#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
AASS	10157	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	121766489	121766489	+	Nonsense_Mutation	SNP	T	T	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr7:121766489T>A	ENST00000393376.1	-	3	507	c.412A>T	c.(412-414)Aaa>Taa	p.K138*	AASS_ENST00000417368.2_Nonsense_Mutation_p.K138*|AASS_ENST00000473553.1_Intron			Q9UDR5	AASS_HUMAN	aminoadipate-semialdehyde synthase	138	Lysine-ketoglutarate reductase.				cellular nitrogen compound metabolic process (GO:0034641)|L-lysine catabolic process to acetyl-CoA via saccharopine (GO:0033512)|lysine catabolic process (GO:0006554)|protein tetramerization (GO:0051262)|small molecule metabolic process (GO:0044281)	intracellular membrane-bounded organelle (GO:0043231)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	saccharopine dehydrogenase (NAD+, L-glutamate-forming) activity (GO:0047131)|saccharopine dehydrogenase (NADP+, L-lysine-forming) activity (GO:0047130)	p.K138*(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(6)|large_intestine(12)|lung(27)|ovary(1)|pancreas(1)|upper_aerodigestive_tract(1)	54						TCCACCATTTTCTCATAATCA	0.398																																																	1	Substitution - Nonsense(1)	kidney(1)											239.0	229.0	232.0					7																	121766489		2203	4300	6503	SO:0001587	stop_gained	10157			AF229180	CCDS5783.1	7q31.3	2010-12-14			ENSG00000008311	ENSG00000008311			17366	protein-coding gene	gene with protein product		605113				10775527	Standard	NM_005763		Approved	LORSDH, LKRSDH	uc003vkb.3	Q9UDR5	OTTHUMG00000157058	ENST00000393376.1:c.412A>T	7.37:g.121766489T>A	ENSP00000377040:p.Lys138*		O95462	Nonsense_Mutation	SNP	ENST00000393376.1	37	CCDS5783.1	.	.	.	.	.	.	.	.	.	.	.	38	6.660256	0.97743	.	.	ENSG00000008311	ENST00000393376;ENST00000417368	.	.	.	5.5	5.5	0.81552	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.26408	T	0.33	-14.728	15.6396	0.76984	0.0:0.0:0.0:1.0	.	.	.	.	X	138	.	ENSP00000351834:K138X	K	-	1	0	AASS	121553725	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	8.000000	0.88501	2.104000	0.64026	0.524000	0.50904	AAA		0.398	AASS-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000347300.1		NM_005763	
ABCD2	225	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	39980001	39980001	+	Missense_Mutation	SNP	C	C	G	rs151149571	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr12:39980001C>G	ENST00000308666.3	-	7	1880	c.1745G>C	c.(1744-1746)cGt>cCt	p.R582P		NM_005164.3	NP_005155.1	Q9UBJ2	ABCD2_HUMAN	ATP-binding cassette, sub-family D (ALD), member 2	582	ABC transporter. {ECO:0000255|PROSITE- ProRule:PRU00434}.				fatty acid beta-oxidation (GO:0006635)|positive regulation of fatty acid beta-oxidation (GO:0032000)|transmembrane transport (GO:0055085)|very long-chain fatty acid catabolic process (GO:0042760)|very long-chain fatty acid metabolic process (GO:0000038)	cytosol (GO:0005829)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|mitochondrion (GO:0005739)|peroxisomal membrane (GO:0005778)|peroxisome (GO:0005777)	ATP binding (GO:0005524)|ATPase activity, coupled to transmembrane movement of substances (GO:0042626)|protein homodimerization activity (GO:0042803)	p.R582P(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(10)|lung(24)|ovary(2)|pancreas(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)	52						GTGTAGGATACGTTCCAGATC	0.363																																																	1	Substitution - Missense(1)	kidney(1)											191.0	159.0	170.0					12																	39980001		2203	4300	6503	SO:0001583	missense	225			U28150	CCDS8734.1	12q12	2012-05-16			ENSG00000173208	ENSG00000173208		"""ATP binding cassette transporters / subfamily D"""	66	protein-coding gene	gene with protein product		601081		ALDL1		8577752	Standard	NM_005164		Approved	ALDR, ALDRP	uc001rmb.2	Q9UBJ2	OTTHUMG00000169337	ENST00000308666.3:c.1745G>C	12.37:g.39980001C>G	ENSP00000310688:p.Arg582Pro		B2RAM3|Q13210|Q2M3H9	Missense_Mutation	SNP	ENST00000308666.3	37	CCDS8734.1	.	.	.	.	.	.	.	.	.	.	C	1.376	-0.584760	0.03827	.	.	ENSG00000173208	ENST00000308666	D	0.94046	-3.34	4.63	-1.75	0.08031	ATPase, AAA+ type, core (1);ABC transporter-like (2);	1.359530	0.04251	N	0.338576	D	0.89897	0.6848	L	0.52823	1.66	0.09310	N	1	B	0.21147	0.052	B	0.30179	0.112	T	0.74121	-0.3767	9	.	.	.	-17.52	2.3556	0.04294	0.1372:0.4061:0.0958:0.3608	.	582	Q9UBJ2	ABCD2_HUMAN	P	582	ENSP00000310688:R582P	.	R	-	2	0	ABCD2	38266268	0.000000	0.05858	0.004000	0.12327	0.119000	0.20118	-0.557000	0.05985	-0.094000	0.12374	-0.424000	0.05967	CGT		0.363	ABCD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403591.1		NM_005164	
ANKRD17	26057	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	73956463	73956463	+	Silent	SNP	T	T	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr4:73956463T>A	ENST00000358602.4	-	29	6998	c.6882A>T	c.(6880-6882)tcA>tcT	p.S2294S	ANKRD17_ENST00000509867.2_Silent_p.S2181S|ANKRD17_ENST00000330838.6_Silent_p.S2043S	NM_032217.3	NP_115593.3	O75179	ANR17_HUMAN	ankyrin repeat domain 17	2294					blood vessel maturation (GO:0001955)|negative regulation of smooth muscle cell differentiation (GO:0051151)|viral process (GO:0016032)	cytoplasm (GO:0005737)|membrane (GO:0016020)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S2294S(1)		NS(3)|breast(2)|central_nervous_system(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(15)|lung(39)|ovary(6)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(3)	96	Breast(15;0.000295)		Epithelial(6;8.86e-07)|OV - Ovarian serous cystadenocarcinoma(6;6.22e-06)|all cancers(17;1.51e-05)|Lung(101;0.103)|LUSC - Lung squamous cell carcinoma(112;0.154)			GTAAAGGATCTGAATTTGGCA	0.433																																																	1	Substitution - coding silent(1)	kidney(1)											138.0	145.0	143.0					4																	73956463		2203	4300	6503	SO:0001819	synonymous_variant	26057			AB014597	CCDS34003.1, CCDS34004.1, CCDS68721.1	4q21.1-q21.21	2013-01-10			ENSG00000132466	ENSG00000132466		"""Ankyrin repeat domain containing"""	23575	protein-coding gene	gene with protein product		615929				11165478	Standard	NM_032217		Approved	GTAR, KIAA0697, FLJ22206, NY-BR-16	uc003hgp.3	O75179	OTTHUMG00000160826	ENST00000358602.4:c.6882A>T	4.37:g.73956463T>A			E7EUV3|G5E964|Q6PJ85|Q6PK85|Q6PKA2|Q86XI3|Q8NDR5|Q96I86|Q9H288|Q9H6J9	Silent	SNP	ENST00000358602.4	37	CCDS34004.1																																																																																				0.433	ANKRD17-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000362475.1		NM_032217	
ANK2	287	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	114290829	114290829	+	Silent	SNP	A	A	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	A	A	A	T	A	A	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr4:114290829A>T	ENST00000357077.4	+	43	11531	c.11478A>T	c.(11476-11478)atA>atT	p.I3826I	ANK2_ENST00000394537.3_Silent_p.I1741I|ANK2_ENST00000506722.1_Silent_p.I1732I|ANK2_ENST00000509550.1_Silent_p.I917I|ANK2_ENST00000264366.6_Silent_p.I3793I|ANK2_ENST00000510275.2_Silent_p.I393I	NM_001148.4	NP_001139.3	Q01484	ANK2_HUMAN	ankyrin 2, neuronal	3826					atrial cardiac muscle cell action potential (GO:0086014)|atrial cardiac muscle cell to AV node cell communication (GO:0086066)|atrial septum development (GO:0003283)|axon guidance (GO:0007411)|cardiac muscle contraction (GO:0060048)|cellular calcium ion homeostasis (GO:0006874)|cellular protein localization (GO:0034613)|membrane depolarization during SA node cell action potential (GO:0086046)|paranodal junction assembly (GO:0030913)|positive regulation of calcium ion transmembrane transporter activity (GO:1901021)|positive regulation of calcium ion transport (GO:0051928)|positive regulation of cation channel activity (GO:2001259)|positive regulation of gene expression (GO:0010628)|positive regulation of potassium ion transmembrane transporter activity (GO:1901018)|positive regulation of potassium ion transport (GO:0043268)|protein localization to cell surface (GO:0034394)|protein localization to endoplasmic reticulum (GO:0070972)|protein localization to M-band (GO:0036309)|protein localization to organelle (GO:0033365)|protein localization to plasma membrane (GO:0072659)|protein localization to T-tubule (GO:0036371)|protein stabilization (GO:0050821)|protein targeting to plasma membrane (GO:0072661)|regulation of calcium ion transmembrane transporter activity (GO:1901019)|regulation of calcium ion transport (GO:0051924)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of cardiac muscle cell membrane potential (GO:0086036)|regulation of cardiac muscle contraction (GO:0055117)|regulation of cardiac muscle contraction by calcium ion signaling (GO:0010882)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of heart rate (GO:0002027)|regulation of heart rate by cardiac conduction (GO:0086091)|regulation of protein stability (GO:0031647)|regulation of release of sequestered calcium ion into cytosol (GO:0051279)|regulation of ventricular cardiac muscle cell membrane repolarization (GO:0060307)|response to methylmercury (GO:0051597)|SA node cell action potential (GO:0086015)|SA node cell to atrial cardiac muscle cell communication (GO:0086070)|sarcoplasmic reticulum calcium ion transport (GO:0070296)|T-tubule organization (GO:0033292)|ventricular cardiac muscle cell action potential (GO:0086005)	A band (GO:0031672)|basolateral plasma membrane (GO:0016323)|costamere (GO:0043034)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|integral component of plasma membrane (GO:0005887)|intercalated disc (GO:0014704)|intracellular (GO:0005622)|M band (GO:0031430)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)|Z disc (GO:0030018)	ATPase binding (GO:0051117)|enzyme binding (GO:0019899)|ion channel binding (GO:0044325)|potassium channel regulator activity (GO:0015459)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|spectrin binding (GO:0030507)|structural constituent of cytoskeleton (GO:0005200)	p.I3826I(1)		NS(1)|biliary_tract(1)|breast(9)|central_nervous_system(10)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(7)|large_intestine(54)|liver(2)|lung(112)|ovary(8)|pancreas(1)|prostate(7)|skin(11)|stomach(2)|upper_aerodigestive_tract(3)|urinary_tract(10)	248		Ovarian(17;0.0448)|Hepatocellular(203;0.218)		OV - Ovarian serous cystadenocarcinoma(123;4.92e-05)		CTCCCATCATACAAGAACCCG	0.582																																																	1	Substitution - coding silent(1)	kidney(1)											66.0	64.0	65.0					4																	114290829		2203	4300	6503	SO:0001819	synonymous_variant	287			M37123	CCDS3702.1, CCDS43261.1, CCDS54796.1	4q25-q26	2014-09-17	2003-03-12		ENSG00000145362	ENSG00000145362		"""Ankyrin repeat domain containing"""	493	protein-coding gene	gene with protein product		106410	"""long (electrocardiographic) QT syndrome 4"""	LQT4		7485162, 12571597	Standard	NM_001148		Approved		uc003ibe.4	Q01484	OTTHUMG00000132912	ENST00000357077.4:c.11478A>T	4.37:g.114290829A>T			Q01485|Q08AC7|Q08AC8|Q7Z3L5	Silent	SNP	ENST00000357077.4	37	CCDS3702.1	.	.	.	.	.	.	.	.	.	.	A	6.380	0.438153	0.12104	.	.	ENSG00000145362	ENST00000514960	.	.	.	5.66	-11.3	0.00108	.	.	.	.	.	T	0.62768	0.2455	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.76764	-0.2839	4	.	.	.	.	18.6757	0.91528	0.0774:0.2487:0.6738:0.0	.	.	.	.	S	743	.	.	T	+	1	0	ANK2	114510278	0.014000	0.17966	0.000000	0.03702	0.008000	0.06430	-1.240000	0.02914	-2.557000	0.00476	-0.924000	0.02725	ACA		0.582	ANK2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000256422.2		NM_001148	
ANO2	57101	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	5672713	5672713	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr12:5672713C>T	ENST00000356134.5	-	27	2823	c.2752G>A	c.(2752-2754)Gtc>Atc	p.V918I	ANO2_ENST00000546188.1_Missense_Mutation_p.V918I|ANO2_ENST00000327087.8_Missense_Mutation_p.V917I	NM_001278596.1	NP_001265525.1	Q9NQ90	ANO2_HUMAN	anoctamin 2, calcium activated chloride channel	922					chloride transmembrane transport (GO:1902476)|ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	chloride channel complex (GO:0034707)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	intracellular calcium activated chloride channel activity (GO:0005229)	p.V918I(2)|p.V917I(2)		central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(11)|lung(23)|ovary(4)|pancreas(1)|prostate(1)|skin(5)|stomach(3)|upper_aerodigestive_tract(1)	58						TCCACGAGGACGCTCAGGAAC	0.557																																																	4	Substitution - Missense(4)	kidney(2)|endometrium(2)											85.0	79.0	81.0					12																	5672713		1968	4163	6131	SO:0001583	missense	57101			AJ272204	CCDS44807.1, CCDS44807.2	12p13.3	2014-04-09	2014-04-09	2008-08-28		ENSG00000047617		"""Ion channels / Chloride channels : Calcium activated : Anoctamins"""	1183	protein-coding gene	gene with protein product	"""transmembrane protein 16B (eight membrane-spanning domains)"""	610109	"""chromosome 12 open reading frame 3"", ""transmembrane protein 16B"", ""anoctamin 2"""	C12orf3, TMEM16B		12739008, 15067359, 24692353	Standard	NM_001278596		Approved		uc001qnm.2	Q9NQ90		ENST00000356134.5:c.2752G>A	12.37:g.5672713C>T	ENSP00000348453:p.Val918Ile		C4N787|Q9H847	Missense_Mutation	SNP	ENST00000356134.5	37		.	.	.	.	.	.	.	.	.	.	C	6.220	0.408776	0.11812	.	.	ENSG00000047617	ENST00000327087;ENST00000356134;ENST00000546188;ENST00000541277;ENST00000543568	T;T;T	0.62941	-0.01;-0.01;-0.01	4.79	4.79	0.61399	.	0.141486	0.48767	D	0.000165	T	0.40743	0.1129	N	0.04746	-0.17	0.31993	N	0.604406	B	0.24651	0.108	B	0.15484	0.013	T	0.39522	-0.9610	10	0.21014	T	0.42	.	17.1807	0.86854	0.0:1.0:0.0:0.0	.	917	Q9NQ90-3	.	I	917;918;918;922;5	ENSP00000314048:V917I;ENSP00000348453:V918I;ENSP00000440981:V918I	ENSP00000314048:V917I	V	-	1	0	ANO2	5542974	0.000000	0.05858	0.994000	0.49952	0.962000	0.63368	0.462000	0.21956	2.369000	0.80426	0.555000	0.69702	GTC		0.557	ANO2-001	KNOWN	basic	protein_coding	protein_coding	OTTHUMT00000399019.4		NM_020373	
APOB	338	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	21242762	21242762	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr2:21242762C>A	ENST00000233242.1	-	19	2959	c.2832G>T	c.(2830-2832)ttG>ttT	p.L944F		NM_000384.2	NP_000375	P04114	APOB_HUMAN	apolipoprotein B	944	Heparin-binding.				artery morphogenesis (GO:0048844)|blood coagulation (GO:0007596)|cellular response to prostaglandin stimulus (GO:0071379)|cellular response to tumor necrosis factor (GO:0071356)|cholesterol efflux (GO:0033344)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|cholesterol transport (GO:0030301)|fertilization (GO:0009566)|in utero embryonic development (GO:0001701)|leukocyte migration (GO:0050900)|lipoprotein biosynthetic process (GO:0042158)|lipoprotein catabolic process (GO:0042159)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|low-density lipoprotein particle clearance (GO:0034383)|low-density lipoprotein particle remodeling (GO:0034374)|nervous system development (GO:0007399)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of lipid storage (GO:0010884)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|post-embryonic development (GO:0009791)|receptor-mediated endocytosis (GO:0006898)|regulation of cholesterol biosynthetic process (GO:0045540)|response to carbohydrate (GO:0009743)|response to lipopolysaccharide (GO:0032496)|response to selenium ion (GO:0010269)|response to virus (GO:0009615)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|sperm motility (GO:0030317)|spermatogenesis (GO:0007283)|triglyceride catabolic process (GO:0019433)|triglyceride mobilization (GO:0006642)|very-low-density lipoprotein particle assembly (GO:0034379)	actin cytoskeleton (GO:0015629)|chylomicron (GO:0042627)|chylomicron remnant (GO:0034360)|clathrin-coated endocytic vesicle membrane (GO:0030669)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|early endosome (GO:0005769)|endocytic vesicle lumen (GO:0071682)|endoplasmic reticulum lumen (GO:0005788)|endoplasmic reticulum membrane (GO:0005789)|endosome lumen (GO:0031904)|endosome membrane (GO:0010008)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|intermediate-density lipoprotein particle (GO:0034363)|intracellular membrane-bounded organelle (GO:0043231)|low-density lipoprotein particle (GO:0034362)|mature chylomicron (GO:0034359)|plasma membrane (GO:0005886)|very-low-density lipoprotein particle (GO:0034361)	cholesterol transporter activity (GO:0017127)|heparin binding (GO:0008201)|lipase binding (GO:0035473)|low-density lipoprotein particle receptor binding (GO:0050750)|phospholipid binding (GO:0005543)	p.L944F(1)		NS(5)|autonomic_ganglia(1)|breast(6)|central_nervous_system(4)|cervix(3)|endometrium(19)|kidney(10)|large_intestine(63)|liver(5)|lung(125)|ovary(16)|pancreas(1)|prostate(5)|skin(31)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(6)	305	Acute lymphoblastic leukemia(172;0.155)|all_hematologic(175;0.215)					TGGTAGAGACCAAATGTAATG	0.448																																																	1	Substitution - Missense(1)	kidney(1)											137.0	128.0	131.0					2																	21242762		2203	4300	6503	SO:0001583	missense	338			M14162	CCDS1703.1	2p24-p23	2013-05-29	2013-05-29		ENSG00000084674	ENSG00000084674		"""Apolipoproteins"""	603	protein-coding gene	gene with protein product		107730	"""apolipoprotein B (including Ag(x) antigen)"""				Standard	NM_000384		Approved		uc002red.3	P04114	OTTHUMG00000090785	ENST00000233242.1:c.2832G>T	2.37:g.21242762C>A	ENSP00000233242:p.Leu944Phe		O00502|P78479|P78480|P78481|Q13779|Q13785|Q13786|Q13787|Q13788|Q4ZG63|Q53QC8|Q7Z600|Q9UMN0	Missense_Mutation	SNP	ENST00000233242.1	37	CCDS1703.1	.	.	.	.	.	.	.	.	.	.	C	14.61	2.586850	0.46110	.	.	ENSG00000084674	ENST00000233242;ENST00000535079	T	0.15718	2.4	5.23	4.34	0.51931	Lipid transport protein, beta-sheet shell (1);Vitellinogen, open beta-sheet, subdomain 2 (1);	0.000000	0.49916	D	0.000130	T	0.35856	0.0946	L	0.54323	1.7	0.80722	D	1	D	0.89917	1.0	D	0.81914	0.995	T	0.06023	-1.0850	10	0.48119	T	0.1	.	13.9811	0.64306	0.0:0.9262:0.0:0.0738	.	944	P04114	APOB_HUMAN	F	944	ENSP00000233242:L944F	ENSP00000233242:L944F	L	-	3	2	APOB	21096267	0.953000	0.32496	0.999000	0.59377	0.364000	0.29643	0.860000	0.27871	1.343000	0.45638	0.655000	0.94253	TTG		0.448	APOB-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207571.1			
ATP1A1	476	broad.mit.edu	37	1	116941357	116941357	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr1:116941357G>A	ENST00000295598.5	+	16	2491	c.2239G>A	c.(2239-2241)Gac>Aac	p.D747N	ATP1A1_ENST00000369496.4_Missense_Mutation_p.D716N|ATP1A1_ENST00000537345.1_Missense_Mutation_p.D747N	NM_000701.7	NP_000692.2	P05023	AT1A1_HUMAN	ATPase, Na+/K+ transporting, alpha 1 polypeptide	747					ATP biosynthetic process (GO:0006754)|cardiac muscle contraction (GO:0060048)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|cellular potassium ion homeostasis (GO:0030007)|cellular response to mechanical stimulus (GO:0071260)|cellular response to steroid hormone stimulus (GO:0071383)|cellular sodium ion homeostasis (GO:0006883)|ion transmembrane transport (GO:0034220)|membrane hyperpolarization (GO:0060081)|membrane repolarization (GO:0086009)|membrane repolarization during cardiac muscle cell action potential (GO:0086013)|negative regulation of glucocorticoid biosynthetic process (GO:0031947)|negative regulation of heart contraction (GO:0045822)|positive regulation of heart contraction (GO:0045823)|positive regulation of striated muscle contraction (GO:0045989)|potassium ion import (GO:0010107)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle cell contraction (GO:0086004)|regulation of sodium ion transport (GO:0002028)|regulation of the force of heart contraction (GO:0002026)|relaxation of cardiac muscle (GO:0055119)|response to drug (GO:0042493)|sodium ion export from cell (GO:0036376)|transmembrane transport (GO:0055085)	apical plasma membrane (GO:0016324)|basolateral plasma membrane (GO:0016323)|caveola (GO:0005901)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|sarcolemma (GO:0042383)|sodium:potassium-exchanging ATPase complex (GO:0005890)|T-tubule (GO:0030315)|vesicle (GO:0031982)	ADP binding (GO:0043531)|ATP binding (GO:0005524)|chaperone binding (GO:0051087)|phosphatase activity (GO:0016791)|potassium ion binding (GO:0030955)|sodium ion binding (GO:0031402)|sodium:potassium-exchanging ATPase activity (GO:0005391)|steroid hormone binding (GO:1990239)	p.D747N(1)|p.D747H(1)		NS(2)|breast(2)|cervix(3)|endometrium(2)|kidney(5)|large_intestine(9)|lung(17)|ovary(1)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	47	Lung SC(450;0.225)	all_cancers(81;1.28e-06)|all_epithelial(167;3.48e-07)|all_lung(203;2.64e-06)|Lung NSC(69;1.98e-05)		Lung(183;0.0164)|LUSC - Lung squamous cell carcinoma(189;0.0548)|Colorectal(144;0.0825)|COAD - Colon adenocarcinoma(174;0.127)|all cancers(265;0.24)	Acetyldigitoxin(DB00511)|Almitrine(DB01430)|Aluminium(DB01370)|Bepridil(DB01244)|Bretylium(DB01158)|Ciclopirox(DB01188)|Deslanoside(DB01078)|Diazoxide(DB01119)|Digitoxin(DB01396)|Digoxin(DB00390)|Ethacrynic acid(DB00903)|Hydroflumethiazide(DB00774)|Ouabain(DB01092)|Trichlormethiazide(DB01021)	GCAAGCTGCTGACATGATTCT	0.463																																																	2	Substitution - Missense(2)	lung(1)|kidney(1)											186.0	177.0	180.0					1																	116941357		2203	4300	6503	SO:0001583	missense	476			D00099	CCDS887.1, CCDS53351.1, CCDS53352.1	1p13	2012-10-22			ENSG00000163399	ENSG00000163399	3.6.3.9	"""ATPases / P-type"""	799	protein-coding gene	gene with protein product	"""sodium/potassium-transporting ATPase subunit alpha-1"", ""sodium pump subunit alpha-1"", ""sodium-potassium ATPase catalytic subunit alpha-1"""	182310					Standard	NM_000701		Approved		uc001ege.3	P05023	OTTHUMG00000012109	ENST00000295598.5:c.2239G>A	1.37:g.116941357G>A	ENSP00000295598:p.Asp747Asn		B2RBR6|B7Z2T5|B7Z3U6|F5H3A1|Q16689|Q6LDM4|Q9UCN1|Q9UJ20|Q9UJ21	Missense_Mutation	SNP	ENST00000295598.5	37	CCDS887.1	.	.	.	.	.	.	.	.	.	.	G	36	5.779031	0.96929	.	.	ENSG00000163399	ENST00000295598;ENST00000537345;ENST00000369496	D;D;D	0.85258	-1.96;-1.96;-1.96	5.23	5.23	0.72850	HAD-like domain (1);ATPase, P-type,  transmembrane domain (1);	0.000000	0.85682	D	0.000000	D	0.93025	0.7780	M	0.90870	3.155	0.80722	D	1	P;P	0.38280	0.625;0.491	P;P	0.56088	0.791;0.623	D	0.93408	0.6766	10	0.87932	D	0	.	19.0012	0.92834	0.0:0.0:1.0:0.0	.	747;747	F5H3A1;P05023	.;AT1A1_HUMAN	N	747;747;716	ENSP00000295598:D747N;ENSP00000445306:D747N;ENSP00000358508:D716N	ENSP00000295598:D747N	D	+	1	0	ATP1A1	116742880	1.000000	0.71417	0.980000	0.43619	0.997000	0.91878	9.657000	0.98554	2.718000	0.92993	0.655000	0.94253	GAC		0.463	ATP1A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000033481.5		NM_001160233	
ATP7A	538	hgsc.bcm.edu	37	X	77284798	77284799	+	Frame_Shift_Ins	INS	-	-	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chrX:77284798_77284799insA	ENST00000341514.6	+	15	3123_3124	c.2968_2969insA	c.(2968-2970)caafs	p.Q990fs	ATP7A_ENST00000350425.4_Intron|ATP7A_ENST00000343533.5_Frame_Shift_Ins_p.Q912fs	NM_000052.5	NP_000043.4	Q04656	ATP7A_HUMAN	ATPase, Cu++ transporting, alpha polypeptide	990					blood vessel development (GO:0001568)|blood vessel remodeling (GO:0001974)|cartilage development (GO:0051216)|catecholamine metabolic process (GO:0006584)|cellular copper ion homeostasis (GO:0006878)|central nervous system neuron development (GO:0021954)|cerebellar Purkinje cell differentiation (GO:0021702)|collagen fibril organization (GO:0030199)|copper ion export (GO:0060003)|copper ion import (GO:0015677)|copper ion transport (GO:0006825)|dendrite morphogenesis (GO:0048813)|detoxification of copper ion (GO:0010273)|dopamine metabolic process (GO:0042417)|elastic fiber assembly (GO:0048251)|elastin biosynthetic process (GO:0051542)|epinephrine metabolic process (GO:0042414)|extracellular matrix organization (GO:0030198)|hair follicle morphogenesis (GO:0031069)|in utero embryonic development (GO:0001701)|ion transmembrane transport (GO:0034220)|lactation (GO:0007595)|locomotory behavior (GO:0007626)|lung alveolus development (GO:0048286)|mitochondrion organization (GO:0007005)|negative regulation of metalloenzyme activity (GO:0048553)|negative regulation of neuron apoptotic process (GO:0043524)|neuron projection morphogenesis (GO:0048812)|norepinephrine biosynthetic process (GO:0042421)|norepinephrine metabolic process (GO:0042415)|peptidyl-lysine modification (GO:0018205)|pigmentation (GO:0043473)|positive regulation of catalytic activity (GO:0043085)|positive regulation of metalloenzyme activity (GO:0048554)|positive regulation of oxidoreductase activity (GO:0051353)|pyramidal neuron development (GO:0021860)|regulation of gene expression (GO:0010468)|regulation of oxidative phosphorylation (GO:0002082)|release of cytochrome c from mitochondria (GO:0001836)|removal of superoxide radicals (GO:0019430)|response to iron(III) ion (GO:0010041)|response to zinc ion (GO:0010043)|serotonin metabolic process (GO:0042428)|skin development (GO:0043588)|T-helper cell differentiation (GO:0042093)|transmembrane transport (GO:0055085)|tryptophan metabolic process (GO:0006568)|tyrosine metabolic process (GO:0006570)	basolateral plasma membrane (GO:0016323)|brush border membrane (GO:0031526)|endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|late endosome (GO:0005770)|membrane (GO:0016020)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|trans-Golgi network (GO:0005802)|trans-Golgi network transport vesicle (GO:0030140)	ATP binding (GO:0005524)|copper ion binding (GO:0005507)|copper ion transmembrane transporter activity (GO:0005375)|copper-dependent protein binding (GO:0032767)|copper-exporting ATPase activity (GO:0004008)|superoxide dismutase copper chaperone activity (GO:0016532)			breast(4)|central_nervous_system(3)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(7)|lung(26)|pancreas(1)|prostate(1)|urinary_tract(1)	53					Carboplatin(DB00958)|Cisplatin(DB00515)|Oxaliplatin(DB00526)	ATTTGCTTTCCAAGCCTCTATC	0.431																																																	0																																										SO:0001589	frameshift_variant	538			L06133	CCDS35339.1, CCDS75997.1	Xq21.1	2012-10-22	2008-07-31		ENSG00000165240	ENSG00000165240	3.6.3.4	"""ATPases / P-type"""	869	protein-coding gene	gene with protein product	"""copper pump 1"", ""copper-transporting ATPase 1"""	300011	"""Menkes syndrome"""	MNK		10079817	Standard	NM_000052		Approved		uc004ecx.4	Q04656	OTTHUMG00000021885	ENST00000341514.6:c.2970dupA	X.37:g.77284800_77284800dupA	ENSP00000345728:p.Gln990fs		B1AT72|O00227|O00745|Q9BYY8	Frame_Shift_Ins	INS	ENST00000341514.6	37	CCDS35339.1																																																																																				0.431	ATP7A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057306.1		NM_000052	
