAN	proline-rich coiled-coil 2A	458	2 X type B repeats.|4 X 57 AA type A repeats.					cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S458P(1)		breast(6)|central_nervous_system(1)|endometrium(7)|kidney(5)|large_intestine(14)|lung(19)|ovary(3)|pancreas(2)|prostate(4)|skin(5)|soft_tissue(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	70						GCAGTCGTCATCTGAGATTTC	0.627																																																	1	Substitution - Missense(1)	kidney(1)											61.0	72.0	68.0					6																	31595623		1510	2708	4218	SO:0001583	missense	7916			M31293	CCDS4708.1	6p21.3	2010-12-09	2010-12-09	2010-12-09	ENSG00000204469	ENSG00000204469			13918	protein-coding gene	gene with protein product		142580	"""HLA-B associated transcript 2"""	BAT2		2156268, 8499947	Standard	NM_080686		Approved	G2, D6S51E	uc003nvc.4	P48634	OTTHUMG00000031168	ENST00000376033.2:c.1372T>C	6.37:g.31595623T>C	ENSP00000365201:p.Ser458Pro		B0UX77|B0UZE9|B0UZL3|O95875|Q05BK4|Q4LE37|Q5SQ29|Q5SQ30|Q5ST84|Q5STX6|Q5STX7|Q68DW9|Q6P9P7|Q6PIN1|Q8MGQ9|Q96QC6	Missense_Mutation	SNP	ENST00000376033.2	37	CCDS4708.1	.	.	.	.	.	.	.	.	.	.	T	11.02	1.516414	0.27123	.	.	ENSG00000204469	ENST00000424184;ENST00000435052;ENST00000376007;ENST00000376033	T;T	0.04049	3.72;3.72	4.38	4.38	0.52667	.	0.000000	0.47093	D	0.000257	T	0.08891	0.0220	M	0.62723	1.935	0.41971	D	0.99075	D	0.65815	0.995	P	0.59115	0.852	T	0.01549	-1.1327	10	0.87932	D	0	-14.9121	12.9926	0.58627	0.0:0.0:0.0:1.0	.	458	P48634	PRC2A_HUMAN	P	458;447;458;458	ENSP00000365175:S458P;ENSP00000365201:S458P	ENSP00000365175:S458P	S	+	1	0	PRRC2A	31703602	0.993000	0.37304	0.978000	0.43139	0.922000	0.55478	2.527000	0.45615	1.985000	0.57927	0.459000	0.35465	TCT		0.627	PRRC2A-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259319.1		NM_080686	
PTPRJ	5795	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	48166241	48166241	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr11:48166241G>A	ENST00000418331.2	+	13	2942	c.2590G>A	c.(2590-2592)Gca>Aca	p.A864T		NM_002843.3	NP_002834.3	Q12913	PTPRJ_HUMAN	protein tyrosine phosphatase, receptor type, J	864	Fibronectin type-III 9. {ECO:0000255|PROSITE-ProRule:PRU00316}.				contact inhibition (GO:0060242)|heart development (GO:0007507)|negative regulation of cell growth (GO:0030308)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of platelet-derived growth factor receptor signaling pathway (GO:0010642)|negative regulation of protein kinase B signaling (GO:0051898)|negative regulation of T cell receptor signaling pathway (GO:0050860)|negative regulation of vascular permeability (GO:0043116)|oligodendrocyte differentiation (GO:0048709)|peptidyl-tyrosine dephosphorylation (GO:0035335)|platelet-derived growth factor receptor signaling pathway (GO:0048008)|positive chemotaxis (GO:0050918)|positive regulation of cell adhesion (GO:0045785)|positive regulation of focal adhesion assembly (GO:0051894)|positive regulation of protein kinase B signaling (GO:0051897)|regulation of cell adhesion (GO:0030155)|vasculogenesis (GO:0001570)	cell projection (GO:0042995)|cell surface (GO:0009986)|cell-cell junction (GO:0005911)|extracellular vesicular exosome (GO:0070062)|immunological synapse (GO:0001772)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-catenin binding (GO:0008013)|delta-catenin binding (GO:0070097)|gamma-catenin binding (GO:0045295)|mitogen-activated protein kinase binding (GO:0051019)|phosphatase activity (GO:0016791)|platelet-derived growth factor receptor binding (GO:0005161)|protein kinase binding (GO:0019901)|protein tyrosine phosphatase activity (GO:0004725)	p.A864T(2)		breast(3)|endometrium(7)|kidney(7)|large_intestine(5)|lung(15)|ovary(1)|prostate(2)|skin(6)|stomach(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	52						TCACCCTTCTGCAGATGTCCT	0.423																																																	2	Substitution - Missense(2)	kidney(2)											82.0	77.0	79.0					11																	48166241		2201	4298	6499	SO:0001583	missense	5795			U10886	CCDS7945.1, CCDS44596.1	11p11.2	2013-02-11			ENSG00000149177	ENSG00000149177		"""CD molecules"", ""Protein tyrosine phosphatases / Class I Cys-based PTPs : Transmembrane receptor-like"", ""Fibronectin type III domain containing"""	9673	protein-coding gene	gene with protein product		600925				7937872, 7994032	Standard	NM_001098503		Approved	DEP1, HPTPeta, CD148	uc001ngp.4	Q12913	OTTHUMG00000166573	ENST00000418331.2:c.2590G>A	11.37:g.48166241G>A	ENSP00000400010:p.Ala864Thr		Q15255|Q6P4H4|Q8NHM2|Q9UDA9	Missense_Mutation	SNP	ENST00000418331.2	37	CCDS7945.1	.	.	.	.	.	.	.	.	.	.	G	6.019	0.371846	0.11409	.	.	ENSG00000149177	ENST00000418331	T	0.13196	2.61	5.45	-5.91	0.02269	Fibronectin, type III (2);	.	.	.	.	T	0.04952	0.0133	N	0.08118	0	0.09310	N	1	B	0.18863	0.031	B	0.11329	0.006	T	0.44390	-0.9331	9	0.15066	T	0.55	.	7.273	0.26268	0.355:0.4356:0.2095:0.0	.	864	Q12913	PTPRJ_HUMAN	T	864	ENSP00000400010:A864T	ENSP00000400010:A864T	A	+	1	0	PTPRJ	48122817	0.000000	0.05858	0.000000	0.03702	0.002000	0.02628	-0.339000	0.07832	-1.366000	0.02155	-0.859000	0.03014	GCA		0.423	PTPRJ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000390525.1			
QRSL1	55278	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	107088233	107088233	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr6:107088233G>A	ENST00000369046.4	+	2	138	c.34G>A	c.(34-36)Gca>Aca	p.A12T	QRSL1_ENST00000369044.1_Missense_Mutation_p.A12T|QRSL1_ENST00000467262.1_3'UTR	NM_018292.4	NP_060762.3			glutaminyl-tRNA synthase (glutamine-hydrolyzing)-like 1									p.A12T(1)		endometrium(2)|kidney(1)|large_intestine(4)|lung(4)	11	Breast(9;0.0107)|all_epithelial(6;0.14)	all_cancers(87;0.00768)|Acute lymphoblastic leukemia(125;2.27e-07)|all_hematologic(75;1.38e-05)|all_epithelial(87;0.248)	Epithelial(6;0.000334)|all cancers(7;0.00157)|BRCA - Breast invasive adenocarcinoma(8;0.00721)|OV - Ovarian serous cystadenocarcinoma(5;0.0152)	BRCA - Breast invasive adenocarcinoma(108;0.118)|all cancers(137;0.167)|Epithelial(106;0.176)		GGTTTCTGCGGCACTGAAACA	0.408																																					NSCLC(192;2127 2142 11668 26277 49545)												1	Substitution - Missense(1)	kidney(1)											85.0	85.0	85.0					6																	107088233		2203	4300	6503	SO:0001583	missense	55278			AK001851	CCDS5057.1	6q21	2014-08-04			ENSG00000130348	ENSG00000130348			21020	protein-coding gene	gene with protein product	"""glutamyl-tRNA(Gln) amidotransferase, subunit A"""					11230166, 19805282	Standard	NM_018292		Approved	GatA, FLJ10989, FLJ12189, DKFZP564C1278, FLJ13447	uc003prm.3	Q9H0R6	OTTHUMG00000015301	ENST00000369046.4:c.34G>A	6.37:g.107088233G>A	ENSP00000358042:p.Ala12Thr			Missense_Mutation	SNP	ENST00000369046.4	37	CCDS5057.1	.	