#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_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	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
ACTN1	87	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	69356966	69356966	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr14:69356966T>G	ENST00000193403.6	-	11	1507	c.1124A>C	c.(1123-1125)gAg>gCg	p.E375A	ACTN1_ENST00000538545.2_Missense_Mutation_p.E375A|ACTN1_ENST00000376839.3_Missense_Mutation_p.E310A|ACTN1_ENST00000394419.4_Missense_Mutation_p.E375A|ACTN1_ENST00000438964.2_Missense_Mutation_p.E375A	NM_001102.3	NP_001093.1	P12814	ACTN1_HUMAN	actinin, alpha 1	375	Interaction with DDN.				actin crosslink formation (GO:0051764)|actin filament bundle assembly (GO:0051017)|blood coagulation (GO:0007596)|cell junction assembly (GO:0034329)|extracellular matrix organization (GO:0030198)|focal adhesion assembly (GO:0048041)|negative regulation of cellular component movement (GO:0051271)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of apoptotic process (GO:0042981)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|dendritic spine (GO:0043197)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|focal adhesion (GO:0005925)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|platelet alpha granule lumen (GO:0031093)|pseudopodium (GO:0031143)|Z disc (GO:0030018)	calcium ion binding (GO:0005509)|double-stranded RNA binding (GO:0003725)|integrin binding (GO:0005178)|ion channel binding (GO:0044325)|vinculin binding (GO:0017166)	p.E375A(1)		breast(1)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(5)|lung(9)|prostate(2)|urinary_tract(1)	27				BRCA - Breast invasive adenocarcinoma(234;0.00605)|all cancers(60;0.00846)|OV - Ovarian serous cystadenocarcinoma(108;0.0654)		ATAGCCCTTCTCCACCTGCTC	0.622																																																	1	Substitution - Missense(1)	kidney(1)											102.0	84.0	90.0					14																	69356966		2203	4300	6503	SO:0001583	missense	87			M95178	CCDS9792.1, CCDS45129.1, CCDS45130.1	14q24.1	2014-08-08			ENSG00000072110	ENSG00000072110		"""EF-hand domain containing"""	163	protein-coding gene	gene with protein product		102575				2349951	Standard	NM_001102		Approved		uc001xkm.3	P12814	OTTHUMG00000171386	ENST00000193403.6:c.1124A>C	14.37:g.69356966T>G	ENSP00000193403:p.Glu375Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B3V8S3|B4DHH3|B7TY16|Q1HE25|Q9BTN1	Missense_Mutation	SNP	ENST00000193403.6	37	CCDS9792.1	.	.	.	.	.	.	.	.	.	.	T	24.3	4.520004	0.85495	.	.	ENSG00000072110	ENST00000193403;ENST00000394419;ENST00000438964;ENST00000376839;ENST00000538545	T;T;T;T;T	0.42131	0.98;0.98;0.98;0.98;0.98	4.7	4.7	0.59300	.	0.000000	0.85682	D	0.000000	T	0.70622	0.3245	M	0.91872	3.25	0.80722	D	1	D;P;D;D	0.71674	0.998;0.862;0.96;0.969	D;D;D;D	0.81914	0.995;0.944;0.944;0.985	T	0.78836	-0.2047	10	0.87932	D	0	.	14.3534	0.66719	0.0:0.0:0.0:1.0	.	375;375;375;375	B7TY16;P12814-2;Q1HE25;P12814	.;.;.;ACTN1_HUMAN	A	375;375;375;310;375	ENSP00000193403:E375A;ENSP00000377941:E375A;ENSP00000414272:E375A;ENSP00000366035:E310A;ENSP00000439828:E375A	ENSP00000193403:E375A	E	-	2	0	ACTN1	68426719	1.000000	0.71417	0.994000	0.49952	0.927000	0.56198	7.868000	0.87116	1.971000	0.57363	0.533000	0.62120	GAG		0.622	ACTN1-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000413233.3		NM_001102	
ADCY1	107	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	45725770	45725770	+	Silent	SNP	G	G	A			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr7:45725770G>A	ENST00000297323.7	+	13	2305	c.2283G>A	c.(2281-2283)acG>acA	p.T761T		NM_021116.2	NP_066939.1	Q08828	ADCY1_HUMAN	adenylate cyclase 1 (brain)	761					activation of phospholipase C activity (GO:0007202)|activation of protein kinase A activity (GO:0034199)|adenylate cyclase-activating G-protein coupled receptor signaling pathway (GO:0007189)|adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|axonogenesis (GO:0007409)|cellular response to glucagon stimulus (GO:0071377)|circadian rhythm (GO:0007623)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|intracellular signal transduction (GO:0035556)|long-term memory (GO:0007616)|neurotrophin TRK receptor signaling pathway (GO:0048011)|regulation of circadian rhythm (GO:0042752)|response to drug (GO:0042493)|response to lithium ion (GO:0010226)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)|water transport (GO:0006833)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|calcium- and calmodulin-responsive adenylate cyclase activity (GO:0008294)|metal ion binding (GO:0046872)	p.T761T(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|large_intestine(14)|lung(33)|ovary(4)|prostate(3)|skin(4)|upper_aerodigestive_tract(1)	71					Adenosine monophosphate(DB00131)|Adenosine triphosphate(DB00171)	GGCTCACCACGTCCTACATCC	0.567																																																	1	Substitution - coding silent(1)	kidney(1)											92.0	86.0	88.0					7																	45725770		2203	4300	6503	SO:0001819	synonymous_variant	107			L05500	CCDS34631.1, CCDS75593.1	7p13-p12	2013-02-04			ENSG00000164742	ENSG00000164742	4.6.1.1	"""Adenylate cyclases"""	232	protein-coding gene	gene with protein product		103072				8314585	Standard	NM_021116		Approved	AC1	uc003tne.4	Q08828	OTTHUMG00000155420	ENST00000297323.7:c.2283G>A	7.37:g.45725770G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A4D2L8|Q75MI1	Silent	SNP	ENST00000297323.7	37	CCDS34631.1																																																																																				0.567	ADCY1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000340055.2		NM_021116	
SLC35G6	643664	hgsc.bcm.edu	37	17	7385682	7385682	+	Missense_Mutation	SNP	G	G	A	rs143401129	byFrequency	TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr17:7385682G>A	ENST00000412468.2	+	2	494	c.379G>A	c.(379-381)Gct>Act	p.A127T	POLR2A_ENST00000322644.6_5'Flank|POLR2A_ENST00000572844.1_5'Flank|ZBTB4_ENST00000311403.4_Intron|ZBTB4_ENST00000380599.4_5'Flank	NM_001102614.1	NP_001096084.1	P0C7Q6	S35G6_HUMAN	solute carrier family 35, member G6	127	EamA 1.					integral component of membrane (GO:0016021)		p.A127T(1)									GGTGGTGCCCGCTGGCAACGC	0.617													G|||	2	0.000399361	0.0	0.0	5008	,	,		18120	0.002		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	skin(1)											117.0	118.0	117.0					17																	7385682		2203	4297	6500	SO:0001583	missense	0				CCDS45603.1	17p13.1	2013-05-22	2011-08-03	2011-08-03		ENSG00000259224		"""Solute carriers"""	31351	protein-coding gene	gene with protein product			"""transmembrane protein 21B"", ""acyl-malonyl condensing enzyme 1-like 3"""	TMEM21B, AMAC1L3			Standard	NM_001102614		Approved		uc010cmj.1	P0C7Q6		ENST00000412468.2:c.379G>A	17.37:g.7385682G>A	ENSP00000396523:p.Ala127Thr	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000412468.2	37	CCDS45603.1	.	.	.	.	.	.	.	.	.	.	G	7.540	0.660468	0.14645	.	.	ENSG00000181222	ENST00000412468	T	0.61040	0.14	4.33	1.16	0.20824	.	.	.	.	.	T	0.34221	0.0890	N	0.19112	0.55	0.09310	N	1	B	0.09022	0.002	B	0.06405	0.002	T	0.18209	-1.0344	9	0.15952	T	0.53	2.672	4.1386	0.10183	0.2674:0.3521:0.3805:0.0	.	127	P0C7Q6	S35G6_HUMAN	T	127	ENSP00000396523:A127T	ENSP00000396523:A127T	A	+	1	0	SLC35G6	7326406	0.000000	0.05858	0.060000	0.19600	0.581000	0.36288	-0.024000	0.12435	0.400000	0.25396	0.563000	0.77884	GCT		0.617	SLC35G6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding			NM_001102614	
TIMMDC1	51300	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	119242475	119242475	+	Nonsense_Mutation	SNP	G	G	T			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr3:119242475G>T	ENST00000494664.1	+	7	932	c.730G>T	c.(730-732)Gag>Tag	p.E244*	TIMMDC1_ENST00000493694.1_Nonsense_Mutation_p.E110*	NM_016589.3	NP_057673.2	Q9NPL8	TIDC1_HUMAN	translocase of inner mitochondrial membrane domain containing 1	244						integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|nucleus (GO:0005634)		p.E244*(1)		autonomic_ganglia(1)|kidney(2)|large_intestine(2)|lung(7)|ovary(1)|stomach(1)|urinary_tract(1)	15						ACAAGTTACTGAGCACCTCCC	0.358																																																	1	Substitution - Nonsense(1)	kidney(1)											105.0	110.0	108.0					3																	119242475		2203	4300	6503	SO:0001587	stop_gained	0			AF210057	CCDS33831.1	3q13.33	2013-12-05	2011-07-05	2011-07-05	ENSG00000113845	ENSG00000113845			1321	protein-coding gene	gene with protein product		615534	"""chromosome 3 open reading frame 1"""	C3orf1		11092749	Standard	NM_016589		Approved	FLJ22597	uc003ecn.3	Q9NPL8	OTTHUMG00000159388	ENST00000494664.1:c.730G>T	3.37:g.119242475G>T	ENSP00000418803:p.Glu244*	Somatic		WXS	Illumina HiSeq	Phase_I	D3DN81|Q6IAJ7|Q6UWU6|Q9NPR3|Q9NPS5|Q9P0Y6	Nonsense_Mutation	SNP	ENST00000494664.1	37	CCDS33831.1	.	.	.	.	.	.	.	.	.	.	G	9.371	1.070611	0.20147	.	.	ENSG00000113845	ENST00000494664;ENST00000493694	.	.	.	5.54	4.66	0.58398	.	0.231484	0.43747	D	0.000539	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.56958	D	0.05	-10.5191	12.3596	0.55194	0.0:0.1687:0.8313:0.0	.	.	.	.	X	244;110	.	ENSP00000419510:E110X	E	+	1	0	TIMMDC1	120725165	1.000000	0.71417	0.358000	0.25811	0.087000	0.18053	2.913000	0.48790	1.566000	0.49654	0.650000	0.86243	GAG		0.358	TIMMDC1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000355077.3		NM_016589	
CATSPER1	117144	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	65792685	65792685	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr11:65792685T>G	ENST00000312106.5	-	1	1303	c.1166A>C	c.(1165-1167)aAa>aCa	p.K389T		NM_053054.3	NP_444282.3	Q8NEC5	CTSR1_HUMAN	cation channel, sperm associated 1	389					calcium ion import (GO:0070509)|cell differentiation (GO:0030154)|fusion of sperm to egg plasma membrane (GO:0007342)|membrane depolarization during action potential (GO:0086010)|multicellular organism reproduction (GO:0032504)|multicellular organismal development (GO:0007275)|regulation of calcium ion transport (GO:0051924)|regulation of cilium beat frequency involved in ciliary motility (GO:0060296)|single fertilization (GO:0007338)|sperm motility (GO:0030317)|sperm-egg recognition (GO:0035036)|spermatogenesis (GO:0007283)	CatSper complex (GO:0036128)|motile cilium (GO:0031514)|plasma membrane (GO:0005886)	calcium activated cation channel activity (GO:0005227)|voltage-gated calcium channel activity (GO:0005245)	p.K389T(1)		breast(3)|central_nervous_system(1)|endometrium(9)|kidney(3)|large_intestine(6)|liver(3)|lung(12)|ovary(3)|prostate(1)|skin(2)|upper_aerodigestive_tract(1)	44						TTCTGAATGTTTGGTGGAGAT	0.552																																																	1	Substitution - Missense(1)	kidney(1)											138.0	122.0	127.0					11																	65792685		2201	4296	6497	SO:0001583	missense	117144			AF407333	CCDS8127.1	11q12.1	2011-07-05			ENSG00000175294	ENSG00000175294		"""Voltage-gated ion channels / Cation channels, sperm associated"""	17116	protein-coding gene	gene with protein product		606389				11675491, 11595941, 16382101	Standard	NM_053054		Approved	CATSPER	uc001ogt.3	Q8NEC5	OTTHUMG00000166668	ENST00000312106.5:c.1166A>C	11.37:g.65792685T>G	ENSP00000309052:p.Lys389Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q96P76	Missense_Mutation	SNP	ENST00000312106.5	37	CCDS8127.1	.	.	.	.	.	.	.	.	.	.	T	12.51	1.960634	0.34565	.	.	ENSG00000175294	ENST00000312106	D	0.97279	-4.32	2.63	-5.26	0.02772	.	.	.	.	.	D	0.96241	0.8774	M	0.65975	2.015	0.09310	N	1	D	0.71674	0.998	P	0.60682	0.878	D	0.89742	0.3934	9	0.66056	D	0.02	-0.5077	1.0597	0.01597	0.1549:0.2387:0.3469:0.2595	.	389	Q8NEC5	CTSR1_HUMAN	T	389	ENSP00000309052:K389T	ENSP00000309052:K389T	K	-	2	0	CATSPER1	65549261	0.000000	0.05858	0.000000	0.03702	0.019000	0.09904	-0.883000	0.04170	-1.390000	0.02087	0.377000	0.23210	AAA		0.552	CATSPER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391055.1		NM_053054	
CCDC18	343099	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	93649561	93649561	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr1:93649561A>G	ENST00000343253.7	+	3	663	c.161A>G	c.(160-162)tAt>tGt	p.Y54C	CCDC18_ENST00000338949.4_5'UTR|CCDC18_ENST00000401026.3_Missense_Mutation_p.Y54C|CCDC18_ENST00000557479.1_Missense_Mutation_p.Y172C|CCDC18_ENST00000334652.5_5'UTR			Q5T9S5	CCD18_HUMAN	coiled-coil domain containing 18	54								p.Y172C(1)		breast(5)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(3)|pancreas(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	42		all_lung(203;0.00196)|Lung NSC(277;0.00903)|Melanoma(281;0.099)|all_neural(321;0.185)|Glioma(108;0.203)		all cancers(265;0.00166)|GBM - Glioblastoma multiforme(16;0.00551)|Epithelial(280;0.0967)		AATTCTGATTATGCCCCTAAT	0.323																																																	1	Substitution - Missense(1)	kidney(1)											134.0	123.0	127.0					1																	93649561		1816	4078	5894	SO:0001583	missense	343099					1p22.1	2008-02-05			ENSG00000122483	ENSG00000122483			30370	protein-coding gene	gene with protein product						12601173	Standard	XM_006710609		Approved	NY-SAR-41	uc021opx.1	Q5T9S5	OTTHUMG00000010598	ENST00000343253.7:c.161A>G	1.37:g.93649561A>G	ENSP00000343377:p.Tyr54Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q6ZU17	Missense_Mutation	SNP	ENST00000343253.7	37		.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.59|14.59	2.579560|2.579560	0.46006|0.46006	.|.	.|.	ENSG00000122483|ENSG00000122483	ENST00000370276|ENST00000343253;ENST00000401026;ENST00000557479	.|.	.|.	.|.	6.02|6.02	1.07|1.07	0.20283|0.20283	.|.	.|0.493890	.|0.19883	.|N	.|0.103921	T|T	0.13628|0.13628	0.0330|0.0330	L|L	0.44542|0.44542	1.39|1.39	0.18873|0.18873	N|N	0.999988|0.999988	.|P	.|0.50272	.|0.933	.|P	.|0.46339	.|0.513	T|T	0.06826|0.06826	-1.0805|-1.0805	5|9	.|0.40728	.|T	.|0.16	.|.	3.1298|3.1298	0.06419|0.06419	0.5347:0.0:0.1488:0.3165|0.5347:0.0:0.1488:0.3165	.|.	.|172	.|G3V388	.|.	V|C	108|54;54;172	.|.	.|ENSP00000343377:Y54C	M|Y	+|+	1|2	0|0	CCDC18|CCDC18	93422149|93422149	0.005000|0.005000	0.15991|0.15991	0.819000|0.819000	0.32651|0.32651	0.855000|0.855000	0.48748|0.48748	0.554000|0.554000	0.23407|0.23407	0.461000|0.461000	0.27071|0.27071	0.482000|0.482000	0.46254|0.46254	ATG|TAT		0.323	CCDC18-008	PUTATIVE	basic|appris_principal|exp_conf	protein_coding	protein_coding	OTTHUMT00000382327.1		NM_206886	
