#version 2.4
## 
## Oncotator v1.8.0.0 | Flat File Reference hg19 | GENCODE v19 EFFECT | UniProt_AAxform 2014_12 | ClinVar 12.03.20 | ESP 6500SI-V2 | ORegAnno UCSC Track | dbSNP build 142 | CCLE_By_GP 09292010 | COSMIC v62_291112 | 1000gp3 20130502 | UniProt_AA 2014_12 | dbNSFP v2.4 | ESP 6500SI-V2 | COSMIC_FusionGenes v62_291112 | gencode_xref_refseq metadata_v19 | CCLE_By_Gene 09292010 | ACHILLES_Lineage_Results 110303 | CGC full_2012-03-15 | UniProt 2014_12 | HumanDNARepairGenes 20110905 | HGNC Sept172014 | COSMIC_Tissue 291112 | Familial_Cancer_Genes 20110905 | TUMORScape 20100104 | Ensembl ICGC MUCOPA | TCGAScape 110405 | MutSig Published Results 20110905 
Hugo_Symbol	Entrez_Gene_Id	Center	NCBI_Build	Chromosome	Start_position	End_position	Strand	Variant_Classification	Variant_Type	Reference_Allele	Tumor_Seq_Allele1	Tumor_Seq_Allele2	dbSNP_RS	dbSNP_Val_Status	Tumor_Sample_Barcode	Matched_Norm_Sample_Barcode	Match_Norm_Seq_Allele1	Match_Norm_Seq_Allele2	Tumor_Validation_Allele1	Tumor_Validation_Allele2	Match_Norm_Validation_Allele1	Match_Norm_Validation_Allele2	Verification_Status	Validation_Status	Mutation_Status	Sequencing_Phase	Sequence_Source	Validation_Method	Score	BAM_file	Sequencer	Tumor_Sample_UUID	Matched_Norm_Sample_UUID	Genome_Change	Annotation_Transcript	Transcript_Strand	Transcript_Exon	Transcript_Position	cDNA_Change	Codon_Change	Protein_Change	Other_Transcripts	Refseq_mRNA_Id	Refseq_prot_Id	SwissProt_acc_Id	SwissProt_entry_Id	Description	UniProt_AApos	UniProt_Region	UniProt_Site	UniProt_Natural_Variations	UniProt_Experimental_Info	GO_Biological_Process	GO_Cellular_Component	GO_Molecular_Function	COSMIC_overlapping_mutations	COSMIC_fusion_genes	COSMIC_tissue_types_affected	COSMIC_total_alterations_in_gene	Tumorscape_Amplification_Peaks	Tumorscape_Deletion_Peaks	TCGAscape_Amplification_Peaks	TCGAscape_Deletion_Peaks	DrugBank	ref_context	gc_content	CCLE_ONCOMAP_overlapping_mutations	CCLE_ONCOMAP_total_mutations_in_gene	CGC_Mutation_Type	CGC_Translocation_Partner	CGC_Tumor_Types_Somatic	CGC_Tumor_Types_Germline	CGC_Other_Diseases	DNARepairGenes_Role	FamilialCancerDatabase_Syndromes	MUTSIG_Published_Results	OREGANNO_ID	OREGANNO_Values	i_1000gp3_AA	i_1000gp3_AC	i_1000gp3_AF	i_1000gp3_AFR_AF	i_1000gp3_AMR_AF	i_1000gp3_AN	i_1000gp3_CIEND	i_1000gp3_CIPOS	i_1000gp3_CS	i_1000gp3_DP	i_1000gp3_EAS_AF	i_1000gp3_END	i_1000gp3_EUR_AF	i_1000gp3_IMPRECISE	i_1000gp3_MC	i_1000gp3_MEINFO	i_1000gp3_MEND	i_1000gp3_MLEN	i_1000gp3_MSTART	i_1000gp3_NS	i_1000gp3_SAS_AF	i_1000gp3_SVLEN	i_1000gp3_SVTYPE	i_1000gp3_TSD	i_ACHILLES_Lineage_Results_Top_Genes	i_BAM_File	i_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_Mutation_Status	i_ORegAnno_bin	i_Sequence_Source	i_Sequencer	i_Sequencing_Phase	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_match_norm_validation_allele1	i_refseq_mrna_id	i_secondary_variant_classification
ABAT	18	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	8844355	8844355	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr16:8844355G>A	ENST00000396600.2	+	5	1213	c.275G>A	c.(274-276)cGa>cAa	p.R92Q	ABAT_ENST00000569156.1_Missense_Mutation_p.R92Q|ABAT_ENST00000567812.1_Missense_Mutation_p.R107Q|ABAT_ENST00000425191.2_Missense_Mutation_p.R92Q|ABAT_ENST00000268251.8_Missense_Mutation_p.R92Q	NM_000663.4	NP_000654.2	P80404	GABT_HUMAN	4-aminobutyrate aminotransferase	92					behavioral response to cocaine (GO:0048148)|copulation (GO:0007620)|gamma-aminobutyric acid catabolic process (GO:0009450)|locomotory behavior (GO:0007626)|negative regulation of blood pressure (GO:0045776)|neurotransmitter catabolic process (GO:0042135)|neurotransmitter secretion (GO:0007269)|response to drug (GO:0042493)|response to ethanol (GO:0045471)|response to hypoxia (GO:0001666)|response to iron ion (GO:0010039)|response to nicotine (GO:0035094)|synaptic transmission (GO:0007268)	4-aminobutyrate transaminase complex (GO:0032144)|extracellular vesicular exosome (GO:0070062)|mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)|neuron projection (GO:0043005)	(S)-3-amino-2-methylpropionate transaminase activity (GO:0047298)|4-aminobutyrate transaminase activity (GO:0003867)|protein homodimerization activity (GO:0042803)|pyridoxal phosphate binding (GO:0030170)|succinate-semialdehyde dehydrogenase binding (GO:0032145)	p.R92Q(1)		breast(2)|endometrium(3)|kidney(1)|large_intestine(5)|lung(10)|skin(3)|upper_aerodigestive_tract(2)	26					L-Alanine(DB00160)|Phenelzine(DB00780)|Pyruvic acid(DB00119)|Valproic Acid(DB00313)|Vigabatrin(DB01080)	GACGGCAACCGAATGCTGGAT	0.463																																																	1	Substitution - Missense(1)	kidney(1)											199.0	179.0	186.0					16																	8844355		2197	4300	6497	SO:0001583	missense	18			L32961	CCDS10534.1	16p13.2	2011-01-10			ENSG00000183044	ENSG00000183044	2.6.1.19		23	protein-coding gene	gene with protein product	"""4-aminobutyrate transaminase"""	137150				7721088	Standard	NM_020686		Approved	GABAT	uc002czc.4	P80404	OTTHUMG00000048201	ENST00000396600.2:c.275G>A	16.37:g.8844355G>A	ENSP00000379845:p.Arg92Gln	Somatic		WXS	Illumina HiSeq	Phase_I	A8K386|Q16260|Q8N5W2|Q96BG2|Q99800	Missense_Mutation	SNP	ENST00000396600.2	37	CCDS10534.1	.	.	.	.	.	.	.	.	.	.	G	26.5	4.748304	0.89663	.	.	ENSG00000183044	ENST00000268251;ENST00000396600;ENST00000425191	D;D;D	0.86865	-2.18;-2.18;-2.18	5.93	5.93	0.95920	Pyridoxal phosphate-dependent transferase, major region, subdomain 2 (1);Pyridoxal phosphate-dependent transferase, major domain (1);	0.000000	0.85682	D	0.000000	D	0.92051	0.7481	M	0.72479	2.2	0.80722	D	1	D	0.89917	1.0	D	0.66847	0.947	D	0.88276	0.2933	10	0.13108	T	0.6	-11.1913	18.8949	0.92419	0.0:0.0:1.0:0.0	.	92	P80404	GABT_HUMAN	Q	92	ENSP00000268251:R92Q;ENSP00000379845:R92Q;ENSP00000411916:R92Q	ENSP00000268251:R92Q	R	+	2	0	ABAT	8751856	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	9.388000	0.97237	2.803000	0.96430	0.650000	0.86243	CGA		0.463	ABAT-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000433620.2		NM_020686	
ACSM2B	348158	broad.mit.edu;hgsc.bcm.edu	37	16	20548590	20548590	+	Missense_Mutation	SNP	C	C	T	rs371889197		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr16:20548590C>T	ENST00000329697.6	-	14	1892	c.1724G>A	c.(1723-1725)cGt>cAt	p.R575H	ACSM2B_ENST00000565322.1_Missense_Mutation_p.R496H|ACSM2B_ENST00000567001.1_Missense_Mutation_p.R575H|ACSM2B_ENST00000565232.1_Missense_Mutation_p.R575H	NM_001105069.1	NP_001098539.1	Q68CK6	ACS2B_HUMAN	acyl-CoA synthetase medium-chain family member 2B	575					fatty acid metabolic process (GO:0006631)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|butyrate-CoA ligase activity (GO:0047760)|metal ion binding (GO:0046872)	p.R575H(1)		breast(4)|central_nervous_system(2)|endometrium(5)|kidney(2)|large_intestine(4)|lung(33)|ovary(1)|prostate(1)|skin(5)	57						TCACTGCGCACGGGCTTTTCC	0.468													c|||	1	0.000199681	0.0	0.0	5008	,	,		18720	0.0		0.0	False		,,,				2504	0.001																1	Substitution - Missense(1)	kidney(1)						C	HIS/ARG,HIS/ARG	0,4404		0,0,2202	249.0	228.0	235.0		1724,1724	-3.1	0.0	16		235	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense	ACSM2B	NM_001105069.1,NM_182617.3	29,29	0,1,6501	TT,TC,CC		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging	575/578,575/578	20548590	1,13003	2202	4300	6502	SO:0001583	missense	348158			AY160217	CCDS10586.1	16p12.3	2014-08-08	2007-06-20	2007-06-20	ENSG00000066813	ENSG00000066813		"""Acyl-CoA synthetase family"""	30931	protein-coding gene	gene with protein product	"""xenobiotic/medium chain fatty acid:CoA ligase"""	614359	"""acyl-CoA synthetase medium-chain family member 2"""	ACSM2		12616642	Standard	NM_182617		Approved	HXMA, HYST1046	uc002dhk.4	Q68CK6	OTTHUMG00000131555	ENST00000329697.6:c.1724G>A	16.37:g.20548590C>T	ENSP00000327453:p.Arg575His	Somatic		WXS	Illumina HiSeq	Phase_I	Q86YT1	Missense_Mutation	SNP	ENST00000329697.6	37	CCDS10586.1	.	.	.	.	.	.	.	.	.	.	C	8.074	0.770993	0.15983	0.0	1.16E-4	ENSG00000066813	ENST00000329697	T	0.47869	0.83	2.53	-3.09	0.05331	.	.	.	.	.	T	0.24967	0.0606	N	0.08118	0	0.09310	N	1	B	0.13145	0.007	B	0.06405	0.002	T	0.17107	-1.0380	9	0.59425	D	0.04	-0.2477	9.4274	0.38588	0.0:0.233:0.0:0.767	.	575	Q68CK6	ACS2B_HUMAN	H	575	ENSP00000327453:R575H	ENSP00000327453:R575H	R	-	2	0	ACSM2B	20456091	0.000000	0.05858	0.000000	0.03702	0.003000	0.03518	-1.847000	0.01675	-0.819000	0.04323	-0.192000	0.12808	CGT		0.468	ACSM2B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254417.2		NM_182617	
AKAP9	10142	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	91709305	91709305	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr7:91709305A>T	ENST00000359028.2	+	32	8119	c.7894A>T	c.(7894-7896)Act>Tct	p.T2632S	AKAP9_ENST00000356239.3_Missense_Mutation_p.T2620S|AKAP9_ENST00000358100.2_Missense_Mutation_p.T2632S			Q99996	AKAP9_HUMAN	A kinase (PRKA) anchor protein 9	2632	Glu-rich.				G2/M transition of mitotic cell cycle (GO:0000086)|mitotic cell cycle (GO:0000278)|Sertoli cell development (GO:0060009)|signal transduction (GO:0007165)|spermatogenesis (GO:0007283)|synaptic transmission (GO:0007268)|transport (GO:0006810)	centrosome (GO:0005813)|ciliary basal body (GO:0036064)|cytoskeleton (GO:0005856)|cytosol (GO:0005829)|Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|pericentriolar material (GO:0000242)|voltage-gated potassium channel complex (GO:0008076)	ion channel binding (GO:0044325)|protein complex scaffold (GO:0032947)|receptor binding (GO:0005102)	p.T2632S(1)|p.T2620S(1)		NS(1)|autonomic_ganglia(2)|breast(14)|central_nervous_system(3)|cervix(1)|endometrium(13)|kidney(12)|large_intestine(35)|lung(49)|ovary(8)|prostate(6)|skin(8)|stomach(1)|urinary_tract(2)	155	all_cancers(62;2.46e-09)|all_epithelial(64;4.42e-08)|Breast(17;0.00206)|all_lung(186;0.185)|all_hematologic(106;0.215)|Lung NSC(181;0.249)		STAD - Stomach adenocarcinoma(171;6.16e-05)|Lung(22;0.123)|LUSC - Lung squamous cell carcinoma(200;0.225)			TGAAATGCATACTAGTTTGAT	0.323			T	BRAF	papillary thyroid																																			Dom	yes		7	7q21-q22	10142	A kinase (PRKA) anchor protein (yotiao) 9		E	2	Substitution - Missense(2)	kidney(2)											60.0	65.0	64.0					7																	91709305		2202	4299	6501	SO:0001583	missense	10142			AF091711	CCDS5622.1	7q21-q22	2014-09-17	2013-09-25		ENSG00000127914	ENSG00000127914		"""A-kinase anchor proteins"", ""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	379	protein-coding gene	gene with protein product	"""A-kinase anchoring protein 450"", ""AKAP9-BRAF fusion protein"", ""AKAP120-like protein"", ""centrosome- and golgi-localized protein kinase N-associated protein"", ""protein kinase A anchoring protein 9"", ""A-kinase anchor protein, 350kDa"", ""protein phosphatase 1, regulatory subunit 45"", ""yotiao"""	604001				9482789, 10390370, 24475373	Standard	NM_147185		Approved	KIAA0803, AKAP350, AKAP450, CG-NAP, YOTIAO, HYPERION, PRKA9, MU-RMS-40.16A, PPP1R45, LQT11	uc003ulg.3	Q99996	OTTHUMG00000131127	ENST00000359028.2:c.7894A>T	7.37:g.91709305A>T	ENSP00000351922:p.Thr2632Ser	Somatic		WXS	Illumina HiSeq	Phase_I	A4D1F0|A4D1F2|A4D1F4|O14869|O43355|O94895|Q75N20|Q9UQH3|Q9UQQ4|Q9Y6B8|Q9Y6Y2	Missense_Mutation	SNP	ENST00000359028.2	37		.	.	.	.	.	.	.	.	.	.	A	0.389	-0.924603	0.02377	.	.	ENSG00000127914	ENST00000356239;ENST00000359028;ENST00000358100;ENST00000413120;ENST00000394534	T;T;T;T	0.03094	4.13;4.13;4.13;4.05	4.63	-9.16	0.00694	.	0.919567	0.08926	N	0.873681	T	0.01092	0.0036	N	0.05124	-0.11	0.09310	N	1	B;B;B;B	0.02656	0.0;0.0;0.0;0.0	B;B;B;B	0.04013	0.0;0.0;0.001;0.0	T	0.45396	-0.9264	10	0.07644	T	0.81	.	0.5793	0.00709	0.2:0.1946:0.2025:0.4029	.	2624;2632;2620;2612	Q99996-6;Q99996;Q99996-2;Q99996-3	.;AKAP9_HUMAN;.;.	S	2620;2632;2632;2624;466	ENSP00000348573:T2620S;ENSP00000351922:T2632S;ENSP00000350813:T2632S;ENSP00000378042:T466S	ENSP00000348573:T2620S	T	+	1	0	AKAP9	91547241	0.000000	0.05858	0.002000	0.10522	0.006000	0.05464	-1.269000	0.02834	-1.309000	0.02315	-2.334000	0.00248	ACT		0.323	AKAP9-202	KNOWN	basic	protein_coding	protein_coding			NM_005751	
ATP7A	538	hgsc.bcm.edu	37	X	77284798	77284799	+	Frame_Shift_Ins	INS	-	-	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chrX:77284798_77284799insA	ENST00000341514.6	+	15	3123_3124	c.2968_2969insA	c.(2968-2970)caafs	p.Q990fs	ATP7A_ENST00000343533.5_Frame_Shift_Ins_p.Q912fs|ATP7A_ENST00000350425.4_Intron	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	Somatic		WXS	Illumina HiSeq	Phase_I	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	
BAHCC1	57597	broad.mit.edu;hgsc.bcm.edu	37	17	79426336	79426336	+	Silent	SNP	G	G	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr17:79426336G>A	ENST00000307745.7	+	26	5778	c.5778G>A	c.(5776-5778)gaG>gaA	p.E1926E	RP11-1055B8.8_ENST00000572590.1_RNA														p.E1926E(1)									ACTCACTGGAGCAGCTGCTGC	0.677																																																	1	Substitution - coding silent(1)	kidney(1)											28.0	35.0	33.0					17																	79426336		2020	4165	6185	SO:0001819	synonymous_variant	57597																														ENST00000307745.7:c.5778G>A	17.37:g.79426336G>A		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000307745.7	37																																																																																					0.677	RP11-1055B8.7-201	KNOWN	basic|appris_principal	protein_coding	protein_coding				
BOC	91653	broad.mit.edu;hgsc.bcm.edu	37	3	112998705	112998705	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr3:112998705C>A	ENST00000495514.1	+	13	2759	c.2055C>A	c.(2053-2055)aaC>aaA	p.N685K	BOC_ENST00000273395.4_Missense_Mutation_p.N686K|BOC_ENST00000355385.3_Missense_Mutation_p.N685K			Q9BWV1	BOC_HUMAN	BOC cell adhesion associated, oncogene regulated	685	Fibronectin type-III 2. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|cell adhesion (GO:0007155)|muscle cell differentiation (GO:0042692)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of myoblast differentiation (GO:0045663)|smoothened signaling pathway (GO:0007224)	axonal growth cone (GO:0044295)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|plasma membrane (GO:0005886)		p.N685K(1)		NS(1)|breast(1)|central_nervous_system(3)|cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(3)|kidney(4)|large_intestine(17)|lung(18)|ovary(4)|pancreas(1)|prostate(2)|skin(2)|stomach(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	68			Epithelial(53;0.227)			GGGCTCTGAACATGCTGGGGG	0.602																																																	1	Substitution - Missense(1)	kidney(1)											71.0	78.0	76.0					3																	112998705		2203	4300	6503	SO:0001583	missense	91653			AY027658	CCDS2971.1	3q13.2	2013-02-11	2012-12-07		ENSG00000144857	ENSG00000144857		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	17173	protein-coding gene	gene with protein product	"""brother of CDO"", ""brother of CDON"", ""cell adhesion associated, oncogene regulated 2"""	608708	"""Boc homolog (mouse)"""			11782431	Standard	NM_033254		Approved	CDON2	uc003dzy.3	Q9BWV1	OTTHUMG00000159305	ENST00000495514.1:c.2055C>A	3.37:g.112998705C>A	ENSP00000418663:p.Asn685Lys	Somatic		WXS	Illumina HiSeq	Phase_I	A6NJ30|B2RMS8|D3DN70|Q6UXJ5|Q8N2P7|Q8NF26	Missense_Mutation	SNP	ENST00000495514.1	37	CCDS2971.1	.	.	.	.	.	.	.	.	.	.	C	21.9	4.214663	0.79352	.	.	ENSG00000144857	ENST00000495514;ENST00000273395;ENST00000355385	T;T;T	0.62232	0.04;0.04;0.04	5.53	2.76	0.32466	Fibronectin, type III (4);Immunoglobulin-like fold (1);	0.153118	0.56097	D	0.000032	D	0.82600	0.5072	H	0.95504	3.68	0.58432	D	0.999997	D;D	0.89917	1.0;0.999	D;D	0.79784	0.993;0.993	D	0.84372	0.0544	10	0.66056	D	0.02	.	10.0769	0.42366	0.0:0.783:0.0:0.217	.	686;685	Q9BWV1-3;Q9BWV1	.;BOC_HUMAN	K	685;686;685	ENSP00000418663:N685K;ENSP00000273395:N686K;ENSP00000347546:N685K	ENSP00000273395:N686K	N	+	3	2	BOC	114481395	1.000000	0.71417	1.000000	0.80357	0.964000	0.63967	1.830000	0.39131	0.690000	0.31570	0.563000	0.77884	AAC		0.602	BOC-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000354485.3		NM_033254	
C19orf12	83636	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	30193856	30193856	+	Silent	SNP	G	G	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr19:30193856G>T	ENST00000392278.2	-	3	348	c.222C>A	c.(220-222)gcC>gcA	p.A74A	C19orf12_ENST00000323670.9_Silent_p.A63A|C19orf12_ENST00000592153.1_Silent_p.A63A|C19orf12_ENST00000392275.1_5'UTR|C19orf12_ENST00000392276.1_De_novo_Start_OutOfFrame	NM_001031726.3	NP_001026896.2	Q9NSK7	CS012_HUMAN	chromosome 19 open reading frame 12	74					cell death (GO:0008219)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)		p.A74A(1)				Ovarian(5;0.000567)|Breast(6;0.0203)|Esophageal squamous(110;0.239)		UCEC - Uterine corpus endometrioid carcinoma (4;2.65e-06)|STAD - Stomach adenocarcinoma(5;1.7e-06)|Lung(7;0.0435)|LUAD - Lung adenocarcinoma(5;0.0989)|BRCA - Breast invasive adenocarcinoma(6;0.183)			TTGTCATCCAGGCACCTAACA	0.522																																																	1	Substitution - coding silent(1)	kidney(1)											80.0	84.0	83.0					19																	30193856		2203	4300	6503	SO:0001819	synonymous_variant	83636			AK057185	CCDS12418.2, CCDS42542.1, CCDS59373.1, CCDS74325.1	19q13.11	2013-07-24			ENSG00000131943	ENSG00000131943			25443	protein-coding gene	gene with protein product	"""neurodegeneration with brain iron accumulation 4"""	614297	"""spastic paraplegia 43 (autosomal recessive)"""	SPG43		21981780, 23857908	Standard	NM_031448		Approved	MGC10922, DKFZP762D096, NBIA4	uc002nsj.3	Q9NSK7	OTTHUMG00000149838	ENST00000392278.2:c.222C>A	19.37:g.30193856G>T		Somatic		WXS	Illumina HiSeq	Phase_I	B3KQ16|Q0D2Q0|Q6P4C5|Q9BSL7	Silent	SNP	ENST00000392278.2	37	CCDS42542.1																																																																																				0.522	C19orf12-003	KNOWN	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313509.2		NM_031448	
SDE2	163859	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	226180697	226180697	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr1:226180697C>A	ENST00000272091.7	-	3	263	c.245G>T	c.(244-246)gGa>gTa	p.G82V		NM_152608.3	NP_689821.3	Q6IQ49	SDE2_HUMAN	SDE2 telomere maintenance homolog (S. pombe)	82								p.G70V(1)|p.G82V(1)									GAGCATAGATCCAAAACCTGA	0.413																																																	2	Substitution - Missense(2)	kidney(2)											66.0	58.0	61.0					1																	226180697		1862	4097	5959	SO:0001583	missense	0			BC071563	CCDS41473.1	1q42.12	2012-06-26	2012-06-26	2012-06-26	ENSG00000143751	ENSG00000143751			26643	protein-coding gene	gene with protein product			"""chromosome 1 open reading frame 55"""	C1orf55		21333630	Standard	NM_152608		Approved	FLJ35382	uc001hpu.4	Q6IQ49	OTTHUMG00000037504	ENST00000272091.7:c.245G>T	1.37:g.226180697C>A	ENSP00000272091:p.Gly82Val	Somatic		WXS	Illumina HiSeq	Phase_I	A8K4P3|Q5TD36|Q6ZS26|Q8NAG7	Missense_Mutation	SNP	ENST00000272091.7	37	CCDS41473.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	16.40|16.40	3.112605|3.112605	0.56398|0.56398	.|.	.|.	ENSG00000143751|ENSG00000143751	ENST00000366817|ENST00000272091;ENST00000366818	T|D	0.52983|0.89415	0.64|-2.51	5.86|5.86	5.86|5.86	0.93980|0.93980	.|.	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.96312|0.96312	0.8797|0.8797	M|M	0.93808|0.93808	3.46|3.46	0.47441|0.47441	D|D	0.999422|0.999422	.|D;D	.|0.89917	.|1.0;1.0	.|D;D	.|0.97110	.|1.0;0.996	D|D	0.96608|0.96608	0.9450|0.9450	7|10	0.87932|0.87932	D|D	0|0	-18.1297|-18.1297	20.2421|20.2421	0.98377|0.98377	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|70;82	.|Q6IQ49-2;Q6IQ49	.|.;CA055_HUMAN	Y|V	31|82;70	ENSP00000355782:D31Y|ENSP00000272091:G82V	ENSP00000355782:D31Y|ENSP00000272091:G82V	D|G	-|-	1|2	0|0	C1orf55|C1orf55	224247320|224247320	1.000000|1.000000	0.71417|0.71417	0.993000|0.993000	0.49108|0.49108	0.995000|0.995000	0.86356|0.86356	7.729000|7.729000	0.84864|0.84864	2.788000|2.788000	0.95919|0.95919	0.650000|0.650000	0.86243|0.86243	GAT|GGA		0.413	SDE2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000091310.1		NM_152608	
CACNA1A	773	hgsc.bcm.edu;ucsc.edu	37	19	13366037	13366038	+	Frame_Shift_Del	DEL	GC	GC	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	GC	GC	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr19:13366037_13366038delGC	ENST00000360228.5	-	29	4625_4626	c.4626_4627delGC	c.(4624-4629)ccgctgfs	p.L1543fs	CACNA1A_ENST00000573710.2_Frame_Shift_Del_p.L1544fs|CACNA1A_ENST00000574822.1_5'Flank	NM_000068.3|NM_001127222.1|NM_001174080.1|NM_023035.2	NP_000059.3|NP_001120694.1|NP_001167551.1|NP_075461.2	O00555	CAC1A_HUMAN	calcium channel, voltage-dependent, P/Q type, alpha 1A subunit	1544					adult walking behavior (GO:0007628)|behavioral response to pain (GO:0048266)|calcium ion import (GO:0070509)|calcium ion-dependent exocytosis (GO:0017156)|calcium ion-dependent exocytosis of neurotransmitter (GO:0048791)|cell death (GO:0008219)|cell growth (GO:0016049)|cellular chloride ion homeostasis (GO:0030644)|cerebellar molecular layer development (GO:0021679)|cerebellar Purkinje cell differentiation (GO:0021702)|cerebellum maturation (GO:0021590)|dendrite morphogenesis (GO:0048813)|energy reserve metabolic process (GO:0006112)|gamma-aminobutyric acid secretion (GO:0014051)|gamma-aminobutyric acid signaling pathway (GO:0007214)|glucose metabolic process (GO:0006006)|hormone metabolic process (GO:0042445)|membrane depolarization (GO:0051899)|membrane depolarization during action potential (GO:0086010)|musculoskeletal movement, spinal reflex action (GO:0050883)|negative regulation of hormone biosynthetic process (GO:0032353)|negative regulation of neuron apoptotic process (GO:0043524)|neuromuscular process controlling balance (GO:0050885)|neuromuscular synaptic transmission (GO:0007274)|neurotransmitter metabolic process (GO:0042133)|positive regulation of cytosolic calcium ion concentration (GO:0007204)|receptor clustering (GO:0043113)|regulation of acetylcholine secretion, neurotransmission (GO:0014056)|regulation of axonogenesis (GO:0050770)|regulation of calcium ion-dependent exocytosis (GO:0017158)|regulation of insulin secretion (GO:0050796)|rhythmic synaptic transmission (GO:0060024)|small molecule metabolic process (GO:0044281)|spinal cord motor neuron differentiation (GO:0021522)|sulfur amino acid metabolic process (GO:0000096)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)|synaptic transmission, glutamatergic (GO:0035249)|transmission of nerve impulse (GO:0019226)|vestibular nucleus development (GO:0021750)	cell projection (GO:0042995)|cytoplasm (GO:0005737)|dendrite (GO:0030425)|integral component of membrane (GO:0016021)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	high voltage-gated calcium channel activity (GO:0008331)|metal ion binding (GO:0046872)|syntaxin binding (GO:0019905)|voltage-gated calcium channel activity (GO:0005245)			breast(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(3)|lung(25)|prostate(2)|urinary_tract(1)	42			OV - Ovarian serous cystadenocarcinoma(19;5.07e-21)		Bepridil(DB01244)|Loperamide(DB00836)|Pregabalin(DB00230)|Spironolactone(DB00421)|Verapamil(DB00661)	TGTCGGGTCAGCGGCTTGGCGC	0.614																																																	0																																										SO:0001589	frameshift_variant	773			U79666	CCDS45998.1, CCDS45999.1	19p13	2014-09-17			ENSG00000141837	ENSG00000141837		"""Calcium channel subunits"", ""Voltage-gated ion channels / Calcium channels"""	1388	protein-coding gene	gene with protein product		601011		CACNL1A4, SCA6, MHP1, MHP		8825650, 16382099, 23827678	Standard	NM_000068		Approved	Cav2.1, EA2, APCA, HPCA, FHM	uc010xne.2	O00555	OTTHUMG00000044590	ENST00000360228.5:c.4626_4627delGC	19.37:g.13366037_13366038delGC	ENSP00000353362:p.Leu1543fs	Somatic		WXS	Illumina HiSeq	Phase_I	J3KP41|P78510|P78511|Q16290|Q92690|Q99790|Q99791|Q99792|Q99793|Q9NS88|Q9UDC4	Frame_Shift_Del	DEL	ENST00000360228.5	37	CCDS45998.1																																																																																				0.614	CACNA1A-001	KNOWN	non_canonical_U12|basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000104062.2		NM_000068	
CCDC126	90693	broad.mit.edu;ucsc.edu	37	7	23650959	23650959	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr7:23650959A>C	ENST00000307471.3	+	3	482	c.25A>C	c.(25-27)Aat>Cat	p.N9H	CCDC126_ENST00000486109.1_3'UTR|CCDC126_ENST00000409765.1_Missense_Mutation_p.N9H|CCDC126_ENST00000410069.1_Missense_Mutation_p.N9H	NM_138771.3	NP_620126.2	Q96EE4	CC126_HUMAN	coiled-coil domain containing 126	9					protein N-linked glycosylation (GO:0006487)	extracellular region (GO:0005576)|membrane (GO:0016020)	alpha-1,6-mannosylglycoprotein 6-beta-N-acetylglucosaminyltransferase activity (GO:0030144)	p.N9H(1)		endometrium(3)|kidney(1)|large_intestine(1)|ovary(1)|skin(1)	7						CTCAAGAAAAAATATGTCCCA	0.338																																																	1	Substitution - Missense(1)	kidney(1)											79.0	81.0	80.0					7																	23650959		2203	4300	6503	SO:0001583	missense	90693			BC012427	CCDS5384.1	7p15.3	2006-08-15			ENSG00000169193	ENSG00000169193			22398	protein-coding gene	gene with protein product						12477932	Standard	NM_138771		Approved	FLJ23031	uc003swl.3	Q96EE4	OTTHUMG00000128461	ENST00000307471.3:c.25A>C	7.37:g.23650959A>C	ENSP00000304355:p.Asn9His	Somatic		WXS	Illumina GAIIx	Phase_I	A8K1J6|Q6UWP1|Q75MQ6	Missense_Mutation	SNP	ENST00000307471.3	37	CCDS5384.1	.	.	.	.	.	.	.	.	.	.	A	15.52	2.856919	0.51376	.	.	ENSG00000169193	ENST00000307471;ENST00000409765;ENST00000448353;ENST00000410069	.	.	.	5.65	4.49	0.54785	.	0.478186	0.23724	N	0.045200	T	0.63082	0.2481	L	0.54323	1.7	0.38585	D	0.950288	B	0.28880	0.226	B	0.40477	0.33	T	0.64478	-0.6398	9	0.54805	T	0.06	-2.2581	10.103	0.42517	0.7322:0.0:0.0:0.2678	.	9	Q96EE4	CC126_HUMAN	H	9	.	ENSP00000304355:N9H	N	+	1	0	CCDC126	23617484	1.000000	0.71417	0.964000	0.40570	0.987000	0.75469	5.081000	0.64444	0.950000	0.37743	0.455000	0.32223	AAT		0.338	CCDC126-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250259.1		NM_138771	