.	.	.	.	.	.	.	.	.	G	15.35	2.806265	0.50421	.	.	ENSG00000130348	ENST00000369046;ENST00000369044	T;T	0.65732	1.43;-0.17	5.64	5.64	0.86602	.	0.049118	0.85682	D	0.000000	T	0.51719	0.1691	M	0.69248	2.105	0.80722	D	1	B;P	0.40660	0.023;0.726	B;B	0.40565	0.04;0.333	T	0.53528	-0.8426	10	0.15066	T	0.55	-17.6516	19.6932	0.96010	0.0:0.0:1.0:0.0	.	12;12	Q9H0R6;Q9H0R6-2	GATA_HUMAN;.	T	12	ENSP00000358042:A12T;ENSP00000358040:A12T	ENSP00000358040:A12T	A	+	1	0	QRSL1	107194926	1.000000	0.71417	0.422000	0.26621	0.975000	0.68041	9.304000	0.96190	2.660000	0.90430	0.650000	0.86243	GCA		0.408	QRSL1-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000041667.1		NM_018292	
RAPGEF4	11069	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	173879257	173879257	+	Missense_Mutation	SNP	G	G	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr2:173879257G>A	ENST00000397081.3	+	18	1867	c.1724G>A	c.(1723-1725)aGg>aAg	p.R575K	RAPGEF4_ENST00000538974.1_Missense_Mutation_p.R404K|RAPGEF4_ENST00000397087.3_Missense_Mutation_p.R431K|RAPGEF4_ENST00000540783.1_Missense_Mutation_p.R422K|RAPGEF4_ENST00000264111.6_Missense_Mutation_p.R574K|RAPGEF4_ENST00000409036.1_Missense_Mutation_p.R575K|RAPGEF4_ENST00000535187.1_Missense_Mutation_p.R355K|RAPGEF4_ENST00000539331.1_Missense_Mutation_p.R422K	NM_007023.3	NP_008954.2	Q8WZA2	RPGF4_HUMAN	Rap guanine nucleotide exchange factor (GEF) 4	575	N-terminal Ras-GEF. {ECO:0000255|PROSITE- ProRule:PRU00135}.				blood coagulation (GO:0007596)|calcium ion-dependent exocytosis (GO:0017156)|cAMP-mediated signaling (GO:0019933)|energy reserve metabolic process (GO:0006112)|G-protein coupled receptor signaling pathway (GO:0007186)|insulin secretion (GO:0030073)|platelet activation (GO:0030168)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Ras GTPase activity (GO:0032320)|regulation of exocytosis (GO:0017157)|regulation of insulin secretion (GO:0050796)|small GTPase mediated signal transduction (GO:0007264)|small molecule metabolic process (GO:0044281)	cAMP-dependent protein kinase complex (GO:0005952)|cytosol (GO:0005829)|membrane (GO:0016020)|plasma membrane (GO:0005886)	cAMP binding (GO:0030552)|cAMP-dependent protein kinase regulator activity (GO:0008603)|guanyl-nucleotide exchange factor activity (GO:0005085)|Ras GTPase binding (GO:0017016)|Ras guanyl-nucleotide exchange factor activity (GO:0005088)	p.R575K(1)		breast(1)|central_nervous_system(2)|endometrium(5)|kidney(5)|large_intestine(14)|lung(13)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(1)	47			OV - Ovarian serous cystadenocarcinoma(117;0.194)			AACAATAAGAGGCGAGTCATC	0.522																																																	1	Substitution - Missense(1)	kidney(1)											92.0	94.0	94.0					2																	173879257		2043	4195	6238	SO:0001583	missense	11069			U78516	CCDS42775.1, CCDS42776.1, CCDS63060.1, CCDS63061.1, CCDS74604.1	2q31-q32	2008-02-05	2004-03-26		ENSG00000091428	ENSG00000091428			16626	protein-coding gene	gene with protein product	"""cAMP-regulated guanine nucleotide exchange factor II"", "" exchange protein directly activated by cAMP 2"""	606058	"""RAP guanine-nucleotide-exchange factor (GEF) 4"""			10777494, 9856955	Standard	NM_007023		Approved	cAMP-GEFII, CGEF2	uc002uhv.4	Q8WZA2	OTTHUMG00000133677	ENST00000397081.3:c.1724G>A	2.37:g.173879257G>A	ENSP00000380271:p.Arg575Lys		B2R7R3|B7Z283|B7Z3T6|B7Z912|O95636|Q8IXK6|Q8TAA4	Missense_Mutation	SNP	ENST00000397081.3	37	CCDS42775.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.249202	0.80024	.	.	ENSG00000091428	ENST00000264111;ENST00000397081;ENST00000409036;ENST00000397087;ENST00000538974;ENST00000540783;ENST00000539331;ENST00000535187	T;T;T;T;T;T;T;T	0.30714	1.52;1.52;1.52;1.52;1.52;1.52;1.52;1.52	6.17	5.3	0.74995	Ras guanine nucleotide exchange factor, domain (1);Ras-like guanine nucleotide exchange factor, N-terminal (3);	0.042480	0.85682	N	0.000000	T	0.32071	0.0817	L	0.34521	1.04	0.80722	D	1	B;P	0.37500	0.053;0.597	B;P	0.44647	0.111;0.456	T	0.03910	-1.0993	10	0.24483	T	0.36	.	15.8853	0.79244	0.0647:0.0:0.9353:0.0	.	431;575	Q8WZA2-3;Q8WZA2	.;RPGF4_HUMAN	K	574;575;575;431;404;422;422;355	ENSP00000264111:R574K;ENSP00000380271:R575K;ENSP00000387104:R575K;ENSP00000380276:R431K;ENSP00000440135:R404K;ENSP00000440250:R422K;ENSP00000437384:R422K;ENSP00000438011:R355K	ENSP00000264111:R574K	R	+	2	0	RAPGEF4	173587503	1.000000	0.71417	0.992000	0.48379	0.987000	0.75469	6.223000	0.72257	1.627000	0.50400	0.655000	0.94253	AGG		0.522	RAPGEF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257864.2		NM_007023	
SDHB	6390	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	17350478	17350478	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr1:17350478A>G	ENST00000375499.3	-	6	782	c.632T>C	c.(631-633)gTt>gCt	p.V211A		NM_003000.2	NP_002991.2	P21912	SDHB_HUMAN	succinate dehydrogenase complex, subunit B, iron sulfur (Ip)	211					aerobic respiration (GO:0009060)|cellular metabolic process (GO:0044237)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)|succinate metabolic process (GO:0006105)|tricarboxylic acid cycle (GO:0006099)	extracellular vesicular exosome (GO:0070062)|mitochondrial inner membrane (GO:0005743)|mitochondrial respiratory chain complex II (GO:0005749)|mitochondrion (GO:0005739)	2 iron, 2 sulfur cluster binding (GO:0051537)|3 iron, 4 sulfur cluster binding (GO:0051538)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|succinate dehydrogenase (ubiquinone) activity (GO:0008177)|ubiquinone binding (GO:0048039)	p.V211A(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(2)|lung(4)	10		Colorectal(325;3.46e-05)|Breast(348;0.000162)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.00054)|Ovarian(437;0.00669)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0049)|COAD - Colon adenocarcinoma(227;1.18e-05)|BRCA - Breast invasive adenocarcinoma(304;2.41e-05)|Kidney(64;0.000188)|KIRC - Kidney renal clear cell carcinoma(64;0.00273)|STAD - Stomach adenocarcinoma(196;0.00656)|READ - Rectum adenocarcinoma(331;0.0656)|Lung(427;0.19)	Succinic acid(DB00139)	CTGCATAAGAACTGCAGGCCC	0.502			