PHF7	51533	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52443574	52443574	+	5'Flank	SNP	G	G	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	G	A	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr3:52443574G>A	ENST00000327906.3	+	0	0				PHF7_ENST00000347025.2_5'Flank|BAP1_ENST00000460680.1_Nonsense_Mutation_p.Q40*|BAP1_ENST00000296288.5_Nonsense_Mutation_p.Q40*	NM_016483.4	NP_057567.3	Q9BWX1	PHF7_HUMAN	PHD finger protein 7							Golgi apparatus (GO:0005794)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	zinc ion binding (GO:0008270)	p.Q40*(2)		breast(2)|large_intestine(4)|lung(3)	9				BRCA - Breast invasive adenocarcinoma(193;1.71e-05)|Kidney(197;0.00178)|KIRC - Kidney renal clear cell carcinoma(197;0.00201)|OV - Ovarian serous cystadenocarcinoma(275;0.0275)		ACTCACCCCTGACATTTGCTC	0.582																																																	2	Substitution - Nonsense(2)	kidney(1)|pleura(1)											218.0	228.0	224.0					3																	52443574		2203	4300	6503	SO:0001631	upstream_gene_variant	8314			AY014283	CCDS2854.1, CCDS2855.1	3p21.31	2013-01-28			ENSG00000010318	ENSG00000010318		"""Zinc fingers, PHD-type"""	18458	protein-coding gene	gene with protein product						11042152, 11829468	Standard	NM_016483		Approved	NYD-SP6, HSPC226	uc003ddy.3	Q9BWX1	OTTHUMG00000158495		3.37:g.52443574G>A	Exception_encountered		K4DI82	Nonsense_Mutation	SNP	ENST00000327906.3	37	CCDS2854.1	.	.	.	.	.	.	.	.	.	.	G	34	5.352033	0.95830	.	.	ENSG00000163930	ENST00000460680;ENST00000296288	.	.	.	4.97	4.97	0.65823	.	0.114511	0.64402	D	0.000010	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.06099	T	0.92	.	18.2399	0.89963	0.0:0.0:1.0:0.0	.	.	.	.	X	40	.	ENSP00000296288:Q40X	Q	-	1	0	BAP1	52418614	1.000000	0.71417	1.000000	0.80357	0.979000	0.70002	7.607000	0.82883	2.312000	0.78011	0.655000	0.94253	CAG		0.582	PHF7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000351155.1		NM_016483	
BCAS3	54828	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	58786584	58786584	+	Silent	SNP	A	A	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr17:58786584A>T	ENST00000390652.5	+	5	250	c.219A>T	c.(217-219)acA>acT	p.T73T	BCAS3_ENST00000588462.1_Silent_p.T73T|BCAS3_ENST00000589222.1_Silent_p.T73T|BCAS3_ENST00000408905.3_Silent_p.T73T|BCAS3_ENST00000407086.3_Silent_p.T73T	NM_001099432.1	NP_001092902.1			breast carcinoma amplified sequence 3									p.T73T(1)		NS(1)|central_nervous_system(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(24)|ovary(3)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	44			BRCA - Breast invasive adenocarcinoma(1;3.11e-12)|Epithelial(12;8.2e-07)|all cancers(12;5.33e-06)			ATGCAGATACATCAAGAAATC	0.343																																																	1	Substitution - coding silent(1)	kidney(1)											102.0	87.0	92.0					17																	58786584		1849	4093	5942	SO:0001819	synonymous_variant	54828			AF361219	CCDS11626.1, CCDS45749.1	17q23.2	2013-06-25			ENSG00000141376	ENSG00000141376		"""WD repeat domain containing"""	14347	protein-coding gene	gene with protein product		607470				12378525	Standard	NM_017679		Approved	FLJ20128	uc002iyv.4	Q9H6U6	OTTHUMG00000180064	ENST00000390652.5:c.219A>T	17.37:g.58786584A>T				Silent	SNP	ENST00000390652.5	37	CCDS45749.1																																																																																				0.343	BCAS3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000449578.1		NM_017679	
BMP7	655	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	55803435	55803435	+	Missense_Mutation	SNP	C	C	A	rs535214572		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr20:55803435C>A	ENST00000395863.3	-	2	966	c.461G>T	c.(460-462)cGa>cTa	p.R154L	BMP7_ENST00000395864.3_Missense_Mutation_p.R154L|BMP7_ENST00000450594.2_Missense_Mutation_p.R154L	NM_001719.2	NP_001710.1	P18075	BMP7_HUMAN	bone morphogenetic protein 7	154					axon guidance (GO:0007411)|BMP signaling pathway (GO:0030509)|branching involved in salivary gland morphogenesis (GO:0060445)|branching morphogenesis of an epithelial tube (GO:0048754)|cartilage development (GO:0051216)|cellular response to hypoxia (GO:0071456)|dendrite development (GO:0016358)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic limb morphogenesis (GO:0030326)|embryonic pattern specification (GO:0009880)|embryonic skeletal joint morphogenesis (GO:0060272)|epithelial cell differentiation (GO:0030855)|epithelial to mesenchymal transition (GO:0001837)|extracellular matrix organization (GO:0030198)|growth (GO:0040007)|mesenchymal cell differentiation (GO:0048762)|mesenchyme development (GO:0060485)|mesoderm formation (GO:0001707)|mesonephros development (GO:0001823)|metanephric mesenchymal cell proliferation involved in metanephros development (GO:0072136)|metanephric mesenchyme morphogenesis (GO:0072133)|metanephros development (GO:0001656)|monocyte aggregation (GO:0070487)|negative regulation of cell cycle (GO:0045786)|negative regulation of cell death (GO:0060548)|negative regulation of glomerular mesangial cell proliferation (GO:0072125)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of mesenchymal cell apoptotic process involved in nephron morphogenesis (GO:0072040)|negative regulation of mitosis (GO:0045839)|negative regulation of neurogenesis (GO:0050768)|negative regulation of neuron differentiation (GO:0045665)|negative regulation of NF-kappaB import into nucleus (GO:0042347)|negative regulation of NF-kappaB transcription factor activity (GO:0032088)|negative regulation of Notch signaling pathway (GO:0045746)|negative regulation of phosphorylation (GO:0042326)|negative regulation of prostatic bud formation (GO:0060686)|negative regulation of striated muscle cell apoptotic process (GO:0010664)|negative regulation of transcription, DNA-templated (GO:0045892)|nephrogenic mesenchyme morphogenesis (GO:0072134)|neuron projection morphogenesis (GO:0048812)|odontogenesis of dentin-containing tooth (GO:0042475)|ossification (GO:0001503)|positive regulation of apoptotic process (GO:0043065)|positive regulation of bone mineralization (GO:0030501)|positive regulation of dendrite development (GO:1900006)|positive regulation of heterotypic cell-cell adhesion (GO:0034116)|positive regulation of hyaluranon cable assembly (GO:1900106)|positive regulation of neuron differentiation (GO:0045666)|positive regulation of osteoblast differentiation (GO:0045669)|positive regulation of pathway-restricted SMAD protein phosphorylation (GO:0010862)|positive regulation of peptidyl-threonine phosphorylation (GO:0010800)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|protein localization to nucleus (GO:0034504)|regulation of branching involved in prostate gland morphogenesis (GO:0060687)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|regulation of removal of superoxide radicals (GO:2000121)|response to estradiol (GO:0032355)|response to peptide hormone (GO:0043434)|response to vitamin D (GO:0033280)|skeletal system development (GO:0001501)|SMAD protein signal transduction (GO:0060395)|steroid hormone mediated signaling pathway (GO:0043401)|ureteric bud development (GO:0001657)	extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|membrane-bounded vesicle (GO:0031988)	heparin binding (GO:0008201)	p.R154L(1)		endometrium(4)|kidney(1)|large_intestine(7)|lung(6)|prostate(1)|skin(1)	20	all_lung(29;0.0133)|Melanoma(10;0.242)		BRCA - Breast invasive adenocarcinoma(4;2.49e-13)|Epithelial(14;1.74e-08)|all cancers(14;2.05e-07)			CCGGAACTCTCGATGGTGGTA	0.512																																																	1	Substitution - Missense(1)	kidney(1)											168.0	165.0	166.0					20																	55803435		2203	4300	6503	SO:0001583	missense	655				CCDS13455.1	20q13	2014-01-30	2008-05-22		ENSG00000101144	ENSG00000101144		"""Bone morphogenetic proteins"", ""Endogenous ligands"""	1074	protein-coding gene	gene with protein product	"""osteogenic protein 1"""	112267				1427904	Standard	NM_001719		Approved	OP-1	uc010gip.1	P18075	OTTHUMG00000032812	ENST00000395863.3:c.461G>T	20.37:g.55803435C>A	ENSP00000379204:p.Arg154Leu		Q9H512|Q9NTQ7	Missense_Mutation	SNP	ENST00000395863.3	37	CCDS13455.1	.	.	.	.	.	.	.	.	.	.	C	25.7	4.662083	0.88251	.	.	ENSG00000101144	ENST00000395863;ENST00000395864;ENST00000450594	T;T;T	0.64618	-0.11;-0.11;-0.11	5.33	5.33	0.75918	Transforming growth factor-beta, N-terminal (1);	0.049704	0.85682	D	0.000000	T	0.69115	0.3075	L	0.49513	1.565	0.80722	D	1	P;P;P	0.46512	0.76;0.59;0.879	B;B;P	0.53593	0.193;0.258;0.73	T	0.62353	-0.6872	10	0.20519	T	0.43	.	19.3842	0.94550	0.0:1.0:0.0:0.0	.	154;154;154	B1AKZ9;P18075;B1AL00	.;BMP7_HUMAN;.	L	154	ENSP00000379204:R154L;ENSP00000379205:R154L;ENSP00000398687:R154L	ENSP00000379204:R154L	R	-	2	0	BMP7	55236842	0.949000	0.32298	0.979000	0.43373	0.941000	0.58515	2.281000	0.43452	2.644000	0.89710	0.655000	0.94253	CGA		0.512	BMP7-001	KNOWN	basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000079831.2			
BTNL9	153579	broad.mit.edu;hgsc.bcm.edu	37	5	180475150	180475150	+	Silent	SNP	C	C	T	rs112433732		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr5:180475150C>T	ENST00000327705.9	+	3	564	c.333C>T	c.(331-333)atC>atT	p.I111I	BTNL9_ENST00000376842.3_Silent_p.I111I|BTNL9_ENST00000515271.1_Silent_p.I42I|BTNL9_ENST00000376841.2_Silent_p.I111I	NM_152547.4	NP_689760.2	Q6UXG8	BTNL9_HUMAN	butyrophilin-like 9	111	Ig-like V-type.					integral component of membrane (GO:0016021)		p.I111I(1)		breast(2)|central_nervous_system(1)|kidney(4)|large_intestine(1)|lung(10)|ovary(1)	19	all_cancers(89;2.45e-05)|all_epithelial(37;3.77e-06)|Renal(175;0.000159)|Lung NSC(126;0.00211)|all_lung(126;0.00371)|Breast(19;0.114)	all_cancers(40;0.0801)|Medulloblastoma(196;0.0392)|all_neural(177;0.0529)|all_hematologic(541;0.191)	Kidney(164;2.23e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000178)			AGGACGACATCGCCTATGGCA	0.587																																																	1	Substitution - coding silent(1)	kidney(1)						C		0,4406		0,0,2203	74.0	61.0	65.0		333	-4.3	0.0	5	dbSNP_132	65	2,8596	2.2+/-6.3	0,2,4297	no	coding-synonymous	BTNL9	NM_152547.4		0,2,6500	TT,TC,CC		0.0233,0.0,0.0154		111/536	180475150	2,13002	2203	4299	6502	SO:0001819	synonymous_variant	153579			AK057097	CCDS4460.2	5q35.3	2014-01-14			ENSG00000165810	ENSG00000165810		"""Immunoglobulin superfamily / V-set domain containing"", ""Butyrophilins"""	24176	protein-coding gene	gene with protein product							Standard	NM_152547		Approved	FLJ32535, BTN8	uc003mmt.3	Q6UXG8	OTTHUMG00000133152	ENST00000327705.9:c.333C>T	5.37:g.180475150C>T			A6NL42|Q6P660|Q96DM5	Silent	SNP	ENST00000327705.9	37	CCDS4460.2																																																																																				0.587	BTNL9-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000157342.3		NM_152547	
CACNA1C	775	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	2778099	2778099	+	Splice_Site	SNP	C	C	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr12:2778099C>T	ENST00000347598.4	+	40	4768	c.4768C>T	c.(4768-4770)Cgc>Tgc	p.R1590C	CACNA1C-AS2_ENST00000545526.1_RNA|CACNA1C_ENST00000399641.1_Splice_Site_p.R1542C|CACNA1C_ENST00000399638.1_Splice_Site_p.R1570C|CACNA1C_ENST00000399649.1_Splice_Site_p.R1529C|CACNA1C_ENST00000399603.1_Splice_Site_p.R1542C|CACNA1C_ENST00000399634.1_Splice_Site_p.R1542C|CACNA1C_ENST00000399629.1_Splice_Site_p.R1559C|CACNA1C_ENST00000399655.1_Splice_Site_p.R1542C|CACNA1C_ENST00000399621.1_Splice_Site_p.R1542C|CACNA1C_ENST00000406454.3_Splice_Site_p.R1542C|CACNA1C_ENST00000399595.1_Splice_Site_p.R1531C|CACNA1C_ENST00000402845.3_Splice_Site_p.R1542C|CACNA1C_ENST00000327702.7_Splice_Site_p.R1542C|CACNA1C_ENST00000399597.1_Splice_Site_p.R1542C|CACNA1C_ENST00000344100.3_Splice_Site_p.R1564C|CACNA1C_ENST00000399637.1_Splice_Site_p.R1542C|CACNA1C_ENST00000399617.1_Splice_Site_p.R1542C|CACNA1C_ENST00000399644.1_Splice_Site_p.R1542C|CACNA1C_ENST00000399601.1_Splice_Site_p.R1542C|CACNA1C_ENST00000335762.5_Splice_Site_p.R1567C|CACNA1C_ENST00000399591.1_Splice_Site_p.R1531C|CACNA1C_ENST00000399606.1_Splice_Site_p.R1562C	NM_001129827.1|NM_199460.2	NP_001123299.1|NP_955630.2	Q13936	CAC1C_HUMAN	calcium channel, voltage-dependent, L type, alpha 1C subunit	1590					adult walking behavior (GO:0007628)|axon guidance (GO:0007411)|calcium ion import (GO:0070509)|calcium ion transport into cytosol (GO:0060402)|calcium ion-dependent exocytosis (GO:0017156)|calcium-mediated signaling using extracellular calcium source (GO:0035585)|cell communication by electrical coupling involved in cardiac conduction (GO:0086064)|energy reserve metabolic process (GO:0006112)|glucose homeostasis (GO:0042593)|growth hormone secretion (GO:0030252)|insulin secretion (GO:0030073)|membrane depolarization during action potential (GO:0086010)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|regulation of blood pressure (GO:0008217)|regulation of cardiac muscle contraction by regulation of the release of sequestered calcium ion (GO:0010881)|regulation of insulin secretion (GO:0050796)|regulation of organ growth (GO:0046620)|regulation of vasoconstriction (GO:0019229)|small molecule metabolic process (GO:0044281)|smooth muscle contraction involved in micturition (GO:0060083)|synaptic transmission (GO:0007268)|visual learning (GO:0008542)	caveolar macromolecular signaling complex (GO:0002095)|cytoplasm (GO:0005737)|dendritic shaft (GO:0043198)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)|postsynaptic density (GO:0014069)|voltage-gated calcium channel complex (GO:0005891)|Z disc (GO:0030018)	alpha-actinin binding (GO:0051393)|calmodulin binding (GO:0005516)|high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|voltage-gated calcium channel activity (GO:0005245)	p.R1590C(1)|p.R1564C(1)|p.R1077C(1)|p.R1542C(1)|p.R1620C(1)		NS(3)|breast(4)|central_nervous_system(4)|cervix(2)|endometrium(12)|kidney(9)|large_intestine(20)|lung(55)|ovary(10)|pancreas(1)|prostate(5)|skin(3)|upper_aerodigestive_tract(4)	132			OV - Ovarian serous cystadenocarcinoma(31;0.00256)	LUAD - Lung adenocarcinoma(1;0.134)	Amlodipine(DB00381)|Cinnarizine(DB00568)|Clevidipine(DB04920)|Dronedarone(DB04855)|Drotaverine(DB06751)|Felodipine(DB01023)|Ibutilide(DB00308)|Isradipine(DB00270)|Magnesium Sulfate(DB00653)|Nicardipine(DB00622)|Nifedipine(DB01115)|Nilvadipine(DB06712)|Nimodipine(DB00393)|Nisoldipine(DB00401)|Nitrendipine(DB01054)|Spironolactone(DB00421)|Verapamil(DB00661)	TCGCCTGCAGCGCCTGGTCTC	0.572																																																	5	Substitution - Missense(5)	kidney(5)											95.0	96.0	96.0					12																	2778099		2197	4298	6495	SO:0001630	splice_region_variant	775			AF070589	CCDS44787.1, CCDS44788.1, CCDS44789.1, CCDS44790.1, CCDS44791.1, CCDS44792.1, CCDS44793.1, CCDS44794.1, CCDS44795.1, CCDS44796.1, CCDS44797.1, CCDS44798.1, CCDS44799.1, CCDS44800.1, CCDS44801.1, CCDS53733.1, CCDS53734.1, CCDS53735.1, CCDS53736.1	12p13.3	2014-09-17			ENSG00000151067	ENSG00000151067		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1390	protein-coding gene	gene with protein product		114205		CCHL1A1, CACNL1A1		1650913, 16382099	Standard	NM_001129832		Approved	Cav1.2, CACH2, CACN2, TS, LQT8	uc001qjy.3	Q13936	OTTHUMG00000150243	ENST00000347598.4:c.4768-1C>T	12.37:g.2778099C>T			B2RUT3|E9PDJ0|Q13917|Q13918|Q13919|Q13920|Q13921|Q13922|Q13923|Q13924|Q13925|Q13926|Q13927|Q13928|Q13929|Q13930|Q13932|Q13933|Q14743|Q14744|Q15877|Q4VMI7|Q4VMI8|Q4VMI9|Q6PKM7|Q8N6C0|Q99025|Q99241|Q99875	Missense_Mutation	SNP	ENST00000347598.4	37	CCDS44788.1	.	.	.	.	.	.	.	.	.	.	C	20.9	4.065211	0.76187	.	.	ENSG00000151067	ENST00000335762;ENST00000399655;ENST00000399644;ENST00000399638;ENST00000399597;ENST00000399621;ENST00000399637;ENST00000399591;ENST00000399641;ENST00000347598;ENST00000399606;ENST00000399601;ENST00000344100;ENST00000399629;ENST00000327702;ENST00000399649;ENST00000402845;ENST00000399603;ENST00000399634;ENST00000399617;ENST00000406454;ENST00000399595;ENST00000322367	D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D;D	0.97016	-4.15;-4.14;-4.13;-4.15;-4.14;-4.17;-4.06;-4.09;-4.14;-4.08;-4.06;-4.14;-4.2;-4.07;-3.98;-4.21;-4.16;-4.14;-4.15;-4.08;-4.15;-4.2	3.71	3.71	0.42584	.	0.000000	0.85682	D	0.000000	D	0.98223	0.9412	M	0.88906	2.99	0.80722	D	1	D;D;D;D;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;D;D;D;D;D;D	0.89917	1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;1.0;0.999;1.0;1.0;0.946;1.0;1.0;1.0;1.0;1.0;1.0;0.998;1.0;1.0;1.0;1.0;1.0	D;D;D;D;D;D;D;D;D;D;D;D;P;D;D;D;D;D;D;P;D;D;D;D;D	0.91635	0.996;0.995;0.998;0.998;0.997;0.999;0.998;0.999;0.999;0.977;0.999;0.998;0.532;0.999;0.993;0.998;0.995;0.998;0.999;0.854;0.998;0.999;0.999;0.999;0.998	D	0.98951	1.0794	9	.	.	.	.	16.106	0.81223	0.0:1.0:0.0:0.0	.	233;1564;1539;1590;1542;1542;1542;1559;1570;1542;1562;1542;1502;1590;1542;1542;1542;1531;1529;1531;1531;1542;1542;1542;1542	B7Z7Z5;Q13936-14;Q13936-35;Q13936;Q13936-33;Q13936-13;Q13936-22;Q13936-32;Q13936-31;Q13936-21;Q13936-30;Q13936-23;Q13936-28;Q13936-11;E9PDJ1;E9PDJ0;F5GY28;Q13936-25;Q13936-15;Q13936-29;Q13936-19;Q13936-24;Q13936-27;Q13936-20;Q13936-12	.;.;.;CAC1C_HUMAN;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.;.	C	1567;1542;1542;1570;1542;1542;1542;1531;1542;1590;1562;1542;1564;1559;1542;1529;1542;1542;1542;1542;1542;1531;1372	ENSP00000336982:R1567C;ENSP00000382563:R1542C;ENSP00000382552:R1542C;ENSP00000382547:R1570C;ENSP00000382506:R1542C;ENSP00000382530:R1542C;ENSP00000382546:R1542C;ENSP00000382500:R1531C;ENSP00000382549:R1542C;ENSP00000266376:R1590C;ENSP00000382515:R1562C;ENSP00000382510:R1542C;ENSP00000341092:R1564C;ENSP00000382537:R1559C;ENSP00000329877:R1542C;ENSP00000382557:R1529C;ENSP00000385724:R1542C;ENSP00000382512:R1542C;ENSP00000382542:R1542C;ENSP00000382526:R1542C;ENSP00000385896:R1542C;ENSP00000382504:R1531C	.	R	+	1	0	CACNA1C	2648360	1.000000	0.71417	1.000000	0.80357	0.958000	0.62258	5.754000	0.68743	2.083000	0.62718	0.552000	0.68991	CGC		0.572	CACNA1C-017	KNOWN	non_canonical_conserved|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000317035.1		NM_000719	Missense_Mutation
CACNA1G	8913	hgsc.bcm.edu	37	17	48692787	48692788	+	Frame_Shift_Ins	INS	-	-	CC	rs200825775	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr17:48692787_48692788insCC	ENST00000359106.5	+	27	4825_4826	c.4825_4826insCC	c.(4825-4827)accfs	p.T1609fs	CACNA1G_ENST00000507510.2_Frame_Shift_Ins_p.T1609fs|CACNA1G_ENST00000515765.1_Frame_Shift_Ins_p.T1598fs|CACNA1G_ENST00000515411.1_Frame_Shift_Ins_p.T1591fs|CACNA1G_ENST00000515165.1_Frame_Shift_Ins_p.T1609fs|CACNA1G_ENST00000358244.5_Frame_Shift_Ins_p.T1575fs|CACNA1G_ENST00000502264.1_Frame_Shift_Ins_p.T1586fs|CACNA1G_ENST00000510366.1_Frame_Shift_Ins_p.T1557fs|CACNA1G_ENST00000513964.1_Frame_Shift_Ins_p.T1564fs|CACNA1G_ENST00000514717.1_Frame_Shift_Ins_p.T1552fs|CACNA1G_ENST00000352832.5_Frame_Shift_Ins_p.T1575fs|CACNA1G_ENST00000429973.2_Frame_Shift_Ins_p.T1591fs|CACNA1G_ENST00000514181.1_Frame_Shift_Ins_p.T1591fs|CACNA1G_ENST00000503485.1_Frame_Shift_Ins_p.T1575fs|CACNA1G_ENST00000514079.1_Frame_Shift_Ins_p.T1616fs|CACNA1G_ENST00000442258.2_Frame_Shift_Ins_p.T1568fs|CACNA1G_ENST00000507609.1_Frame_Shift_Ins_p.T1609fs|CACNA1G_ENST00000505165.1_Frame_Shift_Ins_p.T1609fs|CACNA1G_ENST00000513689.2_Frame_Shift_Ins_p.T1564fs|CACNA1G_ENST00000360761.4_Frame_Shift_Ins_p.T1586fs|CACNA1G_ENST00000510115.1_Frame_Shift_Ins_p.T1575fs|CACNA1G_ENST00000507896.1_Frame_Shift_Ins_p.T1598fs|CACNA1G_ENST00000507336.1_Frame_Shift_Ins_p.T1598fs|CACNA1G_ENST00000512389.1_Frame_Shift_Ins_p.T1598fs|CACNA1G_ENST00000354983.4_Frame_Shift_Ins_p.T1575fs	NM_018896.4	NP_061496.2	O43497	CAC1G_HUMAN	calcium channel, voltage-dependent, T type, alpha 1G subunit	1609					axon guidance (GO:0007411)|calcium ion import (GO:0070509)|membrane depolarization during action potential (GO:0086010)|positive regulation of calcium ion-dependent exocytosis (GO:0045956)|regulation of atrial cardiac muscle cell membrane depolarization (GO:0060371)|regulation of heart rate (GO:0002027)|regulation of membrane potential (GO:0042391)|response to nickel cation (GO:0010045)|synaptic transmission (GO:0007268)|transport (GO:0006810)	plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	low voltage-gated calcium channel activity (GO:0008332)|scaffold protein binding (GO:0097110)			breast(5)|cervix(1)|endometrium(13)|kidney(5)|lung(23)	47	Breast(11;6.7e-17)		BRCA - Breast invasive adenocarcinoma(22;7.52e-09)		Cinnarizine(DB00568)|Ethosuximide(DB00593)|Flunarizine(DB04841)|Methsuximide(DB05246)|Spironolactone(DB00421)|Trimethadione(DB00347)|Verapamil(DB00661)|Zonisamide(DB00909)	CCACTTGTGCACCAGCCACTAC	0.599																																																	0																																										SO:0001589	frameshift_variant	8913			AC004590	CCDS45730.1, CCDS45731.1, CCDS45732.1, CCDS45733.1, CCDS45734.1, CCDS45735.1, CCDS45736.1, CCDS45737.1, CCDS54142.1, CCDS54143.1, CCDS54144.1, CCDS54145.1, CCDS54146.1, CCDS58565.1, CCDS58566.1, CCDS58567.1, CCDS58568.1, CCDS58569.1, CCDS58570.1, CCDS58571.1, CCDS58572.1, CCDS58573.1, CCDS58574.1, CCDS58575.1, CCDS58576.1	17q22	2012-03-07	2007-02-16		ENSG00000006283	ENSG00000006283		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1394	protein-coding gene	gene with protein product		604065				9495342, 16382099	Standard	NM_001256334		Approved	Cav3.1, NBR13	uc002irk.2	O43497	OTTHUMG00000162180	ENST00000359106.5:c.4826_4827dupCC	17.37:g.48692788_48692789dupCC	ENSP00000352011:p.Thr1609fs		D6RA64|E7EPR0|O43498|O94770|Q19QY8|Q19QY9|Q19QZ0|Q19QZ1|Q19QZ2|Q19QZ3|Q19QZ4|Q19QZ5|Q19QZ6|Q19QZ7|Q19QZ8|Q19QZ9|Q19R00|Q19R01|Q19R02|Q19R03|Q19R04|Q19R05|Q19R06|Q19R07|Q19R08|Q19R09|Q19R10|Q19R11|Q19R12|Q19R13|Q19R15|Q19R16|Q19R17|Q19R18|Q2TAC4|Q9NYU4|Q9NYU5|Q9NYU6|Q9NYU7|Q9NYU8|Q9NYU9|Q9NYV0|Q9NYV1|Q9UHN9|Q9UHP0|Q9ULU6|Q9UNG7|Q9Y5T2|Q9Y5T3	Frame_Shift_Ins	INS	ENST00000359106.5	37	CCDS45730.1																																																																																				0.599	CACNA1G-013	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000367895.1		NM_018896	
CAPN11	11131	hgsc.bcm.edu	37	6	44140054	44140055	+	Frame_Shift_Ins	INS	-	-	GGCTGCC	rs397947482|rs57288791|rs111320370	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr6:44140054_44140055insGGCTGCC	ENST00000398776.1	+	5	463_464	c.425_426insGGCTGCC	c.(424-429)ctggctfs	p.-143fs	CAPN11_ENST00000542245.1_Frame_Shift_Ins_p.-143fs	NM_007058.3	NP_008989.2	Q9UMQ6	CAN11_HUMAN	calpain 11						proteolysis (GO:0006508)	acrosomal vesicle (GO:0001669)|cytoplasm (GO:0005737)	calcium ion binding (GO:0005509)|calcium-dependent cysteine-type endopeptidase activity (GO:0004198)|peptidase activity (GO:0008233)			breast(3)|endometrium(5)|kidney(1)|large_intestine(5)|lung(17)|ovary(1)|pancreas(1)|prostate(2)|stomach(1)	36	all_cancers(18;3.19e-06)|Lung NSC(15;0.00108)|all_lung(25;0.00278)|Hepatocellular(11;0.00908)|Ovarian(13;0.0273)		Colorectal(64;0.00337)|COAD - Colon adenocarcinoma(64;0.00536)			TGCTGGCTGCTGGCTGCCATCG	0.584											OREG0017466	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)		330	0.0658946	0.1256	0.0519	5008	,	,		15212	0.0		0.0736	False		,,,				2504	0.0552																0										348,3260		52,244,1508						4.1	1.0		dbSNP_134	14	387,7195		36,315,3440	yes	frameshift	CAPN11	NM_007058.3		88,559,4948	A1A1,A1R,RR		5.1042,9.6452,6.5684				735,10455				SO:0001589	frameshift_variant	11131			AJ242832	CCDS47436.1	6p12	2013-01-10			ENSG00000137225	ENSG00000137225		"""EF-hand domain containing"""	1478	protein-coding gene	gene with protein product		604822				10409436	Standard	NM_007058		Approved		uc003owt.1	Q9UMQ6	OTTHUMG00000014758	ENST00000398776.1:c.426_432dupGGCTGCC	6.37:g.44140055_44140061dupGGCTGCC	ENSP00000381758:p.Ala143fs	921	B2RA64|Q5T3G1|Q8N4R5	Frame_Shift_Ins	INS	ENST00000398776.1	37	CCDS47436.1																																																																																				0.584	CAPN11-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000040714.3			
CD86	942	broad.mit.edu;ucsc.edu	37	3	121825286	121825286	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr3:121825286G>C	ENST00000330540.2	+	4	758	c.642G>C	c.(640-642)atG>atC	p.M214I	CD86_ENST00000493101.1_Missense_Mutation_p.M102I|CD86_ENST00000264468.5_Intron|CD86_ENST00000393627.2_Missense_Mutation_p.M208I|CD86_ENST00000469710.1_Missense_Mutation_p.M132I	NM_175862.4	NP_787058	P42081	CD86_HUMAN	CD86 molecule	214	Ig-like C2-type.				aging (GO:0007568)|B cell activation (GO:0042113)|cell-cell signaling (GO:0007267)|cellular response to cytokine stimulus (GO:0071345)|cellular response to lipopolysaccharide (GO:0071222)|cellular response to metal ion (GO:0071248)|defense response to virus (GO:0051607)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|immune response (GO:0006955)|innate immune response (GO:0045087)|myeloid dendritic cell differentiation (GO:0043011)|negative regulation of T cell anergy (GO:0002668)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of activated T cell proliferation (GO:0042104)|positive regulation of cell proliferation (GO:0008284)|positive regulation of interleukin-2 biosynthetic process (GO:0045086)|positive regulation of interleukin-4 biosynthetic process (GO:0045404)|positive regulation of lymphotoxin A biosynthetic process (GO:0043017)|positive regulation of T-helper 2 cell differentiation (GO:0045630)|positive regulation of transcription, DNA-templated (GO:0045893)|response to drug (GO:0042493)|response to interferon-gamma (GO:0034341)|response to yeast (GO:0001878)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)|T cell proliferation involved in immune response (GO:0002309)|toll-like receptor signaling pathway (GO:0002224)|viral process (GO:0016032)	cell surface (GO:0009986)|external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|plasma membrane (GO:0005886)	coreceptor activity (GO:0015026)|receptor activity (GO:0004872)	p.M214I(1)		breast(2)|endometrium(1)|kidney(1)|lung(11)|ovary(2)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(3)	23				GBM - Glioblastoma multiforme(114;0.156)	Abatacept(DB01281)|Antithymocyte globulin(DB00098)|Belatacept(DB06681)	CGAGCAATATGACCATCTTCT	0.393																																					GBM(67;1379 1389 36064 39806)												1	Substitution - Missense(1)	kidney(1)											202.0	184.0	190.0					3																	121825286		2203	4300	6503	SO:0001583	missense	942				CCDS3009.1, CCDS43138.1, CCDS56272.1, CCDS56273.1, CCDS74991.1	3q21	2013-01-29	2006-03-28		ENSG00000114013	ENSG00000114013		"""CD molecules"", ""Immunoglobulin superfamily / V-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	1705	protein-coding gene	gene with protein product	"""B-lymphocyte antigen B7-2"""	601020	"""CD86 antigen (CD28 antigen ligand 2, B7-2 antigen)"""	CD28LG2		7513726	Standard	NM_006889		Approved	B7.2, B7-2	uc003eet.3	P42081	OTTHUMG00000159482	ENST00000330540.2:c.642G>C	3.37:g.121825286G>C	ENSP00000332049:p.Met214Ile		A0N0P0|B7Z2F3|B7Z702|E7ETN5|E9PC27|Q13655|Q6FHB1|Q6GTS4|Q7M4L5	Missense_Mutation	SNP	ENST00000330540.2	37	CCDS3009.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	8.146|8.146	0.786378|0.786378	0.16189|0.16189	.|.	.|.	ENSG00000114013|ENSG00000114013	ENST00000478741|ENST00000469710;ENST00000493101;ENST00000330540;ENST00000393627	.|T;T;T;T	.|0.12984	.|2.69;2.63;2.69;2.69	5.65|5.65	-1.04|-1.04	0.10068|0.10068	.|.	.|1.570610	.|0.03359	.|N	.|0.197348	T|T	0.07369|0.07369	0.0186|0.0186	N|N	0.20685|0.20685	0.6|0.6	0.20764|0.20764	N|N	0.999859|0.999859	.|B;B	.|0.22541	.|0.038;0.071	.|B;B	.|0.18871	.|0.014;0.023	T|T	0.27640|0.27640	-1.0068|-1.0068	5|10	.|0.18710	.|T	.|0.47	-0.5257|-0.5257	0.5646|0.5646	0.00685|0.00685	0.2446:0.1316:0.328:0.2958|0.2446:0.1316:0.328:0.2958	.|.	.|102;214	.|E9PC27;P42081	.|.;CD86_HUMAN	H|I	210|132;102;214;208	.|ENSP00000418988:M132I;ENSP00000420230:M102I;ENSP00000332049:M214I;ENSP00000377248:M208I	.|ENSP00000332049:M214I	D|M	+|+	1|3	0|0	CD86|CD86	123307976|123307976	0.036000|0.036000	0.19791|0.19791	0.001000|0.001000	0.08648|0.08648	0.033000|0.033000	0.12548|0.12548	0.354000|0.354000	0.20146|0.20146	-0.047000|-0.047000	0.13423|0.13423	-0.181000|-0.181000	0.13052|0.13052	GAC|ATG		0.393	CD86-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000355671.1		NM_006889	