CDK3	1018	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	73999331	73999332	+	Missense_Mutation	DNP	TC	TC	AG			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	T|C	T|C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr17:73999331_73999332TC>AG	ENST00000425876.2	+	6	732_733	c.644_645TC>AG	c.(643-645)aTC>aAG	p.I215K	CDK3_ENST00000448471.1_Missense_Mutation_p.I215K|TEN1-CDK3_ENST00000567351.1_RNA			Q00526	CDK3_HUMAN	cyclin-dependent kinase 3	215	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cell proliferation (GO:0008283)|G0 to G1 transition (GO:0045023)|G1/S transition of mitotic cell cycle (GO:0000082)|mitotic nuclear division (GO:0007067)|regulation of cell cycle (GO:0051726)		ATP binding (GO:0005524)|cyclin-dependent protein serine/threonine kinase activity (GO:0004693)	p.I215M(1)|p.I215N(1)		central_nervous_system(1)	1						CTCTTTCGTATCTTTCGTATGC	0.55																																																	2	Substitution - Missense(2)	kidney(2)																																								SO:0001583	missense	1018			X66357	CCDS11736.1	17q25.1	2012-09-20			ENSG00000250506	ENSG00000250506		"""Cyclin-dependent kinases"""	1772	protein-coding gene	gene with protein product		123828				1639063	Standard	NM_001258		Approved		uc010dgt.3	Q00526	OTTHUMG00000154861	Exception_encountered	17.37:g.73999331_73999332delinsAG	ENSP00000410561:p.Ile215Lys	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000425876.2	37	CCDS11736.1																																																																																				0.550	CDK3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000337389.2		NM_001258	
CLPB	81570	broad.mit.edu;ucsc.edu	37	11	72012879	72012879	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr11:72012879C>T	ENST00000294053.3	-	12	1560	c.1387G>A	c.(1387-1389)Gtg>Atg	p.V463M	CLPB_ENST00000538039.1_Missense_Mutation_p.V433M|CLPB_ENST00000538021.1_Missense_Mutation_p.V71M|CLPB_ENST00000543042.1_Missense_Mutation_p.V262M|CLPB_ENST00000437826.2_Missense_Mutation_p.V418M|CLPB_ENST00000340729.5_Missense_Mutation_p.V404M|AP000593.7_ENST00000546065.1_RNA	NM_001258394.1|NM_030813.4	NP_001245323.1|NP_110440.1	Q9H078	CLPB_HUMAN	ClpB caseinolytic peptidase B homolog (E. coli)	463					cellular response to heat (GO:0034605)	mitochondrion (GO:0005739)	ATP binding (GO:0005524)	p.V463M(1)		endometrium(3)|kidney(3)|large_intestine(2)|lung(7)|ovary(1)|pancreas(1)|skin(1)|urinary_tract(1)	19						ATGGTGAGCACATCTGGATGG	0.557																																																	1	Substitution - Missense(1)	kidney(1)											194.0	170.0	178.0					11																	72012879		2200	4293	6493	SO:0001583	missense	81570			BC006404	CCDS8215.1, CCDS58152.1, CCDS58153.1, CCDS58154.1	11q13.4	2013-01-10			ENSG00000162129	ENSG00000162129		"""Ankyrin repeat domain containing"""	30664	protein-coding gene	gene with protein product	"""suppressor of potassium transport defect 3"""					11230166, 7835694	Standard	NM_030813		Approved	HSP78, SKD3, FLJ13152	uc010rqy.3	Q9H078	OTTHUMG00000167902	ENST00000294053.3:c.1387G>A	11.37:g.72012879C>T	ENSP00000294053:p.Val463Met	Somatic		WXS	Illumina GAIIx	Phase_I	B4DXJ7|B4DXP7|E7EWN6|F8W7P6|Q8ND11|Q9H8Y0	Missense_Mutation	SNP	ENST00000294053.3	37	CCDS8215.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	28.7|28.7	4.944915|4.944915	0.92593|0.92593	.|.	.|.	ENSG00000162129|ENSG00000162129	ENST00000544382|ENST00000294053;ENST00000538039;ENST00000535990;ENST00000340729;ENST00000437826;ENST00000543042;ENST00000538021	.|T;T;T;T;T;T;T	.|0.69685	.|-0.42;-0.42;-0.42;-0.42;-0.42;-0.42;-0.42	5.39|5.39	5.39|5.39	0.77823|0.77823	.|ATPase, AAA-2 (1);ATPase, AAA+ type, core (1);	.|0.000000	.|0.85682	.|D	.|0.000000	D|D	0.87943|0.87943	0.6305|0.6305	H|H	0.95884|0.95884	3.735|3.735	0.80722|0.80722	D|D	1|1	.|D;D;D;D;D;D	.|0.89917	.|1.0;1.0;1.0;1.0;1.0;1.0	.|D;D;D;D;D;D	.|0.97110	.|0.994;0.994;0.999;0.998;1.0;0.993	D|D	0.91633|0.91633	0.5320|0.5320	5|10	.|0.87932	.|D	.|0	-16.9357|-16.9357	17.7622|17.7622	0.88467|0.88467	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|262;404;418;433;463;71	.|B4DXW4;F8W7P6;E7EWN6;Q9H078-2;Q9H078;Q7Z777	.|.;.;.;.;CLPB_HUMAN;.	I|M	240|463;433;468;404;418;262;71	.|ENSP00000294053:V463M;ENSP00000441518:V433M;ENSP00000443822:V468M;ENSP00000340385:V404M;ENSP00000407296:V418M;ENSP00000439746:V262M;ENSP00000445180:V71M	.|ENSP00000294053:V463M	M|V	-|-	3|1	0|0	CLPB|CLPB	71690527|71690527	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.999000|0.999000	0.98932|0.98932	7.818000|7.818000	0.86416|0.86416	2.537000|2.537000	0.85549|0.85549	0.655000|0.655000	0.94253|0.94253	ATG|GTG		0.557	CLPB-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000396889.1		NM_030813	
CNST	163882	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	246797267	246797267	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr1:246797267C>A	ENST00000366513.4	+	5	927	c.658C>A	c.(658-660)Cat>Aat	p.H220N	CNST_ENST00000483271.1_3'UTR|CNST_ENST00000366512.3_Missense_Mutation_p.H220N	NM_152609.2	NP_689822.2	Q6PJW8	CNST_HUMAN	consortin, connexin sorting protein	220					negative regulation of phosphatase activity (GO:0010923)|positive regulation of Golgi to plasma membrane protein transport (GO:0042998)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|plasma membrane (GO:0005886)|protein complex (GO:0043234)|trans-Golgi network (GO:0005802)|transport vesicle (GO:0030133)	connexin binding (GO:0071253)|phosphatase binding (GO:0019902)	p.H220N(1)		breast(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|prostate(1)|urinary_tract(2)	28						ACGATTGTATCATGAGCAATT	0.353																																																	1	Substitution - Missense(1)	kidney(1)											113.0	114.0	114.0					1																	246797267		2203	4300	6503	SO:0001583	missense	163882			AK056563	CCDS1628.1, CCDS44343.1	1q44	2012-04-17	2009-11-03	2009-11-03	ENSG00000162852	ENSG00000162852		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	26486	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 64"""	613439	"""chromosome 1 open reading frame 71"""	C1orf71		19864490	Standard	NM_152609		Approved	FLJ32001, PPP1R64	uc001ibp.3	Q6PJW8	OTTHUMG00000040090	ENST00000366513.4:c.658C>A	1.37:g.246797267C>A	ENSP00000355470:p.His220Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VSY9|Q5VTM7|Q8IYA9|Q8N3L5|Q8NB09|Q8TEI2|Q96MR5	Missense_Mutation	SNP	ENST00000366513.4	37	CCDS1628.1	.	.	.	.	.	.	.	.	.	.	C	25.2	4.612830	0.87258	.	.	ENSG00000162852	ENST00000366513;ENST00000366512	T;T	0.26223	1.75;1.75	5.75	5.75	0.90469	.	0.000000	0.85682	D	0.000000	T	0.55049	0.1896	M	0.78801	2.425	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.56257	-0.8009	10	0.66056	D	0.02	-0.4146	18.5555	0.91083	0.0:1.0:0.0:0.0	.	220;220	Q6PJW8;Q6PJW8-2	CNST_HUMAN;.	N	220	ENSP00000355470:H220N;ENSP00000355469:H220N	ENSP00000355469:H220N	H	+	1	0	CNST	244863890	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	5.912000	0.69948	2.726000	0.93360	0.644000	0.83932	CAT		0.353	CNST-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096780.1		NM_152609	
DCC	1630	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	50683750	50683750	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr18:50683750C>A	ENST00000442544.2	+	8	1902	c.1286C>A	c.(1285-1287)cCt>cAt	p.P429H	DCC_ENST00000581580.1_Missense_Mutation_p.P84H|DCC_ENST00000580146.1_3'UTR|DCC_ENST00000412726.1_Missense_Mutation_p.P277H	NM_005215.3	NP_005206.2	P43146	DCC_HUMAN	DCC netrin 1 receptor	429					anterior/posterior axon guidance (GO:0033564)|apoptotic process (GO:0006915)|axon guidance (GO:0007411)|axonogenesis (GO:0007409)|dorsal/ventral axon guidance (GO:0033563)|negative regulation of collateral sprouting (GO:0048671)|negative regulation of dendrite development (GO:2000171)|negative regulation of neuron projection development (GO:0010977)|neuron migration (GO:0001764)|positive regulation of apoptotic process (GO:0043065)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|positive regulation of neuron projection development (GO:0010976)|regulation of apoptotic process (GO:0042981)|response to amphetamine (GO:0001975)|spinal cord ventral commissure morphogenesis (GO:0021965)	axon (GO:0030424)|cytosol (GO:0005829)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|membrane raft (GO:0045121)|plasma membrane (GO:0005886)	netrin receptor activity (GO:0005042)|transcription coactivator activity (GO:0003713)|transmembrane signaling receptor activity (GO:0004888)	p.P429H(1)		NS(3)|breast(2)|central_nervous_system(1)|cervix(2)|endometrium(13)|haematopoietic_and_lymphoid_tissue(2)|kidney(5)|large_intestine(23)|liver(1)|lung(56)|ovary(7)|pancreas(3)|prostate(2)|skin(16)|stomach(2)|upper_aerodigestive_tract(4)|urinary_tract(6)	148		all_cancers(7;0.11)|all_epithelial(6;0.00126)		Colorectal(16;0.0251)|COAD - Colon adenocarcinoma(17;0.0942)		AGTGTCCTCCCTTCGGCTCCC	0.542																																																	1	Substitution - Missense(1)	kidney(1)											191.0	178.0	183.0					18																	50683750		2203	4300	6503	SO:0001583	missense	1630			X76132	CCDS11952.1	18q21.1	2014-06-20	2014-06-20		ENSG00000187323	ENSG00000187323		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	2701	protein-coding gene	gene with protein product	"""immunoglobulin superfamily, DCC subclass, member 1"""	120470	"""deleted in colorectal carcinoma"""			2294591, 24400119	Standard	NM_005215		Approved	IGDCC1, NTN1R1	uc002lfe.2	P43146	OTTHUMG00000132698	ENST00000442544.2:c.1286C>A	18.37:g.50683750C>A	ENSP00000389140:p.Pro429His	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000442544.2	37	CCDS11952.1	.	.	.	.	.	.	.	.	.	.	C	15.52	2.857617	0.51376	.	.	ENSG00000187323	ENST00000442544;ENST00000304775;ENST00000412726	T;T	0.67523	-0.22;-0.27	5.34	5.34	0.76211	Fibronectin, type III (2);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000001	D	0.89347	0.6689	H	0.98507	4.25	0.58432	D	0.999991	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.999;0.999	D	0.93441	0.6794	10	0.87932	D	0	.	17.8248	0.88661	0.0:1.0:0.0:0.0	.	277;277;429	E7EQM8;B4DYX2;P43146	.;.;DCC_HUMAN	H	429;362;277	ENSP00000389140:P429H;ENSP00000397322:P277H	ENSP00000304146:P362H	P	+	2	0	DCC	48937748	1.000000	0.71417	1.000000	0.80357	0.984000	0.73092	7.027000	0.76463	2.510000	0.84645	0.561000	0.74099	CCT		0.542	DCC-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255996.3		NM_005215	
DENND4C	55667	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	9	19305459	19305459	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr9:19305459delA	ENST00000380432.2	+	6	746	c.713delA	c.(712-714)tatfs	p.Y238fs	DENND4C_ENST00000434457.2_Frame_Shift_Del_p.Y474fs|DENND4C_ENST00000602925.1_Frame_Shift_Del_p.Y474fs			Q5VZ89	DEN4C_HUMAN	DENN/MADD domain containing 4C	238	DENN. {ECO:0000255|PROSITE- ProRule:PRU00304}.				cellular response to insulin stimulus (GO:0032869)|positive regulation of Rab GTPase activity (GO:0032851)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)	cytosol (GO:0005829)|insulin-responsive compartment (GO:0032593)|plasma membrane (GO:0005886)|retromer complex (GO:0030904)	Rab guanyl-nucleotide exchange factor activity (GO:0017112)			breast(1)|endometrium(8)|kidney(1)|large_intestine(7)|liver(2)|lung(13)|ovary(1)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(1)	40						GACTCAAGGTATTTTGATCTT	0.383																																																	0													212.0	201.0	205.0					9																	19305459		2203	4300	6503	SO:0001589	frameshift_variant	55667			AK000693	CCDS6491.2, CCDS6491.3	9p22.1	2012-10-03	2006-01-27	2006-01-27	ENSG00000137145	ENSG00000137145		"""DENN/MADD domain containing"""	26079	protein-coding gene	gene with protein product			"""chromosome 9 open reading frame 55B"", ""chromosome 9 open reading frame 55"""	C9orf55B, C9orf55		12906859	Standard	NM_017925		Approved	FLJ20686, bA513M16.3	uc031tcw.1	Q5VZ89	OTTHUMG00000019627	ENST00000380432.2:c.713delA	9.37:g.19305459delA	ENSP00000369797:p.Tyr238fs	Somatic		WXS	Illumina HiSeq	Phase_I	A2A3R1|A2A3R2|A2A3R3|A2A3R9|Q6AI48|Q6ZUB3|Q8NCY7|Q9H6N4|Q9NUT1|Q9NWA5|Q9NWT3	Frame_Shift_Del	DEL	ENST00000380432.2	37																																																																																					0.383	DENND4C-201	KNOWN	basic	protein_coding	protein_coding			NM_017925	
DPAGT1	1798	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	118968667	118968667	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr11:118968667C>T	ENST00000409993.2	-	8	2366	c.815G>A	c.(814-816)aGc>aAc	p.S272N	DPAGT1_ENST00000445653.1_5'Flank|H2AFX_ENST00000530167.1_5'Flank|DPAGT1_ENST00000354202.4_Missense_Mutation_p.S272N|DPAGT1_ENST00000432443.2_Missense_Mutation_p.S165N			Q9H3H5	GPT_HUMAN	dolichyl-phosphate (UDP-N-acetylglucosamine) N-acetylglucosaminephosphotransferase 1 (GlcNAc-1-P transferase)	272					cellular protein metabolic process (GO:0044267)|dolichol biosynthetic process (GO:0019408)|dolichol-linked oligosaccharide biosynthetic process (GO:0006488)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation (GO:0006487)|protein N-linked glycosylation via asparagine (GO:0018279)|protein oligomerization (GO:0051259)|UDP-N-acetylglucosamine metabolic process (GO:0006047)	endoplasmic reticulum membrane (GO:0005789)|integral component of endoplasmic reticulum membrane (GO:0030176)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)	phospho-N-acetylmuramoyl-pentapeptide-transferase activity (GO:0008963)|transferase activity, transferring glycosyl groups (GO:0016757)|UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975)	p.S272N(1)		breast(2)|endometrium(1)|kidney(2)|large_intestine(3)|lung(5)|ovary(1)|prostate(1)|skin(2)	17	all_hematologic(175;0.0977)	Medulloblastoma(222;0.0425)|Breast(348;0.052)|all_neural(223;0.112)		BRCA - Breast invasive adenocarcinoma(274;7.55e-05)		CATGGTCTTGCTGAAGTGTCC	0.547																																																	1	Substitution - Missense(1)	kidney(1)											194.0	174.0	181.0					11																	118968667		2200	4295	6495	SO:0001583	missense	1798			Z82022	CCDS8411.1	11q23.3	2007-12-14			ENSG00000172269	ENSG00000172269	2.7.8.15		2995	protein-coding gene	gene with protein product		191350		DPAGT2, DPAGT		8244387	Standard	NM_001382		Approved	GPT, D11S366, DGPT, ALG7, CDG-Ij	uc001pvi.3	Q9H3H5	OTTHUMG00000153533	ENST00000409993.2:c.815G>A	11.37:g.118968667C>T	ENSP00000386597:p.Ser272Asn	Somatic		WXS	Illumina HiSeq	Phase_I	O15216|Q86WV9|Q9BWE6	Missense_Mutation	SNP	ENST00000409993.2	37	CCDS8411.1	.	.	.	.	.	.	.	.	.	.	C	34	5.304760	0.95601	.	.	ENSG00000172269	ENST00000409993;ENST00000354202;ENST00000432443	D;D;D	0.92699	-3.09;-3.09;-2.96	5.9	5.9	0.94986	.	0.000000	0.85682	D	0.000000	D	0.97492	0.9179	H	0.95151	3.63	0.80722	D	1	D;D	0.89917	0.998;1.0	D;D	0.79108	0.969;0.992	D	0.98098	1.0413	10	0.87932	D	0	-24.7629	19.2671	0.93993	0.0:1.0:0.0:0.0	.	165;272	E7EW40;Q9H3H5	.;GPT_HUMAN	N	272;272;165	ENSP00000386597:S272N;ENSP00000346142:S272N;ENSP00000404036:S165N	ENSP00000346142:S272N	S	-	2	0	DPAGT1	118473877	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.818000	0.86416	2.788000	0.95919	0.650000	0.86243	AGC		0.547	DPAGT1-002	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000331527.2		NM_001382	
EEA1	8411	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	93171332	93171332	+	Frame_Shift_Del	DEL	T	T	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr12:93171332delT	ENST00000322349.8	-	27	4265	c.4001delA	c.(4000-4002)aacfs	p.N1334fs		NM_003566.3	NP_003557	Q15075	EEA1_HUMAN	early endosome antigen 1	1334					early endosome to late endosome transport (GO:0045022)|endocytosis (GO:0006897)|synaptic vesicle to endosome fusion (GO:0016189)|vesicle fusion (GO:0006906)	axonal spine (GO:0044308)|cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|early endosome (GO:0005769)|extracellular vesicular exosome (GO:0070062)|extrinsic component of plasma membrane (GO:0019897)|membrane (GO:0016020)|recycling endosome (GO:0055037)|serine-pyruvate aminotransferase complex (GO:0005969)	1-phosphatidylinositol binding (GO:0005545)|calmodulin binding (GO:0005516)|GTP-dependent protein binding (GO:0030742)|protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)			endometrium(5)|kidney(5)|large_intestine(11)|lung(7)|ovary(2)|prostate(1)|skin(2)|upper_aerodigestive_tract(3)	36						AAGTGATTGGTTTTCTCTGCC	0.358																																																	0													146.0	133.0	137.0					12																	93171332		2203	4300	6503	SO:0001589	frameshift_variant	8411			L40157	CCDS31874.1	12q22	2007-02-23	2007-02-23			ENSG00000102189		"""Zinc fingers, FYVE domain containing"""	3185	protein-coding gene	gene with protein product		605070	"""early endosome antigen 1, 162kD"""			7768953, 9697774	Standard	NM_003566		Approved	ZFYVE2	uc001tck.3	Q15075	OTTHUMG00000170110	ENST00000322349.8:c.4001delA	12.37:g.93171332delT	ENSP00000317955:p.Asn1334fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q14221	Frame_Shift_Del	DEL	ENST00000322349.8	37	CCDS31874.1																																																																																				0.358	EEA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407304.1		NM_003566	
COL26A1	136227	hgsc.bcm.edu	37	7	101063320	101063320	+	RNA	SNP	C	C	T	rs369792846		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr7:101063320C>T	ENST00000397927.3	+	0	434				COL26A1_ENST00000528707.1_RNA|COL26A1_ENST00000313669.7_RNA	NM_001278563.1	NP_001265492.1	Q96A83	COQA1_HUMAN	collagen, type XXVI, alpha 1						collagen catabolic process (GO:0030574)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|positive regulation of cell-substrate adhesion (GO:0010811)	collagen trimer (GO:0005581)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|Golgi apparatus (GO:0005794)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)											GGCTCGGAGACGGTGGTCCAG	0.647																																																	0								C	MET/THR	0,4164		0,0,2082	28.0	38.0	35.0		221	4.9	1.0	7		35	1,8411		0,1,4205	no	missense	EMID2	NM_133457.2	81	0,1,6287	TT,TC,CC		0.0119,0.0,0.0080	probably-damaging	74/440	101063320	1,12575	2082	4206	6288			136227			AJ416091	CCDS64739.1	7q22.1	2013-01-16	2013-01-16	2013-01-16	ENSG00000160963	ENSG00000160963		"""Collagens"", ""EMI domain containing"""	18038	protein-coding gene	gene with protein product	"""Emu2 gene"""	608927	"""EMI domain containing 2"""	EMID2		12221002, 12145293	Standard	NM_001278563		Approved	Emu2, EMI6	uc003uyo.1	Q96A83	OTTHUMG00000150033		7.37:g.101063320C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q32M90	Missense_Mutation	SNP	ENST00000397927.3	37		.	.	.	.	.	.	.	.	.	.	C	26.0	4.694517	0.88830	0.0	1.19E-4	ENSG00000160963	ENST00000313669	T	0.46451	0.87	4.95	4.95	0.65309	EMI domain (2);	0.000000	0.38217	U	0.001773	T	0.67524	0.2902	M	0.84326	2.69	0.32682	N	0.515394	D;D	0.89917	1.0;1.0	D;D	0.87578	0.998;0.998	T	0.78326	-0.2247	10	0.87932	D	0	.	15.7219	0.77718	0.0:1.0:0.0:0.0	.	74;74	Q96A83;C9JPW4	EMID2_HUMAN;.	M	74	ENSP00000318234:T74M	ENSP00000318234:T74M	T	+	2	0	EMID2	100850040	1.000000	0.71417	0.999000	0.59377	0.994000	0.84299	7.079000	0.76829	2.310000	0.77875	0.558000	0.71614	ACG		0.647	COL26A1-002	KNOWN	basic	polymorphic_pseudogene	polymorphic_pseudogene	OTTHUMT00000315898.2		NM_133457	
FAM73A	374986	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	78249000	78249000	+	Silent	SNP	T	T	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr1:78249000T>C	ENST00000370791.3	+	2	191	c.159T>C	c.(157-159)ttT>ttC	p.F53F	FAM73A_ENST00000443751.2_Intron	NM_001270384.1|NM_198549.3	NP_001257313.1|NP_940951.1	Q8NAN2	FA73A_HUMAN	family with sequence similarity 73, member A	53						integral component of membrane (GO:0016021)		p.F53F(1)		breast(2)|kidney(2)|large_intestine(5)|lung(6)|ovary(2)|skin(1)|urinary_tract(1)	19				Colorectal(170;0.226)		TAAGAGTGTTTGATCTTCCTC	0.353																																																	1	Substitution - coding silent(1)	kidney(1)											151.0	145.0	147.0					1																	78249000		2203	4300	6503	SO:0001819	synonymous_variant	374986				CCDS681.1, CCDS72809.1	1p31.1	2008-02-05			ENSG00000180488	ENSG00000180488			24741	protein-coding gene	gene with protein product							Standard	NM_001270384		Approved	FLJ35093	uc010ork.3	Q8NAN2	OTTHUMG00000009766	ENST00000370791.3:c.159T>C	1.37:g.78249000T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q6MZG0	Silent	SNP	ENST00000370791.3	37	CCDS681.1																																																																																				0.353	FAM73A-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000026931.1		NM_198549	
FBN3	84467	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	8162185	8162185	+	Silent	SNP	G	G	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr19:8162185G>A	ENST00000600128.1	-	42	5689	c.5275C>T	c.(5275-5277)Ctg>Ttg	p.L1759L	FBN3_ENST00000601739.1_Silent_p.L1759L|FBN3_ENST00000270509.2_Silent_p.L1759L			Q75N90	FBN3_HUMAN	fibrillin 3	1759	EGF-like 26; calcium-binding. {ECO:0000255|PROSITE-ProRule:PRU00076}.					proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)|extracellular matrix structural constituent (GO:0005201)	p.L1759L(1)		NS(1)|breast(9)|central_nervous_system(2)|cervix(1)|endometrium(11)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(15)|lung(53)|ovary(7)|pancreas(2)|prostate(3)|skin(10)|stomach(1)|upper_aerodigestive_tract(5)|urinary_tract(2)	132						TCACAAGCCAGCAGGATGCTG	0.587																																																	1	Substitution - coding silent(1)	kidney(1)											41.0	38.0	39.0					19																	8162185		2203	4299	6502	SO:0001819	synonymous_variant	84467				CCDS12196.1	19p13	2008-02-05							18794	protein-coding gene	gene with protein product		608529					Standard	NM_032447		Approved		uc002mjf.3	Q75N90		ENST00000600128.1:c.5275C>T	19.37:g.8162185G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q75N91|Q75N92|Q75N93|Q86SJ5|Q96JP8	Silent	SNP	ENST00000600128.1	37	CCDS12196.1																																																																																				0.587	FBN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000461428.2		NM_032447	
FBXO30	84085	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	146126842	146126842	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr6:146126842T>C	ENST00000237281.4	-	2	866	c.700A>G	c.(700-702)Aaa>Gaa	p.K234E		NM_032145.4	NP_115521.3	Q8TB52	FBX30_HUMAN	F-box protein 30	234							ubiquitin-protein transferase activity (GO:0004842)|zinc ion binding (GO:0008270)	p.K234E(1)		NS(1)|endometrium(3)|kidney(1)|large_intestine(5)|lung(11)|ovary(2)|prostate(1)|skin(1)|upper_aerodigestive_tract(1)	26		Ovarian(120;0.0776)		OV - Ovarian serous cystadenocarcinoma(155;1.95e-07)|GBM - Glioblastoma multiforme(68;0.0149)		TCTTGGTCTTTCAAGTTTTGA	0.393																																																	1	Substitution - Missense(1)	kidney(1)											191.0	193.0	192.0					6																	146126842		2203	4300	6503	SO:0001583	missense	84085			AF248640	CCDS5208.1	6q24	2008-02-05	2004-06-15		ENSG00000118496	ENSG00000118496		"""F-boxes /  ""other"""""	15600	protein-coding gene	gene with protein product		609101	"""F-box only protein, helicase, 18"""				Standard	XM_005267159		Approved	MGC21674, Fbx30	uc003qla.3	Q8TB52	OTTHUMG00000015749	ENST00000237281.4:c.700A>G	6.37:g.146126842T>C	ENSP00000237281:p.Lys234Glu	Somatic		WXS	Illumina HiSeq	Phase_I	Q9BXZ7	Missense_Mutation	SNP	ENST00000237281.4	37	CCDS5208.1	.	.	.	.	.	.	.	.	.	.	T	1.972	-0.436340	0.04636	.	.	ENSG00000118496	ENST00000237281	T	0.19250	2.16	5.62	5.62	0.85841	.	0.637186	0.18398	N	0.142437	T	0.10766	0.0263	L	0.54323	1.7	0.42127	D	0.991457	B	0.20368	0.044	B	0.15870	0.014	T	0.04242	-1.0966	10	0.31617	T	0.26	-17.8953	11.8513	0.52413	0.1382:0.0:0.0:0.8618	.	234	Q8TB52	FBX30_HUMAN	E	234	ENSP00000237281:K234E	ENSP00000237281:K234E	K	-	1	0	FBXO30	146168535	0.992000	0.36948	0.926000	0.36857	0.568000	0.35870	3.538000	0.53597	2.255000	0.74692	0.533000	0.62120	AAA		0.393	FBXO30-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000042570.2			