"""Mis, N, F"""			"""paraganglioma, pheochromocytoma"""			Familial Paragangliomas;Cowden syndrome;Carney-Stratakis syndrome																														yes	Rec		Familial paraganglioma	1	1p36.1-p35	6390	"""succinate dehydrogenase complex, subunit B, iron sulfur (Ip)"""		O	1	Substitution - Missense(1)	kidney(1)											46.0	46.0	46.0					1																	17350478		2203	4300	6503	SO:0001583	missense	6390	Familial Cancer Database	Hereditary Glomus Tumors, Familial Paragangliomas, Hereditary Paragangliomas, type 1-3: PGL1, PGL2, PGL3, incl. Familial Carotid Body Paraganglioma and Sensorineural Hearing Loss;CS, Cowden disease, Multiple Hamartoma Syndrome, incl.: Lhermitte-Duclos; part of PTEN hamartoma tumour syndrome (PHTS) / PTEN-MATCHS, Cowden-like syndrome;Carney-Stratakis dyad, Paraganglioma-Gastric Stromal Sarcoma dyad	U17248	CCDS176.1	1p36.1-p35	2014-09-17			ENSG00000117118	ENSG00000117118	1.3.99.1	"""Mitochondrial respiratory chain complex / Complex II"""	10681	protein-coding gene	gene with protein product		185470		SDH1, SDH			Standard	NM_003000		Approved		uc001bae.3	P21912	OTTHUMG00000002289	ENST00000375499.3:c.632T>C	1.37:g.17350478A>G	ENSP00000364649:p.Val211Ala		B2R545|Q0QEY7|Q9NQ12	Missense_Mutation	SNP	ENST00000375499.3	37	CCDS176.1	.	.	.	.	.	.	.	.	.	.	A	21.8	4.208657	0.79240	.	.	ENSG00000117118	ENST00000375499	D	0.96459	-4.02	5.49	5.49	0.81192	Fumarate reductase, C-terminal (1);Alpha-helical ferredoxin (1);	0.000000	0.85682	D	0.000000	D	0.91640	0.7358	N	0.03281	-0.365	0.80722	D	1	P	0.35684	0.515	P	0.44921	0.464	D	0.90871	0.4746	10	0.22706	T	0.39	-22.0733	14.7068	0.69198	1.0:0.0:0.0:0.0	.	211	P21912	DHSB_HUMAN	A	211	ENSP00000364649:V211A	ENSP00000364649:V211A	V	-	2	0	SDHB	17223065	1.000000	0.71417	0.293000	0.24932	0.976000	0.68499	8.269000	0.89878	2.208000	0.71279	0.482000	0.46254	GTT		0.502	SDHB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000006603.1		NM_003000	
SEMG2	6407	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	43850086	43850086	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr20:43850086C>T	ENST00000372769.3	+	1	146	c.56C>T	c.(55-57)gCa>gTa	p.A19V		NM_003008.2	NP_002999.1	Q02383	SEMG2_HUMAN	semenogelin II	19					sexual reproduction (GO:0019953)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|secretory granule (GO:0030141)	structural molecule activity (GO:0005198)	p.A19V(1)		autonomic_ganglia(1)|breast(3)|endometrium(6)|kidney(2)|large_intestine(6)|lung(9)|prostate(2)|skin(1)|stomach(2)|upper_aerodigestive_tract(2)|urinary_tract(2)	36		Myeloproliferative disorder(115;0.0122)				GAGAAGCAAGCAGCTGTGATG	0.443																																																	1	Substitution - Missense(1)	kidney(1)											75.0	70.0	72.0					20																	43850086		2203	4300	6503	SO:0001583	missense	6407				CCDS13346.1	20q12-q13.1	2008-07-02			ENSG00000124157	ENSG00000124157			10743	protein-coding gene	gene with protein product	"""Semenogelin 2"""	182141				1517240, 9523691	Standard	NM_003008		Approved	SGII	uc002xnk.3	Q02383	OTTHUMG00000032566	ENST00000372769.3:c.56C>T	20.37:g.43850086C>T	ENSP00000361855:p.Ala19Val		Q53ZU2|Q6X2M5|Q6X2M6	Missense_Mutation	SNP	ENST00000372769.3	37	CCDS13346.1	.	.	.	.	.	.	.	.	.	.	C	15.79	2.936551	0.52972	.	.	ENSG00000124157	ENST00000372769	T	0.13196	2.61	2.43	0.4	0.16331	.	.	.	.	.	T	0.29914	0.0748	M	0.71036	2.16	0.09310	N	1	D;D	0.69078	0.997;0.997	D;D	0.80764	0.994;0.994	T	0.07829	-1.0752	9	0.87932	D	0	.	5.2866	0.15704	0.0:0.7377:0.0:0.2623	.	19;19	Q6IRW3;Q02383	.;SEMG2_HUMAN	V	19	ENSP00000361855:A19V	ENSP00000361855:A19V	A	+	2	0	SEMG2	43283500	0.000000	0.05858	0.023000	0.16930	0.367000	0.29736	-0.885000	0.04161	0.119000	0.18210	0.462000	0.41574	GCA		0.443	SEMG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000079417.1		NM_003008	
SFXN2	118980	broad.mit.edu;hgsc.bcm.edu	37	10	104489089	104489089	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr10:104489089T>C	ENST00000369893.5	+	5	612	c.445T>C	c.(445-447)Tcc>Ccc	p.S149P		NM_178858.4	NP_849189.1	Q96NB2	SFXN2_HUMAN	sideroflexin 2	149				QMALSYFTATTTAVATAVGMNMLTKKAPPLVGRWVPFAAVA AANCVNIPMMRQQELIKGI -> KRRPWWAAGCPLPLWLRL TVSISP (in Ref. 4). {ECO:0000305}.	iron ion homeostasis (GO:0055072)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)	cation transmembrane transporter activity (GO:0008324)	p.S149P(1)		endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)|prostate(1)	13		Colorectal(252;0.207)		Epithelial(162;4.53e-09)|all cancers(201;1.2e-07)|BRCA - Breast invasive adenocarcinoma(275;0.218)		GATGGCCCTTTCCTACTTCAC	0.637											OREG0020485	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - Missense(1)	kidney(1)											51.0	43.0	46.0					10																	104489089		2203	4300	6503	SO:0001583	missense	118980			AF462052	CCDS7539.1	10q24.32	2006-03-13			ENSG00000156398	ENSG00000156398		"""Sideroflexins"""	16086	protein-coding gene	gene with protein product		615570					Standard	NM_178858		Approved		uc001kwb.2	Q96NB2	OTTHUMG00000018967	ENST00000369893.5:c.445T>C	10.37:g.104489089T>C	ENSP00000358909:p.Ser149Pro	1382	Q5JSM6	Missense_Mutation	SNP	ENST00000369893.5	37	CCDS7539.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.189692	0.78789	.	.	ENSG00000156398	ENST00000369893	T	0.36878	1.23	5.72	3.25	0.37280	.	0.096018	0.64402	D	0.000001	T	0.48804	0.1520	M	0.70275	2.135	0.50813	D	0.99989	P	0.41265	0.744	P	0.50896	0.653	T	0.51911	-0.8645	10	0.62326	D	0.03	-6.8454	11.6282	0.51158	0.0:0.0:0.5093:0.4907	.	149	Q96NB2	SFXN2_HUMAN	P	149	ENSP00000358909:S149P	ENSP00000358909:S149P	S	+	1	0	SFXN2	104479079	1.000000	0.71417	1.000000	0.80357	0.798000	0.45092	4.959000	0.63666	0.990000	0.38787	0.482000	0.46254	TCC		0.637	SFXN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050096.2		XM_058359	