CCDC54	84692	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	107097368	107097368	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr3:107097368A>G	ENST00000261058.1	+	1	1181	c.934A>G	c.(934-936)Aac>Gac	p.N312D		NM_032600.2	NP_115989.1	Q8NEL0	CCD54_HUMAN	coiled-coil domain containing 54	312								p.N312D(1)		NS(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(8)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)	19						CTCCATCTTCAACAATATTTA	0.423																																																	1	Substitution - Missense(1)	kidney(1)											81.0	82.0	82.0					3																	107097368		2138	4273	6411	SO:0001583	missense	84692			AF367469	CCDS2949.1	3q13.12	2013-10-11			ENSG00000138483	ENSG00000138483			30703	protein-coding gene	gene with protein product	"""sperm protein 17"""					15257753	Standard	NM_032600		Approved	NYD-SP17, FLJ25362, SP17	uc003dwi.1	Q8NEL0	OTTHUMG00000159169	ENST00000261058.1:c.934A>G	3.37:g.107097368A>G	ENSP00000261058:p.Asn312Asp	Somatic		WXS	Illumina HiSeq	Phase_I	Q96A43	Missense_Mutation	SNP	ENST00000261058.1	37	CCDS2949.1	.	.	.	.	.	.	.	.	.	.	A	11.90	1.777246	0.31411	.	.	ENSG00000138483	ENST00000261058	T	0.52983	0.64	5.09	2.51	0.30379	.	0.110120	0.39834	N	0.001260	T	0.51126	0.1656	M	0.64997	1.995	0.22066	N	0.999385	D	0.57257	0.979	P	0.53518	0.728	T	0.41610	-0.9499	10	0.59425	D	0.04	-10.4542	5.9448	0.19213	0.6684:0.1692:0.0:0.1624	.	312	Q8NEL0	CCD54_HUMAN	D	312	ENSP00000261058:N312D	ENSP00000261058:N312D	N	+	1	0	CCDC54	108580058	1.000000	0.71417	0.974000	0.42286	0.046000	0.14306	1.230000	0.32612	0.742000	0.32697	0.377000	0.23210	AAC		0.423	CCDC54-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000353651.1		NM_032600	
CCDC91	55297	broad.mit.edu;ucsc.edu	37	12	28636996	28636996	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr12:28636996G>T	ENST00000545336.1	+	15	1532	c.1113G>T	c.(1111-1113)aaG>aaT	p.K371N	CCDC91_ENST00000540401.1_3'UTR|CCDC91_ENST00000381259.1_Missense_Mutation_p.K371N|CCDC91_ENST00000539107.1_Missense_Mutation_p.K335N|CCDC91_ENST00000306172.5_Missense_Mutation_p.K341N|CCDC91_ENST00000381256.1_Missense_Mutation_p.K335N			Q7Z6B0	CCD91_HUMAN	coiled-coil domain containing 91	371	Homodimerization.				protein transport (GO:0015031)	Golgi apparatus (GO:0005794)|membrane (GO:0016020)|nucleus (GO:0005634)		p.K371N(1)		NS(1)|breast(3)|central_nervous_system(1)|endometrium(1)|kidney(2)|large_intestine(5)|lung(8)|skin(1)	22	Acute lymphoblastic leukemia(23;0.00718)|all_hematologic(23;0.0113)|Lung SC(9;0.184)					AAACTGTTAAGGCAGCAATAA	0.388																																																	1	Substitution - Missense(1)	kidney(1)											68.0	72.0	71.0					12																	28636996		2203	4300	6503	SO:0001583	missense	55297			AK093152	CCDS8716.1	12p11.22	2006-03-17				ENSG00000123106			24855	protein-coding gene	gene with protein product	"""GGA binding partner"""					12808037	Standard	XM_005253413		Approved	p56, FLJ11088, DKFZp779L1558	uc001riq.3	Q7Z6B0		ENST00000545336.1:c.1113G>T	12.37:g.28636996G>T	ENSP00000438040:p.Lys371Asn	Somatic		WXS	Illumina GAIIx	Phase_I	B3KSA3|C9JR07|Q68D43|Q6IA78|Q8NEN7|Q9NUW9	Missense_Mutation	SNP	ENST00000545336.1	37	CCDS8716.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	18.98|18.98	3.737717|3.737717	0.69304|0.69304	.|.	.|.	ENSG00000123106|ENSG00000123106	ENST00000536154;ENST00000539107;ENST00000545336;ENST00000381259;ENST00000381256;ENST00000306172;ENST00000535212|ENST00000542801	T;T;T;T;T;T;T|.	0.55234|.	0.85;0.93;1.18;1.18;0.93;1.16;0.53|.	5.83|5.83	4.93|4.93	0.64822|0.64822	.|.	0.090217|.	0.48286|.	D|.	0.000197|.	T|T	0.33469|0.33469	0.0864|0.0864	N|N	0.24115|0.24115	0.695|0.695	0.31213|0.31213	N|N	0.698464|0.698464	B;P;P|.	0.40731|.	0.081;0.728;0.728|.	B;B;B|.	0.41988|.	0.064;0.372;0.372|.	T|T	0.22906|0.22906	-1.0203|-1.0203	10|5	0.87932|.	D|.	0|.	-6.9287|-6.9287	9.8479|9.8479	0.41039|0.41039	0.0904:0.0:0.9096:0.0|0.0904:0.0:0.9096:0.0	.|.	335;371;341|.	Q7Z6B0-3;Q7Z6B0;Q7Z6B0-2|.	.;CCD91_HUMAN;.|.	N|M	111;335;371;371;335;341;70|42	ENSP00000444440:K111N;ENSP00000440513:K335N;ENSP00000438040:K371N;ENSP00000370658:K371N;ENSP00000370655:K335N;ENSP00000305075:K341N;ENSP00000445999:K70N|.	ENSP00000305075:K341N|.	K|R	+|+	3|2	2|0	CCDC91|CCDC91	28528263|28528263	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.994000|0.994000	0.84299|0.84299	0.701000|0.701000	0.25616|0.25616	2.756000|2.756000	0.94617|0.94617	0.655000|0.655000	0.94253|0.94253	AAG|AGG		0.388	CCDC91-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402447.1		NM_018318	
CDK12	51755	broad.mit.edu;hgsc.bcm.edu	37	17	37681129	37681129	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr17:37681129G>A	ENST00000447079.4	+	12	3331	c.3298G>A	c.(3298-3300)Gat>Aat	p.D1100N	CDK12_ENST00000430627.2_Missense_Mutation_p.D1100N	NM_015083.1|NM_016507.2	NP_055898.1|NP_057591.2	Q9NYV4	CDK12_HUMAN	cyclin-dependent kinase 12	1100					mRNA processing (GO:0006397)|phosphorylation of RNA polymerase II C-terminal domain (GO:0070816)|protein autophosphorylation (GO:0046777)|regulation of MAP kinase activity (GO:0043405)|RNA splicing (GO:0008380)	cyclin K-CDK12 complex (GO:0002944)|nuclear cyclin-dependent protein kinase holoenzyme complex (GO:0019908)|nuclear speck (GO:0016607)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|cyclin binding (GO:0030332)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)|protein kinase activity (GO:0004672)|RNA polymerase II carboxy-terminal domain kinase activity (GO:0008353)	p.D1100N(1)		NS(4)|breast(3)|endometrium(5)|kidney(4)|large_intestine(11)|lung(23)|ovary(11)|prostate(4)|skin(2)|urinary_tract(3)	70						TGGGGCTGGGGATGCAATAGG	0.517			"""Mis, N, F"""		serous ovarian					TCGA Ovarian(9;0.13)																														Rec	yes		17	17q12	51755	cyclin-dependent kinase 12		E	1	Substitution - Missense(1)	kidney(1)											52.0	53.0	53.0					17																	37681129		2203	4300	6503	SO:0001583	missense	51755			AF227198	CCDS11337.1, CCDS45666.1	17q12	2011-10-25	2009-12-16	2009-12-16	ENSG00000167258	ENSG00000167258		"""Cyclin-dependent kinases"""	24224	protein-coding gene	gene with protein product	"""CDC2 related protein kinase 7"""	615514	"""Cdc2-related kinase, arginine/serine-rich"""	CRKRS		10048485, 11683387, 19884882	Standard	XM_005257456		Approved	CRK7, CRKR, KIAA0904	uc010cvv.3	Q9NYV4	OTTHUMG00000133214	ENST00000447079.4:c.3298G>A	17.37:g.37681129G>A	ENSP00000398880:p.Asp1100Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A7E2B2|B4DYX4|B9EIQ6|O94978	Missense_Mutation	SNP	ENST00000447079.4	37	CCDS11337.1	.	.	.	.	.	.	.	.	.	.	G	11.97	1.797025	0.31777	.	.	ENSG00000167258	ENST00000430627;ENST00000447079	T;T	0.67698	-0.28;-0.27	4.98	4.98	0.66077	.	0.000000	0.44688	D	0.000421	T	0.52565	0.1742	N	0.24115	0.695	0.29262	N	0.871275	B;B;B	0.23650	0.089;0.037;0.062	B;B;B	0.24155	0.023;0.023;0.051	T	0.40608	-0.9554	10	0.18276	T	0.48	-4.5654	16.2155	0.82211	0.0:0.0:1.0:0.0	.	1099;1100;1100	E7EUM9;Q9NYV4;Q9NYV4-2	.;CDK12_HUMAN;.	N	1100	ENSP00000407720:D1100N;ENSP00000398880:D1100N	ENSP00000407720:D1100N	D	+	1	0	CDK12	34934655	1.000000	0.71417	1.000000	0.80357	0.927000	0.56198	3.779000	0.55379	2.591000	0.87537	0.563000	0.77884	GAT		0.517	CDK12-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000256941.4		NM_016507	
CGGBP1	8545	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	88104822	88104822	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr3:88104822C>G	ENST00000398392.2	-	1	1637	c.305G>C	c.(304-306)aGt>aCt	p.S102T	CGGBP1_ENST00000474441.1_5'Flank|CGGBP1_ENST00000462901.1_Missense_Mutation_p.S102T|CGGBP1_ENST00000309534.6_Missense_Mutation_p.S102T|CGGBP1_ENST00000482016.1_Missense_Mutation_p.S102T			Q9UFW8	CGBP1_HUMAN	CGG triplet repeat binding protein 1	102					negative regulation of transcription from RNA polymerase II promoter (GO:0000122)	nucleus (GO:0005634)	double-stranded DNA binding (GO:0003690)|RNA polymerase II regulatory region sequence-specific DNA binding (GO:0000977)|RNA polymerase II transcription regulatory region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001227)	p.S102T(2)		kidney(1)|large_intestine(2)|lung(2)	5		Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00359)|Lung(72;0.00677)		CTGGATAACACTGACTTTCTC	0.483																																																	2	Substitution - Missense(2)	kidney(2)											118.0	120.0	119.0					3																	88104822		1998	4172	6170	SO:0001583	missense	8545			AJ000258	CCDS43111.1	3p12-p11.1	2008-07-18			ENSG00000163320	ENSG00000163320			1888	protein-coding gene	gene with protein product	"""p20-CGG binding protein"""	603363				9201980, 14667814	Standard	NM_001195308		Approved	p20-CGGBP, CGGBP	uc003dqt.3	Q9UFW8	OTTHUMG00000159009	ENST00000398392.2:c.305G>C	3.37:g.88104822C>G	ENSP00000381429:p.Ser102Thr	Somatic		WXS	Illumina HiSeq	Phase_I	D3DU38|O15183	Missense_Mutation	SNP	ENST00000398392.2	37	CCDS43111.1	.	.	.	.	.	.	.	.	.	.	C	8.408	0.843614	0.16963	.	.	ENSG00000163320	ENST00000309534;ENST00000398392;ENST00000482016;ENST00000462901;ENST00000467332	.	.	.	5.86	5.86	0.93980	.	0.000000	0.45867	U	0.000336	T	0.39911	0.1096	N	0.14661	0.345	0.37924	D	0.931794	B	0.29955	0.263	B	0.21360	0.034	T	0.36407	-0.9749	9	0.20519	T	0.43	-16.0985	17.392	0.87434	0.0:1.0:0.0:0.0	.	102	Q9UFW8	CGBP1_HUMAN	T	102	.	ENSP00000381428:S102T	S	-	2	0	CGGBP1	88187512	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	2.483000	0.45233	2.787000	0.95880	0.650000	0.86243	AGT		0.483	CGGBP1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352955.1		NM_001008390	
CKS2	1164	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	91931300	91931300	+	Missense_Mutation	SNP	T	T	G			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr9:91931300T>G	ENST00000314355.6	+	3	295	c.200T>G	c.(199-201)cTt>cGt	p.L67R	SECISBP2_ENST00000534113.2_5'Flank|SECISBP2_ENST00000375807.3_5'Flank|SECISBP2_ENST00000339901.4_5'Flank	NM_001827.1	NP_001818.1	P33552	CKS2_HUMAN	CDC28 protein kinase regulatory subunit 2	67					cell proliferation (GO:0008283)|meiosis I (GO:0007127)|regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0000079)		cyclin-dependent protein serine/threonine kinase regulator activity (GO:0016538)	p.L67R(1)		kidney(1)|large_intestine(1)	2						CCACATATTCTTCTCTTTAGA	0.289																																																	1	Substitution - Missense(1)	kidney(1)											37.0	35.0	36.0					9																	91931300		2199	4287	6486	SO:0001583	missense	1164			X54942	CCDS6682.1	9q22	2008-02-05	2002-10-07		ENSG00000123975	ENSG00000123975			2000	protein-coding gene	gene with protein product		116901	"""CDC28 protein kinase 2"""			2227411, 8697818	Standard	NM_001827		Approved		uc004aqh.3	P33552	OTTHUMG00000020180	ENST00000314355.6:c.200T>G	9.37:g.91931300T>G	ENSP00000364976:p.Leu67Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q6FGI9|Q6LET5	Missense_Mutation	SNP	ENST00000314355.6	37	CCDS6682.1	.	.	.	.	.	.	.	.	.	.	T	20.4	3.976008	0.74360	.	.	ENSG00000123975	ENST00000314355	.	.	.	4.97	4.97	0.65823	.	0.000000	0.64402	D	0.000002	T	0.79845	0.4516	.	.	.	0.80722	D	1	D	0.76494	0.999	D	0.91635	0.999	T	0.83125	-0.0116	8	0.87932	D	0	-8.6307	15.156	0.72743	0.0:0.0:0.0:1.0	.	67	P33552	CKS2_HUMAN	R	67	.	ENSP00000364976:L67R	L	+	2	0	CKS2	91121120	1.000000	0.71417	1.000000	0.80357	0.978000	0.69477	7.326000	0.79133	2.223000	0.72356	0.456000	0.33151	CTT		0.289	CKS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052988.1		NM_001827	
CPXM1	56265	broad.mit.edu	37	20	2779142	2779142	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr20:2779142T>C	ENST00000380605.2	-	3	446	c.382A>G	c.(382-384)Agc>Ggc	p.S128G		NM_001184699.1|NM_019609.4	NP_001171628.1|NP_062555.1	Q96SM3	CPXM1_HUMAN	carboxypeptidase X (M14 family), member 1	128	F5/8 type C. {ECO:0000255|PROSITE- ProRule:PRU00081}.				cell adhesion (GO:0007155)	extracellular space (GO:0005615)	metallocarboxypeptidase activity (GO:0004181)|zinc ion binding (GO:0008270)	p.S128G(1)		endometrium(5)|kidney(5)|large_intestine(8)|lung(17)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	43						TCAAGCCGGCTATCTGAAACT	0.602																																																	1	Substitution - Missense(1)	kidney(1)											56.0	56.0	56.0					20																	2779142		2203	4300	6503	SO:0001583	missense	56265			AL035460	CCDS13033.1	20p13	2012-02-10	2006-08-24	2006-08-24	ENSG00000088882	ENSG00000088882			15771	protein-coding gene	gene with protein product	"""carboxypeptidase-like protein X1"""	609555	"""carboxypeptidase X (M14 family)"""	CPXM		14702039	Standard	NM_019609		Approved	CPX-1, CPX1	uc002wgu.3	Q96SM3	OTTHUMG00000031706	ENST00000380605.2:c.382A>G	20.37:g.2779142T>C	ENSP00000369979:p.Ser128Gly	Somatic		WXS	Illumina GAIIx	Phase_I	Q6P4G8|Q6UW65|Q9NUB5	Missense_Mutation	SNP	ENST00000380605.2	37	CCDS13033.1	.	.	.	.	.	.	.	.	.	.	T	1.644	-0.515704	0.04200	.	.	ENSG00000088882	ENST00000380605	D	0.99051	-5.37	4.6	-0.622	0.11560	Coagulation factor 5/8 C-terminal type domain (2);Galactose-binding domain-like (1);	0.994225	0.08175	N	0.986453	D	0.95884	0.8660	L	0.48362	1.52	0.20403	N	0.999909	B;B	0.09022	0.002;0.0	B;B	0.06405	0.002;0.001	D	0.88609	0.3155	10	0.13853	T	0.58	-1.5627	0.1085	0.00054	0.3137:0.1857:0.1616:0.3389	.	128;128	Q8N2E1;Q96SM3	.;CPXM1_HUMAN	G	128	ENSP00000369979:S128G	ENSP00000369979:S128G	S	-	1	0	CPXM1	2727142	0.000000	0.05858	0.866000	0.34008	0.391000	0.30476	-0.951000	0.03885	-0.038000	0.13624	-0.490000	0.04691	AGC		0.602	CPXM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077643.2		NM_019609	
