#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
ANKRD26	22852	hgsc.bcm.edu;ucsc.edu	37	10	27303499	27303499	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr10:27303499delT	ENST00000376087.4	-	31	4813	c.4648delA	c.(4648-4650)accfs	p.T1550fs	ANKRD26_ENST00000436985.2_Frame_Shift_Del_p.T1566fs|ANKRD26_ENST00000376070.3_Frame_Shift_Del_p.T1107fs	NM_001256053.1|NM_014915.2	NP_001242982.1|NP_055730.2	Q9UPS8	ANR26_HUMAN	ankyrin repeat domain 26	1549					glucose homeostasis (GO:0042593)|negative regulation of ERK1 and ERK2 cascade (GO:0070373)|negative regulation of fat cell differentiation (GO:0045599)|negative regulation of insulin receptor signaling pathway (GO:0046627)|negative regulation of multicellular organism growth (GO:0040015)|negative regulation of organ growth (GO:0046621)|regulation of fatty acid metabolic process (GO:0019217)|regulation of feeding behavior (GO:0060259)	actin filament (GO:0005884)|centrosome (GO:0005813)				breast(4)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(14)|lung(30)|ovary(1)|pancreas(1)|prostate(3)|skin(2)|urinary_tract(2)	70						TCCAGTTCGGTTTTATTAAAG	0.284																																																	0													52.0	48.0	49.0					10																	27303499		1779	4050	5829	SO:0001589	frameshift_variant	22852			AB028997	CCDS41499.1	10p12.1	2014-09-17			ENSG00000107890	ENSG00000107890		"""Ankyrin repeat domain containing"""	29186	protein-coding gene	gene with protein product		610855	"""thrombocytopenia 2 (autosomal dominant)"""	THC2		10470851, 21211618	Standard	NM_014915		Approved	KIAA1074	uc009xku.1	Q9UPS8	OTTHUMG00000017851	ENST00000376087.4:c.4648delA	10.37:g.27303499delT	ENSP00000365255:p.Thr1550fs	Somatic		WXS	Illumina HiSeq	Phase_I	A6NH29|Q2TAZ3|Q6ZR14|Q9H1Q1|Q9NSK9|Q9NTD5|Q9NW69	Frame_Shift_Del	DEL	ENST00000376087.4	37	CCDS41499.1																																																																																				0.284	ANKRD26-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000047296.1			
AOC2	314	hgsc.bcm.edu	37	17	40996867	40996868	+	Frame_Shift_Ins	INS	-	-	G			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr17:40996867_40996868insG	ENST00000253799.3	+	1	251_252	c.224_225insG	c.(223-228)ctggggfs	p.LG75fs	AOC2_ENST00000452774.2_Frame_Shift_Ins_p.LG75fs	NM_009590.2	NP_033720.2	O75106	AOC2_HUMAN	amine oxidase, copper containing 2 (retina-specific)	75					amine metabolic process (GO:0009308)|catecholamine metabolic process (GO:0006584)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|plasma membrane (GO:0005886)	aliphatic-amine oxidase activity (GO:0052595)|aminoacetone:oxygen oxidoreductase(deaminating) activity (GO:0052594)|copper ion binding (GO:0005507)|electron carrier activity (GO:0009055)|phenethylamine:oxygen oxidoreductase (deaminating) activity (GO:0052596)|primary amine oxidase activity (GO:0008131)|quinone binding (GO:0048038)|tryptamine:oxygen oxidoreductase (deaminating) activity (GO:0052593)			NS(1)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(6)|lung(14)|ovary(4)|skin(2)	30		Breast(137;0.000143)		BRCA - Breast invasive adenocarcinoma(366;0.156)		ACCCAGCGGCTGGGGCCAGGGC	0.668																																																	0																																										SO:0001589	frameshift_variant	314			AF081363	CCDS11443.1, CCDS45690.1	17q21	2012-07-13				ENSG00000131480	1.4.3.21		549	protein-coding gene	gene with protein product		602268				9119395, 9722954	Standard	NM_001158		Approved	RAO, DAO2	uc002ibu.3	O75106		ENST00000253799.3:c.228dupG	17.37:g.40996871_40996871dupG	ENSP00000253799:p.Leu75fs	Somatic		WXS	Illumina HiSeq	Phase_I	A5PKW2|O00120|O75105|Q4TTW5|Q9UNY0	Frame_Shift_Ins	INS	ENST00000253799.3	37	CCDS11443.1																																																																																				0.668	AOC2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000452442.1		NM_009590, NM_001158	
AP4E1	23431	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	51216161	51216161	+	Missense_Mutation	SNP	G	G	T			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr15:51216161G>T	ENST00000261842.5	+	4	486	c.380G>T	c.(379-381)aGt>aTt	p.S127I	AP4E1_ENST00000560508.1_Missense_Mutation_p.S52I	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	127					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)		p.S127I(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		CTACATGAAAGTCATGAATTA	0.318																																																	1	Substitution - Missense(1)	kidney(1)											191.0	177.0	182.0					15																	51216161		2194	4294	6488	SO:0001583	missense	23431			AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.380G>T	15.37:g.51216161G>T	ENSP00000261842:p.Ser127Ile	Somatic		WXS	Illumina HiSeq	Phase_I	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Missense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	G	15.29	2.790627	0.50102	.	.	ENSG00000081014	ENST00000261842	T	0.28895	1.59	5.55	0.128	0.14733	Clathrin/coatomer adaptor, adaptin-like, N-terminal (1);Armadillo-like helical (1);Armadillo-type fold (1);	0.385848	0.33631	N	0.004704	T	0.30665	0.0772	L	0.38175	1.15	0.34723	D	0.728923	P;P	0.39071	0.57;0.658	B;P	0.48598	0.27;0.583	T	0.40384	-0.9566	10	0.62326	D	0.03	-2.2854	9.4165	0.38525	0.7657:0.0:0.2343:0.0	.	127;127	B4DM48;Q9UPM8	.;AP4E1_HUMAN	I	127	ENSP00000261842:S127I	ENSP00000261842:S127I	S	+	2	0	AP4E1	49003453	1.000000	0.71417	0.996000	0.52242	0.998000	0.95712	0.835000	0.27531	-0.075000	0.12798	0.591000	0.81541	AGT		0.318	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			
AP4E1	23431	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	15	51217400	51217400	+	Nonsense_Mutation	SNP	A	A	T			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr15:51217400A>T	ENST00000261842.5	+	5	632	c.526A>T	c.(526-528)Aaa>Taa	p.K176*	AP4E1_ENST00000560508.1_Nonsense_Mutation_p.K101*	NM_001252127.1|NM_007347.4	NP_001239056.1|NP_031373.2	Q9UPM8	AP4E1_HUMAN	adaptor-related protein complex 4, epsilon 1 subunit	176					intracellular protein transport (GO:0006886)|vesicle-mediated transport (GO:0016192)	coated pit (GO:0005905)|Golgi apparatus (GO:0005794)|membrane coat (GO:0030117)		p.K176*(1)		breast(1)|endometrium(6)|kidney(3)|large_intestine(10)|lung(5)|skin(2)	27				all cancers(107;0.000893)|GBM - Glioblastoma multiforme(94;0.00364)		AATAGAAGATAAACTTCAACA	0.353																																																	1	Substitution - Nonsense(1)	kidney(1)											91.0	83.0	86.0					15																	51217400		2196	4294	6490	SO:0001587	stop_gained	23431			AB030653	CCDS32240.1, CCDS58362.1	15q21.2	2014-09-17			ENSG00000081014	ENSG00000081014			573	protein-coding gene	gene with protein product		607244				10436028, 21620353	Standard	NM_007347		Approved	AP-4-EPSILON, SPG51	uc001zyx.2	Q9UPM8	OTTHUMG00000172458	ENST00000261842.5:c.526A>T	15.37:g.51217400A>T	ENSP00000261842:p.Lys176*	Somatic		WXS	Illumina HiSeq	Phase_I	A0AVD6|A1L4A9|A6NNX7|H0YKX4|Q68D31|Q9Y588	Nonsense_Mutation	SNP	ENST00000261842.5	37	CCDS32240.1	.	.	.	.	.	.	.	.	.	.	A	37	6.300420	0.97453	.	.	ENSG00000081014	ENST00000261842	.	.	.	5.53	5.53	0.82687	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.19147	T	0.46	-23.0417	14.8349	0.70175	1.0:0.0:0.0:0.0	.	.	.	.	X	176	.	ENSP00000261842:K176X	K	+	1	0	AP4E1	49004692	1.000000	0.71417	1.000000	0.80357	0.992000	0.81027	8.932000	0.92897	2.099000	0.63709	0.377000	0.23210	AAA		0.353	AP4E1-001	KNOWN	non_canonical_U12|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000418656.1			
B4GALT3	8703	hgsc.bcm.edu;ucsc.edu	37	1	161141850	161141851	+	Frame_Shift_Ins	INS	-	-	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr1:161141850_161141851insA	ENST00000319769.5	-	8	1159_1160	c.937_938insT	c.(937-939)tccfs	p.S313fs	PPOX_ENST00000535223.1_Intron|PPOX_ENST00000495483.1_Intron|B4GALT3_ENST00000367998.1_Frame_Shift_Ins_p.S313fs|PPOX_ENST00000432542.2_Intron|B4GALT3_ENST00000470882.1_5'UTR	NM_001199873.1|NM_003779.3	NP_001186802.1|NP_003770.1	O60512	B4GT3_HUMAN	UDP-Gal:betaGlcNAc beta 1,4- galactosyltransferase, polypeptide 3	313					carbohydrate metabolic process (GO:0005975)|cellular protein metabolic process (GO:0044267)|glycosaminoglycan metabolic process (GO:0030203)|keratan sulfate biosynthetic process (GO:0018146)|keratan sulfate metabolic process (GO:0042339)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|extracellular vesicular exosome (GO:0070062)|Golgi apparatus (GO:0005794)|Golgi membrane (GO:0000139)|integral component of membrane (GO:0016021)	beta-N-acetylglucosaminylglycopeptide beta-1,4-galactosyltransferase activity (GO:0003831)|galactosyltransferase activity (GO:0008378)|metal ion binding (GO:0046872)|N-acetyllactosamine synthase activity (GO:0003945)			cervix(1)|endometrium(5)|large_intestine(6)|lung(6)	18	all_cancers(52;3.73e-19)|Breast(13;0.000577)|all_hematologic(112;0.093)		BRCA - Breast invasive adenocarcinoma(70;0.00275)		N-Acetyl-D-glucosamine(DB00141)	TTGCGTCCAGGAATTCTGGGTA	0.505																																																	0																																										SO:0001589	frameshift_variant	8703			BC006099	CCDS1222.1	1q21-q23	2013-02-19			ENSG00000158850	ENSG00000158850		"""Beta 4-glycosyltransferases"""	926	protein-coding gene	gene with protein product		604014				9405390, 9597550	Standard	NM_001199873		Approved	beta4Gal-T3	uc001fys.2	O60512	OTTHUMG00000034348	ENST00000319769.5:c.938dupT	1.37:g.161141852_161141852dupA	ENSP00000320965:p.Ser313fs	Somatic		WXS	Illumina HiSeq	Phase_I	D3DVG3|O60910|Q9BPZ4|Q9H8T2	Frame_Shift_Ins	INS	ENST00000319769.5	37	CCDS1222.1																																																																																				0.505	B4GALT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083054.1		NM_003779	
C11orf24	53838	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	68029634	68029634	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr11:68029634G>A	ENST00000304271.6	-	4	1231	c.829C>T	c.(829-831)Ccc>Tcc	p.P277S	C11orf24_ENST00000530166.1_5'Flank|C11orf24_ENST00000533310.1_Intron	NM_022338.3	NP_071733.1	Q96F05	CK024_HUMAN	chromosome 11 open reading frame 24	277	Pro-rich.					Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)		p.P277S(1)		endometrium(3)|kidney(3)|large_intestine(3)|lung(3)|ovary(1)	13						GTGTTTGAGGGCATGGGTGTG	0.592																																					NSCLC(21;855 905 4198 36694)												1	Substitution - Missense(1)	kidney(1)											86.0	91.0	90.0					11																	68029634		2200	4294	6494	SO:0001583	missense	53838			AF264781	CCDS8180.1, CCDS73338.1	11q13.2	2014-01-08			ENSG00000171067	ENSG00000171067			1174	protein-coding gene	gene with protein product		610880				11401438, 24312644	Standard	NM_022338		Approved	DM4E3	uc001onr.4	Q96F05	OTTHUMG00000167478	ENST00000304271.6:c.829C>T	11.37:g.68029634G>A	ENSP00000307264:p.Pro277Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q9H2K4	Missense_Mutation	SNP	ENST00000304271.6	37	CCDS8180.1	.	.	.	.	.	.	.	.	.	.	G	14.87	2.665218	0.47677	.	.	ENSG00000171067	ENST00000304271	T	0.35048	1.33	4.5	2.59	0.31030	.	0.254221	0.20840	N	0.084728	T	0.24198	0.0586	L	0.34521	1.04	0.09310	N	0.999998	P	0.41784	0.762	B	0.42555	0.391	T	0.11251	-1.0595	10	0.10111	T	0.7	-7.1457	7.0504	0.25069	0.0936:0.334:0.5725:0.0	.	277	Q96F05	CK024_HUMAN	S	277	ENSP00000307264:P277S	ENSP00000307264:P277S	P	-	1	0	C11orf24	67786210	0.727000	0.28069	0.082000	0.20525	0.145000	0.21501	3.458000	0.53014	0.464000	0.27142	0.289000	0.19496	CCC		0.592	C11orf24-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000394750.1		NM_022338	