SLC25A25	114789	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	130868093	130868093	+	Missense_Mutation	SNP	G	G	A	rs201242773		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr9:130868093G>A	ENST00000373064.5	+	6	994	c.731G>A	c.(730-732)cGg>cAg	p.R244Q	SLC25A25_ENST00000373066.5_Missense_Mutation_p.R276Q|SLC25A25_ENST00000373068.2_Missense_Mutation_p.R278Q|SLC25A25_ENST00000432073.2_Missense_Mutation_p.R264Q|SLC25A25_ENST00000373069.5_Missense_Mutation_p.R290Q|SLC25A25_ENST00000433501.1_Missense_Mutation_p.R141Q|RP11-395P17.11_ENST00000602939.1_RNA	NM_052901.4	NP_443133.2	Q6KCM7	SCMC2_HUMAN	solute carrier family 25 (mitochondrial carrier; phosphate carrier), member 25	244					adipose tissue development (GO:0060612)|ATP metabolic process (GO:0046034)|calcium ion transmembrane transport (GO:0070588)|camera-type eye development (GO:0043010)|cellular respiration (GO:0045333)|multicellular organism growth (GO:0035264)|response to activity (GO:0014823)|response to dietary excess (GO:0002021)|response to food (GO:0032094)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)	calcium ion binding (GO:0005509)	p.R244Q(1)|p.R264Q(1)|p.R278Q(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)	10						TCACTCTGGCGGGGCAATGGC	0.592													G|||	1	0.000199681	0.0	0.0014	5008	,	,		18982	0.0		0.0	False		,,,				2504	0.0																3	Substitution - Missense(3)	kidney(3)											79.0	69.0	73.0					9																	130868093		2203	4300	6503	SO:0001583	missense	114789			AJ619963	CCDS6890.1, CCDS35151.1, CCDS48031.1, CCDS59146.1	9q34	2013-05-22			ENSG00000148339	ENSG00000148339		"""Solute carriers"", ""EF-hand domain containing"""	20663	protein-coding gene	gene with protein product		608745				15123600	Standard	NM_052901		Approved	KIAA1896, PCSCL, MCSC	uc004btb.4	Q6KCM7	OTTHUMG00000020736	ENST00000373064.5:c.731G>A	9.37:g.130868093G>A	ENSP00000362155:p.Arg244Gln		Q5SYW7|Q5SYW8|Q5SYX3|Q5VWU2|Q5VWU3|Q5VWU4|Q6KCM4|Q6KCM6|Q6UX48|Q705K2|Q96PZ1|Q9BSA6	Missense_Mutation	SNP	ENST00000373064.5	37	CCDS6890.1	1	4.578754578754579E-4	0	0.0	1	0.0027624309392265192	0	0.0	0	0.0	G	34	5.396477	0.96009	.	.	ENSG00000148339	ENST00000373068;ENST00000373069;ENST00000432073;ENST00000373066;ENST00000373064;ENST00000433501	D;D;D;D;D;D	0.81659	-1.52;-1.52;-1.52;-1.52;-1.52;-1.52	5.77	4.86	0.63082	Mitochondrial carrier domain (2);	0.000000	0.85682	D	0.000000	D	0.90466	0.7014	M	0.85630	2.765	0.80722	D	1	D;D;D;D	0.89917	1.0;0.999;1.0;1.0	D;D;D;D	0.97110	0.954;0.953;0.977;1.0	D	0.91980	0.5594	10	0.72032	D	0.01	-19.1579	15.7548	0.78015	0.0:0.1367:0.8633:0.0	.	244;276;264;278	Q6KCM7;Q6KCM7-5;Q6KCM7-4;Q6KCM7-2	SCMC2_HUMAN;.;.;.	Q	278;290;264;276;244;141	ENSP00000362159:R278Q;ENSP00000362160:R290Q;ENSP00000410053:R264Q;ENSP00000362157:R276Q;ENSP00000362155:R244Q;ENSP00000401672:R141Q	ENSP00000362155:R244Q	R	+	2	0	SLC25A25	129907914	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.961000	0.87903	1.402000	0.46780	0.561000	0.74099	CGG		0.592	SLC25A25-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054407.1		NM_052901	
SLC6A5	9152	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	20629130	20629130	+	Missense_Mutation	SNP	T	T	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr11:20629130T>C	ENST00000525748.1	+	5	1190	c.917T>C	c.(916-918)cTa>cCa	p.L306P		NM_004211.3	NP_004202.2	Q9Y345	SC6A5_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 5	306			L -> V (in HKPX3; compound heterozygote with S-509; impairment of glycine transport when coexpressed with S-509 in vitro). {ECO:0000269|PubMed:16751771}.		glycine import (GO:0036233)|synaptic transmission (GO:0007268)|synaptic transmission, glycinergic (GO:0060012)|transmembrane transport (GO:0055085)|transport (GO:0006810)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycine:sodium symporter activity (GO:0015375)|neurotransmitter:sodium symporter activity (GO:0005328)	p.L306P(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(13)|lung(34)|ovary(2)|prostate(3)|skin(3)|upper_aerodigestive_tract(1)	63					Glycine(DB00145)	GTGTCTGTACTACCCTGGGGC	0.418																																																	1	Substitution - Missense(1)	kidney(1)											171.0	159.0	163.0					11																	20629130		2203	4300	6503	SO:0001583	missense	9152			AF085412	CCDS7854.1	11p15.1	2013-07-19	2013-07-19		ENSG00000165970	ENSG00000165970		"""Solute carriers"""	11051	protein-coding gene	gene with protein product	"""glycine transporter 2"""	604159	"""solute carrier family 6 (neurotransmitter transporter, glycine), member 5"""	NET1		9845349	Standard	NM_004211		Approved	GLYT2	uc001mqd.3	Q9Y345	OTTHUMG00000166024	ENST00000525748.1:c.917T>C	11.37:g.20629130T>C	ENSP00000434364:p.Leu306Pro		O95288|Q4VAM7|Q9BX77	Missense_Mutation	SNP	ENST00000525748.1	37	CCDS7854.1	.	.	.	.	.	.	.	.	.	.	T	22.4	4.287097	0.80803	.	.	ENSG00000165970	ENST00000525748	D	0.84146	-1.81	5.72	5.72	0.89469	.	0.000000	0.85682	D	0.000000	D	0.94318	0.8174	M	0.94063	3.49	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95616	0.8676	10	0.87932	D	0	.	15.658	0.77158	0.0:0.0:0.0:1.0	.	306	Q9Y345	SC6A5_HUMAN	P	306	ENSP00000434364:L306P	ENSP00000434364:L306P	L	+	2	0	SLC6A5	20585706	1.000000	0.71417	1.000000	0.80357	0.920000	0.55202	8.040000	0.89188	2.179000	0.69175	0.460000	0.39030	CTA		0.418	SLC6A5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387497.2		NM_004211	
RPS3A	6189	broad.mit.edu;hgsc.bcm.edu	37	4	152025029	152025029	+	3'UTR	SNP	C	C	T	rs191265801	byFrequency	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr4:152025029C>T	ENST00000322686.6	+	0	1346				RPS3A_ENST00000274065.4_Intron|RPS3A_ENST00000514682.1_Intron|RPS3A_ENST00000509736.1_Intron|RPS3A_ENST00000512690.1_Intron|SNORD73A_ENST00000386062.1_RNA|RPS3A_ENST00000506126.1_Intron|SNORD73_ENST00000364394.1_RNA					ribosomal protein S3A											endometrium(1)|lung(1)|ovary(1)|pancreas(1)	4	all_hematologic(180;0.093)					GTGATAACAACATTTTTCTGA	0.378													C|||	3	0.000599042	0.0008	0.0	5008	,	,		18420	0.0		0.0	False		,,,				2504	0.002																0													53.0	46.0	48.0					4																	152025029		876	1991	2867	SO:0001624	3_prime_UTR_variant	8944			X87373	CCDS3775.1	4q31.2-q31.3	2011-04-05			ENSG00000145425	ENSG00000145425		"""S ribosomal proteins"""	10421	protein-coding gene	gene with protein product		180478		MFTL		8647443, 1398113	Standard	NM_001006		Approved	S3A	uc003ilz.4	P61247	OTTHUMG00000161445	ENST00000322686.6:c.*794C>T	4.37:g.152025029C>T				RNA	SNP	ENST00000322686.6	37																																																																																					0.378	RPS3A-201	KNOWN	basic	protein_coding	protein_coding				