DYNC2H1	79659	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	103229065	103229065	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr11:103229065A>G	ENST00000375735.2	+	83	12278	c.12134A>G	c.(12133-12135)aAt>aGt	p.N4045S	DYNC2H1_ENST00000334267.7_Intron|DYNC2H1_ENST00000398093.3_Missense_Mutation_p.N4052S	NM_001080463.1|NM_001377.2	NP_001073932.1|NP_001368.2	Q8NCM8	DYHC2_HUMAN	dynein, cytoplasmic 2, heavy chain 1	4045					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|asymmetric protein localization (GO:0008105)|cilium assembly (GO:0042384)|determination of left/right symmetry (GO:0007368)|dorsal/ventral pattern formation (GO:0009953)|embryonic limb morphogenesis (GO:0030326)|forebrain development (GO:0030900)|Golgi organization (GO:0007030)|intraciliary retrograde transport (GO:0035721)|positive regulation of smoothened signaling pathway (GO:0045880)|protein processing (GO:0016485)|spinal cord motor neuron differentiation (GO:0021522)	apical part of cell (GO:0045177)|axoneme (GO:0005930)|cytosol (GO:0005829)|dynein complex (GO:0030286)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|microtubule (GO:0005874)|motile primary cilium (GO:0031512)|plasma membrane (GO:0005886)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)|motor activity (GO:0003774)	p.N1485S(1)		NS(1)|endometrium(4)|kidney(5)|large_intestine(9)|lung(9)|ovary(1)|prostate(2)|upper_aerodigestive_tract(2)	33		Acute lymphoblastic leukemia(157;0.000966)|all_hematologic(158;0.00348)		BRCA - Breast invasive adenocarcinoma(274;0.000177)|Epithelial(105;0.0785)		CCTGTCCTCAATCTCTGGAAG	0.408																																																	1	Substitution - Missense(1)	kidney(1)											72.0	63.0	66.0					11																	103229065		1843	4089	5932	SO:0001583	missense	79659			AB082528	CCDS44717.1, CCDS53701.1	11q21-q22.1	2011-06-02	2005-11-24	2005-11-24	ENSG00000187240	ENSG00000187240		"""Cytoplasmic dyneins"""	2962	protein-coding gene	gene with protein product		603297	"""dynein, cytoplasmic, heavy polypeptide 2"""	DNCH2		9763680, 9373155	Standard	NM_001080463		Approved	hdhc11, DHC2, DHC1b, DYH1B	uc001phn.1	Q8NCM8	OTTHUMG00000165941	ENST00000375735.2:c.12134A>G	11.37:g.103229065A>G	ENSP00000364887:p.Asn4045Ser	Somatic		WXS	Illumina HiSeq	Phase_I	O00432|Q16693|Q3C1U8|Q4AC93|Q6ZMX7|Q6ZUM6|Q7Z363|Q8N977|Q92815|Q9HAE4	Missense_Mutation	SNP	ENST00000375735.2	37	CCDS53701.1	.	.	.	.	.	.	.	.	.	.	A	6.514	0.462988	0.12402	.	.	ENSG00000187240	ENST00000375735;ENST00000398093;ENST00000540621;ENST00000533197	T;T;T	0.44881	3.16;3.16;0.91	5.62	2.13	0.27403	Dynein heavy chain (1);	0.765819	0.13228	N	0.403843	T	0.24044	0.0582	N	0.12746	0.255	0.40134	D	0.976751	B;B	0.02656	0.0;0.0	B;B	0.10450	0.005;0.001	T	0.04870	-1.0921	10	0.41790	T	0.15	.	8.4061	0.32616	0.7689:0.0:0.2311:0.0	.	4045;4052	Q8NCM8;Q8NCM8-2	DYHC2_HUMAN;.	S	4045;4052;291;32	ENSP00000364887:N4045S;ENSP00000381167:N4052S;ENSP00000436736:N32S	ENSP00000364887:N4045S	N	+	2	0	DYNC2H1	102734275	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	3.180000	0.50895	0.435000	0.26365	0.459000	0.35465	AAT		0.408	DYNC2H1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000387196.1		XM_370652	
FAM91A1	157769	hgsc.bcm.edu;ucsc.edu	37	8	124792237	124792237	+	Frame_Shift_Del	DEL	C	C	-			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr8:124792237delC	ENST00000334705.7	+	7	808	c.562delC	c.(562-564)cctfs	p.P188fs	FAM91A1_ENST00000521166.1_Frame_Shift_Del_p.P188fs	NM_144963.2	NP_659400	Q658Y4	F91A1_HUMAN	family with sequence similarity 91, member A1	188										breast(4)|central_nervous_system(3)|endometrium(6)|kidney(2)|large_intestine(3)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(1)	28	Lung NSC(37;8.76e-13)|Ovarian(258;0.00744)|all_neural(195;0.0741)		STAD - Stomach adenocarcinoma(47;0.00192)			ATGCACTTTGCCTGAGAAATG	0.338																																																	0													111.0	101.0	104.0					8																	124792237		1853	4101	5954	SO:0001589	frameshift_variant	157769			AK074370	CCDS6346.2	8q24.13	2005-10-04			ENSG00000176853	ENSG00000176853			26306	protein-coding gene	gene with protein product						12477932	Standard	XM_005250806		Approved	FLJ23790	uc003yqv.3	Q658Y4	OTTHUMG00000133021	ENST00000334705.7:c.562delC	8.37:g.124792237delC	ENSP00000335082:p.Pro188fs	Somatic		WXS	Illumina HiSeq	Phase_I	B6YY23|Q658T5|Q8TE89	Frame_Shift_Del	DEL	ENST00000334705.7	37	CCDS6346.2																																																																																				0.338	FAM91A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256607.1		NM_144963	
FBXL17	64839	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	107703606	107703606	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr5:107703606C>G	ENST00000542267.1	-	2	1448	c.1042G>C	c.(1042-1044)Gtt>Ctt	p.V348L	FBXL17_ENST00000359660.5_5'UTR|FBXL17_ENST00000496714.1_5'UTR	NM_001163315.2	NP_001156787.2	Q9UF56	FXL17_HUMAN	F-box and leucine-rich repeat protein 17	348	F-box. {ECO:0000255|PROSITE- ProRule:PRU00080}.							p.V348L(1)		endometrium(1)|large_intestine(4)|lung(1)	6		all_cancers(142;0.00273)|all_epithelial(76;0.000362)|Prostate(80;0.0115)|Myeloproliferative disorder(839;0.0393)|Ovarian(225;0.232)		OV - Ovarian serous cystadenocarcinoma(64;9.63e-11)|Epithelial(69;4.02e-10)		TACTTGCAAACCAATGATGCG	0.403																																																	1	Substitution - Missense(1)	kidney(1)											172.0	135.0	146.0					5																	107703606		692	1591	2283	SO:0001583	missense	64839			AL133602	CCDS54886.1	5q21.3	2011-06-09	2004-06-15	2004-06-16	ENSG00000145743	ENSG00000145743		"""F-boxes / Leucine-rich repeats"""	13615	protein-coding gene	gene with protein product		609083	"""F-box only protein 13"""	FBXO13			Standard	NM_001163315		Approved	DKFZP434C1715, Fbx13, Fbl17	uc011cvc.2	Q9UF56	OTTHUMG00000159785	ENST00000542267.1:c.1042G>C	5.37:g.107703606C>G	ENSP00000437464:p.Val348Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A1A4E3	Missense_Mutation	SNP	ENST00000542267.1	37	CCDS54886.1	.	.	.	.	.	.	.	.	.	.	C	29.5	5.011224	0.93346	.	.	ENSG00000145743	ENST00000542267	T	0.54479	0.57	4.92	4.92	0.64577	F-box domain, cyclin-like (2);F-box domain, Skp2-like (1);	.	.	.	.	T	0.79052	0.4381	M	0.91872	3.25	0.80722	D	1	D	0.69078	0.997	D	0.80764	0.994	D	0.84560	0.0649	9	0.87932	D	0	.	18.4748	0.90788	0.0:1.0:0.0:0.0	.	348	Q9UF56	FXL17_HUMAN	L	348	ENSP00000437464:V348L	ENSP00000437464:V348L	V	-	1	0	FBXL17	107731505	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.421000	0.80204	2.435000	0.82474	0.563000	0.77884	GTT		0.403	FBXL17-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding				
FECH	2235	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	55233773	55233773	+	Silent	SNP	A	A	G			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr18:55233773A>G	ENST00000262093.5	-	5	655	c.504T>C	c.(502-504)ccT>ccC	p.P168P	FECH_ENST00000382873.3_Silent_p.P174P|FECH_ENST00000585699.1_5'Flank	NM_000140.3|NM_001012515.2	NP_000131.2|NP_001012533.1	P22830	HEMH_HUMAN	ferrochelatase	168					cellular response to dexamethasone stimulus (GO:0071549)|cholesterol metabolic process (GO:0008203)|detection of UV (GO:0009589)|erythrocyte differentiation (GO:0030218)|generation of precursor metabolites and energy (GO:0006091)|heme biosynthetic process (GO:0006783)|iron ion homeostasis (GO:0055072)|porphyrin-containing compound metabolic process (GO:0006778)|protoporphyrinogen IX metabolic process (GO:0046501)|regulation of eIF2 alpha phosphorylation by heme (GO:0010999)|regulation of gene expression (GO:0010468)|regulation of hemoglobin biosynthetic process (GO:0046984)|response to arsenic-containing substance (GO:0046685)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to insecticide (GO:0017085)|response to lead ion (GO:0010288)|response to light stimulus (GO:0009416)|response to methylmercury (GO:0051597)|response to platinum ion (GO:0070541)|small molecule metabolic process (GO:0044281)|very-low-density lipoprotein particle assembly (GO:0034379)	mitochondrial inner membrane (GO:0005743)|mitochondrial matrix (GO:0005759)	2 iron, 2 sulfur cluster binding (GO:0051537)|ferrochelatase activity (GO:0004325)|ferrous iron binding (GO:0008198)|heme binding (GO:0020037)|iron-responsive element binding (GO:0030350)	p.P174P(1)		central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|lung(5)|prostate(1)|upper_aerodigestive_tract(1)	15		Colorectal(73;0.227)				CTTCTGTTAAAGGATGGACGT	0.428																																																	1	Substitution - coding silent(1)	kidney(1)											189.0	153.0	165.0					18																	55233773		2203	4300	6503	SO:0001819	synonymous_variant	2235			D00726	CCDS11964.1, CCDS32836.1	18q21.2-q21.3	2010-05-11	2010-05-11		ENSG00000066926	ENSG00000066926	4.99.1.1		3647	protein-coding gene	gene with protein product	"""protoporphyria"""	612386	"""ferrochelatase (protoporphyria)"""			1838349	Standard	NM_001012515		Approved		uc002lgp.4	P22830	OTTHUMG00000132740	ENST00000262093.5:c.504T>C	18.37:g.55233773A>G		Somatic		WXS	Illumina HiSeq	Phase_I	A8KA72|Q8IXN1|Q8NAN0	Silent	SNP	ENST00000262093.5	37	CCDS11964.1																																																																																				0.428	FECH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256098.1			
GJB6	10804	broad.mit.edu;hgsc.bcm.edu	37	13	20797320	20797320	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr13:20797320G>T	ENST00000356192.6	-	5	920	c.300C>A	c.(298-300)caC>caA	p.H100Q	GJB6_ENST00000400066.3_Missense_Mutation_p.H100Q|GJB6_ENST00000241124.6_Missense_Mutation_p.H100Q|GJB6_ENST00000400065.3_Missense_Mutation_p.H100Q	NM_001110219.2	NP_001103689.1	O95452	CXB6_HUMAN	gap junction protein, beta 6, 30kDa	100					apoptotic process (GO:0006915)|cell communication (GO:0007154)|ear morphogenesis (GO:0042471)|inner ear development (GO:0048839)|negative regulation of cell proliferation (GO:0008285)|sensory perception of sound (GO:0007605)	apical plasma membrane (GO:0016324)|connexon complex (GO:0005922)|cytosol (GO:0005829)|integral component of membrane (GO:0016021)		p.H100Q(1)		biliary_tract(1)|endometrium(2)|kidney(2)|large_intestine(1)|lung(2)|ovary(1)	9		all_cancers(29;2.04e-22)|all_epithelial(30;1.19e-19)|all_lung(29;2.27e-18)|Lung SC(185;0.0257)|Ovarian(182;0.0822)		all cancers(112;2.17e-05)|Epithelial(112;0.00075)|OV - Ovarian serous cystadenocarcinoma(117;0.00978)|Lung(94;0.0238)|GBM - Glioblastoma multiforme(144;0.0323)|LUSC - Lung squamous cell carcinoma(192;0.0744)		GAGTGGTTTCGTGCCTGTAGT	0.547																																																	1	Substitution - Missense(1)	kidney(1)											58.0	50.0	53.0					13																	20797320		2203	4300	6503	SO:0001583	missense	10804			AJ005585	CCDS9291.1	13q12	2010-01-06	2007-11-06		ENSG00000121742	ENSG00000121742		"""Ion channels / Gap junction proteins (connexins)"""	4288	protein-coding gene	gene with protein product	"""connexin 30"""	604418	"""ectodermal dysplasia 2, hidrotic (Clouston syndrome)"", ""gap junction protein, beta 6 (connexin 30)"", ""gap junction protein, beta 6"""	DFNA3, ED2		10471490, 8845850	Standard	NM_006783		Approved	EDH, HED, CX30	uc001und.4	O95452	OTTHUMG00000016515	ENST00000356192.6:c.300C>A	13.37:g.20797320G>T	ENSP00000348521:p.His100Gln	Somatic		WXS	Illumina HiSeq	Phase_I	B3KQN2|Q5Q1H9|Q5Q1I0|Q5Q1I1|Q5T5U0|Q8IUP0	Missense_Mutation	SNP	ENST00000356192.6	37	CCDS9291.1	.	.	.	.	.	.	.	.	.	.	G	7.444	0.641263	0.14451	.	.	ENSG00000121742	ENST00000241124;ENST00000400065;ENST00000400066;ENST00000356192	D;D;D;D	0.99032	-5.35;-5.35;-5.35;-5.35	5.28	-10.6	0.00265	Connexin, N-terminal (1);	0.128062	0.51477	D	0.000092	D	0.96393	0.8823	M	0.78456	2.415	0.21967	N	0.999445	P	0.50066	0.931	B	0.43575	0.424	D	0.87905	0.2693	10	0.46703	T	0.11	.	2.2252	0.03982	0.4648:0.1496:0.2286:0.157	.	100	O95452	CXB6_HUMAN	Q	100	ENSP00000241124:H100Q;ENSP00000382938:H100Q;ENSP00000382939:H100Q;ENSP00000348521:H100Q	ENSP00000241124:H100Q	H	-	3	2	GJB6	19695320	0.000000	0.05858	0.008000	0.14137	0.270000	0.26580	-4.338000	0.00250	-2.330000	0.00633	-0.824000	0.03097	CAC		0.547	GJB6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000272906.1			
