#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
BMPER	168667	hgsc.bcm.edu	37	7	34118719	34118730	+	In_Frame_Del	DEL	GCGCATCGCGCT	GCGCATCGCGCT	-			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	GCGCATCGCGCT	GCGCATCGCGCT	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr7:34118719_34118730delGCGCATCGCGCT	ENST00000297161.2	+	13	1703_1714	c.1329_1340delGCGCATCGCGCT	c.(1327-1341)tcgcgcatcgcgctc>tcc	p.RIAL444del	BMPER_ENST00000426693.1_In_Frame_Del_p.RIAL444del	NM_133468.4	NP_597725.1	Q8N8U9	BMPER_HUMAN	BMP binding endothelial regulator	444	VWFD. {ECO:0000255|PROSITE- ProRule:PRU00580}.				blood vessel endothelial cell proliferation involved in sprouting angiogenesis (GO:0002043)|endothelial cell activation (GO:0042118)|inner ear development (GO:0048839)|negative regulation of BMP signaling pathway (GO:0030514)|positive regulation of ERK1 and ERK2 cascade (GO:0070374)|regulation of endothelial cell migration (GO:0010594)|regulation of pathway-restricted SMAD protein phosphorylation (GO:0060393)|ureteric bud development (GO:0001657)	extracellular space (GO:0005615)		p.A446A(1)		breast(1)|central_nervous_system(1)|cervix(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(2)|kidney(1)|large_intestine(7)|lung(24)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	48						GGAACGGCTCGCGCATCGCGCTCCCCTGCCGC	0.656																																																	1	Substitution - coding silent(1)	lung(1)																																								SO:0001651	inframe_deletion	168667				CCDS5442.1	7p14.3	2009-02-18			ENSG00000164619	ENSG00000164619			24154	protein-coding gene	gene with protein product	"""crossveinless-2"""	608699				12897139, 14766204	Standard	NM_133468		Approved	Cv2, CRIM3	uc011kap.2	Q8N8U9	OTTHUMG00000128675	ENST00000297161.2:c.1329_1340delGCGCATCGCGCT	7.37:g.34118719_34118730delGCGCATCGCGCT	ENSP00000297161:p.Arg444_Leu447del	Somatic		WXS	Illumina HiSeq	Phase_I	A8K1P8|Q8TF36	In_Frame_Del	DEL	ENST00000297161.2	37	CCDS5442.1																																																																																				0.656	BMPER-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000250570.2		NM_133468	
C17orf80	55028	hgsc.bcm.edu	37	17	71241322	71241325	+	Intron	DEL	GTAA	GTAA	-	rs150601360|rs202220073	byFrequency	TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	GTAA	GTAA	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr17:71241322_71241325delGTAA	ENST00000535032.2	+	5	1842				C17orf80_ENST00000359042.2_Intron|C17orf80_ENST00000268942.8_Intron|C17orf80_ENST00000255557.4_Frame_Shift_Del_p.RK546fs|C17orf80_ENST00000577615.1_Intron|RP11-661C3.2_ENST00000579037.1_RNA|C17orf80_ENST00000426147.2_Frame_Shift_Del_p.RK582fs|C17orf80_ENST00000582793.1_Intron			Q9BSJ5	CQ080_HUMAN	chromosome 17 open reading frame 80							extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)				kidney(1)|large_intestine(5)|lung(2)|skin(2)|stomach(2)|urinary_tract(2)	14			LUSC - Lung squamous cell carcinoma(166;0.197)			CAGCGGTGGCGTAAGTAGTGTTGA	0.422														21	0.00419329	0.0008	0.0029	5008	,	,		17069	0.0		0.0159	False		,,,				2504	0.002																0									,,	10,3874		0,10,1932					,,	4.8	1.0			80	93,7941		2,89,3926	no	intron,frameshift,intron	C17orf80	NM_017941.4,NM_001100622.1,NM_001100621.1	,,	2,99,5858	A1A1,A1R,RR		1.1576,0.2575,0.8642	,,	,,		103,11815				SO:0001627	intron_variant	55028			AY163812	CCDS11694.1, CCDS42377.1, CCDS45767.1, CCDS74145.1	17q25.1	2012-02-24	2012-02-24	2012-02-24	ENSG00000141219	ENSG00000141219			29601	protein-coding