SOAT2	8435	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	53512684	53512685	+	Missense_Mutation	DNP	GT	GT	TG			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G|T	G|T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr12:53512684_53512685GT>TG	ENST00000301466.3	+	9	934_935	c.874_875GT>TG	c.(874-876)GTc>TGc	p.V292C		NM_003578.3	NP_003569.1	O75908	SOAT2_HUMAN	sterol O-acyltransferase 2	292					cholesterol efflux (GO:0033344)|cholesterol esterification (GO:0034435)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|intestinal cholesterol absorption (GO:0030299)|macrophage derived foam cell differentiation (GO:0010742)|very-low-density lipoprotein particle assembly (GO:0034379)	brush border (GO:0005903)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	cholesterol binding (GO:0015485)|cholesterol O-acyltransferase activity (GO:0034736)|fatty-acyl-CoA binding (GO:0000062)|transferase activity, transferring acyl groups (GO:0016746)	p.V292F(1)|p.V292G(1)|p.V292>?(1)		endometrium(5)|kidney(3)|large_intestine(2)|liver(1)|lung(5)|ovary(1)|skin(1)	18					Hesperetin(DB01094)	GACGCCCTATGTCAGGTGGAAT	0.535																																																	3	Substitution - Missense(2)|Complex(1)	kidney(3)																																								SO:0001583	missense	8435			AF059203	CCDS8847.1	12q13.13	2012-09-20			ENSG00000167780	ENSG00000167780	2.3.1.26		11178	protein-coding gene	gene with protein product		601311				9756920	Standard	NM_003578		Approved	ACAT2	uc001sbv.3	O75908	OTTHUMG00000169774	Exception_encountered	12.37:g.53512684_53512685delinsTG	ENSP00000301466:p.Val292Cys		F5H7W4|I6L9H9|Q4VB99|Q4VBA1|Q96TD4|Q9UNR2	Missense_Mutation	SNP	ENST00000301466.3	37	CCDS8847.1																																																																																				0.535	SOAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405817.1			
SORCS1	114815	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	108366996	108366996	+	Silent	SNP	A	A	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr10:108366996A>G	ENST00000263054.6	-	23	3100	c.3093T>C	c.(3091-3093)acT>acC	p.T1031T	SORCS1_ENST00000369698.1_Silent_p.T566T|SORCS1_ENST00000344440.6_Silent_p.T1031T|SORCS1_ENST00000478809.2_5'UTR	NM_001206570.1|NM_052918.4	NP_001193499.1|NP_443150.3	Q8WY21	SORC1_HUMAN	sortilin-related VPS10 domain containing receptor 1	1031					neuropeptide signaling pathway (GO:0007218)	integral component of membrane (GO:0016021)|membrane (GO:0016020)	neuropeptide receptor activity (GO:0008188)	p.T1031T(2)		breast(5)|central_nervous_system(1)|cervix(2)|endometrium(9)|kidney(2)|large_intestine(24)|lung(69)|ovary(1)|prostate(8)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	127		Breast(234;0.0256)|Colorectal(252;0.09)|Lung NSC(174;0.168)		Epithelial(162;1.66e-05)|all cancers(201;0.000689)		AGAGTTCAGCAGTGGTGGGTA	0.557																																																	2	Substitution - coding silent(2)	kidney(2)											83.0	79.0	80.0					10																	108366996		2203	4300	6503	SO:0001819	synonymous_variant	114815			AF284756	CCDS7559.1	10q23-q25	2004-04-20			ENSG00000108018	ENSG00000108018			16697	protein-coding gene	gene with protein product		606283				11499680	Standard	NM_001206570		Approved	sorCS1	uc001kyl.3	Q8WY21	OTTHUMG00000019018	ENST00000263054.6:c.3093T>C	10.37:g.108366996A>G			A2RRF4|Q59GG7|Q5JVT7|Q5JVT8|Q5VY14|Q86WQ1|Q86WQ2|Q9H1Y1|Q9H1Y2	Silent	SNP	ENST00000263054.6	37	CCDS7559.1	.	.	.	.	.	.	.	.	.	.	A	9.074	0.997610	0.19043	.	.	ENSG00000108018	ENST00000452214	.	.	.	5.92	-2.95	0.05564	.	.	.	.	.	T	0.36358	0.0964	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.37126	-0.9719	4	.	.	.	-10.4163	0.3049	0.00279	0.398:0.1521:0.1918:0.2581	.	.	.	.	P	46	.	.	L	-	2	0	SORCS1	108356986	0.897000	0.30589	0.896000	0.35187	0.770000	0.43624	0.021000	0.13489	-0.089000	0.12484	0.533000	0.62120	CTG		0.557	SORCS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050232.4		NM_052918	
SPIB	6689	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	50926246	50926246	+	Silent	SNP	C	C	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr19:50926246C>A	ENST00000595883.1	+	4	316	c.291C>A	c.(289-291)gcC>gcA	p.A97A	CTD-2545M3.6_ENST00000599632.1_Missense_Mutation_p.P232T|SPIB_ENST00000596074.1_Intron|SPIB_ENST00000270632.7_Silent_p.A97A|SPIB_ENST00000439922.2_Intron|SPIB_ENST00000597855.1_Silent_p.A97A	NM_001243999.1|NM_001244000.1|NM_003121.4	NP_001230928.1|NP_001230929.1|NP_003112.2	Q01892	SPIB_HUMAN	Spi-B transcription factor (Spi-1/PU.1 related)	97					cell differentiation (GO:0030154)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.A97A(1)		breast(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(1)|lung(8)	14		all_neural(266;0.131)		OV - Ovarian serous cystadenocarcinoma(262;0.00757)|GBM - Glioblastoma multiforme(134;0.0186)		GCCTGGAGGCCCCGGGGCCTG	0.642																																																	1	Substitution - coding silent(1)	kidney(1)											29.0	33.0	32.0					19																	50926246		2196	4279	6475	SO:0001819	synonymous_variant	6689				CCDS33080.1, CCDS58674.1, CCDS59412.1	19q13.3-q13.4	2008-07-22				ENSG00000269404			11242	protein-coding gene	gene with protein product		606802				1406622	Standard	NM_003121		Approved	SPI-B	uc002psd.3	Q01892		ENST00000595883.1:c.291C>A	19.37:g.50926246C>A			A8K9C9|B4DUG6|Q15359	Silent	SNP	ENST00000595883.1	37	CCDS33080.1																																																																																				0.642	SPIB-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000464744.1		NM_003121	
STMN3	50861	broad.mit.edu;hgsc.bcm.edu	37	20	62275107	62275107	+	Splice_Site	SNP	G	G	T	rs368408629		TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr20:62275107G>T	ENST00000370053.1	-	3	373		c.e3+1		STMN3_ENST00000540534.1_Splice_Site	NM_001276310.1|NM_015894.2	NP_001263239.1|NP_056978.2	Q9NZ72	STMN3_HUMAN	stathmin-like 3						cytoplasmic microtubule organization (GO:0031122)|negative regulation of Rac protein signal transduction (GO:0035021)|nervous system development (GO:0007399)|neuron projection development (GO:0031175)|regulation of cytoskeleton organization (GO:0051493)|regulation of microtubule polymerization or depolymerization (GO:0031110)|regulation of Rac GTPase activity (GO:0032314)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|Golgi apparatus (GO:0005794)	protein domain specific binding (GO:0019904)	p.?(1)		kidney(1)|large_intestine(1)|lung(5)|prostate(1)	8	all_cancers(38;2.31e-11)|all_epithelial(29;7.76e-13)		Epithelial(9;1.9e-09)|all cancers(9;1.22e-08)|BRCA - Breast invasive adenocarcinoma(10;8.86e-06)|OV - Ovarian serous cystadenocarcinoma(5;0.00559)			AGGACTCCTTGCCTTCCTCCG	0.657																																																	1	Unknown(1)	kidney(1)											30.0	32.0	31.0					20																	62275107		2203	4300	6503	SO:0001630	splice_region_variant	50861			AF069709	CCDS13529.1, CCDS63330.1	20q13.3	2007-01-22			ENSG00000197457	ENSG00000197457			15926	protein-coding gene	gene with protein product		608362				9603203, 10655513	Standard	NM_001276310		Approved	SCLIP	uc002yfr.2	Q9NZ72	OTTHUMG00000032985	ENST00000370053.1:c.291+1C>A	20.37:g.62275107G>T			B3KSQ5|B7WP52|B7Z5G4|O75527|Q969Y4	Splice_Site	SNP	ENST00000370053.1	37	CCDS13529.1	.	.	.	.	.	.	.	.	.	.	G	11.65	1.701941	0.30232	.	.	ENSG00000197457	ENST00000370053;ENST00000540534	.	.	.	4.42	3.36	0.38483	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	5.1854	0.15182	0.8158:0.0:0.1842:0.0	.	.	.	.	.	-1	.	.	.	-	.	.	STMN3	61745551	1.000000	0.71417	0.893000	0.35052	0.274000	0.26718	6.182000	0.71995	0.676000	0.31285	0.313000	0.20887	.		0.657	STMN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000080163.1		NM_015894	Intron