CECR2	27443	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	17978494	17978494	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr22:17978494G>T	ENST00000400573.5	+	4	399	c.392G>T	c.(391-393)gGg>gTg	p.G131V	CECR2_ENST00000262608.8_Missense_Mutation_p.G112V|CECR2_ENST00000400585.2_5'UTR|CECR2_ENST00000342247.5_Missense_Mutation_p.G111V			Q9BXF3	CECR2_HUMAN	cat eye syndrome chromosome region, candidate 2	153					apoptotic DNA fragmentation (GO:0006309)|ATP-dependent chromatin remodeling (GO:0043044)|cytokinesis (GO:0000910)|cytoskeleton organization (GO:0007010)|execution phase of apoptosis (GO:0097194)|neural tube development (GO:0021915)|vesicle-mediated transport (GO:0016192)	CERF complex (GO:0090537)|nucleus (GO:0005634)		p.G131V(2)		NS(1)|breast(2)|central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(11)|lung(22)|ovary(1)|pancreas(1)|prostate(2)|skin(5)|stomach(1)|urinary_tract(1)	59		all_epithelial(15;0.139)		Lung(27;0.146)		GACAATTCTGGGGCACTATAT	0.488																																																	2	Substitution - Missense(2)	lung(1)|kidney(1)											94.0	90.0	91.0					22																	17978494		1866	4110	5976	SO:0001583	missense	27443			AF336133		22q11.2	2012-04-19			ENSG00000099954	ENSG00000099954			1840	protein-coding gene	gene with protein product		607576				11381032	Standard	XM_006724077		Approved	KIAA1740	uc002zml.2	Q9BXF3	OTTHUMG00000150072	ENST00000400573.5:c.392G>T	22.37:g.17978494G>T	ENSP00000383417:p.Gly131Val		A8MS90|A8MX16|Q658Z4|Q96P58|Q9C0C3	Missense_Mutation	SNP	ENST00000400573.5	37		.	.	.	.	.	.	.	.	.	.	G	31	5.076467	0.94000	.	.	ENSG00000099954	ENST00000342247;ENST00000400573;ENST00000262608	T;T;T	0.48201	0.82;0.82;0.82	6.01	6.01	0.97437	.	0.000000	0.36591	U	0.002510	T	0.73187	0.3555	M	0.81112	2.525	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.74671	-0.3587	10	0.87932	D	0	-13.9556	20.5141	0.99211	0.0:0.0:1.0:0.0	.	153	Q9BXF3	CECR2_HUMAN	V	111;131;112	ENSP00000341219:G111V;ENSP00000383417:G131V;ENSP00000262608:G112V	ENSP00000262608:G112V	G	+	2	0	CECR2	16358494	1.000000	0.71417	0.926000	0.36857	0.874000	0.50279	9.381000	0.97205	2.850000	0.98022	0.655000	0.94253	GGG		0.488	CECR2-001	NOVEL	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000316104.5		NM_031413	
CLCA1	1179	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	86957042	86957042	+	Silent	SNP	G	G	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr1:86957042G>A	ENST00000234701.3	+	10	1803	c.1452G>A	c.(1450-1452)caG>caA	p.Q484Q	CLCA1_ENST00000394711.1_Silent_p.Q484Q			A8K7I4	CLCA1_HUMAN	chloride channel accessory 1	484					calcium ion transport (GO:0006816)|cellular response to hypoxia (GO:0071456)|chloride transmembrane transport (GO:1902476)|chloride transport (GO:0006821)|transport (GO:0006810)	extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)|microvillus (GO:0005902)|zymogen granule membrane (GO:0042589)	chloride channel activity (GO:0005254)	p.Q484Q(1)		NS(1)|breast(3)|endometrium(1)|kidney(3)|large_intestine(9)|lung(14)|ovary(2)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	38		Lung NSC(277;0.239)		all cancers(265;0.0249)|Epithelial(280;0.0476)		CTGTCTCTCAGCGCTCCATCC	0.388																																																	1	Substitution - coding silent(1)	kidney(1)											104.0	101.0	102.0					1																	86957042		2203	4300	6503	SO:0001819	synonymous_variant	1179				CCDS709.1	1p22.3	2012-02-26	2009-01-29		ENSG00000016490	ENSG00000016490			2015	protein-coding gene	gene with protein product		603906	"""chloride channel, calcium activated, family member 1"", ""chloride channel regulator 1"""			9828122	Standard	NM_001285		Approved	CaCC, CLCRG1	uc001dlt.3	A8K7I4	OTTHUMG00000010254	ENST00000234701.3:c.1452G>A	1.37:g.86957042G>A			B2RAV5|O95151|Q5TDF4|Q9UNF6|Q9UPC6	Silent	SNP	ENST00000234701.3	37	CCDS709.1																																																																																				0.388	CLCA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028277.1		NM_001285	
CNOT1	23019	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	58571103	58571106	+	Frame_Shift_Del	DEL	TACT	TACT	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	TACT	TACT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr16:58571103_58571106delTACT	ENST00000317147.5	-	39	5765_5768	c.5433_5436delAGTA	c.(5431-5436)gaagtafs	p.EV1811fs	CNOT1_ENST00000245138.4_Frame_Shift_Del_p.EV662fs|CNOT1_ENST00000569240.1_Frame_Shift_Del_p.EV1806fs	NM_001265612.1|NM_016284.4	NP_001252541.1|NP_057368.3	A5YKK6	CNOT1_HUMAN	CCR4-NOT transcription complex, subunit 1	1811					gene expression (GO:0010467)|gene silencing by RNA (GO:0031047)|mRNA metabolic process (GO:0016071)|negative regulation of intracellular estrogen receptor signaling pathway (GO:0033147)|negative regulation of retinoic acid receptor signaling pathway (GO:0048387)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:0000288)|nuclear-transcribed mRNA poly(A) tail shortening (GO:0000289)|positive regulation of cytoplasmic mRNA processing body assembly (GO:0010606)|positive regulation of nuclear-transcribed mRNA catabolic process, deadenylation-dependent decay (GO:1900153)|positive regulation of nuclear-transcribed mRNA poly(A) tail shortening (GO:0060213)|regulation of stem cell maintenance (GO:2000036)|regulation of translation (GO:0006417)|RNA metabolic process (GO:0016070)|RNA phosphodiester bond hydrolysis, exonucleolytic (GO:0090503)|transcription, DNA-templated (GO:0006351)|trophectodermal cell differentiation (GO:0001829)	CCR4-NOT complex (GO:0030014)|cytoplasmic mRNA processing body (GO:0000932)|cytosol (GO:0005829)|extracellular space (GO:0005615)|membrane (GO:0016020)|nucleus (GO:0005634)|peroxisomal membrane (GO:0005778)	estrogen receptor binding (GO:0030331)|poly(A) RNA binding (GO:0044822)|retinoic acid receptor binding (GO:0042974)			breast(1)|central_nervous_system(2)|endometrium(9)|haematopoietic_and_lymphoid_tissue(4)|kidney(7)|large_intestine(24)|lung(25)|ovary(4)|prostate(6)|skin(3)|upper_aerodigestive_tract(2)	87				Kidney(780;0.0722)|OV - Ovarian serous cystadenocarcinoma(108;0.173)|Epithelial(162;0.239)		TGGATCGCACTACTTCCATCAGCT	0.422																																																	0																																										SO:0001589	frameshift_variant	23019			AL833549	CCDS10799.1, CCDS45501.1, CCDS58468.1	16q21	2008-02-05			ENSG00000125107	ENSG00000125107			7877	protein-coding gene	gene with protein product		604917		NOT1		14702039	Standard	NM_016284		Approved	CDC39, NOT1H, KIAA1007, AD-005	uc002env.4	A5YKK6	OTTHUMG00000133487	ENST00000317147.5:c.5433_5436delAGTA	16.37:g.58571103_58571106delTACT	ENSP00000320949:p.Glu1811fs		Q68DX7|Q7Z3K2|Q8IWB8|Q8TB53|Q9BVZ6|Q9UFR8|Q9UI27|Q9Y2L0	Frame_Shift_Del	DEL	ENST00000317147.5	37	CCDS10799.1																																																																																				0.422	CNOT1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257385.3		NM_016284	
COL14A1	7373	hgsc.bcm.edu;ucsc.edu	37	8	121259910	121259910	+	Silent	SNP	C	C	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	C	T	C	C	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr8:121259910C>T	ENST00000297848.3	+	21	2808	c.2538C>T	c.(2536-2538)cgC>cgT	p.R846R	COL14A1_ENST00000247781.3_Silent_p.R751R|COL14A1_ENST00000432943.2_3'UTR|COL14A1_ENST00000309791.4_Silent_p.R846R	NM_021110.1	NP_066933.1			collagen, type XIV, alpha 1											NS(1)|autonomic_ganglia(1)|breast(11)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(9)|large_intestine(31)|lung(42)|ovary(5)|pancreas(1)|prostate(1)|skin(8)|stomach(2)|upper_aerodigestive_tract(2)	119	Lung NSC(37;6.52e-07)|Ovarian(258;0.00769)|Hepatocellular(40;0.161)		OV - Ovarian serous cystadenocarcinoma(1;6.47e-38)|STAD - Stomach adenocarcinoma(47;0.00503)			ACCGGTTGCGCATTACGTGGG	0.458																																																	0													108.0	96.0	100.0					8																	121259910		2203	4300	6503	SO:0001819	synonymous_variant	7373				CCDS34938.1	8q23	2013-02-11	2008-02-04		ENSG00000187955	ENSG00000187955		"""Collagens"", ""Fibronectin type III domain containing"""	2191	protein-coding gene	gene with protein product		120324	"""undulin"""	UND		1716629, 9427527	Standard	NM_021110		Approved		uc003yox.4	Q05707	OTTHUMG00000149877	ENST00000297848.3:c.2538C>T	8.37:g.121259910C>T				Silent	SNP	ENST00000297848.3	37	CCDS34938.1																																																																																				0.458	COL14A1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000313657.2		NM_021110	
COL22A1	169044	hgsc.bcm.edu	37	8	139824126	139824127	+	In_Frame_Ins	INS	-	-	GGTGGA	rs548885226	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr8:139824126_139824127insGGTGGA	ENST00000303045.6	-	9	1810_1811	c.1364_1365insTCCACC	c.(1363-1365)ccc>ccTCCACCc	p.455_455P>PPP	COL22A1_ENST00000435777.1_In_Frame_Ins_p.455_455P>PPP	NM_152888.1	NP_690848.1	Q8NFW1	COMA1_HUMAN	collagen, type XXII, alpha 1	455	Pro-rich.				extracellular matrix organization (GO:0030198)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|proteinaceous extracellular matrix (GO:0005578)				breast(1)|endometrium(10)|haematopoietic_and_lymphoid_tissue(2)|kidney(14)|large_intestine(29)|lung(107)|ovary(13)|pancreas(1)|prostate(3)|skin(12)|upper_aerodigestive_tract(15)|urinary_tract(4)	211	all_epithelial(106;1.55e-12)|Lung NSC(106;1.67e-05)|all_lung(105;3.39e-05)|Ovarian(258;0.00672)|Acute lymphoblastic leukemia(118;0.155)		BRCA - Breast invasive adenocarcinoma(115;0.0517)			GCTGGGGTGGGGGTGGAGGTGG	0.599										HNSCC(7;0.00092)				22	0.00439297	0.0008	0.013	5008	,	,		8677	0.0		0.0119	False		,,,				2504	0.0																0										10,4142		2,6,2068						-2.7	0.0			16	104,7944		5,94,3925	no	coding	COL22A1	NM_152888.1		7,100,5993	A1A1,A1R,RR		1.2922,0.2408,0.9344				114,12086				SO:0001652	inframe_insertion	169044			AF406780	CCDS6376.1	8q24.3	2013-01-16			ENSG00000169436	ENSG00000169436		"""Collagens"""	22989	protein-coding gene	gene with protein product		610026					Standard	NM_152888		Approved		uc003yvd.3	Q8NFW1	OTTHUMG00000150035	ENST00000303045.6:c.1359_1364dupTCCACC	8.37:g.139824127_139824132dupGGTGGA	ENSP00000303153:p.ProPro457dup		B7ZMH0|C9K0G4|Q8IVT9	In_Frame_Ins	INS	ENST00000303045.6	37	CCDS6376.1																																																																																				0.599	COL22A1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000315905.2		XM_291257	
COL4A5	1287	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	107924995	107924995	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chrX:107924995C>T	ENST00000361603.2	+	45	4319	c.4075C>T	c.(4075-4077)Cct>Tct	p.P1359S	COL4A5_ENST00000328300.6_Missense_Mutation_p.P1365S	NM_000495.4	NP_000486.1	P29400	CO4A5_HUMAN	collagen, type IV, alpha 5	1359	Triple-helical region.				axon guidance (GO:0007411)|collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|neuromuscular junction development (GO:0007528)	basal lamina (GO:0005605)|collagen type IV trimer (GO:0005587)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|neuromuscular junction (GO:0031594)	extracellular matrix structural constituent (GO:0005201)	p.P1359S(2)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(25)|lung(32)|ovary(4)|prostate(2)|skin(8)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(1)	99						CATAGGTCCTCCTGGATTACC	0.463									Alport syndrome with Diffuse Leiomyomatosis																																								2	Substitution - Missense(2)	breast(1)|kidney(1)											133.0	118.0	123.0					X																	107924995		2203	4300	6503	SO:0001583	missense	1287	Familial Cancer Database		M90464	CCDS14543.1, CCDS35366.1	Xq22	2014-09-17	2008-07-28		ENSG00000188153	ENSG00000188153		"""Collagens"""	2207	protein-coding gene	gene with protein product		303630	"""Alport syndrome"""	ASLN, ATS			Standard	NM_000495		Approved		uc004enz.2	P29400	OTTHUMG00000022182	ENST00000361603.2:c.4075C>T	X.37:g.107924995C>T	ENSP00000354505:p.Pro1359Ser		Q16006|Q16126|Q6LD84|Q7Z700|Q9NUB7	Missense_Mutation	SNP	ENST00000361603.2	37	CCDS14543.1	.	.	.	.	.	.	.	.	.	.	C	18.15	3.559496	0.65538	.	.	ENSG00000188153	ENST00000328300;ENST00000361603;ENST00000508186	D;D	0.93019	-3.15;-3.15	4.86	4.86	0.63082	.	0.000000	0.85682	D	0.000000	D	0.96408	0.8828	M	0.75884	2.315	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.91635	0.999;0.994	D	0.96571	0.9423	10	0.52906	T	0.07	.	17.4297	0.87536	0.0:1.0:0.0:0.0	.	1362;1359	E7EVY4;P29400	.;CO4A5_HUMAN	S	1365;1359;1365	ENSP00000331902:P1365S;ENSP00000354505:P1359S	ENSP00000331902:P1365S	P	+	1	0	COL4A5	107811651	1.000000	0.71417	1.000000	0.80357	0.939000	0.58152	6.772000	0.75001	2.128000	0.65567	0.506000	0.49869	CCT		0.463	COL4A5-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000057880.2			
DENND1C	79958	broad.mit.edu;ucsc.edu	37	19	6467951	6467951	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr19:6467951G>C	ENST00000381480.2	-	23	2082	c.1970C>G	c.(1969-1971)tCc>tGc	p.S657C	DENND1C_ENST00000543576.1_Missense_Mutation_p.S613C	NM_024898.2	NP_079174.2	Q8IV53	DEN1C_HUMAN	DENN/MADD domain containing 1C	657					positive regulation of Rab GTPase activity (GO:0032851)	cytoplasmic vesicle (GO:0031410)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)	p.S683C(1)|p.S657C(1)		endometrium(3)|kidney(3)|large_intestine(1)|lung(3)	10						AGCTGTTGAGGACTGGGATGG	0.557																																																	2	Substitution - Missense(2)	kidney(2)											52.0	54.0	53.0					19																	6467951		2017	4162	6179	SO:0001583	missense	79958			AL713770	CCDS45938.1	19p13.3	2014-02-06	2005-08-17	2005-08-17	ENSG00000205744	ENSG00000205744		"""DENN/MADD domain containing"""	26225	protein-coding gene	gene with protein product		613634	"""family with sequence similarity 31, member C"""	FAM31C		12477932	Standard	XM_005259646		Approved	FLJ22757	uc002mfe.3	Q8IV53	OTTHUMG00000180853	ENST00000381480.2:c.1970C>G	19.37:g.6467951G>C	ENSP00000370889:p.Ser657Cys		B4E051|D3PFD4|Q8NDB1|Q9H5Z2	Missense_Mutation	SNP	ENST00000381480.2	37	CCDS45938.1	.	.	.	.	.	.	.	.	.	.	G	10.43	1.347062	0.24426	.	.	ENSG00000205744	ENST00000381480;ENST00000543576	T;T	0.10573	3.03;2.86	4.18	-0.718	0.11205	.	24.883700	0.00166	N	0.000000	T	0.09335	0.0230	L	0.27053	0.805	0.09310	N	1	B	0.28512	0.214	B	0.25405	0.06	T	0.35724	-0.9777	10	0.62326	D	0.03	0.1265	7.4608	0.27294	0.365:0.0:0.635:0.0	.	657	Q8IV53	DEN1C_HUMAN	C	657;613	ENSP00000370889:S657C;ENSP00000437805:S613C	ENSP00000370889:S657C	S	-	2	0	DENND1C	6418951	0.000000	0.05858	0.000000	0.03702	0.027000	0.11550	0.149000	0.16243	-0.216000	0.10048	0.298000	0.19748	TCC		0.557	DENND1C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000453332.2		NM_024898	
DYSF	8291	broad.mit.edu	37	2	71801334	71801335	+	In_Frame_Ins	INS	-	-	AGGCGG	rs398123779|rs373644336|rs202034789	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr2:71801334_71801335insAGGCGG	ENST00000258104.3	+	30	3458_3459	c.3181_3182insAGGCGG	c.(3181-3183)cag>cAGGCGGag	p.1065_1066insAE	DYSF_ENST00000410020.3_In_Frame_Ins_p.1083_1084insAE|DYSF_ENST00000413539.2_In_Frame_Ins_p.1096_1097insAE|DYSF_ENST00000409366.1_In_Frame_Ins_p.1066_1067insAE|DYSF_ENST00000394120.2_In_Frame_Ins_p.1066_1067insAE|DYSF_ENST00000429174.2_In_Frame_Ins_p.1065_1066insAE|DYSF_ENST00000409582.3_In_Frame_Ins_p.1082_1083insAE|DYSF_ENST00000409651.1_In_Frame_Ins_p.1097_1098insAE|DYSF_ENST00000409762.1_In_Frame_Ins_p.1082_1083insAE|DYSF_ENST00000410041.1_In_Frame_Ins_p.1083_1084insAE|DYSF_ENST00000409744.1_In_Frame_Ins_p.1052_1053insAE	NM_001130976.1|NM_003494.3	NP_001124448.1|NP_003485.1	O75923	DYSF_HUMAN	dysferlin	1065	Arg-rich.		E -> EAE. {ECO:0000269|PubMed:16996541}.		plasma membrane repair (GO:0001778)|vesicle fusion (GO:0006906)	cytoplasmic vesicle (GO:0031410)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|lamellipodium (GO:0030027)|plasma membrane (GO:0005886)|sarcolemma (GO:0042383)|T-tubule (GO:0030315)	calcium ion binding (GO:0005509)|calcium-dependent phospholipid binding (GO:0005544)|phospholipid binding (GO:0005543)			autonomic_ganglia(2)|breast(3)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(22)|lung(57)|ovary(3)|pancreas(1)|prostate(2)|skin(6)|upper_aerodigestive_tract(3)|urinary_tract(2)	111						GCAGCACAGGCAGGCGGAGGCG	0.639														113	0.0225639	0.0008	0.049	5008	,	,		19492	0.0		0.0596	False		,,,				2504	0.0184																0									,,,,,,,,,,,,,	64,4110		3,58,2026					,,,,,,,,,,,,,	4.6	1.0			53	453,7697		31,391,3653	no	coding,coding,coding,coding,coding,coding,coding,coding,coding,coding,coding,coding,coding,coding	DYSF	NM_003494.3,NM_001130987.1,NM_001130986.1,NM_001130985.1,NM_001130984.1,NM_001130983.1,NM_001130982.1,NM_001130981.1,NM_001130980.1,NM_001130979.1,NM_001130978.1,NM_001130977.1,NM_001130976.1,NM_001130455.1	,,,,,,,,,,,,,	34,449,5679	A1A1,A1R,RR		5.5583,1.5333,4.1951	,,,,,,,,,,,,,	,,,,,,,,,,,,,		517,11807				SO:0001652	inframe_insertion	8291			AF075575	CCDS1918.1, CCDS46323.1, CCDS46324.1, CCDS46325.1, CCDS46326.1, CCDS46327.1, CCDS46328.1, CCDS46329.1, CCDS46330.1, CCDS46331.1, CCDS46332.1	2p13.3	2014-09-17	2013-09-12		ENSG00000135636	ENSG00000135636			3097	protein-coding gene	gene with protein product	"""fer-1-like family member 1"""	603009	"""limb girdle muscular dystrophy 2B (autosomal recessive)"""	LGMD2B		8320700	Standard	NM_003494		Approved	FER1L1	uc010fen.3	O75923	OTTHUMG00000129757	ENST00000258104.3:c.3188_3193dupAGGCGG	2.37:g.71801335_71801340dupAGGCGG	ENSP00000258104:p.Ala1064_Glu1065dup		A0FK00|B1PZ70|B1PZ71|B1PZ72|B1PZ73|B1PZ74|B1PZ75|B1PZ76|B1PZ77|B1PZ78|B1PZ79|B1PZ80|B1PZ81|B3KQB9|O75696|Q09EX5|Q0H395|Q53QY3|Q53TD2|Q8TEL8|Q9UEN7	In_Frame_Ins	INS	ENST00000258104.3	37	CCDS1918.1																																																																																				0.639	DYSF-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000251970.3		NM_003494	
DPP4	1803	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	162894910	162894910	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr2:162894910A>C	ENST00000360534.3	-	8	1075	c.515T>G	c.(514-516)aTt>aGt	p.I172S		NM_001935.3	NP_001926.2	P27487	DPP4_HUMAN	dipeptidyl-peptidase 4	172					cell adhesion (GO:0007155)|endothelial cell migration (GO:0043542)|negative regulation of extracellular matrix disassembly (GO:0010716)|positive regulation of cell proliferation (GO:0008284)|regulation of cell-cell adhesion mediated by integrin (GO:0033632)|response to hypoxia (GO:0001666)|T cell activation (GO:0042110)|T cell costimulation (GO:0031295)	apical plasma membrane (GO:0016324)|cell surface (GO:0009986)|endocytic vesicle (GO:0030139)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intercellular canaliculus (GO:0046581)|invadopodium membrane (GO:0071438)|lamellipodium (GO:0030027)|lysosomal membrane (GO:0005765)|membrane (GO:0016020)|plasma membrane (GO:0005886)	dipeptidyl-peptidase activity (GO:0008239)|identical protein binding (GO:0042802)|protease binding (GO:0002020)|protein homodimerization activity (GO:0042803)|receptor binding (GO:0005102)|serine-type endopeptidase activity (GO:0004252)|serine-type peptidase activity (GO:0008236)	p.I172S(1)		breast(3)|central_nervous_system(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|liver(1)|lung(21)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	48					Alogliptin(DB06203)|Atorvastatin(DB01076)|Linagliptin(DB08882)|Liraglutide(DB06655)|Saxagliptin(DB06335)|Sitagliptin(DB01261)|Vildagliptin(DB04876)	TTTAACATAAATGTCATTGTT	0.303																																																	1	Substitution - Missense(1)	kidney(1)											61.0	60.0	60.0					2																	162894910		2201	4284	6485	SO:0001583	missense	1803			M74777	CCDS2216.1	2q24.2	2013-09-19	2008-08-01		ENSG00000197635	ENSG00000197635	3.4.14.5	"""CD molecules"""	3009	protein-coding gene	gene with protein product		102720	"""dipeptidylpeptidase IV (CD26, adenosine deaminase complexing protein 2)"", ""adenosine deaminase complexing protein 2"""	CD26, ADCP2		8101391	Standard	NM_001935		Approved	DPPIV	uc002ubz.3	P27487	OTTHUMG00000132056	ENST00000360534.3:c.515T>G	2.37:g.162894910A>C	ENSP00000353731:p.Ile172Ser		Q53TN1	Missense_Mutation	SNP	ENST00000360534.3	37	CCDS2216.1	.	.	.	.	.	.	.	.	.	.	A	25.9	4.686706	0.88639	.	.	ENSG00000197635	ENST00000360534	T	0.37752	1.18	6.03	6.03	0.97812	Peptidase S9B, dipeptidylpeptidase IV N-terminal (1);	0.613796	0.17661	N	0.166325	T	0.68238	0.2979	M	0.90309	3.105	0.80722	D	1	D	0.63880	0.993	D	0.72338	0.977	T	0.74278	-0.3717	10	0.87932	D	0	-6.6896	16.2458	0.82445	1.0:0.0:0.0:0.0	.	172	P27487	DPP4_HUMAN	S	172	ENSP00000353731:I172S	ENSP00000353731:I172S	I	-	2	0	DPP4	162603156	1.000000	0.71417	0.999000	0.59377	0.993000	0.82548	7.725000	0.84808	2.313000	0.78055	0.455000	0.32223	ATT		0.303	DPP4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255079.2			
EPHB6	2051	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	142563846	142563846	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr7:142563846G>T	ENST00000392957.2	+	9	2021	c.1234G>T	c.(1234-1236)Ggc>Tgc	p.G412C	EPHB6_ENST00000411471.2_Missense_Mutation_p.G135C|EPHB6_ENST00000442129.1_Missense_Mutation_p.G412C	NM_004445.3	NP_004436.3	O15197	EPHB6_HUMAN	EPH receptor B6	412	Fibronectin type-III 1. {ECO:0000255|PROSITE-ProRule:PRU00316}.					extracellular region (GO:0005576)|integral component of plasma membrane (GO:0005887)	ATP binding (GO:0005524)|ephrin receptor activity (GO:0005003)|receptor activity (GO:0004872)	p.G397C(1)		NS(1)|breast(1)|central_nervous_system(4)|cervix(1)|endometrium(5)|kidney(4)|large_intestine(9)|lung(46)|ovary(2)|pancreas(2)|prostate(1)|skin(9)|stomach(1)|upper_aerodigestive_tract(1)	87	Melanoma(164;0.059)					GGAGTGTGAAGGCCGCCAGGA	0.642																																																	1	Substitution - Missense(1)	kidney(1)											37.0	32.0	34.0					7																	142563846		2203	4299	6502	SO:0001583	missense	2051			D83492	CCDS5873.2, CCDS75672.1	7q33-q35	2013-02-11	2004-10-28		ENSG00000106123	ENSG00000106123		"""EPH receptors"", ""Sterile alpha motif (SAM) domain containing"", ""Fibronectin type III domain containing"""	3396	protein-coding gene	gene with protein product		602757	"""EphB6"""				Standard	XM_006715881		Approved	HEP	uc011kst.2	O15197	OTTHUMG00000155707	ENST00000392957.2:c.1234G>T	7.37:g.142563846G>T	ENSP00000376684:p.Gly412Cys		A4D2I7|A8CDT5|D3DXD3|Q2TB23|Q2TB24	Missense_Mutation	SNP	ENST00000392957.2	37	CCDS5873.2	.	.	.	.	.	.	.	.	.	.	G	12.76	2.033367	0.35893	.	.	ENSG00000106123	ENST00000392957;ENST00000442129;ENST00000411471	T;T;T	0.59638	0.25;0.25;0.25	5.25	4.37	0.52481	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.505173	0.16953	N	0.192781	T	0.65616	0.2708	L	0.54323	1.7	0.09310	N	1	D	0.61080	0.989	P	0.59546	0.859	T	0.56111	-0.8033	10	0.49607	T	0.09	.	9.7619	0.40537	0.096:0.0:0.904:0.0	.	412	O15197	EPHB6_HUMAN	C	412;412;135	ENSP00000376684:G412C;ENSP00000410789:G412C;ENSP00000409061:G135C	ENSP00000376684:G412C	G	+	1	0	EPHB6	142273968	0.462000	0.25791	0.003000	0.11579	0.340000	0.28889	0.923000	0.28757	1.201000	0.43203	0.462000	0.41574	GGC		0.642	EPHB6-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000341329.1			
ETV6	2120	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	11905414	11905414	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr12:11905414A>T	ENST00000396373.4	+	2	338	c.64A>T	c.(64-66)Agc>Tgc	p.S22C	ETV6_ENST00000544715.1_3'UTR	NM_001987.4	NP_001978.1	P41212	ETV6_HUMAN	ets variant 6	22					cell differentiation (GO:0030154)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleolus (GO:0005730)	protein domain specific binding (GO:0019904)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II 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)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.S22C(1)	ETV6/JAK2(11)|ETV6/ITPR2(2)|ETV6/NTRK3(238)	breast(3)|endometrium(1)|haematopoietic_and_lymphoid_tissue(15)|kidney(1)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|skin(3)|upper_aerodigestive_tract(2)|urinary_tract(1)	45		all_cancers(2;1.88e-12)|Acute lymphoblastic leukemia(2;6.91e-39)|all_hematologic(2;2.7e-36)				ACCTCCAGAGAGCCCAGTGCC	0.547			T	"""NTRK3, RUNX1, PDGFRB, ABL1, MN1, ABL2, FACL6, CHIC2, ARNT, JAK2, EVI1, CDX2, STL, HLXB9, MDS2, PER1, SYK, TTL, FGFR3, PAX5"""	"""congenital fibrosarcoma, multiple leukemia and lymphoma,  secretory breast, MDS, ALL"""																																			Dom	yes		12	12p13	2120	ets variant gene 6 (TEL oncogene)		"""L, E, M"""	1	Substitution - Missense(1)	kidney(1)											90.0	84.0	86.0					12																	11905414		2203	4300	6503	SO:0001583	missense	2120			BC043399	CCDS8643.1	12p13	2014-09-17	2008-09-12		ENSG00000139083	ENSG00000139083			3495	protein-coding gene	gene with protein product	"""TEL oncogene"""	600618	"""ets variant gene 6 (TEL oncogene)"""			7731705	Standard	NM_001987		Approved	TEL	uc001qzz.3	P41212	OTTHUMG00000168538	ENST00000396373.4:c.64A>T	12.37:g.11905414A>T	ENSP00000379658:p.Ser22Cys		A3QVP6|A8K076|Q9UMF6|Q9UMF7|Q9UMG0	Missense_Mutation	SNP	ENST00000396373.4	37	CCDS8643.1	.	.	.	.	.	.	.	.	.	.	A	27.3	4.818856	0.90873	.	.	ENSG00000139083	ENST00000396373	T	0.09723	2.95	5.73	5.73	0.89815	Sterile alpha motif/pointed domain (1);	0.143629	0.64402	D	0.000008	T	0.10252	0.0251	L	0.29908	0.895	0.47476	D	0.999437	B	0.24963	0.115	B	0.17098	0.017	T	0.07385	-1.0775	10	0.52906	T	0.07	.	15.6788	0.77352	1.0:0.0:0.0:0.0	.	22	P41212	ETV6_HUMAN	C	22	ENSP00000379658:S22C	ENSP00000379658:S22C	S	+	1	0	ETV6	11796681	1.000000	0.71417	1.000000	0.80357	0.985000	0.73830	6.384000	0.73177	2.186000	0.69663	0.533000	0.62120	AGC		0.547	ETV6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000400130.2		NM_001987	