FBXO3	26273	broad.mit.edu;ucsc.edu	37	11	33790514	33790514	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr11:33790514C>A	ENST00000265651.3	-	3	259	c.241G>T	c.(241-243)Gat>Tat	p.D81Y	FBXO3_ENST00000534136.1_Missense_Mutation_p.D81Y|FBXO3_ENST00000526785.1_5'UTR|FBXO3_ENST00000530401.1_Missense_Mutation_p.D76Y|FBXO3_ENST00000448981.2_Missense_Mutation_p.D81Y|FBXO3_ENST00000533103.1_5'UTR	NM_012175.3	NP_036307.2	Q9UK99	FBX3_HUMAN	F-box protein 3	81					proteolysis (GO:0006508)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	ubiquitin-protein transferase activity (GO:0004842)	p.D81Y(1)		NS(1)|breast(2)|central_nervous_system(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(3)|lung(2)|pancreas(1)|stomach(1)	13		Lung NSC(402;0.0804)		BRCA - Breast invasive adenocarcinoma(625;0.00315)|Lung(977;0.00488)|LUSC - Lung squamous cell carcinoma(625;0.008)		GAGTAAGTATCTATGAAGAGA	0.338																																																	1	Substitution - Missense(1)	kidney(1)											189.0	185.0	186.0					11																	33790514		2202	4298	6500	SO:0001583	missense	26273			AK001943	CCDS7887.1, CCDS44566.1	11p13	2006-07-07	2004-06-15		ENSG00000110429	ENSG00000110429		"""F-boxes /  ""other"""""	13582	protein-coding gene	gene with protein product		609089	"""F-box only protein 3"""			10531037	Standard	NM_033406		Approved	FBX3, FBA	uc001muz.3	Q9UK99	OTTHUMG00000166244	ENST00000265651.3:c.241G>T	11.37:g.33790514C>A	ENSP00000265651:p.Asp81Tyr	Somatic		WXS	Illumina GAIIx	Phase_I	B3KY16|D3DR05|Q86X90|Q9H0V2|Q9NUX2	Missense_Mutation	SNP	ENST00000265651.3	37	CCDS7887.1	.	.	.	.	.	.	.	.	.	.	C	13.61	2.287289	0.40494	.	.	ENSG00000110429	ENST00000265651;ENST00000321458;ENST00000530401;ENST00000534136;ENST00000448981	T;T;T;T	0.54071	0.59;0.59;0.59;0.59	5.99	5.99	0.97316	F-box domain, Skp2-like (1);	0.569812	0.21575	N	0.072350	T	0.36744	0.0978	N	0.14661	0.345	0.33385	D	0.575313	B;B;B	0.18968	0.032;0.032;0.019	B;B;B	0.11329	0.005;0.005;0.006	T	0.44605	-0.9317	10	0.45353	T	0.12	-13.2404	12.866	0.57939	0.0:0.9238:0.0:0.0762	.	76;81;81	Q9UK99-3;Q9UK99-2;Q9UK99	.;.;FBX3_HUMAN	Y	81;78;76;81;81	ENSP00000265651:D81Y;ENSP00000433781:D76Y;ENSP00000431745:D81Y;ENSP00000408836:D81Y	ENSP00000265651:D81Y	D	-	1	0	FBXO3	33747090	1.000000	0.71417	0.993000	0.49108	0.990000	0.78478	3.087000	0.50167	2.840000	0.97914	0.655000	0.94253	GAT		0.338	FBXO3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388665.1		NM_012175	
FDPS	2224	broad.mit.edu;hgsc.bcm.edu	37	1	155279736	155279736	+	Silent	SNP	A	A	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr1:155279736A>G	ENST00000356657.6	+	2	318	c.156A>G	c.(154-156)caA>caG	p.Q52Q	FDPS_ENST00000368356.4_Silent_p.Q52Q|FDPS_ENST00000447866.1_Intron|FDPS_ENST00000487002.1_3'UTR	NM_001135821.1	NP_001129293.1	P14324	FPPS_HUMAN	farnesyl diphosphate synthase	52					cholesterol biosynthetic process (GO:0006695)|farnesyl diphosphate biosynthetic process (GO:0045337)|geranyl diphosphate biosynthetic process (GO:0033384)|small molecule metabolic process (GO:0044281)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|mitochondrion (GO:0005739)|nucleus (GO:0005634)	dimethylallyltranstransferase activity (GO:0004161)|geranyltranstransferase activity (GO:0004337)|metal ion binding (GO:0046872)|poly(A) RNA binding (GO:0044822)	p.Q52Q(1)		cervix(1)|endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|prostate(1)	10	Hepatocellular(266;0.0877)|all_hematologic(923;0.145)		Epithelial(20;2.03e-10)|all cancers(21;5.23e-10)|BRCA - Breast invasive adenocarcinoma(34;0.000549)|LUSC - Lung squamous cell carcinoma(543;0.127)		Alendronate(DB00630)|Ibandronate(DB00710)|Pamidronate(DB00282)|Risedronate(DB00884)|Zoledronate(DB00399)	GCTGGTGCCAAGCGTGGACAG	0.637																																																	1	Substitution - coding silent(1)	kidney(1)											21.0	22.0	22.0					1																	155279736		2202	4300	6502	SO:0001819	synonymous_variant	2224			J05262	CCDS1110.1, CCDS44241.1, CCDS72940.1	1q22	2012-07-13	2010-06-24		ENSG00000160752	ENSG00000160752	2.5.1.1, 2.5.1.10		3631	protein-coding gene	gene with protein product	"""farnesyl pyrophosphate synthetase, dimethylallyltranstransferase, geranyltranstransferase"""	134629				1968462	Standard	NM_002004		Approved		uc001fkc.2	P14324	OTTHUMG00000013909	ENST00000356657.6:c.156A>G	1.37:g.155279736A>G		Somatic		WXS	Illumina HiSeq	Phase_I	D3DV91|E9PCI9|Q96G29	Silent	SNP	ENST00000356657.6	37	CCDS1110.1																																																																																				0.637	FDPS-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000039053.1		NM_002004	
GLRA3	8001	broad.mit.edu;ucsc.edu	37	4	175649781	175649781	+	Silent	SNP	A	A	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr4:175649781A>G	ENST00000274093.3	-	4	838	c.336T>C	c.(334-336)ccT>ccC	p.P112P	GLRA3_ENST00000436738.1_5'UTR|GLRA3_ENST00000340217.5_Silent_p.P112P	NM_006529.2	NP_006520.2	O75311	GLRA3_HUMAN	glycine receptor, alpha 3	112					ion transmembrane transport (GO:0034220)|transmembrane transport (GO:0055085)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)	extracellular-glycine-gated chloride channel activity (GO:0016934)|glycine binding (GO:0016594)|transmitter-gated ion channel activity (GO:0022824)	p.P112P(1)		endometrium(2)|kidney(1)|large_intestine(12)|lung(11)|ovary(3)|prostate(1)|skin(3)|stomach(1)|urinary_tract(1)	35		Prostate(90;0.00601)|Breast(14;0.0091)|Melanoma(52;0.00959)|Renal(120;0.0183)|all_neural(102;0.0891)|all_hematologic(60;0.107)		all cancers(43;4.99e-18)|Epithelial(43;1.18e-16)|OV - Ovarian serous cystadenocarcinoma(60;5.88e-09)|STAD - Stomach adenocarcinoma(60;0.00442)|GBM - Glioblastoma multiforme(59;0.0102)|LUSC - Lung squamous cell carcinoma(193;0.0421)	Glycine(DB00145)|Ivermectin(DB00602)|Lindane(DB00431)	AAGAGTCGTCAGGATATTCAC	0.398																																																	1	Substitution - coding silent(1)	kidney(1)											99.0	109.0	106.0					4																	175649781		2203	4300	6503	SO:0001819	synonymous_variant	8001			AF017724	CCDS3822.1, CCDS43283.1	4q34.1	2012-02-07			ENSG00000145451	ENSG00000145451		"""Ligand-gated ion channels / Glycine receptors"""	4328	protein-coding gene	gene with protein product		600421				9677400	Standard	NM_001042543		Approved		uc003ity.1	O75311	OTTHUMG00000149816	ENST00000274093.3:c.336T>C	4.37:g.175649781A>G		Somatic		WXS	Illumina GAIIx	Phase_I	D3DP44|O75816|Q5D0E3	Silent	SNP	ENST00000274093.3	37	CCDS3822.1																																																																																				0.398	GLRA3-001	KNOWN	basic|appris_candidate_longest|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000313427.1			
HIAT1	64645	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	100503796	100503796	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr1:100503796A>T	ENST00000370152.3	+	1	144	c.8A>T	c.(7-9)cAg>cTg	p.Q3L	RP4-714D9.5_ENST00000564623.1_RNA	NM_033055.2	NP_149044.2	Q96MC6	HIAT1_HUMAN	hippocampus abundant transcript 1	3					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	transporter activity (GO:0005215)	p.Q3L(1)		breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(8)|skin(1)	16		all_epithelial(167;2.96e-06)|all_lung(203;0.00125)|Lung NSC(277;0.00131)		Epithelial(280;0.0832)|all cancers(265;0.136)|COAD - Colon adenocarcinoma(174;0.148)|Lung(183;0.195)		AAAATGACCCAGGGGAAGAAG	0.632																																																	1	Substitution - Missense(1)	kidney(1)											64.0	58.0	60.0					1																	100503796		2179	4238	6417	SO:0001583	missense	64645			AK096669	CCDS763.1	1p21.3	2008-02-05			ENSG00000156875	ENSG00000156875			23363	protein-coding gene	gene with protein product						9299464	Standard	NM_033055		Approved	DKFZP564L0864	uc001dst.3	Q96MC6	OTTHUMG00000010755	ENST00000370152.3:c.8A>T	1.37:g.100503796A>T	ENSP00000359171:p.Gln3Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q6P2N7|Q8N8K2|Q8NBV3|Q96NY0|Q9NT25	Missense_Mutation	SNP	ENST00000370152.3	37	CCDS763.1	.	.	.	.	.	.	.	.	.	.	A	15.69	2.907314	0.52333	.	.	ENSG00000156875	ENST00000370152	T	0.30182	1.54	4.8	2.5	0.30297	Major facilitator superfamily domain, general substrate transporter (1);	0.290951	0.28006	N	0.016966	T	0.08582	0.0213	L	0.29908	0.895	0.45261	D	0.998265	B	0.09022	0.002	B	0.04013	0.001	T	0.07462	-1.0771	10	0.36615	T	0.2	-0.3119	7.1971	0.25860	0.8187:0.0:0.1813:0.0	.	3	Q96MC6	HIAT1_HUMAN	L	3	ENSP00000359171:Q3L	ENSP00000359171:Q3L	Q	+	2	0	HIAT1	100276384	1.000000	0.71417	0.999000	0.59377	0.991000	0.79684	2.096000	0.41738	0.682000	0.31407	0.379000	0.24179	CAG		0.632	HIAT1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000029657.1		NM_033055	
GPSM2	29899	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	109466798	109466798	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr1:109466798G>A	ENST00000406462.2	+	15	2550	c.1777G>A	c.(1777-1779)Gct>Act	p.A593T	GPSM2_ENST00000264126.3_Missense_Mutation_p.A593T|AKNAD1_ENST00000357393.4_Intron			P81274	GPSM2_HUMAN	G-protein signaling modulator 2	593					establishment of mitotic spindle orientation (GO:0000132)|G-protein coupled receptor signaling pathway (GO:0007186)|lung epithelial cell differentiation (GO:0060487)	apical part of cell (GO:0045177)|cytoplasm (GO:0005737)|nucleus (GO:0005634)	GTPase regulator activity (GO:0030695)|identical protein binding (GO:0042802)	p.A586T(1)		breast(2)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(4)|liver(2)|lung(3)	14		all_epithelial(167;7.64e-05)|all_lung(203;0.000321)|Lung NSC(277;0.000626)		Colorectal(144;0.0353)|Lung(183;0.0984)|COAD - Colon adenocarcinoma(174;0.129)|Epithelial(280;0.175)|all cancers(265;0.209)		CAACAAAGAGGCTGATGAAGA	0.408																																																	1	Substitution - Missense(1)	kidney(1)											100.0	89.0	92.0					1																	109466798		2203	4300	6503	SO:0001583	missense	29899			AY136740	CCDS792.2	1p13.3	2013-10-11	2010-06-24		ENSG00000121957	ENSG00000121957		"""Tetratricopeptide (TTC) repeat domain containing"""	29501	protein-coding gene	gene with protein product		609245	"""G-protein signalling modulator 2 (AGS3-like, C. elegans)"", ""deafness, autosomal recessive 82"""	DFNB82		11832491, 8973305, 19888295, 20602914, 21348867	Standard	NM_013296		Approved	LGN, Pins	uc010ovc.2	P81274	OTTHUMG00000011730	ENST00000406462.2:c.1777G>A	1.37:g.109466798G>A	ENSP00000385510:p.Ala593Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5T1N8|Q6IBL7|Q8N0Z5	Missense_Mutation	SNP	ENST00000406462.2	37	CCDS792.2	.	.	.	.	.	.	.	.	.	.	G	14.35	2.509213	0.44660	.	.	ENSG00000121957	ENST00000406462;ENST00000264126	D;D	0.93307	-3.2;-3.2	5.62	3.74	0.42951	.	0.288557	0.39274	N	0.001406	T	0.79919	0.4529	N	0.14661	0.345	0.26972	N	0.965562	B	0.24823	0.112	B	0.20184	0.028	T	0.71649	-0.4529	10	0.72032	D	0.01	-2.8453	16.2361	0.82375	0.0:0.7387:0.2613:0.0	.	593	P81274	GPSM2_HUMAN	T	593	ENSP00000385510:A593T;ENSP00000264126:A593T	ENSP00000264126:A593T	A	+	1	0	GPSM2	109268321	1.000000	0.71417	0.999000	0.59377	0.253000	0.25986	3.077000	0.50089	0.730000	0.32425	-0.165000	0.13383	GCT		0.408	GPSM2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000032400.3		NM_013296	
HTR1E	3354	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	87725912	87725912	+	Missense_Mutation	SNP	G	G	A	rs61735411		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr6:87725912G>A	ENST00000305344.5	+	2	1563	c.860G>A	c.(859-861)cGg>cAg	p.R287Q		NM_000865.2	NP_000856.1	P28566	5HT1E_HUMAN	5-hydroxytryptamine (serotonin) receptor 1E, G protein-coupled	287					adenylate cyclase-inhibiting G-protein coupled receptor signaling pathway (GO:0007193)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|negative regulation of cAMP metabolic process (GO:0030815)|serotonin receptor signaling pathway (GO:0007210)|synaptic transmission (GO:0007268)	integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|serotonin binding (GO:0051378)|serotonin receptor activity (GO:0004993)	p.R287Q(1)		breast(3)|endometrium(2)|kidney(3)|large_intestine(11)|lung(15)|ovary(2)|prostate(2)|skin(3)	41		all_cancers(76;7.11e-06)|Acute lymphoblastic leukemia(125;1.2e-09)|Prostate(29;3.51e-09)|all_hematologic(105;7.43e-06)|all_epithelial(107;0.00819)		BRCA - Breast invasive adenocarcinoma(108;0.055)	Aripiprazole(DB01238)|Clozapine(DB00363)|Eletriptan(DB00216)|Ergoloid mesylate(DB01049)|Ketamine(DB01221)|Loxapine(DB00408)|Methysergide(DB00247)|Olanzapine(DB00334)|Quetiapine(DB01224)|Ziprasidone(DB00246)	ACCAGGGAACGGAAGGCAGCA	0.502																																																	1	Substitution - Missense(1)	kidney(1)											175.0	162.0	167.0					6																	87725912		2203	4300	6503	SO:0001583	missense	3354				CCDS5006.1	6q14-q15	2013-06-19	2012-02-03		ENSG00000168830	ENSG00000168830		"""5-HT (serotonin) receptors"", ""GPCR / Class A : 5-HT (serotonin) receptors, GPCR only"""	5291	protein-coding gene	gene with protein product		182132	"""5-hydroxytryptamine (serotonin) receptor 1E"""			1608964	Standard	NM_000865		Approved	5-HT1E	uc003pli.3	P28566	OTTHUMG00000015154	ENST00000305344.5:c.860G>A	6.37:g.87725912G>A	ENSP00000307766:p.Arg287Gln	Somatic		WXS	Illumina HiSeq	Phase_I	E1P503|Q9P1Y1	Missense_Mutation	SNP	ENST00000305344.5	37	CCDS5006.1	.	.	.	.	.	.	.	.	.	.	G	15.93	2.979157	0.53827	.	.	ENSG00000168830	ENST00000305344;ENST00000369584	T;T	0.72835	-0.69;-0.69	4.44	3.53	0.40419	GPCR, rhodopsin-like superfamily (1);	0.000000	0.64402	U	0.000016	T	0.75384	0.3842	M	0.68593	2.085	0.47819	D	0.999527	D	0.89917	1.0	D	0.74674	0.984	T	0.77153	-0.2692	10	0.49607	T	0.09	.	13.4304	0.61051	0.0:0.0:0.8416:0.1583	rs61735411	287	P28566	5HT1E_HUMAN	Q	287	ENSP00000307766:R287Q;ENSP00000358597:R287Q	ENSP00000307766:R287Q	R	+	2	0	HTR1E	87782631	1.000000	0.71417	0.997000	0.53966	0.314000	0.28054	9.219000	0.95173	0.821000	0.34540	0.205000	0.17691	CGG		0.502	HTR1E-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000472488.2		NM_000865	
KRT13	3860	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	39659227	39659227	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr17:39659227T>C	ENST00000246635.3	-	4	905	c.859A>G	c.(859-861)Agg>Ggg	p.R287G	KRT13_ENST00000336861.3_Missense_Mutation_p.R287G|KRT13_ENST00000587544.1_Missense_Mutation_p.R287G|KRT13_ENST00000587118.1_5'Flank|AC019349.5_ENST00000411759.1_RNA	NM_153490.2	NP_705694	P13646	K1C13_HUMAN	keratin 13	287	Coil 2.|Rod.				cellular response to retinoic acid (GO:0071300)|cytoskeleton organization (GO:0007010)|response to radiation (GO:0009314)|tongue morphogenesis (GO:0043587)	extracellular vesicular exosome (GO:0070062)|intermediate filament cytoskeleton (GO:0045111)|keratin filament (GO:0045095)|nucleus (GO:0005634)	structural molecule activity (GO:0005198)	p.R287G(1)		NS(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|prostate(2)|skin(4)|urinary_tract(1)	33		Breast(137;0.000286)				CGGCGGTTCCTCTCTGCCATG	0.647																																																	1	Substitution - Missense(1)	kidney(1)											174.0	163.0	167.0					17																	39659227		2203	4300	6503	SO:0001583	missense	3860				CCDS11396.1, CCDS11397.1	17q21.2	2013-06-20			ENSG00000171401	ENSG00000171401		"""-"", ""Intermediate filaments type I, keratins (acidic)"""	6415	protein-coding gene	gene with protein product	"""keratin, type I cytoskeletal 13"", ""cytokeratin 13"""	148065				16831889	Standard	NM_153490		Approved	K13, CK13, MGC3781, MGC161462	uc002hwu.1	P13646	OTTHUMG00000133434	ENST00000246635.3:c.859A>G	17.37:g.39659227T>C	ENSP00000246635:p.Arg287Gly	Somatic		WXS	Illumina HiSeq	Phase_I	Q53G54|Q6AZK5|Q8N240	Missense_Mutation	SNP	ENST00000246635.3	37	CCDS11396.1	.	.	.	.	.	.	.	.	.	.	T	12.48	1.950032	0.34377	.	.	ENSG00000171401	ENST00000246635;ENST00000336861;ENST00000157775	T;T	0.78816	-1.21;-1.21	4.32	3.23	0.37069	Filament (1);	0.135136	0.32918	N	0.005494	T	0.79499	0.4456	M	0.83852	2.665	0.24730	N	0.993092	B;B;B;B	0.28378	0.209;0.126;0.104;0.126	B;B;B;B	0.37346	0.236;0.247;0.159;0.247	T	0.73824	-0.3861	10	0.72032	D	0.01	.	7.3808	0.26854	0.0:0.0806:0.2099:0.7096	.	275;287;287;287	P13646-2;A1A4E9;P13646-3;P13646	.;.;.;K1C13_HUMAN	G	287;287;275	ENSP00000246635:R287G;ENSP00000336604:R287G	ENSP00000157775:R275G	R	-	1	2	KRT13	36912753	1.000000	0.71417	0.998000	0.56505	0.330000	0.28571	2.744000	0.47450	0.801000	0.34066	0.459000	0.35465	AGG		0.647	KRT13-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000257297.1		NM_153490	
KRT82	3888	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	52795073	52795075	+	Splice_Site	DEL	CTT	CTT	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	CTT	CTT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr12:52795073_52795075delCTT	ENST00000257974.2	-	3	756_758	c.679_681delAAG	c.(679-681)aagdel	p.K227del	RP3-416H24.4_ENST00000547174.1_RNA	NM_033033.3	NP_149022.3	Q9NSB4	KRT82_HUMAN	keratin 82	227	Coil 1B.|Rod.					keratin filament (GO:0045095)	structural constituent of epidermis (GO:0030280)			endometrium(1)|kidney(2)|large_intestine(6)|liver(2)|lung(13)|ovary(1)|skin(3)|upper_aerodigestive_tract(1)	29				BRCA - Breast invasive adenocarcinoma(357;0.193)		TCCTCCTTACCTTCTTCAAGGCA	0.552																																																	0																																										SO:0001630	splice_region_variant	3888			Y19207	CCDS8826.1	12q13	2013-01-16	2006-07-17	2006-07-17		ENSG00000161850		"""-"", ""Intermediate filaments type II, keratins (basic)"""	6459	protein-coding gene	gene with protein product	"""hard keratin type II 2"""	601078	"""keratin, hair, basic, 2"""	KRTHB2		2431943, 16831889	Standard	NM_033033		Approved	Hb-2	uc001sai.1	Q9NSB4	OTTHUMG00000169636	ENST00000257974.2:c.681+1AAG>-	12.37:g.52795076_52795078delCTT		Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000257974.2	37	CCDS8826.1																																																																																				0.552	KRT82-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000405189.1		NM_033033	In_Frame_Del
LRP1	4035	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	57548478	57548478	+	Silent	SNP	C	C	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr12:57548478C>T	ENST00000243077.3	+	8	1687	c.1221C>T	c.(1219-1221)ggC>ggT	p.G407G	LRP1_ENST00000554174.1_Silent_p.G407G	NM_002332.2	NP_002323.2	Q07954	LRP1_HUMAN	low density lipoprotein receptor-related protein 1	407					aging (GO:0007568)|aorta morphogenesis (GO:0035909)|apoptotic cell clearance (GO:0043277)|beta-amyloid clearance (GO:0097242)|cell proliferation (GO:0008283)|cholesterol metabolic process (GO:0008203)|lipoprotein metabolic process (GO:0042157)|lipoprotein transport (GO:0042953)|negative regulation of neuron apoptotic process (GO:0043524)|negative regulation of platelet-derived growth factor receptor-beta signaling pathway (GO:2000587)|negative regulation of smooth muscle cell migration (GO:0014912)|negative regulation of Wnt signaling pathway (GO:0030178)|phototransduction, visible light (GO:0007603)|positive regulation of cholesterol efflux (GO:0010875)|positive regulation of lipid transport (GO:0032370)|positive regulation of protein transport (GO:0051222)|protein kinase C-activating G-protein coupled receptor signaling pathway (GO:0007205)|receptor-mediated endocytosis (GO:0006898)|regulation of actin cytoskeleton organization (GO:0032956)|regulation of cholesterol transport (GO:0032374)|regulation of phospholipase A2 activity (GO:0032429)|retinoid metabolic process (GO:0001523)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|dendrite (GO:0030425)|endocytic vesicle membrane (GO:0030666)|endosome (GO:0005768)|focal adhesion (GO:0005925)|integral component of plasma membrane (GO:0005887)|lysosomal membrane (GO:0005765)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	apolipoprotein binding (GO:0034185)|calcium ion binding (GO:0005509)|lipoprotein particle receptor binding (GO:0070325)|lipoprotein transporter activity (GO:0042954)|poly(A) RNA binding (GO:0044822)|protein complex binding (GO:0032403)|receptor activity (GO:0004872)	p.G407G(1)		NS(1)|breast(9)|central_nervous_system(3)|cervix(3)|endometrium(33)|haematopoietic_and_lymphoid_tissue(4)|kidney(10)|large_intestine(26)|lung(58)|ovary(10)|pancreas(2)|prostate(11)|skin(7)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(5)	184				BRCA - Breast invasive adenocarcinoma(357;0.0103)	Antihemophilic Factor(DB00025)|Coagulation Factor IX(DB00100)|Tenecteplase(DB00031)	TCATCCAGGGCATCCTGGTGA	0.577																																																	1	Substitution - coding silent(1)	kidney(1)											32.0	29.0	30.0					12																	57548478		2192	4291	6483	SO:0001819	synonymous_variant	4035			X13916	CCDS8932.1	12q13.3	2013-05-28	2010-01-26		ENSG00000123384	ENSG00000123384		"""CD molecules"", ""Low density lipoprotein receptors"""	6692	protein-coding gene	gene with protein product		107770	"""alpha-2-macroglobulin receptor"""	APR, A2MR		2548950	Standard	NM_002332		Approved	LRP, CD91, LRP1A, APOER	uc001snd.3	Q07954	OTTHUMG00000044412	ENST00000243077.3:c.1221C>T	12.37:g.57548478C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q2PP12|Q86SW0|Q8IVG8	Silent	SNP	ENST00000243077.3	37	CCDS8932.1																																																																																				0.577	LRP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000412772.2		NM_002332	
LRP2	4036	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	170026249	170026249	+	Silent	SNP	G	G	A	rs371738642		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr2:170026249G>A	ENST00000263816.3	-	60	11745	c.11460C>T	c.(11458-11460)tcC>tcT	p.S3820S		NM_004525.2	NP_004516.2	P98164	LRP2_HUMAN	low density lipoprotein receptor-related protein 2	3820	LDL-receptor class A 33. {ECO:0000255|PROSITE-ProRule:PRU00124}.				cell proliferation (GO:0008283)|endocytosis (GO:0006897)|forebrain development (GO:0030900)|lipid metabolic process (GO:0006629)|phototransduction, visible light (GO:0007603)|protein glycosylation (GO:0006486)|receptor-mediated endocytosis (GO:0006898)|retinoid metabolic process (GO:0001523)|small molecule metabolic process (GO:0044281)|steroid metabolic process (GO:0008202)|vitamin D metabolic process (GO:0042359)	apical plasma membrane (GO:0016324)|brush border membrane (GO:0031526)|coated pit (GO:0005905)|endocytic vesicle (GO:0030139)|endoplasmic reticulum (GO:0005783)|endosome (GO:0005768)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|lysosomal membrane (GO:0005765)|lysosome (GO:0005764)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	calcium ion binding (GO:0005509)	p.S3820S(1)		biliary_tract(1)|breast(16)|central_nervous_system(6)|cervix(2)|endometrium(24)|haematopoietic_and_lymphoid_tissue(2)|kidney(17)|large_intestine(70)|liver(1)|lung(117)|ovary(19)|pancreas(1)|prostate(2)|skin(17)|upper_aerodigestive_tract(7)|urinary_tract(13)	315				STAD - Stomach adenocarcinoma(1183;0.000766)|COAD - Colon adenocarcinoma(177;0.0101)	"""""""Insulin(DB00071)|Gentamicin(DB00798)|Insulin Regular(DB00030)|Urokinase(DB00013)"""	AACAGTCAGCGGATCCATCGC	0.423																																																	1	Substitution - coding silent(1)	kidney(1)						G		1,4405	2.1+/-5.4	0,1,2202	224.0	175.0	192.0		11460	-12.3	0.0	2		192	0,8600		0,0,4300	no	coding-synonymous	LRP2	NM_004525.2		0,1,6502	AA,AG,GG		0.0,0.0227,0.0077		3820/4656	170026249	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	4036				CCDS2232.1	2q31.1	2013-05-28	2010-01-26		ENSG00000081479	ENSG00000081479		"""Low density lipoprotein receptors"""	6694	protein-coding gene	gene with protein product	"""megalin"""	600073				7959795	Standard	NM_004525		Approved	gp330, DBS	uc002ues.3	P98164	OTTHUMG00000132179	ENST00000263816.3:c.11460C>T	2.37:g.170026249G>A		Somatic		WXS	Illumina HiSeq	Phase_I	O00711|Q16215	Silent	SNP	ENST00000263816.3	37	CCDS2232.1																																																																																				0.423	LRP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000255231.2		NM_004525	