C17orf49	124944	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	6919830	6919830	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr17:6919830A>G	ENST00000439424.2	+	4	311	c.235A>G	c.(235-237)Act>Gct	p.T79A	RP11-589P10.7_ENST00000572547.1_RNA|MIR497HG_ENST00000572453.1_RNA|C17orf49_ENST00000546495.1_Missense_Mutation_p.T79A|MIR497HG_ENST00000443997.1_RNA|MIR497HG_ENST00000385194.1_RNA|C17orf49_ENST00000546760.1_Missense_Mutation_p.T79A|C17orf49_ENST00000552402.1_Missense_Mutation_p.T45A|C17orf49_ENST00000552775.1_Missense_Mutation_p.T53A|MIR497HG_ENST00000385056.1_RNA|C17orf49_ENST00000547709.1_3'UTR|RNASEK-C17orf49_ENST00000547302.2_Silent_p.P119P|AC040977.1_ENST00000593646.1_5'Flank	NM_001142798.2|NM_174893.3	NP_001136270.1|NP_777553.1	Q8IXM2	BAP18_HUMAN	chromosome 17 open reading frame 49	79	SANT.				chromatin modification (GO:0016568)	MLL1 complex (GO:0071339)|NURF complex (GO:0016589)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)	p.T79A(2)		kidney(1)|large_intestine(2)|ovary(1)	4						GATAAAGGCCACTGTGAAACG	0.527																																																	2	Substitution - Missense(2)	kidney(2)											117.0	123.0	121.0					17																	6919830		2203	4300	6503	SO:0001583	missense	124944			AK055800	CCDS32542.1, CCDS45595.1, CCDS45596.1	17p13.1	2013-02-11			ENSG00000258315	ENSG00000258315			28737	protein-coding gene	gene with protein product	"""BPTF associated protein of 18 kDa"", ""human embryo lung cellular protein interacting with SARS-CoV nsp-10"""						Standard	NM_174893		Approved	MGC49942, BAP18, HEPIS		Q8IXM2	OTTHUMG00000170147	ENST00000439424.2:c.235A>G	17.37:g.6919830A>G	ENSP00000411851:p.Thr79Ala	Somatic		WXS	Illumina HiSeq	Phase_I	B4DIV3|C9J4G0|E9PB29	Missense_Mutation	SNP	ENST00000439424.2	37	CCDS32542.1	.	.	.	.	.	.	.	.	.	.	A	11.45	1.642278	0.29246	.	.	ENSG00000161939;ENSG00000161939;ENSG00000258315;ENSG00000258315;ENSG00000258315;ENSG00000258315;ENSG00000258315	ENST00000293804;ENST00000455303;ENST00000546495;ENST00000546760;ENST00000552402;ENST00000439424;ENST00000552775	.	.	.	4.89	4.89	0.63831	SANT domain, DNA binding (1);	0.057545	0.64402	D	0.000002	T	0.30008	0.0751	N	0.21282	0.65	0.30126	N	0.805252	B;B;B;B	0.23854	0.009;0.092;0.004;0.038	B;B;B;B	0.29176	0.022;0.099;0.009;0.069	T	0.35624	-0.9781	8	0.11485	T	0.65	-18.4508	7.3075	0.26455	0.9012:0.0:0.0988:0.0	.	45;79;79;53	E9PB29;C9J4G0;Q8IXM2;F8W1H0	.;.;BAP18_HUMAN;.	A	79;45;79;79;45;79;53	.	ENSP00000411851:T79A	T	+	1	0	AC040977.1;C17orf49	6860554	1.000000	0.71417	1.000000	0.80357	0.998000	0.95712	6.161000	0.71868	1.828000	0.53243	0.533000	0.62120	ACT		0.527	C17orf49-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000407666.1		NM_174893	
LAMP5	24141	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	20	9496942	9496942	+	Missense_Mutation	SNP	A	A	G			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr20:9496942A>G	ENST00000246070.2	+	4	901	c.409A>G	c.(409-411)Agg>Ggg	p.R137G	RP5-1119D9.4_ENST00000443469.1_RNA|LAMP5_ENST00000427562.2_Missense_Mutation_p.R93G	NM_012261.3	NP_036393.1	Q9UJQ1	LAMP5_HUMAN	lysosomal-associated membrane protein family, member 5	137						cytoplasmic vesicle membrane (GO:0030659)|dendrite membrane (GO:0032590)|early endosome membrane (GO:0031901)|endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116)|endosome membrane (GO:0010008)|growth cone membrane (GO:0032584)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|recycling endosome membrane (GO:0055038)		p.R137G(1)									GGCGACTTGGAGGCTGAGCAA	0.582																																																	1	Substitution - Missense(1)	kidney(1)											98.0	89.0	92.0					20																	9496942		2203	4300	6503	SO:0001583	missense	0			AL121740	CCDS13106.1, CCDS56177.1	20p12	2013-03-14	2011-11-25	2011-11-25	ENSG00000125869	ENSG00000125869			16097	protein-coding gene	gene with protein product	"""brain and dendritic cell associated LAMP"""	614641	"""chromosome 20 open reading frame 103"""	C20orf103		11780052, 21642595	Standard	NM_012261		Approved	dJ1119D9.3, BAD-LAMP, UNC-43	uc002wni.2	Q9UJQ1	OTTHUMG00000031851	ENST00000246070.2:c.409A>G	20.37:g.9496942A>G	ENSP00000246070:p.Arg137Gly	Somatic		WXS	Illumina HiSeq	Phase_I	B4DHZ7|B7Z9Z9	Missense_Mutation	SNP	ENST00000246070.2	37	CCDS13106.1	.	.	.	.	.	.	.	.	.	.	A	14.66	2.601091	0.46423	.	.	ENSG00000125869	ENST00000246070;ENST00000427562	T;T	0.32988	1.43;1.43	5.98	4.88	0.63580	.	0.234407	0.52532	D	0.000070	T	0.17408	0.0418	N	0.14661	0.345	0.44956	D	0.997972	B;B	0.29136	0.01;0.234	B;B	0.26969	0.033;0.075	T	0.07177	-1.0786	9	.	.	.	-7.3705	11.4518	0.50158	0.8492:0.1508:0.0:0.0	.	93;137	Q9UJQ1-2;Q9UJQ1	.;CT103_HUMAN	G	137;93	ENSP00000246070:R137G;ENSP00000406360:R93G	.	R	+	1	2	C20orf103	9444942	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	6.590000	0.74085	1.076000	0.40961	0.482000	0.46254	AGG		0.582	LAMP5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000077946.2		NM_012261	
CACHD1	57685	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	65143848	65143848	+	Silent	SNP	T	T	C			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr1:65143848T>C	ENST00000371073.2	+	23	3099	c.3099T>C	c.(3097-3099)tgT>tgC	p.C1033C	CACHD1_ENST00000495994.1_3'UTR|CACHD1_ENST00000290039.5_Silent_p.C982C			Q5VU97	CAHD1_HUMAN	cache domain containing 1	1033					calcium ion transport (GO:0006816)	integral component of membrane (GO:0016021)		p.C982C(1)		breast(4)|endometrium(3)|kidney(3)|large_intestine(20)|lung(14)|ovary(2)|pancreas(1)|prostate(5)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	55						GCAGGGACTGTTTTGGGGTGC	0.507																																																	1	Substitution - coding silent(1)	kidney(1)											118.0	108.0	111.0					1																	65143848		2203	4300	6503	SO:0001819	synonymous_variant	57685			AB046793	CCDS628.2	1p31.3	2008-02-05	2005-10-11	2005-10-11	ENSG00000158966	ENSG00000158966			29314	protein-coding gene	gene with protein product			"""von Willebrand factor type A and cache domain containing 1"""	VWCD1		10997877	Standard	NM_020925		Approved	KIAA1573	uc001dbo.1	Q5VU97	OTTHUMG00000009030	ENST00000371073.2:c.3099T>C	1.37:g.65143848T>C		Somatic		WXS	Illumina HiSeq	Phase_I	Q49AE9|Q658T4|Q7Z3P2|Q9H7W4|Q9H9W3|Q9HCJ9	Silent	SNP	ENST00000371073.2	37																																																																																					0.507	CACHD1-201	KNOWN	basic	protein_coding	protein_coding			NM_020925	
CACNG2	10369	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	36960524	36960524	+	Silent	SNP	G	G	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr22:36960524G>A	ENST00000300105.6	-	4	1827	c.846C>T	c.(844-846)acC>acT	p.T282T	RP5-1119A7.17_ENST00000562756.1_RNA	NM_006078.3	NP_006069.1	Q9Y698	CCG2_HUMAN	calcium channel, voltage-dependent, gamma subunit 2	282					membrane depolarization (GO:0051899)|membrane hyperpolarization (GO:0060081)|neuromuscular junction development (GO:0007528)|regulation of alpha-amino-3-hydroxy-5-methyl-4-isoxazole propionate selective glutamate receptor activity (GO:2000311)|synaptic transmission (GO:0007268)|transmission of nerve impulse (GO:0019226)|transport (GO:0006810)	alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid selective glutamate receptor complex (GO:0032281)|endocytic vesicle membrane (GO:0030666)|plasma membrane (GO:0005886)|voltage-gated calcium channel complex (GO:0005891)	voltage-gated calcium channel activity (GO:0005245)	p.T282T(1)		breast(1)|endometrium(2)|kidney(1)|large_intestine(7)|lung(4)|prostate(1)|skin(1)|urinary_tract(1)	18						CGGTGGGCGTGGTGGCGGCCT	0.607																																																	1	Substitution - coding silent(1)	kidney(1)											66.0	64.0	65.0					22																	36960524		2203	4300	6503	SO:0001819	synonymous_variant	10369			AF096322	CCDS13931.1	22q13.1	2006-08-01			ENSG00000166862	ENSG00000166862		"""Calcium channel subunits"""	1406	protein-coding gene	gene with protein product		602911					Standard	NM_006078		Approved	stargazin, MGC138502, MGC138504	uc003aps.2	Q9Y698	OTTHUMG00000030612	ENST00000300105.6:c.846C>T	22.37:g.36960524G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q2M1M1|Q5TGT3|Q9UGZ7	Silent	SNP	ENST00000300105.6	37	CCDS13931.1																																																																																				0.607	CACNG2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000075500.2			
CBLN1	869	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	16	49313372	49313372	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr16:49313372G>C	ENST00000219197.6	-	3	890	c.525C>G	c.(523-525)aaC>aaG	p.N175K	CBLN1_ENST00000536749.1_Missense_Mutation_p.N175K	NM_004352.3	NP_004343.1	P23435	CBLN1_HUMAN	cerebellin 1 precursor	175	C1q. {ECO:0000255|PROSITE- ProRule:PRU00368}.|Necessary for interaction with CBLN3, and homotrimerization. {ECO:0000250}.				cerebellar granule cell differentiation (GO:0021707)|heterophilic cell-cell adhesion (GO:0007157)|nervous system development (GO:0007399)|positive regulation of synapse assembly (GO:0051965)|protein secretion (GO:0009306)|synaptic transmission (GO:0007268)	cell junction (GO:0030054)|extracellular region (GO:0005576)|postsynaptic membrane (GO:0045211)		p.N175K(1)		breast(1)|kidney(3)|large_intestine(2)|lung(3)	9		all_cancers(37;0.0766)|all_lung(18;0.24)				CCCCCATCAAGTTTCCCCGCT	0.612																																																	1	Substitution - Missense(1)	kidney(1)											112.0	106.0	108.0					16																	49313372		2200	4300	6500	SO:0001583	missense	869			M58583	CCDS10736.1	16q12.1	2008-02-05			ENSG00000102924	ENSG00000102924			1543	protein-coding gene	gene with protein product		600432				7877445, 1704129	Standard	NM_004352		Approved		uc002efq.3	P23435	OTTHUMG00000133148	ENST00000219197.6:c.525C>G	16.37:g.49313372G>C	ENSP00000219197:p.Asn175Lys	Somatic		WXS	Illumina HiSeq	Phase_I	B2RAN9|P02682|Q52M09	Missense_Mutation	SNP	ENST00000219197.6	37	CCDS10736.1	.	.	.	.	.	.	.	.	.	.	G	19.87	3.908140	0.72868	.	.	ENSG00000102924	ENST00000219197;ENST00000536749	T;T	0.37058	1.22;1.22	5.49	5.49	0.81192	Tumour necrosis factor-like (2);Complement C1q protein (3);	0.000000	0.85682	D	0.000000	T	0.38719	0.1051	L	0.28740	0.885	0.80722	D	1	P	0.50156	0.932	P	0.56216	0.794	T	0.03025	-1.1081	10	0.15952	T	0.53	-19.617	13.0149	0.58751	0.0741:0.0:0.9259:0.0	.	175	P23435	CBLN1_HUMAN	K	175	ENSP00000219197:N175K;ENSP00000444651:N175K	ENSP00000219197:N175K	N	-	3	2	CBLN1	47870873	1.000000	0.71417	1.000000	0.80357	0.997000	0.91878	7.901000	0.87382	2.716000	0.92895	0.655000	0.94253	AAC		0.612	CBLN1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256845.4		NM_004352	