TATDN3	128387	hgsc.bcm.edu;ucsc.edu	37	1	212981154	212981154	+	Frame_Shift_Del	DEL	C	C	-			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr1:212981154delC	ENST00000366974.4	+	8	658	c.564delC	c.(562-564)ttcfs	p.F189fs	TATDN3_ENST00000526641.1_Frame_Shift_Del_p.F168fs|TATDN3_ENST00000525569.1_3'UTR|TATDN3_ENST00000531963.1_Frame_Shift_Del_p.F189fs|TATDN3_ENST00000532324.1_Frame_Shift_Del_p.F189fs|TATDN3_ENST00000526997.1_Intron|TATDN3_ENST00000366973.4_Frame_Shift_Del_p.F189fs	NM_001042552.2|NM_001042553.2|NM_001146169.1|NM_001146171.1	NP_001036017.1|NP_001036018.1|NP_001139641.1|NP_001139643.1	Q17R31	TATD3_HUMAN	TatD DNase domain containing 3	189					DNA catabolic process (GO:0006308)	intracellular organelle (GO:0043229)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	deoxyribonuclease activity (GO:0004536)|endodeoxyribonuclease activity, producing 5'-phosphomonoesters (GO:0016888)|metal ion binding (GO:0046872)			endometrium(1)|large_intestine(2)|lung(6)	9				OV - Ovarian serous cystadenocarcinoma(81;0.00699)|all cancers(67;0.0118)|GBM - Glioblastoma multiforme(131;0.0801)|Epithelial(68;0.104)		CTGGGTACTTCTTCTCAATTC	0.373																																																	0													132.0	129.0	130.0					1																	212981154		2203	4300	6503	SO:0001589	frameshift_variant	128387			AL832248	CCDS31019.1, CCDS41465.1, CCDS53475.1, CCDS53476.1, CCDS53477.1	1q32.3	2008-02-05			ENSG00000203705	ENSG00000203705			27010	protein-coding gene	gene with protein product							Standard	NM_001042552		Approved		uc001hjo.2	Q17R31	OTTHUMG00000036805	ENST00000366974.4:c.564delC	1.37:g.212981154delC	ENSP00000355941:p.Phe189fs		A6NGS3|B7Z1C1|B7Z978|B7ZLQ6|E9PJE5|E9PNH3|G3V151|Q4G0L1	Frame_Shift_Del	DEL	ENST00000366974.4	37	CCDS31019.1																																																																																				0.373	TATDN3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000089396.2		XM_375838	
TEX13A	56157	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	104464656	104464656	+	Silent	SNP	C	C	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chrX:104464656C>T	ENST00000413579.1	-	2	537	c.426G>A	c.(424-426)gaG>gaA	p.E142E	IL1RAPL2_ENST00000372582.1_Intron|TEX13A_ENST00000372578.3_Silent_p.E142E|TEX13A_ENST00000372575.1_Silent_p.E142E|IL1RAPL2_ENST00000344799.4_Intron			Q9BXU3	TX13A_HUMAN	testis expressed 13A	142							zinc ion binding (GO:0008270)			large_intestine(5)|ovary(2)|upper_aerodigestive_tract(1)	8						CCTTGTCTCTCTCTTTCTGCA	0.612																																																	0													33.0	33.0	33.0					X																	104464656		2128	4196	6324	SO:0001819	synonymous_variant	56157			AF285597	CCDS76005.1	Xq28	2012-04-20	2007-03-13		ENSG00000133149	ENSG00000268629			11735	protein-coding gene	gene with protein product		300312	"""testis expressed sequence 13A"""			11279525	Standard	NM_031274		Approved		uc004ema.3	Q9BXU3	OTTHUMG00000022133	ENST00000413579.1:c.426G>A	X.37:g.104464656C>T			B1B1G8|Q32NB6	Silent	SNP	ENST00000413579.1	37																																																																																					0.612	TEX13A-201	KNOWN	basic|appris_principal	protein_coding	protein_coding			NM_031274	
TNRC18	84629	broad.mit.edu	37	7	5347894	5347894	+	Missense_Mutation	SNP	A	A	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr7:5347894A>G	ENST00000430969.1	-	30	9098	c.8750T>C	c.(8749-8751)gTg>gCg	p.V2917A	TNRC18_ENST00000399537.4_Missense_Mutation_p.V2917A	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2917	BAH. {ECO:0000255|PROSITE- ProRule:PRU00370}.						chromatin binding (GO:0003682)	p.V2917A(2)		central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CTTGTGCGACACCGTCTGCAC	0.627																																																	2	Substitution - Missense(2)	kidney(2)											39.0	42.0	41.0					7																	5347894		2120	4225	6345	SO:0001583	missense	84629			U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.8750T>C	7.37:g.5347894A>G	ENSP00000395538:p.Val2917Ala		A8MX41|Q96JH1|Q96K91	Missense_Mutation	SNP	ENST00000430969.1	37	CCDS47534.1	.	.	.	.	.	.	.	.	.	.	a	16.15	3.041908	0.55003	.	.	ENSG00000182095	ENST00000399537;ENST00000430969	D;D	0.88277	-2.36;-2.36	4.65	4.65	0.58169	Bromo adjacent homology (BAH) domain (3);	.	.	.	.	D	0.88005	0.6321	N	0.17631	0.505	0.36377	D	0.861657	D	0.56968	0.978	P	0.57911	0.829	D	0.91649	0.5333	9	0.87932	D	0	.	13.7161	0.62697	1.0:0.0:0.0:0.0	.	2917	O15417	TNC18_HUMAN	A	2917	ENSP00000382452:V2917A;ENSP00000395538:V2917A	ENSP00000382452:V2917A	V	-	2	0	TNRC18	5314420	1.000000	0.71417	1.000000	0.80357	0.742000	0.42306	8.686000	0.91250	1.705000	0.51264	0.454000	0.30748	GTG		0.627	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				