HSPA8	3312	broad.mit.edu;hgsc.bcm.edu	37	11	122931975	122931975	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr11:122931975C>G	ENST00000532636.1	-	2	177	c.58G>C	c.(58-60)Gtt>Ctt	p.V20L	HSPA8_ENST00000227378.3_Missense_Mutation_p.V20L|HSPA8_ENST00000534624.1_Missense_Mutation_p.V20L|SNORD14D_ENST00000384390.1_RNA|HSPA8_ENST00000533540.1_Missense_Mutation_p.V20L|HSPA8_ENST00000526110.1_Missense_Mutation_p.V20L|HSPA8_ENST00000526862.1_5'Flank|SNORD14C_ENST00000365382.1_RNA|HSPA8_ENST00000534319.1_5'Flank|HSPA8_ENST00000453788.2_Missense_Mutation_p.V20L			P11142	HSP7C_HUMAN	heat shock 70kDa protein 8	20					ATP catabolic process (GO:0006200)|axon guidance (GO:0007411)|chaperone mediated protein folding requiring cofactor (GO:0051085)|clathrin coat disassembly (GO:0072318)|gene expression (GO:0010467)|membrane organization (GO:0061024)|mRNA metabolic process (GO:0016071)|mRNA processing (GO:0006397)|negative regulation of fibril organization (GO:1902904)|negative regulation of transcription, DNA-templated (GO:0045892)|neurotransmitter secretion (GO:0007269)|post-Golgi vesicle-mediated transport (GO:0006892)|protein folding (GO:0006457)|protein refolding (GO:0042026)|regulation of cell cycle (GO:0051726)|response to unfolded protein (GO:0006986)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|synaptic transmission (GO:0007268)|transcription, DNA-templated (GO:0006351)|viral process (GO:0016032)	blood microparticle (GO:0072562)|clathrin-sculpted gamma-aminobutyric acid transport vesicle membrane (GO:0061202)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|intracellular (GO:0005622)|membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Prp19 complex (GO:0000974)|ribonucleoprotein complex (GO:0030529)|spliceosomal complex (GO:0005681)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|ATPase activity, coupled (GO:0042623)|enzyme binding (GO:0019899)|G-protein coupled receptor binding (GO:0001664)|heat shock protein binding (GO:0031072)|MHC class II protein complex binding (GO:0023026)|poly(A) RNA binding (GO:0044822)|ubiquitin protein ligase binding (GO:0031625)|unfolded protein binding (GO:0051082)	p.V20L(1)		breast(1)|central_nervous_system(7)|endometrium(1)|kidney(9)|large_intestine(4)|lung(13)|upper_aerodigestive_tract(1)	36		Breast(109;0.00249)|Lung NSC(97;0.0177)|all_lung(97;0.0179)|Medulloblastoma(222;0.0425)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;4.88e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0279)		TGCTGGAAAACACCCACACAA	0.438																																					Colon(21;486 594 5900 6733 14272)												1	Substitution - Missense(1)	kidney(1)											67.0	59.0	62.0					11																	122931975		2202	4299	6501	SO:0001583	missense	3312			Y00371	CCDS8440.1, CCDS44754.1	11q24.1	2011-09-02	2002-08-29		ENSG00000109971	ENSG00000109971		"""Heat shock proteins / HSP70"""	5241	protein-coding gene	gene with protein product		600816	"""heat shock 70kD protein 8"""	HSPA10		8530083, 3037489	Standard	NM_006597		Approved	HSC71, HSC70, HSP73	uc001pyo.3	P11142	OTTHUMG00000166030	ENST00000532636.1:c.58G>C	11.37:g.122931975C>G	ENSP00000437125:p.Val20Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q9H3R6	Missense_Mutation	SNP	ENST00000532636.1	37	CCDS8440.1	.	.	.	.	.	.	.	.	.	.	C	23.5	4.421477	0.83559	.	.	ENSG00000109971	ENST00000532636;ENST00000533540;ENST00000534624;ENST00000453788;ENST00000227378;ENST00000526110;ENST00000525463;ENST00000525624;ENST00000534567;ENST00000527387;ENST00000532182;ENST00000524590;ENST00000530391	T;T;T;T;T;T;T;T;T;T;T;T;T	0.04275	4.8;4.8;4.8;4.8;4.8;4.8;3.66;4.8;4.8;4.8;4.8;4.8;4.8	4.42	4.42	0.53409	.	0.000000	0.64402	D	0.000001	T	0.24699	0.0599	H	0.95079	3.62	0.80722	D	1	B;B;B;B;B	0.22003	0.063;0.062;0.007;0.002;0.062	B;B;B;B;B	0.40741	0.17;0.339;0.015;0.009;0.339	T	0.28202	-1.0051	10	0.87932	D	0	-20.9376	17.4081	0.87479	0.0:1.0:0.0:0.0	.	20;20;20;20;20	B4DTX2;Q53GZ6;E7ET08;P11142-2;P11142	.;.;.;.;HSP7C_HUMAN	L	20	ENSP00000437125:V20L;ENSP00000437189:V20L;ENSP00000432083:V20L;ENSP00000404372:V20L;ENSP00000227378:V20L;ENSP00000433584:V20L;ENSP00000436762:V20L;ENSP00000435154:V20L;ENSP00000431641:V20L;ENSP00000436183:V20L;ENSP00000434415:V20L;ENSP00000434565:V20L;ENSP00000434851:V20L	ENSP00000227378:V20L	V	-	1	0	HSPA8	122437185	1.000000	0.71417	1.000000	0.80357	0.990000	0.78478	6.079000	0.71291	2.151000	0.67156	0.484000	0.47621	GTT		0.438	HSPA8-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000387515.1			
ITGAM	3684	hgsc.bcm.edu;ucsc.edu	37	16	31309149	31309149	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr16:31309149delG	ENST00000287497.8	+	14	1656	c.1581delG	c.(1579-1581)ctgfs	p.L527fs	ITGAM_ENST00000544665.3_Frame_Shift_Del_p.L528fs			P11215	ITAM_HUMAN	integrin, alpha M (complement component 3 receptor 3 subunit)	527					activated T cell proliferation (GO:0050798)|blood coagulation (GO:0007596)|cell adhesion (GO:0007155)|cellular extravasation (GO:0045123)|ectodermal cell differentiation (GO:0010668)|extracellular matrix organization (GO:0030198)|innate immune response (GO:0045087)|integrin-mediated signaling pathway (GO:0007229)|leukocyte cell-cell adhesion (GO:0007159)|leukocyte migration (GO:0050900)|leukocyte migration involved in inflammatory response (GO:0002523)|microglia development (GO:0014005)|neutrophil chemotaxis (GO:0030593)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor signaling pathway (GO:0002224)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integrin complex (GO:0008305)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	glycoprotein binding (GO:0001948)|heparin binding (GO:0008201)|metal ion binding (GO:0046872)			endometrium(7)|kidney(1)|large_intestine(10)|lung(32)|ovary(1)|prostate(4)|skin(1)	56						TAACAGTGCTGGGGGACGTAA	0.607																																																	0													72.0	77.0	75.0					16																	31309149		2185	4291	6476	SO:0001589	frameshift_variant	3684			J03925	CCDS45470.1, CCDS54004.1	16p11.2	2010-03-23	2006-02-10			ENSG00000169896		"""CD molecules"", ""Complement system"", ""Integrins"""	6149	protein-coding gene	gene with protein product		120980	"""integrin, alpha M (complement component receptor 3, alpha; also known as CD11b (p170), macrophage antigen alpha polypeptide)"""	CR3A, CD11B			Standard	NM_001145808		Approved	MAC-1, CD11b	uc002ebr.3	P11215		ENST00000287497.8:c.1581delG	16.37:g.31309149delG	ENSP00000287497:p.Leu527fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q4VAK0|Q4VAK1|Q4VAK2	Frame_Shift_Del	DEL	ENST00000287497.8	37	CCDS45470.1																																																																																				0.607	ITGAM-002	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000432816.1		NM_000632	
KRTAP9-9	81870	hgsc.bcm.edu	37	17	39412063	39412063	+	Silent	SNP	C	C	A			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr17:39412063C>A	ENST00000394008.1	+	1	428	c.426C>A	c.(424-426)ccC>ccA	p.P142P		NM_030975.2	NP_112237.2	Q9BYP9	KRA99_HUMAN	keratin associated protein 9-9	127	14 X 5 AA repeats of C-C-[RQVGE]- [SPSTNQ]-[TASL].					keratin filament (GO:0045095)				endometrium(3)|skin(2)|upper_aerodigestive_tract(1)	6		Breast(137;0.000496)	STAD - Stomach adenocarcinoma(17;0.000397)			GCTGCCGCCCCGCCTGCTGTG	0.607																																																	0													155.0	163.0	160.0					17																	39412063		2203	4300	6503	SO:0001819	synonymous_variant	81870			AJ406951	CCDS54127.1	17q21.2	2010-06-03			ENSG00000198083	ENSG00000198083		"""Keratin associated proteins"""	16773	protein-coding gene	gene with protein product			"""keratin associated protein 9-5"""	KRTAP9-5		11279113	Standard	NM_030975		Approved	KAP9.9, KAP9.5	uc021txh.1	Q9BYP9	OTTHUMG00000133602	ENST00000394008.1:c.426C>A	17.37:g.39412063C>A		Somatic		WXS	Illumina HiSeq	Phase_I	B5MDD6|Q9BYQ1	Silent	SNP	ENST00000394008.1	37	CCDS54127.1																																																																																				0.607	KRTAP9-9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000257710.1		NM_030975	
KANSL1	284058	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	44116407	44116407	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr17:44116407G>C	ENST00000262419.6	-	9	2848	c.2378C>G	c.(2377-2379)tCt>tGt	p.S793C	KANSL1_ENST00000432791.1_Missense_Mutation_p.S793C|KANSL1_ENST00000575318.1_Intron|KANSL1_ENST00000572904.1_Missense_Mutation_p.S793C|KANSL1_ENST00000393476.3_Intron|KANSL1_ENST00000574590.1_Missense_Mutation_p.S793C	NM_001193466.1	NP_001180395	Q7Z3B3	KANL1_HUMAN	KAT8 regulatory NSL complex subunit 1	793					chromatin organization (GO:0006325)|histone H4-K16 acetylation (GO:0043984)|histone H4-K5 acetylation (GO:0043981)|histone H4-K8 acetylation (GO:0043982)	histone acetyltransferase complex (GO:0000123)|MLL1 complex (GO:0071339)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)		p.S793C(1)									ACTTCTCTCAGATGAATGGTC	0.567																																																	1	Substitution - Missense(1)	kidney(1)											226.0	190.0	202.0					17																	44116407		2203	4300	6503	SO:0001583	missense	0			BX538006	CCDS11503.1, CCDS11503.2, CCDS74084.1	17q21.31	2012-02-20	2012-02-20	2012-02-20	ENSG00000120071	ENSG00000120071			24565	protein-coding gene	gene with protein product	"""centromere protein 36"""	612452	"""KIAA1267"""	KIAA1267		10574462	Standard	NM_015443		Approved	DKFZP727C091, MSL1v1, CENP-36, NSL1	uc002ikd.3	Q7Z3B3		ENST00000262419.6:c.2378C>G	17.37:g.44116407G>C	ENSP00000262419:p.Ser793Cys	Somatic		WXS	Illumina HiSeq	Phase_I	A8K5E4|Q6AW85|Q8IYH1|Q9BRH0|Q9NTE7|Q9UFT0|Q9ULF3	Missense_Mutation	SNP	ENST00000262419.6	37	CCDS11503.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.400270	0.62177	.	.	ENSG00000120071	ENST00000262419;ENST00000432791	T;T	0.12569	2.67;2.67	6.17	6.17	0.99709	.	0.170029	0.45867	D	0.000330	T	0.18718	0.0449	N	0.14661	0.345	0.80722	D	1	D;P;P	0.67145	0.996;0.91;0.91	P;P;P	0.56474	0.799;0.646;0.646	T	0.01256	-1.1404	10	0.54805	T	0.06	-10.6566	17.6123	0.88058	0.0:0.0:1.0:0.0	.	124;793;793	Q7Z3B3-2;C9JHY2;Q7Z3B3	.;.;K1267_HUMAN	C	793	ENSP00000262419:S793C;ENSP00000387393:S793C	ENSP00000262419:S793C	S	-	2	0	KIAA1267	41472254	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	5.370000	0.66144	2.941000	0.99782	0.655000	0.94253	TCT		0.567	KANSL1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440274.1		NM_015443	
Unknown	0	broad.mit.edu	37	9	66502883	66502884	+	IGR	DEL	AT	AT	-	rs202240604		TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	AT	AT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr9:66502883_66502884delAT								RP11-262H14.1 (33573 upstream) : RP11-262H14.7 (14321 downstream)																							TTAGTGGCAAATATTTTTTTTT	0.307																																																	0																																										SO:0001628	intergenic_variant	0																															9.37:g.66502885_66502886delAT		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL		37																																																																																				0	0.307									
Unknown	0	broad.mit.edu	37	9	66502886	66502886	+	IGR	DEL	T	T	-			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr9:66502886delT								RP11-262H14.1 (33576 upstream) : RP11-262H14.7 (14319 downstream)																							GTGGCAAATATTTTTTTTTTG	0.313																																																	0																																										SO:0001628	intergenic_variant	0																															9.37:g.66502886delT		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL		37																																																																																				0	0.313									
TSSC2	650368	broad.mit.edu	37	11	3427845	3427845	+	RNA	SNP	C	C	T			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr11:3427845C>T	ENST00000529482.1	+	0	962									tumor suppressing subtransferable candidate 2 pseudogene																		CTTCAAGTGGCAGGAGCAGAA	0.587																																																	0																																												650368					11p15.4	2014-06-05	2008-06-30		ENSG00000223756	ENSG00000223756			12384	pseudogene	pseudogene	"""tumor-supressing STF cDNA 2"", ""asparagine-linked glycosylation 1 homolog (yeast, beta-1,4-mannosyltransferase) (ALG1) pseudogene"""	608999	"""tumor suppressing subtransferable candidate 2"""			9403053	Standard	NR_024248		Approved				OTTHUMG00000011705		11.37:g.3427845C>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000529482.1	37																																																																																					0.587	TSSC2-003	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000392020.1			
LRRC40	55631	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	70618119	70618119	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr1:70618119A>C	ENST00000370952.3	-	12	1515	c.1436T>G	c.(1435-1437)cTc>cGc	p.L479R		NM_017768.4	NP_060238.3	Q9H9A6	LRC40_HUMAN	leucine rich repeat containing 40	479						membrane (GO:0016020)		p.L479R(1)		breast(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(5)|lung(10)|ovary(1)|prostate(1)|skin(2)	27						TAAATACCTGAGATCTAAAAA	0.294																																																	1	Substitution - Missense(1)	kidney(1)											61.0	60.0	60.0					1																	70618119		2203	4295	6498	SO:0001583	missense	55631				CCDS646.1	1p31.1	2008-02-05			ENSG00000066557	ENSG00000066557			26004	protein-coding gene	gene with protein product						12477932	Standard	NM_017768		Approved	FLJ20331	uc001der.2	Q9H9A6	OTTHUMG00000009348	ENST00000370952.3:c.1436T>G	1.37:g.70618119A>C	ENSP00000359990:p.Leu479Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q9BTR7|Q9NSK1|Q9NXC1	Missense_Mutation	SNP	ENST00000370952.3	37	CCDS646.1	.	.	.	.	.	.	.	.	.	.	A	21.6	4.179436	0.78564	.	.	ENSG00000066557	ENST00000370952	T	0.71461	-0.57	5.55	5.55	0.83447	.	0.177570	0.47852	D	0.000218	D	0.88474	0.6446	H	0.98178	4.165	0.52099	D	0.999949	D	0.69078	0.997	D	0.69824	0.966	D	0.92812	0.6265	10	0.87932	D	0	.	15.6901	0.77442	1.0:0.0:0.0:0.0	.	479	Q9H9A6	LRC40_HUMAN	R	479	ENSP00000359990:L479R	ENSP00000359990:L479R	L	-	2	0	LRRC40	70390707	1.000000	0.71417	1.000000	0.80357	0.976000	0.68499	7.283000	0.78640	2.114000	0.64651	0.528000	0.53228	CTC		0.294	LRRC40-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000025914.1		NM_017768	