gene	gene with protein product	"""sperm-expressed protein 1"", ""migration-inducing protein 3"""					12477932	Standard	NM_017941		Approved	HLC-8, MIG3, FLJ20721, SPEP1	uc002jjl.4	Q9BSJ5		ENST00000535032.2:c.1730-2055GTAA>-	17.37:g.71241322_71241325delGTAA		Somatic		WXS	Illumina HiSeq	Phase_I	A8K9X3|Q5JB45|Q6YAU3|Q9H0L9|Q9H5E6|Q9NWN5	Frame_Shift_Del	DEL	ENST00000535032.2	37	CCDS11694.1																																																																																				0.422	C17orf80-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000441893.1		NM_017941	
CLDN3	1365	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	7	73183930	73183930	+	Silent	SNP	C	C	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr7:73183930C>G	ENST00000395145.2	-	1	670	c.450G>C	c.(448-450)gtG>gtC	p.V150V		NM_001306.3	NP_001297.1	O15551	CLD3_HUMAN	claudin 3	150					calcium-independent cell-cell adhesion (GO:0016338)|response to hypoxia (GO:0001666)|signal transduction (GO:0007165)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|integral component of plasma membrane (GO:0005887)|lateral plasma membrane (GO:0016328)|tight junction (GO:0005923)	structural molecule activity (GO:0005198)|transmembrane signaling receptor activity (GO:0004888)	p.V150V(1)		kidney(1)|lung(1)	2		Lung NSC(55;0.159)				CCTCGGGCACCACGGGGTTGT	0.706																																																	1	Substitution - coding silent(1)	kidney(1)											25.0	25.0	25.0					7																	73183930		2198	4299	6497	SO:0001819	synonymous_variant	1365			AF007189	CCDS5559.1	7q11	2008-07-18			ENSG00000165215	ENSG00000165215		"""Claudins"""	2045	protein-coding gene	gene with protein product	"""Clostridium perfringens enterotoxin receptor 2"", ""ventral prostate.1-like protein"", ""claudin-3"", ""CPE-receptor 2"""	602910		C7orf1, CPETR2		9441748, 9892664	Standard	NM_001306		Approved	RVP1, CPE-R2, HRVP1	uc003tzg.4	O15551	OTTHUMG00000023424	ENST00000395145.2:c.450G>C	7.37:g.73183930C>G		Somatic		WXS	Illumina HiSeq	Phase_I		Silent	SNP	ENST00000395145.2	37	CCDS5559.1																																																																																				0.706	CLDN3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252310.1		NM_001306	
DNAH7	56171	broad.mit.edu;hgsc.bcm.edu	37	2	196723250	196723250	+	Missense_Mutation	SNP	G	G	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr2:196723250G>T	ENST00000312428.6	-	43	8115	c.8015C>A	c.(8014-8016)gCc>gAc	p.A2672D		NM_018897.2	NP_061720.2	Q8WXX0	DYH7_HUMAN	dynein, axonemal, heavy chain 7	2672	Stalk. {ECO:0000250}.				cilium movement (GO:0003341)|cilium or flagellum-dependent cell motility (GO:0001539)|metabolic process (GO:0008152)	axonemal dynein complex (GO:0005858)|cilium (GO:0005929)|microtubule (GO:0005874)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|calcium ion binding (GO:0005509)|microtubule motor activity (GO:0003777)	p.A2672D(2)		NS(4)|breast(2)|endometrium(12)|haematopoietic_and_lymphoid_tissue(1)|kidney(15)|large_intestine(28)|liver(3)|lung(100)|ovary(4)|prostate(5)|skin(26)|upper_aerodigestive_tract(2)|urinary_tract(3)	205						TATTGGCAAGGCACCTGCCAG	0.453																																																	2	Substitution - Missense(2)	kidney(2)											78.0	74.0	76.0					2																	196723250		1970	4159	6129	SO:0001583	missense	56171			AF327442	CCDS42794.1	2q33.1	2013-01-10	2006-09-04		ENSG00000118997	ENSG00000118997		"""Axonemal dyneins"", ""EF-hand domain containing"""	18661	protein-coding gene	gene with protein product		610061	"""dynein, axonemal, heavy polypeptide 7"""			9373155, 11877439	Standard	NM_018897		Approved	KIAA0944	uc002utj.4	Q8WXX0	OTTHUMG00000154438	ENST00000312428.6:c.8015C>A	2.37:g.196723250G>T	ENSP00000311273:p.Ala2672Asp	Somatic		WXS	Illumina HiSeq	Phase_I	B8ZZX8|O00433|O95492|Q4G152|Q53QX7|Q53S64|Q53T02|Q68CY5|Q8N1Z2|Q9UMS3|Q9Y2F3	Missense_Mutation	SNP	ENST00000312428.6	37	CCDS42794.1	.	