FAM47A	158724	hgsc.bcm.edu	37	X	34149658	34149693	+	In_Frame_Del	DEL	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	-	rs367563899|rs201090915|rs201363312|rs373732464		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chrX:34149658_34149693delATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ENST00000346193.3	-	1	754_789	c.703_738delCTCCGCCCGGAGCCTCCAGAGACTGGAGTGTCCCAT	c.(703-738)ctccgcccggagcctccagagactggagtgtcccatdel	p.LRPEPPETGVSH235del		NM_203408.3	NP_981953.2	Q5JRC9	FA47A_HUMAN	family with sequence similarity 47, member A	235	Pro-rich.							p.L235_H246delLRPEPPETGVSH(1)|p.P240P(1)		NS(1)|biliary_tract(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(5)|large_intestine(17)|lung(44)|ovary(5)|prostate(2)|skin(4)|upper_aerodigestive_tract(4)|urinary_tract(2)	97						CCGGGCGGATATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAGATGGGACACT	0.627														5	0.0013245	0.0	0.0	3775	,	,		15035	0.0		0.004	False		,,,				2504	0.001																2	Substitution - coding silent(1)|Deletion - In frame(1)	ovary(1)|lung(1)								33,3667		0,20,13,1562,523						-0.3	0.0			32	98,6373		2,62,32,2290,1731	no	coding	FAM47A	NM_203408.3		2,82,45,3852,2254	A1A1,A1R,A1,RR,R		1.5144,0.8919,1.288				131,10040				SO:0001651	inframe_deletion	158724			BC026171	CCDS43926.1	Xp21.1	2004-08-09			ENSG00000185448	ENSG00000185448			29962	protein-coding gene	gene with protein product	"""similar to hypothetical protein FLJ35782"""					12477932	Standard	NM_203408		Approved	MGC27003	uc004ddg.3	Q5JRC9	OTTHUMG00000021339	ENST00000346193.3:c.703_738delCTCCGCCCGGAGCCTCCAGAGACTGGAGTGTCCCAT	X.37:g.34149658_34149693delATGGGACACTCCAGTCTCTGGAGGCTCCGGGCGGAG	ENSP00000345029:p.Leu235_His246del		A8K8I9|Q8TAA0	In_Frame_Del	DEL	ENST00000346193.3	37	CCDS43926.1																																																																																				0.627	FAM47A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056205.1		NM_203408	
GAREM	64762	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	29867878	29867878	+	Missense_Mutation	SNP	G	G	C	rs370225304		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr18:29867878G>C	ENST00000269209.6	-	4	685	c.682C>G	c.(682-684)Cag>Gag	p.Q228E	RP11-344B2.2_ENST00000579580.1_RNA|GAREM_ENST00000578619.1_5'UTR|GAREM_ENST00000399218.4_Missense_Mutation_p.Q228E			Q9H706	GAREM_HUMAN	GRB2 associated, regulator of MAPK1	228	CABIT.				cellular response to epidermal growth factor stimulus (GO:0071364)|epidermal growth factor receptor signaling pathway (GO:0007173)|positive regulation of cell division (GO:0051781)|positive regulation of cell proliferation (GO:0008284)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)	plasma membrane (GO:0005886)	proline-rich region binding (GO:0070064)	p.Q228E(1)									TCTTGCATCTGAAGTTCCAGG	0.517																																																	1	Substitution - Missense(1)	kidney(1)						G	GLU/GLN,GLU/GLN	1,4405	2.1+/-5.4	0,1,2202	138.0	117.0	124.0		682,682	5.7	1.0	18		124	0,8600		0,0,4300	no	missense,missense	FAM59A	NM_001242409.1,NM_022751.2	29,29	0,1,6502	CC,CG,GG		0.0,0.0227,0.0077	benign,benign	228/877,228/876	29867878	1,13005	2203	4300	6503	SO:0001583	missense	0			AK025263	CCDS11905.1, CCDS56057.1	18q12.1	2012-11-30	2012-11-30	2012-11-30	ENSG00000141441	ENSG00000141441			26136	protein-coding gene	gene with protein product	"""Grb2-associated and regulator of Erk/MAPK"""		"""chromosome 18 open reading frame 11"", ""family with sequence similarity 59, member A"""	C18orf11, FAM59A		19509291	Standard	NM_001242409		Approved	FLJ21610	uc002kxl.3	Q9H706	OTTHUMG00000132273	ENST00000269209.6:c.682C>G	18.37:g.29867878G>C	ENSP00000269209:p.Gln228Glu		Q0VAG3|Q0VAG4|Q8ND03|Q9BSF5	Missense_Mutation	SNP	ENST00000269209.6	37	CCDS56057.1	.	.	.	.	.	.	.	.	.	.	G	24.6	4.549955	0.86127	2.27E-4	0.0	ENSG00000141441	ENST00000399218;ENST00000269209	T;T	0.15139	2.45;2.45	5.67	5.67	0.87782	.	0.000000	0.85682	D	0.000000	T	0.40979	0.1139	L	0.55481	1.735	0.80722	D	1	D;D	0.63046	0.992;0.97	D;P	0.76071	0.987;0.798	T	0.06006	-1.0851	10	0.72032	D	0.01	-25.6247	20.1095	0.97908	0.0:0.0:1.0:0.0	.	228;228	Q9H706;Q9H706-3	FA59A_HUMAN;.	E	228	ENSP00000382165:Q228E;ENSP00000269209:Q228E	ENSP00000269209:Q228E	Q	-	1	0	FAM59A	28121876	1.000000	0.71417	0.998000	0.56505	0.996000	0.88848	9.357000	0.97099	2.831000	0.97527	0.655000	0.94253	CAG		0.517	GAREM-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000255365.1		NM_022751	
FMN2	56776	hgsc.bcm.edu	37	1	240371112	240371112	+	Silent	SNP	G	G	T	rs71646889	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr1:240371112G>T	ENST00000319653.9	+	5	3230	c.3000G>T	c.(2998-3000)ccG>ccT	p.P1000P		NM_020066.4	NP_064450.3	Q9NZ56	FMN2_HUMAN	formin 2	1000	FH1.|Pro-rich.				cellular response to DNA damage stimulus (GO:0006974)|cellular response to hypoxia (GO:0071456)|establishment of meiotic spindle localization (GO:0051295)|formin-nucleated actin cable assembly (GO:0070649)|homologous chromosome movement towards spindle pole involved in homologous chromosome segregation (GO:0051758)|intracellular signal transduction (GO:0035556)|intracellular transport (GO:0046907)|multicellular organismal development (GO:0007275)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein catabolic process (GO:0042177)|oogenesis (GO:0048477)|polar body extrusion after meiotic divisions (GO:0040038)|protein transport (GO:0015031)|vesicle-mediated transport (GO:0016192)	cell cortex (GO:0005938)|cytoplasmic vesicle membrane (GO:0030659)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|microvillus (GO:0005902)|nucleolus (GO:0005730)|plasma membrane (GO:0005886)|spindle (GO:0005819)	actin binding (GO:0003779)	p.P1143P(1)		NS(1)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(10)|large_intestine(13)|lung(87)|ovary(6)|pancreas(3)|prostate(12)|skin(7)|stomach(2)|upper_aerodigestive_tract(6)|urinary_tract(2)	178	Ovarian(103;0.127)	all_cancers(173;0.013)	OV - Ovarian serous cystadenocarcinoma(106;0.0106)			TACCCCCTCCGCCCCCACTTC	0.716													G|||	1341	0.267772	0.357	0.1873	5008	,	,		4654	0.2927		0.2008	False		,,,				2504	0.2474																1	Substitution - coding silent(1)	prostate(1)											4.0	6.0	6.0					1																	240371112		1774	3850	5624	SO:0001819	synonymous_variant	56776			AF218942	CCDS31069.2	1q43	2008-02-05			ENSG00000155816	ENSG00000155816			14074	protein-coding gene	gene with protein product		606373				10781961	Standard	NM_020066		Approved		uc010pyd.2	Q9NZ56	OTTHUMG00000039883	ENST00000319653.9:c.3000G>T	1.37:g.240371112G>T			B0QZA7|B4DP05|Q59GF6|Q5VU37|Q9NZ55	Silent	SNP	ENST00000319653.9	37	CCDS31069.2																																																																																				0.716	FMN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096217.2		XM_371352	
GPR98	84059	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	89989763	89989763	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr5:89989763T>A	ENST00000405460.2	+	33	7286	c.7190T>A	c.(7189-7191)gTg>gAg	p.V2397E		NM_032119.3	NP_115495.3	Q8WXG9	GPR98_HUMAN	G protein-coupled receptor 98	2397					detection of mechanical stimulus involved in sensory perception of sound (GO:0050910)|G-protein coupled receptor signaling pathway (GO:0007186)|inner ear receptor stereocilium organization (GO:0060122)|maintenance of organ identity (GO:0048496)|nervous system development (GO:0007399)|neurological system process (GO:0050877)|neuropeptide signaling pathway (GO:0007218)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)|single organismal cell-cell adhesion (GO:0016337)|visual perception (GO:0007601)	cell surface (GO:0009986)|cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)|stereocilia ankle link complex (GO:0002142)	calcium ion binding (GO:0005509)|G-protein coupled receptor activity (GO:0004930)	p.V2397E(1)		NS(4)|breast(7)|central_nervous_system(6)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(3)|kidney(18)|large_intestine(46)|liver(2)|lung(80)|ovary(12)|pancreas(5)|prostate(1)|skin(50)|stomach(7)|upper_aerodigestive_tract(8)|urinary_tract(6)	269		all_cancers(142;1.05e-09)|all_epithelial(76;1.81e-12)|all_lung(232;5.41e-06)|Lung NSC(167;1.72e-05)|Ovarian(174;0.00948)|Colorectal(57;0.133)|Breast(839;0.192)		OV - Ovarian serous cystadenocarcinoma(54;7.01e-30)|Epithelial(54;6.79e-25)|all cancers(79;1.88e-20)		ATTGATGTAGTGGCTCTGGCA	0.448																																																	1	Substitution - Missense(1)	kidney(1)											68.0	65.0	66.0					5																	89989763		1903	4125	6028	SO:0001583	missense	84059			AB014586	CCDS47246.1	5q13	2014-08-08	2006-05-26	2006-05-26	ENSG00000164199	ENSG00000164199		"""-"", ""GPCR / Class B : Orphans"""	17416	protein-coding gene	gene with protein product		602851	"""monogenic, audiogenic seizure susceptibility 1 homolog (mouse)"""	USH2C, MASS1		10976914, 14740321	Standard	NM_032119		Approved	DKFZp761P0710, KIAA0686, FEB4, VLGR1b	uc003kju.3	Q8WXG9	OTTHUMG00000162668	ENST00000405460.2:c.7190T>A	5.37:g.89989763T>A	ENSP00000384582:p.Val2397Glu		O75171|Q8TF58|Q9H0X5|Q9UL61	Missense_Mutation	SNP	ENST00000405460.2	37	CCDS47246.1	.	.	.	.	.	.	.	.	.	.	T	21.7	4.193576	0.78902	.	.	ENSG00000164199	ENST00000405460;ENST00000296619	T	0.35605	1.3	6.08	6.08	0.98989	.	0.051301	0.85682	D	0.000000	T	0.47563	0.1452	M	0.69823	2.125	0.80722	D	1	D	0.54207	0.965	P	0.50082	0.63	T	0.52756	-0.8533	10	0.87932	D	0	.	11.6508	0.51288	0.0:0.0684:0.0:0.9316	.	2397	Q8WXG9	GPR98_HUMAN	E	2397	ENSP00000384582:V2397E	ENSP00000296619:V2397E	V	+	2	0	GPR98	90025519	1.000000	0.71417	1.000000	0.80357	0.959000	0.62525	6.101000	0.71479	2.333000	0.79357	0.482000	0.46254	GTG		0.448	GPR98-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000369993.2		NM_032119	
HECTD1	25831	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	31613394	31613394	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr14:31613394T>G	ENST00000399332.1	-	17	3189	c.2701A>C	c.(2701-2703)Aag>Cag	p.K901Q	RNU6-541P_ENST00000384709.1_RNA|HECTD1_ENST00000553700.1_Missense_Mutation_p.K901Q	NM_015382.2	NP_056197.2	Q9ULT8	HECD1_HUMAN	HECT domain containing E3 ubiquitin protein ligase 1	901					neural tube closure (GO:0001843)|protein ubiquitination involved in ubiquitin-dependent protein catabolic process (GO:0042787)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ligase activity (GO:0016874)|metal ion binding (GO:0046872)|ubiquitin-protein transferase activity (GO:0004842)	p.K901Q(1)		breast(10)|endometrium(7)|kidney(5)|large_intestine(12)|lung(23)|ovary(4)|prostate(3)|skin(1)|upper_aerodigestive_tract(2)|urinary_tract(3)	70	Hepatocellular(127;0.0877)|Breast(36;0.176)		LUAD - Lung adenocarcinoma(48;0.00292)|Lung(238;0.0164)|BRCA - Breast invasive adenocarcinoma(188;0.111)|STAD - Stomach adenocarcinoma(7;0.173)	GBM - Glioblastoma multiforme(265;0.00617)		TTTTCATCCTTCAAAAGTACA	0.313																																																	1	Substitution - Missense(1)	kidney(1)											46.0	45.0	45.0					14																	31613394		1823	4073	5896	SO:0001583	missense	25831			AB032957	CCDS41939.1	14q12	2013-01-10	2012-02-23		ENSG00000092148	ENSG00000092148		"""Ankyrin repeat domain containing"""	20157	protein-coding gene	gene with protein product			"""HECT domain containing 1"""			10574461	Standard	XM_005267502		Approved	KIAA1131	uc001wrc.1	Q9ULT8	OTTHUMG00000170670	ENST00000399332.1:c.2701A>C	14.37:g.31613394T>G	ENSP00000382269:p.Lys901Gln		D3DS86|Q6P445|Q86VJ1|Q96F34|Q9UFZ7	Missense_Mutation	SNP	ENST00000399332.1	37	CCDS41939.1	.	.	.	.	.	.	.	.	.	.	T	14.72	2.618888	0.46736	.	.	ENSG00000092148	ENST00000553700;ENST00000261312;ENST00000399332;ENST00000553957;ENST00000556224	T;T;T;T	0.65364	-0.15;-0.15;1.51;-0.15	5.66	5.66	0.87406	Armadillo-like helical (1);Armadillo-type fold (1);	0.000000	0.85682	U	0.000000	T	0.58308	0.2113	N	0.04959	-0.14	0.80722	D	1	B;D	0.57899	0.099;0.981	B;D	0.67231	0.019;0.95	T	0.58612	-0.7606	10	0.14656	T	0.56	-9.4393	15.8889	0.79276	0.0:0.0:0.0:1.0	.	901;901	D3DS86;Q9ULT8	.;HECD1_HUMAN	Q	901;901;901;375;901	ENSP00000450697:K901Q;ENSP00000382269:K901Q;ENSP00000451860:K375Q;ENSP00000452015:K901Q	ENSP00000261312:K901Q	K	-	1	0	HECTD1	30683145	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	8.036000	0.88901	2.143000	0.66587	0.533000	0.62120	AAG		0.313	HECTD1-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000409942.1			
HK2	3099	broad.mit.edu;ucsc.edu	37	2	75107668	75107668	+	Silent	SNP	C	C	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr2:75107668C>T	ENST00000290573.2	+	10	2142	c.1542C>T	c.(1540-1542)acC>acT	p.T514T	HK2_ENST00000409174.1_Silent_p.T486T	NM_000189.4	NP_000180.2	P52789	HXK2_HUMAN	hexokinase 2	514	Catalytic.|Hexokinase type-1 2.				apoptotic mitochondrial changes (GO:0008637)|carbohydrate metabolic process (GO:0005975)|cellular glucose homeostasis (GO:0001678)|glucose 6-phosphate metabolic process (GO:0051156)|glucose metabolic process (GO:0006006)|glucose transport (GO:0015758)|glycolytic process (GO:0006096)|hexose transport (GO:0008645)|lactation (GO:0007595)|regulation of glucose import (GO:0046324)|small molecule metabolic process (GO:0044281)|transmembrane transport (GO:0055085)	cytosol (GO:0005829)|membrane (GO:0016020)|mitochondrial outer membrane (GO:0005741)	ATP binding (GO:0005524)|fructokinase activity (GO:0008865)|glucokinase activity (GO:0004340)|glucose binding (GO:0005536)|hexokinase activity (GO:0004396)|mannokinase activity (GO:0019158)	p.T514T(1)		breast(2)|central_nervous_system(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(22)|ovary(2)|prostate(1)|skin(2)|stomach(1)|urinary_tract(1)	43						TGCTGCCCACCTACGTGTGTG	0.597																																																	1	Substitution - coding silent(1)	kidney(1)											65.0	64.0	65.0					2																	75107668		2203	4300	6503	SO:0001819	synonymous_variant	3099				CCDS1956.1	2p13	2010-03-19			ENSG00000159399	ENSG00000159399	2.7.1.1		4923	protein-coding gene	gene with protein product		601125					Standard	NM_000189		Approved		uc002snd.3	P52789	OTTHUMG00000129972	ENST00000290573.2:c.1542C>T	2.37:g.75107668C>T			D6W5J2|Q8WU87|Q9UN82	Silent	SNP	ENST00000290573.2	37	CCDS1956.1																																																																																				0.597	HK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252238.2		NM_000189	
CSF1R	1436	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	149431465	149431465	+	IGR	SNP	T	T	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr5:149431465T>A	ENST00000286301.3	-	0	3989				HMGXB3_ENST00000502717.1_Missense_Mutation_p.L1197M|HMGXB3_ENST00000503427.1_Missense_Mutation_p.L1165M	NM_005211.3	NP_005202.2	P07333	CSF1R_HUMAN	colony stimulating factor 1 receptor						cell proliferation (GO:0008283)|cell-cell junction maintenance (GO:0045217)|cellular response to cytokine stimulus (GO:0071345)|cellular response to macrophage colony-stimulating factor stimulus (GO:0036006)|cytokine-mediated signaling pathway (GO:0019221)|hemopoiesis (GO:0030097)|inflammatory response (GO:0006954)|innate immune response (GO:0045087)|macrophage differentiation (GO:0030225)|mammary gland duct morphogenesis (GO:0060603)|monocyte differentiation (GO:0030224)|multicellular organismal development (GO:0007275)|osteoclast differentiation (GO:0030316)|peptidyl-tyrosine phosphorylation (GO:0018108)|phosphatidylinositol metabolic process (GO:0046488)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of cell migration (GO:0030335)|positive regulation of cell motility (GO:2000147)|positive regulation of cell proliferation (GO:0008284)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of protein phosphorylation (GO:0001934)|positive regulation of protein serine/threonine kinase activity (GO:0071902)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of tyrosine phosphorylation of Stat3 protein (GO:0042517)|protein autophosphorylation (GO:0046777)|regulation of actin cytoskeleton reorganization (GO:2000249)|regulation of bone resorption (GO:0045124)|regulation of cell shape (GO:0008360)|ruffle organization (GO:0031529)|signal transduction (GO:0007165)|transmembrane receptor protein tyrosine kinase signaling pathway (GO:0007169)	cell surface (GO:0009986)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	ATP binding (GO:0005524)|cytokine binding (GO:0019955)|macrophage colony-stimulating factor receptor activity (GO:0005011)|protein homodimerization activity (GO:0042803)	p.L1443M(1)		NS(2)|breast(2)|central_nervous_system(3)|endometrium(3)|haematopoietic_and_lymphoid_tissue(38)|kidney(2)|large_intestine(6)|liver(3)|lung(23)|ovary(2)|pancreas(1)|prostate(3)|upper_aerodigestive_tract(2)|urinary_tract(3)	93			KIRC - Kidney renal clear cell carcinoma(527;0.000962)|Kidney(363;0.00147)		Imatinib(DB00619)|Sunitinib(DB01268)	GTGCCCTGAATTGGCACCTTA	0.602																																																	1	Substitution - Missense(1)	kidney(1)											108.0	106.0	106.0					5																	149431465		692	1591	2283	SO:0001628	intergenic_variant	22993			U63963	CCDS4302.1	5q32	2013-01-11	2008-08-01		ENSG00000182578	ENSG00000182578		"""CD molecules"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"""	2433	protein-coding gene	gene with protein product		164770	"""McDonough feline sarcoma viral (v-fms) oncogene homolog"""	FMS		1611909	Standard	NM_005211		Approved	C-FMS, CSFR, CD115	uc003lrm.3	P07333	OTTHUMG00000130050		5.37:g.149431465T>A			B5A955|D3DQG2|Q6LDW5|Q6LDY4|Q86VW7	Missense_Mutation	SNP	ENST00000286301.3	37	CCDS4302.1	.	.	.	.	.	.	.	.	.	.	T	18.02	3.530350	0.64860	.	.	ENSG00000113716	ENST00000503427;ENST00000502717	.	.	.	5.97	-2.5	0.06384	.	0.000000	0.85682	D	0.000000	T	0.75671	0.3881	M	0.68952	2.095	0.47862	D	0.999537	D	0.89917	1.0	D	0.91635	0.999	T	0.75584	-0.3267	9	0.87932	D	0	-9.4179	18.919	0.92518	0.0:0.8717:0.0:0.1283	.	1443	Q12766	HMGX3_HUMAN	M	1165;1197	.	ENSP00000421917:L1197M	L	+	1	2	HMGXB3	149411658	0.982000	0.34865	0.840000	0.33206	0.681000	0.39784	0.317000	0.19487	-1.033000	0.03299	-0.250000	0.11733	TTG		0.602	CSF1R-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252329.2		NM_005211	
HOOK2	29911	broad.mit.edu	37	19	12883813	12883813	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr19:12883813G>C	ENST00000397668.3	-	4	323	c.250C>G	c.(250-252)Cag>Gag	p.Q84E	HOOK2_ENST00000264827.5_Missense_Mutation_p.Q84E|HOOK2_ENST00000589965.1_Intron	NM_013312.2	NP_037444.2	Q96ED9	HOOK2_HUMAN	hook microtubule-tethering protein 2	84	Required for localization to the centrosome and induction of aggresome formation.|Sufficient for interaction with microtubules.				early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|endosome organization (GO:0007032)|endosome to lysosome transport (GO:0008333)|lysosome organization (GO:0007040)|protein transport (GO:0015031)	centrosome (GO:0005813)|FHF complex (GO:0070695)|microtubule (GO:0005874)	identical protein binding (GO:0042802)	p.Q84E(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|prostate(5)|skin(1)	20						CTCACATCCTGGGAGTACTCT	0.557																																																	1	Substitution - Missense(1)	kidney(1)											83.0	80.0	81.0					19																	12883813		1903	4106	6009	SO:0001583	missense	29911			AF044924	CCDS42507.1, CCDS42508.1	19p13.2	2013-08-21	2013-08-21						19885	protein-coding gene	gene with protein product		607824	"""hook homolog 2 (Drosophila)"""			9927460	Standard	NM_013312		Approved	HK2	uc002muy.2	Q96ED9		ENST00000397668.3:c.250C>G	19.37:g.12883813G>C	ENSP00000380785:p.Gln84Glu		O60562	Missense_Mutation	SNP	ENST00000397668.3	37	CCDS42508.1	.	.	.	.	.	.	.	.	.	.	G	13.44	2.237238	0.39498	.	.	ENSG00000095066	ENST00000397668;ENST00000264827	T;T	0.18174	2.23;2.23	3.66	2.57	0.30868	.	0.220521	0.38959	N	0.001511	T	0.20700	0.0498	M	0.74881	2.28	0.27900	N	0.939	B;B	0.29378	0.204;0.243	B;B	0.34452	0.073;0.183	T	0.17623	-1.0363	10	0.16420	T	0.52	-20.6551	10.943	0.47285	0.0:0.0:0.8034:0.1966	.	84;84	Q96ED9-2;Q96ED9	.;HOOK2_HUMAN	E	84	ENSP00000380785:Q84E;ENSP00000264827:Q84E	ENSP00000264827:Q84E	Q	-	1	0	HOOK2	12744813	1.000000	0.71417	0.987000	0.45799	0.884000	0.51177	4.659000	0.61504	0.555000	0.29079	0.555000	0.69702	CAG		0.557	HOOK2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000451008.1		NM_013312	
HTR1F	3355	hgsc.bcm.edu;ucsc.edu	37	3	88040822	88040823	+	Frame_Shift_Ins	INS	-	-	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr3:88040822_88040823insT	ENST00000319595.4	+	1	977_978	c.923_924insT	c.(922-927)ccttttfs	p.PF308fs		NM_000866.3	NP_000857.1	P30939	5HT1F_HUMAN	5-hydroxytryptamine (serotonin) receptor 1F, G protein-coupled	308	Agonist binding. {ECO:0000250}.				adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)			breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(4)|lung(12)|ovary(3)|skin(1)|upper_aerodigestive_tract(1)	25	all_cancers(8;0.147)	Lung NSC(201;0.0283)		LUSC - Lung squamous cell carcinoma(29;0.00353)|Lung(72;0.00664)	Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ergotamine(DB00696)|Ketamine(DB01221)|Methysergide(DB00247)|Mianserin(DB06148)|Naratriptan(DB00952)|Rizatriptan(DB00953)|Sumatriptan(DB00669)|Zolmitriptan(DB00315)	TGTTGGCTTCCTTTTTTTGTAA	0.371																																																	0																																										SO:0001589	frameshift_variant	3355			L05597	CCDS2920.1	3p12	2012-08-08	2012-02-03		ENSG00000179097	ENSG00000179097		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5292	protein-coding gene	gene with protein product		182134	"""5-hydroxytryptamine (serotonin) receptor 1F"""			8384716, 8380639	Standard	NM_000866		Approved	HTR1EL, 5-HT1F	uc003dqr.2	P30939	OTTHUMG00000159008	ENST00000319595.4:c.930dupT	3.37:g.88040829_88040829dupT	ENSP00000322924:p.Pro308fs			Frame_Shift_Ins	INS	ENST00000319595.4	37	CCDS2920.1																																																																																				0.371	HTR1F-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000352890.1		NM_000866	
IL33	90865	broad.mit.edu;ucsc.edu	37	9	6251225	6251225	+	Silent	SNP	C	C	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr9:6251225C>G	ENST00000381434.3	+	3	316	c.303C>G	c.(301-303)gtC>gtG	p.V101V	IL33_ENST00000456383.2_Silent_p.V101V|IL33_ENST00000417746.2_Intron	NM_033439.3	NP_254274.1	O95760	IL33_HUMAN	interleukin 33	101	Interaction with RELA. {ECO:0000250}.				extrinsic apoptotic signaling pathway (GO:0097191)|negative regulation of immunoglobulin secretion (GO:0051025)|negative regulation of interferon-gamma production (GO:0032689)|negative regulation of leukocyte migration (GO:0002686)|negative regulation of T-helper 1 type immune response (GO:0002826)|positive regulation of chemokine secretion (GO:0090197)|positive regulation of immunoglobulin secretion (GO:0051024)|positive regulation of inflammatory response (GO:0050729)|positive regulation of interleukin-13 production (GO:0032736)|positive regulation of interleukin-4 production (GO:0032753)|positive regulation of interleukin-5 production (GO:0032754)|positive regulation of interleukin-6 production (GO:0032755)|positive regulation of macrophage activation (GO:0043032)|positive regulation of proteasomal ubiquitin-dependent protein catabolic process (GO:0032436)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of type 2 immune response (GO:0002830)|transcription, DNA-templated (GO:0006351)	chromosome (GO:0005694)|cytoplasmic vesicle (GO:0031410)|extracellular space (GO:0005615)|nucleus (GO:0005634)	cytokine activity (GO:0005125)	p.V101V(1)		breast(3)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(2)|lung(4)|stomach(1)|urinary_tract(1)	16		Acute lymphoblastic leukemia(23;0.158)|Prostate(43;0.167)		GBM - Glioblastoma multiforme(50;0.0161)|Lung(218;0.105)		TATCAGGGGTCCAGAAATATA	0.502																																																	1	Substitution - coding silent(1)	kidney(1)											177.0	160.0	165.0					9																	6251225		2203	4300	6503	SO:0001819	synonymous_variant	90865			AB024518	CCDS6468.1, CCDS56563.1, CCDS56564.1	9p24.1	2014-01-28	2006-11-20	2006-11-20	ENSG00000137033	ENSG00000137033		"""Interleukins and interleukin receptors"""	16028	protein-coding gene	gene with protein product	"""DVS27-related protein"", ""nuclear factor for high endothelial venules"", ""interleukin-1 family, member 11"""	608678	"""chromosome 9 open reading frame 26 (NF-HEV)"""	C9orf26		10566975, 12819012	Standard	NM_033439		Approved	DVS27, DKFZp586H0523, NF-HEV, IL1F11	uc003zjt.3	O95760	OTTHUMG00000019516	ENST00000381434.3:c.303C>G	9.37:g.6251225C>G			B2R8L1|B4DJ35|B4E1Q9|D3DRI5|E7EAX4|Q2YEJ5	Silent	SNP	ENST00000381434.3	37	CCDS6468.1																																																																																				0.502	IL33-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051655.1		NM_033439	
KCNJ12	3768	hgsc.bcm.edu	37	17	21319527	21319527	+	Silent	SNP	C	C	T	rs80022364	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr17:21319527C>T	ENST00000583088.1	+	3	1768	c.873C>T	c.(871-873)gaC>gaT	p.D291D	KCNJ12_ENST00000331718.5_Silent_p.D291D	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	291					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)			NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	TGGAGACGGACGACTTTGAGA	0.617										Prostate(3;0.18)			.|||	2	0.000399361	0.0015	0.0	5008	,	,		35812	0.0		0.0	False		,,,				2504	0.0																0													96.0	88.0	91.0					17																	21319527		2203	4300	6503	SO:0001819	synonymous_variant	100134444			L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.873C>T	17.37:g.21319527C>T			O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																				0.617	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2		NM_021012	
KCNJ12	3768	hgsc.bcm.edu	37	17	21319743	21319743	+	Silent	SNP	A	A	G	rs76267885	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr17:21319743A>G	ENST00000583088.1	+	3	1984	c.1089A>G	c.(1087-1089)gtA>gtG	p.V363V	KCNJ12_ENST00000331718.5_Silent_p.V363V	NM_021012.4	NP_066292.2	Q14500	KCJ12_HUMAN	potassium inwardly-rectifying channel, subfamily J, member 12	363					muscle contraction (GO:0006936)|potassium ion transmembrane transport (GO:0071805)|potassium ion transport (GO:0006813)|protein homotetramerization (GO:0051289)|regulation of heart contraction (GO:0008016)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|intrinsic component of membrane (GO:0031224)|plasma membrane (GO:0005886)	inward rectifier potassium channel activity (GO:0005242)	p.V363V(1)		NS(1)|breast(4)|endometrium(4)|kidney(1)|large_intestine(5)|lung(39)|ovary(5)|skin(8)|stomach(3)	70				Colorectal(15;0.0183)|COAD - Colon adenocarcinoma(3;0.0732)	Dofetilide(DB00204)|Yohimbine(DB01392)	AGGATCTGGTAGAGAACAAGT	0.577										Prostate(3;0.18)																																							1	Substitution - coding silent(1)	lung(1)											100.0	95.0	97.0					17																	21319743		2203	4300	6503	SO:0001819	synonymous_variant	100134444			L36069	CCDS11219.1	17p11.1	2011-07-05	2004-01-13		ENSG00000184185	ENSG00000184185		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels, Inwardly rectifying"""	6258	protein-coding gene	gene with protein product		602323	"""potassium inwardly-rectifying channel, subfamily J, inhibitor 1"""	KCNJN1		7859381, 12417321, 16382105	Standard	NM_021012		Approved	Kir2.2, Kir2.2v, IRK2, hIRK1	uc021tss.1	Q14500	OTTHUMG00000132039	ENST00000583088.1:c.1089A>G	17.37:g.21319743A>G			O43401|Q15756|Q8NG63	Silent	SNP	ENST00000583088.1	37	CCDS11219.1																																																																																				0.577	KCNJ12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255060.2		NM_021012	