MAP2K3	5606	hgsc.bcm.edu	37	17	21215483	21215483	+	Silent	SNP	C	C	T	rs55935757	byFrequency	TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr17:21215483C>T	ENST00000342679.4	+	10	1053	c.804C>T	c.(802-804)taC>taT	p.Y268Y	MAP2K3_ENST00000316920.6_Silent_p.Y239Y|MAP2K3_ENST00000361818.5_Silent_p.Y239Y	NM_145109.2	NP_659731.1	P46734	MP2K3_HUMAN	mitogen-activated protein kinase kinase 3	268	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				activation of MAPK activity (GO:0000187)|cardiac muscle contraction (GO:0060048)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|MyD88-dependent toll-like receptor signaling pathway (GO:0002755)|MyD88-independent toll-like receptor signaling pathway (GO:0002756)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of cytokine biosynthetic process (GO:0042035)|signal transduction (GO:0007165)|stress-activated MAPK cascade (GO:0051403)|toll-like receptor 10 signaling pathway (GO:0034166)|toll-like receptor 2 signaling pathway (GO:0034134)|toll-like receptor 3 signaling pathway (GO:0034138)|toll-like receptor 4 signaling pathway (GO:0034142)|toll-like receptor 5 signaling pathway (GO:0034146)|toll-like receptor 9 signaling pathway (GO:0034162)|toll-like receptor signaling pathway (GO:0002224)|toll-like receptor TLR1:TLR2 signaling pathway (GO:0038123)|toll-like receptor TLR6:TLR2 signaling pathway (GO:0038124)|TRIF-dependent toll-like receptor signaling pathway (GO:0035666)	cytosol (GO:0005829)|membrane (GO:0016020)|nucleoplasm (GO:0005654)	ATP binding (GO:0005524)|MAP kinase kinase activity (GO:0004708)|protein kinase binding (GO:0019901)|protein serine/threonine kinase activity (GO:0004674)|protein tyrosine kinase activity (GO:0004713)								COAD - Colon adenocarcinoma(3;0.0131)|Colorectal(15;0.0553)		GGTTCCCTTACGAGTCCTGGG	0.657													C|||	40	0.00798722	0.0	0.0	5008	,	,		16127	0.0357		0.004	False		,,,				2504	0.0																0																																										SO:0001819	synonymous_variant	5606			L36719	CCDS11217.1, CCDS11218.1	17q11.2	2011-06-09			ENSG00000034152	ENSG00000034152		"""Mitogen-activated protein kinase cascade / Kinase kinases"""	6843	protein-coding gene	gene with protein product	"""MAPK/ERK kinase 3"", ""MAP kinase kinase 3"", ""dual specificity mitogen activated protein kinase kinase 3"""	602315		PRKMK3		9465908	Standard	NM_145109		Approved	MEK3, MKK3, MAPKK3	uc002gys.3	P46734	OTTHUMG00000134322	ENST00000342679.4:c.804C>T	17.37:g.21215483C>T		Somatic		WXS	Illumina HiSeq	Phase_I	B3KSK7|Q99441|Q9UE71|Q9UE72	Silent	SNP	ENST00000342679.4	37	CCDS11217.1																																																																																				0.657	MAP2K3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000259374.2		NM_145109	
MEN1	4221	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	64573234	64573234	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr11:64573234delT	ENST00000337652.1	-	8	1576	c.1073delA	c.(1072-1074)tacfs	p.Y358fs	MEN1_ENST00000315422.4_Frame_Shift_Del_p.Y353fs|MEN1_ENST00000394374.2_Frame_Shift_Del_p.Y358fs|MEN1_ENST00000312049.6_Frame_Shift_Del_p.Y353fs|MEN1_ENST00000394376.1_Frame_Shift_Del_p.Y358fs|MEN1_ENST00000478548.1_5'UTR|MEN1_ENST00000377326.3_Frame_Shift_Del_p.Y353fs|MEN1_ENST00000443283.1_Frame_Shift_Del_p.Y358fs|MAP4K2_ENST00000377350.3_5'Flank|MAP4K2_ENST00000294066.2_5'Flank|MAP4K2_ENST00000468062.1_5'Flank|MEN1_ENST00000377316.2_Frame_Shift_Del_p.Y353fs|MEN1_ENST00000377321.1_Frame_Shift_Del_p.Y318fs|MEN1_ENST00000377313.1_Frame_Shift_Del_p.Y358fs	NM_130803.2	NP_570715	O00255	MEN1_HUMAN	multiple endocrine neoplasia I	358	Interaction with FANCD2.		Y -> D (in MEN1). {ECO:0000269|PubMed:10993647}.		brain development (GO:0007420)|cell cycle arrest (GO:0007050)|cellular response to DNA damage stimulus (GO:0006974)|chromatin remodeling (GO:0006338)|DNA repair (GO:0006281)|embryonic skeletal system morphogenesis (GO:0048704)|gene expression (GO:0010467)|hemopoiesis (GO:0030097)|histone lysine methylation (GO:0034968)|leukocyte homeostasis (GO:0001776)|MAPK cascade (GO:0000165)|maternal process involved in female pregnancy (GO:0060135)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cyclin-dependent protein serine/threonine kinase activity (GO:0045736)|negative regulation of JNK cascade (GO:0046329)|negative regulation of organ growth (GO:0046621)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein phosphorylation (GO:0001933)|negative regulation of sequence-specific DNA binding transcription factor activity (GO:0043433)|negative regulation of telomerase activity (GO:0051974)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoblast development (GO:0002076)|osteoblast fate commitment (GO:0002051)|palate development (GO:0060021)|positive regulation of apoptotic process (GO:0043065)|positive regulation of cell division (GO:0051781)|positive regulation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0043280)|positive regulation of histone methylation (GO:0031062)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of protein binding (GO:0032092)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transforming growth factor beta receptor signaling pathway (GO:0030511)|regulation of activin receptor signaling pathway (GO:0032925)|response to gamma radiation (GO:0010332)|response to UV (GO:0009411)|transcription initiation from RNA polymerase II promoter (GO:0006367)|transcription, DNA-templated (GO:0006351)|transforming growth factor beta receptor signaling pathway (GO:0007179)	chromatin (GO:0000785)|cleavage furrow (GO:0032154)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|histone methyltransferase complex (GO:0035097)|nuclear matrix (GO:0016363)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|protein complex (GO:0043234)	chromatin binding (GO:0003682)|double-stranded DNA binding (GO:0003690)|four-way junction DNA binding (GO:0000400)|protein binding, bridging (GO:0030674)|protein N-terminus binding (GO:0047485)|R-SMAD binding (GO:0070412)|sequence-specific DNA binding (GO:0043565)|transcription regulatory region DNA binding (GO:0044212)|Y-form DNA binding (GO:0000403)			NS(7)|adrenal_gland(5)|breast(2)|central_nervous_system(5)|endometrium(1)|gastrointestinal_tract_(site_indeterminate)(15)|large_intestine(2)|lung(21)|ovary(1)|pancreas(64)|parathyroid(181)|pituitary(7)|prostate(4)|retroperitoneum(1)|skin(1)|small_intestine(13)|soft_tissue(4)|stomach(1)|thymus(2)	337						TTCCCGGCAGTAGTTGTAGCT	0.612			"""D, Mis, N, F, S"""		"""parathyroid tumors, Pancreatic neuroendocrine tumors"""	"""parathyroid adenoma, pituitary adenoma, pancreatic islet cell, carcinoid"""			Multiple Endocrine Neoplasia, type 1;Hyperparathyroidism, Familial Isolated																												Esophageal Squamous(1;83 158 15500 18603 18803 29295)		yes	Rec	yes	Multiple Endocrine Neoplasia Type 1	11	11q13	4221	multiple endocrine neoplasia type 1 gene		E	0													111.0	113.0	112.0					11																	64573234		2201	4297	6498	SO:0001589	frameshift_variant	4221	Familial Cancer Database	MEN1, Wermer disease;FIHP, FIHPT, HRPT1, Familial Isolated Primary Hyperparathyroidism	U93236	CCDS8083.1, CCDS31600.1	11q13	2014-09-17			ENSG00000133895	ENSG00000133895			7010	protein-coding gene	gene with protein product	"""menin"""	613733					Standard	NM_130799		Approved		uc001obn.3	O00255	OTTHUMG00000045366	ENST00000337652.1:c.1073delA	11.37:g.64573234delT	ENSP00000337088:p.Tyr358fs	Somatic		WXS	Illumina HiSeq	Phase_I	A5HBC6|A5HBC7|A5HBC8|A5HBC9|A5HBD0|A5HBD1|A5HBD2|O00632|Q9BUF0|Q9BUK2	Frame_Shift_Del	DEL	ENST00000337652.1	37	CCDS8083.1																																																																																				0.612	MEN1-201	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000143881.1			
Unknown	0	broad.mit.edu	37	1	16976641	16976641	+	IGR	SNP	C	C	T	rs1057417		TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr1:16976641C>T								CROCCP2 (15587 upstream) : RNU1-3 (16638 downstream)																							AATCCCCAACCGAGTATGCGC	0.577																																																	0																																										SO:0001628	intergenic_variant	11209																															1.37:g.16976641C>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.577									
MUC20	200958	broad.mit.edu	37	3	195452619	195452619	+	Missense_Mutation	SNP	C	C	T	rs200883738	byFrequency	TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr3:195452619C>T	ENST00000447234.2	+	2	1271	c.1145C>T	c.(1144-1146)gCc>gTc	p.A382V	MUC20_ENST00000320736.6_Missense_Mutation_p.A211V|MUC20_ENST00000445522.2_Missense_Mutation_p.A347V|MUC20_ENST00000436408.1_Missense_Mutation_p.A382V	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	382	12 X 20 AA approximate tandem repeats of S-S-E-S-S-A-S-S-D-S-P-H-P-V-I-T-P-S-R-A.|Ser-rich.				activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)		p.A382V(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CCGTCACGGGCCTCAGAGAGC	0.662																																																	1	Substitution - Missense(1)	kidney(1)											2.0	2.0	2.0					3																	195452619		1026	2268	3294	SO:0001583	missense	200958			AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1145C>T	3.37:g.195452619C>T	ENSP00000414350:p.Ala382Val	Somatic		WXS	Illumina GAIIx	Phase_I	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	C	9.944	1.218251	0.22373	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.15372	2.92;2.43;3.11;2.5	0.602	0.602	0.17535	.	.	.	.	.	T	0.07007	0.0178	.	.	.	0.09310	N	1	P	0.35481	0.504	B	0.27380	0.079	T	0.35151	-0.9800	7	0.14656	T	0.56	.	.	.	.	.	211	E9PH32	.	V	382;211;382;347	ENSP00000414350:A382V;ENSP00000325431:A211V;ENSP00000396774:A382V;ENSP00000405629:A347V	ENSP00000325431:A211V	A	+	2	0	MUC20	196938290	0.028000	0.19301	0.007000	0.13788	0.025000	0.11179	1.554000	0.36266	0.567000	0.29293	0.411000	0.27672	GCC		0.662	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1		NM_152673	
MUC20	200958	broad.mit.edu	37	3	195452645	195452645	+	Missense_Mutation	SNP	G	G	A	rs200616967	byFrequency	TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr3:195452645G>A	ENST00000447234.2	+	2	1297	c.1171G>A	c.(1171-1173)Ggc>Agc	p.G391S	MUC20_ENST00000320736.6_Missense_Mutation_p.G220S|MUC20_ENST00000445522.2_Missense_Mutation_p.G356S|MUC20_ENST00000436408.1_Missense_Mutation_p.G391S	NM_001282506.1	NP_001269435.1	Q8N307	MUC20_HUMAN	mucin 20, cell surface associated	391	12 X 20 AA approximate tandem repeats of S-S-E-S-S-A-S-S-D-S-P-H-P-V-I-T-P-S-R-A.				activation of MAPK activity (GO:0000187)|cellular protein metabolic process (GO:0044267)|hepatocyte growth factor receptor signaling pathway (GO:0048012)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)|protein homooligomerization (GO:0051260)	basal plasma membrane (GO:0009925)|cell projection (GO:0042995)|extracellular region (GO:0005576)|Golgi lumen (GO:0005796)		p.G391S(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(4)|skin(4)|stomach(3)|upper_aerodigestive_tract(1)	23	all_cancers(143;1.8e-08)|Ovarian(172;0.0634)	Lung NSC(153;0.191)	Epithelial(36;1e-21)|all cancers(36;9.02e-20)|OV - Ovarian serous cystadenocarcinoma(49;1.6e-18)|Lung(62;0.000104)|LUSC - Lung squamous cell carcinoma(58;0.000128)	GBM - Glioblastoma multiforme(46;1.66e-05)		CTCTTCCGACGGCCCCCATCC	0.622																																																	1	Substitution - Missense(1)	kidney(1)											3.0	2.0	2.0					3																	195452645		1453	3082	4535	SO:0001583	missense	200958			AB037780	CCDS63877.1	3q29	2008-08-07	2006-03-14		ENSG00000176945	ENSG00000176945		"""Mucins"""	23282	protein-coding gene	gene with protein product		610360				14565953	Standard	NM_001282506		Approved	FLJ14408, KIAA1359	uc010hzo.3	Q8N307	OTTHUMG00000155823	ENST00000447234.2:c.1171G>A	3.37:g.195452645G>A	ENSP00000414350:p.Gly391Ser	Somatic		WXS	Illumina GAIIx	Phase_I	Q6UX97|Q76I83|Q76I85|Q86ST8|Q8NBY6|Q96KA1|Q9P2I8	Missense_Mutation	SNP	ENST00000447234.2	37		.	.	.	.	.	.	.	.	.	.	G	0.012	-1.663601	0.00772	.	.	ENSG00000176945	ENST00000447234;ENST00000320736;ENST00000436408;ENST00000445522	T;T;T;T	0.19806	2.98;2.12;3.1;2.58	0.669	-0.281	0.12882	.	.	.	.	.	T	0.07548	0.0190	.	.	.	0.09310	N	1	B	0.14012	0.009	B	0.08055	0.003	T	0.40421	-0.9564	7	0.07175	T	0.84	.	.	.	.	.	220	E9PH32	.	S	391;220;391;356	ENSP00000414350:G391S;ENSP00000325431:G220S;ENSP00000396774:G391S;ENSP00000405629:G356S	ENSP00000325431:G220S	G	+	1	0	MUC20	196938316	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-3.519000	0.00444	-0.171000	0.10797	-0.363000	0.07495	GGC		0.622	MUC20-001	KNOWN	basic|appris_candidate	protein_coding	protein_coding	OTTHUMT00000341835.1		NM_152673	
NHLRC2	374354	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	115614767	115614767	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr10:115614767G>A	ENST00000369301.3	+	1	348	c.136G>A	c.(136-138)Gac>Aac	p.D46N	DCLRE1A_ENST00000369305.1_5'Flank|DCLRE1A_ENST00000476112.1_5'Flank|DCLRE1A_ENST00000361384.2_5'Flank	NM_198514.3	NP_940916.2	Q8NBF2	NHLC2_HUMAN	NHL repeat containing 2	46	Thioredoxin. {ECO:0000255|PROSITE- ProRule:PRU00691}.							p.D46N(1)		breast(1)|endometrium(2)|kidney(4)|large_intestine(3)|lung(3)|ovary(1)|upper_aerodigestive_tract(1)	15				Epithelial(162;0.017)|all cancers(201;0.0187)		GCAGAAGGTGGACGGCTGGGA	0.677																																																	1	Substitution - Missense(1)	kidney(1)											49.0	43.0	45.0					10																	115614767		2164	4190	6354	SO:0001583	missense	374354			AK090631	CCDS7585.1	10q26.11	2006-03-31			ENSG00000196865	ENSG00000196865			24731	protein-coding gene	gene with protein product						12477932	Standard	NM_198514		Approved	FLJ25621, FLJ20147, FLJ33312, MGC45492, DKFZp779F115	uc001lax.2	Q8NBF2	OTTHUMG00000019078	ENST00000369301.3:c.136G>A	10.37:g.115614767G>A	ENSP00000358307:p.Asp46Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q8N1H1|Q8N5A6	Missense_Mutation	SNP	ENST00000369301.3	37	CCDS7585.1	.	.	.	.	.	.	.	.	.	.	G	24.3	4.517901	0.85495	.	.	ENSG00000196865	ENST00000369301	T	0.51817	0.69	5.21	5.21	0.72293	Thioredoxin-like fold (2);	0.000000	0.85682	D	0.000000	T	0.60779	0.2295	L	0.57536	1.79	0.80722	D	1	D	0.67145	0.996	P	0.58331	0.837	T	0.59252	-0.7489	10	0.38643	T	0.18	-18.4967	16.93	0.86188	0.0:0.0:1.0:0.0	.	46	Q8NBF2	NHLC2_HUMAN	N	46	ENSP00000358307:D46N	ENSP00000358307:D46N	D	+	1	0	NHLRC2	115604757	1.000000	0.71417	1.000000	0.80357	0.994000	0.84299	6.471000	0.73562	2.410000	0.81850	0.561000	0.74099	GAC		0.677	NHLRC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000050446.1		NM_198514	