.	.	.	.	.	.	.	.	.	G	18.92	3.725919	0.69074	.	.	ENSG00000118997	ENST00000312428	T	0.80653	-1.4	5.64	5.64	0.86602	Dynein heavy chain, coiled coil stalk (1);	0.000000	0.85682	D	0.000000	D	0.95118	0.8418	H	0.99668	4.69	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.96858	0.9630	10	0.87932	D	0	.	19.4873	0.95035	0.0:0.0:1.0:0.0	.	2672	Q8WXX0	DYH7_HUMAN	D	2672	ENSP00000311273:A2672D	ENSP00000311273:A2672D	A	-	2	0	DNAH7	196431495	1.000000	0.71417	0.996000	0.52242	0.004000	0.04260	9.544000	0.98092	2.937000	0.99478	0.650000	0.86243	GCC		0.453	DNAH7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000335202.3		NM_018897	
GLYCTK	132158	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	3	52324497	52324497	+	Missense_Mutation	SNP	G	G	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr3:52324497G>A	ENST00000436784.2	+	2	199	c.139G>A	c.(139-141)Ggt>Agt	p.G47S	GLYCTK_ENST00000354773.4_Missense_Mutation_p.G47S|GLYCTK-AS1_ENST00000493616.1_RNA|GLYCTK_ENST00000477382.1_Missense_Mutation_p.G47S|GLYCTK_ENST00000471180.1_Intron|GLYCTK_ENST00000461183.1_Intron|GLYCTK_ENST00000305690.8_Missense_Mutation_p.G47S|GLYCTK_ENST00000473032.1_Missense_Mutation_p.G47S			Q8IVS8	GLCTK_HUMAN	glycerate kinase	47					protein phosphorylation (GO:0006468)	cytoplasm (GO:0005737)|mitochondrion (GO:0005739)	ATP binding (GO:0005524)|glycerate kinase activity (GO:0008887)	p.G47S(1)		NS(1)|breast(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(3)|urinary_tract(1)	9				BRCA - Breast invasive adenocarcinoma(193;3.56e-05)|Kidney(197;0.00171)|KIRC - Kidney renal clear cell carcinoma(197;0.00194)|OV - Ovarian serous cystadenocarcinoma(275;0.235)		GAGTGCTGTAGGTGCAGTGCT	0.642																																																	1	Substitution - Missense(1)	kidney(1)											31.0	30.0	30.0					3																	52324497		2203	4300	6503	SO:0001583	missense	132158				CCDS2852.1, CCDS46841.1	3p21.1	2008-01-22			ENSG00000168237	ENSG00000168237	2.7.1.31		24247	protein-coding gene	gene with protein product		610516				16753811	Standard	NM_145262		Approved	HBEBP4, HBEBP2	uc003ddo.3	Q8IVS8	OTTHUMG00000158380	ENST00000436784.2:c.139G>A	3.37:g.52324497G>A	ENSP00000389175:p.Gly47Ser	Somatic		WXS	Illumina HiSeq	Phase_I	Q0P630|Q2EZ43|Q6Y2K6|Q7Z6G5|Q86YR8|Q8TED2|Q8WTY2	Missense_Mutation	SNP	ENST00000436784.2	37	CCDS2852.1	.	.	.	.	.	.	.	.	.	.	G	11.21	1.571865	0.28003	.	.	ENSG00000168237	ENST00000473032;ENST00000305690;ENST00000354773;ENST00000436784;ENST00000477382;ENST00000411757	T;T;T;T;T	0.39787	1.06;1.06;1.06;1.06;1.06	5.4	3.44	0.39384	.	0.220732	0.47852	D	0.000201	T	0.16471	0.0396	N	0.04508	-0.205	0.34918	D	0.748133	P;B;B	0.51933	0.949;0.066;0.014	B;B;B	0.42495	0.389;0.018;0.038	T	0.10200	-1.0640	10	0.10111	T	0.7	-7.8395	5.9756	0.19377	0.074:0.1335:0.6546:0.1379	.	47;47;47	Q8IVS8-2;Q8IVS8-4;Q8IVS8	.;.;GLCTK_HUMAN	S	47	ENSP00000418951:G47S;ENSP00000301965:G47S;ENSP00000346825:G47S;ENSP00000389175:G47S;ENSP00000419008:G47S	ENSP00000301965:G47S	G	+	1	0	GLYCTK	52299537	1.000000	0.71417	0.989000	0.46669	0.669000	0.39330	1.605000	0.36815	2.527000	0.85204	0.643000	0.83706	GGT		0.642	GLYCTK-005	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000350835.1		NM_145262	