CFH	3075	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	196695938	196695938	+	Missense_Mutation	SNP	G	G	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr1:196695938G>A	ENST00000367429.4	+	14	2344	c.2104G>A	c.(2104-2106)Gcc>Acc	p.A702T		NM_000186.3	NP_000177.2	P08603	CFAH_HUMAN	complement factor H	702	Sushi 12. {ECO:0000255|PROSITE- ProRule:PRU00302}.				complement activation (GO:0006956)|complement activation, alternative pathway (GO:0006957)|innate immune response (GO:0045087)|regulation of complement activation (GO:0030449)	blood microparticle (GO:0072562)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)	heparan sulfate proteoglycan binding (GO:0043395)|heparin binding (GO:0008201)	p.A702T(1)		NS(3)|breast(4)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(8)|large_intestine(24)|lung(33)|ovary(1)|prostate(5)|skin(9)|stomach(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	101						ACATGGCTGGGCCCAGCTTTC	0.363																																																	1	Substitution - Missense(1)	kidney(1)											120.0	120.0	120.0					1																	196695938		2203	4300	6503	SO:0001583	missense	3075			Y00716	CCDS1385.1	1q32	2014-09-17	2004-08-09	2004-08-12	ENSG00000000971	ENSG00000000971		"""Complement system"""	4883	protein-coding gene	gene with protein product	"""beta-1H"", ""H factor 2 (complement)"", ""age-related maculopathy susceptibility 1"""	134370	"""H factor 1 (complement)"""	HF, HF1, HF2		2889480, 2963625	Standard	NM_000186		Approved	HUS, FHL1, ARMS1, ARMD4	uc001gtj.4	P08603	OTTHUMG00000035607	ENST00000367429.4:c.2104G>A	1.37:g.196695938G>A	ENSP00000356399:p.Ala702Thr	Somatic		WXS	Illumina HiSeq	Phase_I	A5PL14|P78435|Q14570|Q2TAZ5|Q38G77|Q5TFM3|Q8N708|Q9NU86	Missense_Mutation	SNP	ENST00000367429.4	37	CCDS1385.1	.	.	.	.	.	.	.	.	.	.	G	11.06	1.528785	0.27387	.	.	ENSG00000000971	ENST00000367429	T	0.63417	-0.04	5.8	0.301	0.15781	Complement control module (2);Sushi/SCR/CCP (3);	.	.	.	.	T	0.44561	0.1299	L	0.33668	1.02	0.09310	N	1	B	0.19706	0.038	B	0.16289	0.015	T	0.23940	-1.0174	9	0.22706	T	0.39	.	6.3376	0.21304	0.2985:0.0:0.5767:0.1248	.	702	P08603	CFAH_HUMAN	T	702	ENSP00000356399:A702T	ENSP00000356399:A702T	A	+	1	0	CFH	194962561	0.000000	0.05858	0.000000	0.03702	0.000000	0.00434	-0.122000	0.10627	0.036000	0.15547	-2.134000	0.00341	GCC		0.363	CFH-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000086412.2		NM_000186	
COL11A2	1302	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	33133477	33133477	+	Silent	SNP	G	G	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr6:33133477G>A	ENST00000374708.4	-	61	4599	c.4341C>T	c.(4339-4341)gcC>gcT	p.A1447A	COL11A2_ENST00000374714.1_Silent_p.A1507A|COL11A2_ENST00000361917.1_Silent_p.A1426A|COL11A2_ENST00000395197.1_Silent_p.A1473A|COL11A2_ENST00000341947.2_Silent_p.A1533A|COL11A2_ENST00000374712.1_Silent_p.A1452A|COL11A2_ENST00000357486.1_Silent_p.A1512A|COL11A2_ENST00000374713.1_Silent_p.A1486A|COL11A2_ENST00000477772.1_5'UTR	NM_080681.2	NP_542412.2	P13942	COBA2_HUMAN	collagen, type XI, alpha 2	1533	Collagen-like 8.|Triple-helical region.				cartilage development (GO:0051216)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|palate development (GO:0060021)|sensory perception of sound (GO:0007605)|skeletal system development (GO:0001501)|soft palate development (GO:0060023)	collagen type XI trimer (GO:0005592)|endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)	extracellular matrix structural constituent conferring tensile strength (GO:0030020)|metal ion binding (GO:0046872)|protein binding, bridging (GO:0030674)	p.A1533A(1)		biliary_tract(1)|breast(1)|cervix(2)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|liver(1)|lung(27)|ovary(5)|prostate(5)|skin(6)	68						GACTGCCGGGGGCTCCCCCGG	0.642																																					Melanoma(1;90 116 3946 5341 17093)												1	Substitution - coding silent(1)	kidney(1)											52.0	54.0	53.0					6																	33133477		2203	4300	6503	SO:0001819	synonymous_variant	1302			U32169	CCDS43452.1, CCDS54992.1	6p21.3	2013-01-16			ENSG00000204248	ENSG00000204248		"""Collagens"""	2187	protein-coding gene	gene with protein product		120290		DFNA13, DFNB53		7559422, 10581026	Standard	NM_080679		Approved	HKE5	uc003ocx.1	P13942	OTTHUMG00000031036	ENST00000374708.4:c.4341C>T	6.37:g.33133477G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A6NLX2|E7ER90|Q07751|Q13271|Q13272|Q13273|Q5JP94|Q5SUI8|Q7Z6C3|Q99866|Q9UIP9	Silent	SNP	ENST00000374708.4	37	CCDS43452.1																																																																																				0.642	COL11A2-001	KNOWN	not_organism_supported|basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000076032.2			
CYTH1	9267	broad.mit.edu;ucsc.edu	37	17	76677108	76677108	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr17:76677108C>A	ENST00000446868.3	-	12	978	c.908G>T	c.(907-909)gGa>gTa	p.G303V	CYTH1_ENST00000589297.1_Missense_Mutation_p.G244V|CYTH1_ENST00000586175.1_5'UTR|CYTH1_ENST00000585509.1_Missense_Mutation_p.G244V|CYTH1_ENST00000591455.1_Missense_Mutation_p.G302V|CYTH1_ENST00000589296.1_Intron|CYTH1_ENST00000361101.4_Missense_Mutation_p.G303V			Q15438	CYH1_HUMAN	cytohesin 1	303	PH. {ECO:0000255|PROSITE- ProRule:PRU00145}.				establishment of epithelial cell polarity (GO:0090162)|positive regulation of GTPase activity (GO:0043547)|regulation of ARF protein signal transduction (GO:0032012)|regulation of cell adhesion (GO:0030155)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|extrinsic component of cytoplasmic side of plasma membrane (GO:0031234)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ARF guanyl-nucleotide exchange factor activity (GO:0005086)|lipid binding (GO:0008289)	p.G303V(1)		endometrium(4)|kidney(1)|large_intestine(2)|lung(7)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)	19						AGGGATGATTCCACGGGGCTC	0.468																																																	1	Substitution - Missense(1)	kidney(1)											99.0	103.0	102.0					17																	76677108		2203	4300	6503	SO:0001583	missense	9267			M85169	CCDS32754.1, CCDS42392.2	17q25	2014-05-02	2008-08-14	2008-08-14	ENSG00000108669	ENSG00000108669		"""Pleckstrin homology (PH) domain containing"""	9501	protein-coding gene	gene with protein product		182115	"""pleckstrin homology, Sec7 and coiled-coil domains 1"""	PSCD1		1511013, 8449036, 21628335, 20018626	Standard	XM_006722180		Approved	B2-1, D17S811E, cytohesin-1	uc002jvw.3	Q15438	OTTHUMG00000150253	ENST00000446868.3:c.908G>T	17.37:g.76677108C>A	ENSP00000389095:p.Gly303Val	Somatic		WXS	Illumina GAIIx	Phase_I	A6NFW7|B7Z1T4|Q9P123|Q9P124	Missense_Mutation	SNP	ENST00000446868.3	37		.	.	.	.	.	.	.	.	.	.	C	25.2	4.608780	0.87258	.	.	ENSG00000108669	ENST00000446868;ENST00000361101;ENST00000539525;ENST00000537048;ENST00000262763;ENST00000392453	T;T	0.77489	-1.1;-1.1	4.91	4.91	0.64330	.	0.000000	0.85682	D	0.000000	D	0.92499	0.7618	H	0.97465	4.01	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.95046	0.8182	10	0.62326	D	0.03	.	17.6968	0.88283	0.0:1.0:0.0:0.0	.	302	Q15438-2	.	V	303;303;244;244;302;140	ENSP00000389095:G303V;ENSP00000354398:G303V	ENSP00000262763:G302V	G	-	2	0	CYTH1	74188703	1.000000	0.71417	0.806000	0.32338	0.980000	0.70556	7.667000	0.83888	2.265000	0.75225	0.467000	0.42956	GGA		0.468	CYTH1-001	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000317099.1		NM_004762	
SNIP1	79753	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	38022628	38022628	+	5'Flank	SNP	C	C	T			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr1:38022628C>T	ENST00000296215.6	-	0	0				DNALI1_ENST00000296218.7_Silent_p.Y33Y|DNALI1_ENST00000541606.1_5'UTR|SNIP1_ENST00000468040.1_5'Flank	NM_024700.3	NP_078976.2	Q8TAD8	SNIP1_HUMAN	Smad nuclear interacting protein 1						I-kappaB kinase/NF-kappaB signaling (GO:0007249)|production of miRNAs involved in gene silencing by miRNA (GO:0035196)|regulation of transcription, DNA-templated (GO:0006355)	nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.Y33Y(1)		breast(2)|cervix(2)|endometrium(1)|large_intestine(3)|lung(15)|ovary(1)|upper_aerodigestive_tract(1)	25		Myeloproliferative disorder(586;0.0393)				TGCTCAAGTACGACACCCCAG	0.602																																																	1	Substitution - coding silent(1)	kidney(1)											68.0	66.0	67.0					1																	38022628		2203	4300	6503	SO:0001631	upstream_gene_variant	7802				CCDS419.1	1p34.3	2010-07-06			ENSG00000163877	ENSG00000163877			30587	protein-coding gene	gene with protein product		608241				10887155, 15378006	Standard	NM_024700		Approved		uc001cbi.4	Q8TAD8	OTTHUMG00000004225		1.37:g.38022628C>T	Exception_encountered	Somatic		WXS	Illumina HiSeq	Phase_I	Q96SP9|Q9H9T7	Silent	SNP	ENST00000296215.6	37	CCDS419.1																																																																																				0.602	SNIP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000012169.2		NM_024700	
DNTTIP2	30836	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	94335473	94335473	+	Silent	SNP	G	G	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr1:94335473G>A	ENST00000436063.2	-	7	2262	c.2205C>T	c.(2203-2205)atC>atT	p.I735I		NM_014597.4	NP_055412.2	Q5QJE6	TDIF2_HUMAN	deoxynucleotidyltransferase, terminal, interacting protein 2	735					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleolus (GO:0005730)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.I735I(1)		NS(1)|cervix(1)|endometrium(4)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(8)|lung(15)|ovary(1)|prostate(2)|upper_aerodigestive_tract(1)	38		all_lung(203;0.0111)|Lung NSC(277;0.0347)		all cancers(265;0.00679)|GBM - Glioblastoma multiforme(16;0.0278)|Epithelial(280;0.128)		TTTCAGCCATGATCTCTGAGT	0.333																																																	1	Substitution - coding silent(1)	kidney(1)											117.0	109.0	112.0					1																	94335473		1830	4076	5906	SO:0001819	synonymous_variant	30836			AY394925	CCDS44174.1	1p22.1	2008-02-05			ENSG00000067334	ENSG00000067334			24013	protein-coding gene	gene with protein product	"""acidic 82 kDa protein mRNA"""	611199				15047147	Standard	NM_014597		Approved	HSU15552, ERBP, TdIF2	uc001dqf.3	Q5QJE6	OTTHUMG00000010268	ENST00000436063.2:c.2205C>T	1.37:g.94335473G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q12987|Q53H59|Q5TFJ4|Q6TLI0|Q76MJ8|Q86WX9	Silent	SNP	ENST00000436063.2	37	CCDS44174.1																																																																																				0.333	DNTTIP2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000028317.2		NM_014597	