LRP5	4041	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	68183829	68183829	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr11:68183829C>A	ENST00000294304.7	+	13	2967	c.2861C>A	c.(2860-2862)tCt>tAt	p.S954Y		NM_002335.2	NP_002326.2	O75197	LRP5_HUMAN	low density lipoprotein receptor-related protein 5	954	Beta-propeller 4.				adipose tissue development (GO:0060612)|anatomical structure regression (GO:0060033)|anterior/posterior pattern specification (GO:0009952)|apoptotic process involved in patterning of blood vessels (GO:1902262)|bone marrow development (GO:0048539)|bone morphogenesis (GO:0060349)|bone remodeling (GO:0046849)|branching involved in mammary gland duct morphogenesis (GO:0060444)|canonical Wnt signaling pathway (GO:0060070)|cell migration involved in gastrulation (GO:0042074)|cell-cell signaling involved in mammary gland development (GO:0060764)|cholesterol homeostasis (GO:0042632)|cholesterol metabolic process (GO:0008203)|embryonic camera-type eye morphogenesis (GO:0048596)|embryonic digit morphogenesis (GO:0042733)|embryonic limb morphogenesis (GO:0030326)|embryonic retina morphogenesis in camera-type eye (GO:0060059)|endocytosis (GO:0006897)|extracellular matrix-cell signaling (GO:0035426)|gastrulation with mouth forming second (GO:0001702)|glucose catabolic process (GO:0006007)|negative regulation of osteoblast differentiation (GO:0045668)|negative regulation of protein serine/threonine kinase activity (GO:0071901)|osteoblast development (GO:0002076)|positive regulation of cell proliferation (GO:0008284)|positive regulation of fat cell differentiation (GO:0045600)|positive regulation of mesenchymal cell proliferation (GO:0002053)|positive regulation of mitosis (GO:0045840)|positive regulation of osteoblast proliferation (GO:0033690)|positive regulation of sequence-specific DNA binding transcription factor activity (GO:0051091)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of transcription, DNA-templated (GO:0045893)|regulation of apoptotic process (GO:0042981)|regulation of blood pressure (GO:0008217)|regulation of bone remodeling (GO:0046850)|regulation of canonical Wnt signaling pathway (GO:0060828)|regulation of insulin secretion involved in cellular response to glucose stimulus (GO:0061178)|response to peptide hormone (GO:0043434)|retina morphogenesis in camera-type eye (GO:0060042)|retinal blood vessel morphogenesis (GO:0061304)|somatic stem cell maintenance (GO:0035019)|Wnt signaling pathway (GO:0016055)|Wnt signaling pathway involved in dorsal/ventral axis specification (GO:0044332)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)|mitochondrion (GO:0005739)|plasma membrane (GO:0005886)|receptor complex (GO:0043235)	coreceptor activity (GO:0015026)|Wnt-activated receptor activity (GO:0042813)|Wnt-protein binding (GO:0017147)	p.S954Y(1)		autonomic_ganglia(1)|breast(3)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(9)|lung(24)|ovary(5)|pancreas(1)|prostate(1)|skin(6)|upper_aerodigestive_tract(1)|urinary_tract(1)	63						AGCCAGAAATCTGCCATCAGT	0.587																																																	1	Substitution - Missense(1)	kidney(1)											101.0	92.0	95.0					11																	68183829		2200	4294	6494	SO:0001583	missense	4041			AF064548	CCDS8181.1	11q13.4	2014-01-28	2003-03-12		ENSG00000162337	ENSG00000162337		"""Low density lipoprotein receptors"""	6697	protein-coding gene	gene with protein product		603506	"""osteoporosis pseudoglioma syndrome"", ""exudative vitreoretinopathy 1"""	LRP7, OPPG, EVR1		9714764, 10049586	Standard	XM_005273994		Approved	LR3, BMND1, HBM, OPS, OPTA1, VBCH2, EVR4	uc001ont.3	O75197	OTTHUMG00000167570	ENST00000294304.7:c.2861C>A	11.37:g.68183829C>A	ENSP00000294304:p.Ser954Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	Q96TD6|Q9UES7|Q9UP66	Missense_Mutation	SNP	ENST00000294304.7	37	CCDS8181.1	.	.	.	.	.	.	.	.	.	.	C	15.24	2.774110	0.49786	.	.	ENSG00000162337	ENST00000294304	D	0.91464	-2.85	4.49	0.372	0.16173	Six-bladed beta-propeller, TolB-like (1);	1.245830	0.05989	N	0.645741	D	0.87410	0.6170	L	0.56124	1.755	0.19300	N	0.999977	P;P	0.36199	0.543;0.543	B;B	0.39217	0.294;0.294	T	0.75048	-0.3455	10	0.52906	T	0.07	.	2.996	0.05998	0.1799:0.436:0.264:0.1201	.	954;954	Q9UES7;O75197	.;LRP5_HUMAN	Y	954	ENSP00000294304:S954Y	ENSP00000294304:S954Y	S	+	2	0	LRP5	67940405	0.000000	0.05858	0.321000	0.25320	0.926000	0.56050	0.693000	0.25497	-0.089000	0.12484	-0.165000	0.13383	TCT		0.587	LRP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000395088.1		NM_002335	
MAGI3	260425	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	114193677	114193677	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr1:114193677A>T	ENST00000307546.9	+	14	2364	c.2289A>T	c.(2287-2289)aaA>aaT	p.K763N	MAGI3_ENST00000369615.1_Missense_Mutation_p.K763N|MAGI3_ENST00000369611.4_Missense_Mutation_p.K763N|MAGI3_ENST00000369617.4_Missense_Mutation_p.K788N	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	788	Interaction with BAI1.|PDZ 4. {ECO:0000255|PROSITE- ProRule:PRU00143}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)	p.K763N(2)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		CAGCTGAGAAAGATGGTCGGC	0.428																																																	2	Substitution - Missense(2)	kidney(2)											108.0	105.0	106.0					1																	114193677		2203	4300	6503	SO:0001583	missense	260425			AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.2289A>T	1.37:g.114193677A>T	ENSP00000304604:p.Lys763Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Missense_Mutation	SNP	ENST00000307546.9	37	CCDS44196.1	.	.	.	.	.	.	.	.	.	.	A	16.23	3.064842	0.55432	.	.	ENSG00000081026	ENST00000369617;ENST00000307546;ENST00000369615;ENST00000369611	T;T;T;T	0.29142	1.58;1.58;1.58;1.58	5.74	-2.26	0.06867	.	0.000000	0.85682	D	0.000000	T	0.35098	0.0920	L	0.61218	1.895	0.58432	D	0.999999	D;D;P	0.89917	0.99;1.0;0.507	P;D;P	0.87578	0.841;0.998;0.549	T	0.30357	-0.9981	10	0.52906	T	0.07	-0.3518	12.9047	0.58145	0.5267:0.0:0.4733:0.0	.	763;763;788	Q5TCQ9-4;Q5TCQ9-3;Q5TCQ9-2	.;.;.	N	788;763;763;763	ENSP00000358630:K788N;ENSP00000304604:K763N;ENSP00000358628:K763N;ENSP00000358624:K763N	ENSP00000304604:K763N	K	+	3	2	MAGI3	113995200	0.955000	0.32602	0.973000	0.42090	0.999000	0.98932	0.127000	0.15790	-0.694000	0.05113	0.533000	0.62120	AAA		0.428	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1		NM_152900	
METTL17	64745	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	21461323	21461323	+	Missense_Mutation	SNP	T	T	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr14:21461323T>G	ENST00000339374.6	+	6	808	c.575T>G	c.(574-576)tTt>tGt	p.F192C	METTL17_ENST00000382985.4_Missense_Mutation_p.F192C|RP11-84C10.4_ENST00000557335.1_RNA|METTL17_ENST00000556670.2_Missense_Mutation_p.F192C	NM_001029991.1|NM_022734.2	NP_001025162.1|NP_073571.1	Q9H7H0	MET17_HUMAN	methyltransferase like 17	192					translation (GO:0006412)	mitochondrion (GO:0005739)|ribosome (GO:0005840)	copper ion binding (GO:0005507)|methyltransferase activity (GO:0008168)	p.F192C(1)		central_nervous_system(1)|endometrium(3)|kidney(1)|large_intestine(2)|lung(8)|ovary(2)|prostate(1)|skin(2)	20						TTGATGGACTTTGGCTCAGGT	0.418																																																	1	Substitution - Missense(1)	kidney(1)											205.0	184.0	191.0					14																	21461323		2203	4300	6503	SO:0001583	missense	0			AK024512	CCDS9562.1, CCDS41913.1	14q11.2	2011-03-03	2011-03-02	2011-03-02	ENSG00000165792	ENSG00000165792			19280	protein-coding gene	gene with protein product			"""methyltransferase 11 domain containing 1"""	METT11D1		11278769	Standard	XM_006720235		Approved	FLJ20859	uc001vyn.3	Q9H7H0	OTTHUMG00000029610	ENST00000339374.6:c.575T>G	14.37:g.21461323T>G	ENSP00000343041:p.Phe192Cys	Somatic		WXS	Illumina HiSeq	Phase_I	Q9BSH1|Q9BZH2|Q9BZH3	Missense_Mutation	SNP	ENST00000339374.6	37	CCDS9562.1	.	.	.	.	.	.	.	.	.	.	T	20.5	4.000419	0.74818	.	.	ENSG00000165792	ENST00000339374;ENST00000382985;ENST00000553564;ENST00000555670	T;T;T;T	0.42900	0.96;0.96;1.97;0.96	5.29	5.29	0.74685	.	0.000000	0.85682	D	0.000000	T	0.68016	0.2955	M	0.87038	2.855	0.58432	D	0.999998	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.91635	0.999;0.998;0.998	T	0.73600	-0.3931	10	0.59425	D	0.04	.	13.1812	0.59655	0.0:0.0:0.0:1.0	.	192;192;192	Q9H7H0-3;Q9H7H0;Q9H7H0-2	.;MET17_HUMAN;.	C	192;192;110;110	ENSP00000343041:F192C;ENSP00000372445:F192C;ENSP00000451478:F110C;ENSP00000451049:F110C	ENSP00000343041:F192C	F	+	2	0	METTL17	20531163	1.000000	0.71417	1.000000	0.80357	0.944000	0.59088	4.897000	0.63231	1.999000	0.58509	0.482000	0.46254	TTT		0.418	METTL17-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000073804.4		NM_022734	
MAX	4149	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	65569042	65569042	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr14:65569042C>A	ENST00000358664.4	-	1	146	c.16G>T	c.(16-18)Gac>Tac	p.D6Y	MAX_ENST00000284165.6_Missense_Mutation_p.D6Y|MAX_ENST00000555419.1_Missense_Mutation_p.D6Y|MAX_ENST00000358402.4_Missense_Mutation_p.D6Y|MAX_ENST00000556979.1_Missense_Mutation_p.D6Y|MAX_ENST00000557277.1_Intron|MAX_ENST00000555932.1_Missense_Mutation_p.D6Y|MAX_ENST00000556443.1_Missense_Mutation_p.D6Y|MAX_ENST00000246163.2_Missense_Mutation_p.D6Y|MAX_ENST00000557746.1_Missense_Mutation_p.D6Y|MAX_ENST00000341653.2_Missense_Mutation_p.D6Y|MAX_ENST00000555667.1_Missense_Mutation_p.D6Y	NM_002382.4	NP_002373.3	P61244	MAX_HUMAN	MYC associated factor X	6					cellular response to peptide hormone stimulus (GO:0071375)|cellular response to starvation (GO:0009267)|negative regulation of gene expression (GO:0010629)|neuron apoptotic process (GO:0051402)|protein complex assembly (GO:0006461)|response to axon injury (GO:0048678)|response to insulin (GO:0032868)|retina development in camera-type eye (GO:0060041)|transcription from RNA polymerase II promoter (GO:0006366)	cytoplasm (GO:0005737)|dendrite (GO:0030425)|MLL1 complex (GO:0071339)|nucleus (GO:0005634)|PML body (GO:0016605)	sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|transcription coactivator activity (GO:0003713)|transcription cofactor activity (GO:0003712)	p.D6Y(3)		breast(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(1)|lung(3)|prostate(1)|skin(1)	17				all cancers(60;0.000776)|OV - Ovarian serous cystadenocarcinoma(108;0.00359)|BRCA - Breast invasive adenocarcinoma(234;0.00999)		ACCTCGATGTCATCGTTATCG	0.672																																																	3	Substitution - Missense(3)	kidney(3)											74.0	63.0	66.0					14																	65569042		2203	4300	6503	SO:0001583	missense	4149				CCDS9770.1, CCDS9771.1, CCDS9772.1, CCDS9774.1, CCDS41965.1	14q23	2014-09-17	2005-02-08		ENSG00000125952	ENSG00000125952		"""Basic helix-loop-helix proteins"""	6913	protein-coding gene	gene with protein product		154950	"""MAX protein"""			1557420	Standard	NM_002382		Approved	bHLHd4, bHLHd5, bHLHd6, bHLHd7, bHLHd8	uc001xif.2	P61244	OTTHUMG00000142809	ENST00000358664.4:c.16G>T	14.37:g.65569042C>A	ENSP00000351490:p.Asp6Tyr	Somatic		WXS	Illumina HiSeq	Phase_I	A6NH73|A8K265|A8K4G4|A8K824|P25912|P52163|Q14803|Q96CY8	Missense_Mutation	SNP	ENST00000358664.4	37	CCDS9771.1	.	.	.	.	.	.	.	.	.	.	C	21.0	4.076344	0.76415	.	.	ENSG00000125952	ENST00000341653;ENST00000358402;ENST00000555932;ENST00000284165;ENST00000358664;ENST00000555419;ENST00000556979;ENST00000555667;ENST00000557746;ENST00000556443;ENST00000246163	D;D;D;D;D;D;D;D;D;D	0.99745	-4.35;-4.5;-4.86;-5.1;-3.95;-6.61;-4.29;-4.4;-4.38;-4.22	4.91	4.01	0.46588	.	0.000000	0.85682	D	0.000000	D	0.99591	0.9852	M	0.80982	2.52	0.80722	D	1	D;D;D;D;D;D;D;D	0.89917	0.998;1.0;1.0;1.0;1.0;0.996;1.0;1.0	D;D;D;D;D;D;D;D	0.87578	0.919;0.987;0.976;0.963;0.968;0.928;0.982;0.998	D	0.98346	1.0541	10	0.87932	D	0	-5.0444	10.8962	0.47023	0.0:0.909:0.0:0.091	.	6;6;6;6;6;6;6;6	G3V2N4;Q96CY8;Q14803;Q6V3B1;P61244-2;P61244;P61244-3;A6NH73	.;.;.;.;.;MAX_HUMAN;.;.	Y	6	ENSP00000342482:D6Y;ENSP00000351175:D6Y;ENSP00000284165:D6Y;ENSP00000351490:D6Y;ENSP00000452405:D6Y;ENSP00000452378:D6Y;ENSP00000452286:D6Y;ENSP00000452197:D6Y;ENSP00000450818:D6Y;ENSP00000246163:D6Y	ENSP00000246163:D6Y	D	-	1	0	MAX	64638795	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	5.538000	0.67193	1.186000	0.42985	0.585000	0.79938	GAC		0.672	MAX-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000286386.1		NM_197957	
KMT2C	58508	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	151877902	151877902	+	Missense_Mutation	SNP	T	T	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	T	T	T	C	T	T	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr7:151877902T>C	ENST00000262189.6	-	36	7261	c.7043A>G	c.(7042-7044)cAg>cGg	p.Q2348R	KMT2C_ENST00000355193.2_Missense_Mutation_p.Q2348R	NM_170606.2	NP_733751.2	Q8NEZ4	KMT2C_HUMAN	lysine (K)-specific methyltransferase 2C	2348					histone H3-K4 methylation (GO:0051568)|intracellular signal transduction (GO:0035556)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	histone methyltransferase complex (GO:0035097)|nucleus (GO:0005634)	DNA binding (GO:0003677)|histone methyltransferase activity (H3-K4 specific) (GO:0042800)|poly(A) RNA binding (GO:0044822)|zinc ion binding (GO:0008270)	p.Q2348R(2)									ACCAGAGAACTGCTGGCCTTG	0.488																																																	2	Substitution - Missense(2)	kidney(2)											98.0	86.0	90.0					7																	151877902		2203	4300	6503	SO:0001583	missense	58508			AF264750	CCDS5931.1	7q36	2013-05-09	2013-05-09	2013-05-09	ENSG00000055609	ENSG00000055609		"""Chromatin-modifying enzymes / K-methyltransferases"", ""Zinc fingers, PHD-type"""	13726	protein-coding gene	gene with protein product		606833	"""myeloid/lymphoid or mixed-lineage leukemia 3"""	MLL3		10819331	Standard	XM_005250026		Approved	KIAA1506, HALR		Q8NEZ4	OTTHUMG00000150553	ENST00000262189.6:c.7043A>G	7.37:g.151877902T>C	ENSP00000262189:p.Gln2348Arg	Somatic		WXS	Illumina HiSeq	Phase_I	Q8NC02|Q8NDF6|Q9H9P4|Q9NR13|Q9P222|Q9UDR7	Missense_Mutation	SNP	ENST00000262189.6	37	CCDS5931.1	.	.	.	.	.	.	.	.	.	.	T	8.430	0.848402	0.17034	.	.	ENSG00000055609	ENST00000262189;ENST00000355193	D;D	0.83506	-1.73;-1.73	5.25	1.34	0.21922	.	0.524101	0.15729	N	0.247528	T	0.75774	0.3895	L	0.51422	1.61	0.80722	D	1	B;P	0.38420	0.361;0.63	B;B	0.29077	0.081;0.098	T	0.74435	-0.3666	10	0.52906	T	0.07	.	14.8266	0.70117	0.0:0.0:0.5742:0.4258	.	2348;1409	Q8NEZ4;Q8NEZ4-2	MLL3_HUMAN;.	R	2348	ENSP00000262189:Q2348R;ENSP00000347325:Q2348R	ENSP00000262189:Q2348R	Q	-	2	0	MLL3	151508835	1.000000	0.71417	0.143000	0.22291	0.893000	0.52053	1.494000	0.35616	0.397000	0.25310	0.528000	0.53228	CAG		0.488	KMT2C-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000318887.3			
MOGAT2	80168	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	75438650	75438650	+	Silent	SNP	G	G	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr11:75438650G>T	ENST00000198801.5	+	3	511	c.441G>T	c.(439-441)cgG>cgT	p.R147R	MOGAT2_ENST00000526712.1_Silent_p.R65R	NM_025098.2	NP_079374.2	Q3SYC2	MOGT2_HUMAN	monoacylglycerol O-acyltransferase 2	147					diacylglycerol biosynthetic process (GO:0006651)|glycerol metabolic process (GO:0006071)|intestinal absorption (GO:0050892)|triglyceride biosynthetic process (GO:0019432)	endoplasmic reticulum (GO:0005783)|integral component of membrane (GO:0016021)	2-acylglycerol O-acyltransferase activity (GO:0003846)|acetyltransferase activity (GO:0016407)	p.R147R(1)		NS(1)|kidney(2)|large_intestine(2)|lung(11)|ovary(2)|skin(1)|urinary_tract(1)	20	Ovarian(111;0.103)					TGTGGTTCCGGGCCCCCTTCT	0.532																																																	1	Substitution - coding silent(1)	kidney(1)											117.0	111.0	113.0					11																	75438650		2200	4293	6493	SO:0001819	synonymous_variant	80168			AY157608	CCDS8240.1	11q13.5	2008-02-05			ENSG00000166391	ENSG00000166391			23248	protein-coding gene	gene with protein product		610270				14970677	Standard	NM_025098		Approved	MGAT2, DGAT2L5, FLJ22644	uc010rru.2	Q3SYC2	OTTHUMG00000165341	ENST00000198801.5:c.441G>T	11.37:g.75438650G>T		Somatic		WXS	Illumina HiSeq	Phase_I	A8K7I3|Q3SYC1|Q6ZQZ2|Q86UH6|Q9H630	Silent	SNP	ENST00000198801.5	37	CCDS8240.1																																																																																				0.532	MOGAT2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000383520.1		NM_025098	
MTMR7	9108	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	17157530	17157530	+	Silent	SNP	G	G	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr8:17157530G>A	ENST00000180173.5	-	14	1858	c.1824C>T	c.(1822-1824)gaC>gaT	p.D608D	MTMR7_ENST00000398099.3_Silent_p.D199D|VPS37A_ENST00000521162.1_3'UTR	NM_004686.4	NP_004677.3	Q9Y216	MTMR7_HUMAN	myotubularin related protein 7	608					inositol phosphate dephosphorylation (GO:0046855)|peptidyl-tyrosine dephosphorylation (GO:0035335)|phosphatidylinositol biosynthetic process (GO:0006661)|phosphatidylinositol dephosphorylation (GO:0046856)|phospholipid metabolic process (GO:0006644)|protein dephosphorylation (GO:0006470)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|membrane (GO:0016020)	protein tyrosine phosphatase activity (GO:0004725)	p.D608D(1)		breast(1)|endometrium(5)|kidney(2)|large_intestine(5)|liver(1)|lung(8)|prostate(3)|skin(5)|stomach(1)|upper_aerodigestive_tract(1)	32				Colorectal(111;0.112)		TTTTCAGATTGTCTTGGGTTA	0.498																																																	1	Substitution - coding silent(1)	kidney(1)											122.0	113.0	116.0					8																	17157530		2203	4300	6503	SO:0001819	synonymous_variant	9108			AF073482	CCDS34851.1	8p22	2011-06-09			ENSG00000003987	ENSG00000003987		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Myotubularins"""	7454	protein-coding gene	gene with protein product		603562				9736772, 12890864	Standard	NM_004686		Approved		uc003wxm.3	Q9Y216	OTTHUMG00000163771	ENST00000180173.5:c.1824C>T	8.37:g.17157530G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A1L4K9|B4DG87|Q68DX4	Silent	SNP	ENST00000180173.5	37	CCDS34851.1																																																																																				0.498	MTMR7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000375311.1		NM_004686	
MUC13	56667	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	124635228	124635228	+	Silent	SNP	C	C	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr3:124635228C>T	ENST00000311075.3	-	6	935	c.897G>A	c.(895-897)aaG>aaA	p.K299K		NM_033049.3	NP_149038	Q9H3R2	MUC13_HUMAN	mucin 13, cell surface associated	300	SEA. {ECO:0000255|PROSITE- ProRule:PRU00188}.				cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	apical plasma membrane (GO:0016324)|cytosol (GO:0005829)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of membrane (GO:0016021)	protein homodimerization activity (GO:0042803)	p.K299K(1)		breast(1)|central_nervous_system(1)|cervix(1)|kidney(1)|large_intestine(6)|lung(5)|prostate(1)|skin(1)|stomach(1)	18						CAGTCACAGTCTTCTCATTGT	0.333																																																	1	Substitution - coding silent(1)	kidney(1)											118.0	108.0	112.0					3																	124635228		2202	4299	6501	SO:0001819	synonymous_variant	56667			AF286113		3q21.2	2007-01-17	2006-03-14		ENSG00000173702	ENSG00000173702		"""Mucins"""	7511	protein-coding gene	gene with protein product		612181	"""down-regulated in colon cancer 1"", ""mucin 13, epithelial transmembrane"""	DRCC1		11278439	Standard	NM_033049		Approved		uc003ehq.2	Q9H3R2	OTTHUMG00000159484	ENST00000311075.3:c.897G>A	3.37:g.124635228C>T		Somatic		WXS	Illumina HiSeq	Phase_I	Q6UWD9|Q9NXT5	Silent	SNP	ENST00000311075.3	37																																																																																					0.333	MUC13-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000355714.1		NM_033049	
MUC4	4585	hgsc.bcm.edu	37	3	195514998	195515045	+	In_Frame_Del	DEL	GGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGA	GGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGA	-	rs200518052|rs538504516|rs199975352|rs200763050|rs552771790|rs570974278|rs368837663|rs201206859|rs199883835|rs78683709|rs201451131|rs76196931	byFrequency	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	GGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGA	GGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr3:195514998_195515045delGGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGA	ENST00000463781.3	-	2	3865_3912	c.3406_3453delTCTCTTCCTGTCACCGACACTTCCTCAGTATCCACAGGTCACACCACC	c.(3406-3453)tctcttcctgtcaccgacacttcctcagtatccacaggtcacaccaccdel	p.SLPVTDTSSVSTGHTT1136del	MUC4_ENST00000346145.4_Intron|MUC4_ENST00000349607.4_Intron|MUC4_ENST00000475231.1_In_Frame_Del_p.SLPVTDTSSVSTGHTT1136del	NM_018406.6	NP_060876.5	Q99102	MUC4_HUMAN	mucin 4, cell surface associated	603					cell-matrix adhesion (GO:0007160)|cellular protein metabolic process (GO:0044267)|maintenance of gastrointestinal epithelium (GO:0030277)|O-glycan processing (GO:0016266)|post-translational protein modification (GO:0043687)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|Golgi lumen (GO:0005796)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|proteinaceous extracellular matrix (GO:0005578)|vesicle (GO:0031982)	ErbB-2 class receptor binding (GO:0005176)|extracellular matrix constituent, lubricant activity (GO:0030197)	p.T1142S(3)|p.V1145A(2)|p.P1138L(1)|p.H1149H(1)|p.T1142T(1)|p.T1150A(1)		NS(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(3)|kidney(1)|large_intestine(5)|lung(23)|ovary(3)|prostate(8)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	51	all_cancers(143;1.11e-08)|Ovarian(172;0.0634)|Breast(254;0.206)	Lung NSC(153;0.191)	Epithelial(36;3.72e-24)|all cancers(36;6.22e-22)|OV - Ovarian serous cystadenocarcinoma(49;1.1e-18)|Lung(62;4.65e-05)|LUSC - Lung squamous cell carcinoma(58;5.31e-05)	GBM - Glioblastoma multiforme(46;2.37e-05)		CATGAAGAGGGGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGAGGTGGCGTGA	0.569																																																	9	Substitution - Missense(7)|Substitution - coding silent(2)	endometrium(4)|stomach(2)|skin(2)|kidney(1)							,,	1034,2304		279,476,914					,,	-1.1	0.0			8	2849,3303		990,869,1217	no	intron,coding,intron	MUC4	NM_138297.4,NM_018406.6,NM_004532.5	,,	1269,1345,2131	A1A1,A1R,RR		46.3101,30.9766,40.9168	,,	,,		3883,5607				SO:0001651	inframe_deletion	4585			AJ276359	CCDS3310.1, CCDS3311.1, CCDS54700.1	3q29	2007-01-19	2006-03-14		ENSG00000145113	ENSG00000145113		"""Mucins"""	7514	protein-coding gene	gene with protein product		158372	"""mucin 4, tracheobronchial"""			1673336	Standard	NM_004532		Approved		uc021xjp.1	Q99102	OTTHUMG00000151827	ENST00000463781.3:c.3406_3453delTCTCTTCCTGTCACCGACACTTCCTCAGTATCCACAGGTCACACCACC	3.37:g.195514998_195515045delGGTGGTGTGACCTGTGGATACTGAGGAAGTGTCGGTGACAGGAAGAGA	ENSP00000417498:p.Ser1136_Thr1151del	Somatic		WXS	Illumina HiSeq	Phase_I	O95938|Q9GZM2|Q9GZV6|Q9H481|Q9H482|Q9H483|Q9H484|Q9H485|Q9H486|Q9H487|Q9H4D6|Q9H4D8|Q9NPJ0|Q9NY09|Q9NY75|Q9NY76|Q9NY77|Q9NY78|Q9NY79|Q9NY80|Q9NY81	In_Frame_Del	DEL	ENST00000463781.3	37	CCDS54700.1																																																																																				0.569	MUC4-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000324081.6		NM_018406	
MYO5A	4644	broad.mit.edu;ucsc.edu	37	15	52720650	52720650	+	Silent	SNP	C	C	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr15:52720650C>G	ENST00000399231.3	-	3	498	c.255G>C	c.(253-255)gtG>gtC	p.V85V	MYO5A_ENST00000356338.6_Silent_p.V85V|MYO5A_ENST00000358212.6_Silent_p.V85V|MYO5A_ENST00000399233.2_Silent_p.V85V|MYO5A_ENST00000553916.1_Silent_p.V85V	NM_000259.3	NP_000250	Q9Y4I1	MYO5A_HUMAN	myosin VA (heavy chain 12, myoxin)	85	Myosin motor.				actin filament-based movement (GO:0030048)|anagen (GO:0042640)|cellular protein metabolic process (GO:0044267)|cellular response to insulin stimulus (GO:0032869)|endoplasmic reticulum localization (GO:0051643)|exocytosis (GO:0006887)|insulin secretion (GO:0030073)|locomotion involved in locomotory behavior (GO:0031987)|long-chain fatty acid biosynthetic process (GO:0042759)|melanin biosynthetic process (GO:0042438)|melanocyte differentiation (GO:0030318)|melanosome transport (GO:0032402)|membrane organization (GO:0061024)|myelination (GO:0042552)|odontogenesis (GO:0042476)|post-Golgi vesicle-mediated transport (GO:0006892)|protein localization to plasma membrane (GO:0072659)|protein transport (GO:0015031)|regulation of inositol 1,4,5-trisphosphate-sensitive calcium-release channel activity (GO:0031585)|secretory granule localization (GO:0032252)|synapse organization (GO:0050808)|synaptic transmission (GO:0007268)|transport (GO:0006810)|vesicle transport along actin filament (GO:0030050)|vesicle-mediated transport (GO:0016192)|visual perception (GO:0007601)	actomyosin (GO:0042641)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|filopodium tip (GO:0032433)|Golgi apparatus (GO:0005794)|growth cone (GO:0030426)|insulin-responsive compartment (GO:0032593)|intermediate filament (GO:0005882)|melanosome (GO:0042470)|membrane (GO:0016020)|microtubule plus-end (GO:0035371)|myosin complex (GO:0016459)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)|photoreceptor outer segment (GO:0001750)|ruffle (GO:0001726)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|microfilament motor activity (GO:0000146)|poly(A) RNA binding (GO:0044822)|Rab GTPase binding (GO:0017137)	p.V85V(1)		breast(4)|central_nervous_system(1)|cervix(2)|endometrium(5)|kidney(7)|large_intestine(12)|lung(19)|ovary(3)|skin(3)|stomach(1)	57				all cancers(107;0.0085)|Colorectal(133;0.077)|READ - Rectum adenocarcinoma(133;0.196)		GATTATGGAGCACAGCAGGCT	0.428																																																	1	Substitution - coding silent(1)	kidney(1)											159.0	147.0	151.0					15																	52720650		1952	4163	6115	SO:0001819	synonymous_variant	4644				CCDS42037.1, CCDS45262.1	15q21	2014-09-17	2006-09-29		ENSG00000197535	ENSG00000197535		"""Myosins / Myosin superfamily : Class V"""	7602	protein-coding gene	gene with protein product	"""myosin, heavy polypeptide kinase"", ""myosin heavy chain 12"", ""myoxin"", ""myosin V"""	160777	"""myosin VA (heavy polypeptide 12, myoxin)"""	MYH12		8188282, 8022818	Standard	NM_000259		Approved	MYO5, GS1, MYR12	uc002aby.2	Q9Y4I1	OTTHUMG00000137383	ENST00000399231.3:c.255G>C	15.37:g.52720650C>G		Somatic		WXS	Illumina GAIIx	Phase_I	A8MZC5|O60653|Q07902|Q16249|Q9UE30|Q9UE31	Silent	SNP	ENST00000399231.3	37	CCDS42037.1																																																																																				0.428	MYO5A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000268102.1		NM_000259	