JMJD6	23210	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	74720100	74720100	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr17:74720100G>T	ENST00000397625.4	-	3	673	c.559C>A	c.(559-561)Cac>Aac	p.H187N	METTL23_ENST00000590964.1_5'Flank|METTL23_ENST00000588302.1_5'Flank|METTL23_ENST00000586752.1_5'Flank|METTL23_ENST00000588783.1_5'Flank|METTL23_ENST00000586200.1_5'Flank|METTL23_ENST00000589977.1_5'Flank|METTL23_ENST00000591571.1_5'Flank|METTL23_ENST00000586738.1_5'Flank|JMJD6_ENST00000585429.1_Missense_Mutation_p.H187N|JMJD6_ENST00000445478.2_Missense_Mutation_p.H187N|METTL23_ENST00000341249.6_5'Flank|METTL23_ENST00000588822.1_5'Flank	NM_015167.2	NP_055982.2	Q6NYC1	JMJD6_HUMAN	jumonji domain containing 6	187	JmjC. {ECO:0000255|PROSITE- ProRule:PRU00538}.				cell surface receptor signaling pathway (GO:0007166)|erythrocyte development (GO:0048821)|heart development (GO:0007507)|histone H3-R2 demethylation (GO:0070078)|histone H4-R3 demethylation (GO:0070079)|kidney development (GO:0001822)|lung development (GO:0030324)|macrophage activation (GO:0042116)|mRNA processing (GO:0006397)|peptidyl-lysine hydroxylation to 5-hydroxy-L-lysine (GO:0018395)|recognition of apoptotic cell (GO:0043654)|regulation of mRNA splicing, via spliceosome (GO:0048024)|regulation of transcription, DNA-templated (GO:0006355)|retina development in camera-type eye (GO:0060041)|RNA splicing (GO:0008380)|sprouting angiogenesis (GO:0002040)|T cell differentiation in thymus (GO:0033077)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	histone demethylase activity (H3-R2 specific) (GO:0033746)|histone demethylase activity (H4-R3 specific) (GO:0033749)|identical protein binding (GO:0042802)|iron ion binding (GO:0005506)|peptidyl-lysine 5-dioxygenase activity (GO:0070815)|receptor activity (GO:0004872)|RNA binding (GO:0003723)|single-stranded RNA binding (GO:0003727)	p.H187N(2)		endometrium(2)|kidney(5)|large_intestine(2)|lung(3)|ovary(2)|skin(2)	16						GGGTCGATGTGAATCCCAGTT	0.507																																																	2	Substitution - Missense(2)	kidney(2)											106.0	104.0	105.0					17																	74720100		1938	4144	6082	SO:0001583	missense	23210			AB011157	CCDS42383.1, CCDS42384.1	17q25	2007-11-20	2007-02-16	2007-02-16	ENSG00000070495	ENSG00000070495			19355	protein-coding gene	gene with protein product		604914	"""phosphatidylserine receptor"""	PTDSR		11877474	Standard	NM_015167		Approved	PTDSR1, KIAA0585	uc002jsn.1	Q6NYC1	OTTHUMG00000169267	ENST00000397625.4:c.559C>A	17.37:g.74720100G>T	ENSP00000380750:p.His187Asn		B3KMN8|B4DGX1|Q86VY0|Q8IUM5|Q9Y4E2	Missense_Mutation	SNP	ENST00000397625.4	37	CCDS42384.1	.	.	.	.	.	.	.	.	.	.	G	29.7	5.026418	0.93518	.	.	ENSG00000070495	ENST00000445478;ENST00000344991;ENST00000397625	D;D	0.99259	-5.64;-5.64	5.35	5.35	0.76521	Transcription factor jumonji/aspartyl beta-hydroxylase (2);Transcription factor jumonji (1);	0.150898	0.64402	D	0.000017	D	0.99725	0.9893	H	0.98833	4.345	0.80722	D	1	D;D;D	0.69078	0.997;0.975;0.996	D;P;D	0.79784	0.993;0.89;0.988	D	0.97051	0.9764	10	0.87932	D	0	-8.3945	19.0951	0.93248	0.0:0.0:1.0:0.0	.	187;187;187	B2WTI3;Q6NYC1;Q6NYC1-3	.;JMJD6_HUMAN;.	N	187	ENSP00000394085:H187N;ENSP00000380750:H187N	ENSP00000302916:H187N	H	-	1	0	JMJD6	72231695	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	9.855000	0.99526	2.491000	0.84063	0.643000	0.83706	CAC		0.507	JMJD6-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000403211.1		NM_015167	
KCNV2	169522	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	2729659	2729659	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr9:2729659G>A	ENST00000382082.3	+	2	1808	c.1570G>A	c.(1570-1572)Gcc>Acc	p.A524T		NM_133497.3	NP_598004.1	Q8TDN2	KCNV2_HUMAN	potassium channel, subfamily V, member 2	524					protein homooligomerization (GO:0051260)|synaptic transmission (GO:0007268)	plasma membrane (GO:0005886)|voltage-gated potassium channel complex (GO:0008076)	delayed rectifier potassium channel activity (GO:0005251)	p.A524T(2)		NS(1)|breast(1)|central_nervous_system(3)|endometrium(5)|kidney(4)|large_intestine(7)|lung(9)|ovary(1)|prostate(2)|skin(2)	35				GBM - Glioblastoma multiforme(50;0.0257)		CATGCAGAGAGCCAGAAAGAA	0.453																																																	2	Substitution - Missense(2)	NS(1)|kidney(1)											114.0	104.0	107.0					9																	2729659		2203	4300	6503	SO:0001583	missense	169522			AF348983	CCDS6447.1	9p24.2	2011-07-05			ENSG00000168263	ENSG00000168263		"""Potassium channels"", ""Voltage-gated ion channels / Potassium channels"""	19698	protein-coding gene	gene with protein product		607604				12060745, 16382104	Standard	NM_133497		Approved	Kv8.2	uc003zho.2	Q8TDN2	OTTHUMG00000019449	ENST00000382082.3:c.1570G>A	9.37:g.2729659G>A	ENSP00000371514:p.Ala524Thr		Q5T6X0	Missense_Mutation	SNP	ENST00000382082.3	37	CCDS6447.1	.	.	.	.	.	.	.	.	.	.	G	33	5.197423	0.94960	.	.	ENSG00000168263	ENST00000382082	D	0.96992	-4.2	5.37	5.37	0.77165	.	1.184800	0.06247	N	0.691438	D	0.96414	0.8830	M	0.77820	2.39	0.80722	D	1	P	0.40660	0.726	B	0.35607	0.206	D	0.91557	0.5261	10	0.52906	T	0.07	.	19.47	0.94959	0.0:0.0:1.0:0.0	.	524	Q8TDN2	KCNV2_HUMAN	T	524	ENSP00000371514:A524T	ENSP00000371514:A524T	A	+	1	0	KCNV2	2719659	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	7.951000	0.87819	2.681000	0.91329	0.655000	0.94253	GCC		0.453	KCNV2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000051528.1		NM_133497	
KIAA0586	9786	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	58949396	58949396	+	Missense_Mutation	SNP	C	C	T	rs367811307		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr14:58949396C>T	ENST00000556134.1	+	22	3339	c.3065C>T	c.(3064-3066)tCt>tTt	p.S1022F	KIAA0586_ENST00000354386.6_Missense_Mutation_p.S1090F|KIAA0586_ENST00000538571.2_3'UTR|KIAA0586_ENST00000423743.3_Missense_Mutation_p.S993F|KIAA0586_ENST00000261244.5_Missense_Mutation_p.S961F	NM_001244190.1|NM_001244193.1	NP_001231119.1|NP_001231122.1	Q9BVV6	TALD3_HUMAN	KIAA0586	1022					cilium assembly (GO:0042384)|cilium morphogenesis (GO:0060271)|regulation of establishment of protein localization (GO:0070201)|smoothened signaling pathway (GO:0007224)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoplasm (GO:0005737)		p.S961F(1)|p.S1090F(1)		endometrium(4)|kidney(6)|large_intestine(8)|lung(12)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	34						ACAGGTGTTTCTGGGGATGCT	0.388																																																	2	Substitution - Missense(2)	kidney(2)											121.0	120.0	120.0					14																	58949396		1852	4112	5964	SO:0001583	missense	9786			AB011158	CCDS45115.1, CCDS58320.1, CCDS58321.1, CCDS58322.1, CCDS73639.1	14q23.1	2012-12-06			ENSG00000100578	ENSG00000100578			19960	protein-coding gene	gene with protein product		610178				16702409	Standard	NM_014749		Approved	Talpid3	uc010trr.2	Q9BVV6	OTTHUMG00000171141	ENST00000556134.1:c.3065C>T	14.37:g.58949396C>T	ENSP00000452351:p.Ser1022Phe		B4DZB6|E7EWM8|J3KQH9|O60328|Q6NYC6|Q6UV20	Missense_Mutation	SNP	ENST00000556134.1	37	CCDS58321.1	.	.	.	.	.	.	.	.	.	.	C	13.24	2.178245	0.38511	.	.	ENSG00000100578	ENST00000354386;ENST00000556134;ENST00000423743;ENST00000261244;ENST00000546216	T;T;T;T	0.48201	0.82;0.82;0.82;0.82	5.72	3.9	0.45041	.	1.213970	0.05662	N	0.587149	T	0.59032	0.2164	M	0.68317	2.08	0.09310	N	1	P;P;D;P;P;P	0.53151	0.681;0.681;0.958;0.925;0.799;0.799	B;B;P;P;B;B	0.53809	0.281;0.281;0.66;0.735;0.281;0.366	T	0.34004	-0.9846	10	0.62326	D	0.03	.	5.9295	0.19130	0.1425:0.6463:0.1373:0.074	.	897;897;1090;961;1022;993	F5GWA3;B7Z7W7;E7EWM8;E9PGW8;Q9BVV6;Q6UV20	.;.;.;.;K0586_HUMAN;.	F	1090;1022;993;961;897	ENSP00000346359:S1090F;ENSP00000452351:S1022F;ENSP00000399427:S993F;ENSP00000261244:S961F	ENSP00000261244:S961F	S	+	2	0	KIAA0586	58019149	0.888000	0.30383	0.147000	0.22382	0.008000	0.06430	2.805000	0.47939	0.768000	0.33290	-0.885000	0.02943	TCT		0.388	KIAA0586-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000411887.1		NM_014749	
KL	9365	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	33634984	33634984	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr13:33634984G>A	ENST00000380099.3	+	4	1776	c.1768G>A	c.(1768-1770)Gtt>Att	p.V590I	KL_ENST00000487852.1_3'UTR|KL_ENST00000426690.2_3'UTR	NM_004795.3	NP_004786.2	Q9UEF7	KLOT_HUMAN	klotho	590	Glycosyl hydrolase-1 2.				acute inflammatory response (GO:0002526)|aging (GO:0007568)|calcium ion homeostasis (GO:0055074)|carbohydrate metabolic process (GO:0005975)|energy reserve metabolic process (GO:0006112)|epidermal growth factor receptor signaling pathway (GO:0007173)|Fc-epsilon receptor signaling pathway (GO:0038095)|fibroblast growth factor receptor signaling pathway (GO:0008543)|innate immune response (GO:0045087)|insulin receptor signaling pathway (GO:0008286)|neurotrophin TRK receptor signaling pathway (GO:0048011)|phosphatidylinositol-mediated signaling (GO:0048015)|positive regulation of bone mineralization (GO:0030501)|positive regulation of MAPKKK cascade by fibroblast growth factor receptor signaling pathway (GO:0090080)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	beta-glucosidase activity (GO:0008422)|beta-glucuronidase activity (GO:0004566)|fibroblast growth factor binding (GO:0017134)|signal transducer activity (GO:0004871)|vitamin D binding (GO:0005499)	p.V590I(1)		breast(2)|endometrium(5)|kidney(3)|large_intestine(10)|lung(14)|ovary(2)|skin(5)	41	all_epithelial(80;0.133)	Ovarian(182;1.78e-06)|Breast(139;4.08e-05)|Hepatocellular(188;0.00886)|Lung SC(185;0.0262)		GBM - Glioblastoma multiforme(144;7.13e-230)|all cancers(112;1.33e-165)|OV - Ovarian serous cystadenocarcinoma(117;1.09e-113)|Epithelial(112;3.79e-112)|Lung(94;8.52e-27)|LUSC - Lung squamous cell carcinoma(192;1.4e-13)|Kidney(163;3.04e-09)|KIRC - Kidney renal clear cell carcinoma(186;5.63e-08)|BRCA - Breast invasive adenocarcinoma(63;1.41e-05)		GGAAATGCACGTTACACATTT	0.517																																																	1	Substitution - Missense(1)	kidney(1)											166.0	141.0	149.0					13																	33634984		2203	4300	6503	SO:0001583	missense	9365			AB005142	CCDS9347.1	13q12	2008-02-05			ENSG00000133116	ENSG00000133116			6344	protein-coding gene	gene with protein product		604824				9464267	Standard	NM_004795		Approved		uc001uus.3	Q9UEF7	OTTHUMG00000017408	ENST00000380099.3:c.1768G>A	13.37:g.33634984G>A	ENSP00000369442:p.Val590Ile		Q5VZ95|Q96KV5|Q96KW5|Q9UEI9|Q9Y4F0	Missense_Mutation	SNP	ENST00000380099.3	37	CCDS9347.1	.	.	.	.	.	.	.	.	.	.	g	3.320	-0.138854	0.06669	.	.	ENSG00000133116	ENST00000380099	T	0.31769	1.48	5.44	0.784	0.18578	Glycoside hydrolase, subgroup, catalytic domain (1);Glycoside hydrolase, superfamily (1);	0.235838	0.42821	N	0.000655	T	0.25457	0.0619	L	0.53617	1.68	0.09310	N	1	B	0.27951	0.195	B	0.25884	0.064	T	0.17379	-1.0371	10	0.42905	T	0.14	-17.3704	9.7991	0.40753	0.4701:0.0:0.5299:0.0	.	590	Q9UEF7	KLOT_HUMAN	I	590	ENSP00000369442:V590I	ENSP00000369442:V590I	V	+	1	0	KL	32532984	0.994000	0.37717	0.001000	0.08648	0.001000	0.01503	2.837000	0.48191	0.313000	0.23062	-2.003000	0.00443	GTT		0.517	KL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045987.1			
KLHL42	57542	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	27933951	27933951	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr12:27933951T>C	ENST00000381271.2	+	1	999	c.688T>C	c.(688-690)Ttc>Ctc	p.F230L	RP11-860B13.1_ENST00000545904.1_RNA	NM_020782.1	NP_065833.1	Q9P2K6	KLH42_HUMAN	kelch-like family member 42	230					mitotic nuclear division (GO:0007067)|proteasome-mediated ubiquitin-dependent protein catabolic process (GO:0043161)|protein polyubiquitination (GO:0000209)|regulation of microtubule-based process (GO:0032886)	Cul3-RING ubiquitin ligase complex (GO:0031463)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)		p.F230L(1)									TGAGCGTTGGTTCCCGCTGGC	0.637																																																	1	Substitution - Missense(1)	kidney(1)											76.0	56.0	63.0					12																	27933951		2203	4300	6503	SO:0001583	missense	57542			AB037761	CCDS31763.1	12p11.22	2013-04-24	2013-02-22	2013-01-30	ENSG00000087448	ENSG00000087448		"""Kelch-like"""	29252	protein-coding gene	gene with protein product			"""kelch domain containing 5"""	KLHDC5		19261606	Standard	NM_020782		Approved	KIAA1340, Ctb9	uc001rij.3	Q9P2K6	OTTHUMG00000169217	ENST00000381271.2:c.688T>C	12.37:g.27933951T>C	ENSP00000370671:p.Phe230Leu		Q2VPK1|Q8N334	Missense_Mutation	SNP	ENST00000381271.2	37	CCDS31763.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	T|T	15.99|15.99	2.994140|2.994140	0.54041|0.54041	.|.	.|.	ENSG00000087448|ENSG00000087448	ENST00000381271|ENST00000543254	T|.	0.65178|.	-0.14|.	4.73|4.73	2.29|2.29	0.28610|0.28610	Kelch-type beta propeller (1);|.	0.344763|.	0.30781|.	N|.	0.008895|.	T|T	0.16041|0.16041	0.0386|0.0386	N|N	0.02539|0.02539	-0.55|-0.55	0.33912|0.33912	D|D	0.639838|0.639838	B|.	0.02656|.	0.0|.	B|.	0.01281|.	0.0|.	T|T	0.23013|0.23013	-1.0200|-1.0200	10|5	0.09338|.	T|.	0.73|.	.|.	6.3285|6.3285	0.21257|0.21257	0.0:0.3567:0.0:0.6433|0.0:0.3567:0.0:0.6433	.|.	230|.	Q9P2K6|.	KLDC5_HUMAN|.	L|A	230|51	ENSP00000370671:F230L|.	ENSP00000370671:F230L|.	F|V	+|+	1|2	0|0	KLHDC5|KLHDC5	27825218|27825218	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.998000|0.998000	0.95712|0.95712	1.358000|1.358000	0.34102|0.34102	0.845000|0.845000	0.35118|0.35118	0.477000|0.477000	0.44152|0.44152	TTC|GTT		0.637	KLHL42-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000402904.1		NM_020782	
KRT4	3851	hgsc.bcm.edu	37	12	53207602	53207603	+	Frame_Shift_Ins	INS	-	-	G	rs7135148|rs71092788		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr12:53207602_53207603insG	ENST00000551956.1	-	1	732_733	c.240_241insC	c.(238-243)tttggcfs	p.G81fs	KRT4_ENST00000458244.2_Frame_Shift_Ins_p.G61fs|KRT4_ENST00000293774.4_Frame_Shift_Ins_p.G155fs			P19013	K2C4_HUMAN	keratin 4	81	Gly-rich.|Head.				cytoskeleton organization (GO:0007010)|epithelial cell differentiation (GO:0030855)|negative regulation of epithelial cell proliferation (GO:0050680)	cell surface (GO:0009986)|intermediate filament (GO:0005882)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)			endometrium(3)|kidney(4)|large_intestine(6)|lung(8)|ovary(4)|prostate(2)|skin(2)	29						CCACCAGTGCCAAAGCCTCCAG	0.599																																					Pancreas(190;284 2995 41444 45903)												0																																										SO:0001589	frameshift_variant	3851				CCDS41787.1, CCDS41787.2	12q13.13	2013-01-16			ENSG00000170477	ENSG00000170477		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6441	protein-coding gene	gene with protein product	"""cytokeratin 4"", ""keratin, type II cytoskeletal 4"""	123940		CYK4		16831889	Standard	NM_002272		Approved	CK4, K4	uc031qhk.1	P19013		ENST00000551956.1:c.240_241insC	12.37:g.53207602_53207603insG	ENSP00000448220:p.Gly81fs		F8VS64|Q6GTR8|Q96LA7|Q9BTL1	Frame_Shift_Ins	INS	ENST00000551956.1	37	CCDS41787.2																																																																																				0.599	KRT4-001	KNOWN	upstream_ATG|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000405931.1		NM_002272	
MATN2	4147	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	99028778	99028778	+	Silent	SNP	T	T	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr8:99028778T>C	ENST00000520016.1	+	10	1708	c.1584T>C	c.(1582-1584)tcT>tcC	p.S528S	MATN2_ENST00000522025.2_Silent_p.S244S|MATN2_ENST00000524308.1_Silent_p.S487S|MATN2_ENST00000521689.1_Silent_p.S528S|MATN2_ENST00000254898.5_Silent_p.S528S			O00339	MATN2_HUMAN	matrilin 2	528	EGF-like 8. {ECO:0000255|PROSITE- ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.S528S(2)		breast(1)|endometrium(4)|kidney(1)|large_intestine(5)|lung(17)|ovary(2)|urinary_tract(1)	31	Breast(36;1.43e-06)		OV - Ovarian serous cystadenocarcinoma(57;0.244)			AATTGGACTCTTGTGCTCTGG	0.393																																																	2	Substitution - coding silent(2)	kidney(2)											76.0	71.0	73.0					8																	99028778		1862	4107	5969	SO:0001819	synonymous_variant	4147			U69263	CCDS55264.1, CCDS55265.1	8q22.1-q22.2	2008-05-15							6908	protein-coding gene	gene with protein product		602108				9083061, 11852232	Standard	XM_005250920		Approved		uc003yic.3	O00339		ENST00000520016.1:c.1584T>C	8.37:g.99028778T>C			A8K106|E7EW74|E9PD48|E9PGL2|Q6UWA5|Q7Z5X1|Q8NDE6|Q96FT5|Q9NSZ1	Silent	SNP	ENST00000520016.1	37	CCDS55264.1																																																																																				0.393	MATN2-004	KNOWN	non_canonical_conserved|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000380332.1			
MCM3AP	8888	broad.mit.edu;hgsc.bcm.edu	37	21	47692488	47692488	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr21:47692488C>T	ENST00000397708.1	-	9	2706	c.2452G>A	c.(2452-2454)Gga>Aga	p.G818R	MCM3AP_ENST00000291688.1_Missense_Mutation_p.G818R			O60318	GANP_HUMAN	minichromosome maintenance complex component 3 associated protein	818	SAC3 homology.				DNA replication (GO:0006260)|immune system process (GO:0002376)|mRNA transport (GO:0051028)|protein import into nucleus (GO:0006606)	cytosol (GO:0005829)|nuclear pore (GO:0005643)|nucleus (GO:0005634)	DNA binding (GO:0003677)|transferase activity, transferring acyl groups (GO:0016746)	p.G818R(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(10)|kidney(5)|large_intestine(17)|lung(24)|ovary(4)|skin(4)|upper_aerodigestive_tract(2)|urinary_tract(2)	72	Breast(49;0.112)					AGGATGTCTCCCTTGTTGAGA	0.498																																																	1	Substitution - Missense(1)	kidney(1)											145.0	127.0	133.0					21																	47692488		2203	4300	6503	SO:0001583	missense	8888			AB005543	CCDS13734.1	21q22.3	2012-12-19	2007-04-04		ENSG00000160294	ENSG00000160294			6946	protein-coding gene	gene with protein product	"""germinal-centre associated nuclear protein"""	603294	"""minichromosome maintenance deficient (S. cerevisiae) 3-associated protein"", ""MCM3 minichromosome maintenance deficient 3 (S. cerevisiae) associated protein"""			9712829, 16914116, 21195085	Standard	XM_005261205		Approved	Map80, KIAA0572, GANP, SAC3	uc002zir.1	O60318	OTTHUMG00000090630	ENST00000397708.1:c.2452G>A	21.37:g.47692488C>T	ENSP00000380820:p.Gly818Arg		C9JL56|Q2M3C1|Q6PJP6|Q9BSY5|Q9UMT4	Missense_Mutation	SNP	ENST00000397708.1	37	CCDS13734.1	.	.	.	.	.	.	.	.	.	.	C	16.19	3.052832	0.55218	.	.	ENSG00000160294	ENST00000397708;ENST00000291688	T;T	0.30981	1.51;1.51	5.72	4.84	0.62591	.	0.096427	0.64402	D	0.000001	T	0.46983	0.1421	L	0.43598	1.365	0.80722	D	1	D	0.76494	0.999	D	0.85130	0.997	T	0.34129	-0.9841	10	0.36615	T	0.2	-32.0768	14.7567	0.69569	0.0:0.9309:0.0:0.0691	.	818	O60318	MCM3A_HUMAN	R	818	ENSP00000380820:G818R;ENSP00000291688:G818R	ENSP00000291688:G818R	G	-	1	0	MCM3AP	46516916	1.000000	0.71417	1.000000	0.80357	0.119000	0.20118	7.559000	0.82265	1.440000	0.47531	-0.140000	0.14226	GGA		0.498	MCM3AP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000207254.1		NM_003906	
MOAP1	64112	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	93650048	93650050	+	In_Frame_Del	DEL	TTC	TTC	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	TTC	TTC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr14:93650048_93650050delTTC	ENST00000556883.1	-	2	1022_1024	c.538_540delGAA	c.(538-540)gaadel	p.E180del	TMEM251_ENST00000415050.2_5'Flank|MOAP1_ENST00000298894.4_In_Frame_Del_p.E180del|TMEM251_ENST00000283534.4_5'Flank|RP11-371E8.4_ENST00000557574.1_5'Flank			Q96BY2	MOAP1_HUMAN	modulator of apoptosis 1	180					apoptotic signaling pathway (GO:0097190)|extrinsic apoptotic signaling pathway in absence of ligand (GO:0097192)|extrinsic apoptotic signaling pathway via death domain receptors (GO:0008625)|intrinsic apoptotic signaling pathway in response to DNA damage (GO:0008630)|positive regulation of apoptotic process (GO:0043065)|positive regulation of release of cytochrome c from mitochondria (GO:0090200)|protein insertion into mitochondrial membrane involved in apoptotic signaling pathway (GO:0001844)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrial outer membrane (GO:0005741)|mitochondrion (GO:0005739)	ubiquitin protein ligase binding (GO:0031625)			central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(1)|lung(4)|ovary(1)|skin(2)	13		all_cancers(154;0.00528)|Acute lymphoblastic leukemia(33;0.0497)|all_epithelial(191;0.125)|all_neural(303;0.13)		Epithelial(152;0.178)|all cancers(159;0.2)|COAD - Colon adenocarcinoma(157;0.204)		agcgtccaaattcttcttctcct	0.512																																																	0																																										SO:0001651	inframe_deletion	64112			BC015044	CCDS9908.1	14q32.12	2012-02-09			ENSG00000165943	ENSG00000165943		"""Paraneoplastic Ma antigens"""	16658	protein-coding gene	gene with protein product	"""paraneoplastic Ma antigen family member 4"""	609485				11060313	Standard	NM_022151		Approved	MAP-1, PNMA4	uc001ybj.3	Q96BY2	OTTHUMG00000169184	ENST00000556883.1:c.538_540delGAA	14.37:g.93650054_93650056delTTC	ENSP00000451594:p.Glu180del		B2RDF6|Q9H833|Q9HAS1	In_Frame_Del	DEL	ENST00000556883.1	37	CCDS9908.1																																																																																				0.512	MOAP1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412685.1			
MSMP	692094	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	35753713	35753713	+	Silent	SNP	G	G	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr9:35753713G>A	ENST00000436428.2	-	2	322	c.183C>T	c.(181-183)cgC>cgT	p.R61R	MSMP_ENST00000414286.1_5'UTR|RP11-112J3.15_ENST00000425499.2_RNA|RGP1_ENST00000378078.4_3'UTR	NM_001044264.2	NP_001037729.1	Q1L6U9	MSMP_HUMAN	microseminoprotein, prostate associated	61						cytoplasm (GO:0005737)|extracellular space (GO:0005615)		p.R61R(1)		endometrium(2)|kidney(1)|lung(3)|prostate(3)	9						AACAGTCCTTGCGGAGCCAAG	0.512																																																	1	Substitution - coding silent(1)	kidney(1)											45.0	46.0	46.0					9																	35753713		2058	4215	6273	SO:0001819	synonymous_variant	692094			DQ012170	CCDS43797.1	9p13.3	2012-10-02			ENSG00000215183	ENSG00000215183			29663	protein-coding gene	gene with protein product		612191				17338636	Standard	NM_001044264		Approved	PC-3, PSMP	uc003zyb.2	Q1L6U9	OTTHUMG00000019882	ENST00000436428.2:c.183C>T	9.37:g.35753713G>A				Missense_Mutation	SNP	ENST00000436428.2	37	CCDS43797.1																																																																																				0.512	MSMP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000052384.2		NM_001044264	
MUTYH	4595	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	45796978	45796978	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr1:45796978A>G	ENST00000372098.3	-	14	1476	c.1343T>C	c.(1342-1344)cTg>cCg	p.L448P	MUTYH_ENST00000456914.2_Missense_Mutation_p.L423P|MUTYH_ENST00000372104.1_Missense_Mutation_p.L423P|MUTYH_ENST00000528332.2_Missense_Mutation_p.L132P|MUTYH_ENST00000372110.3_Missense_Mutation_p.L438P|MUTYH_ENST00000372115.3_Missense_Mutation_p.L437P|MUTYH_ENST00000354383.6_Missense_Mutation_p.L424P|MUTYH_ENST00000529984.1_Missense_Mutation_p.L118P|MUTYH_ENST00000372100.5_Missense_Mutation_p.L434P|MUTYH_ENST00000531105.1_Intron|MUTYH_ENST00000528013.2_Missense_Mutation_p.L437P|MUTYH_ENST00000450313.1_Missense_Mutation_p.L451P|MUTYH_ENST00000448481.1_Missense_Mutation_p.L434P|MUTYH_ENST00000488731.2_Missense_Mutation_p.L118P|MUTYH_ENST00000355498.2_Missense_Mutation_p.L423P			Q9UIF7	MUTYH_HUMAN	mutY homolog	448	Nudix hydrolase. {ECO:0000255|PROSITE- ProRule:PRU00794}.				base-excision repair (GO:0006284)|base-excision repair, AP site formation (GO:0006285)|depurination (GO:0045007)|DNA repair (GO:0006281)|mismatch repair (GO:0006298)	mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	4 iron, 4 sulfur cluster binding (GO:0051539)|hydrolase activity, acting on glycosyl bonds (GO:0016798)|metal ion binding (GO:0046872)|MutSalpha complex binding (GO:0032407)	p.L448P(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(5)|lung(8)|urinary_tract(1)	19	Acute lymphoblastic leukemia(166;0.155)					TTGATATGTCAGCTTGATGTG	0.537			Mis			colorectal		Base excision repair (BER), DNA glycosylases	MUTYH-associated polyposis																														yes	Rec		Adenomatous polyposis coli	1	1p34.3-1p32.1	4595	mutY homolog (E. coli)		E	1	Substitution - Missense(1)	kidney(1)											91.0	88.0	89.0					1																	45796978		2203	4300	6503	SO:0001583	missense	4595	Familial Cancer Database	MAP, MYH-associated polyposis	U63329	CCDS520.1, CCDS41320.1, CCDS41321.1, CCDS41322.1, CCDS72776.1, CCDS72777.1	1p34.1	2014-09-17	2013-09-12		ENSG00000132781	ENSG00000132781			7527	protein-coding gene	gene with protein product		604933	"""mutY (E. coli) homolog"", ""mutY homolog (E. coli)"""			7823963, 10684930	Standard	NM_012222		Approved	MYH	uc009vxp.3	Q9UIF7	OTTHUMG00000007682	ENST00000372098.3:c.1343T>C	1.37:g.45796978A>G	ENSP00000361170:p.Leu448Pro		D3DPZ4|Q15830|Q9UBP2|Q9UBS7|Q9UIF4|Q9UIF5|Q9UIF6	Missense_Mutation	SNP	ENST00000372098.3	37	CCDS520.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	14.71|14.71	2.617635|2.617635	0.46736|0.46736	.|.	.|.	ENSG00000132781|ENSG00000132781	ENST00000529984;ENST00000528332;ENST00000372104;ENST00000448481;ENST00000456914;ENST00000354383;ENST00000355498;ENST00000372098;ENST00000372110;ENST00000372115;ENST00000488731;ENST00000450313;ENST00000372100|ENST00000529892	D;D;D;D;D;D;D;D;D;D;D;D;D|.	0.95554|.	-3.74;-3.74;-3.74;-3.74;-3.74;-3.74;-3.74;-3.74;-3.74;-3.74;-3.74;-3.74;-3.74|.	5.16|5.16	3.91|3.91	0.45181|0.45181	NUDIX hydrolase domain (2);NUDIX hydrolase domain-like (1);|.	0.206122|.	0.42172|.	D|.	0.000742|.	T|.	0.78836|.	0.4346|.	M|M	0.91663|0.91663	3.23|3.23	0.58432|0.58432	D|D	0.999997|0.999997	D;D;D;D;D;D;P;D|.	0.76494|.	0.999;0.97;0.972;0.982;0.972;0.97;0.93;0.986|.	D;D;D;D;D;D;P;D|.	0.77004|.	0.989;0.916;0.916;0.962;0.916;0.916;0.881;0.916|.	T|.	0.82163|.	-0.0593|.	10|.	0.51188|.	T|.	0.08|.	-5.17|-5.17	9.2488|9.2488	0.37543|0.37543	0.706:0.0:0.0:0.294|0.706:0.0:0.0:0.294	.|.	132;451;448;438;448;437;331;424|.	B4DEX2;E5KP25;E5KP26;Q9UIF7-2;Q9UIF7;E5KP27;D3DPZ6;E5KP28|.	.;.;.;.;MUTYH_HUMAN;.;.;.|.	P|R	118;132;423;434;423;424;423;448;438;437;118;451;434|115	ENSP00000437093:L118P;ENSP00000433076:L132P;ENSP00000361176:L423P;ENSP00000409718:L434P;ENSP00000407590:L423P;ENSP00000346354:L424P;ENSP00000347685:L423P;ENSP00000361170:L448P;ENSP00000361182:L438P;ENSP00000361187:L437P;ENSP00000432330:L118P;ENSP00000408176:L451P;ENSP00000361172:L434P|.	ENSP00000346354:L424P|.	L|X	-|-	2|1	0|0	MUTYH|MUTYH	45569565|45569565	1.000000|1.000000	0.71417|0.71417	0.999000|0.999000	0.59377|0.59377	0.952000|0.952000	0.60782|0.60782	4.919000|4.919000	0.63383|0.63383	1.955000|1.955000	0.56771|0.56771	0.533000|0.533000	0.62120|0.62120	CTG|TGA		0.537	MUTYH-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000020529.1		NM_012222	