ELFN2	114794	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	22	37770000	37770000	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr22:37770000C>G	ENST00000402918.2	-	3	2360	c.1575G>C	c.(1573-1575)gaG>gaC	p.E525D	ELFN2_ENST00000435824.1_5'Flank|RP1-63G5.5_ENST00000430883.1_RNA|RP1-63G5.8_ENST00000609322.1_RNA	NM_052906.3	NP_443138.2	Q5R3F8	PPR29_HUMAN	extracellular leucine-rich repeat and fibronectin type III domain containing 2	525					negative regulation of phosphatase activity (GO:0010923)	extracellular space (GO:0005615)|integral component of membrane (GO:0016021)	phosphatase binding (GO:0019902)|protein phosphatase inhibitor activity (GO:0004864)	p.E525D(1)		NS(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(4)|lung(13)|ovary(1)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(3)|urinary_tract(1)	35	Melanoma(58;0.0574)					CCTGGCCGTTCTCGAGGTCCG	0.602																																																	1	Substitution - Missense(1)	kidney(1)											70.0	70.0	70.0					22																	37770000		2203	4300	6503	SO:0001583	missense	114794			BC041596	CCDS33642.1	22q13.1	2013-02-11	2011-10-27	2011-10-27	ENSG00000166897	ENSG00000166897		"""Serine/threonine phosphatases / Protein phosphatase 1, regulatory subunits"", ""Fibronectin type III domain containing"""	29396	protein-coding gene	gene with protein product			"""leucine rich repeat containing 62"", ""extracellular leucine-rich repeat and fibronectin type III containing 2"", ""extracellular leucine-rich repeat and fibronectin type III domain containing 2"", ""protein phosphatase 1, regulatory subunit 29"""	LRRC62, PPP1R29		17868438	Standard	XR_244427		Approved	dJ63G5.3, KIAA1904	uc003asq.4	Q5R3F8	OTTHUMG00000150558	ENST00000402918.2:c.1575G>C	22.37:g.37770000C>G	ENSP00000385277:p.Glu525Asp	Somatic		WXS	Illumina HiSeq	Phase_I	Q96PY3	Missense_Mutation	SNP	ENST00000402918.2	37	CCDS33642.1	.	.	.	.	.	.	.	.	.	.	C	0.019	-1.454188	0.01071	.	.	ENSG00000166897	ENST00000349653;ENST00000402918	T;T	0.29917	1.55;1.55	4.79	1.25	0.21368	.	0.165305	0.51477	D	0.000083	T	0.05868	0.0153	N	0.00392	-1.555	0.30131	N	0.804813	B	0.06786	0.001	B	0.04013	0.001	T	0.28776	-1.0033	10	0.11794	T	0.64	-32.2327	3.528	0.07766	0.1328:0.4055:0.3604:0.1013	.	525	Q5R3F8	PPR29_HUMAN	D	525	ENSP00000300147:E525D;ENSP00000385277:E525D	ENSP00000300147:E525D	E	-	3	2	ELFN2	36099946	1.000000	0.71417	0.999000	0.59377	0.179000	0.23085	0.688000	0.25422	0.969000	0.38237	0.511000	0.50034	GAG		0.602	ELFN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000318900.2		NM_052906	
FAM83C	128876	broad.mit.edu;hgsc.bcm.edu	37	20	33875579	33875579	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr20:33875579C>T	ENST00000374408.3	-	4	1099	c.1003G>A	c.(1003-1005)Gtc>Atc	p.V335I	FAM83C-AS1_ENST00000429167.1_RNA|EIF6_ENST00000374450.3_5'Flank	NM_178468.5	NP_848563.1	Q9BQN1	FA83C_HUMAN	family with sequence similarity 83, member C	335								p.V335I(1)|p.V335F(1)		central_nervous_system(2)|endometrium(3)|kidney(1)|large_intestine(6)|lung(19)|ovary(2)|prostate(2)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	40			BRCA - Breast invasive adenocarcinoma(18;0.00252)			GGGCTTGGGACATCAGGCCTG	0.667																																																	2	Substitution - Missense(2)	lung(1)|kidney(1)											103.0	83.0	90.0					20																	33875579		2203	4300	6503	SO:0001583	missense	128876			AL121753	CCDS13251.1	20q11.22	2011-04-01	2006-03-23	2006-03-23	ENSG00000125998	ENSG00000125998			16121	protein-coding gene	gene with protein product			"""chromosome 20 open reading frame 128"""	C20orf128			Standard	NM_178468		Approved	dJ614O4.7	uc021wck.1	Q9BQN1	OTTHUMG00000032332	ENST00000374408.3:c.1003G>A	20.37:g.33875579C>T	ENSP00000363529:p.Val335Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q14D67|Q5JWN6|Q8N276	Missense_Mutation	SNP	ENST00000374408.3	37	CCDS13251.1	.	.	.	.	.	.	.	.	.	.	C	0.004	-2.365599	0.00212	.	.	ENSG00000125998	ENST00000374408	T	0.06687	3.27	4.53	-4.06	0.03986	.	1.148530	0.06725	N	0.775559	T	0.02727	0.0082	N	0.03050	-0.425	0.09310	N	1	B	0.02656	0.0	B	0.01281	0.0	T	0.47674	-0.9099	10	0.09843	T	0.71	-4.7306	7.0441	0.25037	0.0:0.4394:0.1348:0.4259	.	335	Q9BQN1	FA83C_HUMAN	I	335	ENSP00000363529:V335I	ENSP00000363529:V335I	V	-	1	0	FAM83C	33338993	0.000000	0.05858	0.000000	0.03702	0.032000	0.12392	0.120000	0.15647	-0.488000	0.06726	-0.340000	0.08031	GTC		0.667	FAM83C-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000078854.3			
GABRQ	55879	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	X	151815617	151815617	+	Missense_Mutation	SNP	G	G	C			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chrX:151815617G>C	ENST00000370306.2	+	4	535	c.515G>C	c.(514-516)cGg>cCg	p.R172P		NM_018558.2	NP_061028.3	Q9UN88	GBRT_HUMAN	gamma-aminobutyric acid (GABA) A receptor, theta	172					neurotransmitter transport (GO:0006836)|signal transduction (GO:0007165)	cell junction (GO:0030054)|chloride channel complex (GO:0034707)|integral component of plasma membrane (GO:0005887)|postsynaptic membrane (GO:0045211)|receptor complex (GO:0043235)	chloride channel activity (GO:0005254)|extracellular ligand-gated ion channel activity (GO:0005230)|GABA-A receptor activity (GO:0004890)|neurotransmitter transporter activity (GO:0005326)|transmembrane signaling receptor activity (GO:0004888)	p.R172P(1)		breast(1)|central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(9)|lung(25)|ovary(3)|pancreas(2)|prostate(2)|skin(3)|upper_aerodigestive_tract(1)	52	Acute lymphoblastic leukemia(192;6.56e-05)				Acamprosate(DB00659)|Alprazolam(DB00404)|Amoxapine(DB00543)|Bromazepam(DB01558)|Butabarbital(DB00237)|Butalbital(DB00241)|Chlordiazepoxide(DB00475)|Clobazam(DB00349)|Clonazepam(DB01068)|Clorazepate(DB00628)|Desflurane(DB01189)|Diazepam(DB00829)|Enflurane(DB00228)|Ergoloid mesylate(DB01049)|Estazolam(DB01215)|Eszopiclone(DB00402)|Ethchlorvynol(DB00189)|Etomidate(DB00292)|Flumazenil(DB01205)|Flurazepam(DB00690)|Glutethimide(DB01437)|Halazepam(DB00801)|Halothane(DB01159)|Isoflurane(DB00753)|Lorazepam(DB00186)|Meprobamate(DB00371)|Methoxyflurane(DB01028)|Methyprylon(DB01107)|Midazolam(DB00683)|Nitrazepam(DB01595)|Olanzapine(DB00334)|Oxazepam(DB00842)|Pentobarbital(DB00312)|Prazepam(DB01588)|Primidone(DB00794)|Propofol(DB00818)|Quazepam(DB01589)|Sevoflurane(DB01236)|Talbutal(DB00306)|Temazepam(DB00231)|Topiramate(DB00273)|Triazolam(DB00897)	GGAACGGTGCGGTACGGCATC	0.517																																																	1	Substitution - Missense(1)	kidney(1)											150.0	109.0	123.0					X																	151815617		2203	4300	6503	SO:0001583	missense	55879			U47334	CCDS14707.1	Xq28	2012-06-22	2012-02-03		ENSG00000147402	ENSG00000268089		"""GABA receptors"", ""Ligand-gated ion channels / GABA(A) receptors"""	14454	protein-coding gene	gene with protein product	"""GABA(A) receptor, theta"""	300349	"""gamma-aminobutyric acid (GABA) receptor, theta"""			10804200, 10449790	Standard	NM_018558		Approved	THETA	uc004ffp.1	Q9UN88	OTTHUMG00000022649	ENST00000370306.2:c.515G>C	X.37:g.151815617G>C	ENSP00000359329:p.Arg172Pro	Somatic		WXS	Illumina HiSeq	Phase_I	A6NFN1|Q32MB4|Q9NZK8	Missense_Mutation	SNP	ENST00000370306.2	37	CCDS14707.1	.	.	.	.	.	.	.	.	.	.	G	9.661	1.144021	0.21205	.	.	ENSG00000147402	ENST00000370306	T	0.78126	-1.15	5.19	-4.81	0.03180	Neurotransmitter-gated ion-channel ligand-binding (3);	0.882556	0.09422	N	0.804240	T	0.74688	0.3749	L	0.52573	1.65	0.19300	N	0.999977	P	0.42941	0.794	P	0.50109	0.631	T	0.69289	-0.5184	10	0.66056	D	0.02	.	6.8973	0.24262	0.6136:0.0:0.1978:0.1886	.	172	Q9UN88	GBRT_HUMAN	P	172	ENSP00000359329:R172P	ENSP00000359329:R172P	R	+	2	0	GABRQ	151566273	0.222000	0.23652	0.005000	0.12908	0.006000	0.05464	1.825000	0.39081	-1.042000	0.03262	-0.269000	0.10298	CGG		0.517	GABRQ-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000058763.2		NM_018558	
HIST1H2BO	8348	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	27861305	27861305	+	Missense_Mutation	SNP	C	C	T			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr6:27861305C>T	ENST00000303806.4	+	1	103	c.65C>T	c.(64-66)gCc>gTc	p.A22V	HIST1H2AM_ENST00000359611.2_5'Flank|HIST1H3J_ENST00000359303.2_5'Flank|HIST1H3J_ENST00000479986.1_5'Flank	NM_003527.4	NP_003518.2	P23527	H2B1O_HUMAN	histone cluster 1, H2bo	22					chromatin organization (GO:0006325)|nucleosome assembly (GO:0006334)	nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)	DNA binding (GO:0003677)	p.A22V(1)									GTAACCAAGGCCCAGAAAAAG	0.547																																																	1	Substitution - Missense(1)	kidney(1)											87.0	87.0	87.0					6																	27861305		2203	4300	6503	SO:0001583	missense	8348			X57138	CCDS4640.1	6p22.1	2011-01-27	2006-10-11	2003-02-21	ENSG00000196331			"""Histones / Replication-dependent"""	4758	protein-coding gene	gene with protein product		602808	"""H2B histone family, member N"", ""histone 1, H2bo"""	H2BFN		1768865, 12408966	Standard	NM_003527		Approved	H2B/n, H2B.2	uc003nkc.1	P23527	OTTHUMG00000014493	ENST00000303806.4:c.65C>T	6.37:g.27861305C>T	ENSP00000303408:p.Ala22Val	Somatic		WXS	Illumina HiSeq	Phase_I	Q3KPI7|Q8TCV6	Missense_Mutation	SNP	ENST00000303806.4	37	CCDS4640.1	.	.	.	.	.	.	.	.	.	.	C	15.74	2.922265	0.52653	.	.	ENSG00000196331	ENST00000303806	T	0.23147	1.92	3.7	3.7	0.42460	Histone-fold (2);	.	.	.	.	T	0.09555	0.0235	N	0.25094	0.71	0.33794	D	0.625829	B	0.21225	0.053	B	0.12837	0.008	T	0.08785	-1.0705	9	0.48119	T	0.1	.	15.2409	0.73468	0.0:1.0:0.0:0.0	.	22	P23527	H2B1O_HUMAN	V	22	ENSP00000303408:A22V	ENSP00000303408:A22V	A	+	2	0	HIST1H2BO	27969284	1.000000	0.71417	1.000000	0.80357	0.077000	0.17291	5.329000	0.65892	2.356000	0.79943	0.561000	0.74099	GCC		0.547	HIST1H2BO-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000040161.1		NM_003527	
MYPN	84665	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	10	69926368	69926368	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr10:69926368C>A	ENST00000358913.5	+	10	2406	c.1918C>A	c.(1918-1920)Cca>Aca	p.P640T	MYPN_ENST00000540630.1_Missense_Mutation_p.P640T|MYPN_ENST00000354393.2_Missense_Mutation_p.P365T	NM_001256267.1|NM_032578.3	NP_001243196.1|NP_115967.2	Q86TC9	MYPN_HUMAN	myopalladin	640					sarcomere organization (GO:0045214)	I band (GO:0031674)|nucleus (GO:0005634)|Z disc (GO:0030018)	cytoskeletal protein binding (GO:0008092)|muscle alpha-actinin binding (GO:0051371)|SH3 domain binding (GO:0017124)	p.P640T(1)		breast(2)|central_nervous_system(1)|endometrium(13)|kidney(6)|large_intestine(13)|liver(1)|lung(43)|ovary(3)|prostate(1)|skin(6)|upper_aerodigestive_tract(5)	94						AACAAAAACCCCAGAGCCTTC	0.517																																																	1	Substitution - Missense(1)	kidney(1)											54.0	52.0	53.0					10																	69926368		2203	4300	6503	SO:0001583	missense	84665			AL834247	CCDS7275.1, CCDS73142.1	10q22.1	2014-09-17			ENSG00000138347	ENSG00000138347		"""Immunoglobulin superfamily / I-set domain containing"""	23246	protein-coding gene	gene with protein product	"""sarcomeric protein myopalladin, 145 kDa"""	608517				11309420, 12482578	Standard	NM_032578		Approved	MYOP	uc001jnm.5	Q86TC9	OTTHUMG00000018344	ENST00000358913.5:c.1918C>A	10.37:g.69926368C>A	ENSP00000351790:p.Pro640Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q5VV35|Q5VV36|Q86T37|Q8N3L4|Q96K90|Q96KF5	Missense_Mutation	SNP	ENST00000358913.5	37	CCDS7275.1	.	.	.	.	.	.	.	.	.	.	C	3.102	-0.184610	0.06340	.	.	ENSG00000138347	ENST00000354393;ENST00000542332;ENST00000358913;ENST00000540630	T;T;T	0.60672	0.17;0.32;0.29	5.43	-2.49	0.06403	.	0.923109	0.09184	N	0.837058	T	0.52191	0.1719	M	0.68593	2.085	0.09310	N	1	B;B;B	0.30686	0.29;0.034;0.02	B;B;B	0.29077	0.098;0.033;0.014	T	0.39663	-0.9603	9	.	.	.	.	11.4434	0.50110	0.0:0.4588:0.0:0.5412	.	640;365;640	F5GWA6;Q86TC9-2;Q86TC9	.;.;MYPN_HUMAN	T	365;365;640;640	ENSP00000346369:P365T;ENSP00000351790:P640T;ENSP00000441668:P640T	.	P	+	1	0	MYPN	69596374	0.000000	0.05858	0.000000	0.03702	0.122000	0.20287	-0.470000	0.06639	-0.911000	0.03843	-0.345000	0.07892	CCA		0.517	MYPN-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000048307.1		NM_032578	