NAA16	79612	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	41932483	41932483	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr13:41932483G>C	ENST00000379406.3	+	11	1455	c.1131G>C	c.(1129-1131)caG>caC	p.Q377H	NAA16_ENST00000379367.3_Missense_Mutation_p.Q377H|NAA16_ENST00000403412.3_Missense_Mutation_p.Q377H	NM_024561.4	NP_078837.3	Q6N069	NAA16_HUMAN	N(alpha)-acetyltransferase 16, NatA auxiliary subunit	377					N-terminal protein amino acid acetylation (GO:0006474)|negative regulation of apoptotic process (GO:0043066)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|NatA complex (GO:0031415)|nucleus (GO:0005634)|transcription factor complex (GO:0005667)	ribosome binding (GO:0043022)	p.Q377H(1)		breast(2)|central_nervous_system(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(10)|lung(8)|prostate(1)|urinary_tract(2)	31						TCTGGGTTCAGTATTTCCTGG	0.348																																																	1	Substitution - Missense(1)	kidney(1)											92.0	91.0	92.0					13																	41932483		2203	4300	6503	SO:0001583	missense	79612			AL833341	CCDS9379.1, CCDS45044.1	13q14.11	2013-01-10	2010-01-14	2010-01-14	ENSG00000172766	ENSG00000172766		"""N(alpha)-acetyltransferase subunits"", ""Tetratricopeptide (TTC) repeat domain containing"""	26164	protein-coding gene	gene with protein product			"""NMDA receptor regulated 1-like"""	NARG1L		11483580, 19660095	Standard	NM_024561		Approved	FLJ22054, MGC40612, PRO2435	uc001uyf.2	Q6N069	OTTHUMG00000016791	ENST00000379406.3:c.1131G>C	13.37:g.41932483G>C	ENSP00000368716:p.Gln377His	Somatic		WXS	Illumina HiSeq	Phase_I	B0QZ59|Q5VSP9|Q6P2D5|Q8N5J3|Q8N870	Missense_Mutation	SNP	ENST00000379406.3	37	CCDS9379.1	.	.	.	.	.	.	.	.	.	.	G	2.086	-0.409573	0.04799	.	.	ENSG00000172766	ENST00000379367;ENST00000379406;ENST00000403412	T;T;T	0.53857	0.6;0.6;0.97	5.02	-0.738	0.11125	Tetratricopeptide repeat-containing (1);	0.196932	0.33875	N	0.004463	T	0.48169	0.1485	L	0.33485	1.01	0.30860	N	0.733571	B;P	0.40032	0.162;0.699	B;P	0.55455	0.315;0.776	T	0.50882	-0.8775	10	0.17369	T	0.5	-0.1734	6.9989	0.24799	0.2481:0.3293:0.4226:0.0	.	377;377	Q6N069;Q6N069-4	NAA16_HUMAN;.	H	377	ENSP00000368674:Q377H;ENSP00000368716:Q377H;ENSP00000386103:Q377H	ENSP00000368674:Q377H	Q	+	3	2	NAA16	40830483	0.988000	0.35896	0.996000	0.52242	0.036000	0.12997	0.173000	0.16724	-0.098000	0.12285	0.484000	0.47621	CAG		0.348	NAA16-003	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000044672.2		NM_018527	
NEFH	4744	hgsc.bcm.edu	37	22	29885572	29885573	+	In_Frame_Ins	INS	-	-	CCCTGAGAAGGCCAAGTC			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr22:29885572_29885573insCCCTGAGAAGGCCAAGTC	ENST00000310624.6	+	4	1976_1977	c.1943_1944insCCCTGAGAAGGCCAAGTC	c.(1942-1947)tcccct>tcCCCTGAGAAGGCCAAGTCccct	p.648_649SP>SPEKAKSP		NM_021076.3	NP_066554.2	P12036	NFH_HUMAN	neurofilament, heavy polypeptide	654	30 X 6 AA repeats of K-S-P-[AEPV]-[EAK]- [AEVK].|Tail.			Missing (in Ref. 1; CAA33366 and 5; AC000035). {ECO:0000305}.	axon development (GO:0061564)|axonogenesis (GO:0007409)|cell death (GO:0008219)|cell projection assembly (GO:0030031)|microtubule cytoskeleton organization (GO:0000226)|neurofilament bundle assembly (GO:0033693)|peripheral nervous system neuron axonogenesis (GO:0048936)|regulation of organelle transport along microtubule (GO:1902513)	axon (GO:0030424)|cytoplasm (GO:0005737)|mitochondrion (GO:0005739)|neurofibrillary tangle (GO:0097418)|neurofilament (GO:0005883)	dynein binding (GO:0045502)|kinesin binding (GO:0019894)|microtubule binding (GO:0008017)|protein binding, bridging (GO:0030674)|protein kinase binding (GO:0019901)|structural constituent of cytoskeleton (GO:0005200)|structural molecule activity (GO:0005198)			cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(3)	30						GAAGCAAAGTCCCCTGAGAAGG	0.569																																																	0																																										SO:0001652	inframe_insertion	4744				CCDS13858.1	22q12.2	2013-01-16	2008-09-19		ENSG00000100285	ENSG00000100285		"""Intermediate filaments type IV"""	7737	protein-coding gene	gene with protein product		162230	"""neurofilament, heavy polypeptide 200kDa"""				Standard	NM_021076		Approved		uc003afo.3	P12036	OTTHUMG00000151155	ENST00000310624.6:c.1944_1961dupCCCTGAGAAGGCCAAGTC	22.37:g.29885572_29885573insCCCTGAGAAGGCCAAGTC	ENSP00000311997:p.Pro643_Ser648dup	Somatic		WXS	Illumina HiSeq	Phase_I	B4DYY4|Q96HF8|Q9UJS7|Q9UQ14	In_Frame_Ins	INS	ENST00000310624.6	37	CCDS13858.1																																																																																				0.569	NEFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000321553.2		NM_021076	
NFASC	23114	broad.mit.edu;hgsc.bcm.edu	37	1	204955082	204955082	+	Silent	SNP	G	G	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr1:204955082G>A	ENST00000404076.1	+	21	2990	c.2568G>A	c.(2566-2568)gtG>gtA	p.V856V	NFASC_ENST00000367169.4_Intron|NFASC_ENST00000367172.4_Silent_p.V877V|NFASC_ENST00000513543.1_Silent_p.V873V|NFASC_ENST00000367170.4_Silent_p.V877V|NFASC_ENST00000404907.1_Silent_p.V873V|NFASC_ENST00000539706.1_Silent_p.V873V|NFASC_ENST00000338586.6_Silent_p.V877V|NFASC_ENST00000401399.1_Intron|NFASC_ENST00000339876.6_Intron|NFASC_ENST00000360049.4_Silent_p.V873V|NFASC_ENST00000338515.6_Silent_p.V877V|NFASC_ENST00000367171.4_Silent_p.V862V			O94856	NFASC_HUMAN	neurofascin	877	Fibronectin type-III 3. {ECO:0000255|PROSITE-ProRule:PRU00316}.				axon guidance (GO:0007411)|clustering of voltage-gated sodium channels (GO:0045162)|heterotypic cell-cell adhesion (GO:0034113)|myelination (GO:0042552)|paranodal junction assembly (GO:0030913)|peripheral nervous system development (GO:0007422)|protein localization to juxtaparanode region of axon (GO:0071205)|protein localization to paranode region of axon (GO:0002175)|synapse organization (GO:0050808)|transmission of nerve impulse (GO:0019226)	axon initial segment (GO:0043194)|extracellular vesicular exosome (GO:0070062)|focal adhesion (GO:0005925)|integral component of membrane (GO:0016021)|intracellular (GO:0005622)|node of Ranvier (GO:0033268)|paranodal junction (GO:0033010)|paranode region of axon (GO:0033270)|plasma membrane (GO:0005886)		p.V873V(1)		NS(1)|breast(4)|central_nervous_system(1)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(22)|liver(1)|lung(24)|ovary(3)|pancreas(1)|prostate(3)|skin(5)|upper_aerodigestive_tract(1)	81	all_cancers(21;0.0375)|Breast(84;0.0437)|all_epithelial(62;0.171)|Prostate(682;0.19)		KIRC - Kidney renal clear cell carcinoma(13;0.0584)|Kidney(21;0.0934)|BRCA - Breast invasive adenocarcinoma(75;0.158)			ACCTGTGGGTGTCTCAGAAGA	0.602																																																	1	Substitution - coding silent(1)	kidney(1)											59.0	48.0	52.0					1																	204955082		2203	4300	6503	SO:0001819	synonymous_variant	23114			AK027553	CCDS30982.1, CCDS53460.1, CCDS53461.1, CCDS53462.1	1q32.1	2013-02-11	2010-06-24		ENSG00000163531	ENSG00000163531		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	29866	protein-coding gene	gene with protein product		609145	"""neurofascin homolog (chicken)"""			1377696, 8672144	Standard	NM_015090		Approved	NRCAML, KIAA0756, FLJ46866, NF	uc001hbj.3	O94856	OTTHUMG00000151697	ENST00000404076.1:c.2568G>A	1.37:g.204955082G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B2RNN8|B3KQZ1|B5MDP6|B5MDR6|B7ZMD8|Q149P5|Q5T2F0|Q5T2F1|Q5T2F2|Q5T2F3|Q5T2F4|Q5T2F5|Q5T2F6|Q5T2F7|Q5T2F9|Q5T2G0|Q5W9F8|Q68DH3|Q6ZQV6|Q7Z3K1|Q96HT1|Q96K50	Silent	SNP	ENST00000404076.1	37																																																																																					0.602	NFASC-012	NOVEL	not_organism_supported|basic	protein_coding	protein_coding	OTTHUMT00000131243.1		NM_001005388	
NOM1	64434	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	156759742	156759742	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr7:156759742G>A	ENST00000275820.3	+	9	2269	c.2254G>A	c.(2254-2256)Gcc>Acc	p.A752T		NM_138400.1	NP_612409.1	Q5C9Z4	NOM1_HUMAN	nucleolar protein with MIF4G domain 1	752	MI. {ECO:0000255|PROSITE- ProRule:PRU00698}.					nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.A752T(1)		endometrium(5)|kidney(4)|large_intestine(9)|lung(7)|ovary(1)|prostate(2)|skin(2)|urinary_tract(1)	31	Ovarian(565;0.218)	all_hematologic(28;0.0749)	OV - Ovarian serous cystadenocarcinoma(82;0.00301)	UCEC - Uterine corpus endometrioid carcinoma (81;0.169)		TCATCTGGTGGCCCACTTGTT	0.388																																																	1	Substitution - Missense(1)	kidney(1)											142.0	130.0	134.0					7																	156759742		2203	4300	6503	SO:0001583	missense	64434			AF107455	CCDS34787.1	7q36.3	2014-06-13	2005-03-30	2005-03-30	ENSG00000146909	ENSG00000146909			13244	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 113"""	611269	"""chromosome 7 open reading frame 3"""	C7orf3		10329000	Standard	XM_005249560		Approved	SGD1, PPP1R113	uc003wmy.3	Q5C9Z4	OTTHUMG00000152639	ENST00000275820.3:c.2254G>A	7.37:g.156759742G>A	ENSP00000275820:p.Ala752Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q96I08	Missense_Mutation	SNP	ENST00000275820.3	37	CCDS34787.1	.	.	.	.	.	.	.	.	.	.	G	7.675	0.687856	0.14973	.	.	ENSG00000146909	ENST00000275820	T	0.35421	1.31	4.97	4.09	0.47781	Initiation factor eIF-4 gamma, MA3 (3);	0.459092	0.25081	N	0.033297	T	0.26412	0.0645	L	0.38692	1.165	0.34351	D	0.689855	B	0.28400	0.21	B	0.26094	0.066	T	0.32322	-0.9911	10	0.28530	T	0.3	-20.584	9.6189	0.39710	0.1601:0.0:0.8399:0.0	.	752	Q5C9Z4	NOM1_HUMAN	T	752	ENSP00000275820:A752T	ENSP00000275820:A752T	A	+	1	0	NOM1	156452503	0.994000	0.37717	0.997000	0.53966	0.677000	0.39632	3.930000	0.56522	1.198000	0.43158	0.655000	0.94253	GCC		0.388	NOM1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000327098.1		NM_138400	
OBSCN	84033	broad.mit.edu;hgsc.bcm.edu	37	1	228403481	228403481	+	Silent	SNP	G	G	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr1:228403481G>C	ENST00000422127.1	+	6	2090	c.2046G>C	c.(2044-2046)ctG>ctC	p.L682L	OBSCN_ENST00000366709.4_5'UTR|OBSCN_ENST00000570156.2_Silent_p.L682L|C1orf145_ENST00000295012.5_5'Flank|OBSCN_ENST00000284548.11_Silent_p.L682L|OBSCN_ENST00000366707.4_5'UTR	NM_001098623.2	NP_001092093.2	Q5VST9	OBSCN_HUMAN	obscurin, cytoskeletal calmodulin and titin-interacting RhoGEF	682	Ig-like 6.				apoptotic signaling pathway (GO:0097190)|multicellular organismal development (GO:0007275)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|protein localization to M-band (GO:0036309)|regulation of small GTPase mediated signal transduction (GO:0051056)|sarcomere organization (GO:0045214)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|M band (GO:0031430)|myofibril (GO:0030016)|Z disc (GO:0030018)	ankyrin binding (GO:0030506)|ATP binding (GO:0005524)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)|structural constituent of muscle (GO:0008307)|titin binding (GO:0031432)	p.L682L(4)		NS(2)|breast(7)|central_nervous_system(5)|cervix(2)|endometrium(30)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(37)|lung(89)|ovary(8)|pancreas(3)|prostate(13)|skin(6)|stomach(11)|upper_aerodigestive_tract(2)|urinary_tract(3)	223		Prostate(94;0.0405)				GGGCGCAGCTGAAGTTCGTGG	0.652																																																	4	Substitution - coding silent(4)	kidney(4)											20.0	25.0	23.0					1																	228403481		2110	4233	6343	SO:0001819	synonymous_variant	84033			AJ002535	CCDS1570.2, CCDS58065.1, CCDS59204.1	1q42	2014-09-17			ENSG00000154358	ENSG00000154358		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	15719	protein-coding gene	gene with protein product		608616				11448995, 11814696	Standard	NM_001098623		Approved	KIAA1556, UNC89, KIAA1639, ARHGEF30	uc001hsq.2	Q5VST9	OTTHUMG00000039772	ENST00000422127.1:c.2046G>C	1.37:g.228403481G>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q2A664|Q5T7G8|Q5T7G9|Q5VSU2|Q86YC7|Q8NHN0|Q8NHN1|Q8NHN2|Q8NHN3|Q8NHN4|Q8NHN5|Q8NHN6|Q8NHN7|Q8NHN8|Q8NHN9|Q96AA2|Q9HCD3|Q9HCL6	Silent	SNP	ENST00000422127.1	37	CCDS58065.1																																																																																				0.652	OBSCN-204	KNOWN	basic|CCDS	protein_coding	protein_coding			NM_052843	
OR7C1	26664	hgsc.bcm.edu	37	19	14910638	14910638	+	Frame_Shift_Del	DEL	A	A	-	rs534928853	byFrequency	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr19:14910638delA	ENST00000248073.2	-	1	385	c.311delT	c.(310-312)ttcfs	p.F104fs	OR7A5_ENST00000601611.1_Intron	NM_198944.1	NP_945182.1	O76099	OR7C1_HUMAN	olfactory receptor, family 7, subfamily C, member 1	104					spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			breast(2)|central_nervous_system(1)|endometrium(2)|large_intestine(8)|lung(2)|ovary(2)|prostate(1)	18						AAATGAAGTGAAAAAAAAAAT	0.443													|||unknown(HR)	63	0.0125799	0.0076	0.0043	5008	,	,		21296	0.0109		0.002	False		,,,				2504	0.0378																0										3,45,4216		0,0,3,0,45,2084	59.0	60.0	60.0			2.6	0.1	19		61	16,32,8204		0,0,16,2,28,4080	no	codingComplex	OR7C1	NM_198944.1		0,0,19,2,73,6164	A1A1,A1A2,A1R,A2A2,A2R,RR		0.5817,1.1257,0.767			14910638	19,77,12420	2203	4300	6503	SO:0001589	frameshift_variant	26664			X89676	CCDS12317.1	19p13.1	2012-08-09						"""GPCR / Class A : Olfactory receptors"""	8373	protein-coding gene	gene with protein product				OR7C4			Standard	NM_198944		Approved	OR19-5	uc010xnz.2	O76099		ENST00000248073.2:c.311delT	19.37:g.14910638delA	ENSP00000248073:p.Phe104fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q15621|Q6IFP2|Q96R94	Frame_Shift_Del	DEL	ENST00000248073.2	37	CCDS12317.1																																																																																				0.443	OR7C1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466519.1			
PAPSS1	9061	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	4	108574727	108574727	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr4:108574727C>T	ENST00000265174.4	-	9	1429	c.1157G>A	c.(1156-1158)cGa>cAa	p.R386Q	PAPSS1_ENST00000511304.1_5'UTR	NM_005443.4	NP_005434.4	O43252	PAPS1_HUMAN	3'-phosphoadenosine 5'-phosphosulfate synthase 1	386					3'-phosphoadenosine 5'-phosphosulfate biosynthetic process (GO:0050428)|3'-phosphoadenosine 5'-phosphosulfate metabolic process (GO:0050427)|carbohydrate metabolic process (GO:0005975)|glycosaminoglycan metabolic process (GO:0030203)|skeletal system development (GO:0001501)|small molecule metabolic process (GO:0044281)|sulfate assimilation (GO:0000103)|xenobiotic metabolic process (GO:0006805)	cytosol (GO:0005829)	adenylylsulfate kinase activity (GO:0004020)|ATP binding (GO:0005524)|nucleotidyltransferase activity (GO:0016779)|sulfate adenylyltransferase (ATP) activity (GO:0004781)	p.R386Q(2)		NS(1)|endometrium(2)|kidney(5)|large_intestine(2)|lung(5)|ovary(1)	16		Hepatocellular(203;0.217)		OV - Ovarian serous cystadenocarcinoma(123;5.49e-05)		CCAATAAACTCGATCCAAGAC	0.348																																																	2	Substitution - Missense(2)	large_intestine(1)|kidney(1)											141.0	124.0	130.0					4																	108574727		2203	4300	6503	SO:0001583	missense	9061			Y10387	CCDS3676.1	4q24	2012-07-13			ENSG00000138801	ENSG00000138801	2.7.7.4, 2.7.1.25		8603	protein-coding gene	gene with protein product		603262				9576487, 9771708	Standard	NM_005443		Approved	ATPSK1, PAPSS	uc003hyk.3	O43252	OTTHUMG00000131210	ENST00000265174.4:c.1157G>A	4.37:g.108574727C>T	ENSP00000265174:p.Arg386Gln	Somatic		WXS	Illumina HiSeq	Phase_I	O43841|O75332|Q96FB1|Q96TF4|Q9P1P9|Q9UE98	Missense_Mutation	SNP	ENST00000265174.4	37	CCDS3676.1	.	.	.	.	.	.	.	.	.	.	C	33	5.212722	0.95069	.	.	ENSG00000138801	ENST00000265174	T	0.23348	1.91	5.47	5.47	0.80525	Sulphate adenylyltransferase (2);PUA-like domain (1);	0.114505	0.56097	D	0.000027	T	0.31263	0.0791	M	0.78801	2.425	0.80722	D	1	P	0.37441	0.595	B	0.23419	0.046	T	0.34354	-0.9832	10	0.66056	D	0.02	-11.9101	19.3341	0.94307	0.0:1.0:0.0:0.0	.	386	O43252	PAPS1_HUMAN	Q	386	ENSP00000265174:R386Q	ENSP00000265174:R386Q	R	-	2	0	PAPSS1	108794176	1.000000	0.71417	1.000000	0.80357	0.968000	0.65278	4.442000	0.59988	2.558000	0.86282	0.557000	0.71058	CGA		0.348	PAPSS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253946.2			
PCDH15	65217	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	55779999	55779999	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr10:55779999A>T	ENST00000320301.6	-	20	3098	c.2704T>A	c.(2704-2706)Tat>Aat	p.Y902N	PCDH15_ENST00000395438.1_Missense_Mutation_p.Y902N|PCDH15_ENST00000414778.1_Missense_Mutation_p.Y907N|PCDH15_ENST00000373965.2_Missense_Mutation_p.Y909N|PCDH15_ENST00000361849.3_Missense_Mutation_p.Y902N|PCDH15_ENST00000373955.1_Missense_Mutation_p.Y902N|PCDH15_ENST00000395433.1_Missense_Mutation_p.Y880N|PCDH15_ENST00000373957.3_Intron|PCDH15_ENST00000395445.1_Missense_Mutation_p.Y909N|PCDH15_ENST00000409834.1_Missense_Mutation_p.Y513N|PCDH15_ENST00000395430.1_Missense_Mutation_p.Y902N|PCDH15_ENST00000395432.2_Missense_Mutation_p.Y865N|PCDH15_ENST00000395446.1_Intron|PCDH15_ENST00000395442.1_Intron|PCDH15_ENST00000437009.1_Missense_Mutation_p.Y831N|PCDH15_ENST00000395440.1_Intron	NM_033056.3	NP_149045.3	Q96QU1	PCD15_HUMAN	protocadherin-related 15	902	Cadherin 8. {ECO:0000255|PROSITE- ProRule:PRU00043}.				equilibrioception (GO:0050957)|homophilic cell adhesion (GO:0007156)|photoreceptor cell maintenance (GO:0045494)|sensory perception of light stimulus (GO:0050953)|sensory perception of sound (GO:0007605)	extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|photoreceptor outer segment (GO:0001750)|plasma membrane (GO:0005886)|stereocilium (GO:0032420)|synapse (GO:0045202)	calcium ion binding (GO:0005509)	p.Y907N(2)|p.Y902N(2)		NS(3)|breast(6)|central_nervous_system(1)|cervix(3)|endometrium(18)|haematopoietic_and_lymphoid_tissue(4)|kidney(13)|large_intestine(39)|lung(108)|ovary(5)|pancreas(6)|prostate(6)|skin(12)|upper_aerodigestive_tract(12)|urinary_tract(1)	237		Melanoma(3;0.117)|Lung SC(717;0.238)				ATTGTTCCATAAATATCAAAG	0.418										HNSCC(58;0.16)																																							4	Substitution - Missense(4)	kidney(4)											151.0	138.0	142.0					10																	55779999		2203	4300	6503	SO:0001583	missense	65217			AY029205	CCDS7248.1, CCDS44400.1, CCDS44401.1, CCDS44403.1, CCDS44404.1, CCDS73134.1, CCDS73135.1, CCDS73136.1, CCDS73137.1, CCDS73138.1	10q21.1	2013-01-08	2010-01-25		ENSG00000150275	ENSG00000150275		"""Cadherins / Cadherin-related"""	14674	protein-coding gene	gene with protein product	"""cadherin-related family member 15"""	605514	"""deafness, autosomal recessive 23"", ""protocadherin 15"""	USH1F, DFNB23		11398101, 14570705	Standard	NM_033056		Approved	CDHR15	uc010qhy.1	Q96QU1	OTTHUMG00000018259	ENST00000320301.6:c.2704T>A	10.37:g.55779999A>T	ENSP00000322604:p.Tyr902Asn	Somatic		WXS	Illumina HiSeq	Phase_I	A6NL19|C6ZEF5|C6ZEF6|C6ZEF7|Q5VY38|Q5VY39|Q6TRH8|Q8NDB9|Q96QT8	Missense_Mutation	SNP	ENST00000320301.6	37	CCDS7248.1	.	.	.	.	.	.	.	.	.	.	A	14.78	2.637672	0.47049	.	.	ENSG00000150275	ENST00000373965;ENST00000414778;ENST00000455746;ENST00000395438;ENST00000409834;ENST00000395445;ENST00000395432;ENST00000361849;ENST00000395433;ENST00000320301;ENST00000395430;ENST00000417177;ENST00000437009;ENST00000373955	T;T;T;T;T;T;T;T;T;T;T;T	0.36340	1.26;1.26;1.26;1.26;1.26;1.26;1.26;1.26;1.26;1.26;1.26;1.26	6.06	4.96	0.65561	Cadherin (4);Cadherin-like (1);	.	.	.	.	T	0.22475	0.0542	N	0.03194	-0.395	0.32456	N	0.544729	P;B;B;B;P;P;P;B;B;B;B;B;B;B	0.46987	0.853;0.409;0.409;0.1;0.888;0.584;0.741;0.041;0.124;0.124;0.124;0.409;0.062;0.409	P;B;B;B;P;B;P;B;B;B;B;B;B;B	0.52710	0.568;0.348;0.348;0.115;0.707;0.348;0.568;0.14;0.247;0.247;0.247;0.348;0.085;0.348	T	0.06625	-1.0816	9	0.10902	T	0.67	.	6.9538	0.24560	0.5418:0.343:0.0:0.1152	.	880;902;902;907;831;865;902;902;909;909;902;907;902;902	A2A3E8;E7EMG4;A2A3E7;C9JIG1;E7EM53;E7EMG0;A2A3E6;A2A3E3;C6ZEF5;A2A3E2;C6ZEF7;C9J4F3;Q96QU1-3;Q96QU1	.;.;.;.;.;.;.;.;.;.;.;.;.;PCD15_HUMAN	N	909;907;902;902;513;909;865;902;880;902;902;907;831;902	ENSP00000363076:Y909N;ENSP00000410304:Y907N;ENSP00000378826:Y902N;ENSP00000386693:Y513N;ENSP00000378832:Y909N;ENSP00000378820:Y865N;ENSP00000354950:Y902N;ENSP00000378821:Y880N;ENSP00000322604:Y902N;ENSP00000378818:Y902N;ENSP00000412628:Y831N;ENSP00000363066:Y902N	ENSP00000322604:Y902N	Y	-	1	0	PCDH15	55450005	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	3.926000	0.56491	2.323000	0.78572	0.528000	0.53228	TAT		0.418	PCDH15-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000048121.2		NM_033056	
PCDHB14	56122	broad.mit.edu;hgsc.bcm.edu	37	5	140605198	140605198	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr5:140605198delG	ENST00000239449.4	+	1	2121	c.2121delG	c.(2119-2121)ctgfs	p.L707fs	PCDHB14_ENST00000515856.2_Frame_Shift_Del_p.L554fs	NM_018934.2	NP_061757.1	Q9Y5E9	PCDBE_HUMAN	protocadherin beta 14	707					calcium-dependent cell-cell adhesion (GO:0016339)|homophilic cell adhesion (GO:0007156)|synapse assembly (GO:0007416)|synaptic transmission (GO:0007268)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)			NS(1)|breast(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(10)|lung(21)|ovary(2)|prostate(3)|skin(6)|urinary_tract(1)	49			KIRC - Kidney renal clear cell carcinoma(527;0.00185)|Kidney(363;0.00339)			CGGTGCTCCTGTTCGTGGCGG	0.701																																					Ovarian(141;50 1831 27899 33809 37648)												0													75.0	89.0	84.0					5																	140605198		2195	4282	6477	SO:0001589	frameshift_variant	56122			AF152493	CCDS4256.1	5q31	2010-01-26			ENSG00000120327	ENSG00000120327		"""Cadherins / Protocadherins : Clustered"""	8685	other	protocadherin		606340				10380929	Standard	NM_018934		Approved	PCDH-BETA14	uc003ljb.3	Q9Y5E9	OTTHUMG00000129619	ENST00000239449.4:c.2121delG	5.37:g.140605198delG	ENSP00000239449:p.Leu707fs	Somatic		WXS	Illumina HiSeq	Phase_I	B4DPE2|Q4FZA4|Q4KN11	Frame_Shift_Del	DEL	ENST00000239449.4	37	CCDS4256.1																																																																																				0.701	PCDHB14-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251814.2		NM_018934	
PDK2	5164	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	48183306	48183306	+	Missense_Mutation	SNP	G	G	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr17:48183306G>T	ENST00000503176.1	+	4	551	c.390G>T	c.(388-390)atG>atT	p.M130I	PDK2_ENST00000007708.3_Missense_Mutation_p.M66I	NM_002611.4	NP_002602.2	Q15119	PDK2_HUMAN	pyruvate dehydrogenase kinase, isozyme 2	130					cellular metabolic process (GO:0044237)|cellular response to nutrient (GO:0031670)|cellular response to reactive oxygen species (GO:0034614)|glucose homeostasis (GO:0042593)|glucose metabolic process (GO:0006006)|insulin receptor signaling pathway (GO:0008286)|intrinsic apoptotic signaling pathway by p53 class mediator (GO:0072332)|protein phosphorylation (GO:0006468)|pyruvate metabolic process (GO:0006090)|regulation of acetyl-CoA biosynthetic process from pyruvate (GO:0010510)|regulation of cellular ketone metabolic process (GO:0010565)|regulation of gluconeogenesis (GO:0006111)|regulation of glucose metabolic process (GO:0010906)|regulation of pH (GO:0006885)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrial pyruvate dehydrogenase complex (GO:0005967)	ATP binding (GO:0005524)|protein homodimerization activity (GO:0042803)|protein kinase activity (GO:0004672)|protein serine/threonine kinase activity (GO:0004674)|pyruvate dehydrogenase (acetyl-transferring) kinase activity (GO:0004740)	p.M130I(1)		central_nervous_system(4)|endometrium(2)|kidney(1)|large_intestine(2)|lung(7)|prostate(2)|skin(1)|urinary_tract(1)	20						TGCCCACCATGGCACAAGGCG	0.602									Autosomal Dominant Polycystic Kidney Disease																																								1	Substitution - Missense(1)	kidney(1)											122.0	73.0	90.0					17																	48183306		2203	4300	6503	SO:0001583	missense	5164	Familial Cancer Database	ADPKD	L42451	CCDS11559.1, CCDS56039.1	17q21.33	2012-07-18	2005-11-16		ENSG00000005882	ENSG00000005882			8810	protein-coding gene	gene with protein product		602525	"""pyruvate dehydrogenase kinase, isoenzyme 2"""			7499431	Standard	NM_001199898		Approved	PDHK2	uc002iqc.3	Q15119	OTTHUMG00000161948	ENST00000503176.1:c.390G>T	17.37:g.48183306G>T	ENSP00000420927:p.Met130Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A8K3A7|B3KNW0|Q6P515|Q9BS05	Missense_Mutation	SNP	ENST00000503176.1	37	CCDS11559.1	.	.	.	.	.	.	.	.	.	.	G	20.5	4.002121	0.74932	.	.	ENSG00000005882	ENST00000007708;ENST00000508030;ENST00000503176;ENST00000503614;ENST00000505440;ENST00000512238;ENST00000510219	T;T;T;T;T;T;T	0.30714	1.52;1.52;1.53;1.52;1.52;1.53;1.53	4.26	4.26	0.50523	Branched-chain alpha-ketoacid dehydrogenase kinase/Pyruvate dehydrogenase kinase, N-terminal (3);	0.101514	0.64402	D	0.000004	T	0.52885	0.1762	M	0.76328	2.33	0.80722	D	1	B	0.30068	0.267	P	0.50109	0.631	T	0.59590	-0.7426	10	0.66056	D	0.02	-19.3221	15.4621	0.75366	0.0:0.0:1.0:0.0	.	130	Q15119	PDK2_HUMAN	I	66;66;130;66;66;66;35	ENSP00000007708:M66I;ENSP00000427682:M66I;ENSP00000420927:M130I;ENSP00000425265:M66I;ENSP00000425615:M66I;ENSP00000421178:M66I;ENSP00000423310:M35I	ENSP00000007708:M66I	M	+	3	0	PDK2	45538305	1.000000	0.71417	1.000000	0.80357	0.970000	0.65996	7.792000	0.85828	1.926000	0.55796	0.393000	0.25936	ATG		0.602	PDK2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000366492.2		NM_002611	