HIST1H3I	8354	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	6	27839911	27839911	+	Silent	SNP	C	C	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr6:27839911C>T	ENST00000328488.2	-	1	188	c.183G>A	c.(181-183)ctG>ctA	p.L61L		NM_003533.2	NP_003524.1	P68431	H31_HUMAN	histone cluster 1, H3i	61					blood coagulation (GO:0007596)|chromatin organization (GO:0006325)|DNA replication-dependent nucleosome assembly (GO:0006335)|regulation of gene silencing (GO:0060968)	extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nuclear chromosome (GO:0000228)|nucleoplasm (GO:0005654)|nucleosome (GO:0000786)|nucleus (GO:0005634)|protein complex (GO:0043234)	DNA binding (GO:0003677)	p.L61L(1)		endometrium(2)|kidney(1)|lung(4)|ovary(1)|prostate(1)|upper_aerodigestive_tract(1)|urinary_tract(1)	11						TCCGGATTAGCAGCTCGGTCG	0.652																																																	1	Substitution - coding silent(1)	kidney(1)											69.0	75.0	73.0					6																	27839911		2203	4300	6503	SO:0001819	synonymous_variant	8354			X83550	CCDS4636.1	6p22.1	2011-01-27	2006-10-11	2003-02-14	ENSG00000182572	ENSG00000275379		"""Histones / Replication-dependent"""	4771	protein-coding gene	gene with protein product		602814	"""H3 histone family, member F"", ""histone 1, H3i"""	H3FF		9031620, 9439656, 12408966	Standard	NM_003533		Approved	H3/f, H3.f	uc003njy.3	P68431	OTTHUMG00000016184	ENST00000328488.2:c.183G>A	6.37:g.27839911C>T		Somatic		WXS	Illumina HiSeq	Phase_I	A0PJT7|A5PLR1|P02295|P02296|P16106|Q6ISV8|Q6NWP8|Q6NWP9|Q6NXU4|Q71DJ3|Q93081	Silent	SNP	ENST00000328488.2	37	CCDS4636.1																																																																																				0.652	HIST1H3I-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043452.1		NM_003533	
MTCL1	23255	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	18	8825236	8825236	+	Missense_Mutation	SNP	C	C	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr18:8825236C>T	ENST00000306329.11	+	13	4685	c.4685C>T	c.(4684-4686)cCc>cTc	p.P1562L	SOGA2_ENST00000400050.3_Missense_Mutation_p.P1202L|SOGA2_ENST00000518815.1_Missense_Mutation_p.P568L|SOGA2_ENST00000359865.3_Missense_Mutation_p.P1243L|SOGA2_ENST00000306285.7_Missense_Mutation_p.P568L|SOGA2_ENST00000517570.1_Missense_Mutation_p.P1202L														p.P1243L(2)									TGCACCTCCCCCAGGCACTCC	0.662																																																	2	Substitution - Missense(2)	kidney(2)											18.0	21.0	20.0					18																	8825236		2197	4295	6492	SO:0001583	missense	0																														ENST00000306329.11:c.4685C>T	18.37:g.8825236C>T	ENSP00000305027:p.Pro1562Leu	Somatic		WXS	Illumina HiSeq	Phase_I		Missense_Mutation	SNP	ENST00000306329.11	37		.	.	.	.	.	.	.	.	.	.	C	3.248	-0.153816	0.06585	.	.	ENSG00000168502	ENST00000306329;ENST00000517570;ENST00000359865;ENST00000400050;ENST00000306285	T;T;T;T	0.29397	2.58;2.58;2.58;1.57	5.24	4.35	0.52113	.	0.802924	0.10887	N	0.623129	T	0.25494	0.0620	L	0.34521	1.04	0.09310	N	1	B;B	0.25955	0.138;0.002	B;B	0.21708	0.036;0.006	T	0.19844	-1.0293	10	0.66056	D	0.02	-4.5397	10.3939	0.44190	0.144:0.6963:0.1596:0.0	.	1553;1243	Q9Y4B5;Q9Y4B5-3	CC165_HUMAN;.	L	1264;1202;1243;1202;568	ENSP00000429556:P1202L;ENSP00000352927:P1243L;ENSP00000382924:P1202L;ENSP00000303670:P568L	ENSP00000303670:P568L	P	+	2	0	CCDC165	8815236	0.805000	0.28982	0.092000	0.20876	0.024000	0.10985	1.319000	0.33655	1.176000	0.42840	0.655000	0.94253	CCC		0.662	SOGA2-015	PUTATIVE	basic|appris_candidate_longest|exp_conf	protein_coding	protein_coding	OTTHUMT00000444141.1			