NDUFS1	4719	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	2	206997774	206997774	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr2:206997774C>A	ENST00000233190.6	-	14	1714	c.1448G>T	c.(1447-1449)aGa>aTa	p.R483I	NDUFS1_ENST00000423725.1_Missense_Mutation_p.R426I|NDUFS1_ENST00000455934.2_Missense_Mutation_p.R497I|NDUFS1_ENST00000457011.1_Missense_Mutation_p.R367I|NDUFS1_ENST00000449699.1_Missense_Mutation_p.R483I|NDUFS1_ENST00000432169.1_Missense_Mutation_p.R372I|NDUFS1_ENST00000440274.1_Missense_Mutation_p.R447I	NM_005006.6	NP_004997.4	P28331	NDUS1_HUMAN	NADH dehydrogenase (ubiquinone) Fe-S protein 1, 75kDa (NADH-coenzyme Q reductase)	483					apoptotic mitochondrial changes (GO:0008637)|ATP metabolic process (GO:0046034)|cellular metabolic process (GO:0044237)|cellular respiration (GO:0045333)|mitochondrial electron transport, NADH to ubiquinone (GO:0006120)|reactive oxygen species metabolic process (GO:0072593)|regulation of mitochondrial membrane potential (GO:0051881)|respiratory electron transport chain (GO:0022904)|small molecule metabolic process (GO:0044281)	mitochondrial inner membrane (GO:0005743)|mitochondrial intermembrane space (GO:0005758)|mitochondrial respiratory chain complex I (GO:0005747)	2 iron, 2 sulfur cluster binding (GO:0051537)|4 iron, 4 sulfur cluster binding (GO:0051539)|electron carrier activity (GO:0009055)|metal ion binding (GO:0046872)|NADH dehydrogenase (ubiquinone) activity (GO:0008137)	p.R483I(1)		breast(1)|central_nervous_system(1)|endometrium(6)|kidney(2)|large_intestine(7)|lung(15)|ovary(1)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	38						TCCATCATTTCTTTGGAGTGC	0.343																																																	1	Substitution - Missense(1)	kidney(1)											87.0	78.0	81.0					2																	206997774		2203	4300	6503	SO:0001583	missense	4719				CCDS2366.1, CCDS56162.1, CCDS56163.1, CCDS56164.1, CCDS56165.1	2q33-q34	2011-07-04	2002-08-29		ENSG00000023228	ENSG00000023228	1.6.5.3	"""Mitochondrial respiratory chain complex / Complex I"""	7707	protein-coding gene	gene with protein product	"""complex I 75kDa subunit"", ""NADH-ubiquinone oxidoreductase 75 kDa subunit, mitochondrial"""	157655	"""NADH dehydrogenase (ubiquinone) Fe-S protein 1 (75kD) (NADH-coenzyme Q reductase)"""			1935949	Standard	NM_005006		Approved	CI-75k	uc010ziq.2	P28331	OTTHUMG00000132892	ENST00000233190.6:c.1448G>T	2.37:g.206997774C>A	ENSP00000233190:p.Arg483Ile	Somatic		WXS	Illumina HiSeq	Phase_I	B4DIN9|B4DJA0|B4DPG1|B4DUC1|E7ENF3|Q53TR8|Q8N1C4|Q8TCC9	Missense_Mutation	SNP	ENST00000233190.6	37	CCDS2366.1	.	.	.	.	.	.	.	.	.	.	C	29.7	5.025251	0.93518	.	.	ENSG00000023228	ENST00000233190;ENST00000423725;ENST00000457011;ENST00000440274;ENST00000455934;ENST00000449699;ENST00000432169	D;D;D;D;D;D;D	0.89343	-2.5;-2.5;-2.5;-2.5;-2.5;-2.5;-2.5	6.17	6.17	0.99709	Molybdopterin oxidoreductase (1);	0.044888	0.85682	D	0.000000	D	0.96043	0.8711	M	0.92507	3.315	0.80722	D	1	P;D;D;D	0.60575	0.943;0.963;0.988;0.988	P;P;D;D	0.67231	0.828;0.896;0.95;0.928	D	0.95812	0.8842	10	0.72032	D	0.01	-13.1041	20.8794	0.99867	0.0:1.0:0.0:0.0	.	372;447;497;483	B4DPG1;E7ENF3;B4DJA0;P28331	.;.;.;NDUS1_HUMAN	I	483;426;367;447;497;483;372	ENSP00000233190:R483I;ENSP00000397760:R426I;ENSP00000400976:R367I;ENSP00000409766:R447I;ENSP00000392709:R497I;ENSP00000399912:R483I;ENSP00000409689:R372I	ENSP00000233190:R483I	R	-	2	0	NDUFS1	206706019	1.000000	0.71417	1.000000	0.80357	0.982000	0.71751	5.454000	0.66651	2.941000	0.99782	0.655000	0.94253	AGA		0.343	NDUFS1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000256391.4		NM_005006	
NEXN	91624	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	78383401	78383401	+	Missense_Mutation	SNP	C	C	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr1:78383401C>A	ENST00000334785.7	+	3	362	c.178C>A	c.(178-180)Caa>Aaa	p.Q60K	NEXN_ENST00000457030.1_Missense_Mutation_p.Q60K|NEXN_ENST00000330010.8_Intron|NEXN_ENST00000294624.8_Missense_Mutation_p.Q60K	NM_144573.3	NP_653174.3			nexilin (F actin binding protein)									p.Q60K(1)		breast(2)|central_nervous_system(1)|endometrium(5)|kidney(2)|large_intestine(5)|lung(7)|ovary(3)|prostate(2)|skin(2)|upper_aerodigestive_tract(1)	30				Colorectal(170;0.114)		AAGAAAAGAACAATATATTAG	0.333																																																	1	Substitution - Missense(1)	kidney(1)											58.0	53.0	55.0					1																	78383401		1814	4076	5890	SO:0001583	missense	91624			AK057954	CCDS41351.1, CCDS53335.1	1p31.1	2014-09-17			ENSG00000162614	ENSG00000162614		"""Immunoglobulin superfamily / I-set domain containing"""	29557	protein-coding gene	gene with protein product		613121				12053183, 8227983	Standard	NM_144573		Approved	nexilin, NELIN	uc001dic.4	Q0ZGT2	OTTHUMG00000040533	ENST00000334785.7:c.178C>A	1.37:g.78383401C>A	ENSP00000333938:p.Gln60Lys	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000334785.7	37	CCDS41351.1	.	.	.	.	.	.	.	.	.	.	C	22.6	4.315433	0.81358	.	.	ENSG00000162614	ENST00000457030;ENST00000294624;ENST00000334785;ENST00000440324	T;T;T;T	0.66280	0.2;-0.2;0.19;-0.13	5.36	5.36	0.76844	.	0.000000	0.47455	D	0.000236	T	0.68906	0.3052	L	0.49126	1.545	0.49389	D	0.999783	D	0.64830	0.994	D	0.69654	0.965	T	0.63743	-0.6568	10	0.33141	T	0.24	-28.8025	19.4565	0.94892	0.0:1.0:0.0:0.0	.	60	Q0ZGT2	NEXN_HUMAN	K	60	ENSP00000388048:Q60K;ENSP00000294624:Q60K;ENSP00000333938:Q60K;ENSP00000411902:Q60K	ENSP00000294624:Q60K	Q	+	1	0	NEXN	78155989	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	7.319000	0.79040	2.682000	0.91365	0.650000	0.86243	CAA		0.333	NEXN-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000097549.1		NM_144573	
NR5A2	2494	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	200014711	200014711	+	Splice_Site	SNP	A	A	C			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr1:200014711A>C	ENST00000367362.3	+	4	708	c.462A>C	c.(460-462)gaA>gaC	p.E154D	NR5A2_ENST00000544748.1_Splice_Site_p.E82D|NR5A2_ENST00000236914.3_Splice_Site_p.E108D	NM_001276464.1|NM_205860.1	NP_001263393.1|NP_995582.1	O00482	NR5A2_HUMAN	nuclear receptor subfamily 5, group A, member 2	154					bile acid metabolic process (GO:0008206)|cholesterol homeostasis (GO:0042632)|embryo development (GO:0009790)|endocrine pancreas development (GO:0031018)|gene expression (GO:0010467)|homeostatic process (GO:0042592)|intracellular receptor signaling pathway (GO:0030522)|positive regulation of transcription, DNA-templated (GO:0045893)|positive regulation of viral genome replication (GO:0045070)|regulation of cell proliferation (GO:0042127)|regulation of transcription, DNA-templated (GO:0006355)|transcription initiation from RNA polymerase II promoter (GO:0006367)	cytoplasm (GO:0005737)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	DNA binding (GO:0003677)|ligand-activated sequence-specific DNA binding RNA polymerase II transcription factor activity (GO:0004879)|phospholipid binding (GO:0005543)|RNA polymerase II core promoter proximal region sequence-specific DNA binding (GO:0000978)|RNA polymerase II core promoter proximal region sequence-specific DNA binding transcription factor activity involved in positive regulation of transcription (GO:0001077)|RNA polymerase II distal enhancer sequence-specific DNA binding transcription factor activity (GO:0003705)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)|steroid hormone receptor activity (GO:0003707)|transcription regulatory region DNA binding (GO:0044212)|zinc ion binding (GO:0008270)	p.E154D(1)		cervix(1)|endometrium(1)|kidney(3)|large_intestine(6)|lung(15)|ovary(1)|prostate(1)|skin(2)|urinary_tract(1)	31	Prostate(682;0.19)					TGAAGCTAGAAGGTAAGATTC	0.358																																					Melanoma(179;1138 2773 15678 26136)												1	Substitution - Missense(1)	kidney(1)											74.0	75.0	75.0					1																	200014711		2203	4300	6503	SO:0001630	splice_region_variant	2494			U93553	CCDS1400.1, CCDS1401.1, CCDS60383.1	1q32.11	2013-01-16			ENSG00000116833	ENSG00000116833		"""Nuclear hormone receptors"""	7984	protein-coding gene	gene with protein product	"""liver receptor homolog-1"""	604453		FTF		9858833, 7680097	Standard	NM_205860		Approved	FTZ-F1beta, hB1F, LRH-1, FTZ-F1, hB1F-2, B1F2	uc001gvb.4	O00482	OTTHUMG00000035635	ENST00000367362.3:c.463+1A>C	1.37:g.200014711A>C		Somatic		WXS	Illumina HiSeq	Phase_I	B4E2P3|O95642|Q147U3	Missense_Mutation	SNP	ENST00000367362.3	37	CCDS1401.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	22.0|22.0	4.225230|4.225230	0.79576|0.79576	.|.	.|.	ENSG00000116833|ENSG00000116833	ENST00000367362;ENST00000236914;ENST00000544748;ENST00000235480|ENST00000367357	T;T;T|.	0.52526|.	0.66;0.66;0.66|.	5.5|5.5	4.34|4.34	0.51931|0.51931	Zinc finger, NHR/GATA-type (1);Nuclear hormone receptor, ligand-binding (1);Zinc finger, nuclear hormone receptor-type (2);|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72922|0.72922	0.3521|0.3521	M|M	0.78344|0.78344	2.41|2.41	0.80722|0.80722	D|D	1|1	P;P|.	0.45594|.	0.862;0.721|.	P;P|.	0.53954|.	0.738;0.733|.	T|T	0.72827|0.72827	-0.4175|-0.4175	9|5	.|.	.|.	.|.	.|.	11.8418|11.8418	0.52359|0.52359	0.9302:0.0:0.0698:0.0|0.9302:0.0:0.0698:0.0	.|.	108;154|.	F1D8R9;O00482|.	.;NR5A2_HUMAN|.	D|T	154;108;82;74|75	ENSP00000356331:E154D;ENSP00000236914:E108D;ENSP00000439116:E82D|.	.|.	E|K	+|+	3|2	2|0	NR5A2|NR5A2	198281334|198281334	1.000000|1.000000	0.71417|0.71417	1.000000|1.000000	0.80357|0.80357	0.997000|0.997000	0.91878|0.91878	6.189000|6.189000	0.72051|0.72051	0.980000|0.980000	0.38523|0.38523	0.533000|0.533000	0.62120|0.62120	GAA|AAG		0.358	NR5A2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000086497.2			Missense_Mutation
TENM4	26011	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	11	78412936	78412936	+	Silent	SNP	G	G	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr11:78412936G>A	ENST00000278550.7	-	28	5184	c.4722C>T	c.(4720-4722)aaC>aaT	p.N1574N		NM_001098816.2	NP_001092286.2	Q6N022	TEN4_HUMAN	teneurin transmembrane protein 4	1574					cardiac cell fate specification (GO:0060912)|cardiac muscle cell proliferation (GO:0060038)|central nervous system myelin formation (GO:0032289)|gastrulation with mouth forming second (GO:0001702)|neuron development (GO:0048666)|positive regulation of gastrulation (GO:2000543)|positive regulation of myelination (GO:0031643)|positive regulation of oligodendrocyte differentiation (GO:0048714)|self proteolysis (GO:0097264)|signal transduction (GO:0007165)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|neuron projection (GO:0043005)|nucleus (GO:0005634)	protein homodimerization activity (GO:0042803)	p.N1574N(2)									GCTCATACATGTTCTGGGTGT	0.527																																																	2	Substitution - coding silent(2)	kidney(2)											115.0	121.0	119.0					11																	78412936		2069	4188	6257	SO:0001819	synonymous_variant	0			AB037723	CCDS44688.1	11q13	2012-10-02	2012-10-02	2012-10-02		ENSG00000149256			29945	protein-coding gene	gene with protein product		610084	"""odz, odd Oz/ten-m homolog 4 (Drosophila)"""	ODZ4		12000766, 10625539	Standard	NM_001098816		Approved	KIAA1302, Ten-M4	uc001ozl.4	Q6N022		ENST00000278550.7:c.4722C>T	11.37:g.78412936G>A		Somatic		WXS	Illumina HiSeq	Phase_I	A6ND26|Q7Z3C7|Q96MS6|Q9P2P4|Q9Y4S2	Silent	SNP	ENST00000278550.7	37	CCDS44688.1																																																																																				0.527	TENM4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000391406.2			