PIGQ	9091	hgsc.bcm.edu	37	16	632283	632283	+	Intron	SNP	G	G	A	rs7187227	byFrequency	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr16:632283G>A	ENST00000026218.5	+	10	1619				PIGQ_ENST00000409527.2_Missense_Mutation_p.G523S|PIGQ_ENST00000321878.5_Missense_Mutation_p.G523S	NM_148920.2	NP_683721.1	Q9BRB3	PIGQ_HUMAN	phosphatidylinositol glycan anchor biosynthesis, class Q						C-terminal protein lipidation (GO:0006501)|carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|post-translational protein modification (GO:0043687)|preassembly of GPI anchor in ER membrane (GO:0016254)	endoplasmic reticulum membrane (GO:0005789)|glycosylphosphatidylinositol-N-acetylglucosaminyltransferase (GPI-GnT) complex (GO:0000506)|integral component of membrane (GO:0016021)	phosphatidylinositol N-acetylglucosaminyltransferase activity (GO:0017176)			central_nervous_system(1)|endometrium(3)|kidney(2)|large_intestine(1)|lung(4)|prostate(1)|upper_aerodigestive_tract(1)	13		Hepatocellular(780;0.00335)				GCACGAGGCCGGCAGGCCCCT	0.692													G|||	696	0.138978	0.1377	0.0793	5008	,	,		17264	0.0248		0.1799	False		,,,				2504	0.2587																0								G	SER/GLY,	675,3717		50,575,1571	25.0	26.0	26.0		1567,	5.1	1.0	16	dbSNP_116	26	1560,7032		144,1272,2880	yes	missense,intron	PIGQ	NM_004204.3,NM_148920.1	56,	194,1847,4451	AA,AG,GG		18.1564,15.3689,17.2135	,	523/582,	632283	2235,10749	2196	4296	6492	SO:0001627	intron_variant	9091			AB003723	CCDS10411.1, CCDS10412.1	16p13.3	2013-03-28	2006-06-28		ENSG00000007541	ENSG00000007541		"""Phosphatidylinositol glycan anchor biosynthesis"""	14135	protein-coding gene	gene with protein product		605754	"""phosphatidylinositol glycan, class Q"""			9463366, 9729469	Standard	NM_004204		Approved	hGPI1, GPI1	uc002cho.3	Q9BRB3	OTTHUMG00000168047	ENST00000026218.5:c.1532-600G>A	16.37:g.632283G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A2IDE1|D3DU52|O14927|Q96G00|Q96S22|Q9UJH4	Missense_Mutation	SNP	ENST00000026218.5	37	CCDS10411.1	268	0.1227106227106227	73	0.1483739837398374	32	0.08839779005524862	18	0.03146853146853147	145	0.19129287598944592	G	22.4	4.284826	0.80803	0.153689	0.181564	ENSG00000007541	ENST00000409527;ENST00000321878;ENST00000540241	T;T	0.44482	0.92;0.92	5.08	5.08	0.68730	.	.	.	.	.	T	0.00178	0.0005	M	0.73598	2.24	0.09310	P	1.0	D	0.89917	1.0	D	0.76575	0.988	T	0.08743	-1.0707	8	0.10636	T	0.68	.	17.4349	0.87548	0.0:0.0:1.0:0.0	rs7187227	523	Q9BRB3-2	.	S	523;523;81	ENSP00000386760:G523S;ENSP00000326674:G523S	ENSP00000326674:G523S	G	+	1	0	PIGQ	572284	1.000000	0.71417	0.995000	0.50966	0.430000	0.31655	5.884000	0.69729	2.361000	0.80049	0.561000	0.74099	GGC		0.692	PIGQ-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000239270.2		NM_004204	
PPP2R1A	5518	hgsc.bcm.edu;ucsc.edu	37	19	52723429	52723429	+	Intron	SNP	G	G	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr19:52723429G>A	ENST00000322088.6	+	11	1360				CTD-2525I3.3_ENST00000593857.1_RNA|PPP2R1A_ENST00000444322.2_Intron|PPP2R1A_ENST00000462990.1_Intron	NM_014225.5	NP_055040.2	P30153	2AAA_HUMAN	protein phosphatase 2, regulatory subunit A, alpha						apoptotic process (GO:0006915)|ceramide metabolic process (GO:0006672)|chromosome segregation (GO:0007059)|fibroblast growth factor receptor signaling pathway (GO:0008543)|G2/M transition of mitotic cell cycle (GO:0000086)|gene expression (GO:0010467)|inactivation of MAPK activity (GO:0000188)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope reassembly (GO:0007084)|mRNA metabolic process (GO:0016071)|negative regulation of cell growth (GO:0030308)|negative regulation of tyrosine phosphorylation of Stat3 protein (GO:0042518)|nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (GO:0000184)|peptidyl-serine dephosphorylation (GO:0070262)|positive regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001241)|protein complex assembly (GO:0006461)|protein dephosphorylation (GO:0006470)|regulation of cell adhesion (GO:0030155)|regulation of cell differentiation (GO:0045595)|regulation of DNA replication (GO:0006275)|regulation of growth (GO:0040008)|regulation of transcription, DNA-templated (GO:0006355)|regulation of Wnt signaling pathway (GO:0030111)|response to organic substance (GO:0010033)|RNA metabolic process (GO:0016070)|RNA splicing (GO:0008380)|second-messenger-mediated signaling (GO:0019932)	chromosome, centromeric region (GO:0000775)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|microtubule cytoskeleton (GO:0015630)|mitochondrion (GO:0005739)|nucleus (GO:0005634)|protein phosphatase type 2A complex (GO:0000159)	antigen binding (GO:0003823)|protein heterodimerization activity (GO:0046982)|protein phosphatase type 2A regulator activity (GO:0008601)|protein serine/threonine phosphatase activity (GO:0004722)			NS(1)|breast(4)|cervix(2)|endometrium(62)|kidney(1)|large_intestine(7)|lung(21)|ovary(32)|pancreas(1)|prostate(2)|skin(1)|urinary_tract(1)	135				GBM - Glioblastoma multiforme(134;0.00456)|OV - Ovarian serous cystadenocarcinoma(262;0.015)		GGAACCCTTGGTTTCTCCTGT	0.522			Mis		clear cell ovarian carcinoma																																			Dom?	yes		19	19q13.41	5518	"""protein phosphatase 2, regulatory subunit A, alpha"""		E	0													142.0	124.0	130.0					19																	52723429		2203	4300	6503	SO:0001627	intron_variant	5518				CCDS12849.1	19q13	2010-06-18	2010-04-14		ENSG00000105568	ENSG00000105568	3.1.3.16	"""Serine/threonine phosphatases / Protein phosphatase 2, regulatory subunits"""	9302	protein-coding gene	gene with protein product	"""protein phosphatase 2A, regulatory subunit A, alpha isoform"", ""protein phosphatase 2, 65kDa regulatory subunit A"""	605983	"""protein phosphatase 2 (formerly 2A), regulatory subunit A (PR 65), alpha isoform"", ""protein phosphatase 2 (formerly 2A), regulatory subunit A, alpha isoform"""				Standard	NR_033500		Approved	PR65A, PP2A-Aalpha	uc002pyp.3	P30153	OTTHUMG00000137367	ENST00000322088.6:c.1303-13G>A	19.37:g.52723429G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q13773|Q6ICQ3|Q96DH3	RNA	SNP	ENST00000322088.6	37	CCDS12849.1																																																																																				0.522	PPP2R1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000267967.2		NM_014225	
RASA3	22821	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	13	114782719	114782719	+	Silent	SNP	G	G	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr13:114782719G>T	ENST00000334062.7	-	12	1321	c.1200C>A	c.(1198-1200)atC>atA	p.I400I	RASA3_ENST00000389544.4_Silent_p.I368I	NM_007368.2	NP_031394.2	Q14644	RASA3_HUMAN	RAS p21 protein activator 3	400	Ras-GAP. {ECO:0000255|PROSITE- ProRule:PRU00167}.				calcium ion transmembrane transport (GO:0070588)|intracellular signal transduction (GO:0035556)|negative regulation of Ras protein signal transduction (GO:0046580)|positive regulation of Ras GTPase activity (GO:0032320)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|intrinsic component of the cytoplasmic side of the plasma membrane (GO:0031235)	calcium-release channel activity (GO:0015278)|GTPase activator activity (GO:0005096)|metal ion binding (GO:0046872)|Ras GTPase activator activity (GO:0005099)	p.I400I(1)		breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|kidney(2)|large_intestine(8)|lung(20)|ovary(3)|prostate(2)|skin(3)|upper_aerodigestive_tract(2)	47	Lung NSC(43;0.00814)|all_neural(89;0.0337)|Medulloblastoma(90;0.163)|Lung SC(71;0.218)	all_cancers(25;0.016)|all_epithelial(44;0.00577)|all_lung(25;0.0173)|Lung NSC(25;0.0634)|Breast(118;0.188)	BRCA - Breast invasive adenocarcinoma(86;0.128)			TCACCTCCTCGATGGCGGGCT	0.617											OREG0022538	type=REGULATORY REGION|TFbs=CTCF|Dataset=CTCF ChIP-chip sites (Ren lab)|EvidenceSubtype=ChIP-on-chip (ChIP-chip)																																					1	Substitution - coding silent(1)	kidney(1)											139.0	111.0	121.0					13																	114782719		2203	4300	6503	SO:0001819	synonymous_variant	22821				CCDS32016.1	13q34	2013-01-10			ENSG00000185989	ENSG00000185989		"""Pleckstrin homology (PH) domain containing"""	20331	protein-coding gene	gene with protein product		605182				7637787, 9382842	Standard	NM_007368		Approved	GAP1IP4BP, GAPIII	uc001vui.3	Q14644	OTTHUMG00000017399	ENST00000334062.7:c.1200C>A	13.37:g.114782719G>T		Somatic	1460	WXS	Illumina HiSeq	Phase_I	A6NL15|F8W6X8|Q8IUY2	Silent	SNP	ENST00000334062.7	37	CCDS32016.1																																																																																				0.617	RASA3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000045957.2		NM_007368	
RBAK	57786	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	5105059	5105059	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr7:5105059A>G	ENST00000353796.3	+	6	2296	c.1972A>G	c.(1972-1974)Aaa>Gaa	p.K658E	RBAK-RBAKDN_ENST00000407184.1_Intron|RBAK-RBAKDN_ENST00000396904.2_Intron|RBAK_ENST00000396912.1_Missense_Mutation_p.K658E	NM_001204456.1	NP_001191385.1	Q9NYW8	RBAK_HUMAN	RB-associated KRAB zinc finger	658	Interaction with AR.				negative regulation of transcription, DNA-templated (GO:0045892)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	nucleic acid binding (GO:0003676)|zinc ion binding (GO:0008270)	p.K658E(1)		NS(1)|kidney(1)|large_intestine(2)|ovary(4)|skin(1)|upper_aerodigestive_tract(1)	10		Ovarian(82;0.0175)		UCEC - Uterine corpus endometrioid carcinoma (126;0.0916)|OV - Ovarian serous cystadenocarcinoma(56;2.44e-14)		TGAATGTGGGAAAGTCTTTTC	0.408																																																	1	Substitution - Missense(1)	kidney(1)											114.0	122.0	119.0					7																	5105059		2203	4300	6503	SO:0001583	missense	57786			AF226869	CCDS5337.1	7p22.1	2013-01-08			ENSG00000146587	ENSG00000146587		"""Zinc fingers, C2H2-type"", ""-"""	17680	protein-coding gene	gene with protein product		608191					Standard	NM_021163		Approved	ZNF769	uc003sns.1	Q9NYW8	OTTHUMG00000121155	ENST00000353796.3:c.1972A>G	7.37:g.5105059A>G	ENSP00000275423:p.Lys658Glu	Somatic		WXS	Illumina HiSeq	Phase_I	A6NDF2|A8KAK4|B2RN44|B9EGS1|F8W6M7	Missense_Mutation	SNP	ENST00000353796.3	37	CCDS5337.1	.	.	.	.	.	.	.	.	.	.	A	19.54	3.847343	0.71603	.	.	ENSG00000146587	ENST00000353796;ENST00000396912	T;T	0.27104	1.69;1.69	3.81	3.81	0.43845	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.51477	D	0.000088	T	0.48447	0.1500	M	0.83012	2.62	0.32662	N	0.517907	D	0.61080	0.989	D	0.63381	0.914	T	0.64740	-0.6336	8	.	.	.	.	11.1491	0.48447	1.0:0.0:0.0:0.0	rs34448026	658	Q9NYW8	RBAK_HUMAN	E	658	ENSP00000275423:K658E;ENSP00000380120:K658E	.	K	+	1	0	RBAK	5071585	0.995000	0.38212	0.993000	0.49108	0.979000	0.70002	6.613000	0.74192	1.952000	0.56665	0.528000	0.53228	AAA		0.408	RBAK-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000241640.2		NM_021163	
RPTN	126638	broad.mit.edu;ucsc.edu	37	1	152127611	152127611	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr1:152127611C>T	ENST00000316073.3	-	3	2028	c.1964G>A	c.(1963-1965)aGc>aAc	p.S655N		NM_001122965.1	NP_001116437.1	Q6XPR3	RPTN_HUMAN	repetin	655	Gln-rich.					cornified envelope (GO:0001533)|proteinaceous extracellular matrix (GO:0005578)	calcium ion binding (GO:0005509)	p.S655N(1)		breast(2)|central_nervous_system(1)|endometrium(14)|kidney(2)|large_intestine(1)|lung(32)|prostate(1)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)	59						GTGATGTTGGCTATCCTCTTC	0.517																																																	1	Substitution - Missense(1)	kidney(1)											256.0	207.0	222.0					1																	152127611		1568	3582	5150	SO:0001583	missense	126638			AK096436	CCDS41397.1	1q21.3	2013-01-10			ENSG00000215853	ENSG00000215853		"""EF-hand domain containing"""	26809	protein-coding gene	gene with protein product		613259				15854042	Standard	NM_001122965		Approved	FLJ39117	uc001ezs.1	Q6XPR3	OTTHUMG00000154095	ENST00000316073.3:c.1964G>A	1.37:g.152127611C>T	ENSP00000317895:p.Ser655Asn	Somatic		WXS	Illumina GAIIx	Phase_I	B7ZBZ3	Missense_Mutation	SNP	ENST00000316073.3	37	CCDS41397.1	.	.	.	.	.	.	.	.	.	.	C	6.887	0.533041	0.13188	.	.	ENSG00000215853	ENST00000316073;ENST00000541545	T	0.17691	2.26	5.07	-4.6	0.03390	.	1.463310	0.04884	N	0.448257	T	0.02649	0.0080	L	0.43923	1.385	0.09310	N	1	P	0.38922	0.651	B	0.30401	0.115	T	0.30119	-0.9989	10	0.07644	T	0.81	-1.0E-4	6.7378	0.23419	0.0:0.2051:0.226:0.5689	.	655	Q6XPR3	RPTN_HUMAN	N	655;310	ENSP00000317895:S655N	ENSP00000317895:S655N	S	-	2	0	RPTN	150394235	0.000000	0.05858	0.003000	0.11579	0.074000	0.17049	-0.961000	0.03845	-0.549000	0.06191	0.643000	0.83706	AGC		0.517	RPTN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333867.1		XM_371312	
RNASEL	6041	broad.mit.edu;ucsc.edu	37	1	182551376	182551376	+	Silent	SNP	G	G	A	rs200818153		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr1:182551376G>A	ENST00000367559.3	-	4	1837	c.1584C>T	c.(1582-1584)gtC>gtT	p.V528V	RNASEL_ENST00000444138.1_Silent_p.V528V|RNASEL_ENST00000539397.1_Silent_p.V528V	NM_021133.3	NP_066956.1	Q05823	RN5A_HUMAN	ribonuclease L (2',5'-oligoisoadenylate synthetase-dependent)	528	Protein kinase. {ECO:0000255|PROSITE- ProRule:PRU00159}.				cytokine-mediated signaling pathway (GO:0019221)|defense response to virus (GO:0051607)|mRNA processing (GO:0006397)|negative regulation of viral genome replication (GO:0045071)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|protein phosphorylation (GO:0006468)|RNA phosphodiester bond hydrolysis, endonucleolytic (GO:0090502)|rRNA processing (GO:0006364)|type I interferon signaling pathway (GO:0060337)	cytosol (GO:0005829)|mitochondrion (GO:0005739)|nuclear matrix (GO:0016363)	ATP binding (GO:0005524)|endoribonuclease activity (GO:0004521)|metal ion binding (GO:0046872)|protein kinase activity (GO:0004672)|RNA binding (GO:0003723)|rRNA binding (GO:0019843)	p.V528V(1)		NS(1)|breast(1)|endometrium(3)|kidney(3)|large_intestine(3)|lung(9)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(1)	27						CCACATAGAGGACCAGCCGTC	0.443																																																	1	Substitution - coding silent(1)	kidney(1)											119.0	114.0	116.0					1																	182551376		2203	4300	6503	SO:0001819	synonymous_variant	6041			L10381	CCDS1347.1	1q25	2013-01-10			ENSG00000135828	ENSG00000135828	3.1.26.-	"""Ankyrin repeat domain containing"""	10050	protein-coding gene	gene with protein product		180435	"""prostate cancer 1"""	RNS4, PRCA1		7514564	Standard	NM_021133		Approved		uc009wxz.2	Q05823	OTTHUMG00000035213	ENST00000367559.3:c.1584C>T	1.37:g.182551376G>A		Somatic		WXS	Illumina GAIIx	Phase_I	Q5W0L2|Q6AI46	Silent	SNP	ENST00000367559.3	37	CCDS1347.1	.	.	.	.	.	.	.	.	.	.	G	8.179	0.793506	0.16327	.	.	ENSG00000135828	ENST00000543858	.	.	.	5.1	1.06	0.20224	.	.	.	.	.	T	0.50548	0.1622	.	.	.	0.80722	D	1	.	.	.	.	.	.	T	0.26503	-1.0101	5	0.22109	T	0.4	-24.6326	7.9837	0.30198	0.3489:0.0:0.6511:0.0	.	.	.	.	S	144	.	ENSP00000443960:P144S	P	-	1	0	RNASEL	180817999	1.000000	0.71417	0.565000	0.28409	0.903000	0.53119	0.489000	0.22387	0.006000	0.14734	-0.143000	0.13931	CCT		0.443	RNASEL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000085189.1		NM_021133	
RYR3	6263	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	33842489	33842489	+	Missense_Mutation	SNP	C	C	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr15:33842489C>G	ENST00000389232.4	+	10	1014	c.944C>G	c.(943-945)tCc>tGc	p.S315C	RYR3_ENST00000415757.3_Missense_Mutation_p.S315C	NM_001036.3	NP_001027.3	Q15413	RYR3_HUMAN	ryanodine receptor 3	315	MIR 4. {ECO:0000255|PROSITE- ProRule:PRU00131}.				calcium ion transmembrane transport (GO:0070588)|calcium ion transport (GO:0006816)|cellular response to ATP (GO:0071318)|cellular response to caffeine (GO:0071313)|cellular response to calcium ion (GO:0071277)|cellular response to magnesium ion (GO:0071286)|ion transmembrane transport (GO:0034220)|negative regulation of cytosolic calcium ion concentration (GO:0051481)|protein homotetramerization (GO:0051289)|striated muscle contraction (GO:0006941)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|junctional membrane complex (GO:0030314)|perinuclear region of cytoplasm (GO:0048471)|sarcoplasmic reticulum membrane (GO:0033017)	calcium ion binding (GO:0005509)|calcium-induced calcium release activity (GO:0048763)|calcium-release channel activity (GO:0015278)|ryanodine-sensitive calcium-release channel activity (GO:0005219)	p.S315C(1)		NS(3)|breast(9)|central_nervous_system(8)|cervix(2)|endometrium(29)|haematopoietic_and_lymphoid_tissue(2)|kidney(18)|large_intestine(55)|lung(148)|ovary(7)|pancreas(1)|prostate(13)|skin(4)|stomach(1)|upper_aerodigestive_tract(8)|urinary_tract(3)	311		all_lung(180;7.18e-09)		all cancers(64;8.95e-12)|GBM - Glioblastoma multiforme(186;0.00109)|BRCA - Breast invasive adenocarcinoma(123;0.0363)		GACACCAAGTCCACAGCTTTC	0.498																																																	1	Substitution - Missense(1)	kidney(1)											41.0	43.0	42.0					15																	33842489		2133	4258	6391	SO:0001583	missense	6263				CCDS45210.1, CCDS58351.1	15q14-q15	2013-01-10				ENSG00000198838		"""Ion channels / Ryanodine receptors"", ""EF-hand domain containing"""	10485	protein-coding gene	gene with protein product		180903				8276408	Standard	NM_001036		Approved		uc001zhi.3	Q15413		ENST00000389232.4:c.944C>G	15.37:g.33842489C>G	ENSP00000373884:p.Ser315Cys	Somatic		WXS	Illumina HiSeq	Phase_I	O15175|Q15412	Missense_Mutation	SNP	ENST00000389232.4	37	CCDS45210.1	.	.	.	.	.	.	.	.	.	.	C	20.3	3.966131	0.74131	.	.	ENSG00000198838	ENST00000389232;ENST00000415757;ENST00000361728	D;D	0.86956	-2.19;-2.19	5.29	4.36	0.52297	MIR motif (2);MIR (2);	0.141336	0.48286	D	0.000185	D	0.88983	0.6586	L	0.42245	1.32	0.41158	D	0.986077	D;P	0.53151	0.958;0.927	P;P	0.56474	0.799;0.69	D	0.90299	0.4328	10	0.66056	D	0.02	.	15.7724	0.78180	0.0:0.8632:0.1368:0.0	.	315;315	Q15413-2;Q15413	.;RYR3_HUMAN	C	315	ENSP00000373884:S315C;ENSP00000399610:S315C	ENSP00000354735:S315C	S	+	2	0	RYR3	31629781	1.000000	0.71417	1.000000	0.80357	0.995000	0.86356	7.234000	0.78134	1.451000	0.47736	0.591000	0.81541	TCC		0.498	RYR3-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000417514.1			
SDK1	221935	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	4218194	4218194	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr7:4218194G>A	ENST00000404826.2	+	35	5213	c.5074G>A	c.(5074-5076)Gtg>Atg	p.V1692M	SDK1_ENST00000389531.3_Missense_Mutation_p.V1672M	NM_152744.3	NP_689957.3	Q7Z5N4	SDK1_HUMAN	sidekick cell adhesion molecule 1	1692	Fibronectin type-III 10. {ECO:0000255|PROSITE-ProRule:PRU00316}.				cell adhesion (GO:0007155)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)		p.V1692M(1)		NS(1)|breast(6)|central_nervous_system(3)|cervix(1)|endometrium(13)|haematopoietic_and_lymphoid_tissue(1)|kidney(8)|large_intestine(42)|lung(55)|ovary(4)|pancreas(1)|prostate(4)|skin(6)|upper_aerodigestive_tract(4)|urinary_tract(4)	153		all_cancers(1;0.127)|Ovarian(82;0.0177)|Myeloproliferative disorder(862;0.194)		UCEC - Uterine corpus endometrioid carcinoma (126;0.121)|OV - Ovarian serous cystadenocarcinoma(56;9.65e-15)		CAGCGCGCCCGTGGAGGTCTT	0.592																																																	1	Substitution - Missense(1)	kidney(1)											74.0	83.0	80.0					7																	4218194		2203	4300	6503	SO:0001583	missense	221935			AK074077	CCDS34590.1	7p22.3	2013-02-11	2011-12-09		ENSG00000146555	ENSG00000146555		"""Immunoglobulin superfamily / I-set domain containing"", ""Immunoglobulin superfamily / Immunoglobulin-like domain containing"", ""Fibronectin type III domain containing"""	19307	protein-coding gene	gene with protein product		607216	"""sidekick homolog 1 (chicken)"", ""sidekick homolog 1, cell adhesion molecule (chicken)"""			12230981, 17307840, 15213259	Standard	NM_001079653		Approved	FLJ31425	uc003smx.3	Q7Z5N4	OTTHUMG00000151733	ENST00000404826.2:c.5074G>A	7.37:g.4218194G>A	ENSP00000385899:p.Val1692Met	Somatic		WXS	Illumina HiSeq	Phase_I	Q8TEN9|Q8TEP5|Q96N44	Missense_Mutation	SNP	ENST00000404826.2	37	CCDS34590.1	.	.	.	.	.	.	.	.	.	.	G	17.73	3.461279	0.63513	.	.	ENSG00000146555	ENST00000404826;ENST00000389531	T;T	0.57752	0.38;0.38	5.09	5.09	0.68999	Fibronectin, type III (3);Immunoglobulin-like fold (1);	0.000000	0.64402	D	0.000008	T	0.71476	0.3344	M	0.80183	2.485	0.38647	D	0.951745	D;D;D	0.76494	0.978;0.992;0.999	P;P;D	0.63113	0.738;0.557;0.911	T	0.74028	-0.3796	10	0.36615	T	0.2	.	17.0409	0.86489	0.0:0.0:1.0:0.0	.	1672;179;1692	F8W6X9;F2Z3E9;Q7Z5N4	.;.;SDK1_HUMAN	M	1692;1672	ENSP00000385899:V1692M;ENSP00000374182:V1672M	ENSP00000374182:V1672M	V	+	1	0	SDK1	4184720	1.000000	0.71417	0.901000	0.35422	0.370000	0.29829	5.763000	0.68818	2.525000	0.85131	0.655000	0.94253	GTG		0.592	SDK1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000323702.1		NM_152744	
SCAF4	57466	hgsc.bcm.edu	37	21	33058544	33058544	+	Intron	SNP	A	A	C	rs200491574|rs80021168		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	A	C	A	A	Unknown	Valid	Somatic	Phase_I	WXS	PGM			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr21:33058544A>C	ENST00000286835.7	-	17	2426				SCAF4_ENST00000434667.3_Intron|SCAF4_ENST00000399804.1_Intron	NM_020706.2	NP_065757.1	O95104	SFR15_HUMAN	SR-related CTD-associated factor 4							nucleus (GO:0005634)	nucleotide binding (GO:0000166)|poly(A) RNA binding (GO:0044822)			NS(1)|breast(2)|endometrium(9)|kidney(9)|large_intestine(11)|lung(15)|prostate(1)|skin(2)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	54						aaaaaaaaaaaGGAAAGAAAG	0.388																																																	0													86.0	82.0	83.0					21																	33058544		692	1591	2283	SO:0001627	intron_variant	0			AB032998	CCDS33537.1, CCDS46644.1, CCDS54482.1	21q22.1	2013-02-12	2011-01-10	2011-01-10	ENSG00000156304	ENSG00000156304		"""RNA binding motif (RRM) containing"""	19304	protein-coding gene	gene with protein product			"""splicing factor, arginine/serine-rich 15"""	SFRS15		10574461	Standard	NM_020706		Approved	KIAA1172, DKFZp434E098, SRA4	uc002ypd.2	O95104	OTTHUMG00000084903	ENST00000286835.7:c.2044-498T>G	21.37:g.33058544A>C		Somatic		WXS	Illumina HiSeq	Phase_I	C9JLZ0|Q0P5W8|Q6P1M5|Q8N3I8|Q9UFM1|Q9ULP8	Intron	SNP	ENST00000286835.7	37	CCDS33537.1																																																																																				0.388	SCAF4-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000192659.1		XM_047889	
SLC23A2	9962	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	4839999	4839999	+	Silent	SNP	G	G	A	rs368342772		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr20:4839999G>A	ENST00000379333.1	-	16	2048	c.1656C>T	c.(1654-1656)gtC>gtT	p.V552V	SLC23A2_ENST00000424750.2_Silent_p.V438V|SLC23A2_ENST00000338244.1_Silent_p.V552V	NM_203327.1	NP_976072.1	Q9UGH3	S23A2_HUMAN	solute carrier family 23 (ascorbic acid transporter), member 2	552					L-ascorbic acid metabolic process (GO:0019852)|L-ascorbic acid transport (GO:0015882)|molecular hydrogen transport (GO:0015993)|nucleobase transport (GO:0015851)|nucleobase-containing compound metabolic process (GO:0006139)|response to oxidative stress (GO:0006979)|small molecule metabolic process (GO:0044281)|transepithelial L-ascorbic acid transport (GO:0070904)|vitamin metabolic process (GO:0006766)|vitamin transmembrane transport (GO:0035461)|water-soluble vitamin metabolic process (GO:0006767)	apical plasma membrane (GO:0016324)|basal plasma membrane (GO:0009925)|basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|membrane (GO:0016020)|plasma membrane (GO:0005886)	L-ascorbate:sodium symporter activity (GO:0008520)|L-ascorbic acid transporter activity (GO:0015229)|nucleobase transmembrane transporter activity (GO:0015205)|sodium-dependent L-ascorbate transmembrane transporter activity (GO:0070890)|sodium-dependent multivitamin transmembrane transporter activity (GO:0008523)	p.V552V(1)		endometrium(1)|kidney(3)|large_intestine(9)|lung(7)|ovary(3)|prostate(1)|upper_aerodigestive_tract(2)|urinary_tract(1)	27						TTGTGAGAAGGACGTTCAACA	0.453																																																	1	Substitution - coding silent(1)	kidney(1)						G	,	0,4406		0,0,2203	173.0	152.0	159.0		1656,1656	1.9	1.0	20		159	1,8599	1.2+/-3.3	0,1,4299	no	coding-synonymous,coding-synonymous	SLC23A2	NM_005116.5,NM_203327.1	,	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	,	552/651,552/651	4839999	1,13005	2203	4300	6503	SO:0001819	synonymous_variant	9962			AF058319	CCDS13085.1	20p13	2013-07-18	2013-07-18	2003-03-21	ENSG00000089057	ENSG00000089057		"""Solute carriers"""	10973	protein-coding gene	gene with protein product		603791	"""solute carrier family 23 (nucleobase transporters), member 1"""	SLC23A1		9804989, 10331392	Standard	NM_005116		Approved	SVCT2, KIAA0238, YSPL2	uc002wlh.1	Q9UGH3	OTTHUMG00000031793	ENST00000379333.1:c.1656C>T	20.37:g.4839999G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B4DJZ1|Q8WWR4|Q92512|Q96D54|Q9UNU1|Q9UP85	Silent	SNP	ENST00000379333.1	37	CCDS13085.1																																																																																				0.453	SLC23A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077832.1			