TOX2	84969	broad.mit.edu;hgsc.bcm.edu	37	20	42680130	42680130	+	Missense_Mutation	SNP	C	C	T			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr20:42680130C>T	ENST00000358131.5	+	4	831	c.623C>T	c.(622-624)gCg>gTg	p.A208V	TOX2_ENST00000341197.4_Missense_Mutation_p.A199V|TOX2_ENST00000372999.1_Missense_Mutation_p.A157V|TOX2_ENST00000423191.2_Missense_Mutation_p.A157V|TOX2_ENST00000435864.2_3'UTR	NM_001098798.1	NP_001092268.1	Q96NM4	TOX2_HUMAN	TOX high mobility group box family member 2	208					female gonad development (GO:0008585)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|response to gonadotropin (GO:0034698)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A208V(1)|p.A157V(1)		NS(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(13)|ovary(1)|skin(2)	26		Myeloproliferative disorder(115;0.00452)	COAD - Colon adenocarcinoma(18;0.00189)			AGCAAGTCAGCGACCCCCTCT	0.627																																																	2	Substitution - Missense(2)	kidney(2)											41.0	37.0	38.0					20																	42680130		2203	4300	6503	SO:0001583	missense	84969			BC007636	CCDS13324.1, CCDS42875.1, CCDS46603.1	20q13.12	2007-03-20	2007-03-20	2007-03-20					16095	protein-coding gene	gene with protein product	"""granulosa cell HMG box 1"""	611163	"""chromosome 20 open reading frame 100"""	C20orf100		14764631	Standard	NM_001098796		Approved	dJ1108D11.2, GCX-1	uc010ggo.3	Q96NM4		ENST00000358131.5:c.623C>T	20.37:g.42680130C>T	ENSP00000350849:p.Ala208Val		A8K1J1|E1P5X0|G3XAC7|Q5TE33|Q5TE34|Q5TE35|Q96IC9|Q9BQN5	Missense_Mutation	SNP	ENST00000358131.5	37	CCDS42875.1	.	.	.	.	.	.	.	.	.	.	C	20.7	4.036137	0.75617	.	.	ENSG00000124191	ENST00000341197;ENST00000442881;ENST00000423191;ENST00000372999;ENST00000358131;ENST00000435864	T;T;T;T;T;T	0.43294	1.94;0.95;1.94;1.94;1.94;2.16	5.67	5.67	0.87782	.	0.163089	0.53938	D	0.000051	T	0.65595	0.2706	M	0.69823	2.125	0.80722	D	1	D;D;P;D;D	0.89917	0.982;1.0;0.807;0.999;1.0	B;D;B;P;D	0.80764	0.383;0.994;0.15;0.881;0.986	T	0.65672	-0.6111	10	0.54805	T	0.06	.	18.758	0.91839	0.0:1.0:0.0:0.0	.	77;199;157;208;157	B4DQV8;G3XAC7;A8K1J1;Q96NM4;E1P5X0	.;.;.;TOX2_HUMAN;.	V	199;157;157;157;208;77	ENSP00000344724:A199V;ENSP00000396584:A157V;ENSP00000390278:A157V;ENSP00000362090:A157V;ENSP00000350849:A208V;ENSP00000396777:A77V	ENSP00000344724:A199V	A	+	2	0	TOX2	42113544	1.000000	0.71417	0.561000	0.28357	0.014000	0.08584	7.771000	0.85420	2.659000	0.90383	0.655000	0.94253	GCG		0.627	TOX2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000079329.2			
TSSK4	283629	hgsc.bcm.edu	37	14	24677344	24677346	+	In_Frame_Del	DEL	ACG	ACG	-	rs35244223|rs34067514|rs56356156|rs532876491|rs368797011	byFrequency	TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	ACG	ACG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr14:24677344_24677346delACG	ENST00000287913.6	+	4	1147_1149	c.979_981delACG	c.(979-981)acgdel	p.T328del	TSSK4_ENST00000339917.5_In_Frame_Del_p.T338del|CHMP4A_ENST00000542700.2_5'Flank|TSSK4_ENST00000428351.2_In_Frame_Del_p.T135del|AL136419.6_ENST00000565988.1_RNA|TM9SF1_ENST00000556387.1_Intron|TSSK4_ENST00000556621.1_In_Frame_Del_p.T252del|TM9SF1_ENST00000530611.1_Intron			Q6SA08	TSSK4_HUMAN	testis-specific serine kinase 4	328					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|positive regulation of CREB transcription factor activity (GO:0032793)|protein phosphorylation (GO:0006468)|spermatogenesis (GO:0007283)		ATP binding (GO:0005524)|magnesium ion binding (GO:0000287)|protein serine/threonine kinase activity (GO:0004674)			cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(2)	8				GBM - Glioblastoma multiforme(265;0.018)		CTTGCAAATTACGACCTGAAAAT	0.473														191	0.038139	0.1399	0.0086	5008	,	,		22221	0.0		0.0	False		,,,				2504	0.0																0									,	543,3721		26,491,1615					,	0.8	0.0		dbSNP_126	53	4,8250		0,4,4123	no	coding,coding	TSSK4	NM_174944.3,NM_001184739.1	,	26,495,5738	A1A1,A1R,RR		0.0485,12.7345,4.3697	,	,		547,11971				SO:0001651	inframe_deletion	283629			AF542390	CCDS9618.1, CCDS53890.1	14q11.2	2006-03-31	2005-03-10	2005-03-12	ENSG00000139908	ENSG00000139908			19825	protein-coding gene	gene with protein product	"""chromosome 14 open reading frame 20"""	610711	"""serine/threonine kinase 22E"""	C14orf20, STK22E			Standard	NM_174944		Approved		uc001wnh.3	Q6SA08	OTTHUMG00000029323	ENST00000287913.6:c.979_981delACG	14.37:g.24677344_24677346delACG	ENSP00000287913:p.Thr328del		Q2TA60|Q6ZNM2	In_Frame_Del	DEL	ENST00000287913.6	37	CCDS9618.1																																																																																				0.473	TSSK4-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000073139.3		NM_174944	
UBR1	197131	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	43317589	43317589	+	Missense_Mutation	SNP	G	G	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr15:43317589G>C	ENST00000290650.4	-	24	2652	c.2574C>G	c.(2572-2574)aaC>aaG	p.N858K	UBR1_ENST00000382177.2_3'UTR	NM_174916.2	NP_777576.1	Q8IWV7	UBR1_HUMAN	ubiquitin protein ligase E3 component n-recognin 1	858					cellular response to leucine (GO:0071233)|negative regulation of TOR signaling (GO:0032007)|ubiquitin-dependent protein catabolic process (GO:0006511)	cytoplasm (GO:0005737)|proteasome complex (GO:0000502)|ubiquitin ligase complex (GO:0000151)	leucine binding (GO:0070728)|ligase activity (GO:0016874)|ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.N858K(1)		NS(2)|endometrium(2)|kidney(7)|large_intestine(12)|lung(25)|pancreas(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(3)|urinary_tract(1)	58		all_cancers(109;4.32e-15)|all_epithelial(112;4.05e-13)|Lung NSC(122;1.75e-08)|all_lung(180;2e-07)|Melanoma(134;0.0179)|Colorectal(260;0.215)		GBM - Glioblastoma multiforme(94;4.08e-07)|COAD - Colon adenocarcinoma(120;0.185)|Colorectal(105;0.214)		CTTCATCTTTGTTTTCTTGTT	0.294																																																	1	Substitution - Missense(1)	kidney(1)											192.0	162.0	172.0					15																	43317589		2196	4297	6493	SO:0001583	missense	197131				CCDS10091.1	15q13	2008-06-23			ENSG00000159459	ENSG00000159459		"""Ubiquitin protein ligase E3 component n-recognins"""	16808	protein-coding gene	gene with protein product		605981				9653112	Standard	NM_174916		Approved		uc001zqq.3	Q8IWV7	OTTHUMG00000130702	ENST00000290650.4:c.2574C>G	15.37:g.43317589G>C	ENSP00000290650:p.Asn858Lys		O60708|O75492|Q14D45|Q68DN9|Q8IWY6|Q96JY4	Missense_Mutation	SNP	ENST00000290650.4	37	CCDS10091.1	.	.	.	.	.	.	.	.	.	.	G	9.598	1.127884	0.20959	.	.	ENSG00000159459	ENST00000290650;ENST00000546274	T	0.45276	0.9	4.97	4.02	0.46733	.	0.216529	0.48767	D	0.000178	T	0.18341	0.0440	N	0.11560	0.145	0.80722	D	1	B;B	0.19331	0.035;0.0	B;B	0.17098	0.017;0.001	T	0.11227	-1.0596	10	0.02654	T	1	-8.9371	7.8304	0.29338	0.13:0.0:0.87:0.0	.	858;858	B4DYL2;Q8IWV7	.;UBR1_HUMAN	K	858	ENSP00000290650:N858K	ENSP00000290650:N858K	N	-	3	2	UBR1	41104881	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	2.220000	0.42908	1.119000	0.41883	0.655000	0.94253	AAC		0.294	UBR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253202.1		NM_174916	