P2RX1	5023	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	3807223	3807223	+	Splice_Site	SNP	G	G	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr17:3807223G>A	ENST00000225538.3	-	5	797	c.523C>T	c.(523-525)Cgc>Tgc	p.R175C		NM_002558.2	NP_002549.1	P51575	P2RX1_HUMAN	purinergic receptor P2X, ligand-gated ion channel, 1	175					activation of cysteine-type endopeptidase activity involved in apoptotic process (GO:0006919)|blood coagulation (GO:0007596)|calcium ion transmembrane transport (GO:0070588)|cation transmembrane transport (GO:0098655)|cation transport (GO:0006812)|ceramide biosynthetic process (GO:0046513)|insemination (GO:0007320)|ion transport (GO:0006811)|neuronal action potential (GO:0019228)|platelet activation (GO:0030168)|positive regulation of ion transport (GO:0043270)|protein heterooligomerization (GO:0051291)|protein homooligomerization (GO:0051260)|purinergic nucleotide receptor signaling pathway (GO:0035590)|regulation of blood pressure (GO:0008217)|regulation of calcium ion transport (GO:0051924)|regulation of vascular smooth muscle contraction (GO:0003056)|response to ATP (GO:0033198)|serotonin secretion by platelet (GO:0002554)|signal transduction (GO:0007165)|synaptic transmission, glutamatergic (GO:0035249)|transport (GO:0006810)|vasoconstriction (GO:0042310)	external side of cell outer membrane (GO:0031240)|integral component of nuclear inner membrane (GO:0005639)|integral component of plasma membrane (GO:0005887)|membrane raft (GO:0045121)|neuron projection (GO:0043005)|plasma membrane (GO:0005886)|postsynaptic membrane (GO:0045211)|protein complex (GO:0043234)	ATP binding (GO:0005524)|calcium channel activity (GO:0005262)|cation channel activity (GO:0005261)|drug binding (GO:0008144)|extracellular ATP-gated cation channel activity (GO:0004931)|purinergic nucleotide receptor activity (GO:0001614)|zinc ion binding (GO:0008270)	p.R175C(1)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(1)|lung(4)|ovary(1)|prostate(1)|skin(2)	13				LUAD - Lung adenocarcinoma(2;1.9e-05)|Lung(3;0.0173)		GAGTGTTACCGCGGGATGTCG	0.572																																																	1	Substitution - Missense(1)	kidney(1)											93.0	76.0	82.0					17																	3807223		2203	4300	6503	SO:0001630	splice_region_variant	5023			X83688	CCDS11040.1	17p13.3	2012-01-17				ENSG00000108405		"""Purinergic receptors"", ""Ligand-gated ion channels / Purinergic receptors, ionotropic"""	8533	protein-coding gene	gene with protein product		600845				8834001	Standard	NM_002558		Approved	P2X1	uc002fww.3	P51575		ENST00000225538.3:c.524+1C>T	17.37:g.3807223G>A		Somatic		WXS	Illumina HiSeq	Phase_I	Q9UK84	Missense_Mutation	SNP	ENST00000225538.3	37	CCDS11040.1	.	.	.	.	.	.	.	.	.	.	G	14.16	2.451602	0.43531	.	.	ENSG00000108405	ENST00000225538	T	0.04502	3.61	5.44	-5.31	0.02730	.	0.608667	0.18136	N	0.150576	T	0.04452	0.0122	M	0.62723	1.935	0.21105	N	0.999781	B	0.10296	0.003	B	0.08055	0.003	T	0.33752	-0.9856	10	0.59425	D	0.04	-23.7932	4.5038	0.11878	0.076:0.1558:0.2074:0.5608	.	175	P51575	P2RX1_HUMAN	C	175	ENSP00000225538:R175C	ENSP00000225538:R175C	R	-	1	0	P2RX1	3753972	0.520000	0.26250	0.042000	0.18584	0.018000	0.09664	0.789000	0.26886	-0.439000	0.07222	0.655000	0.94253	CGC		0.572	P2RX1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000438391.1		NM_002558	Missense_Mutation
PBRM1	55193	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52621519	52621519	+	Frame_Shift_Del	DEL	T	T	-			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr3:52621519delT	ENST00000296302.7	-	19	2974	c.2973delA	c.(2971-2973)aaafs	p.K991fs	PBRM1_ENST00000409057.1_Frame_Shift_Del_p.K991fs|PBRM1_ENST00000356770.4_Frame_Shift_Del_p.K959fs|PBRM1_ENST00000409114.3_Frame_Shift_Del_p.K1006fs|PBRM1_ENST00000337303.4_Frame_Shift_Del_p.K991fs|PBRM1_ENST00000409767.1_Frame_Shift_Del_p.K1006fs|PBRM1_ENST00000394830.3_Intron|PBRM1_ENST00000410007.1_Intron			Q86U86	PB1_HUMAN	polybromo 1	991	BAH 1. {ECO:0000255|PROSITE- ProRule:PRU00370}.				chromatin remodeling (GO:0006338)|heart development (GO:0007507)|mitotic nuclear division (GO:0007067)|negative regulation of cell proliferation (GO:0008285)|placenta development (GO:0001890)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	kinetochore (GO:0000776)|nuclear chromosome (GO:0000228)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)			breast(5)|endometrium(5)|kidney(301)|liver(1)|lung(22)|pancreas(1)	335				BRCA - Breast invasive adenocarcinoma(193;1.8e-05)|Kidney(197;0.00105)|KIRC - Kidney renal clear cell carcinoma(197;0.00122)|OV - Ovarian serous cystadenocarcinoma(275;0.0613)		CATACAACCATTTTTCACCTC	0.353			"""Mis, N, F, S, D, O"""		"""clear cell renal carcinoma, breast"""																																			Rec	yes		3	3p21	55193	polybromo 1		E	0													41.0	44.0	43.0					3																	52621519		2203	4300	6503	SO:0001589	frameshift_variant	55193			BC015323	CCDS43099.1	3p21	2007-03-29			ENSG00000163939	ENSG00000163939			30064	protein-coding gene	gene with protein product		606083				11078522, 11483580	Standard	NM_018313		Approved	BAF180, PB1	uc003der.2	Q86U86	OTTHUMG00000152663	ENST00000296302.7:c.2973delA	3.37:g.52621519delT	ENSP00000296302:p.Lys991fs	Somatic		WXS	Illumina HiSeq	Phase_I	A1L381|A1L382|A4FUJ7|Q1RMD1|Q1RMD2|Q96MS2|Q9H2T3|Q9H2T4|Q9H2T5|Q9H301|Q9H314	Frame_Shift_Del	DEL	ENST00000296302.7	37																																																																																					0.353	PBRM1-008	KNOWN	basic|appris_candidate_longest	protein_coding	protein_coding	OTTHUMT00000327232.1		NM_018165	
FAM13B	51306	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	137275829	137275829	+	3'UTR	SNP	G	G	T	rs200078301		TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr5:137275829G>T	ENST00000033079.3	-	0	3284				PKD2L2_ENST00000508638.1_3'UTR|PKD2L2_ENST00000502810.1_3'UTR|PKD2L2_ENST00000508883.1_Intron|PKD2L2_ENST00000290431.5_Missense_Mutation_p.R612L	NM_016603.2	NP_057687.2	Q9NYF5	FA13B_HUMAN	family with sequence similarity 13, member B						regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cytosol (GO:0005829)	GTPase activator activity (GO:0005096)	p.R612L(1)		endometrium(4)|kidney(2)|lung(5)	11						CTGACAAAACGAATTTAAGTA	0.388																																																	1	Substitution - Missense(1)	kidney(1)											134.0	133.0	133.0					5																	137275829		2203	4300	6503	SO:0001624	3_prime_UTR_variant	27039			AF251038	CCDS4195.1, CCDS47269.1, CCDS47270.1	5q31	2011-09-07	2009-01-20	2009-01-20	ENSG00000031003	ENSG00000031003		"""Rho GTPase activating proteins"""	1335	protein-coding gene	gene with protein product		609371	"""chromosome 5 open reading frame 5"", ""family with sequence similarity 13, member B1"""	C5orf5, FAM13B1		11087669, 11161817	Standard	NM_016603		Approved	N61, KHCHP, ARHGAP49	uc003lbz.2	Q9NYF5	OTTHUMG00000129202	ENST00000033079.3:c.*85C>A	5.37:g.137275829G>T		Somatic		WXS	Illumina HiSeq	Phase_I	D3DQB5|G3V0H9|Q3ZCR0|Q6PGQ2|Q9P0I7	Missense_Mutation	SNP	ENST00000033079.3	37	CCDS4195.1	.	.	.	.	.	.	.	.	.	.	G	12.64	1.999647	0.35320	.	.	ENSG00000078795	ENST00000290431	T	0.66995	-0.24	5.34	4.47	0.54385	.	.	.	.	.	T	0.51890	0.1701	.	.	.	0.80722	D	1	P	0.45594	0.862	B	0.31946	0.138	T	0.57985	-0.7716	8	0.66056	D	0.02	.	10.4298	0.44400	0.1495:0.0:0.8505:0.0	.	612	Q9NZM6-5	.	L	612	ENSP00000290431:R612L	ENSP00000290431:R612L	R	+	2	0	PKD2L2	137303728	1.000000	0.71417	1.000000	0.80357	0.365000	0.29674	1.800000	0.38833	1.386000	0.46466	-0.218000	0.12543	CGA		0.388	FAM13B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000251279.1			
PRR12	57479	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	19	50118189	50118189	+	Silent	SNP	C	C	T			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr19:50118189C>T	ENST00000418929.2	+	8	4959	c.4947C>T	c.(4945-4947)ttC>ttT	p.F1649F		NM_020719.1	NP_065770.1	Q9ULL5	PRR12_HUMAN	proline rich 12	828							DNA binding (GO:0003677)	p.F829F(1)|p.F1649F(1)		NS(1)|central_nervous_system(1)|endometrium(2)|kidney(1)|large_intestine(1)|lung(2)|pancreas(1)|prostate(2)	11		all_lung(116;2.45e-07)|Lung NSC(112;1.24e-06)|Ovarian(192;0.0728)|all_neural(266;0.0887)		OV - Ovarian serous cystadenocarcinoma(262;0.00319)|GBM - Glioblastoma multiforme(134;0.0132)		ATGTAAAGTTCCTGGAAAATG	0.512																																																	2	Substitution - coding silent(2)	kidney(2)											73.0	72.0	72.0					19																	50118189		1890	4108	5998	SO:0001819	synonymous_variant	57479			AB033031	CCDS46143.1	19q13.33	2008-07-02	2006-02-06	2006-02-06		ENSG00000126464			29217	protein-coding gene	gene with protein product			"""KIAA1205"""	KIAA1205		10574462	Standard	NM_020719		Approved		uc002poo.4	Q9ULL5		ENST00000418929.2:c.4947C>T	19.37:g.50118189C>T		Somatic		WXS	Illumina HiSeq	Phase_I	E9PB06|Q8N4J6	Silent	SNP	ENST00000418929.2	37	CCDS46143.1																																																																																				0.512	PRR12-001	NOVEL	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000465915.1		NM_020719	
REG1B	5968	hgsc.bcm.edu;ucsc.edu	37	2	79314032	79314032	+	Frame_Shift_Del	DEL	G	G	-			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr2:79314032delG	ENST00000305089.3	-	3	169	c.89delC	c.(88-90)cctfs	p.P30fs		NM_006507.3	NP_006498.1	P48304	REG1B_HUMAN	regenerating islet-derived 1 beta	30					cell proliferation (GO:0008283)	extracellular vesicular exosome (GO:0070062)	carbohydrate binding (GO:0030246)	p.P30H(1)		central_nervous_system(1)|cervix(1)|endometrium(1)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(2)|lung(40)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(2)	51						TCGGGGATTAGGCAGCTCTGT	0.493																																																	1	Substitution - Missense(1)	lung(1)											123.0	126.0	125.0					2																	79314032		2203	4300	6503	SO:0001589	frameshift_variant	5968				CCDS1963.1	2p12	2008-06-04	2008-06-04		ENSG00000172023	ENSG00000172023			9952	protein-coding gene	gene with protein product	"""lithostathine 1 beta"", ""secretory pancreatic stone protein 2"""	167771	"""regenerating islet-derived 1 beta (pancreatic stone protein, pancreatic thread protein)"""			8110835	Standard	NM_006507		Approved	REGL, PSPS2, REGH, REGI-BETA	uc002sny.2	P48304	OTTHUMG00000130019	ENST00000305089.3:c.89delC	2.37:g.79314032delG	ENSP00000303206:p.Pro30fs	Somatic		WXS	Illumina HiSeq	Phase_I		Frame_Shift_Del	DEL	ENST00000305089.3	37	CCDS1963.1																																																																																				0.493	REG1B-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252292.2		NM_006507	