NBPF10	100132406	broad.mit.edu	37	1	145302695	145302695	+	Missense_Mutation	SNP	C	C	T	rs587628031	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr1:145302695C>T	ENST00000369339.3	+	5	573	c.320C>T	c.(319-321)aCc>aTc	p.T107I	NBPF10_ENST00000342960.5_Missense_Mutation_p.T378I|NBPF10_ENST00000369338.1_Missense_Mutation_p.T107I|RP11-458D21.5_ENST00000468030.1_3'UTR			Q6P3W6	NBPFA_HUMAN	neuroblastoma breakpoint family, member 10	378						cytoplasm (GO:0005737)	poly(A) RNA binding (GO:0044822)	p.T378I(1)|p.T107I(1)		NS(3)|breast(1)|central_nervous_system(3)|endometrium(12)|kidney(23)|lung(15)|ovary(1)|prostate(7)|skin(6)|urinary_tract(2)	73	all_hematologic(923;0.032)			Colorectal(1306;1.36e-07)|KIRC - Kidney renal clear cell carcinoma(1967;0.00258)		CGAGAGCTGACCCAGTTAAAG	0.507													.|||	668	0.133387	0.0696	0.1758	5008	,	,		14673	0.1577		0.1769	False		,,,				2504	0.1196																2	Substitution - Missense(2)	kidney(2)																																								SO:0001583	missense	100132406			BC021111		1q21.1	2013-01-17			ENSG00000163386	ENSG00000271425		"""neuroblastoma breakpoint family"""	31992	protein-coding gene	gene with protein product		614000				16079250	Standard	NM_001039703		Approved	AG1		Q6P3W6	OTTHUMG00000013757	ENST00000369339.3:c.320C>T	1.37:g.145302695C>T	ENSP00000358345:p.Thr107Ile		Q5RHC0|Q9NWN6	Missense_Mutation	SNP	ENST00000369339.3	37		.	.	.	.	.	.	.	.	.	.	.	10.68	1.419456	0.25552	.	.	ENSG00000163386	ENST00000448873;ENST00000369338;ENST00000369334;ENST00000342960	T;T	0.08984	3.03;3.87	0.712	0.712	0.18167	.	.	.	.	.	T	0.09423	0.0232	L	0.49513	1.565	0.09310	N	1	D	0.76494	0.999	D	0.79108	0.992	T	0.17592	-1.0364	8	0.46703	T	0.11	.	.	.	.	.	107	A8MQ30	.	I	303;107;107;378	ENSP00000358344:T107I;ENSP00000345684:T378I	ENSP00000345684:T378I	T	+	2	0	NBPF10	144014052	0.175000	0.23083	0.036000	0.18154	0.003000	0.03518	0.222000	0.17699	0.672000	0.31204	0.409000	0.27619	ACC		0.507	NBPF10-001	KNOWN	not_best_in_genome_evidence|basic	protein_coding	protein_coding	OTTHUMT00000038550.3		NM_001039703	
NEIL3	55247	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	178283613	178283613	+	Silent	SNP	T	T	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr4:178283613T>A	ENST00000264596.3	+	10	1924	c.1806T>A	c.(1804-1806)atT>atA	p.I602I		NM_018248.2	NP_060718	Q8TAT5	NEIL3_HUMAN	nei endonuclease VIII-like 3 (E. coli)	602					base-excision repair (GO:0006284)|DNA catabolic process, endonucleolytic (GO:0000737)|nucleotide-excision repair (GO:0006289)	nucleus (GO:0005634)	bubble DNA binding (GO:0000405)|damaged DNA binding (GO:0003684)|DNA N-glycosylase activity (GO:0019104)|DNA-(apurinic or apyrimidinic site) lyase activity (GO:0003906)|double-stranded DNA binding (GO:0003690)|single-stranded DNA binding (GO:0003697)|zinc ion binding (GO:0008270)	p.I602I(1)		breast(1)|central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(4)|lung(14)|ovary(1)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	29		Breast(14;6.27e-05)|Melanoma(52;0.00102)|Renal(120;0.00988)|Prostate(90;0.00996)|all_hematologic(60;0.014)|all_neural(102;0.164)		all cancers(43;1.96e-23)|Epithelial(43;2.52e-20)|OV - Ovarian serous cystadenocarcinoma(60;1.89e-11)|GBM - Glioblastoma multiforme(59;9.49e-05)|Colorectal(24;0.00013)|COAD - Colon adenocarcinoma(29;0.000696)|STAD - Stomach adenocarcinoma(60;0.00308)|LUSC - Lung squamous cell carcinoma(193;0.0398)|READ - Rectum adenocarcinoma(43;0.191)		TAAAAATTATTCCTGGATGCT	0.358								Base excision repair (BER), DNA glycosylases																																									1	Substitution - coding silent(1)	kidney(1)											57.0	64.0	62.0					4																	178283613		2203	4300	6503	SO:0001819	synonymous_variant	55247			AB079071	CCDS3828.1	4q34	2014-02-18			ENSG00000109674	ENSG00000109674			24573	protein-coding gene	gene with protein product	"""zinc finger, GRF-type containing 3"""	608934				12713815, 12509226	Standard	NM_018248		Approved	FLJ10858, hFPG2, FPG2, hNEI3, ZGRF3	uc003iut.2	Q8TAT5	OTTHUMG00000160722	ENST00000264596.3:c.1806T>A	4.37:g.178283613T>A			Q2PPJ3|Q8NG51|Q9NV95	Silent	SNP	ENST00000264596.3	37	CCDS3828.1																																																																																				0.358	NEIL3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000361914.1		NM_018248	
NF2	4771	broad.mit.edu;hgsc.bcm.edu	37	22	30050715	30050715	+	Splice_Site	SNP	G	G	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr22:30050715G>C	ENST00000338641.4	+	5	957		c.e5+1		NF2_ENST00000361166.4_Splice_Site|NF2_ENST00000353887.4_Splice_Site|NF2_ENST00000334961.7_Splice_Site|NF2_ENST00000403435.1_Splice_Site|NF2_ENST00000403999.3_Splice_Site|NF2_ENST00000413209.2_Intron|NF2_ENST00000397789.3_Splice_Site|NF2_ENST00000347330.5_Intron|NF2_ENST00000361676.4_Splice_Site|NF2_ENST00000361452.4_Splice_Site	NM_000268.3|NM_016418.5|NM_181832.2	NP_000259.1|NP_057502.2|NP_861970.1	P35240	MERL_HUMAN	neurofibromin 2 (merlin)						actin cytoskeleton organization (GO:0030036)|cell-cell junction organization (GO:0045216)|ectoderm development (GO:0007398)|hippocampus development (GO:0021766)|lens fiber cell differentiation (GO:0070306)|mesoderm formation (GO:0001707)|negative regulation of cell migration (GO:0030336)|negative regulation of cell proliferation (GO:0008285)|negative regulation of cell-cell adhesion (GO:0022408)|negative regulation of cell-matrix adhesion (GO:0001953)|negative regulation of DNA replication (GO:0008156)|negative regulation of JAK-STAT cascade (GO:0046426)|negative regulation of MAPK cascade (GO:0043409)|negative regulation of protein kinase activity (GO:0006469)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|negative regulation of tyrosine phosphorylation of Stat5 protein (GO:0042524)|odontogenesis of dentin-containing tooth (GO:0042475)|positive regulation of cell differentiation (GO:0045597)|positive regulation of stress fiber assembly (GO:0051496)|regulation of hippo signaling (GO:0035330)|regulation of neural precursor cell proliferation (GO:2000177)|regulation of protein localization to nucleus (GO:1900180)|regulation of protein stability (GO:0031647)|Schwann cell proliferation (GO:0014010)	adherens junction (GO:0005912)|apical part of cell (GO:0045177)|cleavage furrow (GO:0032154)|cortical actin cytoskeleton (GO:0030864)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|early endosome (GO:0005769)|extrinsic component of membrane (GO:0019898)|filopodium (GO:0030175)|lamellipodium (GO:0030027)|membrane (GO:0016020)|nucleolus (GO:0005730)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|ruffle (GO:0001726)		p.?(9)		NS(1)|bone(2)|breast(5)|central_nervous_system(21)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(3)|kidney(17)|large_intestine(9)|liver(1)|lung(9)|meninges(372)|ovary(2)|pituitary(1)|pleura(9)|prostate(1)|skin(7)|soft_tissue(303)|stomach(2)|thyroid(2)|upper_aerodigestive_tract(1)|urinary_tract(4)	776						TCCAAAAAGGGTAAGAGATTA	0.423			"""D, Mis, N, F, S, O"""		"""meningioma, acoustic neuroma, renal """	"""meningioma, acoustic neuroma"""			Neurofibromatosis, type 2																														yes	Rec	yes	Neurofibromatosis type 2	22	22q12.2	4771	neurofibromatosis type 2 gene		O	9	Unknown(9)	meninges(3)|kidney(2)|large_intestine(1)|soft_tissue(1)|central_nervous_system(1)|stomach(1)	GRCh37	CS951485	NF2	S							108.0	108.0	108.0					22																	30050715		2203	4300	6503	SO:0001630	splice_region_variant	4771	Familial Cancer Database	NF2, Central Neurofibromatosis, Bilateral Acoustic Neurofibromatosis	L11353	CCDS13861.1, CCDS13862.1, CCDS13863.1, CCDS13864.1, CCDS13865.1, CCDS54516.1	22q12.2	2014-09-17	2007-12-17		ENSG00000186575	ENSG00000186575		"""A-kinase anchor proteins"""	7773	protein-coding gene	gene with protein product	"""moesin-ezrin-radixin like"", ""schwannomin"""	607379	"""neurofibromin 2 (bilateral acoustic neuroma)"""			10591208	Standard	NM_000268		Approved	merlin	uc003age.4	P35240	OTTHUMG00000030727	ENST00000338641.4:c.516+1G>C	22.37:g.30050715G>C			O95683|Q8WUJ2|Q969N0|Q969Q3|Q96T30|Q96T31|Q96T32|Q96T33|Q9BTW3|Q9UNG9|Q9UNH3|Q9UNH4	Splice_Site	SNP	ENST00000338641.4	37	CCDS13861.1	.	.	.	.	.	.	.	.	.	.	G	28.1	4.894105	0.91889	.	.	ENSG00000186575	ENST00000338641;ENST00000403435;ENST00000361452;ENST00000397822;ENST00000403999;ENST00000334961;ENST00000353887;ENST00000397789;ENST00000361676;ENST00000361166	.	.	.	5.92	5.92	0.95590	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	20.3325	0.98724	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	NF2	28380715	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	9.705000	0.98719	2.805000	0.96524	0.655000	0.94253	.		0.423	NF2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075615.3		NM_000268	Intron
NKD1	85407	broad.mit.edu;ucsc.edu	37	16	50664121	50664121	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr16:50664121A>G	ENST00000268459.3	+	7	711	c.487A>G	c.(487-489)Atc>Gtc	p.I163V		NM_033119.4	NP_149110.1	Q969G9	NKD1_HUMAN	naked cuticle homolog 1 (Drosophila)	163	EF-hand. {ECO:0000255|PROSITE- ProRule:PRU00448}.|Interaction with DVL1, DVL2 and DVL3. {ECO:0000250}.				eye photoreceptor cell differentiation (GO:0001754)|negative regulation of canonical Wnt signaling pathway (GO:0090090)|negative regulation of convergent extension involved in axis elongation (GO:1901233)|positive regulation of non-canonical Wnt signaling pathway via JNK cascade (GO:1901231)|positive regulation of protein catabolic process (GO:0045732)|positive regulation of Wnt signaling pathway, planar cell polarity pathway (GO:2000096)|regulation of cell motility involved in somitogenic axis elongation (GO:0090249)|somatic muscle development (GO:0007525)|Wnt signaling pathway (GO:0016055)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.I163V(1)		NS(1)|central_nervous_system(1)|endometrium(1)|kidney(3)|large_intestine(5)|lung(9)|prostate(1)|urinary_tract(2)	23		all_cancers(37;0.229)		GBM - Glioblastoma multiforme(240;0.243)		GCTGCACACCATCTATGAGGT	0.572																																																	1	Substitution - Missense(1)	kidney(1)											86.0	73.0	77.0					16																	50664121		2198	4300	6498	SO:0001583	missense	85407			AF358135	CCDS10743.1	16q12.1	2013-01-10			ENSG00000140807	ENSG00000140807		"""EF-hand domain containing"""	17045	protein-coding gene	gene with protein product		607851				11356022	Standard	NM_033119		Approved		uc002egg.2	Q969G9	OTTHUMG00000133169	ENST00000268459.3:c.487A>G	16.37:g.50664121A>G	ENSP00000268459:p.Ile163Val		B2RC39|Q8WZ08	Missense_Mutation	SNP	ENST00000268459.3	37	CCDS10743.1	.	.	.	.	.	.	.	.	.	.	A	23.7	4.443732	0.83993	.	.	ENSG00000140807	ENST00000268459	T	0.44482	0.92	4.85	4.85	0.62838	EF-hand-like domain (1);	0.049810	0.85682	D	0.000000	T	0.66858	0.2832	M	0.84326	2.69	0.80722	D	1	D	0.67145	0.996	D	0.77557	0.99	T	0.73322	-0.4019	10	0.87932	D	0	-21.286	14.7298	0.69372	1.0:0.0:0.0:0.0	.	163	Q969G9	NKD1_HUMAN	V	163	ENSP00000268459:I163V	ENSP00000268459:I163V	I	+	1	0	NKD1	49221622	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	9.148000	0.94652	1.936000	0.56123	0.533000	0.62120	ATC		0.572	NKD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256873.1			
OR10H5	284433	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	15904911	15904911	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr19:15904911C>G	ENST00000308940.8	+	1	151	c.53C>G	c.(52-54)tCt>tGt	p.S18C		NM_001004466.1	NP_001004466.1	Q8NGA6	O10H5_HUMAN	olfactory receptor, family 10, subfamily H, member 5	18						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.S18C(1)		breast(1)|central_nervous_system(1)|endometrium(2)|kidney(2)|large_intestine(3)|liver(1)|lung(9)|ovary(1)	20						GTTGGCTTCTCTGCCTTCCCC	0.572																																																	1	Substitution - Missense(1)	kidney(1)											253.0	211.0	225.0					19																	15904911		2203	4300	6503	SO:0001583	missense	284433			AC011537	CCDS32940.1	19p13.12	2013-09-24			ENSG00000172519	ENSG00000172519		"""GPCR / Class A : Olfactory receptors"""	15389	protein-coding gene	gene with protein product							Standard	NM_001004466		Approved		uc010xos.2	Q8NGA6	OTTHUMG00000182284	ENST00000308940.8:c.53C>G	19.37:g.15904911C>G	ENSP00000310704:p.Ser18Cys		Q6IFJ0|Q96R60	Missense_Mutation	SNP	ENST00000308940.8	37	CCDS32940.1	.	.	.	.	.	.	.	.	.	.	.	12.51	1.960603	0.34565	.	.	ENSG00000172519	ENST00000308940	T	0.01106	5.33	3.45	3.45	0.39498	.	0.000000	0.49305	D	0.000151	T	0.08358	0.0208	M	0.90198	3.095	0.30252	N	0.793989	D	0.89917	1.0	D	0.91635	0.999	T	0.00904	-1.1520	10	0.87932	D	0	.	12.7772	0.57455	0.0:1.0:0.0:0.0	.	18	Q8NGA6	O10H5_HUMAN	C	18	ENSP00000310704:S18C	ENSP00000310704:S18C	S	+	2	0	OR10H5	15765911	0.000000	0.05858	0.930000	0.37139	0.245000	0.25701	0.966000	0.29331	1.637000	0.50538	0.573000	0.79308	TCT		0.572	OR10H5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000460363.1			
OR4C12	283093	broad.mit.edu;hgsc.bcm.edu	37	11	50003858	50003858	+	Silent	SNP	G	G	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr11:50003858G>A	ENST00000335238.4	-	1	213	c.180C>T	c.(178-180)ttC>ttT	p.F60F		NM_001005270.2	NP_001005270.2	Q96R67	OR4CC_HUMAN	olfactory receptor, family 4, subfamily C, member 12	60						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)	p.F60F(1)		NS(1)|kidney(4)|large_intestine(3)|liver(1)|lung(19)|ovary(2)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)	36						GGTGGGTCAGGAAGAAGTACA	0.408																																																	1	Substitution - coding silent(1)	kidney(1)											64.0	67.0	66.0					11																	50003858		2201	4296	6497	SO:0001819	synonymous_variant	283093			BK004413	CCDS31496.1	11p11.12	2012-08-09			ENSG00000221954	ENSG00000221954		"""GPCR / Class A : Olfactory receptors"""	15168	protein-coding gene	gene with protein product							Standard	NM_001005270		Approved		uc010ria.2	Q96R67	OTTHUMG00000166687	ENST00000335238.4:c.180C>T	11.37:g.50003858G>A			B2RNF0|Q6IF49	Silent	SNP	ENST00000335238.4	37	CCDS31496.1																																																																																				0.408	OR4C12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391104.1		NM_001005270	
AKAP2	11217	hgsc.bcm.edu	37	9	112900341	112900342	+	In_Frame_Ins	INS	-	-	GAAGCT	rs373159646|rs34665027|rs150402481	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr9:112900341_112900342insGAAGCT	ENST00000259318.7	+	2	2031_2032	c.1824_1825insGAAGCT	c.(1825-1827)gaa>GAAGCTgaa	p.609_609E>EAE	AKAP2_ENST00000374525.1_In_Frame_Ins_p.698_698E>EAE|PALM2-AKAP2_ENST00000302798.7_In_Frame_Ins_p.840_840E>EAE|AKAP2_ENST00000434623.2_In_Frame_Ins_p.698_698E>EAE|PALM2-AKAP2_ENST00000374530.3_In_Frame_Ins_p.840_840E>EAE|AKAP2_ENST00000555236.1_In_Frame_Ins_p.840_840E>EAE|AKAP2_ENST00000510514.5_In_Frame_Ins_p.840_840E>EAE	NM_001136562.2	NP_001130034.1	Q9Y2D5	AKAP2_HUMAN	A kinase (PRKA) anchor protein 2	609								p.E839_E840insEA(1)|p.E697_E698insEA(1)		breast(1)|endometrium(3)|kidney(2)|large_intestine(5)|lung(16)|ovary(3)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	33						CGACTGTAGAGGAAGCTGAAGC	0.505														656	0.13099	0.1309	0.0821	5008	,	,		20174	0.2133		0.1362	False		,,,				2504	0.0757																2	Insertion - In frame(2)	lung(2)							,,,,	550,3714		39,472,1621					,,,,	2.7	0.9		dbSNP_134	39	1146,7108		82,982,3063	no	coding,coding,coding,coding,coding	AKAP2,PALM2-AKAP2	NM_147150.2,NM_007203.4,NM_001198656.1,NM_001136562.2,NM_001004065.4	,,,,	121,1454,4684	A1A1,A1R,RR		13.8842,12.8987,13.5485	,,,,	,,,,		1696,10822				SO:0001652	inframe_insertion	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.1831_1836dupGAAGCT	9.37:g.112900342_112900347dupGAAGCT	Exception_encountered		B1ALX9|B2RTU4|B3KQ00|B4DTZ2|B7ZW07|B9EJB5|Q9UG26	In_Frame_Ins	INS	ENST00000259318.7	37	CCDS48003.1																																																																																				0.505	AKAP2-003	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000346067.3		NM_001004065	
PEG3	5178	broad.mit.edu;ucsc.edu	37	19	57330017	57330017	+	Missense_Mutation	SNP	G	G	T	rs80150589	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr19:57330017G>T	ENST00000326441.9	-	8	1086	c.723C>A	c.(721-723)caC>caA	p.H241Q	PEG3_ENST00000598410.1_Missense_Mutation_p.H116Q|ZIM2_ENST00000221722.5_Missense_Mutation_p.H116Q|PEG3_ENST00000423103.2_Missense_Mutation_p.H241Q|ZIM2_ENST00000601070.1_Missense_Mutation_p.H116Q|ZIM2_ENST00000599935.1_Missense_Mutation_p.H116Q|PEG3_ENST00000593695.1_Missense_Mutation_p.H115Q|ZIM2_ENST00000593711.1_Missense_Mutation_p.H116Q|ZIM2_ENST00000391708.3_Missense_Mutation_p.H116Q	NM_006210.2	NP_006201.1	Q9GZU2	PEG3_HUMAN	paternally expressed 3	241					apoptotic process (GO:0006915)|genetic imprinting (GO:0071514)|in utero embryonic development (GO:0001701)|multicellular organism growth (GO:0035264)|regulation of transcription from RNA polymerase II promoter (GO:0006357)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	metal ion binding (GO:0046872)|nucleic acid binding (GO:0003676)|sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0000981)	p.H241Q(2)|p.H116Q(1)		NS(1)|biliary_tract(4)|breast(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(9)|large_intestine(27)|lung(84)|ovary(8)|pancreas(5)|prostate(6)|skin(8)|stomach(2)|upper_aerodigestive_tract(6)	170		Colorectal(82;0.000256)|all_neural(62;0.103)|Ovarian(87;0.243)		GBM - Glioblastoma multiforme(193;0.0269)		GGATTGTGTTGTGAGGTTTCC	0.493													G|||	7	0.00139776	0.0053	0.0	5008	,	,		17872	0.0		0.0	False		,,,				2504	0.0																3	Substitution - Missense(3)	kidney(3)						G	GLN/HIS,GLN/HIS,GLN/HIS,GLN/HIS,GLN/HIS,GLN/HIS,GLN/HIS,GLN/HIS	7,4399	12.9+/-30.5	0,7,2196	358.0	290.0	313.0		723,345,723,348,348,348,723,348	3.0	1.0	19	dbSNP_131	313	0,8600		0,0,4300	yes	missense,missense,missense,missense,missense,missense,missense,missense	PEG3,ZIM2	NM_001146184.1,NM_001146185.1,NM_001146186.1,NM_001146187.1,NM_001146326.1,NM_001146327.1,NM_006210.2,NM_015363.4	24,24,24,24,24,24,24,24	0,7,6496	TT,TG,GG		0.0,0.1589,0.0538	benign,benign,benign,benign,benign,benign,benign,benign	241/1589,115/1463,241/1589,116/1465,116/528,116/528,241/1589,116/528	57330017	7,12999	2203	4300	6503	SO:0001583	missense	5178			AB006625	CCDS12948.1, CCDS58684.1, CCDS58685.1	19q13.4	2013-01-09				ENSG00000198300		"""Zinc fingers, C2H2-type"", ""-"", ""-"", ""-"""	8826	protein-coding gene	gene with protein product		601483				9149948	Standard	NM_006210		Approved	ZKSCAN22, KIAA0287, ZNF904, ZSCAN24	uc010etr.2	Q9GZU2		ENST00000326441.9:c.723C>A	19.37:g.57330017G>T	ENSP00000326581:p.His241Gln		A7E2B8|B4DIM4|C9JP50|P78418|Q5H9P9|Q7Z7H7|Q8TF75|Q9GZY2	Missense_Mutation	SNP	ENST00000326441.9	37	CCDS12948.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	14.74	2.625235	0.46840	0.001589	0.0	ENSG00000198300	ENST00000391708;ENST00000221722;ENST00000326441;ENST00000423103;ENST00000292074	T;T;T;T	0.03330	3.97;3.97;4.39;4.39	4.0	2.96	0.34315	.	0.177425	0.27636	N	0.018492	T	0.01353	0.0044	N	0.01576	-0.805	.	.	.	B;B;B;B	0.06786	0.0;0.0;0.0;0.001	B;B;B;B	0.01281	0.0;0.0;0.0;0.0	T	0.34403	-0.9830	9	0.09590	T	0.72	-27.7987	9.4612	0.38785	0.0:0.7417:0.2583:0.0	.	116;241;175;116	A7E2B8;Q9GZU2;Q96Q96;Q9NZV7	.;PEG3_HUMAN;.;ZIM2_HUMAN	Q	116;116;241;241;241	ENSP00000375589:H116Q;ENSP00000221722:H116Q;ENSP00000326581:H241Q;ENSP00000403051:H241Q	ENSP00000221722:H116Q	H	-	3	2	ZIM2	62021829	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	0.599000	0.24089	1.278000	0.44430	0.557000	0.71058	CAC		0.493	PEG3-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000416099.2			
PER1	5187	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	8047092	8047092	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr17:8047092T>C	ENST00000317276.4	-	19	2801	c.2564A>G	c.(2563-2565)tAt>tGt	p.Y855C	PER1_ENST00000578089.1_5'UTR|PER1_ENST00000581082.1_Missense_Mutation_p.Y832C	NM_002616.2	NP_002607.2	O15534	PER1_HUMAN	period circadian clock 1	855	Pro-rich.				circadian regulation of gene expression (GO:0032922)|circadian regulation of translation (GO:0097167)|circadian rhythm (GO:0007623)|entrainment of circadian clock (GO:0009649)|entrainment of circadian clock by photoperiod (GO:0043153)|histone H3 acetylation (GO:0043966)|histone H3 deacetylation (GO:0070932)|histone H4 acetylation (GO:0043967)|negative regulation of glucocorticoid receptor signaling pathway (GO:2000323)|negative regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043124)|negative regulation of JNK cascade (GO:0046329)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|posttranscriptional regulation of gene expression (GO:0010608)|regulation of circadian rhythm (GO:0042752)|regulation of cytokine production involved in inflammatory response (GO:1900015)|regulation of hair cycle (GO:0042634)|regulation of p38MAPK cascade (GO:1900744)|regulation of sodium ion transport (GO:0002028)|transcription, DNA-templated (GO:0006351)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	chromatin DNA binding (GO:0031490)|E-box binding (GO:0070888)|kinase binding (GO:0019900)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|signal transducer activity (GO:0004871)|transcription factor binding transcription factor activity (GO:0000989)|ubiquitin protein ligase binding (GO:0031625)	p.Y855C(1)		breast(4)|central_nervous_system(1)|endometrium(2)|kidney(7)|large_intestine(3)|lung(15)|ovary(4)|pancreas(1)|prostate(5)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	47						GTGTGAGACATAGCAGGGCGC	0.692			T	ETV6	"""AML, CMML"""			Other conserved DNA damage response genes																																Dom	yes		17	17p13.1-17p12	5187	period homolog 1 (Drosophila)		L	1	Substitution - Missense(1)	kidney(1)											33.0	37.0	36.0					17																	8047092		2203	4300	6503	SO:0001583	missense	5187			AB002107	CCDS11131.1	17p13.1	2012-12-13	2012-12-13			ENSG00000179094			8845	protein-coding gene	gene with protein product		602260	"""period (Drosophila) homolog 1"", ""period homolog 1 (Drosophila)"""	PER		9323128	Standard	NM_002616		Approved	RIGUI	uc002gkd.3	O15534		ENST00000317276.4:c.2564A>G	17.37:g.8047092T>C	ENSP00000314420:p.Tyr855Cys		B2RPA8|B4DI49|D3DTR3	Missense_Mutation	SNP	ENST00000317276.4	37	CCDS11131.1	.	.	.	.	.	.	.	.	.	.	T	6.260	0.416119	0.11870	.	.	ENSG00000179094	ENST00000317276	T	0.12569	2.67	5.24	0.515	0.17013	.	0.312394	0.32430	N	0.006116	T	0.06826	0.0174	N	0.19112	0.55	0.38767	D	0.954466	B	0.02656	0.0	B	0.04013	0.001	T	0.28332	-1.0047	10	0.38643	T	0.18	0.3024	4.0574	0.09823	0.1463:0.2526:0.0:0.6012	.	855	O15534	PER1_HUMAN	C	855	ENSP00000314420:Y855C	ENSP00000314420:Y855C	Y	-	2	0	PER1	7987817	0.425000	0.25498	0.235000	0.24058	0.503000	0.33858	0.310000	0.19356	0.017000	0.15025	-0.371000	0.07208	TAT		0.692	PER1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441481.2			
JADE2	23338	hgsc.bcm.edu	37	5	133895609	133895610	+	Frame_Shift_Ins	INS	-	-	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr5:133895609_133895610insC	ENST00000402835.1	+	5	656_657	c.401_402insC	c.(400-405)ggcagcfs	p.S135fs	PHF15_ENST00000361895.2_Frame_Shift_Ins_p.S135fs|PHF15_ENST00000395003.1_Frame_Shift_Ins_p.S135fs|PHF15_ENST00000282605.4_Frame_Shift_Ins_p.S135fs																NS(1)|breast(1)|cervix(1)|endometrium(4)|kidney(2)|large_intestine(5)|lung(6)|prostate(1)|skin(1)	22			KIRC - Kidney renal clear cell carcinoma(527;0.0186)|Kidney(363;0.0365)			TGGCCAGGGGGCAGCCGCTATG	0.579																																																	0																																										SO:0001589	frameshift_variant	23338																														ENST00000402835.1:c.402dupC	5.37:g.133895610_133895610dupC	ENSP00000384671:p.Ser135fs			Frame_Shift_Ins	INS	ENST00000402835.1	37																																																																																					0.579	PHF15-007	PUTATIVE	alternative_5_UTR|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000318543.1			
PLIN4	729359	hgsc.bcm.edu;ucsc.edu	37	19	4512636	4512636	+	Missense_Mutation	SNP	A	A	C	rs140230284|rs386806138	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr19:4512636A>C	ENST00000301286.3	-	3	1293	c.1294T>G	c.(1294-1296)Ttg>Gtg	p.L432V		NM_001080400.1	NP_001073869.1	Q96Q06	PLIN4_HUMAN	perilipin 4	432	27 X 33 AA approximate tandem repeat.					cytoplasm (GO:0005737)|lipid particle (GO:0005811)|plasma membrane (GO:0005886)				NS(2)|breast(4)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(7)|lung(14)|ovary(1)|skin(2)|soft_tissue(1)|stomach(2)	41						CCTCTGGCCAAATTCATGGCA	0.552																																																	0								A	VAL/LEU	240,3794		55,130,1832	122.0	147.0	139.0		1294	-9.5	0.0	19	dbSNP_134	139	165,8197		33,99,4049	no	missense	PLIN4	NM_001080400.1	32	88,229,5881	CC,CA,AA		1.9732,5.9494,3.2672	benign	432/1358	4512636	405,11991	2017	4181	6198	SO:0001583	missense	729359			AB067468	CCDS45927.1	19p13.3	2009-10-06	2009-08-12	2009-08-12	ENSG00000167676	ENSG00000167676		"""Perilipins"""	29393	protein-coding gene	gene with protein product		613247	"""KIAA1881"""	KIAA1881		11572484, 19638644	Standard	NM_001080400		Approved	S3-12	uc002mar.1	Q96Q06	OTTHUMG00000167571	ENST00000301286.3:c.1294T>G	19.37:g.4512636A>C	ENSP00000301286:p.Leu432Val		A6NEI2	Missense_Mutation	SNP	ENST00000301286.3	37	CCDS45927.1	56	0.02564102564102564	36	0.07317073170731707	6	0.016574585635359115	0	0.0	14	0.018469656992084433	C	0.046	-1.266936	0.01433	0.059494	0.019732	ENSG00000167676	ENST00000301286	T	0.03065	4.06	4.73	-9.46	0.00597	.	0.585786	0.15154	N	0.277551	T	0.00073	0.0002	N	0.00135	-2.02	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.20706	-1.0267	10	0.02654	T	1	-14.0824	6.7295	0.23375	0.1975:0.1757:0.0:0.6268	.	432	Q96Q06	PLIN4_HUMAN	V	432	ENSP00000301286:L432V	ENSP00000301286:L432V	L	-	1	2	PLIN4	4463636	0.000000	0.05858	0.001000	0.08648	0.001000	0.01503	-4.177000	0.00279	-1.887000	0.01115	-2.171000	0.00323	TTG		0.552	PLIN4-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395095.1		XM_170901	
PREX1	57580	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	47309286	47309286	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr20:47309286G>C	ENST00000371941.3	-	8	982	c.960C>G	c.(958-960)atC>atG	p.I320M	PREX1_ENST00000396220.1_Missense_Mutation_p.I320M	NM_020820.3	NP_065871	Q8TCU6	PREX1_HUMAN	phosphatidylinositol-3,4,5-trisphosphate-dependent Rac exchange factor 1	320	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				actin filament polymerization (GO:0030041)|G-protein coupled receptor signaling pathway (GO:0007186)|intracellular signal transduction (GO:0035556)|neutrophil activation (GO:0042119)|neutrophil chemotaxis (GO:0030593)|positive regulation of Rac GTPase activity (GO:0032855)|positive regulation of substrate adhesion-dependent cell spreading (GO:1900026)|regulation of actin filament polymerization (GO:0030833)|regulation of dendrite development (GO:0050773)|superoxide metabolic process (GO:0006801)|T cell differentiation (GO:0030217)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|dendritic shaft (GO:0043198)|growth cone (GO:0030426)|intracellular membrane-bounded organelle (GO:0043231)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)	enzyme binding (GO:0019899)|phospholipid binding (GO:0005543)|Rho GTPase activator activity (GO:0005100)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)	p.I320M(2)		breast(3)|central_nervous_system(1)|endometrium(4)|kidney(6)|large_intestine(27)|lung(53)|ovary(3)|pancreas(1)|prostate(1)|skin(2)|stomach(5)|upper_aerodigestive_tract(3)|urinary_tract(1)	110			BRCA - Breast invasive adenocarcinoma(12;0.0135)|Colorectal(8;0.198)			GGGAGCCGTTGATGGATTTGG	0.542																																																	2	Substitution - Missense(2)	kidney(2)											281.0	222.0	242.0					20																	47309286		2203	4300	6503	SO:0001583	missense	57580			AB037836	CCDS13410.1	20q13.13	2013-01-10	2008-09-15		ENSG00000124126	ENSG00000124126		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	32594	protein-coding gene	gene with protein product		606905				11955434, 15545267, 16301320	Standard	NM_020820		Approved	KIAA1415, P-REX1	uc002xtw.1	Q8TCU6	OTTHUMG00000032685	ENST00000371941.3:c.960C>G	20.37:g.47309286G>C	ENSP00000361009:p.Ile320Met		E1P5X9|Q5JS95|Q5JS96|Q69YL2|Q7Z2L9|Q9BQH0|Q9BX55|Q9H4Q6|Q9P2D2|Q9UGQ4	Missense_Mutation	SNP	ENST00000371941.3	37	CCDS13410.1	.	.	.	.	.	.	.	.	.	.	G	14.92	2.678920	0.47886	.	.	ENSG00000124126	ENST00000371941;ENST00000396220	D;D	0.88354	-2.37;-2.37	5.5	4.54	0.55810	Pleckstrin homology-type (1);Pleckstrin homology domain (3);	0.000000	0.56097	U	0.000035	T	0.79690	0.4489	N	0.04508	-0.205	0.58432	D	0.999999	P	0.36837	0.571	B	0.38921	0.285	T	0.82068	-0.0640	10	0.52906	T	0.07	.	16.5982	0.84802	0.0:0.1305:0.8695:0.0	.	320	Q8TCU6	PREX1_HUMAN	M	320	ENSP00000361009:I320M;ENSP00000379522:I320M	ENSP00000361009:I320M	I	-	3	3	PREX1	46742693	1.000000	0.71417	1.000000	0.80357	0.993000	0.82548	2.917000	0.48821	1.433000	0.47394	0.650000	0.86243	ATC		0.542	PREX1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000079623.1		NM_020820	