SLC35A4	113829	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	139946853	139946853	+	Silent	SNP	T	T	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr5:139946853T>C	ENST00000514199.1	+	2	1785	c.99T>C	c.(97-99)caT>caC	p.H33H	APBB3_ENST00000507279.1_Intron|APBB3_ENST00000357560.4_5'Flank|APBB3_ENST00000358580.5_5'Flank|SLC35A4_ENST00000508770.1_3'UTR|APBB3_ENST00000508496.2_5'Flank|SLC35A4_ENST00000323146.3_Silent_p.H33H			Q96G79	S35A4_HUMAN	solute carrier family 35, member A4	33	Leu-rich.					Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	sugar:proton symporter activity (GO:0005351)	p.H33H(1)		endometrium(4)|kidney(2)|large_intestine(3)|lung(4)	13			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			ACGGTGCCCATGCCCCATTGC	0.632																																																	1	Substitution - coding silent(1)	kidney(1)											82.0	76.0	78.0					5																	139946853		2203	4300	6503	SO:0001819	synonymous_variant	113829			AJ420598	CCDS4231.1	5q31.3	2013-05-22			ENSG00000176087	ENSG00000176087		"""Solute carriers"""	20753	protein-coding gene	gene with protein product							Standard	NM_080670		Approved		uc003lgg.1	Q96G79	OTTHUMG00000129495	ENST00000514199.1:c.99T>C	5.37:g.139946853T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A8K013	Silent	SNP	ENST00000514199.1	37	CCDS4231.1																																																																																				0.632	SLC35A4-004	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000372815.1		NM_080670	
SLC47A2	146802	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	19610039	19610039	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr17:19610039A>G	ENST00000325411.5	-	9	921	c.871T>C	c.(871-873)Ttc>Ctc	p.F291L	SLC47A2_ENST00000350657.5_Missense_Mutation_p.F255L|SLC47A2_ENST00000463318.1_5'UTR	NM_152908.3	NP_690872.2	Q86VL8	S47A2_HUMAN	solute carrier family 47 (multidrug and toxin extrusion), member 2	291					transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	antiporter activity (GO:0015297)|drug transmembrane transporter activity (GO:0015238)	p.F291L(1)|p.F255L(1)		endometrium(2)|kidney(3)|large_intestine(2)|lung(1)|ovary(1)	9	all_cancers(12;2.3e-05)|all_epithelial(12;0.0024)|Breast(13;0.245)				Aciclovir(DB00787)	AGGGAGAAGAAGGGGCCCCAG	0.617																																																	2	Substitution - Missense(2)	kidney(2)											85.0	79.0	81.0					17																	19610039		2203	4300	6503	SO:0001583	missense	146802			AB250364	CCDS11211.1, CCDS58530.1	17p11.2	2013-07-17	2013-07-17		ENSG00000180638	ENSG00000180638		"""Solute carriers"""	26439	protein-coding gene	gene with protein product	"""multidrug and toxin extrusion 2"""	609833				16996621, 16807400	Standard	NM_152908		Approved	FLJ31196, MATE2, MATE2-K	uc002gwf.4	Q86VL8	OTTHUMG00000059464	ENST00000325411.5:c.871T>C	17.37:g.19610039A>G	ENSP00000326671:p.Phe291Leu	Somatic		WXS	Illumina HiSeq	Phase_I	A0JBX9|A0P8Z7|Q63HJ9|Q8IV44|Q96NA1	Missense_Mutation	SNP	ENST00000325411.5	37	CCDS11211.1	.	.	.	.	.	.	.	.	.	.	A	26.2	4.710541	0.89112	.	.	ENSG00000180638	ENST00000350657;ENST00000325411;ENST00000456947;ENST00000433844	T;T;T	0.40756	1.48;1.54;1.02	5.36	5.36	0.76844	.	0.052658	0.85682	D	0.000000	T	0.48114	0.1482	N	0.16656	0.425	0.46241	D	0.99894	D;D;P	0.76494	0.999;0.999;0.866	D;D;P	0.76071	0.987;0.987;0.688	T	0.54262	-0.8320	10	0.72032	D	0.01	-26.4937	13.5869	0.61937	1.0:0.0:0.0:0.0	.	255;255;291	Q86VL8-3;Q86VL8-4;Q86VL8	.;.;S47A2_HUMAN	L	255;291;206;255	ENSP00000338084:F255L;ENSP00000326671:F291L;ENSP00000391848:F255L	ENSP00000326671:F291L	F	-	1	0	SLC47A2	19550631	1.000000	0.71417	0.693000	0.30195	0.669000	0.39330	8.302000	0.89953	2.165000	0.68154	0.379000	0.24179	TTC		0.617	SLC47A2-002	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000132242.2		NM_152908	
SYT12	91683	hgsc.bcm.edu	37	11	66816101	66816101	+	Missense_Mutation	SNP	G	G	A	rs141165304		TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr11:66816101G>A	ENST00000393946.2	+	11	2301	c.1139G>A	c.(1138-1140)cGt>cAt	p.R380H	SYT12_ENST00000525457.1_Missense_Mutation_p.R380H|SYT12_ENST00000527043.1_Missense_Mutation_p.R380H			Q8IV01	SYT12_HUMAN	synaptotagmin XII	380	C2 2. {ECO:0000255|PROSITE- ProRule:PRU00041}.					cell junction (GO:0030054)|cytoplasmic vesicle (GO:0031410)|integral component of membrane (GO:0016021)|synapse (GO:0045202)				NS(1)|breast(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(9)|ovary(1)|urinary_tract(1)	20						AGCGACGGCCGTGGGGACAAC	0.627													G|||	1	0.000199681	0.0008	0.0	5008	,	,		18972	0.0		0.0	False		,,,				2504	0.0				Ovarian(65;2862 3307)												0								G	HIS/ARG,HIS/ARG	0,4400		0,0,2200	104.0	80.0	88.0		1139,1139	3.7	1.0	11	dbSNP_134	88	6,8584	5.0+/-18.6	0,6,4289	yes	missense,missense	SYT12	NM_001177880.1,NM_177963.3	29,29	0,6,6489	AA,AG,GG		0.0698,0.0,0.0462	probably-damaging,probably-damaging	380/422,380/422	66816101	6,12984	2200	4295	6495	SO:0001583	missense	91683			AK024280	CCDS8154.1	11q13.2	2014-07-02			ENSG00000173227	ENSG00000173227		"""Synaptotagmins"""	18381	protein-coding gene	gene with protein product		606436				8987811	Standard	NM_177963		Approved	SRG1	uc001oju.3	Q8IV01	OTTHUMG00000167101	ENST00000393946.2:c.1139G>A	11.37:g.66816101G>A	ENSP00000377520:p.Arg380His	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000393946.2	37	CCDS8154.1	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	G	10.90	1.480761	0.26598	0.0	6.98E-4	ENSG00000173227	ENST00000393946;ENST00000525457;ENST00000527043	T;T;T	0.09163	3.01;3.01;3.01	4.59	3.68	0.42216	C2 membrane targeting protein (1);C2 calcium-dependent membrane targeting (2);C2 calcium/lipid-binding domain, CaLB (1);	0.000000	0.85682	D	0.000000	T	0.10035	0.0246	L	0.54965	1.715	0.58432	D	0.999999	B	0.15930	0.015	B	0.17098	0.017	T	0.07290	-1.0780	10	0.07325	T	0.83	.	10.7693	0.46312	0.095:0.0:0.905:0.0	.	380	Q8IV01	SYT12_HUMAN	H	380	ENSP00000377520:R380H;ENSP00000431400:R380H;ENSP00000435316:R380H	ENSP00000377520:R380H	R	+	2	0	SYT12	66572677	1.000000	0.71417	1.000000	0.80357	0.908000	0.53690	5.596000	0.67570	1.061000	0.40601	0.462000	0.41574	CGT		0.627	SYT12-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000393129.1		NM_177963	
TCP11	6954	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	35086231	35086231	+	Nonsense_Mutation	SNP	G	G	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr6:35086231G>A	ENST00000512012.1	-	9	1483	c.1327C>T	c.(1327-1329)Cag>Tag	p.Q443*	TCP11_ENST00000244645.3_Nonsense_Mutation_p.Q381*|TCP11_ENST00000311875.5_Nonsense_Mutation_p.Q456*|TCP11_ENST00000444780.2_Nonsense_Mutation_p.Q451*|TCP11_ENST00000373974.4_Nonsense_Mutation_p.Q410*|TCP11_ENST00000373979.2_Nonsense_Mutation_p.Q381*|TCP11_ENST00000412155.2_Nonsense_Mutation_p.Q405*|TCP11_ENST00000418521.2_Nonsense_Mutation_p.Q380*			Q8WWU5	TCP11_HUMAN	t-complex 11, testis-specific	443					cell differentiation (GO:0030154)|multicellular organismal development (GO:0007275)|spermatogenesis (GO:0007283)	integral component of membrane (GO:0016021)		p.Q381*(1)|p.Q456*(1)		breast(1)|kidney(5)|large_intestine(3)|lung(10)|ovary(3)|prostate(1)|skin(4)	27						AGAGACCGCTGCACACCAAGA	0.458																																																	2	Substitution - Nonsense(2)	kidney(2)											76.0	73.0	74.0					6																	35086231		2203	4300	6503	SO:0001587	stop_gained	6954				CCDS4799.1, CCDS47413.1, CCDS59015.1, CCDS59016.1, CCDS59017.1, CCDS59018.1	6p21.31	2012-09-20	2012-09-20		ENSG00000124678	ENSG00000124678			11658	protein-coding gene	gene with protein product	"""fertilization-promoting peptide receptor"""	186982	"""t-complex 11 (a murine tcp homolog)"", ""t-complex 11 homolog (mouse)"""	D6S230E		1427894, 11756566, 21597245	Standard	NM_001093728		Approved	KIAA0229, FPPR	uc003okd.2	Q8WWU5	OTTHUMG00000014560	ENST00000512012.1:c.1327C>T	6.37:g.35086231G>A	ENSP00000425995:p.Gln443*	Somatic		WXS	Illumina HiSeq	Phase_I	B2RCE9|B3KQ27|B7Z7B5|B7Z7G1|B7Z7H4|B7Z7S8|E7EP29|J3KNG1|Q8NF85|Q9NQZ9|Q9NR39	Nonsense_Mutation	SNP	ENST00000512012.1	37		.	.	.	.	.	.	.	.	.	.	G	40	8.278068	0.98740	.	.	ENSG00000124678	ENST00000373979;ENST00000412155;ENST00000244645;ENST00000311875;ENST00000444780;ENST00000373974;ENST00000418521;ENST00000512012	.	.	.	5.42	5.42	0.78866	.	0.284856	0.30940	N	0.008571	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	0.07644	T	0.81	.	14.5631	0.68153	0.0:0.0:0.8532:0.1468	.	.	.	.	X	381;405;381;456;451;410;380;443	.	ENSP00000244645:Q381X	Q	-	1	0	TCP11	35194209	0.902000	0.30710	1.000000	0.80357	0.985000	0.73830	3.057000	0.49931	2.537000	0.85549	0.563000	0.77884	CAG		0.458	TCP11-014	PUTATIVE	basic	protein_coding	protein_coding	OTTHUMT00000370354.1		NM_001093728	
TDP1	55775	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	14	90437547	90437547	+	Missense_Mutation	SNP	G	G	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr14:90437547G>A	ENST00000335725.4	+	6	938	c.688G>A	c.(688-690)Gat>Aat	p.D230N	TDP1_ENST00000393452.3_Missense_Mutation_p.D230N|TDP1_ENST00000393454.2_Missense_Mutation_p.D230N|TDP1_ENST00000555565.1_3'UTR|TDP1_ENST00000555880.1_Missense_Mutation_p.D230N|TDP1_ENST00000357382.3_Silent_p.V2V	NM_018319.3	NP_060789.2	Q9NUW8	TYDP1_HUMAN	tyrosyl-DNA phosphodiesterase 1	230					cell death (GO:0008219)|DNA repair (GO:0006281)|double-strand break repair (GO:0006302)|single strand break repair (GO:0000012)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	3'-tyrosyl-DNA phosphodiesterase activity (GO:0017005)|double-stranded DNA binding (GO:0003690)|exonuclease activity (GO:0004527)|single-stranded DNA binding (GO:0003697)	p.D230N(1)		NS(1)|endometrium(3)|kidney(2)|large_intestine(4)|lung(10)|ovary(3)|prostate(1)|urinary_tract(1)	25		all_cancers(154;0.185)		COAD - Colon adenocarcinoma(157;0.23)		TGTGCATGGTGATAAGCGAGA	0.507								Repair of DNA-protein crosslinks																																									1	Substitution - Missense(1)	kidney(1)											109.0	86.0	94.0					14																	90437547		2203	4300	6503	SO:0001583	missense	55775			AF182002	CCDS9888.1	14q32.11	2008-08-11				ENSG00000042088			18884	protein-coding gene	gene with protein product		607198				11839309, 12244316	Standard	XM_005267847		Approved	FLJ11090, SCAN1	uc001xxz.3	Q9NUW8		ENST00000335725.4:c.688G>A	14.37:g.90437547G>A	ENSP00000337353:p.Asp230Asn	Somatic		WXS	Illumina HiSeq	Phase_I	Q2HXX4|Q86TV8|Q96BK7|Q9NZM7|Q9NZM8	Missense_Mutation	SNP	ENST00000335725.4	37	CCDS9888.1	.	.	.	.	.	.	.	.	.	.	G	20.4	3.987871	0.74589	.	.	ENSG00000042088	ENST00000393452;ENST00000554180;ENST00000393454;ENST00000553617;ENST00000335725;ENST00000555880	T;T;T;T;T;T	0.30448	1.53;1.53;1.53;1.53;1.53;1.53	5.7	5.7	0.88788	.	0.094598	0.64402	D	0.000001	T	0.39545	0.1082	L	0.54323	1.7	0.80722	D	1	B;B;P	0.45126	0.344;0.396;0.851	B;B;P	0.47251	0.152;0.236;0.542	T	0.03364	-1.1044	10	0.19590	T	0.45	-8.4541	19.8344	0.96650	0.0:0.0:1.0:0.0	.	230;230;230	G3V2F4;E7EPD8;Q9NUW8	.;.;TYDP1_HUMAN	N	230;230;230;131;230;230	ENSP00000377098:D230N;ENSP00000450872:D230N;ENSP00000377099:D230N;ENSP00000450708:D131N;ENSP00000337353:D230N;ENSP00000450628:D230N	ENSP00000337353:D230N	D	+	1	0	TDP1	89507300	1.000000	0.71417	0.611000	0.29010	0.925000	0.55904	8.937000	0.92936	2.696000	0.92011	0.561000	0.74099	GAT		0.507	TDP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000411239.1		NM_018319	
TMEM132B	114795	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	12	125834194	125834194	+	Silent	SNP	T	T	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr12:125834194T>C	ENST00000299308.3	+	2	257	c.249T>C	c.(247-249)atT>atC	p.I83I	TMEM132B_ENST00000418253.2_3'UTR	NM_052907.2	NP_443139.2	Q14DG7	T132B_HUMAN	transmembrane protein 132B	83						integral component of membrane (GO:0016021)		p.I83I(1)		NS(1)|breast(9)|central_nervous_system(1)|cervix(1)|endometrium(7)|kidney(2)|large_intestine(11)|liver(1)|lung(45)|ovary(5)|pancreas(1)|prostate(4)|skin(15)|upper_aerodigestive_tract(3)|urinary_tract(1)	107	all_neural(191;0.101)|Medulloblastoma(191;0.163)			OV - Ovarian serous cystadenocarcinoma(86;0.000423)|Epithelial(86;0.00394)|all cancers(50;0.0362)		CACCCCCTATTATCAATGCCA	0.498																																																	1	Substitution - coding silent(1)	kidney(1)											106.0	105.0	105.0					12																	125834194		1868	4104	5972	SO:0001819	synonymous_variant	114795			AB067493	CCDS41859.1, CCDS66501.1	12q24.31	2006-03-02							29397	protein-coding gene	gene with protein product						11572484	Standard	NM_001286219		Approved	KIAA1906, KIAA1786	uc001uhe.1	Q14DG7		ENST00000299308.3:c.249T>C	12.37:g.125834194T>C		Somatic		WXS	Illumina HiSeq	Phase_I	A2RRG8|Q8NA73|Q96JN9|Q96PY1	Silent	SNP	ENST00000299308.3	37	CCDS41859.1																																																																																				0.498	TMEM132B-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000400043.1		NM_052907	
TNFAIP6	7130	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	152220485	152220485	+	Missense_Mutation	SNP	A	A	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr2:152220485A>C	ENST00000243347.3	+	2	198	c.123A>C	c.(121-123)gaA>gaC	p.E41D		NM_007115.3	NP_009046.2	P98066	TSG6_HUMAN	tumor necrosis factor, alpha-induced protein 6	41	Link. {ECO:0000255|PROSITE- ProRule:PRU00323}.				cell adhesion (GO:0007155)|cell-cell signaling (GO:0007267)|inflammatory response (GO:0006954)|signal transduction (GO:0007165)		hyaluronic acid binding (GO:0005540)	p.E41D(1)		endometrium(1)|kidney(1)|large_intestine(3)|lung(4)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	13				BRCA - Breast invasive adenocarcinoma(221;0.131)	Hyaluronan(DB08818)	ACCACAGAGAAGCACGGTCTG	0.502																																																	1	Substitution - Missense(1)	kidney(1)											85.0	80.0	82.0					2																	152220485		2203	4300	6503	SO:0001583	missense	7130				CCDS2193.1	2q23.3	2008-11-18			ENSG00000123610	ENSG00000123610			11898	protein-coding gene	gene with protein product		600410				1730767, 8568267, 15060082	Standard	NM_007115		Approved	TSG6, TSG-6	uc002txk.3	P98066	OTTHUMG00000131884	ENST00000243347.3:c.123A>C	2.37:g.152220485A>C	ENSP00000243347:p.Glu41Asp	Somatic		WXS	Illumina HiSeq	Phase_I	Q53TI7|Q8WWI9	Missense_Mutation	SNP	ENST00000243347.3	37	CCDS2193.1	.	.	.	.	.	.	.	.	.	.	A	17.73	3.460544	0.63513	.	.	ENSG00000123610	ENST00000243347	T	0.31769	1.48	5.85	4.69	0.59074	C-type lectin fold (1);Link (3);C-type lectin-like (1);	0.000000	0.85682	D	0.000000	T	0.47581	0.1453	L	0.55481	1.735	0.47065	D	0.999304	D	0.69078	0.997	D	0.79108	0.992	T	0.43718	-0.9374	10	0.66056	D	0.02	.	9.6059	0.39632	0.8481:0.0:0.1519:0.0	.	41	P98066	TSG6_HUMAN	D	41	ENSP00000243347:E41D	ENSP00000243347:E41D	E	+	3	2	TNFAIP6	151928731	1.000000	0.71417	0.997000	0.53966	0.519000	0.34347	3.639000	0.54339	1.033000	0.39918	-0.297000	0.09499	GAA		0.502	TNFAIP6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254834.2		NM_007115	
TPH1	7166	broad.mit.edu;ucsc.edu	37	11	18045491	18045491	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr11:18045491C>A	ENST00000250018.2	-	8	1532	c.970G>T	c.(970-972)Gat>Tat	p.D324Y	TPH1_ENST00000525406.1_5'Flank|RP1-59M18.2_ENST00000525523.1_RNA|TPH1_ENST00000341556.2_Missense_Mutation_p.D324Y	NM_004179.2	NP_004170.1	P17752	TPH1_HUMAN	tryptophan hydroxylase 1	324					aromatic amino acid family metabolic process (GO:0009072)|bone remodeling (GO:0046849)|cellular nitrogen compound metabolic process (GO:0034641)|circadian rhythm (GO:0007623)|indolalkylamine biosynthetic process (GO:0046219)|mammary gland alveolus development (GO:0060749)|negative regulation of ossification (GO:0030279)|response to immobilization stress (GO:0035902)|serotonin biosynthetic process (GO:0042427)|small molecule metabolic process (GO:0044281)	cytosol (GO:0005829)|neuron projection (GO:0043005)	amino acid binding (GO:0016597)|iron ion binding (GO:0005506)|tryptophan 5-monooxygenase activity (GO:0004510)	p.D324Y(1)		NS(1)|breast(1)|endometrium(1)|kidney(3)|large_intestine(3)|lung(14)|prostate(1)|stomach(1)	25					L-Tryptophan(DB00150)|Tetrahydrobiopterin(DB00360)	AGCTGTCCATCTTGTTTACAT	0.343																																																	1	Substitution - Missense(1)	kidney(1)											124.0	118.0	120.0					11																	18045491		2200	4293	6493	SO:0001583	missense	7166			X52836	CCDS7829.1	11p15.3-p14	2012-10-02	2008-07-31	2003-04-04	ENSG00000129167	ENSG00000129167	1.14.16.4		12008	protein-coding gene	gene with protein product	"""tryptophan 5-monooxygenase"""	191060	"""tryptophan hydroxylase (tryptophan 5-monooxygenase)"""	TPRH, TPH		1463016	Standard	NM_004179		Approved		uc001mnp.2	P17752	OTTHUMG00000166421	ENST00000250018.2:c.970G>T	11.37:g.18045491C>A	ENSP00000250018:p.Asp324Tyr	Somatic		WXS	Illumina GAIIx	Phase_I	D3DQX6|O95188|O95189|Q16736|Q3KPG8	Missense_Mutation	SNP	ENST00000250018.2	37	CCDS7829.1	.	.	.	.	.	.	.	.	.	.	C	33	5.241598	0.95272	.	.	ENSG00000129167	ENST00000250018;ENST00000341556	D;D	0.99574	-6.2;-6.2	5.92	5.92	0.95590	Aromatic amino acid hydroxylase, C-terminal (3);	0.129096	0.64402	D	0.000001	D	0.99648	0.9870	M	0.90759	3.145	0.80722	D	1	D	0.61697	0.99	P	0.59357	0.856	D	0.98281	1.0508	10	0.87932	D	0	-16.9992	20.3128	0.98645	0.0:1.0:0.0:0.0	.	324	P17752	TPH1_HUMAN	Y	324	ENSP00000250018:D324Y;ENSP00000343550:D324Y	ENSP00000250018:D324Y	D	-	1	0	TPH1	18002067	1.000000	0.71417	1.000000	0.80357	0.971000	0.66376	7.773000	0.85462	2.808000	0.96608	0.561000	0.74099	GAT		0.343	TPH1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000389696.1		NM_004179	
URB1	9875	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	21	33744827	33744827	+	Silent	SNP	A	A	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr21:33744827A>T	ENST00000382751.3	-	8	1105	c.990T>A	c.(988-990)ggT>ggA	p.G330G		NM_014825.2	NP_055640.2	O60287	NPA1P_HUMAN	URB1 ribosome biogenesis 1 homolog (S. cerevisiae)	330						nucleolus (GO:0005730)	poly(A) RNA binding (GO:0044822)	p.G330G(2)		NS(1)|autonomic_ganglia(1)|breast(2)|central_nervous_system(1)|endometrium(9)|kidney(3)|skin(1)|stomach(1)	19						TGCCAAAGGTACCCAAAGATG	0.443																																																	2	Substitution - coding silent(2)	kidney(2)											102.0	85.0	90.0					21																	33744827		692	1591	2283	SO:0001819	synonymous_variant	9875			AB011111	CCDS46645.1	21q22.11	2006-11-28	2006-11-28	2006-11-28	ENSG00000142207	ENSG00000142207			17344	protein-coding gene	gene with protein product	nucleolar preribosomal-associated protein 1	608865	"""chromosome 21 open reading frame 108"""	C21orf108		9628581	Standard	NM_014825		Approved	KIAA0539, NPA1	uc002ypn.2	O60287	OTTHUMG00000064919	ENST00000382751.3:c.990T>A	21.37:g.33744827A>T		Somatic		WXS	Illumina HiSeq	Phase_I	D3DSE5|Q96NX1|Q9NYQ1	Silent	SNP	ENST00000382751.3	37	CCDS46645.1																																																																																				0.443	URB1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000139400.2			
USP2	9099	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	119243611	119243611	+	Missense_Mutation	SNP	A	A	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr11:119243611A>G	ENST00000260187.2	-	2	874	c.580T>C	c.(580-582)Tac>Cac	p.Y194H	RP11-334E6.3_ENST00000530918.2_RNA|USP2_ENST00000455332.2_Intron	NM_004205.4	NP_004196.4	O75604	UBP2_HUMAN	ubiquitin specific peptidase 2	194	Necessary for interaction with MDM4.				cell cycle (GO:0007049)|muscle organ development (GO:0007517)|negative regulation of skeletal muscle tissue development (GO:0048642)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|positive regulation of mitotic cell cycle (GO:0045931)|positive regulation of skeletal muscle tissue development (GO:0048643)|protein deubiquitination (GO:0016579)|protein stabilization (GO:0050821)|ubiquitin-dependent protein catabolic process (GO:0006511)	cell cortex (GO:0005938)|centrosome (GO:0005813)|nucleus (GO:0005634)|perinuclear region of cytoplasm (GO:0048471)	cyclin binding (GO:0030332)|cysteine-type endopeptidase activity (GO:0004197)|metal ion binding (GO:0046872)|ubiquitin protein ligase binding (GO:0031625)|ubiquitin thiolesterase activity (GO:0004221)|ubiquitin-specific protease activity (GO:0004843)	p.Y194H(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(5)|lung(5)|ovary(2)|prostate(3)|skin(2)|urinary_tract(1)	24		all_hematologic(192;4.65e-05)|Breast(348;0.0101)|all_neural(223;0.0218)|Medulloblastoma(222;0.0425)|Renal(330;0.157)		BRCA - Breast invasive adenocarcinoma(274;3.93e-06)|OV - Ovarian serous cystadenocarcinoma(223;0.000513)|Colorectal(284;0.0116)|Lung(307;0.0853)|LUSC - Lung squamous cell carcinoma(976;0.0889)		TCGACCAGGTATTCAGGGCAG	0.637																																																	1	Substitution - Missense(1)	kidney(1)											66.0	69.0	68.0					11																	119243611		2199	4295	6494	SO:0001583	missense	9099			AF079564	CCDS8422.1, CCDS8423.1, CCDS58189.1	11q23.3	2008-02-05	2005-08-08			ENSG00000036672		"""Ubiquitin-specific peptidases"""	12618	protein-coding gene	gene with protein product		604725	"""ubiquitin specific protease 2"""			12838346	Standard	NM_004205		Approved	UBP41	uc001pwm.4	O75604		ENST00000260187.2:c.580T>C	11.37:g.119243611A>G	ENSP00000260187:p.Tyr194His	Somatic		WXS	Illumina HiSeq	Phase_I	B0YJB8|E9PPM2|Q8IUM2|Q8IW04|Q96MB9|Q9BQ21	Missense_Mutation	SNP	ENST00000260187.2	37	CCDS8422.1	.	.	.	.	.	.	.	.	.	.	A	16.29	3.080656	0.55753	.	.	ENSG00000036672	ENST00000260187;ENST00000530918	T	0.26067	1.76	5.37	5.37	0.77165	.	0.847047	0.10893	N	0.622512	T	0.35885	0.0947	L	0.29908	0.895	0.80722	D	1	D	0.67145	0.996	P	0.59703	0.862	T	0.01626	-1.1309	10	0.40728	T	0.16	-5.887	13.1125	0.59281	1.0:0.0:0.0:0.0	.	194	O75604	UBP2_HUMAN	H	194;164	ENSP00000260187:Y194H	ENSP00000260187:Y194H	Y	-	1	0	USP2	118748821	1.000000	0.71417	0.993000	0.49108	0.711000	0.40976	4.597000	0.61062	2.024000	0.59613	0.533000	0.62120	TAC		0.637	USP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000388361.2		NM_171997	
WDR3	10885	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	118483544	118483544	+	Missense_Mutation	SNP	C	C	T	rs142439174	byFrequency	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr1:118483544C>T	ENST00000349139.5	+	7	817	c.770C>T	c.(769-771)aCg>aTg	p.T257M	WDR3_ENST00000369441.3_3'UTR	NM_006784.2	NP_006775.1	Q9UNX4	WDR3_HUMAN	WD repeat domain 3	257						nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.T257M(1)		breast(2)|cervix(2)|endometrium(5)|kidney(4)|large_intestine(9)|liver(2)|lung(22)|prostate(2)|upper_aerodigestive_tract(1)	49	Esophageal squamous(2;0.162)	all_cancers(81;2.72e-05)|Acute lymphoblastic leukemia(138;1e-08)|all_epithelial(167;4.4e-07)|all_lung(203;1.7e-06)|Lung NSC(69;1.98e-05)|Prostate(1639;0.00955)|Breast(1374;0.244)		OV - Ovarian serous cystadenocarcinoma(397;1.39e-08)|Epithelial(280;1.82e-07)|all cancers(265;2.04e-05)|Lung(183;0.0525)|BRCA - Breast invasive adenocarcinoma(282;0.0695)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.185)		GCCTTTGAGACGGATGAAGCC	0.393													C|||	9	0.00179712	0.0061	0.0	5008	,	,		18644	0.001		0.0	False		,,,				2504	0.0																1	Substitution - Missense(1)	kidney(1)						C	MET/THR	15,4391	21.2+/-45.6	0,15,2188	104.0	104.0	104.0		770	-5.4	0.0	1	dbSNP_134	104	0,8600		0,0,4300	yes	missense	WDR3	NM_006784.2	81	0,15,6488	TT,TC,CC		0.0,0.3404,0.1153	benign	257/944	118483544	15,12991	2203	4300	6503	SO:0001583	missense	10885			AF083217	CCDS898.1	1p12	2013-01-09			ENSG00000065183	ENSG00000065183		"""WD repeat domain containing"""	12755	protein-coding gene	gene with protein product		604737				10395803	Standard	NM_006784		Approved	FLJ12796, UTP12, DIP2	uc010oxe.1	Q9UNX4	OTTHUMG00000012197	ENST00000349139.5:c.770C>T	1.37:g.118483544C>T	ENSP00000308179:p.Thr257Met	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000349139.5	37	CCDS898.1	2	9.157509157509158E-4	1	0.0020325203252032522	0	0.0	1	0.0017482517482517483	0	0.0	C	8.265	0.812106	0.16537	0.003404	0.0	ENSG00000065183	ENST00000349139	T	0.53857	0.6	5.17	-5.45	0.02616	WD40/YVTN repeat-like-containing domain (1);WD40 repeat-like-containing domain (1);WD40-repeat-containing domain (1);	2.293110	0.01313	N	0.010681	T	0.15176	0.0366	N	0.08118	0	0.09310	N	1	B	0.06786	0.001	B	0.04013	0.001	T	0.25984	-1.0116	10	0.52906	T	0.07	0.1146	13.9516	0.64121	0.0:0.5455:0.0:0.4545	.	257	Q9UNX4	WDR3_HUMAN	M	257	ENSP00000308179:T257M	ENSP00000308179:T257M	T	+	2	0	WDR3	118285067	0.001000	0.12720	0.001000	0.08648	0.002000	0.02628	-0.305000	0.08188	-0.878000	0.04007	-2.048000	0.00412	ACG		0.393	WDR3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000033720.2		NM_006784	