CERS2	29956	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	150939585	150939585	+	Missense_Mutation	SNP	T	T	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr1:150939585T>C	ENST00000271688.6	-	8	1092	c.706A>G	c.(706-708)Atg>Gtg	p.M236V	RP11-316M1.12_ENST00000560481.1_RNA|CERS2_ENST00000561294.1_Missense_Mutation_p.M227V|RP11-316M1.12_ENST00000561111.1_RNA|CERS2_ENST00000368954.5_Missense_Mutation_p.M236V|CERS2_ENST00000345896.4_5'UTR	NM_181746.3	NP_859530.1	Q96G23	CERS2_HUMAN	ceramide synthase 2	236	TLC. {ECO:0000255|PROSITE- ProRule:PRU00205}.				ceramide biosynthetic process (GO:0046513)|small molecule metabolic process (GO:0044281)|sphingolipid biosynthetic process (GO:0030148)|sphingolipid metabolic process (GO:0006665)	endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nuclear membrane (GO:0031965)	DNA binding (GO:0003677)|sphingosine N-acyltransferase activity (GO:0050291)	p.M236V(2)									TGCAGAGCCATGATTAGAGTC	0.488																																																	2	Substitution - Missense(2)	kidney(2)											97.0	93.0	95.0					1																	150939585		2203	4300	6503	SO:0001583	missense	0			AF189062	CCDS973.1	1q21.3	2012-09-20	2011-07-08	2011-07-08	ENSG00000143418	ENSG00000143418		"""Homeoboxes / CERS class"""	14076	protein-coding gene	gene with protein product		606920	"""longevity assurance (LAG1, S. cerevisiae) homolog 2"", ""LAG1 longevity assurance homolog 2 (S. cerevisiae)"", ""LAG1 homolog, ceramide synthase 2"""	LASS2		11543633	Standard	NM_181746		Approved	SP260, FLJ10243	uc001evz.3	Q96G23	OTTHUMG00000035064	ENST00000271688.6:c.706A>G	1.37:g.150939585T>C	ENSP00000271688:p.Met236Val	Somatic		WXS	Illumina HiSeq	Phase_I	D3DV06|Q5SZE5|Q9HD96|Q9NW79	Missense_Mutation	SNP	ENST00000271688.6	37	CCDS973.1	.	.	.	.	.	.	.	.	.	.	T	16.34	3.096317	0.56075	.	.	ENSG00000143418	ENST00000368954;ENST00000271688;ENST00000345896;ENST00000368949;ENST00000361419	D;D;D;D;D	0.85861	-2.04;-2.04;-2.04;-2.04;-2.04	5.42	5.42	0.78866	TRAM/LAG1/CLN8 homology domain (3);	0.000000	0.85682	D	0.000000	T	0.82208	0.4987	M	0.82323	2.585	0.80722	D	1	P	0.38148	0.62	B	0.36378	0.223	D	0.86292	0.1674	10	0.87932	D	0	-25.1355	15.1277	0.72494	0.0:0.0:0.0:1.0	.	236	Q96G23	CERS2_HUMAN	V	236;236;86;256;236	ENSP00000357950:M236V;ENSP00000271688:M236V;ENSP00000337842:M86V;ENSP00000357945:M256V;ENSP00000355020:M236V	ENSP00000271688:M236V	M	-	1	0	CERS2	149206209	1.000000	0.71417	1.000000	0.80357	0.886000	0.51366	3.980000	0.56895	2.058000	0.61347	0.533000	0.62120	ATG		0.488	CERS2-201	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000084897.2		NM_022075	
MGST3	4259	hgsc.bcm.edu	37	1	165624711	165624712	+	Frame_Shift_Ins	INS	-	-	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr1:165624711_165624712insT	ENST00000367889.3	+	6	869_870	c.429_430insT	c.(430-432)ttgfs	p.L144fs	MGST3_ENST00000367884.2_Frame_Shift_Ins_p.L144fs|MGST3_ENST00000367885.1_Frame_Shift_Ins_p.L158fs|MGST3_ENST00000367888.4_Intron|MGST3_ENST00000367886.2_Frame_Shift_Ins_p.L158fs|MGST3_ENST00000367883.1_Frame_Shift_Ins_p.L158fs	NM_004528.3	NP_004519.1	O14880	MGST3_HUMAN	microsomal glutathione S-transferase 3	144					glutathione derivative biosynthetic process (GO:1901687)|lipid metabolic process (GO:0006629)|oxidation-reduction process (GO:0055114)|signal transduction (GO:0007165)|small molecule metabolic process (GO:0044281)|xenobiotic metabolic process (GO:0006805)	endoplasmic reticulum membrane (GO:0005789)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|nuclear envelope (GO:0005635)	glutathione peroxidase activity (GO:0004602)|glutathione transferase activity (GO:0004364)|peroxidase activity (GO:0004601)			endometrium(1)|large_intestine(1)|lung(3)|prostate(1)	6	all_hematologic(923;0.0773)|Acute lymphoblastic leukemia(8;0.155)				Glutathione(DB00143)	TTAAAAGTGGCTTGGGCAGTGG	0.455																																																	0																																										SO:0001589	frameshift_variant	4259			AF026977	CCDS1249.1	1q23	2012-06-21			ENSG00000143198	ENSG00000143198	2.5.1.18	"""Glutathione S-transferases / Microsomal"""	7064	protein-coding gene	gene with protein product	"""microsomal glutathione S-transferase III"", ""microsomal GST-3"", ""microsomal GST-III"""	604564				9278457	Standard	NM_004528		Approved	GST-III	uc001gdf.3	O14880	OTTHUMG00000034627	ENST00000367889.3:c.431dupT	1.37:g.165624713_165624713dupT	ENSP00000356864:p.Leu144fs	Somatic		WXS	Illumina HiSeq	Phase_I	B2R592|Q6ICN4	Frame_Shift_Ins	INS	ENST00000367889.3	37	CCDS1249.1																																																																																				0.455	MGST3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000083797.3		NM_004528	
NOSIP	51070	broad.mit.edu;hgsc.bcm.edu	37	19	50060397	50060397	+	Missense_Mutation	SNP	C	C	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr19:50060397C>G	ENST00000596358.1	-	5	426	c.368G>C	c.(367-369)aGc>aCc	p.S123T	NOSIP_ENST00000391853.3_Missense_Mutation_p.S123T|NOSIP_ENST00000339093.3_Missense_Mutation_p.S123T	NM_001270960.1	NP_001257889.1	Q9Y314	NOSIP_HUMAN	nitric oxide synthase interacting protein	123					negative regulation of catalytic activity (GO:0043086)|negative regulation of nitric-oxide synthase activity (GO:0051001)|nitric oxide metabolic process (GO:0046209)|regulation of nitric-oxide synthase activity (GO:0050999)|small molecule metabolic process (GO:0044281)	cytoplasm (GO:0005737)|cytosol (GO:0005829)|Golgi membrane (GO:0000139)|nucleus (GO:0005634)	poly(A) RNA binding (GO:0044822)	p.S123T(2)		cervix(1)|endometrium(1)|kidney(2)|large_intestine(2)|lung(1)|ovary(1)|skin(2)|urinary_tract(1)	11		all_lung(116;7.84e-06)|Lung NSC(112;2.8e-05)|all_neural(266;0.0966)|Ovarian(192;0.231)		OV - Ovarian serous cystadenocarcinoma(262;0.00321)|GBM - Glioblastoma multiforme(134;0.0133)		GAGGGGCCGGCTCACGATAGC	0.697																																																	2	Substitution - Missense(2)	kidney(2)											25.0	28.0	27.0					19																	50060397		2203	4300	6503	SO:0001583	missense	51070			AF132959	CCDS12772.1	19q13.3	2008-02-05				ENSG00000142546			17946	protein-coding gene	gene with protein product						11149895, 10810093	Standard	NM_015953		Approved	CGI-25	uc002pol.4	Q9Y314		ENST00000596358.1:c.368G>C	19.37:g.50060397C>G	ENSP00000470034:p.Ser123Thr	Somatic		WXS	Illumina HiSeq	Phase_I	Q96FD2	Missense_Mutation	SNP	ENST00000596358.1	37	CCDS12772.1	.	.	.	.	.	.	.	.	.	.	C	10.22	1.290280	0.23478	.	.	ENSG00000142546	ENST00000339093;ENST00000391853	T;T	0.78003	-1.14;-1.14	5.15	4.05	0.47172	.	0.104089	0.64402	D	0.000004	T	0.69860	0.3158	L	0.39514	1.22	0.58432	D	0.999998	D	0.52996	0.957	P	0.45712	0.491	T	0.66348	-0.5946	10	0.10636	T	0.68	-55.6421	14.0315	0.64617	0.0:0.8475:0.1524:0.0	.	123	Q9Y314	NOSIP_HUMAN	T	123	ENSP00000343497:S123T;ENSP00000375726:S123T	ENSP00000343497:S123T	S	-	2	0	NOSIP	54752209	1.000000	0.71417	1.000000	0.80357	0.067000	0.16453	1.868000	0.39509	2.409000	0.81822	0.462000	0.41574	AGC		0.697	NOSIP-001	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000465423.1			