VHL	7428	broad.mit.edu	37	3	10183872	10183872	+	Splice_Site	SNP	G	G	C			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	Illumina Miseq			Illumina GAIIx	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr3:10183872G>C	ENST00000256474.2	+	1	1180		c.e1+1		snoU13_ENST00000458986.1_RNA|VHL_ENST00000345392.2_Splice_Site	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase						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.?(15)		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)		AGCTACCGAGGTACGGGCCCG	0.701		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"""	15	Unknown(15)	kidney(15)	GRCh37	CS044968|CS982396	VHL	S							10.0	11.0	10.0					3																	10183872		1852	3825	5677	SO:0001630	splice_region_variant	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.340+1G>C	3.37:g.10183872G>C			B2RE45|Q13599|Q6PDA9	Splice_Site	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	G	22.1	4.244638	0.79912	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	.	.	.	5.08	5.08	0.68730	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	16.0436	0.80701	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	VHL	10158872	1.000000	0.71417	1.000000	0.80357	0.855000	0.48748	4.276000	0.58933	2.377000	0.81083	0.479000	0.44913	.		0.701	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	Intron
ZNF510	22869	broad.mit.edu;ucsc.edu	37	9	99538291	99538291	+	Missense_Mutation	SNP	C	C	A			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr9:99538291C>A	ENST00000375231.1	-	2	711	c.61G>T	c.(61-63)Gca>Tca	p.A21S	ZNF510_ENST00000223428.4_Missense_Mutation_p.A21S			Q9Y2H8	ZN510_HUMAN	zinc finger protein 510	21					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.A21S(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(8)|stomach(1)|urinary_tract(1)	21		Acute lymphoblastic leukemia(62;0.0527)				CCACCTTCTGCAAGTTGGCCC	0.532																																																	1	Substitution - Missense(1)	kidney(1)											168.0	112.0	131.0					9																	99538291		2203	4299	6502	SO:0001583	missense	22869			AB023189	CCDS35074.1	9q22.33	2013-01-08			ENSG00000081386	ENSG00000081386		"""Zinc fingers, C2H2-type"", ""-"""	29161	protein-coding gene	gene with protein product						10231032	Standard	XM_005251807		Approved	KIAA0972	uc004awn.1	Q9Y2H8	OTTHUMG00000020303	ENST00000375231.1:c.61G>T	9.37:g.99538291C>A	ENSP00000364379:p.Ala21Ser		Q5SZP5	Missense_Mutation	SNP	ENST00000375231.1	37	CCDS35074.1	.	.	.	.	.	.	.	.	.	.	c	11.31	1.601870	0.28534	.	.	ENSG00000081386	ENST00000375231;ENST00000223428;ENST00000374641	T;T;T	0.06218	3.33;3.33;5.71	3.04	1.11	0.20524	.	.	.	.	.	T	0.02193	0.0068	N	0.08118	0	0.09310	N	1	P	0.40970	0.734	B	0.31751	0.135	T	0.37314	-0.9711	9	0.08837	T	0.75	.	5.617	0.17436	0.2283:0.5502:0.2215:0.0	.	21	Q9Y2H8	ZN510_HUMAN	S	21	ENSP00000364379:A21S;ENSP00000223428:A21S;ENSP00000363772:A21S	ENSP00000223428:A21S	A	-	1	0	ZNF510	98578112	0.059000	0.20769	0.001000	0.08648	0.015000	0.08874	0.186000	0.16978	0.300000	0.22699	0.561000	0.74099	GCA		0.532	ZNF510-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000053287.1		NM_014930	
SPEN	23013	broad.mit.edu	37	1	16257104	16257104	+	Missense_Mutation	SNP	T	T	G			TCGA-A3-3376-01A-02D-1421-08	TCGA-A3-3376-11A-01D-1421-08	T	T	T	G	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454	.		Illumina GAIIx	31031387-393f-4bf9-ba87-cfe7330afc13	030e8c64-a55c-4996-9372-ad45846be7c0	g.chr1:16257104T>G	ENST00000375759.3	+	11	4573	c.4369T>G	c.(4369-4371)Tct>Gct	p.S1457A		NM_015001.2	NP_055816.2	Q96T58	MINT_HUMAN	spen family transcriptional repressor	1457					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|Notch signaling pathway (GO:0007219)|positive regulation of neurogenesis (GO:0050769)|positive regulation of transcription, DNA-templated (GO:0045893)|viral process (GO:0016032)	extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|transcriptional repressor complex (GO:0017053)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)|RNA polymerase II transcription factor binding (GO:0001085)|RNA polymerase II transcription factor binding transcription factor activity involved in negative regulation of transcription (GO:0001191)|sequence-specific DNA binding transcription factor activity (GO:0003700)|single-stranded DNA binding (GO:0003697)|transcription corepressor activity (GO:0003714)	p.S1457A(1)		NS(1)|breast(13)|central_nervous_system(3)|cervix(5)|endometrium(16)|kidney(18)|large_intestine(27)|liver(2)|lung(37)|ovary(7)|prostate(7)|skin(7)|upper_aerodigestive_tract(5)|urinary_tract(1)	149		Colorectal(325;0.000258)|Breast(348;0.000278)|Lung NSC(340;0.000419)|Renal(390;0.000518)|all_lung(284;0.000567)|Ovarian(437;0.0129)|Myeloproliferative disorder(586;0.0255)		UCEC - Uterine corpus endometrioid carcinoma (279;0.0185)|Colorectal(212;5.96e-07)|COAD - Colon adenocarcinoma(227;3.11e-05)|BRCA - Breast invasive adenocarcinoma(304;0.000115)|Kidney(64;0.000212)|KIRC - Kidney renal clear cell carcinoma(64;0.003)|STAD - Stomach adenocarcinoma(313;0.013)|READ - Rectum adenocarcinoma(331;0.0681)		CCTCTCTTCATCTCGTGAAGA	0.363																																						.											1	Substitution - Missense(1)	kidney(1)											74.0	78.0	76.0					1																	16257104		2202	4300	6502	SO:0001583	missense	23013				CCDS164.1	1p36	2013-10-17	2013-10-17		ENSG00000065526	ENSG00000065526		"""RNA binding motif (RRM) containing"""	17575	protein-coding gene	gene with protein product		613484	"""SPEN homolog, transcriptional regulator (Drosophila)"", ""spen homolog, transcriptional regulator (Drosophila)"""			10451362, 11331609	Standard	NM_015001		Approved	KIAA0929, MINT, SHARP, RBM15C	uc001axk.1	Q96T58	OTTHUMG00000009376	ENST00000375759.3:c.4369T>G	1.37:g.16257104T>G	ENSP00000364912:p.Ser1457Ala		Q9H9A8|Q9NWH5|Q9UQ01|Q9Y556	Missense_Mutation	SNP	ENST00000375759.3	37	CCDS164.1	.	.	.	.	.	.	.	.	.	.	T	14.48	2.548882	0.45383	.	.	ENSG00000065526	ENST00000375759	T	0.23950	1.88	5.27	5.27	0.74061	.	.	.	.	.	T	0.39886	0.1095	L	0.32530	0.975	0.58432	D	0.999994	D	0.64830	0.994	D	0.72625	0.978	T	0.13442	-1.0509	9	0.45353	T	0.12	-17.2612	15.3637	0.74503	0.0:0.0:0.0:1.0	.	1457	Q96T58	MINT_HUMAN	A	1457	ENSP00000364912:S1457A	ENSP00000364912:S1457A	S	+	1	0	SPEN	16129691	1.000000	0.71417	1.000000	0.80357	0.962000	0.63368	7.477000	0.81069	2.216000	0.71823	0.460000	0.39030	TCT		0.363	SPEN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025993.1		NM_015001	