PSMA8	143471	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	23714010	23714010	+	Silent	SNP	G	G	A	rs570532077		TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr18:23714010G>A	ENST00000308268.6	+	1	170	c.81G>A	c.(79-81)gcG>gcA	p.A27A	PSMA8_ENST00000415576.2_Silent_p.A27A|PSMA8_ENST00000343848.6_Silent_p.A27A	NM_001025096.1|NM_144662.2	NP_001020267.1|NP_653263.2	Q8TAA3	PSA7L_HUMAN	proteasome (prosome, macropain) subunit, alpha type, 8	27					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)|gene expression (GO:0010467)|mitotic cell cycle (GO:0000278)|mRNA metabolic process (GO:0016071)|negative regulation of apoptotic process (GO:0043066)|positive regulation of ubiquitin-protein ligase activity involved in mitotic cell cycle (GO:0051437)|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)|viral process (GO:0016032)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|proteasome core complex, alpha-subunit complex (GO:0019773)|spermatoproteasome complex (GO:1990111)	threonine-type endopeptidase activity (GO:0004298)	p.A27A(1)		breast(1)|cervix(1)|endometrium(1)|kidney(1)|large_intestine(3)|lung(7)|skin(2)	16	all_cancers(21;0.000585)|Lung NSC(5;0.00148)|all_lung(6;0.0038)|Ovarian(20;0.124)		OV - Ovarian serous cystadenocarcinoma(3;0.000324)|all cancers(3;0.000954)|LUSC - Lung squamous cell carcinoma(2;0.181)			CCCAGGAAGCGGTGAAGAAAG	0.557													G|||	1	0.000199681	0.0008	0.0	5008	,	,		16883	0.0		0.0	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)											97.0	89.0	92.0					18																	23714010		2203	4300	6503	SO:0001819	synonymous_variant	143471			BC047355	CCDS32808.1, CCDS45842.1, CCDS45843.1	18q11.2	2006-12-18				ENSG00000154611		"""Proteasome (prosome, macropain) subunits"""	22985	protein-coding gene	gene with protein product							Standard	XM_005258199		Approved	MGC26605, PSMA7L	uc002kvq.3	Q8TAA3		ENST00000308268.6:c.81G>A	18.37:g.23714010G>A			B0YJ75|Q8IVP4|Q8TA98|Q8TAA2	Silent	SNP	ENST00000308268.6	37	CCDS32808.1																																																																																				0.557	PSMA8-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000446255.1		NM_144662	
PTPMT1	114971	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	47593082	47593082	+	Silent	SNP	C	C	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr11:47593082C>A	ENST00000326674.9	+	4	529	c.507C>A	c.(505-507)atC>atA	p.I169I	PTPMT1_ENST00000426530.2_Missense_Mutation_p.P142T|PTPMT1_ENST00000326656.8_Silent_p.I105I|PTPMT1_ENST00000534775.1_3'UTR|NDUFS3_ENST00000533507.1_3'UTR|PTPMT1_ENST00000527079.2_3'UTR	NM_175732.2	NP_783859.1	Q8WUK0	PTPM1_HUMAN	protein tyrosine phosphatase, mitochondrial 1	169	Tyrosine-protein phosphatase.				cardiolipin biosynthetic process (GO:0032049)|glycerophospholipid biosynthetic process (GO:0046474)|inositol phosphate dephosphorylation (GO:0046855)|phosphatidylglycerol biosynthetic process (GO:0006655)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	phosphatidylglycerophosphatase activity (GO:0008962)|phosphatidylinositol-4,5-bisphosphate 5-phosphatase activity (GO:0004439)|protein tyrosine phosphatase activity (GO:0004725)|protein tyrosine/serine/threonine phosphatase activity (GO:0008138)	p.I169I(1)		breast(1)|kidney(1)|large_intestine(2)|lung(1)|skin(1)	6						GGTCATACATCCACATCAGGC	0.478																																																	1	Substitution - coding silent(1)	kidney(1)											99.0	94.0	96.0					11																	47593082		1918	4137	6055	SO:0001819	synonymous_variant	114971			BC014048	CCDS41643.1, CCDS44593.1	11p11.2	2011-06-09			ENSG00000110536	ENSG00000110536	3.1.3.36	"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Atypical dual specificity phosphatases"""	26965	protein-coding gene	gene with protein product		609538				12477932	Standard	NM_175732		Approved	PLIP, DUSP23, MOSP	uc001nfs.4	Q8WUK0	OTTHUMG00000166892	ENST00000326674.9:c.507C>A	11.37:g.47593082C>A			E9PAT8|Q7Z557|Q96CR2|Q9BXV8	Missense_Mutation	SNP	ENST00000326674.9	37	CCDS41643.1	.	.	.	.	.	.	.	.	.	.	C	15.58	2.877081	0.51801	.	.	ENSG00000110536	ENST00000426530	.	.	.	6.03	5.11	0.69529	.	.	.	.	.	T	0.50684	0.1630	.	.	.	0.80722	D	1	B	0.28850	0.225	B	0.24394	0.053	T	0.53337	-0.8453	7	0.87932	D	0	-11.3485	13.1472	0.59470	0.0:0.9258:0.0:0.0742	.	142	E9PAT8	.	T	142	.	ENSP00000410272:P142T	P	+	1	0	PTPMT1	47549658	1.000000	0.71417	0.998000	0.56505	0.871000	0.50021	1.694000	0.37752	1.547000	0.49401	0.655000	0.94253	CCA		0.478	PTPMT1-002	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391746.1		XM_374879	
QSOX1	5768	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	180165532	180165532	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr1:180165532T>G	ENST00000367602.3	+	12	1678	c.1604T>G	c.(1603-1605)tTc>tGc	p.F535C	QSOX1_ENST00000367600.5_Missense_Mutation_p.F535C			O00391	QSOX1_HUMAN	quiescin Q6 sulfhydryl oxidase 1	535					cell redox homeostasis (GO:0045454)|protein folding (GO:0006457)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of Golgi membrane (GO:0030173)	flavin-linked sulfhydryl oxidase activity (GO:0016971)|protein disulfide isomerase activity (GO:0003756)	p.F535C(1)		NS(1)|breast(1)|central_nervous_system(1)|endometrium(4)|kidney(3)|large_intestine(7)|lung(9)|ovary(1)|pancreas(1)|skin(2)|upper_aerodigestive_tract(1)	31						AAGGCCCACTTCTCCCCAAGC	0.622																																																	1	Substitution - Missense(1)	kidney(1)											144.0	146.0	145.0					1																	180165532		2203	4300	6503	SO:0001583	missense	5768			U97276	CCDS1337.1, CCDS30950.1	1q24	2008-02-05	2007-04-23	2007-04-23	ENSG00000116260	ENSG00000116260			9756	protein-coding gene	gene with protein product		603120	"""quiescin Q6"""	QSCN6		9878249, 8396966	Standard	NM_002826		Approved		uc001gnz.3	O00391	OTTHUMG00000035256	ENST00000367602.3:c.1604T>G	1.37:g.180165532T>G	ENSP00000356574:p.Phe535Cys		Q59G29|Q5T2X0|Q8TDL6|Q8WVP4	Missense_Mutation	SNP	ENST00000367602.3	37	CCDS1337.1	.	.	.	.	.	.	.	.	.	.	T	17.38	3.376064	0.61735	.	.	ENSG00000116260	ENST00000367602;ENST00000367600	T;T	0.23147	3.29;1.92	5.35	5.35	0.76521	.	0.409870	0.29653	N	0.011559	T	0.39545	0.1082	L	0.43923	1.385	0.41522	D	0.988405	P;P;D;P	0.89917	0.543;0.543;1.0;0.672	B;B;D;B	0.68192	0.186;0.142;0.956;0.274	T	0.27872	-1.0061	10	0.87932	D	0	-7.7381	9.6887	0.40114	0.1552:0.0:0.0:0.8448	.	535;535;535;535	A8K4C2;A8K477;O00391;O00391-2	.;.;QSOX1_HUMAN;.	C	535	ENSP00000356574:F535C;ENSP00000356572:F535C	ENSP00000356572:F535C	F	+	2	0	QSOX1	178432155	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	1.727000	0.38095	2.030000	0.59900	0.418000	0.28097	TTC		0.622	QSOX1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085289.1		NM_002826	
RELN	5649	hgsc.bcm.edu;ucsc.edu	37	7	103243784	103243793	+	Frame_Shift_Del	DEL	GACACCACAC	GACACCACAC	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	GACACCACAC	GACACCACAC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr7:103243784_103243793delGACACCACAC	ENST00000428762.1	-	24	3450_3459	c.3291_3300delGTGTGGTGTC	c.(3289-3300)gggtgtggtgtcfs	p.GCGV1097fs	RELN_ENST00000424685.2_Frame_Shift_Del_p.GCGV1097fs|RELN_ENST00000343529.5_Frame_Shift_Del_p.GCGV1097fs	NM_005045.3	NP_005036.2	P78509	RELN_HUMAN	reelin	1097					associative learning (GO:0008306)|axon guidance (GO:0007411)|brain development (GO:0007420)|cell adhesion (GO:0007155)|cell morphogenesis involved in differentiation (GO:0000904)|central nervous system development (GO:0007417)|cerebral cortex tangential migration (GO:0021800)|dendrite development (GO:0016358)|glial cell differentiation (GO:0010001)|hippocampus development (GO:0021766)|lateral motor column neuron migration (GO:0097477)|layer formation in cerebral cortex (GO:0021819)|long-term memory (GO:0007616)|N-methyl-D-aspartate receptor clustering (GO:0097114)|neuron migration (GO:0001764)|peptidyl-tyrosine phosphorylation (GO:0018108)|positive regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000969)|positive regulation of CREB transcription factor activity (GO:0032793)|positive regulation of dendritic spine morphogenesis (GO:0061003)|positive regulation of excitatory postsynaptic membrane potential (GO:2000463)|positive regulation of lateral motor column neuron migration (GO:1902078)|positive regulation of long-term synaptic potentiation (GO:1900273)|positive regulation of neuron projection development (GO:0010976)|positive regulation of peptidyl-tyrosine phosphorylation (GO:0050731)|positive regulation of phosphatidylinositol 3-kinase signaling (GO:0014068)|positive regulation of protein kinase activity (GO:0045860)|positive regulation of protein tyrosine kinase activity (GO:0061098)|positive regulation of small GTPase mediated signal transduction (GO:0051057)|positive regulation of synapse maturation (GO:0090129)|positive regulation of synaptic transmission, glutamatergic (GO:0051968)|positive regulation of TOR signaling (GO:0032008)|postsynaptic density protein 95 clustering (GO:0097119)|receptor localization to synapse (GO:0097120)|reelin-mediated signaling pathway (GO:0038026)|regulation of behavior (GO:0050795)|regulation of N-methyl-D-aspartate selective glutamate receptor activity (GO:2000310)|regulation of synaptic transmission (GO:0050804)|response to pain (GO:0048265)|spinal cord patterning (GO:0021511)|ventral spinal cord development (GO:0021517)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|extracellular space (GO:0005615)|proteinaceous extracellular matrix (GO:0005578)	lipoprotein particle receptor binding (GO:0070325)|metal ion binding (GO:0046872)|protein serine/threonine/tyrosine kinase activity (GO:0004712)|serine-type peptidase activity (GO:0008236)|very-low-density lipoprotein particle receptor binding (GO:0070326)			NS(3)|breast(8)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(4)|kidney(6)|large_intestine(43)|lung(101)|ovary(9)|pancreas(2)|prostate(4)|skin(14)|stomach(2)|upper_aerodigestive_tract(12)|urinary_tract(2)	227				COAD - Colon adenocarcinoma(1;8.98e-05)|Colorectal(1;0.00184)		CAGAAGAGATGACACCACACCCTTGTTCTG	0.448																																					NSCLC(146;835 1944 15585 22231 52158)												0																																										SO:0001589	frameshift_variant	5649				CCDS34722.1, CCDS47680.1	7q22	2008-07-18			ENSG00000189056	ENSG00000189056			9957	protein-coding gene	gene with protein product		600514				9049633	Standard	NM_005045		Approved	RL, PRO1598	uc010liz.3	P78509	OTTHUMG00000157247	ENST00000428762.1:c.3291_3300delGTGTGGTGTC	7.37:g.103243784_103243793delGACACCACAC	ENSP00000392423:p.Gly1097fs		A4D0P9|A4D0Q0|Q86UJ0|Q86UJ8|Q8NDV0|Q9UDQ2	Frame_Shift_Del	DEL	ENST00000428762.1	37	CCDS47680.1																																																																																				0.448	RELN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000348148.1		NM_005045	
RLF	6018	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	40704122	40704122	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr1:40704122G>A	ENST00000372771.4	+	8	3775	c.3748G>A	c.(3748-3750)Gaa>Aaa	p.E1250K		NM_012421.3	NP_036553.2	Q13129	RLF_HUMAN	rearranged L-myc fusion	1250					chromosome organization (GO:0051276)|DNA integration (GO:0015074)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.E1250K(1)		NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(11)|kidney(4)|large_intestine(18)|lung(18)|ovary(2)|pancreas(1)|prostate(2)|skin(1)|stomach(4)|urinary_tract(2)	68	Lung NSC(20;4.38e-06)|Ovarian(52;0.00167)|all_hematologic(146;0.0501)|Acute lymphoblastic leukemia(166;0.074)	Myeloproliferative disorder(586;0.0255)	OV - Ovarian serous cystadenocarcinoma(33;5.87e-19)|Epithelial(16;7.02e-16)|all cancers(16;1.69e-14)|Lung(16;0.0427)|LUSC - Lung squamous cell carcinoma(16;0.0461)			TAAAAAGGATGAATGTAGTTC	0.393																																																	1	Substitution - Missense(1)	kidney(1)											61.0	58.0	59.0					1																	40704122		2203	4300	6503	SO:0001583	missense	6018				CCDS448.1	1p32	2010-05-07	2005-08-16		ENSG00000117000	ENSG00000117000		"""Zinc fingers, C2H2-type"""	10025	protein-coding gene	gene with protein product		180610	"""rearranged L-myc fusion sequence"""			1649386	Standard	NM_012421		Approved	ZNF292L, Zn-15L	uc001cfc.4	Q13129	OTTHUMG00000005763	ENST00000372771.4:c.3748G>A	1.37:g.40704122G>A	ENSP00000361857:p.Glu1250Lys		Q14CQ1|Q9NU60	Missense_Mutation	SNP	ENST00000372771.4	37	CCDS448.1	.	.	.	.	.	.	.	.	.	.	G	15.38	2.816488	0.50527	.	.	ENSG00000117000	ENST00000372771;ENST00000535839	T	0.16457	2.34	5.91	5.91	0.95273	.	0.428902	0.28877	N	0.013851	T	0.19366	0.0465	N	0.24115	0.695	0.44728	D	0.997727	D;P	0.55605	0.972;0.953	P;P	0.51550	0.673;0.473	T	0.01185	-1.1425	10	0.29301	T	0.29	-19.3448	15.0617	0.71961	0.0:0.0:0.8582:0.1418	.	943;1250	F5H2M5;Q13129	.;RLF_HUMAN	K	1250;943	ENSP00000361857:E1250K	ENSP00000361857:E1250K	E	+	1	0	RLF	40476709	1.000000	0.71417	1.000000	0.80357	0.945000	0.59286	4.688000	0.61715	2.793000	0.96121	0.655000	0.94253	GAA		0.393	RLF-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000015767.1		NM_012421	
SCRN1	9805	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	29963599	29963599	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr7:29963599C>A	ENST00000426154.1	-	8	1395	c.1219G>T	c.(1219-1221)Gac>Tac	p.D407Y	SCRN1_ENST00000434476.2_Missense_Mutation_p.D427Y|SCRN1_ENST00000409497.1_Missense_Mutation_p.D407Y|SCRN1_ENST00000242059.5_Missense_Mutation_p.D407Y|SCRN1_ENST00000425819.2_Missense_Mutation_p.D339Y|SCRN1_ENST00000416113.2_Missense_Mutation_p.D233Y	NM_001145513.1	NP_001138985.1	Q12765	SCRN1_HUMAN	secernin 1	407					exocytosis (GO:0006887)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)	dipeptidase activity (GO:0016805)	p.D427Y(1)|p.D407Y(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(1)|lung(12)|ovary(2)|prostate(2)|skin(2)	25						ATCTCCGTGTCAACACAGTCA	0.483																																																	2	Substitution - Missense(2)	kidney(2)											138.0	142.0	141.0					7																	29963599		2203	4300	6503	SO:0001583	missense	9805			D83777	CCDS5422.1, CCDS47567.1, CCDS47568.1	7p14.3-p14.1	2006-09-06			ENSG00000136193	ENSG00000136193			22192	protein-coding gene	gene with protein product		614965				12221138	Standard	NM_014766		Approved	KIAA0193	uc011kaa.2	Q12765	OTTHUMG00000097093	ENST00000426154.1:c.1219G>T	7.37:g.29963599C>A	ENSP00000409068:p.Asp407Tyr		A8K0E9|B4DHM0|B4DIP5|C9JPG0|Q25QX7|Q8IWD1	Missense_Mutation	SNP	ENST00000426154.1	37	CCDS5422.1	.	.	.	.	.	.	.	.	.	.	C	22.3	4.266527	0.80358	.	.	ENSG00000136193	ENST00000242059;ENST00000426154;ENST00000425819;ENST00000544388;ENST00000409497;ENST00000416113;ENST00000434476	T;T;T;T;T;T	0.13778	3.05;3.05;2.91;3.05;2.56;3.03	4.73	4.73	0.59995	.	0.000000	0.85682	D	0.000000	T	0.37919	0.1021	M	0.69823	2.125	0.80722	D	1	D;D;D;D	0.89917	0.997;0.997;1.0;0.995	D;D;D;D	0.87578	0.96;0.96;0.998;0.928	T	0.24154	-1.0168	10	0.87932	D	0	-24.5607	16.632	0.85036	0.0:1.0:0.0:0.0	.	427;427;339;407	C9JPG0;B4DHM0;B4DIP5;Q12765	.;.;.;SCRN1_HUMAN	Y	407;407;339;211;407;233;427	ENSP00000242059:D407Y;ENSP00000409068:D407Y;ENSP00000414245:D339Y;ENSP00000386872:D407Y;ENSP00000407460:D233Y;ENSP00000388942:D427Y	ENSP00000242059:D407Y	D	-	1	0	SCRN1	29930124	1.000000	0.71417	0.991000	0.47740	0.951000	0.60555	7.302000	0.78861	2.319000	0.78375	0.655000	0.94253	GAC		0.483	SCRN1-202	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000214231.2		NM_014766	
SEC24C	9632	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	75520019	75520019	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr10:75520019G>A	ENST00000339365.2	+	6	887	c.725G>A	c.(724-726)aGc>aAc	p.S242N	SEC24C_ENST00000535742.1_Intron|SEC24C_ENST00000546025.1_Missense_Mutation_p.S100N|SEC24C_ENST00000411652.2_Missense_Mutation_p.S100N|SEC24C_ENST00000540668.1_Intron|SEC24C_ENST00000345254.4_Missense_Mutation_p.S242N	NM_004922.3	NP_004913.2	P53992	SC24C_HUMAN	SEC24 family member C	242					antigen processing and presentation of exogenous peptide antigen via MHC class II (GO:0019886)|antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cellular protein metabolic process (GO:0044267)|COPII vesicle coating (GO:0048208)|ER to Golgi vesicle-mediated transport (GO:0006888)|intracellular protein transport (GO:0006886)|membrane organization (GO:0061024)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	COPII vesicle coat (GO:0030127)|cytosol (GO:0005829)|endoplasmic reticulum membrane (GO:0005789)|ER to Golgi transport vesicle membrane (GO:0012507)|Golgi membrane (GO:0000139)	zinc ion binding (GO:0008270)	p.S242N(1)		breast(2)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(3)|lung(12)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	32	Prostate(51;0.0112)					CCCTCAGTGAGCCAGCCCAAC	0.642																																																	1	Substitution - Missense(1)	kidney(1)											79.0	83.0	82.0					10																	75520019		2203	4300	6503	SO:0001583	missense	9632			D38555	CCDS7332.1	10q22	2013-10-21	2013-10-21		ENSG00000176986	ENSG00000176986			10705	protein-coding gene	gene with protein product		607185	"""SEC24 (S. cerevisiae) related gene family, member C"", ""SEC24 family, member C (S. cerevisiae)"""			10214955, 7584044	Standard	NM_004922		Approved	KIAA0079	uc001jux.3	P53992	OTTHUMG00000018476	ENST00000339365.2:c.725G>A	10.37:g.75520019G>A	ENSP00000343405:p.Ser242Asn		B4DZT4|Q8WV25	Missense_Mutation	SNP	ENST00000339365.2	37	CCDS7332.1	.	.	.	.	.	.	.	.	.	.	G	9.951	1.220085	0.22373	.	.	ENSG00000176986	ENST00000546025;ENST00000345254;ENST00000339365;ENST00000411652	T;T;D	0.82711	-1.2;-1.2;-1.64	5.63	1.42	0.22433	.	0.449627	0.26311	N	0.025105	T	0.68183	0.2973	L	0.29908	0.895	0.80722	D	1	B;B;B	0.06786	0.0;0.001;0.0	B;B;B	0.04013	0.0;0.001;0.001	T	0.51942	-0.8641	10	0.23302	T	0.38	-0.7522	6.0773	0.19923	0.3284:0.2068:0.4648:0.0	.	100;242;242	E7EP00;G5EA31;P53992	.;.;SC24C_HUMAN	N	100;242;242;100	ENSP00000321845:S242N;ENSP00000343405:S242N;ENSP00000402913:S100N	ENSP00000343405:S242N	S	+	2	0	SEC24C	75190025	0.778000	0.28640	0.998000	0.56505	0.995000	0.86356	0.818000	0.27295	0.055000	0.16094	0.561000	0.74099	AGC		0.642	SEC24C-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000048679.1			
SEMA5A	9037	hgsc.bcm.edu;ucsc.edu	37	5	9122825	9122825	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr5:9122825delG	ENST00000382496.5	-	14	2389	c.1724delC	c.(1723-1725)ccgfs	p.P575fs		NM_003966.2	NP_003957.2	Q13591	SEM5A_HUMAN	sema domain, seven thrombospondin repeats (type 1 and type 1-like), transmembrane domain (TM) and short cytoplasmic domain, (semaphorin) 5A	575	TSP type-1 1. {ECO:0000255|PROSITE- ProRule:PRU00210}.				axon guidance (GO:0007411)|axonal fasciculation (GO:0007413)|blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|cell adhesion (GO:0007155)|cell chemotaxis (GO:0060326)|cell-cell signaling (GO:0007267)|diencephalon development (GO:0021536)|negative regulation of axon extension involved in axon guidance (GO:0048843)|negative regulation of cell adhesion (GO:0007162)|negative regulation of endothelial cell apoptotic process (GO:2000352)|nervous system development (GO:0007399)|patterning of blood vessels (GO:0001569)|positive chemotaxis (GO:0050918)|positive regulation of actin filament depolymerization (GO:0030836)|positive regulation of angiogenesis (GO:0045766)|positive regulation of axon extension involved in axon guidance (GO:0048842)|positive regulation of catenin import into nucleus (GO:0035413)|positive regulation of endothelial cell chemotaxis (GO:2001028)|positive regulation of endothelial cell proliferation (GO:0001938)|positive regulation of protein kinase B signaling (GO:0051897)|signal clustering (GO:1990256)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)	axon guidance receptor activity (GO:0008046)|chondroitin sulfate proteoglycan binding (GO:0035373)|heparan sulfate proteoglycan binding (GO:0043395)|semaphorin receptor binding (GO:0030215)|syndecan binding (GO:0045545)			biliary_tract(1)|breast(4)|central_nervous_system(2)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|large_intestine(13)|lung(40)|ovary(2)|prostate(5)|skin(2)|upper_aerodigestive_tract(3)|urinary_tract(1)	81						ACCACACTGCGGGGCCGGGCT	0.632																																																	0													46.0	51.0	49.0					5																	9122825		2203	4300	6503	SO:0001589	frameshift_variant	9037			U52840	CCDS3875.1	5p15.2	2008-05-15			ENSG00000112902	ENSG00000112902		"""Semaphorins"""	10736	protein-coding gene	gene with protein product		609297		SEMAF		8817451, 9464278	Standard	NM_003966		Approved	semF	uc003jek.2	Q13591	OTTHUMG00000090501	ENST00000382496.5:c.1724delC	5.37:g.9122825delG	ENSP00000371936:p.Pro575fs		D3DTC6|O60408|Q1RLL9	Frame_Shift_Del	DEL	ENST00000382496.5	37	CCDS3875.1																																																																																				0.632	SEMA5A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206989.2			
SETD5	55209	hgsc.bcm.edu	37	3	9517686	9517686	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr3:9517686T>C	ENST00000406341.1	+	22	4430	c.4240T>C	c.(4240-4242)Tac>Cac	p.Y1414H	SETD5_ENST00000302463.6_Missense_Mutation_p.Y1316H|SETD5_ENST00000402198.1_Missense_Mutation_p.Y1414H|SETD5_ENST00000402466.1_Missense_Mutation_p.Y1316H|SETD5_ENST00000407969.1_Missense_Mutation_p.Y1433H			Q9C0A6	SETD5_HUMAN	SET domain containing 5	1414										NS(2)|breast(3)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(10)|lung(11)|ovary(3)|prostate(7)|upper_aerodigestive_tract(1)|urinary_tract(1)	47	Medulloblastoma(99;0.227)			OV - Ovarian serous cystadenocarcinoma(96;0.112)		TTCACAGCACTACCCACACCG	0.572																																																	0													48.0	47.0	47.0					3																	9517686		1977	4159	6136	SO:0001583	missense	55209			BC020956	CCDS46741.1, CCDS74892.1	3p25.3	2011-12-13			ENSG00000168137	ENSG00000168137			25566	protein-coding gene	gene with protein product		615743				11214970	Standard	XM_005265299		Approved	FLJ10707	uc003brt.3	Q9C0A6	OTTHUMG00000150491	ENST00000406341.1:c.4240T>C	3.37:g.9517686T>C	ENSP00000383939:p.Tyr1414His		Q6AI17|Q8WUB6|Q9H3X4|Q9H6V7|Q9H7S3|Q9NVI9	Missense_Mutation	SNP	ENST00000406341.1	37	CCDS46741.1	.	.	.	.	.	.	.	.	.	.	T	16.94	3.261601	0.59431	.	.	ENSG00000168137	ENST00000402198;ENST00000402466;ENST00000406341;ENST00000407969;ENST00000302463	D;D;D;D;D	0.93019	-2.82;-3.15;-2.82;-2.81;-3.15	4.96	4.96	0.65561	.	0.092295	0.47455	D	0.000239	D	0.92718	0.7685	N	0.19112	0.55	0.38224	D	0.940844	D;D;D	0.71674	0.996;0.998;0.99	P;D;P	0.64877	0.904;0.93;0.723	D	0.93178	0.6572	10	0.34782	T	0.22	-8.1182	14.9377	0.70970	0.0:0.0:0.0:1.0	.	1083;1316;1414	B3KXG4;Q9C0A6-3;Q9C0A6	.;.;SETD5_HUMAN	H	1414;1316;1414;1433;1316	ENSP00000385852:Y1414H;ENSP00000384429:Y1316H;ENSP00000383939:Y1414H;ENSP00000384114:Y1433H;ENSP00000302028:Y1316H	ENSP00000302028:Y1316H	Y	+	1	0	SETD5	9492686	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.281000	0.72632	1.982000	0.57802	0.383000	0.25322	TAC		0.572	SETD5-001	KNOWN	alternative_5_UTR|not_organism_supported|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318425.1		XM_371614	
SLC7A4	6545	broad.mit.edu	37	22	21385373	21385373	+	Silent	SNP	G	G	C			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr22:21385373G>C	ENST00000382932.2	-	2	796	c.729C>G	c.(727-729)tcC>tcG	p.S243S	SLC7A4_ENST00000403586.1_Silent_p.S243S|AC002472.11_ENST00000450652.1_RNA	NM_004173.2	NP_004164.2	O43246	CTR4_HUMAN	solute carrier family 7, member 4	243					basic amino acid transport (GO:0015802)|cellular amino acid metabolic process (GO:0006520)|transport (GO:0006810)	integral component of membrane (GO:0016021)	basic amino acid transmembrane transporter activity (GO:0015174)	p.S243S(1)		breast(3)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|lung(7)|ovary(1)|prostate(2)	18	all_cancers(11;2.85e-22)|Lung NSC(8;4.21e-14)|all_lung(8;6.08e-13)|Melanoma(16;0.000465)|Ovarian(15;0.0028)|Colorectal(54;0.0968)	Lung SC(17;0.0262)	LUSC - Lung squamous cell carcinoma(15;0.000204)|Lung(15;0.00494)|Epithelial(17;0.195)		L-Arginine(DB00125)|L-Lysine(DB00123)|L-Ornithine(DB00129)	CATAGAAGCAGGAGGCAGTGC	0.637																																																	1	Substitution - coding silent(1)	kidney(1)											50.0	47.0	48.0					22																	21385373		2203	4300	6503	SO:0001819	synonymous_variant	6545			AJ000730	CCDS33608.1	22q11.21	2013-07-19	2013-07-19		ENSG00000099960	ENSG00000099960		"""Solute carriers"""	11062	protein-coding gene	gene with protein product		603752	"""solute carrier family 7 (cationic amino acid transporter, y+ system), member 4"", ""solute carrier family 7 (orphan transporter), member 4"""			9598310, 11665818	Standard	NM_004173		Approved	HCAT3, CAT-4, VH	uc002zud.3	O43246	OTTHUMG00000150896	ENST00000382932.2:c.729C>G	22.37:g.21385373G>C			Q0P5U2|Q3KNQ6|Q4VC45|Q6IBY8|Q96H88	Silent	SNP	ENST00000382932.2	37	CCDS33608.1																																																																																				0.637	SLC7A4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000320467.1		NM_004173	