AKAP2	11217	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	112918733	112918733	+	Nonsense_Mutation	SNP	G	G	T			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr9:112918733G>T	ENST00000259318.7	+	3	2644	c.2437G>T	c.(2437-2439)Gag>Tag	p.E813*	AKAP2_ENST00000374525.1_Nonsense_Mutation_p.E902*|PALM2-AKAP2_ENST00000302798.7_Nonsense_Mutation_p.E1044*|PALM2-AKAP2_ENST00000374530.3_Nonsense_Mutation_p.E1044*|AKAP2_ENST00000510514.5_Nonsense_Mutation_p.E1044*|AKAP2_ENST00000482335.1_Intron|AKAP2_ENST00000434623.2_Nonsense_Mutation_p.E902*|AKAP2_ENST00000555236.1_Nonsense_Mutation_p.E1044*	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	813								p.E1044*(1)|p.E902*(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						GGAAGACTATGAGACACACAA	0.537																																																	2	Substitution - Nonsense(2)	kidney(2)											97.0	96.0	96.0					9																	112918733		2203	4300	6503	SO:0001587	stop_gained	445815			AB023137	CCDS43861.1, CCDS48003.1, CCDS56581.1	9q31.3	2009-10-16			ENSG00000241978	ENSG00000241978		"""A-kinase anchor proteins"""	372	protein-coding gene	gene with protein product	"""protein kinase A2"""	604582		PRKA2		10231032	Standard	NM_001136562		Approved	AKAP-KL, KIAA0920, DKFZp564L0716		Q9Y2D5	OTTHUMG00000156811	ENST00000259318.7:c.2437G>T	9.37:g.112918733G>T	ENSP00000259318:p.Glu813*	Somatic		WXS	Illumina HiSeq	Phase_I	B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	Nonsense_Mutation	SNP	ENST00000259318.7	37	CCDS48003.1	.	.	.	.	.	.	.	.	.	.	G	44	10.711569	0.99454	.	.	ENSG00000157654;ENSG00000157654;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978;ENSG00000241978	ENST00000374530;ENST00000302798;ENST00000555236;ENST00000510514;ENST00000434623;ENST00000374525;ENST00000259318	.	.	.	5.48	5.48	0.80851	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.24483	T	0.36	-34.2128	18.7114	0.91658	0.0:0.0:1.0:0.0	.	.	.	.	X	1044;1044;1044;1044;902;902;813	.	ENSP00000259318:E813X	E	+	1	0	PALM2-AKAP2;AKAP2	111958554	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.051000	0.93849	2.730000	0.93505	0.655000	0.94253	GAG		0.537	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3		NM_001004065	
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52649440	52649440	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr3:52649440delT	ENST00000296302.7	-	15	1852	c.1851delA	c.(1849-1851)ttafs	p.L618fs	PBRM1_ENST00000337303.4_Frame_Shift_Del_p.L618fs|PBRM1_ENST00000409057.1_Frame_Shift_Del_p.L618fs|PBRM1_ENST00000410007.1_Frame_Shift_Del_p.L618fs|PBRM1_ENST00000409767.1_Frame_Shift_Del_p.L633fs|PBRM1_ENST00000394830.3_Frame_Shift_Del_p.L618fs|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.L586fs|PBRM1_ENST00000409114.3_Frame_Shift_Del_p.L633fs			Q86U86	PB1_HUMAN	polybromo 1	618					chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		TCTCCTTGAGTAACTTCTCCA	0.368			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	0													113.0	103.0	106.0					3																	52649440		2203	4300	6503	SO:0001589	frameshift_variant	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.1851delA	3.37:g.52649440delT	ENSP00000296302:p.Leu618fs	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	37																																																																																					0.368	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
PCDH15	65217	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	55587279	55587279	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr10:55587279C>T	ENST00000320301.6	-	32	4635	c.4241G>A	c.(4240-4242)cGa>cAa	p.R1414Q	PCDH15_ENST00000373965.2_Missense_Mutation_p.R1421Q|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000395445.1_Missense_Mutation_p.R1421Q|PCDH15_ENST00000395438.1_Missense_Mutation_p.R1414Q|PCDH15_ENST00000395440.1_Intron|PCDH15_ENST00000361849.3_Missense_Mutation_p.R1414Q|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395433.1_Missense_Mutation_p.R1389Q|PCDH15_ENST00000463095.1_5'UTR|PCDH15_ENST00000395430.1_Missense_Mutation_p.R1411Q|PCDH15_ENST00000437009.1_Missense_Mutation_p.R1343Q|PCDH15_ENST00000409834.1_Missense_Mutation_p.R1025Q|PCDH15_ENST00000414778.1_Missense_Mutation_p.R1416Q|PCDH15_ENST00000395432.2_Missense_Mutation_p.R1374Q|PCDH15_ENST00000395446.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	1414					equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.R1414Q(2)|p.R1419Q(1)|p.R1416Q(1)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				GGCCTGAATTCGTGCAGTCTT	0.542										HNSCC(58;0.16)																																							4	Substitution - Missense(4)	kidney(4)											81.0	85.0	84.0					10																	55587279		2203	4300	6503	SO:0001583	missense	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.4241G>A	10.37:g.55587279C>T	ENSP00000322604:p.Arg1414Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	C	18.75	3.689671	0.68271	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009	T;T;T;T;T;T;T;T;T;T;T	0.63096	0.48;0.42;0.4;0.41;0.42;0.1;0.15;0.13;0.15;0.06;-0.02	5.6	4.68	0.58851	.	.	.	.	.	T	0.55369	0.1916	L	0.32530	0.975	0.45005	D	0.99802	P;P;P;P;B;P;P;B;B;B;B;B;P	0.52061	0.95;0.764;0.764;0.602;0.42;0.764;0.95;0.197;0.448;0.448;0.448;0.448;0.764	P;B;B;B;B;B;P;B;B;B;B;B;B	0.44422	0.449;0.122;0.122;0.062;0.063;0.122;0.449;0.033;0.042;0.042;0.048;0.063;0.122	T	0.61148	-0.7121	9	0.62326	D	0.03	.	15.0921	0.72204	0.0:0.9276:0.0:0.0724	.	1389;1414;1414;1419;1343;1374;1411;1414;1421;1421;1414;1416;1414	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	Q	1421;1416;1414;1414;1025;1421;1374;1414;1389;1414;1411;1419;1343	ENSP00000363076:R1421Q;ENSP00000410304:R1416Q;ENSP00000378826:R1414Q;ENSP00000386693:R1025Q;ENSP00000378832:R1421Q;ENSP00000378820:R1374Q;ENSP00000354950:R1414Q;ENSP00000378821:R1389Q;ENSP00000322604:R1414Q;ENSP00000378818:R1411Q;ENSP00000412628:R1343Q	ENSP00000322604:R1414Q	R	-	2	0	PCDH15	55257285	0.466000	0.25823	0.980000	0.43619	0.860000	0.49131	4.063000	0.57499	2.786000	0.95864	0.561000	0.74099	CGA		0.542	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2		NM_033056	
PCDH19	57526	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	99551562	99551562	+	Frame_Shift_Del	DEL	C	C	-			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chrX:99551562delC	ENST00000373034.4	-	6	4835	c.3160delG	c.(3160-3162)gagfs	p.E1054fs	PCDH19_ENST00000255531.7_Frame_Shift_Del_p.E1007fs|PCDH19_ENST00000420881.2_Frame_Shift_Del_p.E1006fs|PCDH19_ENST00000464981.1_5'Flank	NM_001184880.1	NP_001171809.1	Q8TAB3	PCD19_HUMAN	protocadherin 19	1054					homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			breast(5)|endometrium(11)|kidney(1)|large_intestine(14)|liver(1)|lung(23)|ovary(3)|prostate(2)|skin(5)|upper_aerodigestive_tract(1)|urinary_tract(2)	68						TTGCCTGCCTCCCGGATAACG	0.597																																																	0													53.0	55.0	54.0					X																	99551562		2142	4234	6376	SO:0001589	frameshift_variant	57526			AB037734	CCDS43976.1, CCDS48141.1, CCDS55462.1	Xq22.1	2014-06-28			ENSG00000165194	ENSG00000165194		"""Cadherins / Protocadherins : Non-clustered"""	14270	protein-coding gene	gene with protein product		300460	"""epilepsy, female restricted, with mental retardation (Juberg-Hellman syndrome)"""	EFMR		11549318, 18469813, 19752159	Standard	NM_020766		Approved	KIAA1313, EIEE9	uc010nmz.3	Q8TAB3	OTTHUMG00000022000	ENST00000373034.4:c.3160delG	X.37:g.99551562delC	ENSP00000362125:p.Glu1054fs	Somatic		WXS	Illumina HiSeq	Phase_I	B0LDS4|E9PAM6|Q5JTG1|Q5JTG2|Q68DT7|Q9P2N3	Frame_Shift_Del	DEL	ENST00000373034.4	37	CCDS55462.1																																																																																				0.597	PCDH19-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000057479.2		NM_020766	
PNMA5	114824	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	152159503	152159503	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chrX:152159503C>T	ENST00000439251.1	-	2	1078	c.640G>A	c.(640-642)Gtg>Atg	p.V214M	PNMA5_ENST00000535214.1_Missense_Mutation_p.V214M|PNMA5_ENST00000452693.1_Missense_Mutation_p.V214M|PNMA5_ENST00000361887.5_Missense_Mutation_p.V214M	NM_001103150.1	NP_001096620.1	Q96PV4	PNMA5_HUMAN	paraneoplastic Ma antigen family member 5	214					positive regulation of apoptotic process (GO:0043065)			p.V214M(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(6)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	25	Acute lymphoblastic leukemia(192;6.56e-05)					GCCTGGAGCACCCGCATGATT	0.527																																																	1	Substitution - Missense(1)	kidney(1)											76.0	71.0	73.0					X																	152159503		2203	4300	6503	SO:0001583	missense	114824			AB067521	CCDS14718.1	Xq28	2012-02-09	2012-02-09		ENSG00000198883	ENSG00000198883		"""Paraneoplastic Ma antigens"""	18743	protein-coding gene	gene with protein product	"""paraneoplastic antigen family 5"""	300916	"""paraneoplastic antigen like 5"""			16214224	Standard	NM_052926		Approved	KIAA1934	uc004fgy.4	Q96PV4	OTTHUMG00000024184	ENST00000439251.1:c.640G>A	X.37:g.152159503C>T	ENSP00000388850:p.Val214Met	Somatic		WXS	Illumina HiSeq	Phase_I	B4DI72|B7Z9Y9|Q495L5|Q8NET3	Missense_Mutation	SNP	ENST00000439251.1	37	CCDS14718.1	.	.	.	.	.	.	.	.	.	.	C	9.644	1.139760	0.21205	.	.	ENSG00000198883	ENST00000361887;ENST00000535214;ENST00000439251;ENST00000452693	T;T;T;T	0.10099	2.91;2.91;2.91;2.91	3.29	1.45	0.22620	.	.	.	.	.	T	0.07773	0.0195	L	0.31065	0.9	0.09310	N	1	B	0.19706	0.038	B	0.27170	0.077	T	0.40608	-0.9554	9	0.32370	T	0.25	.	4.1368	0.10174	0.0:0.6231:0.2359:0.141	.	214	Q96PV4	PNMA5_HUMAN	M	214	ENSP00000354834:V214M;ENSP00000445775:V214M;ENSP00000388850:V214M;ENSP00000392342:V214M	ENSP00000354834:V214M	V	-	1	0	PNMA5	151910159	0.000000	0.05858	0.000000	0.03702	0.249000	0.25844	0.225000	0.17757	0.265000	0.21872	-0.497000	0.04613	GTG		0.527	PNMA5-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000060925.1		NM_052926	
PRRC2C	23215	hgsc.bcm.edu	37	1	171511149	171511149	+	Frame_Shift_Del	DEL	A	A	-			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr1:171511149delA	ENST00000338920.4	+	16	4775	c.4538delA	c.(4537-4539)gaafs	p.E1513fs	PRRC2C_ENST00000367742.3_Frame_Shift_Del_p.E1515fs|PRRC2C_ENST00000392078.3_Frame_Shift_Del_p.E1515fs|PRRC2C_ENST00000426496.2_Frame_Shift_Del_p.E1513fs	NM_015172.3	NP_055987.2	Q9Y520	PRC2C_HUMAN	proline-rich coiled-coil 2C	1513					hematopoietic progenitor cell differentiation (GO:0002244)	membrane (GO:0016020)	poly(A) RNA binding (GO:0044822)|protein C-terminus binding (GO:0008022)										GAGAGGGATGAAAAAAAAAAT	0.388																																																	0													59.0	63.0	62.0					1																	171511149		2203	4300	6503	SO:0001589	frameshift_variant	23215			AL096857	CCDS1296.2	1q24.3	2012-07-18	2010-12-09	2010-12-09	ENSG00000117523	ENSG00000117523			24903	protein-coding gene	gene with protein product			"""BAT2 domain containing 1"", ""HLA-B associated transcript 2-like 2"""	BAT2D1, BAT2L2		10470851, 12443540	Standard	NM_015172		Approved	KIAA1096, XTP2	uc010pmg.2	Q9Y520	OTTHUMG00000034665	ENST00000338920.4:c.4538delA	1.37:g.171511149delA	ENSP00000343629:p.Glu1513fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q05DM8|Q49A39|Q6PD54|Q9H2N2|Q9HA05|Q9NSM8|Q9NXL3|Q9UF29|Q9UPQ6	Frame_Shift_Del	DEL	ENST00000338920.4	37	CCDS1296.2																																																																																				0.388	PRRC2C-010	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000314826.4		NM_015172	