RNF145	153830	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	5	158603776	158603776	+	Missense_Mutation	SNP	A	A	C			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr5:158603776A>C	ENST00000424310.2	-	5	844	c.485T>G	c.(484-486)cTt>cGt	p.L162R	RNF145_ENST00000518802.1_Missense_Mutation_p.L192R|RNF145_ENST00000519865.1_Missense_Mutation_p.L162R|RNF145_ENST00000521606.2_Missense_Mutation_p.L179R|RNF145_ENST00000520638.1_Missense_Mutation_p.L176R|RNF145_ENST00000274542.2_Missense_Mutation_p.L190R	NM_001199383.1	NP_001186312.1	Q96MT1	RN145_HUMAN	ring finger protein 145	162						integral component of membrane (GO:0016021)	zinc ion binding (GO:0008270)	p.L190R(1)		endometrium(7)|kidney(2)|large_intestine(5)|lung(9)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)	30	Renal(175;0.00196)	Medulloblastoma(196;0.0523)	Kidney(164;7.83e-05)|KIRC - Kidney renal clear cell carcinoma(164;0.000525)			CAAAGGAACAAGGCAGAGTCG	0.393																																																	1	Substitution - Missense(1)	kidney(1)											54.0	53.0	53.0					5																	158603776		2202	4300	6502	SO:0001583	missense	153830			BC042684	CCDS4344.1, CCDS56390.1, CCDS56391.1, CCDS56392.1, CCDS56393.1	5q33.3	2013-01-09			ENSG00000145860	ENSG00000145860		"""RING-type (C3HC4) zinc fingers"""	20853	protein-coding gene	gene with protein product							Standard	NM_001199380		Approved	FLJ31951	uc003lxo.2	Q96MT1	OTTHUMG00000130306	ENST00000424310.2:c.485T>G	5.37:g.158603776A>C	ENSP00000409064:p.Leu162Arg	Somatic		WXS	Illumina HiSeq	Phase_I	B7Z903|B7Z949|E7EVI7|Q8IVP7	Missense_Mutation	SNP	ENST00000424310.2	37	CCDS56390.1	.	.	.	.	.	.	.	.	.	.	A	15.26	2.780284	0.49891	.	.	ENSG00000145860	ENST00000274542;ENST00000519865;ENST00000424310;ENST00000521606;ENST00000413445;ENST00000518802;ENST00000535312;ENST00000520638	T;T;T;T;T;T;T	0.76968	-1.06;-1.04;-1.04;-1.05;-1.05;-1.06;-1.05	5.46	5.46	0.80206	.	0.000000	0.85682	D	0.000000	T	0.71213	0.3313	N	0.08118	0	0.80722	D	1	D;D;D;D;D;D	0.60160	0.987;0.987;0.987;0.987;0.987;0.983	P;P;P;P;P;P	0.57846	0.828;0.828;0.828;0.828;0.828;0.736	T	0.69018	-0.5256	10	0.12766	T	0.61	-16.6469	15.8333	0.78778	1.0:0.0:0.0:0.0	.	178;179;176;192;162;190	E7EW26;B7Z949;B7Z903;E7EVI7;Q96MT1;Q96MT1-2	.;.;.;.;RN145_HUMAN;.	R	190;162;162;178;179;192;162;176	ENSP00000274542:L190R;ENSP00000430397:L162R;ENSP00000409064:L162R;ENSP00000430753:L178R;ENSP00000445115:L179R;ENSP00000430955:L192R;ENSP00000429071:L176R	ENSP00000274542:L190R	L	-	2	0	RNF145	158536354	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.576000	0.82467	2.200000	0.70718	0.377000	0.23210	CTT		0.393	RNF145-002	PUTATIVE	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374048.1		NM_144726	
SLC6A13	6540	hgsc.bcm.edu;ucsc.edu	37	12	335652	335652	+	Missense_Mutation	SNP	T	T	C			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr12:335652T>C	ENST00000343164.4	-	9	1016	c.964A>G	c.(964-966)Agc>Ggc	p.S322G	SLC6A13_ENST00000539668.1_5'Flank|SLC6A13_ENST00000445055.2_Missense_Mutation_p.S230G	NM_016615.4	NP_057699.2	Q9NSD5	S6A13_HUMAN	solute carrier family 6 (neurotransmitter transporter), member 13	322					neurotransmitter secretion (GO:0007269)|synaptic transmission (GO:0007268)|transmembrane transport (GO:0055085)	extracellular vesicular exosome (GO:0070062)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	gamma-aminobutyric acid:sodium symporter activity (GO:0005332)|neurotransmitter:sodium symporter activity (GO:0005328)			NS(1)|autonomic_ganglia(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(7)|lung(11)|prostate(1)|urinary_tract(1)	28	all_cancers(10;0.0416)|all_epithelial(11;0.0537)|all_lung(10;0.0989)|Lung NSC(10;0.139)|Ovarian(42;0.142)		OV - Ovarian serous cystadenocarcinoma(31;0.00153)|BRCA - Breast invasive adenocarcinoma(9;0.239)			CTGGTGCCGCTGTTGAGGAAG	0.617																																																	0													61.0	54.0	56.0					12																	335652		2203	4300	6503	SO:0001583	missense	6540			U76343	CCDS8502.1, CCDS53729.1, CCDS58198.1	12p13.33	2013-07-19	2013-07-19		ENSG00000010379	ENSG00000010379		"""Solute carriers"""	11046	protein-coding gene	gene with protein product	"""GABA transporter 2"""	615097	"""solute carrier family 6 (neurotransmitter transporter, GABA), member 13"""				Standard	NM_001243392		Approved	GAT2	uc001qic.2	Q9NSD5	OTTHUMG00000168053	ENST00000343164.4:c.964A>G	12.37:g.335652T>C	ENSP00000339260:p.Ser322Gly	Somatic		WXS	Illumina HiSeq	Phase_I	B4DJL1|Q8TCC2|Q8WW56	Missense_Mutation	SNP	ENST00000343164.4	37	CCDS8502.1	.	.	.	.	.	.	.	.	.	.	T	27.8	4.863727	0.91511	.	.	ENSG00000010379	ENST00000445055;ENST00000313154;ENST00000343164	T;T	0.75367	-0.93;-0.93	5.34	5.34	0.76211	.	0.000000	0.85682	D	0.000000	D	0.82967	0.5152	M	0.85630	2.765	0.80722	D	1	B;B	0.31989	0.35;0.251	B;B	0.44163	0.443;0.288	D	0.84117	0.0404	10	0.56958	D	0.05	.	15.3028	0.73966	0.0:0.0:0.0:1.0	.	230;322	B4DJL1;Q9NSD5	.;S6A13_HUMAN	G	230;301;322	ENSP00000407104:S230G;ENSP00000339260:S322G	ENSP00000318097:S301G	S	-	1	0	SLC6A13	205913	1.000000	0.71417	1.000000	0.80357	0.996000	0.88848	7.974000	0.88039	2.010000	0.58986	0.402000	0.26972	AGC		0.617	SLC6A13-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000397801.1		NM_016615	
SP140L	93349	broad.mit.edu;hgsc.bcm.edu	37	2	231254640	231254641	+	Missense_Mutation	DNP	GA	GA	TT			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G|A	G|A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr2:231254640_231254641GA>TT	ENST00000415673.2	+	11	952_953	c.866_867GA>TT	c.(865-867)aGA>aTT	p.R289I	SP140L_ENST00000444636.1_Missense_Mutation_p.R289I|SP140L_ENST00000396563.4_Intron|SP140L_ENST00000243810.6_Missense_Mutation_p.R289I	NM_138402.4	NP_612411.4	Q9H930	SP14L_HUMAN	SP140 nuclear body protein-like	289						nucleus (GO:0005634)	DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.R289I(3)|p.R289S(2)|p.R289>?(1)		central_nervous_system(1)|endometrium(1)|kidney(4)|large_intestine(5)|lung(7)|prostate(1)|skin(1)	20						TCAGCTTCAAGAAAGCACAAAG	0.431																																																	6	Substitution - Missense(5)|Complex(1)	kidney(6)																																								SO:0001583	missense	93349			BC004921	CCDS46538.1	2q37.1	2013-01-28			ENSG00000185404	ENSG00000185404		"""Zinc fingers, PHD-type"""	25105	protein-coding gene	gene with protein product						12477932	Standard	NM_138402		Approved		uc010fxm.1	Q9H930	OTTHUMG00000153730	Exception_encountered	2.37:g.231254640_231254641delinsTT	ENSP00000397911:p.Arg289Ile	Somatic		WXS	Illumina HiSeq	Phase_I	Q2M375|Q4ZG65|Q9BSP3	Missense_Mutation	SNP	ENST00000415673.2	37	CCDS46538.1																																																																																				0.431	SP140L-009	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000374538.1		NM_138402	
TMEM104	54868	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	17	72832324	72832324	+	Missense_Mutation	SNP	G	G	T	rs372516123		TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr17:72832324G>T	ENST00000335464.5	+	10	1151	c.989G>T	c.(988-990)cGc>cTc	p.R330L	TMEM104_ENST00000417024.2_Intron|TMEM104_ENST00000582330.1_Missense_Mutation_p.R330L|TMEM104_ENST00000582773.1_Intron	NM_017728.3	NP_060198.3	Q8NE00	TM104_HUMAN	transmembrane protein 104	330						integral component of membrane (GO:0016021)		p.R330L(1)		NS(1)|cervix(1)|endometrium(1)|kidney(2)|large_intestine(8)|lung(5)|ovary(1)	19	all_lung(278;0.23)					TTCTGCTTCCGCGGCGACAGC	0.622																																																	1	Substitution - Missense(1)	kidney(1)											246.0	193.0	211.0					17																	72832324		2203	4300	6503	SO:0001583	missense	54868			AK074029	CCDS32723.1	17q25.1	2005-12-19				ENSG00000109066			25984	protein-coding gene	gene with protein product							Standard	NM_017728		Approved	FLJ20255, FLJ00021	uc002jls.4	Q8NE00		ENST00000335464.5:c.989G>T	17.37:g.72832324G>T	ENSP00000334849:p.Arg330Leu	Somatic		WXS	Illumina HiSeq	Phase_I	Q8TEU1|Q9NT56|Q9NXH1	Missense_Mutation	SNP	ENST00000335464.5	37	CCDS32723.1	.	.	.	.	.	.	.	.	.	.	g	14.90	2.672838	0.47781	.	.	ENSG00000109066	ENST00000335464	T	0.30448	1.53	5.26	4.27	0.50696	.	0.188602	0.56097	D	0.000021	T	0.22360	0.0539	L	0.36672	1.1	0.30838	N	0.735975	B	0.30851	0.297	B	0.31946	0.138	T	0.08269	-1.0730	10	0.10902	T	0.67	-25.1969	12.3125	0.54935	0.1359:0.0:0.8641:0.0	.	330	Q8NE00	TM104_HUMAN	L	330	ENSP00000334849:R330L	ENSP00000334849:R330L	R	+	2	0	TMEM104	70343919	1.000000	0.71417	1.000000	0.80357	0.983000	0.72400	3.301000	0.51842	2.626000	0.88956	0.556000	0.70494	CGC		0.622	TMEM104-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000444442.1		NM_017728	
TUBB4A	10382	broad.mit.edu;hgsc.bcm.edu	37	19	6501365	6501365	+	Silent	SNP	G	G	A	rs557747150		TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr19:6501365G>A	ENST00000264071.2	-	3	581	c.210C>T	c.(208-210)ccC>ccT	p.P70P	TUBB4A_ENST00000540257.1_Silent_p.P70P|TUBB4A_ENST00000598006.1_Missense_Mutation_p.P56L|TUBB4A_ENST00000601152.1_Missense_Mutation_p.P45L|TUBB4A_ENST00000596926.1_Silent_p.P70P			P04350	TBB4A_HUMAN	tubulin, beta 4A class IVa	70					'de novo' posttranslational protein folding (GO:0051084)|cellular protein metabolic process (GO:0044267)|G2/M transition of mitotic cell cycle (GO:0000086)|microtubule-based process (GO:0007017)|mitotic cell cycle (GO:0000278)|protein folding (GO:0006457)|protein polymerization (GO:0051258)	cilium (GO:0005929)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|internode region of axon (GO:0033269)|microtubule (GO:0005874)|myelin sheath (GO:0043209)|neuronal cell body (GO:0043025)|nucleus (GO:0005634)	GTP binding (GO:0005525)|GTPase activity (GO:0003924)|structural constituent of cytoskeleton (GO:0005200)	p.P70P(1)									CCATGGTGCCGGGTTCCAGGT	0.617													G|||	1	0.000199681	0.0	0.0	5008	,	,		18932	0.0		0.001	False		,,,				2504	0.0																1	Substitution - coding silent(1)	kidney(1)											50.0	48.0	49.0					19																	6501365		2203	4300	6503	SO:0001819	synonymous_variant	0			AK075307	CCDS12168.1	19p13.3	2014-02-05	2011-10-11	2011-10-10	ENSG00000104833	ENSG00000104833		"""Tubulins"""	20774	protein-coding gene	gene with protein product	"""class IVa beta-tubulin"""	602662	"""tubulin, beta 4"", ""tubulin, beta 4 class IVa"", ""dystonia 4, torsion (autosomal dominant)"""	TUBB4, DYT4		6865944, 6462917, 23595291	Standard	NM_001289123		Approved	beta-5	uc002mfg.1	P04350		ENST00000264071.2:c.210C>T	19.37:g.6501365G>A		Somatic		WXS	Illumina HiSeq	Phase_I	B3KQP4|Q969E5	Silent	SNP	ENST00000264071.2	37	CCDS12168.1																																																																																				0.617	TUBB4A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000457841.1		NM_006087	
VHL	7428	broad.mit.edu;ucsc.edu	37	3	10191470	10191470	+	Splice_Site	SNP	G	G	T	rs5030817		TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr3:10191470G>T	ENST00000256474.2	+	3	1303		c.e3-1		VHL_ENST00000345392.2_Splice_Site|VHL_ENST00000477538.1_Splice_Site	NM_000551.3	NP_000542.1	P40337	VHL_HUMAN	von Hippel-Lindau tumor suppressor, E3 ubiquitin protein ligase						cell morphogenesis (GO:0000902)|cellular response to hypoxia (GO:0071456)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061428)|positive regulation of cell differentiation (GO:0045597)|positive regulation of transcription, DNA-templated (GO:0045893)|protein stabilization (GO:0050821)|protein ubiquitination (GO:0016567)|proteolysis (GO:0006508)|regulation of transcription from RNA polymerase II promoter in response to hypoxia (GO:0061418)|regulation of transcription, DNA-templated (GO:0006355)	cytosol (GO:0005829)|endoplasmic reticulum (GO:0005783)|intermediate filament cytoskeleton (GO:0045111)|membrane (GO:0016020)|mitochondrion (GO:0005739)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)	enzyme binding (GO:0019899)|transcription factor binding (GO:0008134)|ubiquitin protein ligase activity (GO:0061630)|ubiquitin-protein transferase activity (GO:0004842)	p.?(23)		adrenal_gland(25)|autonomic_ganglia(3)|central_nervous_system(2)|endometrium(6)|kidney(1662)|large_intestine(14)|lung(6)|pancreas(18)|paratesticular_tissues(1)|pleura(1)|skin(1)|soft_tissue(24)|thyroid(3)|upper_aerodigestive_tract(3)	1769				Kidney(1;0.000404)|KIRC - Kidney renal clear cell carcinoma(1;0.000569)		TGCCCTTCCAGTGTATACTCT	0.493		1	"""D, Mis, N, F, S"""		"""renal, hemangioma, pheochromocytoma"""	"""renal, hemangioma, pheochromocytoma"""			von Hippel-Lindau disease;Pheochromocytoma (Adrenal), Familial;Chuvash Polycythemia																														yes	Rec	yes	von Hippel-Lindau syndrome	3	3p25	7428	von Hippel-Lindau syndrome gene		"""E, M, O"""	23	Unknown(23)	kidney(21)|soft_tissue(2)	GRCh37	CS071276|CS941547|CS961706	VHL	S	rs5030817						88.0	80.0	83.0					3																	10191470		2203	4300	6503	SO:0001630	splice_region_variant	7428	Familial Cancer Database	VHL; ;Erythrocytosis, Familial type 2	L15409	CCDS2597.1, CCDS2598.1	3p25.3	2014-09-17	2012-02-23		ENSG00000134086	ENSG00000134086			12687	protein-coding gene	gene with protein product		608537	"""von Hippel-Lindau syndrome"", ""von Hippel-Lindau tumor suppressor"""			9671762	Standard	NM_000551		Approved	VHL1	uc003bvc.3	P40337	OTTHUMG00000128668	ENST00000256474.2:c.464-1G>T	3.37:g.10191470G>T		Somatic		WXS	Illumina GAIIx	Phase_I	B2RE45|Q13599|Q6PDA9	Splice_Site	SNP	ENST00000256474.2	37	CCDS2597.1	.	.	.	.	.	.	.	.	.	.	G	12.39	1.923007	0.33908	.	.	ENSG00000134086	ENST00000256474;ENST00000345392;ENST00000450183	.	.	.	4.58	4.58	0.56647	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2774	0.73753	0.0:0.0:1.0:0.0	.	.	.	.	.	-1	.	.	.	+	.	.	VHL	10166470	1.000000	0.71417	1.000000	0.80357	0.419000	0.31324	7.062000	0.76706	2.535000	0.85469	0.655000	0.94253	.		0.493	VHL-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250559.1		NM_000551	Intron