ADAMTSL5	339366	broad.mit.edu	37	19	1508023	1508023	+	Frame_Shift_Del	DEL	A	A	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr19:1508023delA	ENST00000413997.2	-	7	604	c.605delT	c.(604-606)ttcfs	p.F202fs	CTB-25B13.9_ENST00000590252.1_RNA|ADAMTSL5_ENST00000590562.1_5'UTR|ADAMTSL5_ENST00000330475.4_Frame_Shift_Del_p.F192fs|ADAMTSL5_ENST00000395467.2_5'UTR			Q6ZMM2	ATL5_HUMAN	ADAMTS-like 5	202						extracellular matrix (GO:0031012)|extracellular region (GO:0005576)|microfibril (GO:0001527)|proteinaceous extracellular matrix (GO:0005578)	heparin binding (GO:0008201)|metalloendopeptidase activity (GO:0004222)|zinc ion binding (GO:0008270)			cervix(1)|kidney(1)|large_intestine(2)|lung(1)|prostate(3)|skin(1)|upper_aerodigestive_tract(1)	10		Acute lymphoblastic leukemia(61;5.61e-13)|all_hematologic(61;2.65e-08)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		GCGCTGCACGAAAAGGCACGA	0.652																																																	0													26.0	22.0	23.0					19																	1508023		2192	4292	6484	SO:0001589	frameshift_variant	339366			BC040620	CCDS12071.1	19p13.3	2008-02-05	2006-02-07	2006-02-07		ENSG00000185761			27912	protein-coding gene	gene with protein product			"""thrombospondin, type I, domain containing 6"""	THSD6			Standard	NM_213604		Approved		uc002ltd.2	Q6ZMM2		ENST00000413997.2:c.605delT	19.37:g.1508023delA	ENSP00000399364:p.Phe202fs	Somatic		WXS	Illumina GAIIx	Phase_I	B4DXK7|Q8IW95	Frame_Shift_Del	DEL	ENST00000413997.2	37																																																																																					0.652	ADAMTSL5-202	KNOWN	basic	protein_coding	protein_coding			XM_294919	
ARHGAP23	57636	broad.mit.edu	37	17	36636039	36636039	+	Silent	SNP	C	C	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr17:36636039C>T	ENST00000431231.2	+	14	2612	c.2544C>T	c.(2542-2544)cgC>cgT	p.R848R	ARHGAP23_ENST00000443378.1_Silent_p.R754R|ARHGAP23_ENST00000437668.3_Silent_p.R848R	NM_001199417.1	NP_001186346.1	Q9P227	RHG23_HUMAN	Rho GTPase activating protein 23	848					regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	GTPase activator activity (GO:0005096)	p.R1173R(1)		breast(2)|endometrium(8)|kidney(6)|lung(1)|skin(1)|stomach(2)	20						AAGGCTCTCGCGGCCTGGGGG	0.622																																																	1	Substitution - coding silent(1)	kidney(1)											2.0	2.0	2.0					17																	36636039		607	1317	1924	SO:0001819	synonymous_variant	57636			AB040934	CCDS56027.1	17q12	2014-05-06			ENSG00000225485	ENSG00000275832		"""Rho GTPase activating proteins"", ""Pleckstrin homology (PH) domain containing"""	29293	protein-coding gene	gene with protein product		610590				10819331, 15254754	Standard	NM_001199417		Approved	KIAA1501	uc021twd.1	Q9P227	OTTHUMG00000188547	ENST00000431231.2:c.2544C>T	17.37:g.36636039C>T		Somatic		WXS	Illumina GAIIx	Phase_I		Silent	SNP	ENST00000431231.2	37	CCDS56027.1																																																																																				0.622	ARHGAP23-006	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441789.1		XM_290799	
AZGP1	563	broad.mit.edu	37	7	99573623	99573623	+	Silent	SNP	G	G	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr7:99573623G>T	ENST00000292401.4	-	1	157	c.21C>A	c.(19-21)gtC>gtA	p.V7V	AZGP1_ENST00000411734.1_Silent_p.V4V	NM_001185.3	NP_001176.1	P25311	ZA2G_HUMAN	alpha-2-glycoprotein 1, zinc-binding	7					antigen processing and presentation of peptide antigen via MHC class I (GO:0002474)|cell adhesion (GO:0007155)|detection of chemical stimulus involved in sensory perception of bitter taste (GO:0001580)|immune response (GO:0006955)|negative regulation of cell proliferation (GO:0008285)|positive regulation of T cell mediated cytotoxicity (GO:0001916)|protein transmembrane transport (GO:0071806)|retina homeostasis (GO:0001895)|RNA phosphodiester bond hydrolysis (GO:0090501)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|MHC class I protein complex (GO:0042612)|nucleus (GO:0005634)	glycoprotein binding (GO:0001948)|peptide antigen binding (GO:0042605)|protein transmembrane transporter activity (GO:0008320)|ribonuclease activity (GO:0004540)	p.V7V(1)		central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(3)|lung(6)|ovary(1)|prostate(1)|stomach(1)	16	Esophageal squamous(72;0.0166)|Lung NSC(181;0.0211)|all_lung(186;0.0323)					GAGACAGCAGGACAGGCACCA	0.587																																																	1	Substitution - coding silent(1)	kidney(1)											170.0	163.0	166.0					7																	99573623		2203	4300	6503	SO:0001819	synonymous_variant	563			BC005306	CCDS5680.1	7q22.1	2013-01-11	2006-11-07		ENSG00000160862	ENSG00000160862		"""Immunoglobulin superfamily / C1-set domain containing"""	910	protein-coding gene	gene with protein product		194460	"""alpha-2-glycoprotein 1, zinc"""			2049092	Standard	NM_001185		Approved	ZA2G, ZAG	uc003ush.3	P25311	OTTHUMG00000023066	ENST00000292401.4:c.21C>A	7.37:g.99573623G>T		Somatic		WXS	Illumina GAIIx	Phase_I	D6W5T8|O60386|Q5XKQ4|Q8N4N0	Silent	SNP	ENST00000292401.4	37	CCDS5680.1																																																																																				0.587	AZGP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000059387.4		NM_001185	
CTAGE6	340307	broad.mit.edu	37	7	143453714	143453714	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr7:143453714G>C	ENST00000470691.2	-	1	1075	c.1038C>G	c.(1036-1038)gaC>gaG	p.D346E	RNU6-267P_ENST00000516714.1_RNA	NM_178561.4	NP_848656.2	Q86UF2	CTGE6_HUMAN	CTAGE family, member 6	346						integral component of membrane (GO:0016021)						Melanoma(164;0.0903)					CCTTTGTTTTGTCCACTTCAG	0.318																																																	0													7.0	7.0	7.0					7																	143453714		1731	3838	5569	SO:0001583	missense	0			BC043153	CCDS64790.1	7q35	2013-05-22	2013-02-25	2013-02-25	ENSG00000271321	ENSG00000271321			28644	protein-coding gene	gene with protein product			"""CTAGE family, member 6, pseudogene"""	CTAGE6P		12477932	Standard	NM_178561		Approved	MGC41943	uc003wdk.4	Q86UF2	OTTHUMG00000157770	ENST00000470691.2:c.1038C>G	7.37:g.143453714G>C	ENSP00000474388:p.Asp346Glu	Somatic		WXS	Illumina GAIIx	Phase_I	A4FU29|Q3ZCM5	Missense_Mutation	SNP	ENST00000470691.2	37																																																																																					0.318	CTAGE6-001	KNOWN	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000349580.2		NM_178561	
HYDIN	54768	broad.mit.edu	37	16	70889122	70889122	+	Missense_Mutation	SNP	A	A	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr16:70889122A>T	ENST00000393567.2	-	73	12502	c.12352T>A	c.(12352-12354)Ttt>Att	p.F4118I	RNU6ATAC25P_ENST00000408798.1_RNA	NM_001270974.1	NP_001257903.1	Q4G0P3	HYDIN_HUMAN	HYDIN, axonemal central pair apparatus protein	4118					cilium assembly (GO:0042384)|cilium movement (GO:0003341)|epithelial cell development (GO:0002064)|trachea development (GO:0060438)|ventricular system development (GO:0021591)	cell projection (GO:0042995)		p.F4069I(1)|p.F4117I(1)		breast(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(17)|lung(12)|ovary(2)|skin(3)|stomach(2)|upper_aerodigestive_tract(1)	43		Ovarian(137;0.0654)				TGGAAGGAAAAATCGAACCCC	0.537																																																	2	Substitution - Missense(2)	kidney(2)											46.0	70.0	63.0					16																	70889122		1699	4092	5791	SO:0001583	missense	54768			AK074472	CCDS10897.1, CCDS56004.1, CCDS56005.1, CCDS59269.1	16q22.2	2014-02-05	2012-01-06		ENSG00000157423	ENSG00000157423		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"""	19368	protein-coding gene	gene with protein product	"""protein phosphatase 1, regulatory subunit 31"""	610812	"""hydrocephalus inducing"", ""hydrocephalus inducing homolog (mouse)"""			12719380, 23022101	Standard	NM_001198542		Approved	DKFZp434D0513, KIAA1864, PPP1R31, CILD5	uc031qwy.1	Q4G0P3	OTTHUMG00000137584	ENST00000393567.2:c.12352T>A	16.37:g.70889122A>T	ENSP00000377197:p.Phe4118Ile	Somatic		WXS	Illumina GAIIx	Phase_I	A6NC70|A6NLZ0|B4DQY4|B4DRN4|F5H6V3|Q8N3H8|Q8N3P6|Q8TC08|Q96JG3|Q96SS4|Q9H5U3|Q9H9B8|Q9NTI0|Q9UBE5	Missense_Mutation	SNP	ENST00000393567.2	37	CCDS59269.1	.	.	.	.	.	.	.	.	.	.	A	24.3	4.518677	0.85495	.	.	ENSG00000157423	ENST00000393567;ENST00000316490	T	0.03358	3.96	5.57	5.57	0.84162	.	0.000000	0.34110	U	0.004257	T	0.20820	0.0501	M	0.83223	2.63	0.80722	D	1	D	0.89917	1.0	D	0.83275	0.996	T	0.00409	-1.1757	10	0.87932	D	0	.	15.6754	0.77316	1.0:0.0:0.0:0.0	.	4117	F8WD23	.	I	4118;4117	ENSP00000377197:F4118I	ENSP00000313052:F4117I	F	-	1	0	HYDIN	69446623	1.000000	0.71417	0.917000	0.36280	0.582000	0.36321	6.807000	0.75201	2.244000	0.73946	0.418000	0.28097	TTT		0.537	HYDIN-001	PUTATIVE	not_organism_supported|basic|appris_principal|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000398624.3			
RNY4P30	100862673	broad.mit.edu	37	13	50466749	50466749	+	RNA	SNP	C	C	G	rs57976037	byFrequency	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr13:50466749C>G	ENST00000410216.1	-	0	0									RNA, Ro-associated Y4 pseudogene 30																		TTTAAATGTGCCTGATTCATC	0.428																																																	0																																												0					13q14.2	2011-08-03			ENSG00000222148	ENSG00000222148			42498	pseudogene	RNA, pseudogene							Standard	NG_032103		Approved						13.37:g.50466749C>G		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000410216.1	37																																																																																					0.428	RNY4P30-201	KNOWN	basic	misc_RNA	misc_RNA				
AC009120.6	0	broad.mit.edu	37	16	74366481	74366481	+	RNA	SNP	A	A	G			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr16:74366481A>G	ENST00000565313.1	-	0	30				AC009120.6_ENST00000561921.1_RNA																							GGGGATGTAGAGCATGAATCC	0.632																																																	0																																												283922																															16.37:g.74366481A>G		Somatic		WXS	Illumina GAIIx	Phase_I		Missense_Mutation	SNP	ENST00000565313.1	37																																																																																					0.632	AC009120.6-003	KNOWN	basic	antisense	antisense	OTTHUMT00000434677.1			
Unknown	0	broad.mit.edu	37	1	16974182	16974182	+	IGR	SNP	C	C	A	rs370176636	byFrequency	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr1:16974182C>A								CROCCP2 (13128 upstream) : RNU1-3 (19097 downstream)																							GAGCATATCCCGTGGAGTACC	0.672													.|||	821	0.163938	0.2769	0.1297	5008	,	,		43125	0.1825		0.0924	False		,,,				2504	0.09																0																																										SO:0001628	intergenic_variant	11209																															1.37:g.16974182C>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.672									
SNX20	124460	broad.mit.edu	37	16	50709790	50709790	+	Missense_Mutation	SNP	C	C	T			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr16:50709790C>T	ENST00000330943.4	-	3	344	c.173G>A	c.(172-174)cGg>cAg	p.R58Q	SNX20_ENST00000423026.2_Missense_Mutation_p.R58Q|SNX20_ENST00000300590.3_Missense_Mutation_p.R58Q	NM_182854.2	NP_878274.1	Q7Z614	SNX20_HUMAN	sorting nexin 20	58					protein transport (GO:0015031)	endosome (GO:0005768)|nucleus (GO:0005634)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)	p.R58Q(2)		kidney(1)|large_intestine(3)|lung(5)|ovary(2)|prostate(1)|skin(2)|stomach(1)	15						CTGAAGCTCCCGCGTGGTCAT	0.552																																																	2	Substitution - Missense(2)	kidney(2)											107.0	96.0	99.0					16																	50709790		2198	4300	6498	SO:0001583	missense	124460			AK055837	CCDS10745.1, CCDS10744.1, CCDS45481.1	16q12.1	2008-03-25	2008-03-25		ENSG00000167208	ENSG00000167208		"""Sorting nexins"""	30390	protein-coding gene	gene with protein product	"""selectin ligand interactor cytoplasmic 1"""	613281				18196517, 16782399	Standard	NM_182854		Approved	SLIC-1, SLIC1	uc002egk.2	Q7Z614	OTTHUMG00000133173	ENST00000330943.4:c.173G>A	16.37:g.50709790C>T	ENSP00000332062:p.Arg58Gln	Somatic		WXS	Illumina GAIIx	Phase_I	A8K9D5|Q08E98|Q6P4H2|Q8IV59	Missense_Mutation	SNP	ENST00000330943.4	37	CCDS10745.1	.	.	.	.	.	.	.	.	.	.	C	19.28	3.797044	0.70567	.	.	ENSG00000167208	ENST00000300590;ENST00000423026;ENST00000330943;ENST00000413750	T;T;T	0.52295	0.67;0.72;1.17	5.66	3.52	0.40303	Phox homologous domain (1);	0.276731	0.33875	N	0.004467	T	0.43809	0.1264	N	0.24115	0.695	0.24938	N	0.991874	D;P;D	0.76494	0.999;0.913;0.993	P;B;P	0.60345	0.873;0.161;0.724	T	0.22138	-1.0225	10	0.62326	D	0.03	-26.6863	4.1732	0.10339	0.0:0.6117:0.0:0.3883	.	58;58;58	Q7Z614-3;Q7Z614;Q7Z614-4	.;SNX20_HUMAN;.	Q	58	ENSP00000300590:R58Q;ENSP00000388875:R58Q;ENSP00000332062:R58Q	ENSP00000300590:R58Q	R	-	2	0	SNX20	49267291	0.996000	0.38824	0.795000	0.32087	0.502000	0.33828	1.772000	0.38552	1.389000	0.46526	0.462000	0.41574	CGG		0.552	SNX20-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256879.2		NM_153337	
SPAG9	9043	broad.mit.edu	37	17	49197990	49197990	+	Missense_Mutation	SNP	G	G	C			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr17:49197990G>C	ENST00000262013.7	-	1	236	c.28C>G	c.(28-30)Cag>Gag	p.Q10E	SPAG9_ENST00000357122.4_Missense_Mutation_p.Q10E|SPAG9_ENST00000505279.1_Missense_Mutation_p.Q10E	NM_001130528.2	NP_001124000.1	O60271	JIP4_HUMAN	sperm associated antigen 9	10					activation of JUN kinase activity (GO:0007257)|muscle cell differentiation (GO:0042692)|negative regulation of protein homodimerization activity (GO:0090074)|positive regulation of cell migration (GO:0030335)|positive regulation of muscle cell differentiation (GO:0051149)|positive regulation of neuron differentiation (GO:0045666)|protein homooligomerization (GO:0051260)|retrograde transport, endosome to Golgi (GO:0042147)|spermatogenesis (GO:0007283)|striated muscle cell differentiation (GO:0051146)	cytoplasm (GO:0005737)|cytoplasmic vesicle (GO:0031410)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|perinuclear region of cytoplasm (GO:0048471)		p.Q10E(1)		NS(1)|breast(3)|endometrium(3)|kidney(4)|large_intestine(8)|lung(14)|ovary(1)|prostate(1)|skin(1)|stomach(1)	37			BRCA - Breast invasive adenocarcinoma(22;4.24e-07)			GGCTCCTCCTGATACACCACA	0.736																																																	1	Substitution - Missense(1)	kidney(1)											15.0	17.0	16.0					17																	49197990		2196	4295	6491	SO:0001583	missense	9043			AB011088	CCDS11577.1, CCDS45740.1, CCDS58577.1, CCDS58578.1	17q21.33	2013-09-23			ENSG00000008294	ENSG00000008294			14524	protein-coding gene	gene with protein product	"""sperm surface protein"", ""JNK/SAPK-associated protein"", ""JNK interacting protein"", ""sperm specific protein"", ""c-Jun NH2-terminal kinase-associated leucine zipper protein"", ""Max-binding protein"", ""JNK-associated leucine-zipper protein"", ""HLC-4 protein"", ""lung cancer oncogene 4"", ""proliferation-inducing gene 6"", ""cancer/testis antigen 89"""	605430				9480848, 11106729	Standard	NM_003971		Approved	HSS, SYD1, KIAA0516, MGC14967, MGC74461, MGC117291, JLP, PHET, HLC4, PIG6, FLJ13450, FLJ14006, FLJ26141, FLJ34602, CT89	uc002itc.3	O60271	OTTHUMG00000162316	ENST00000262013.7:c.28C>G	17.37:g.49197990G>C	ENSP00000262013:p.Gln10Glu	Somatic		WXS	Illumina GAIIx	Phase_I	A6H8U5|A8MSX0|B4DHH2|O60905|Q3KQU8|Q3MKM7|Q86WC7|Q86WC8|Q8IZX7|Q96II0|Q9H811	Missense_Mutation	SNP	ENST00000262013.7	37	CCDS45740.1	.	.	.	.	.	.	.	.	.	.	G	16.95	3.264166	0.59431	.	.	ENSG00000008294	ENST00000262013;ENST00000505279;ENST00000357122;ENST00000546269	T;T;T	0.23552	1.9;1.91;1.91	3.69	3.69	0.42338	.	0.222821	0.28766	U	0.014216	T	0.29355	0.0731	L	0.60455	1.87	0.28486	N	0.914723	B;B;P	0.41131	0.195;0.243;0.739	B;B;B	0.40782	0.122;0.057;0.34	T	0.20472	-1.0274	10	0.45353	T	0.12	-5.6136	15.4447	0.75220	0.0:0.0:1.0:0.0	.	10;10;10	O60271-2;O60271;O60271-4	.;JIP4_HUMAN;.	E	10	ENSP00000262013:Q10E;ENSP00000426900:Q10E;ENSP00000349636:Q10E	ENSP00000262013:Q10E	Q	-	1	0	SPAG9	46552989	1.000000	0.71417	0.997000	0.53966	0.838000	0.47535	6.357000	0.73051	1.770000	0.52166	0.186000	0.17326	CAG		0.736	SPAG9-001	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000368543.2		NM_003971	
TMEM198	130612	broad.mit.edu	37	2	220412692	220412692	+	Frame_Shift_Del	DEL	C	C	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr2:220412692delC	ENST00000344458.2	+	4	1216	c.631delC	c.(631-633)cccfs	p.P212fs	RP11-256I23.1_ENST00000596829.1_RNA|MIR3132_ENST00000581997.1_RNA|TMEM198_ENST00000373883.3_Frame_Shift_Del_p.P212fs			Q66K66	TM198_HUMAN	transmembrane protein 198	212	Leu-rich.				multicellular organismal development (GO:0007275)|positive regulation of canonical Wnt signaling pathway (GO:0090263)|Wnt signaling pathway (GO:0016055)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)				NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(5)|lung(2)|ovary(1)|prostate(1)|skin(2)|upper_aerodigestive_tract(2)	16		Renal(207;0.0376)		Epithelial(149;6.49e-08)|all cancers(144;6.45e-06)|LUSC - Lung squamous cell carcinoma(224;0.008)|Lung(261;0.00802)		TGCTCCTGTGCCCCCACTCTG	0.677																																																	0													10.0	10.0	10.0					2																	220412692		2191	4295	6486	SO:0001589	frameshift_variant	130612			BC068567	CCDS33385.1	2q35	2011-12-06			ENSG00000188760	ENSG00000188760			33704	protein-coding gene	gene with protein product							Standard	NM_001005209		Approved	MGC99813, TMEM198A	uc002vmf.3	Q66K66	OTTHUMG00000059156	ENST00000344458.2:c.631delC	2.37:g.220412692delC	ENSP00000343507:p.Pro212fs	Somatic		WXS	Illumina GAIIx	Phase_I		Frame_Shift_Del	DEL	ENST00000344458.2	37	CCDS33385.1																																																																																				0.677	TMEM198-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131063.1		NM_001005209	
TNRC18	84629	broad.mit.edu	37	7	5352305	5352305	+	Frame_Shift_Del	DEL	G	G	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr7:5352305delG	ENST00000430969.1	-	27	8565	c.8217delC	c.(8215-8217)cccfs	p.P2739fs	TNRC18_ENST00000399537.4_Frame_Shift_Del_p.P2739fs	NM_001080495.2	NP_001073964.2	O15417	TNC18_HUMAN	trinucleotide repeat containing 18	2739							chromatin binding (GO:0003682)			central_nervous_system(1)|endometrium(1)|large_intestine(1)|lung(8)	11		Ovarian(82;0.142)		UCEC - Uterine corpus endometrioid carcinoma (126;0.195)|OV - Ovarian serous cystadenocarcinoma(56;5.32e-15)		CCTGAGCCTTGGGCTGCAGAG	0.736																																																	0													18.0	20.0	20.0					7																	5352305		1465	3290	4755	SO:0001589	frameshift_variant	84629			U80753	CCDS47534.1	7p22.1	2012-04-17			ENSG00000182095	ENSG00000182095		"""Trinucleotide (CAG) repeat containing"""	11962	protein-coding gene	gene with protein product						9225980	Standard	NM_001080495		Approved	CAGL79, TNRC18A, KIAA1856	uc003soi.4	O15417	OTTHUMG00000151831	ENST00000430969.1:c.8217delC	7.37:g.5352305delG	ENSP00000395538:p.Pro2739fs	Somatic		WXS	Illumina GAIIx	Phase_I	A8MX41|Q96JH1|Q96K91	Frame_Shift_Del	DEL	ENST00000430969.1	37	CCDS47534.1																																																																																				0.736	TNRC18-201	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding				
UGT1A4	54657	broad.mit.edu	37	2	234628268	234628268	+	Missense_Mutation	SNP	C	C	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr2:234628268C>A	ENST00000373409.3	+	1	845	c.802C>A	c.(802-804)Ccg>Acg	p.P268T	UGT1A6_ENST00000373424.1_Intron|UGT1A6_ENST00000305139.6_Intron|UGT1A1_ENST00000373450.4_Intron|UGT1A1_ENST00000609637.1_Intron|UGT1A6_ENST00000406651.1_Intron|UGT1A1_ENST00000608381.1_Intron|UGT1A9_ENST00000354728.4_Intron|UGT1A10_ENST00000344644.5_Intron|UGT1A6_ENST00000480628.1_Intron|UGT1A7_ENST00000373426.3_Intron|UGT1A5_ENST00000373414.3_Intron|UGT1A10_ENST00000373445.1_Intron	NM_007120.2	NP_009051.1	P22310	UD14_HUMAN	UDP glucuronosyltransferase 1 family, polypeptide A4	268					cellular glucuronidation (GO:0052695)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)	enzyme binding (GO:0019899)|glucuronosyltransferase activity (GO:0015020)|protein heterodimerization activity (GO:0046982)|protein homodimerization activity (GO:0042803)	p.P268T(1)		autonomic_ganglia(1)|breast(2)|endometrium(3)|kidney(2)|large_intestine(5)|lung(9)|ovary(1)|skin(2)|urinary_tract(1)	26		Breast(86;0.000765)|all_lung(227;0.00266)|Renal(207;0.00339)|all_hematologic(139;0.0116)|Acute lymphoblastic leukemia(138;0.0327)|Lung NSC(271;0.0456)|Lung SC(224;0.128)		Epithelial(121;3.49e-18)|BRCA - Breast invasive adenocarcinoma(100;0.000504)|Lung(119;0.0026)|LUSC - Lung squamous cell carcinoma(224;0.00624)	Asenapine(DB06216)|Clozapine(DB00363)|Ezogabine(DB04953)|Lamotrigine(DB00555)|Midazolam(DB00683)|Paricalcitol(DB00910)|Tamoxifen(DB00675)|Trifluoperazine(DB00831)|Valproic Acid(DB00313)	CTACCCCAGGCCGATCATGCC	0.522																																					Melanoma(99;1011 1962 13201 26492)												1	Substitution - Missense(1)	kidney(1)											162.0	163.0	163.0					2																	234628268		2203	4298	6501	SO:0001583	missense	54657			M84128	CCDS33405.1	2q37.1	2014-01-10	2005-07-20		ENSG00000244474	ENSG00000244474		"""UDP glucuronosyltransferases"""	12536	other	complex locus constituent		606429	"""UDP glycosyltransferase 1 family, polypeptide A4"""			9295054, 1339448	Standard	NM_007120		Approved	HUG-BR2, UGT1D	uc002vux.3	P22310	OTTHUMG00000059119	ENST00000373409.3:c.802C>A	2.37:g.234628268C>A	ENSP00000362508:p.Pro268Thr	Somatic		WXS	Illumina GAIIx	Phase_I	B2R937|B8K288|Q5DT00	Missense_Mutation	SNP	ENST00000373409.3	37	CCDS33405.1	.	.	.	.	.	.	.	.	.	.	C	18.07	3.542389	0.65198	.	.	ENSG00000244474	ENST00000373409	T	0.64618	-0.11	4.49	3.6	0.41247	.	.	.	.	.	D	0.85292	0.5663	H	0.97023	3.925	0.45621	D	0.998557	D;D	0.89917	1.0;1.0	D;D	0.97110	0.999;1.0	D	0.89673	0.3885	9	0.87932	D	0	.	14.3024	0.66362	0.0:0.8499:0.1501:0.0	.	268;268	B8K288;P22310	.;UD14_HUMAN	T	268	ENSP00000362508:P268T	ENSP00000362508:P268T	P	+	1	0	UGT1A4	234293007	0.997000	0.39634	0.989000	0.46669	0.660000	0.38997	5.961000	0.70356	0.842000	0.35045	0.491000	0.48974	CCG		0.522	UGT1A4-001	KNOWN	basic|appris_principal|readthrough_transcript|CCDS	protein_coding	protein_coding	OTTHUMT00000130984.1		NM_007120	
MIR7162	102466227	broad.mit.edu	37	15	62534763	62534764	+	RNA	DEL	TA	TA	-	rs2414766|rs199607552	byFrequency	TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	TA	TA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr15:62534763_62534764delTA	ENST00000408214.1	-	0	83																											TTTTTTTTTTTAAATTTGGTGG	0.332																																																	0																																												0																															15.37:g.62534763_62534764delTA		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL	ENST00000408214.1	37																																																																																					0.332	AC126323.1-201	NOVEL	basic	miRNA	miRNA				
RP11-1102P16.1	0	broad.mit.edu	37	8	72316198	72316198	+	3'UTR	DEL	T	T	-			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chr8:72316198delT	ENST00000523987.1	-	0	1273																											TACATACTTGTTTTTCGTGAC	0.348																																																	0																																										SO:0001624	3_prime_UTR_variant	0																														ENST00000523987.1:c.*842A>-	8.37:g.72316198delT		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	DEL	ENST00000523987.1	37																																																																																					0.348	RP11-1102P16.1-001	PUTATIVE	basic|appris_principal	protein_coding	protein_coding	OTTHUMT00000378846.1			
WASH6P	653440	broad.mit.edu	37	X	155252868	155252868	+	RNA	SNP	T	T	A			TCGA-CJ-5683-01A-11D-1534-10	TCGA-CJ-5683-11A-01D-1535-10	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	b85e29c5-0206-4d65-aa46-179a55c0ceae	fdd52cce-70b6-4f2d-873b-dbfe5323841d	g.chrX:155252868T>A	ENST00000461007.1	+	0	1876				AJ271736.10_ENST00000285718.7_RNA			Q9NQA3	WASH6_HUMAN	WAS protein family homolog 6 pseudogene						Arp2/3 complex-mediated actin nucleation (GO:0034314)|endosomal transport (GO:0016197)|retrograde transport, endosome to Golgi (GO:0042147)	early endosome (GO:0005769)|membrane (GO:0016020)|recycling endosome (GO:0055037)|WASH complex (GO:0071203)	alpha-tubulin binding (GO:0043014)	p.P304P(5)									TAGCCGAGCCTCTCAAGGCAG	0.632																																																	5	Substitution - coding silent(5)	kidney(3)|endometrium(2)																																										0			AI042587		Xq28 and Yq12	2014-08-28	2008-01-16	2008-01-16	ENSG00000182484	ENSG00000182484		"""Pseudoautosomal regions / PAR2"", ""WAS protein homologs"""	31685	pseudogene	pseudogene			"""family with sequence similarity 39, member A"", ""chromosomes X and Y open reading frame 1"""	FAM39A, CXYorf1		10655549, 12566406, 18159949	Standard	NG_008380		Approved			Q9NQA3	OTTHUMG00000022677		X.37:g.155252868T>A		Somatic		WXS	Illumina GAIIx	Phase_I	A6NGF1|Q8N305	Silent	SNP	ENST00000461007.1	37																																																																																					0.632	WASH6P-016	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000058840.1		NG_008380	