PSMD11	5717	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	30806900	30806900	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr17:30806900C>T	ENST00000261712.3	+	11	1333	c.1070C>T	c.(1069-1071)tCc>tTc	p.S357F	PSMD11_ENST00000457654.2_Missense_Mutation_p.S357F	NM_001270482.1|NM_002815.3	NP_001257411.1|NP_002806.2	O00231	PSD11_HUMAN	proteasome (prosome, macropain) 26S subunit, non-ATPase, 11	357	PCI.				anaphase-promoting complex-dependent proteasomal ubiquitin-dependent protein catabolic process (GO:0031145)|antigen processing and presentation of exogenous peptide antigen via MHC class I (GO:0042590)|antigen processing and presentation of exogenous peptide antigen via MHC class I, TAP-dependent (GO:0002479)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|apoptotic process (GO:0006915)|cellular nitrogen compound metabolic process (GO:0034641)|DNA damage response, signal transduction by p53 class mediator resulting in cell cycle arrest (GO:0006977)|G1/S transition of mitotic cell cycle (GO:0000082)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|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)|proteasome assembly (GO:0043248)|protein polyubiquitination (GO:0000209)|regulation of apoptotic process (GO:0042981)|regulation of cellular amino acid metabolic process (GO:0006521)|regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051439)|RNA metabolic process (GO:0016070)|small molecule metabolic process (GO:0044281)|stem cell differentiation (GO:0048863)|ubiquitin-dependent protein catabolic process (GO:0006511)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|proteasome accessory complex (GO:0022624)|proteasome complex (GO:0000502)|proteasome regulatory particle (GO:0005838)		p.S357F(1)		breast(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)	19		Breast(31;0.159)|Ovarian(249;0.182)	BRCA - Breast invasive adenocarcinoma(9;0.109)			ATCAAACTCTCCAAGGTAAGG	0.498																																					Ovarian(130;1038 1716 9294 11987 19279)												1	Substitution - Missense(1)	kidney(1)											111.0	101.0	104.0					17																	30806900		2203	4300	6503	SO:0001583	missense	5717			AB003102	CCDS11272.1	17q12	2008-05-22			ENSG00000108671	ENSG00000108671		"""Proteasome (prosome, macropain) subunits"""	9556	protein-coding gene	gene with protein product		604449				9426256, 9119060	Standard	NM_001270482		Approved	S9, p44.5, MGC3844, Rpn6	uc010cta.2	O00231	OTTHUMG00000132811	ENST00000261712.3:c.1070C>T	17.37:g.30806900C>T	ENSP00000261712:p.Ser357Phe	Somatic		WXS	Illumina HiSeq	Phase_I	A8K3I7|E1P663|O00495|Q53FT5	Missense_Mutation	SNP	ENST00000261712.3	37	CCDS11272.1	.	.	.	.	.	.	.	.	.	.	C	19.13	3.768057	0.69878	.	.	ENSG00000108671	ENST00000261712	T	0.51817	0.69	5.38	5.38	0.77491	Winged helix-turn-helix transcription repressor DNA-binding (1);Proteasome component (PCI) domain (2);	0.059041	0.64402	D	0.000001	T	0.59473	0.2196	M	0.72894	2.215	0.53688	D	0.999978	B	0.25850	0.136	B	0.40677	0.337	T	0.61710	-0.7007	10	0.87932	D	0	-2.9698	16.6652	0.85250	0.0:1.0:0.0:0.0	.	357	O00231	PSD11_HUMAN	F	357	ENSP00000261712:S357F	ENSP00000261712:S357F	S	+	2	0	PSMD11	27831013	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.653000	0.61462	2.786000	0.95864	0.563000	0.77884	TCC		0.498	PSMD11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256252.2		NM_002815	
RFPL4A	342931	broad.mit.edu	37	19	56274095	56274095	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr19:56274095G>A	ENST00000434937.2	+	3	589	c.418G>A	c.(418-420)Gtc>Atc	p.V140I		NM_001145014.1	NP_001138486.1	A6NLU0	RFPLA_HUMAN	ret finger protein-like 4A	140	B30.2/SPRY. {ECO:0000255|PROSITE- ProRule:PRU00548}.						zinc ion binding (GO:0008270)	p.V140I(1)		haematopoietic_and_lymphoid_tissue(1)|stomach(1)	2						TGCCCTGTGCGTCCTGGGCAC	0.562																																																	1	Substitution - Missense(1)	kidney(1)											18.0	15.0	16.0					19																	56274095		690	1576	2266	SO:0001583	missense	342931				CCDS46201.1	19q13.42	2013-02-22	2007-01-19	2007-01-19	ENSG00000223638	ENSG00000223638		"""RING-type (C3HC4) zinc fingers"""	16449	protein-coding gene	gene with protein product		612601	"""ret finger protein-like 4"""	RFPL4		11850190	Standard	NM_001145014		Approved	RNF210	uc010yge.2	A6NLU0	OTTHUMG00000165449	ENST00000434937.2:c.418G>A	19.37:g.56274095G>A	ENSP00000392936:p.Val140Ile	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000434937.2	37	CCDS46201.1	.	.	.	.	.	.	.	.	.	.	G	11.68	1.711064	0.30322	.	.	ENSG00000223638	ENST00000434937	T	0.31510	1.49	2.64	1.53	0.23141	Concanavalin A-like lectin/glucanase (1);SPRY-associated (1);Butyrophylin-like (1);B30.2/SPRY domain (1);	.	.	.	.	T	0.29652	0.0740	M	0.61703	1.905	0.29506	N	0.854559	B	0.29627	0.252	B	0.30316	0.114	T	0.24404	-1.0161	9	0.46703	T	0.11	-22.2301	8.5553	0.33478	0.0:0.0:0.768:0.232	.	140	A6NLU0	RFPLA_HUMAN	I	140	ENSP00000392936:V140I	ENSP00000392936:V140I	V	+	1	0	RFPL4A	60965907	0.997000	0.39634	0.002000	0.10522	0.024000	0.10985	2.908000	0.48750	0.615000	0.30124	0.655000	0.94253	GTC		0.562	RFPL4A-001	NOVEL	upstream_ATG|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000384184.1		XM_292796	
TCEB3C	162699	broad.mit.edu	37	18	44554961	44554961	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr18:44554961C>T	ENST00000330682.2	-	1	1488	c.1253G>A	c.(1252-1254)cGg>cAg	p.R418Q	KATNAL2_ENST00000245121.5_Intron|KATNAL2_ENST00000592005.1_Intron|KATNAL2_ENST00000356157.7_Intron	NM_145653.3	NP_663628.2	Q8NG57	ELOA3_HUMAN	transcription elongation factor B polypeptide 3C (elongin A3)	418	Activation domain. {ECO:0000250}.				regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	integral component of membrane (GO:0016021)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.R418Q(1)		NS(1)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(1)|lung(16)|skin(2)	30						GTCCCGAAGCCGCAGGTACAG	0.557																																																	1	Substitution - Missense(1)	kidney(1)											13.0	13.0	13.0					18																	44554961		1332	2729	4061	SO:0001583	missense	162699			AB076840	CCDS11931.1	18q21.1	2008-08-13			ENSG00000183791	ENSG00000183791			24617	protein-coding gene	gene with protein product	"""elongin A3"""					11932239, 11994304	Standard	NM_145653		Approved	HsT829, TCEB3L2	uc010xdb.2	Q8NG57	OTTHUMG00000132651	ENST00000330682.2:c.1253G>A	18.37:g.44554961C>T	ENSP00000328232:p.Arg418Gln	Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000330682.2	37	CCDS11931.1	.	.	.	.	.	.	.	.	.	.	c	18.71	3.682490	0.68157	.	.	ENSG00000183791	ENST00000330682	T	0.34472	1.36	1.52	1.52	0.23074	.	0.000000	0.46442	D	0.000282	T	0.54679	0.1873	M	0.82056	2.57	0.52501	D	0.999951	D	0.89917	1.0	D	0.72338	0.977	T	0.55062	-0.8199	10	0.36615	T	0.2	-22.4296	9.0622	0.36442	0.0:1.0:0.0:0.0	.	418	Q8NG57	ELOA3_HUMAN	Q	418	ENSP00000328232:R418Q	ENSP00000328232:R418Q	R	-	2	0	TCEB3C	42808959	0.973000	0.33851	0.504000	0.27639	0.017000	0.09413	2.791000	0.47829	1.198000	0.43158	0.485000	0.47835	CGG		0.557	TCEB3C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255902.1		NM_145653	
TOR3A	64222	broad.mit.edu;hgsc.bcm.edu	37	1	179057120	179057120	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr1:179057120G>C	ENST00000367627.3	+	4	1466	c.714G>C	c.(712-714)gaG>gaC	p.E238D	TOR3A_ENST00000352445.6_Missense_Mutation_p.E238D|TOR3A_ENST00000495145.1_3'UTR	NM_022371.3	NP_071766.2	Q9H497	TOR3A_HUMAN	torsin family 3, member A	238					ATP catabolic process (GO:0006200)|chaperone mediated protein folding requiring cofactor (GO:0051085)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum lumen (GO:0005788)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)	p.E238D(1)		endometrium(1)|kidney(2)|large_intestine(4)|lung(4)|pancreas(1)|urinary_tract(1)	13						ATGAAGCGGAGAAGCTGCACC	0.607																																																	1	Substitution - Missense(1)	kidney(1)											69.0	74.0	73.0					1																	179057120		2203	4300	6503	SO:0001583	missense	64222			BC001085	CCDS1329.1	1q25.2	2008-02-05	2003-04-02		ENSG00000186283	ENSG00000186283			11997	protein-coding gene	gene with protein product		607555	"""ATP-dependant interferon responsive"""	ADIR		10644435	Standard	NM_022371		Approved	FLJ22345, ADIR2	uc001gmd.3	Q9H497	OTTHUMG00000035077	ENST00000367627.3:c.714G>C	1.37:g.179057120G>C	ENSP00000356599:p.Glu238Asp	Somatic		WXS	Illumina HiSeq	Phase_I	B4DSY0|B7ZB65|Q5M7Y7|Q8WVA7|Q8WWM2|Q9H495|Q9H6E7	Missense_Mutation	SNP	ENST00000367627.3	37	CCDS1329.1	.	.	.	.	.	.	.	.	.	.	G	1.415	-0.574512	0.03882	.	.	ENSG00000186283	ENST00000367627;ENST00000352445;ENST00000447595	T;T;T	0.25579	1.79;1.79;1.79	5.33	5.33	0.75918	.	0.051299	0.85682	D	0.000000	T	0.17238	0.0414	N	0.19112	0.55	0.58432	D	0.999991	P	0.43826	0.818	B	0.44224	0.444	T	0.02813	-1.1107	10	0.02654	T	1	-29.7458	13.7194	0.62717	0.0:0.1541:0.8459:0.0	.	238	Q9H497	TOR3A_HUMAN	D	238;238;130	ENSP00000356599:E238D;ENSP00000335351:E238D;ENSP00000410195:E130D	ENSP00000335351:E238D	E	+	3	2	TOR3A	177323743	1.000000	0.71417	1.000000	0.80357	0.176000	0.22953	2.129000	0.42055	2.487000	0.83934	0.561000	0.74099	GAG		0.607	TOR3A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084927.1		NM_022371	
TRDMT1	1787	broad.mit.edu	37	10	17195591	17195591	+	Silent	SNP	T	T	C			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr10:17195591T>C	ENST00000377799.3	-	10	1037	c.990A>G	c.(988-990)gaA>gaG	p.E330E	TRDMT1_ENST00000488990.1_Silent_p.E207E|TRDMT1_ENST00000412821.3_Silent_p.E306E|TRDMT1_ENST00000457442.2_Silent_p.E249E|TRDMT1_ENST00000452380.2_5'UTR|TRDMT1_ENST00000351358.4_Silent_p.E284E|TRDMT1_ENST00000377766.5_3'UTR|TRDMT1_ENST00000358282.7_3'UTR	NM_004412.5	NP_004403.1	O14717	TRDMT_HUMAN	tRNA aspartic acid methyltransferase 1	330	SAM-dependent MTase C5-type. {ECO:0000255|PROSITE-ProRule:PRU01016}.				C-5 methylation of cytosine (GO:0090116)|response to amphetamine (GO:0001975)|tRNA methylation (GO:0030488)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	DNA (cytosine-5-)-methyltransferase activity (GO:0003886)|DNA binding (GO:0003677)|RNA binding (GO:0003723)|tRNA methyltransferase activity (GO:0008175)	p.E330E(1)		breast(2)|endometrium(1)|kidney(3)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	18					Pentamidine(DB00738)	TTGTTATCTGTTCTTCTTGTG	0.343																																																	1	Substitution - coding silent(1)	kidney(1)											137.0	130.0	132.0					10																	17195591		2203	4300	6503	SO:0001819	synonymous_variant	1787			AJ223333	CCDS7114.1	10p15.1	2006-10-23	2006-10-23	2006-10-23	ENSG00000107614	ENSG00000107614	2.1.1.37		2977	protein-coding gene	gene with protein product		602478	"""DNA (cytosine-5-)-methyltransferase 2"""	DNMT2		9425235, 9763678, 16424344	Standard	NM_004412		Approved	RNMT1	uc001iop.3	O14717	OTTHUMG00000017745	ENST00000377799.3:c.990A>G	10.37:g.17195591T>C		Somatic		WXS	Illumina GAIIx	Phase_I	B0YJ02|B0YJ03|B0YJ07|B0YJ08|O43669|Q86WW6	Silent	SNP	ENST00000377799.3	37	CCDS7114.1																																																																																				0.343	TRDMT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047024.3		NM_004412	
TTN	7273	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	179398617	179398617	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr2:179398617T>C	ENST00000591111.1	-	308	98026	c.97802A>G	c.(97801-97803)aAg>aGg	p.K32601R	TTN-AS1_ENST00000419746.1_RNA|TTN-AS1_ENST00000586452.1_RNA|TTN-AS1_ENST00000585358.1_RNA|TTN-AS1_ENST00000589391.1_RNA|TTN-AS1_ENST00000591332.1_RNA|TTN-AS1_ENST00000592689.1_RNA|TTN-AS1_ENST00000592836.1_RNA|TTN_ENST00000342175.6_Missense_Mutation_p.K25369R|TTN-AS1_ENST00000431259.2_RNA|TTN-AS1_ENST00000590807.1_RNA|TTN-AS1_ENST00000604571.1_RNA|TTN-AS1_ENST00000589842.1_RNA|TTN-AS1_ENST00000589355.1_RNA|TTN-AS1_ENST00000590040.1_RNA|TTN-AS1_ENST00000586831.1_RNA|TTN-AS1_ENST00000588716.1_RNA|TTN-AS1_ENST00000592630.1_RNA|TTN-AS1_ENST00000585451.1_RNA|TTN-AS1_ENST00000586707.1_RNA|TTN-AS1_ENST00000588804.1_RNA|TTN-AS1_ENST00000591867.1_RNA|TTN_ENST00000359218.5_Missense_Mutation_p.K25302R|TTN_ENST00000460472.2_Missense_Mutation_p.K25177R|TTN-AS1_ENST00000591466.1_RNA|TTN-AS1_ENST00000592600.1_RNA|TTN-AS1_ENST00000587568.1_RNA|TTN-AS1_ENST00000456053.1_RNA|TTN-AS1_ENST00000587944.1_RNA|TTN-AS1_ENST00000588257.1_RNA|TTN-AS1_ENST00000585487.1_RNA|TTN-AS1_ENST00000592182.1_RNA|TTN-AS1_ENST00000589434.1_RNA|TTN_ENST00000342992.6_Missense_Mutation_p.K31674R|TTN-AS1_ENST00000442329.2_RNA|TTN-AS1_ENST00000592750.1_RNA|TTN-AS1_ENST00000585625.1_RNA|TTN-AS1_ENST00000450692.2_RNA|TTN-AS1_ENST00000588244.1_RNA|TTN_ENST00000589042.1_Missense_Mutation_p.K34242R			Q8WZ42	TITIN_HUMAN	titin	32601					adult heart development (GO:0007512)|blood coagulation (GO:0007596)|cardiac muscle contraction (GO:0060048)|cardiac muscle fiber development (GO:0048739)|cardiac muscle hypertrophy (GO:0003300)|cardiac muscle tissue morphogenesis (GO:0055008)|cardiac myofibril assembly (GO:0055003)|detection of muscle stretch (GO:0035995)|forward locomotion (GO:0043056)|in utero embryonic development (GO:0001701)|mitotic chromosome condensation (GO:0007076)|muscle contraction (GO:0006936)|muscle filament sliding (GO:0030049)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|regulation of catalytic activity (GO:0050790)|regulation of protein kinase activity (GO:0045859)|regulation of relaxation of cardiac muscle (GO:1901897)|response to calcium ion (GO:0051592)|sarcomere organization (GO:0045214)|sarcomerogenesis (GO:0048769)|skeletal muscle myosin thick filament assembly (GO:0030241)|skeletal muscle thin filament assembly (GO:0030240)|somitogenesis (GO:0001756)|striated muscle contraction (GO:0006941)	condensed nuclear chromosome (GO:0000794)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|I band (GO:0031674)|M band (GO:0031430)|nucleus (GO:0005634)|striated muscle thin filament (GO:0005865)|Z disc (GO:0030018)	actin filament binding (GO:0051015)|actinin binding (GO:0042805)|ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|calmodulin binding (GO:0005516)|enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|muscle alpha-actinin binding (GO:0051371)|protease binding (GO:0002020)|protein kinase binding (GO:0019901)|protein self-association (GO:0043621)|protein serine/threonine kinase activity (GO:0004674)|structural constituent of muscle (GO:0008307)|structural molecule activity conferring elasticity (GO:0097493)|telethonin binding (GO:0031433)	p.K25369R(1)|p.K25302R(1)|p.K25177R(1)|p.K31672R(1)|p.K31674R(1)		NS(24)|autonomic_ganglia(1)|breast(64)|central_nervous_system(14)|cervix(14)|endometrium(96)|haematopoietic_and_lymphoid_tissue(16)|kidney(91)|large_intestine(303)|liver(1)|lung(595)|ovary(58)|pancreas(17)|prostate(38)|skin(60)|stomach(29)|upper_aerodigestive_tract(1)|urinary_tract(26)	1448			OV - Ovarian serous cystadenocarcinoma(117;0.023)|Epithelial(96;0.0454)|all cancers(119;0.134)			CTTAATTTTCTTCATGGTTCT	0.403																																																	5	Substitution - Missense(5)	kidney(5)											93.0	85.0	88.0					2																	179398617		1892	4108	6000	SO:0001583	missense	7273			X90568	CCDS54421.1, CCDS54422.1, CCDS54423.1, CCDS54424.1, CCDS33337.1, CCDS59435.1, CCDS74610.1	2q31	2014-09-17	2004-02-13		ENSG00000155657	ENSG00000155657		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	12403	protein-coding gene	gene with protein product		188840	"""cardiomyopathy, dilated 1G (autosomal dominant)"""	CMD1G		2129545, 10051295	Standard	NM_003319		Approved	CMPD4, FLJ32040, TMD, CMH9, LGMD2J, MYLK5	uc031rqd.1	Q8WZ42	OTTHUMG00000154448	ENST00000591111.1:c.97802A>G	2.37:g.179398617T>C	ENSP00000465570:p.Lys32601Arg	Somatic		WXS	Illumina HiSeq	Phase_I	A6NKB1|E7EQE6|E7ET18|K7ENY1|Q10465|Q10466|Q15598|Q2XUS3|Q32Q60|Q4U1Z6|Q4ZG20|Q6NSG0|Q6PDB1|Q6PJP0|Q7KYM2|Q7KYN4|Q7KYN5|Q7LDM3|Q7Z2X3|Q8TCG8|Q8WZ42|Q8WZ51|Q8WZ52|Q8WZ53|Q8WZB3|Q92761|Q92762|Q9UD97|Q9UP84|Q9Y6L9	Missense_Mutation	SNP	ENST00000591111.1	37		.	