WNT3	7473	hgsc.bcm.edu	37	17	44851096	44851097	+	Frame_Shift_Ins	INS	-	-	G			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr17:44851096_44851097insG	ENST00000225512.5	-	2	421_422	c.259_260insC	c.(259-261)cgcfs	p.R87fs		NM_030753.4	NP_110380.1	P56703	WNT3_HUMAN	wingless-type MMTV integration site family, member 3	87					anterior/posterior axis specification (GO:0009948)|axon guidance (GO:0007411)|canonical Wnt signaling pathway (GO:0060070)|canonical Wnt signaling pathway involved in mesenchymal stem cell differentiation (GO:0044338)|canonical Wnt signaling pathway involved in osteoblast differentiation (GO:0044339)|cell fate commitment (GO:0045165)|cell morphogenesis (GO:0000902)|cellular response to retinoic acid (GO:0071300)|dorsal/ventral axis specification (GO:0009950)|embryonic forelimb morphogenesis (GO:0035115)|embryonic hindlimb morphogenesis (GO:0035116)|gamete generation (GO:0007276)|head morphogenesis (GO:0060323)|limb bud formation (GO:0060174)|mammary gland epithelium development (GO:0061180)|mesoderm formation (GO:0001707)|negative regulation of axon extension involved in axon guidance (GO:0048843)|neuron differentiation (GO:0030182)|positive regulation of collateral sprouting in absence of injury (GO:0048697)|positive regulation of gene expression (GO:0010628)|Spemann organizer formation at the anterior end of the primitive streak (GO:0060064)	endoplasmic reticulum lumen (GO:0005788)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|Golgi lumen (GO:0005796)|plasma membrane (GO:0005886)|proteinaceous extracellular matrix (GO:0005578)	frizzled binding (GO:0005109)|receptor agonist activity (GO:0048018)			endometrium(2)|large_intestine(6)|lung(4)|prostate(1)	13			BRCA - Breast invasive adenocarcinoma(9;0.0257)			GTTCCAGCGGCGGCCCCGGAAC	0.644																																																	0																																										SO:0001589	frameshift_variant	7473			AY009397	CCDS11505.1	17q21-q22	2013-02-28				ENSG00000108379		"""Wingless-type MMTV integration sites"", ""Endogenous ligands"""	12782	protein-coding gene	gene with protein product	"""WNT-3 proto-oncogene protein"""	165330		INT4		8244403	Standard	NM_030753		Approved	MGC131950, MGC138321, MGC138323	uc002ikv.3	P56703		ENST00000225512.5:c.260dupC	17.37:g.44851098_44851098dupG	ENSP00000225512:p.Arg87fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q2M237|Q9H1J9	Frame_Shift_Ins	INS	ENST00000225512.5	37	CCDS11505.1																																																																																				0.644	WNT3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000440427.1		NM_030753	
ZFHX4	79776	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	8	77766976	77766976	+	Missense_Mutation	SNP	C	C	G			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr8:77766976C>G	ENST00000521891.2	+	10	8267	c.7819C>G	c.(7819-7821)Cgc>Ggc	p.R2607G	ZFHX4_ENST00000050961.6_Missense_Mutation_p.R2562G|ZFHX4_ENST00000518282.1_Missense_Mutation_p.R2581G|ZFHX4_ENST00000455469.2_Missense_Mutation_p.R2562G	NM_024721.4	NP_078997.4	Q86UP3	ZFHX4_HUMAN	zinc finger homeobox 4	2562					regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	nucleus (GO:0005634)	sequence-specific DNA binding (GO:0043565)|zinc ion binding (GO:0008270)	p.R2591G(1)		NS(3)|breast(11)|central_nervous_system(1)|endometrium(36)|haematopoietic_and_lymphoid_tissue(2)|kidney(15)|large_intestine(66)|liver(2)|lung(245)|ovary(11)|pancreas(3)|prostate(11)|skin(7)|upper_aerodigestive_tract(13)|urinary_tract(6)	432			BRCA - Breast invasive adenocarcinoma(89;0.0895)			CCGAGATAAACGCTTGAGAAC	0.423										HNSCC(33;0.089)																																							1	Substitution - Missense(1)	kidney(1)											49.0	48.0	48.0					8																	77766976		1903	4113	6016	SO:0001583	missense	79776				CCDS47878.1, CCDS47878.2	8q21.11	2012-07-02	2007-07-16		ENSG00000091656	ENSG00000091656		"""Homeoboxes / ZF class"""	30939	protein-coding gene	gene with protein product		606940	"""zinc finger homeodomain 4"""			10873665, 11935336	Standard	NM_024721		Approved	ZFH4, FLJ20980	uc003yau.2	Q86UP3	OTTHUMG00000164557	ENST00000521891.2:c.7819C>G	8.37:g.77766976C>G	ENSP00000430497:p.Arg2607Gly	Somatic		WXS	Illumina HiSeq	Phase_I	G3V138|Q18PS0|Q6ZN20	Missense_Mutation	SNP	ENST00000521891.2	37	CCDS47878.2	.	.	.	.	.	.	.	.	.	.	C	12.74	2.029891	0.35797	.	.	ENSG00000091656	ENST00000521891;ENST00000399468;ENST00000455469;ENST00000050961;ENST00000518282	D;D;D;D	0.97089	-4.24;-4.24;-4.24;-4.24	5.38	5.38	0.77491	Homeodomain-related (1);Homeobox (3);Homeodomain-like (1);	0.000000	0.45361	U	0.000365	D	0.98811	0.9599	H	0.94222	3.51	0.80722	D	1	D;D;D	0.89917	1.0;1.0;0.998	D;D;D	0.91635	0.999;0.999;0.998	D	0.99184	1.0868	10	0.87932	D	0	.	14.1941	0.65659	0.1493:0.8506:0.0:0.0	.	2562;2562;2607	Q86UP3;Q86UP3-4;G3V138	ZFHX4_HUMAN;.;.	G	2607;2591;2562;2562;2581	ENSP00000430497:R2607G;ENSP00000399605:R2562G;ENSP00000050961:R2562G;ENSP00000430848:R2581G	ENSP00000050961:R2562G	R	+	1	0	ZFHX4	77929531	1.000000	0.71417	0.985000	0.45067	0.627000	0.37826	5.772000	0.68889	2.791000	0.96007	0.650000	0.86243	CGC		0.423	ZFHX4-002	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000379197.2		NM_024721	
ZZZ3	26009	broad.mit.edu;hgsc.bcm.edu	37	1	78045311	78045311	+	Silent	SNP	T	T	C			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr1:78045311T>C	ENST00000370801.3	-	10	2458	c.1983A>G	c.(1981-1983)aaA>aaG	p.K661K	ZZZ3_ENST00000370798.1_Silent_p.K167K|ZZZ3_ENST00000476275.1_5'UTR	NM_015534.4	NP_056349.1	Q8IYH5	ZZZ3_HUMAN	zinc finger, ZZ-type containing 3	661	HTH myb-type. {ECO:0000255|PROSITE- ProRule:PRU00625}.				chromatin organization (GO:0006325)|regulation of transcription, DNA-templated (GO:0006355)|transcription, DNA-templated (GO:0006351)	Ada2/Gcn5/Ada3 transcription activator complex (GO:0005671)	chromatin binding (GO:0003682)|DNA binding (GO:0003677)|zinc ion binding (GO:0008270)	p.K661K(1)		breast(2)|endometrium(2)|kidney(2)|large_intestine(8)|lung(17)|ovary(4)|prostate(1)|stomach(1)|urinary_tract(2)	39						GTTCCAGCTTTTTCTAAGCCA	0.338																																																	1	Substitution - coding silent(1)	kidney(1)											145.0	140.0	142.0					1																	78045311		2203	4300	6503	SO:0001819	synonymous_variant	26009			AL080063	CCDS677.1	1p31.1	2012-08-13			ENSG00000036549	ENSG00000036549		"""Zinc fingers, ZZ-type"""	24523	protein-coding gene	gene with protein product	"""ATAC component 1 homolog (Drosophila)"""					16428443, 21304275	Standard	NM_015534		Approved	DKFZP564I052, ATAC1	uc001dhq.3	Q8IYH5	OTTHUMG00000009652	ENST00000370801.3:c.1983A>G	1.37:g.78045311T>C		Somatic		WXS	Illumina HiSeq	Phase_I	B7WPC6|Q6N004|Q6N070|Q8IYP0|Q8IYR1|Q8TEK4|Q9Y4U0	Silent	SNP	ENST00000370801.3	37	CCDS677.1																																																																																				0.338	ZZZ3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000026615.1		NM_015534	
Unknown	0	broad.mit.edu	37	13	19413025	19413025	+	IGR	SNP	A	A	G			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr13:19413025A>G								LINC00418 (119156 upstream) : RP11-38M15.11 (20941 downstream)																							AATAACCTGCACATCCATGCA	0.299																																																	0																																										SO:0001628	intergenic_variant	0																															13.37:g.19413025A>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.299									
TRIM51HP	440041	broad.mit.edu	37	11	55062213	55062213	+	RNA	SNP	C	C	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr11:55062213C>A	ENST00000526016.1	-	0	756					NR_038174.2				tripartite motif-containing 51H, pseudogene																		TAATATGTCTCCAAAAGACTG	0.338																																																	0																																												0					11q11	2012-11-02			ENSG00000166007	ENSG00000166007		"""Triparite motif-containing / Pseudogenes"""	43977	pseudogene	pseudogene							Standard	NR_038174		Approved		uc021qjb.1		OTTHUMG00000166775		11.37:g.55062213C>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000526016.1	37																																																																																					0.338	TRIM51HP-002	PUTATIVE	basic|exp_conf	processed_transcript	pseudogene	OTTHUMT00000391438.1			
HERC2P9	440248	broad.mit.edu	37	15	28929371	28929371	+	RNA	SNP	G	G	T			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr15:28929371G>T	ENST00000528584.1	+	0	1908					NR_036443.1				hect domain and RLD 2 pseudogene 9																		GGAAGGAAAAGGCACACGCTG	0.453																																																	0																																												0			BC047911		15q13.1	2011-05-24			ENSG00000206149	ENSG00000206149			30495	pseudogene	pseudogene							Standard	NR_036443		Approved	FLJ59185	uc010azc.3		OTTHUMG00000167114		15.37:g.28929371G>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000528584.1	37																																																																																					0.453	HERC2P9-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000393268.1		NR_036443	
Unknown	0	broad.mit.edu	37	9	88455089	88455089	+	IGR	SNP	G	G	A			TCGA-B0-5113-01A-01D-1421-08	TCGA-B0-5113-11A-01D-1421-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	64b234e0-74f6-453f-b5cb-280e01fba09b	f7b96180-6131-45d9-8a88-771bc7296cde	g.chr9:88455089G>A								RP11-213G2.2 (48640 upstream) : NAA35 (100971 downstream)																							GTTGGATCACGTAGAAGAACG	0.428																																																	0																																										SO:0001628	intergenic_variant	0																															9.37:g.88455089G>A		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP		37																																																																																				0	0.428									