NOXO1	124056	hgsc.bcm.edu	37	16	2031172	2031173	+	Frame_Shift_Ins	INS	-	-	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr16:2031172_2031173insC	ENST00000397280.4	-	1	11_12	c.8_9insG	c.(7-9)ggcfs	p.G3fs	NOXO1_ENST00000566005.1_Frame_Shift_Ins_p.G3fs|AC005606.1_ENST00000598236.1_5'Flank|NOXO1_ENST00000354249.4_Frame_Shift_Ins_p.G3fs|NOXO1_ENST00000356120.4_Frame_Shift_Ins_p.G3fs|TBL3_ENST00000568546.1_3'UTR			Q8NFA2	NOXO1_HUMAN	NADPH oxidase organizer 1	3	PX. {ECO:0000255|PROSITE- ProRule:PRU00147}.				extracellular matrix disassembly (GO:0022617)|regulation of hydrogen peroxide metabolic process (GO:0010310)|regulation of respiratory burst (GO:0060263)|superoxide metabolic process (GO:0006801)	NADPH oxidase complex (GO:0043020)	enzyme binding (GO:0019899)|identical protein binding (GO:0042802)|phosphatidylinositol binding (GO:0035091)|phospholipid binding (GO:0005543)|superoxide-generating NADPH oxidase activator activity (GO:0016176)			lung(2)	2					Ecabet(DB05265)	GGTATCGGGGGCCTGCCATGGC	0.614																																					Pancreas(104;2811 2841 4129)|Esophageal Squamous(25;910 1225 43728)												0																																										SO:0001589	frameshift_variant	124056			AF532985	CCDS10454.1, CCDS10455.1, CCDS42101.1, CCDS58406.1	16p13.3	2008-02-05			ENSG00000196408	ENSG00000196408			19404	protein-coding gene	gene with protein product		611256					Standard	NM_144603		Approved	P41NOXA, P41NOXB, P41NOXC, SH3PXD5, SNX28	uc002cnx.4	Q8NFA2	OTTHUMG00000128707	ENST00000397280.4:c.9dupG	16.37:g.2031174_2031174dupC	ENSP00000380450:p.Gly3fs	Somatic		WXS	Illumina HiSeq	Phase_I	Q86YM1|Q8NFA3|Q96B73	Frame_Shift_Ins	INS	ENST00000397280.4	37	CCDS42101.1																																																																																				0.614	NOXO1-003	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000250612.1			
SBNO2	22904	broad.mit.edu;hgsc.bcm.edu	37	19	1112193	1112193	+	Missense_Mutation	SNP	T	T	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr19:1112193T>C	ENST00000361757.3	-	22	2860	c.2623A>G	c.(2623-2625)Agt>Ggt	p.S875G	SBNO2_ENST00000587024.1_Missense_Mutation_p.S865G|SBNO2_ENST00000438103.2_Missense_Mutation_p.S818G	NM_014963.2	NP_055778.2	Q9Y2G9	SBNO2_HUMAN	strawberry notch homolog 2 (Drosophila)	875					bone mineralization (GO:0030282)|bone trabecula morphogenesis (GO:0061430)|macrophage activation involved in immune response (GO:0002281)|negative regulation of transcription, DNA-templated (GO:0045892)|osteoclast fusion (GO:0072675)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|regulation of inflammatory response (GO:0050727)|transcription, DNA-templated (GO:0006351)			p.S882G(2)|p.S875G(2)		NS(1)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(2)|lung(2)|upper_aerodigestive_tract(1)|urinary_tract(1)	14		Acute lymphoblastic leukemia(61;2.53e-14)|all_hematologic(61;8.18e-10)|Lung NSC(49;7.93e-06)|all_lung(49;1.25e-05)|Breast(49;0.000172)|Hepatocellular(1079;0.137)		UCEC - Uterine corpus endometrioid carcinoma (162;6.64e-05)|OV - Ovarian serous cystadenocarcinoma(105;1.09e-113)|Epithelial(107;3.79e-112)|all cancers(105;1.67e-104)|BRCA - Breast invasive adenocarcinoma(158;0.00136)|STAD - Stomach adenocarcinoma(1328;0.18)		CTCACCAGACTCTCCAGGCGC	0.657																																																	4	Substitution - Missense(4)	kidney(4)											13.0	16.0	15.0					19																	1112193		1935	4127	6062	SO:0001583	missense	22904			AK074102	CCDS45894.1, CCDS45895.1	19p13.3	2008-02-05	2006-10-06	2006-10-06		ENSG00000064932			29158	protein-coding gene	gene with protein product		615729	"""KIAA0963"""	KIAA0963		10231032	Standard	NM_014963		Approved	FLJ00173, Stno, Sno	uc002lrk.4	Q9Y2G9		ENST00000361757.3:c.2623A>G	19.37:g.1112193T>C	ENSP00000354733:p.Ser875Gly	Somatic		WXS	Illumina HiSeq	Phase_I	A8K8P2|B3KWJ1|O75257|Q3KQX0|Q8TEM0	Missense_Mutation	SNP	ENST00000361757.3	37	CCDS45894.1	.	