.	.	.	.	.	.	.	.	.	T	12.46	1.945573	0.34377	.	.	ENSG00000155657	ENST00000342992;ENST00000460472;ENST00000342175;ENST00000359218;ENST00000356127	T;T;T;T	0.65178	-0.14;0.12;0.1;0.07	5.6	4.45	0.53987	Protein kinase-like domain (1);Peptidase C2, calpain, large subunit, domain III (1);Ribonuclease H-like (1);	.	.	.	.	T	0.42086	0.1187	N	0.08118	0	0.42411	D	0.992608	B;B;B;B	0.17465	0.022;0.022;0.022;0.012	B;B;B;B	0.12156	0.007;0.007;0.007;0.007	T	0.33394	-0.9870	9	0.87932	D	0	.	11.0911	0.48117	0.0:0.0734:0.0:0.9266	.	25177;25302;25369;32601	D3DPF9;E7EQE6;E7ET18;Q8WZ42	.;.;.;TITIN_HUMAN	R	31674;25177;25369;25302;25174	ENSP00000343764:K31674R;ENSP00000434586:K25177R;ENSP00000340554:K25369R;ENSP00000352154:K25302R	ENSP00000340554:K25369R	K	-	2	0	TTN	179106863	1.000000	0.71417	0.999000	0.59377	0.981000	0.71138	1.469000	0.35343	0.966000	0.38159	-0.415000	0.06103	AAG		0.403	TTN-019	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000460310.1		NM_133378	
UBQLN1	29979	broad.mit.edu;ucsc.edu	37	9	86276810	86276810	+	Silent	SNP	G	G	C			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr9:86276810G>C	ENST00000376395.4	-	11	2185	c.1662C>G	c.(1660-1662)ctC>ctG	p.L554L	UBQLN1_ENST00000257468.7_Silent_p.L526L	NM_013438.4|NM_053067.2	NP_038466.2|NP_444295.1	Q9UMX0	UBQL1_HUMAN	ubiquilin 1	554	UBA. {ECO:0000255|PROSITE- ProRule:PRU00212}.				cellular response to hypoxia (GO:0071456)|regulation of oxidative stress-induced intrinsic apoptotic signaling pathway (GO:1902175)|regulation of protein ubiquitination (GO:0031396)|response to endoplasmic reticulum stress (GO:0034976)	cytoplasm (GO:0005737)|endoplasmic reticulum (GO:0005783)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|proteasome complex (GO:0000502)|protein complex (GO:0043234)	kinase binding (GO:0019900)	p.L554L(1)		breast(4)|endometrium(2)|kidney(4)|large_intestine(6)|lung(10)|prostate(1)	27						CCATTGCACTGAGTTGTTCCA	0.418																																					Melanoma(186;1284 2073 12755 14558 18426)												1	Substitution - coding silent(1)	kidney(1)											162.0	154.0	157.0					9																	86276810		2203	4300	6503	SO:0001819	synonymous_variant	29979			AF176069	CCDS6663.1, CCDS6664.1	9q22	2013-02-12			ENSG00000135018	ENSG00000135018		"""Ubiquilin family"""	12508	protein-coding gene	gene with protein product		605046				9303440, 10807547	Standard	NM_013438		Approved	DSK2, PLIC-1, XDRP1, DA41	uc004amv.3	Q9UMX0	OTTHUMG00000020104	ENST00000376395.4:c.1662C>G	9.37:g.86276810G>C		Somatic		WXS	Illumina GAIIx	Phase_I	Q5T6J5|Q5T6J9|Q8IXS9|Q8N2Q3|Q9H0T8|Q9H3R4|Q9HAZ5	Silent	SNP	ENST00000376395.4	37	CCDS6663.1																																																																																				0.418	UBQLN1-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000052834.1		NM_013438	
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10188294	10188295	+	Frame_Shift_Ins	INS	-	-	T			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr3:10188294_10188295insT	ENST00000256474.2	+	2	1277_1278	c.437_438insT	c.(436-441)cctattfs	p.I147fs	VHL_ENST00000477538.1_3'UTR|VHL_ENST00000345392.2_Intron	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	147	Involved in binding to CCT complex.		I -> T (in pheochromocytoma). {ECO:0000269|PubMed:9663592}.		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.P146fs*13(3)|p.P146P(2)|p.Q145fs*12(1)|p.I147fs*26(1)|p.P146fs*12(1)|p.P146fs*23(1)|p.S139fs*12(1)|p.G144fs*19(1)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		GACGGACAGCCTATTTTTGCCA	0.411		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"""	11	Deletion - Frameshift(9)|Substitution - coding silent(2)	kidney(11)	GRCh37	CD031548	VHL	D																																				SO:0001589	frameshift_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.438dupT	3.37:g.10188295_10188295dupT	ENSP00000256474:p.Ile147fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2RE45|Q13599|Q6PDA9	Frame_Shift_Ins	INS	ENST00000256474.2	37	CCDS2597.1																																																																																				0.411	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
VPS18	57617	broad.mit.edu	37	15	41191988	41191988	+	Silent	SNP	A	A	C			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr15:41191988A>C	ENST00000220509.5	+	4	1311	c.972A>C	c.(970-972)ccA>ccC	p.P324P	VPS18_ENST00000558474.1_Intron	NM_020857.2	NP_065908.1	Q9P253	VPS18_HUMAN	vacuolar protein sorting 18 homolog (S. cerevisiae)	324					endosome organization (GO:0007032)|intracellular protein transport (GO:0006886)|lysosome organization (GO:0007040)|vesicle-mediated transport (GO:0016192)|viral entry into host cell (GO:0046718)	actin filament (GO:0005884)|early endosome (GO:0005769)|HOPS complex (GO:0030897)|lysosomal membrane (GO:0005765)	metal ion binding (GO:0046872)	p.P324P(2)		autonomic_ganglia(1)|endometrium(5)|kidney(4)|large_intestine(4)|lung(6)|ovary(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	28		all_cancers(109;1.35e-17)|all_epithelial(112;3.78e-15)|Lung NSC(122;9.68e-11)|all_lung(180;2.25e-09)|Melanoma(134;0.0574)|Ovarian(310;0.0822)|Colorectal(260;0.0946)		GBM - Glioblastoma multiforme(113;1.07e-05)|COAD - Colon adenocarcinoma(120;0.15)|BRCA - Breast invasive adenocarcinoma(123;0.164)		GGGCCAGCCCACCCCTAGCCA	0.647																																																	2	Substitution - coding silent(2)	endometrium(1)|kidney(1)											64.0	67.0	66.0					15																	41191988		2203	4300	6503	SO:0001819	synonymous_variant	57617			AF308802	CCDS10069.1	15q14-q15	2006-12-19	2006-12-19		ENSG00000104142	ENSG00000104142			15972	protein-coding gene	gene with protein product		608551	"""vacuolar protein sorting protein 18"""			11250079, 16203730	Standard	NM_020857		Approved	KIAA1475, PEP3	uc001zne.3	Q9P253	OTTHUMG00000130135	ENST00000220509.5:c.972A>C	15.37:g.41191988A>C		Somatic		WXS	Illumina GAIIx	Phase_I	Q8TCG0|Q96DI3|Q9H268	Silent	SNP	ENST00000220509.5	37	CCDS10069.1																																																																																				0.647	VPS18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252443.2			
WBSCR27	155368	hgsc.bcm.edu	37	7	73249165	73249165	+	Missense_Mutation	SNP	T	T	A	rs13246460	byFrequency	TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr7:73249165T>A	ENST00000297873.4	-	6	695	c.646A>T	c.(646-648)Agg>Tgg	p.R216W		NM_152559.2	NP_689772.2	Q8N6F8	WBS27_HUMAN	Williams Beuren syndrome chromosome region 27	216				R -> W (in Ref. 1; AAN63884, 2; AAQ55828 and 4; AAH30295). {ECO:0000305}.						NS(1)|central_nervous_system(1)|lung(2)|prostate(1)	5		Lung NSC(55;0.159)				GGATACCACCTCCAGCTCGGA	0.627													T|||	2910	0.58107	0.4629	0.6124	5008	,	,		15582	0.5813		0.7256	False		,,,				2504	0.5695																0								T	TRP/ARG	2290,2116	597.0+/-388.8	593,1104,506	67.0	61.0	63.0		646	5.2	0.1	7	dbSNP_121	63	6384,2216	708.8+/-405.7	2371,1642,287	yes	missense	WBSCR27	NM_152559.2	101	2964,2746,793	AA,AT,TT		25.7674,48.0254,33.3077	probably-damaging	216/246	73249165	8674,4332	2203	4300	6503	SO:0001583	missense	155368			AF534110	CCDS5561.1	7q11.23	2004-07-05			ENSG00000165171	ENSG00000165171			19068	protein-coding gene	gene with protein product		612546					Standard	NM_152559		Approved		uc003tzj.2	Q8N6F8	OTTHUMG00000130033	ENST00000297873.4:c.646A>T	7.37:g.73249165T>A	ENSP00000297873:p.Arg216Trp	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000297873.4	37	CCDS5561.1	1327	0.6076007326007326	227	0.4613821138211382	218	0.6022099447513812	328	0.5734265734265734	554	0.7308707124010554	T	23.8	4.463481	0.84425	0.519746	0.742326	ENSG00000165171	ENST00000297873	T	0.69685	-0.42	5.25	5.25	0.73442	.	1.356490	0.04448	N	0.372109	T	0.00012	0.0000	N	0.22421	0.69	0.46131	P	0.0011200000000000099	D	0.55800	0.973	B	0.43754	0.43	T	0.38972	-0.9636	9	0.37606	T	0.19	-8.7324	11.6685	0.51387	0.0:0.0:0.0:1.0	rs13246460;rs17845919;rs17858895	216	Q8N6F8	WBS27_HUMAN	W	216	ENSP00000297873:R216W	ENSP00000297873:R216W	R	-	1	2	WBSCR27	72887101	0.999000	0.42202	0.106000	0.21319	0.330000	0.28571	5.701000	0.68325	2.013000	0.59113	0.449000	0.29647	AGG		0.627	WBSCR27-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252312.1		NM_152559	
YTHDC2	64848	broad.mit.edu;hgsc.bcm.edu	37	5	112899759	112899759	+	Silent	SNP	T	T	C			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr5:112899759T>C	ENST00000161863.4	+	20	2859	c.2646T>C	c.(2644-2646)gcT>gcC	p.A882A		NM_022828.3	NP_073739.3	Q9H6S0	YTDC2_HUMAN	YTH domain containing 2	882					ATP catabolic process (GO:0006200)|positive regulation by host of viral genome replication (GO:0044829)|response to interleukin-1 (GO:0070555)|response to tumor necrosis factor (GO:0034612)	endoplasmic reticulum (GO:0005783)	ATP binding (GO:0005524)|helicase activity (GO:0004386)|poly(A) RNA binding (GO:0044822)|RNA polymerase binding (GO:0070063)|RNA-dependent ATPase activity (GO:0008186)	p.A882A(1)		NS(2)|central_nervous_system(2)|cervix(1)|endometrium(2)|kidney(6)|large_intestine(13)|lung(10)|pancreas(1)|prostate(3)|skin(2)|upper_aerodigestive_tract(1)	43		all_cancers(142;7.69e-05)|all_epithelial(76;6.42e-07)|Colorectal(10;0.00278)|Prostate(80;0.00955)|Ovarian(225;0.0444)|Lung NSC(810;0.143)|all_lung(232;0.163)|Breast(839;0.244)		OV - Ovarian serous cystadenocarcinoma(64;7.2e-08)|Epithelial(69;8.83e-08)|all cancers(49;6.9e-06)|COAD - Colon adenocarcinoma(37;0.0458)|Colorectal(14;0.0594)		AACGTGCAGCTATGCTTTGTA	0.418																																																	1	Substitution - coding silent(1)	kidney(1)											144.0	142.0	142.0					5																	112899759		2202	4300	6502	SO:0001819	synonymous_variant	64848			AK000915	CCDS4113.1	5q22.3	2008-02-05			ENSG00000047188	ENSG00000047188			24721	protein-coding gene	gene with protein product						12477932	Standard	NM_022828		Approved	FLJ2194, FLJ10053, DKFZp564A186	uc003kqn.3	Q9H6S0	OTTHUMG00000128837	ENST00000161863.4:c.2646T>C	5.37:g.112899759T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B2RP66	Silent	SNP	ENST00000161863.4	37	CCDS4113.1																																																																																				0.418	YTHDC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250776.2		NM_022828	
ZC3H18	124245	broad.mit.edu;hgsc.bcm.edu	37	16	88688681	88688681	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5693-01A-11D-1534-10	TCGA-B0-5693-11A-01D-1534-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	be92ee16-6288-46c0-aaa7-7a27020cd7ca	51df4667-989b-4611-b869-3d8046d76232	g.chr16:88688681C>A	ENST00000301011.5	+	9	1752	c.1552C>A	c.(1552-1554)Cct>Act	p.P518T	ZC3H18_ENST00000452588.2_Missense_Mutation_p.P542T	NM_144604.3	NP_653205.3	Q86VM9	ZCH18_HUMAN	zinc finger CCCH-type containing 18	518						nucleus (GO:0005634)	metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.P518T(1)		endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(6)|large_intestine(9)|lung(16)|ovary(1)|skin(2)|upper_aerodigestive_tract(1)	42				BRCA - Breast invasive adenocarcinoma(80;0.0542)		GTGGAAGGACCCTTGGCGCCG	0.602																																					Ovarian(121;375 2276 20373 38669)												1	Substitution - Missense(1)	kidney(1)											56.0	58.0	58.0					16																	88688681		2198	4300	6498	SO:0001583	missense	124245			BC001584	CCDS10967.1, CCDS73924.1	16q24.2-q24.3	2012-07-05			ENSG00000158545	ENSG00000158545		"""Zinc fingers, CCCH-type domain containing"""	25091	protein-coding gene	gene with protein product						17579712	Standard	NM_144604		Approved	NHN1	uc002fky.3	Q86VM9	OTTHUMG00000137679	ENST00000301011.5:c.1552C>A	16.37:g.88688681C>A	ENSP00000301011:p.Pro518Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q96DG4|Q96MP7	Missense_Mutation	SNP	ENST00000301011.5	37	CCDS10967.1	.	.	.	.	.	.	.	.	.	.	C	24.0	4.487851	0.84854	.	.	ENSG00000158545	ENST00000301011;ENST00000289509;ENST00000452588	T;T	0.52754	0.65;0.65	5.83	5.83	0.93111	.	0.053091	0.85682	D	0.000000	T	0.67924	0.2945	L	0.59436	1.845	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.999	T	0.68311	-0.5442	10	0.87932	D	0	-15.7866	19.7135	0.96105	0.0:1.0:0.0:0.0	.	542;518	E7ERS3;Q86VM9	.;ZCH18_HUMAN	T	518;486;542	ENSP00000301011:P518T;ENSP00000416951:P542T	ENSP00000289509:P486T	P	+	1	0	ZC3H18	87216182	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	7.321000	0.79088	2.769000	0.95229	0.655000	0.94253	CCT		0.602	ZC3H18-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000269168.1		NM_144604	