SLFN11	91607	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	33690266	33690266	+	Silent	SNP	C	C	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr17:33690266C>T	ENST00000394566.1	-	4	833	c.561G>A	c.(559-561)tcG>tcA	p.S187S	SLFN11_ENST00000308377.4_Silent_p.S187S	NM_001104587.1|NM_001104588.1|NM_001104589.1|NM_001104590.1	NP_001098057.1|NP_001098058.1|NP_001098059.1|NP_001098060.1	Q7Z7L1	SLN11_HUMAN	schlafen family member 11	187					defense response to virus (GO:0051607)|negative regulation of G1/S transition of mitotic cell cycle (GO:2000134)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ATP binding (GO:0005524)|tRNA binding (GO:0000049)	p.S187S(1)		autonomic_ganglia(1)|breast(1)|kidney(3)|large_intestine(14)|lung(17)|ovary(1)|prostate(4)|skin(2)|stomach(5)|upper_aerodigestive_tract(2)	50		Ovarian(249;0.17)		UCEC - Uterine corpus endometrioid carcinoma (308;0.0182)		CAGCAGGATCCGAGTTTGGGT	0.413																																																	1	Substitution - coding silent(1)	kidney(1)											122.0	124.0	124.0					17																	33690266		2203	4300	6503	SO:0001819	synonymous_variant	91607			AK074184	CCDS11294.1	17q12	2006-04-05			ENSG00000172716	ENSG00000172716			26633	protein-coding gene	gene with protein product		614953				12477932	Standard	NM_001104587		Approved	FLJ34922	uc010ctr.3	Q7Z7L1	OTTHUMG00000132948	ENST00000394566.1:c.561G>A	17.37:g.33690266C>T			E1P643|Q8N3S8|Q8N762|Q8TEE0	Silent	SNP	ENST00000394566.1	37	CCDS11294.1																																																																																				0.413	SLFN11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256480.1		NM_152270	
SORBS2	8470	broad.mit.edu;hgsc.bcm.edu	37	4	186508841	186508841	+	Splice_Site	SNP	C	C	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr4:186508841C>T	ENST00000284776.7	-	21	3752	c.3243G>A	c.(3241-3243)ggG>ggA	p.G1081G	SORBS2_ENST00000355634.5_Splice_Site_p.G1181G|SORBS2_ENST00000418609.1_Splice_Site_p.G985G|SORBS2_ENST00000449407.2_Splice_Site_p.G625G|SORBS2_ENST00000393528.3_Splice_Site_p.G647G|SORBS2_ENST00000431808.1_Splice_Site_p.G1081G|SORBS2_ENST00000319471.9_Splice_Site_p.G712G|SORBS2_ENST00000437304.2_Splice_Site_p.G805G|SORBS2_ENST00000448662.2_Splice_Site_p.G642G|RP11-301L8.2_ENST00000411847.1_RNA	NM_021069.4	NP_066547.1	O94875	SRBS2_HUMAN	sorbin and SH3 domain containing 2	1081	SH3 3. {ECO:0000255|PROSITE- ProRule:PRU00192}.				actin filament organization (GO:0007015)|cell adhesion (GO:0007155)|cell migration (GO:0016477)	actin cytoskeleton (GO:0015629)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|Z disc (GO:0030018)	cytoskeletal adaptor activity (GO:0008093)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)|structural constituent of cytoskeleton (GO:0005200)|structural constituent of muscle (GO:0008307)	p.G642G(1)|p.G647G(1)|p.G1081G(1)|p.G805G(1)		endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(9)|lung(21)|ovary(2)|prostate(2)|skin(4)|urinary_tract(1)	53		all_cancers(14;4.27e-52)|all_epithelial(14;6.58e-39)|all_lung(41;1.42e-13)|Lung NSC(41;3.73e-13)|Melanoma(20;1.91e-06)|Colorectal(36;0.00692)|Hepatocellular(41;0.00826)|Renal(120;0.00994)|Prostate(90;0.0101)|all_hematologic(60;0.0174)|all_neural(102;0.244)		OV - Ovarian serous cystadenocarcinoma(60;1.54e-09)|BRCA - Breast invasive adenocarcinoma(30;0.000232)|GBM - Glioblastoma multiforme(59;0.000385)|STAD - Stomach adenocarcinoma(60;0.00109)|LUSC - Lung squamous cell carcinoma(40;0.0205)		TTCTTGAGGTCCCTGAAAATA	0.493																																					Esophageal Squamous(153;41 2433 9491 36028)												4	Substitution - coding silent(4)	kidney(4)											56.0	57.0	57.0					4																	186508841		2203	4300	6503	SO:0001630	splice_region_variant	8470				CCDS3845.1, CCDS43289.2, CCDS47173.1, CCDS47174.1, CCDS47175.1, CCDS47176.1, CCDS54825.1, CCDS59482.1	4q35.1	2008-02-05			ENSG00000154556	ENSG00000154556			24098	protein-coding gene	gene with protein product	"""Arg/Abl interacting protein"""					9211900, 9872452	Standard	NM_021069		Approved	ARGBP2, KIAA0777	uc003iym.3	O94875	OTTHUMG00000157215	ENST00000284776.7:c.3242-1G>A	4.37:g.186508841C>T			A6NEK9|B3KPQ7|B7Z1G5|B7Z3X6|C9JKV9|D3DP62|D3DP63|E9PAS5|E9PAW4|G3XAI0|H7BXR4|J3KNZ5|O60592|O60593|Q96EX0	Silent	SNP	ENST00000284776.7	37	CCDS3845.1																																																																																				0.493	SORBS2-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000347944.3		NM_003603	Silent
SPTAN1	6709	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	131371420	131371420	+	Nonsense_Mutation	SNP	C	C	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr9:131371420C>T	ENST00000372731.4	+	36	4725	c.4615C>T	c.(4615-4617)Cag>Tag	p.Q1539*	SPTAN1_ENST00000372739.3_Nonsense_Mutation_p.Q1539*|SPTAN1_ENST00000358161.5_Nonsense_Mutation_p.Q1539*	NM_001195532.1|NM_003127.3	NP_001182461.1|NP_003118.2	Q13813	SPTN1_HUMAN	spectrin, alpha, non-erythrocytic 1	1539					actin filament capping (GO:0051693)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|cellular component disassembly involved in execution phase of apoptosis (GO:0006921)	cuticular plate (GO:0032437)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|fascia adherens (GO:0005916)|intracellular membrane-bounded organelle (GO:0043231)|lateral plasma membrane (GO:0016328)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|spectrin (GO:0008091)|vesicle (GO:0031982)|Z disc (GO:0030018)	actin binding (GO:0003779)|calcium ion binding (GO:0005509)|structural constituent of cytoskeleton (GO:0005200)	p.Q1539*(1)		NS(2)|breast(8)|cervix(2)|endometrium(6)|kidney(4)|large_intestine(21)|liver(1)|lung(25)|ovary(5)|pancreas(1)|prostate(4)|skin(3)|stomach(1)|upper_aerodigestive_tract(2)|urinary_tract(2)	87						TCTGAAAGCCCAGATGATTGA	0.488																																					NSCLC(120;833 1744 2558 35612 37579)												1	Substitution - Nonsense(1)	kidney(1)											116.0	112.0	113.0					9																	131371420		2203	4300	6503	SO:0001587	stop_gained	6709			M19725	CCDS6905.1, CCDS48036.1, CCDS75914.1	9q34.11	2013-01-10	2012-06-15		ENSG00000197694	ENSG00000197694		"""EF-hand domain containing"""	11273	protein-coding gene	gene with protein product	"""alpha-fodrin"""	182810				3336352	Standard	NM_003127		Approved		uc004bvm.4	Q13813	OTTHUMG00000020754	ENST00000372731.4:c.4615C>T	9.37:g.131371420C>T	ENSP00000361816:p.Gln1539*		Q13186|Q15324|Q16606|Q59EF1|Q5VXV5|Q5VXV6|Q7Z6M5|Q9P0V0	Nonsense_Mutation	SNP	ENST00000372731.4	37	CCDS6905.1	.	.	.	.	.	.	.	.	.	.	C	45	11.525267	0.99572	.	.	ENSG00000197694	ENST00000358161;ENST00000372731;ENST00000372739;ENST00000372719	.	.	.	5.65	5.65	0.86999	.	0.058821	0.64402	D	0.000001	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.06891	T	0.86	.	19.7244	0.96157	0.0:1.0:0.0:0.0	.	.	.	.	X	1539;1539;1539;1519	.	ENSP00000350882:Q1539X	Q	+	1	0	SPTAN1	130411241	1.000000	0.71417	1.000000	0.80357	0.977000	0.68977	5.724000	0.68500	2.659000	0.90383	0.655000	0.94253	CAG		0.488	SPTAN1-004	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000054472.1		NM_003127	
SYNE1	23345	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	152647465	152647465	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr6:152647465G>A	ENST00000367255.5	-	79	15860	c.15259C>T	c.(15259-15261)Cgg>Tgg	p.R5087W	SYNE1_ENST00000423061.1_Missense_Mutation_p.R5016W|SYNE1_ENST00000448038.1_Missense_Mutation_p.R5016W|SYNE1_ENST00000341594.5_Missense_Mutation_p.R4834W|SYNE1_ENST00000265368.4_Missense_Mutation_p.R5087W	NM_182961.3	NP_892006.3	Q8NF91	SYNE1_HUMAN	spectrin repeat containing, nuclear envelope 1	5087					cell death (GO:0008219)|cytoskeletal anchoring at nuclear membrane (GO:0090286)|establishment of nucleus localization (GO:0040023)|Golgi organization (GO:0007030)|muscle cell differentiation (GO:0042692)|nuclear matrix anchoring at nuclear membrane (GO:0090292)|nucleus organization (GO:0006997)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nucleus (GO:0005634)|postsynaptic membrane (GO:0045211)|sarcomere (GO:0030017)|SUN-KASH complex (GO:0034993)	actin binding (GO:0003779)|actin filament binding (GO:0051015)|lamin binding (GO:0005521)|poly(A) RNA binding (GO:0044822)|protein homodimerization activity (GO:0042803)	p.R5087W(2)|p.R5016W(1)		NS(3)|biliary_tract(1)|breast(17)|central_nervous_system(21)|cervix(3)|endometrium(27)|haematopoietic_and_lymphoid_tissue(4)|kidney(16)|large_intestine(138)|liver(1)|lung(190)|ovary(11)|pancreas(5)|prostate(12)|skin(20)|stomach(3)|upper_aerodigestive_tract(33)|urinary_tract(19)	524		Ovarian(120;0.0955)	BRCA - Breast invasive adenocarcinoma(37;0.243)	OV - Ovarian serous cystadenocarcinoma(155;2.24e-10)		CCAGAGTCCCGGCTCATCCTC	0.478										HNSCC(10;0.0054)																																							3	Substitution - Missense(3)	kidney(3)											77.0	81.0	80.0					6																	152647465		2203	4300	6503	SO:0001583	missense	23345			AB018339	CCDS5235.1, CCDS5236.1, CCDS5236.2	6q24.2-q25.3	2014-09-17			ENSG00000131018	ENSG00000131018			17089	protein-coding gene	gene with protein product	"""myocyte nuclear envelope protein 1"", ""nuclear envelope spectrin repeat-1"""	608441	"""chromosome 6 open reading frame 98"""	C6orf98		9872452, 10878022	Standard	NM_182961		Approved	SYNE-1B, KIAA0796, 8B, Nesprin-1, enaptin, MYNE1, CPG2, dJ45H2.2, SCAR8, ARCA1, Nesp1	uc003qou.4	Q8NF91	OTTHUMG00000015841	ENST00000367255.5:c.15259C>T	6.37:g.152647465G>A	ENSP00000356224:p.Arg5087Trp		E7EQI5|O94890|Q5JV19|Q5JV22|Q8N9P7|Q8TCP1|Q8WWW6|Q8WWW7|Q8WXF6|Q96N17|Q9C0A7|Q9H525|Q9H526|Q9NS36|Q9NU50|Q9UJ06|Q9UJ07|Q9ULF8	Missense_Mutation	SNP	ENST00000367255.5	37	CCDS5236.2	.	.	.	.	.	.	.	.	.	.	G	11.31	1.600829	0.28534	.	.	ENSG00000131018	ENST00000367255;ENST00000423061;ENST00000265368;ENST00000448038;ENST00000341594	T;T;T;T;T	0.53857	1.3;1.3;1.3;1.3;0.6	5.56	4.7	0.59300	.	0.401750	0.21710	N	0.070295	T	0.23926	0.0579	N	0.14661	0.345	0.31886	N	0.617761	D;P;P;D	0.58620	0.972;0.903;0.903;0.983	P;B;B;P	0.45712	0.471;0.124;0.124;0.491	T	0.14783	-1.0460	10	0.87932	D	0	.	10.2581	0.43410	0.0711:0.1347:0.7942:0.0	.	5087;5087;5087;5016	Q8NF91-7;Q8NF91;E7EQI5;Q8NF91-4	.;SYNE1_HUMAN;.;.	W	5087;5016;5087;5016;4834	ENSP00000356224:R5087W;ENSP00000396024:R5016W;ENSP00000265368:R5087W;ENSP00000390975:R5016W;ENSP00000341887:R4834W	ENSP00000265368:R5087W	R	-	1	2	SYNE1	152689158	1.000000	0.71417	0.103000	0.21229	0.038000	0.13279	3.948000	0.56660	1.366000	0.46076	-0.194000	0.12790	CGG		0.478	SYNE1-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000334755.2		NM_182961	
TMEM87A	25963	broad.mit.edu;ucsc.edu	37	15	42529668	42529668	+	Missense_Mutation	SNP	T	T	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr15:42529668T>A	ENST00000389834.4	-	9	1094	c.830A>T	c.(829-831)tAt>tTt	p.Y277F	TMEM87A_ENST00000448392.1_Missense_Mutation_p.Y216F	NM_015497.3	NP_056312.2	Q8NBN3	TM87A_HUMAN	transmembrane protein 87A	277						integral component of membrane (GO:0016021)		p.Y277F(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(1)|lung(9)|ovary(1)|prostate(1)|skin(1)|upper_aerodigestive_tract(2)	24		all_cancers(109;4.28e-16)|all_epithelial(112;1.04e-14)|Lung NSC(122;5.01e-09)|all_lung(180;2.24e-08)|Melanoma(134;0.0574)|Colorectal(260;0.152)		GBM - Glioblastoma multiforme(94;1.03e-06)		AAATTCCGCATAGAAGACAGC	0.433																																																	1	Substitution - Missense(1)	kidney(1)											111.0	103.0	106.0					15																	42529668		2203	4299	6502	SO:0001583	missense	25963			AF132733	CCDS32205.1, CCDS45243.1, CCDS66742.1	15q15.1	2005-10-30				ENSG00000103978			24522	protein-coding gene	gene with protein product						12477932	Standard	XM_005254287		Approved	DKFZP564G2022	uc021sjr.1	Q8NBN3		ENST00000389834.4:c.830A>T	15.37:g.42529668T>A	ENSP00000374484:p.Tyr277Phe		Q6NT77|Q8NCA4|Q9BS46|Q9P103|Q9Y3Y7	Missense_Mutation	SNP	ENST00000389834.4	37	CCDS32205.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.867868	0.91587	.	.	ENSG00000103978	ENST00000389834;ENST00000448392;ENST00000535305	.	.	.	5.8	5.8	0.92144	.	0.000000	0.85682	D	0.000000	T	0.79021	0.4376	M	0.74467	2.265	0.80722	D	1	D;P	0.89917	1.0;0.889	D;P	0.87578	0.998;0.749	T	0.79729	-0.1681	9	0.48119	T	0.1	-12.4336	16.1464	0.81575	0.0:0.0:0.0:1.0	.	277;216	Q8NBN3;Q8NBN3-3	TM87A_HUMAN;.	F	277;216;253	.	ENSP00000374484:Y277F	Y	-	2	0	TMEM87A	40316960	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	8.040000	0.89188	2.220000	0.72140	0.383000	0.25322	TAT		0.433	TMEM87A-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000420482.2		NM_015497	
RP11-24M17.5	0	broad.mit.edu	37	15	76074470	76074470	+	RNA	SNP	A	A	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr15:76074470A>G	ENST00000395215.3	+	0	649				RN7SL319P_ENST00000480656.2_RNA														p.Q203R(4)									CGGTTACAGCAGACCATAAAG	0.577																																																	4	Substitution - Missense(4)	kidney(3)|endometrium(1)																																										0																															15.37:g.76074470A>G				Missense_Mutation	SNP	ENST00000395215.3	37		.	.	.	.	.	.	.	.	.	.	.	3.199	-0.164202	0.06502	.	.	ENSG00000187812	ENST00000395215	.	.	.	0.789	0.789	0.18607	.	.	.	.	.	T	0.40222	0.1108	.	.	.	.	.	.	D	0.54964	0.969	P	0.57101	0.813	T	0.45101	-0.9284	6	0.19147	T	0.46	.	2.915	0.05750	0.5938:0.0:0.0:0.4062	.	203	B4DZE6	.	R	203	.	ENSP00000378641:Q203R	Q	+	2	0	AC019294.2	73861525	0.996000	0.38824	0.003000	0.11579	0.003000	0.03518	0.808000	0.27154	0.620000	0.30215	0.228000	0.17796	CAG		0.577	RP11-24M17.5-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000420501.1			
BCRP7	100133163	broad.mit.edu	37	22	18846005	18846005	+	3'UTR	SNP	G	G	A	rs199684265	byFrequency	TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr22:18846005G>A	ENST00000412938.1	+	0	3363																											TGCGCAGGCCGACACTCACTG	0.617																																																	0																																										SO:0001624	3_prime_UTR_variant	0																														ENST00000412938.1:c.*3360G>A	22.37:g.18846005G>A				RNA	SNP	ENST00000412938.1	37																																																																																					0.617	AC008132.13-002	KNOWN	basic	processed_transcript	protein_coding	OTTHUMT00000471615.1			
USP51	158880	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	55514571	55514571	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chrX:55514571C>T	ENST00000500968.3	-	2	884	c.802G>A	c.(802-804)Gaa>Aaa	p.E268K	USP51_ENST00000586165.1_Intron	NM_201286.3	NP_958443.1	Q70EK9	UBP51_HUMAN	ubiquitin specific peptidase 51	268					protein deubiquitination (GO:0016579)|ubiquitin-dependent protein catabolic process (GO:0006511)		ubiquitin-specific protease activity (GO:0004843)|zinc ion binding (GO:0008270)	p.E268K(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(5)|lung(11)|ovary(2)|skin(2)|upper_aerodigestive_tract(2)	30						TGCTTTGTTTCTGCATGTTTG	0.393																																																	1	Substitution - Missense(1)	kidney(1)											135.0	120.0	125.0					X																	55514571		2203	4300	6503	SO:0001583	missense	158880			BF741256	CCDS14370.1	Xp11	2009-03-19	2005-08-08		ENSG00000247746	ENSG00000247746		"""Ubiquitin-specific peptidases"""	23086	protein-coding gene	gene with protein product			"""ubiquitin specific protease 51"""			12838346	Standard	NM_201286		Approved		uc004dun.2	Q70EK9	OTTHUMG00000021656	ENST00000500968.3:c.802G>A	X.37:g.55514571C>T	ENSP00000423333:p.Glu268Lys		Q8IWJ8	Missense_Mutation	SNP	ENST00000500968.3	37	CCDS14370.1	.	.	.	.	.	.	.	.	.	.	.	3.613	-0.079114	0.07141	.	.	ENSG00000247746	ENST00000500968	T	0.43294	0.95	3.18	2.29	0.28610	Zinc finger, RING/FYVE/PHD-type (1);Zinc finger, UBP-type (2);	0.211954	0.37530	U	0.002056	T	0.12902	0.0313	N	0.01297	-0.9	0.33713	D	0.616051	B	0.18741	0.03	B	0.28139	0.086	T	0.20940	-1.0260	10	0.07813	T	0.8	.	5.1627	0.15070	0.0:0.7151:0.0:0.2849	.	268	Q70EK9	UBP51_HUMAN	K	268	ENSP00000423333:E268K	ENSP00000423333:E268K	E	-	1	0	USP51	55531296	1.000000	0.71417	0.953000	0.39169	0.318000	0.28184	3.734000	0.55037	0.707000	0.31934	0.502000	0.49764	GAA		0.393	USP51-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000056871.2		NM_201286	
VHL	7428	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	10188218	10188218	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	G	T	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr3:10188218G>T	ENST00000256474.2	+	2	1201	c.361G>T	c.(361-363)Gat>Tat	p.D121Y	VHL_ENST00000345392.2_Intron|VHL_ENST00000477538.1_3'UTR	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase	121	Involved in binding to CCT complex.		D -> G (in VHLD; type I; dbSNP:rs5030832). {ECO:0000269|PubMed:8956040}.		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.D121Y(6)|p.R120fs*38(1)|p.?(1)|p.D121_A122del(1)|p.R120fs*34(1)|p.R120fs*10(1)|p.L118_G123>P(1)|p.D121fs*38(1)|p.D121*(1)|p.W117fs*1(1)|p.A122fs*7(1)|p.D121fs*35(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)		GCTCTTCAGAGATGCAGGGAC	0.502		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"""	17	Deletion - Frameshift(7)|Substitution - Missense(6)|Deletion - In frame(1)|Substitution - Nonsense(1)|Unknown(1)|Complex - deletion inframe(1)	kidney(17)	GRCh37	CD962176|CM056724	VHL	D|M							184.0	171.0	176.0					3																	10188218		2203	4300	6503	SO:0001583	missense	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.361G>T	3.37:g.10188218G>T	ENSP00000256474:p.Asp121Tyr		B2RE45|Q13599|Q6PDA9	Missense_Mutation	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	G	17.51	3.406908	0.62399	.	.	ENSG00000134086	ENST00000256474;ENST00000450183	D	0.99841	-7.09	5.07	5.07	0.68467	von Hippel-Lindau disease tumor suppressor,  beta domain (1);von Hippel-Lindau disease tumour suppressor, beta/alpha domain (2);	0.050790	0.85682	D	0.000000	D	0.99782	0.9909	M	0.79011	2.435	0.80722	D	1	D	0.89917	1.0	D	0.85130	0.997	D	0.96910	0.9666	10	0.87932	D	0	-24.4217	16.3181	0.82935	0.0:0.0:1.0:0.0	.	121	P40337	VHL_HUMAN	Y	121;39	ENSP00000256474:D121Y	ENSP00000256474:D121Y	D	+	1	0	VHL	10163218	1.000000	0.71417	1.000000	0.80357	0.299000	0.27559	7.274000	0.78538	2.530000	0.85305	0.563000	0.77884	GAT		0.502	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	
XKR6	286046	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	10782282	10782282	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr8:10782282G>A	ENST00000416569.2	-	2	849	c.823C>T	c.(823-825)Cgc>Tgc	p.R275C	XKR6_ENST00000304437.2_De_novo_Start_OutOfFrame	NM_173683.3	NP_775954.2	Q5GH73	XKR6_HUMAN	XK, Kell blood group complex subunit-related family, member 6	275						integral component of membrane (GO:0016021)		p.R275C(1)		breast(1)|endometrium(3)|kidney(3)|large_intestine(10)|lung(8)|ovary(2)|prostate(1)|skin(3)	31				Lung(29;0.0407)|COAD - Colon adenocarcinoma(149;0.0555)		CAGTAGAAGCGTCGCTGGTGT	0.572																																																	1	Substitution - Missense(1)	kidney(1)											119.0	104.0	109.0					8																	10782282		2203	4300	6503	SO:0001583	missense	286046			BC024146	CCDS5978.2	8p23.1	2009-05-27	2006-01-12	2005-07-28	ENSG00000171044	ENSG00000171044			27806	protein-coding gene	gene with protein product			"""chromosome 8 open reading frame 7"", ""chromosome 8 open reading frame 21"", ""X Kell blood group precursor-related family, member 6"", ""chromosome 8 open reading frame 5"""	C8orf7, C8orf21, C8orf5			Standard	NM_173683		Approved		uc003wtk.1	Q5GH73	OTTHUMG00000129351	ENST00000416569.2:c.823C>T	8.37:g.10782282G>A	ENSP00000416707:p.Arg275Cys		Q8TBA0	Missense_Mutation	SNP	ENST00000416569.2	37	CCDS5978.2	.	.	.	.	.	.	.	.	.	.	g	27.9	4.869545	0.91587	.	.	ENSG00000171044	ENST00000416569	T	0.64803	-0.12	4.71	4.71	0.59529	.	0.000000	0.85682	U	0.000000	T	0.78149	0.4238	M	0.73217	2.22	0.80722	D	1	D	0.89917	1.0	D	0.78314	0.991	T	0.81118	-0.1078	10	0.66056	D	0.02	-8.5012	16.6436	0.85155	0.0:0.0:1.0:0.0	.	275	Q5GH73	XKR6_HUMAN	C	275	ENSP00000416707:R275C	ENSP00000416707:R275C	R	-	1	0	XKR6	10819692	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	9.637000	0.98443	2.156000	0.67533	0.457000	0.33378	CGC		0.572	XKR6-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383958.1		NM_173683	
YLPM1	56252	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	75279329	75279329	+	Splice_Site	SNP	A	A	G			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr14:75279329A>G	ENST00000552421.1	+	10	3353		c.e10-1		YLPM1_ENST00000238571.3_Splice_Site|YLPM1_ENST00000325680.7_Splice_Site			P49750	YLPM1_HUMAN	YLP motif containing 1						regulation of telomere maintenance (GO:0032204)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in negative regulation of transcription (GO:0001078)	p.?(2)		breast(4)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(12)|lung(24)|ovary(3)|pancreas(1)|prostate(1)|skin(1)|urinary_tract(1)	62			KIRC - Kidney renal clear cell carcinoma(43;0.238)	BRCA - Breast invasive adenocarcinoma(234;0.00162)		CTGGAATCCTAGGAGAACGAA	0.448																																																	2	Unknown(2)	kidney(2)											36.0	37.0	37.0					14																	75279329		1945	4143	6088	SO:0001630	splice_region_variant	56252			AK090435	CCDS45135.1	14q24.3	2014-06-13	2004-07-15	2004-07-15	ENSG00000119596	ENSG00000119596			17798	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 169"""		"""chromosome 14 open reading frame 170"""	C14orf170		7596406	Standard	NM_019589		Approved	ZAP, PPP1R169	uc001xqj.4	P49750	OTTHUMG00000172503	ENST00000552421.1:c.3230-1A>G	14.37:g.75279329A>G			P49752|Q96I64|Q9P1V7	Splice_Site	SNP	ENST00000552421.1	37		.	.	.	.	.	.	.	.	.	.	A	22.4	4.283193	0.80803	.	.	ENSG00000119596	ENST00000552421;ENST00000325680;ENST00000238571;ENST00000423680;ENST00000547879	.	.	.	5.75	5.75	0.90469	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	14.6341	0.68676	1.0:0.0:0.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	YLPM1	74349082	1.000000	0.71417	0.997000	0.53966	0.969000	0.65631	7.977000	0.88081	2.187000	0.69744	0.528000	0.53228	.		0.448	YLPM1-008	NOVEL	not_organism_supported|basic|exp_conf	protein_coding	protein_coding	OTTHUMT00000404450.1		NM_019589	Intron
ZCCHC16	340595	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	111698754	111698754	+	Silent	SNP	C	C	T			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chrX:111698754C>T	ENST00000340433.2	+	1	1028	c.798C>T	c.(796-798)ctC>ctT	p.L266L		NM_001004308.2	NP_001004308.2	Q6ZR62	ZCH16_HUMAN	zinc finger, CCHC domain containing 16	266							nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.L266L(1)		cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(16)|ovary(1)|skin(1)|upper_aerodigestive_tract(1)	27						AGCTGCCTCTCACCCCAGCCA	0.547																																																	1	Substitution - coding silent(1)	kidney(1)											73.0	75.0	74.0					X																	111698754		2203	4300	6503	SO:0001819	synonymous_variant	340595			AK128465	CCDS35369.1	Xq23	2008-05-02			ENSG00000187823	ENSG00000187823		"""Zinc fingers, CCHC domain containing"""	25214	protein-coding gene	gene with protein product						15716091, 16093683	Standard	NM_001004308		Approved	Mart4, Mar4, FLJ46608	uc004epo.1	Q6ZR62	OTTHUMG00000159706	ENST00000340433.2:c.798C>T	X.37:g.111698754C>T			B2RPG1	Silent	SNP	ENST00000340433.2	37	CCDS35369.1																																																																																				0.547	ZCCHC16-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000356964.1		NM_001004308	
ZNF844	284391	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	12186656	12186656	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr19:12186656C>A	ENST00000439326.3	+	4	896	c.721C>A	c.(721-723)Caa>Aaa	p.Q241K	ZNF844_ENST00000441304.2_3'UTR	NM_001136501.1	NP_001129973.1	Q08AG5	ZN844_HUMAN	zinc finger protein 844	241					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)	p.Q241K(1)		NS(1)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(2)|lung(1)|prostate(1)	10						AACTTCCCTTCAAATACATGA	0.368																																																	1	Substitution - Missense(1)	kidney(1)											34.0	32.0	33.0					19																	12186656		692	1591	2283	SO:0001583	missense	284391			AL832297	CCDS45985.1	19p13.2	2013-01-08			ENSG00000223547	ENSG00000223547		"""Zinc fingers, C2H2-type"", ""-"""	25932	protein-coding gene	gene with protein product							Standard	NM_001136501		Approved	FLJ14959	uc002mtb.2	Q08AG5	OTTHUMG00000156405	ENST00000439326.3:c.721C>A	19.37:g.12186656C>A	ENSP00000392024:p.Gln241Lys		Q5JPI8	Missense_Mutation	SNP	ENST00000439326.3	37	CCDS45985.1	.	.	.	.	.	.	.	.	.	.	C	10.57	1.385928	0.25031	.	.	ENSG00000223547	ENST00000439326;ENST00000541708;ENST00000535505;ENST00000550826	T;T	0.35605	2.76;1.3	2.5	-2.34	0.06704	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.09598	0.0236	N	0.01454	-0.855	0.09310	N	1	B	0.17268	0.021	B	0.16289	0.015	T	0.36311	-0.9753	9	0.05959	T	0.93	.	5.5519	0.17095	0.3137:0.2565:0.4298:0.0	.	241	Q08AG5	ZN844_HUMAN	K	241;241;216;84	ENSP00000392024:Q241K;ENSP00000448588:Q84K	ENSP00000392024:Q241K	Q	+	1	0	ZNF844	12047656	0.000000	0.05858	0.000000	0.03702	0.412000	0.31113	-0.369000	0.07533	-0.072000	0.12864	0.205000	0.17691	CAA		0.368	ZNF844-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000344086.2			
ZNF611	81856	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	53209500	53209500	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-4638-01A-02D-1386-10	TCGA-CJ-4638-11A-01D-1251-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina HiSeq	cbc187b0-fafe-4b1f-9af0-6714942414ab	e87fd364-fa8b-43c5-a572-8b136f8f2086	g.chr19:53209500G>A	ENST00000319783.1	-	7	1124	c.808C>T	c.(808-810)Cac>Tac	p.H270Y	ZNF611_ENST00000453741.2_Missense_Mutation_p.H201Y|ZNF611_ENST00000602162.1_Missense_Mutation_p.H201Y|ZNF611_ENST00000543227.1_Missense_Mutation_p.H270Y|ZNF611_ENST00000595798.1_Missense_Mutation_p.H201Y|ZNF611_ENST00000602046.1_5'Flank|ZNF611_ENST00000540744.1_Missense_Mutation_p.H270Y	NM_030972.3	NP_112234.3	Q8N823	ZN611_HUMAN	zinc finger protein 611	270					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.H270Y(1)		breast(1)|endometrium(4)|kidney(4)|large_intestine(10)|lung(12)|ovary(1)|prostate(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	36				OV - Ovarian serous cystadenocarcinoma(262;0.0233)|GBM - Glioblastoma multiforme(134;0.04)		TATTGCTCGTGATTAAAGAGC	0.413																																																	1	Substitution - Missense(1)	kidney(1)											182.0	178.0	179.0					19																	53209500		2203	4300	6503	SO:0001583	missense	81856			AK091389	CCDS12855.1, CCDS54312.1	19q13.42	2013-01-08			ENSG00000213020	ENSG00000213020		"""Zinc fingers, C2H2-type"", ""-"""	28766	protein-coding gene	gene with protein product						12477932	Standard	NM_030972		Approved	MGC5384	uc010ydq.2	Q8N823	OTTHUMG00000154908	ENST00000319783.1:c.808C>T	19.37:g.53209500G>A	ENSP00000322427:p.His270Tyr		B3KRD5|Q69YG9	Missense_Mutation	SNP	ENST00000319783.1	37	CCDS12855.1	.	.	.	.	.	.	.	.	.	.	.	1.672	-0.508772	0.04231	.	.	ENSG00000213020	ENST00000543227;ENST00000540744;ENST00000453741;ENST00000319783	T;T;T;T	0.06528	3.29;3.29;3.29;3.29	1.2	-2.4	0.06583	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (2);Zinc finger, C2H2-type/integrase, DNA-binding (1);	.	.	.	.	T	0.04407	0.0121	N	0.25380	0.74	0.09310	N	1	B	0.06786	0.001	B	0.10450	0.005	T	0.38156	-0.9674	9	0.41790	T	0.15	.	6.1684	0.20404	0.6045:0.0:0.3955:0.0	.	270	Q8N823	ZN611_HUMAN	Y	270;270;201;270	ENSP00000437616:H270Y;ENSP00000439211:H270Y;ENSP00000443505:H201Y;ENSP00000322427:H270Y	ENSP00000322427:H270Y	H	-	1	0	ZNF611	57901312	.	.	0.000000	0.03702	0.000000	0.00434	.	.	-1.461000	0.01909	-2.696000	0.00138	CAC		0.413	ZNF611-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337612.1		NM_030972	