.	.	.	.	.	.	.	.	.	T	26.6	4.756695	0.89843	.	.	ENSG00000064932	ENST00000361757;ENST00000438103;ENST00000250872	T;T	0.75477	-0.94;-0.94	4.7	4.7	0.59300	.	0.041945	0.85682	D	0.000000	D	0.88695	0.6506	M	0.93062	3.375	0.45733	D	0.998632	D;D	0.89917	1.0;0.999	D;D	0.83275	0.996;0.994	D	0.91337	0.5094	10	0.87932	D	0	-25.4377	13.6202	0.62132	0.0:0.0:0.0:1.0	.	875;818	Q9Y2G9;Q9Y2G9-3	SBNO2_HUMAN;.	G	875;818;882	ENSP00000354733:S875G;ENSP00000400762:S818G	ENSP00000250872:S882G	S	-	1	0	SBNO2	1063193	1.000000	0.71417	1.000000	0.80357	0.874000	0.50279	7.778000	0.85637	1.882000	0.54519	0.368000	0.22195	AGT		0.657	SBNO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000458065.2		NM_014963	
SPAG1	6674	hgsc.bcm.edu	37	8	101206459	101206460	+	In_Frame_Ins	INS	-	-	GAC	rs72062044|rs56246127	byFrequency	TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr8:101206459_101206460insGAC	ENST00000388798.2	+	10	1250_1251	c.1059_1060insGAC	c.(1060-1062)agc>GACagc	p.353_354insD	SPAG1_ENST00000251809.3_In_Frame_Ins_p.353_354insD|SPAG1_ENST00000520508.1_In_Frame_Ins_p.353_354insD|SPAG1_ENST00000520643.1_In_Frame_Ins_p.353_354insD	NM_003114.4	NP_003105.2	Q07617	SPAG1_HUMAN	sperm associated antigen 1	353					axonemal dynein complex assembly (GO:0070286)|single fertilization (GO:0007338)	cytoplasm (GO:0005737)|microtubule cytoskeleton (GO:0015630)|nucleus (GO:0005634)	GTP binding (GO:0005525)|hydrolase activity (GO:0016787)			central_nervous_system(1)|cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(10)|ovary(2)|pancreas(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	30	all_cancers(14;2.35e-05)|all_epithelial(15;5.2e-08)|Lung NSC(17;0.000283)|all_lung(17;0.000823)	Breast(495;0.195)	Epithelial(11;1.12e-09)|all cancers(13;1.26e-07)|OV - Ovarian serous cystadenocarcinoma(57;4.37e-05)|STAD - Stomach adenocarcinoma(118;0.0525)	KIRC - Kidney renal clear cell carcinoma(542;0.00178)|READ - Rectum adenocarcinoma(644;0.236)		AAGAAGGAAAAAGCGGAAGAAA	0.356														753	0.150359	0.0537	0.2392	5008	,	,		16467	0.0734		0.2117	False		,,,				2504	0.2342																0									,	320,3944		14,292,1826					,	0.9	0.0		dbSNP_130	64	1643,6611		162,1319,2646	no	coding,coding	SPAG1	NM_172218.2,NM_003114.4	,	176,1611,4472	A1A1,A1R,RR		19.9055,7.5047,15.6814	,	,		1963,10555				SO:0001652	inframe_insertion	6674			AF311312	CCDS34930.1	8q22	2014-01-21			ENSG00000104450	ENSG00000104450		"""Tetratricopeptide (TTC) repeat domain containing"""	11212	protein-coding gene	gene with protein product		603395				16368546	Standard	NM_172218		Approved	SP75, FLJ32920, HSD-3.8, TPIS, CT140	uc003yjh.2	Q07617	OTTHUMG00000164706	Exception_encountered	8.37:g.101206459_101206460insGAC	ENSP00000373450:p.Lys353_Ser354insAsp	Somatic		WXS	Illumina HiSeq	Phase_I	A6NP70|B3KQ58|G3XAM3|Q7Z5G1	In_Frame_Ins	INS	ENST00000388798.2	37	CCDS34930.1																																																																																				0.356	SPAG1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000379853.2		NM_172218	
ESPNP	284729	broad.mit.edu	37	1	17034125	17034126	+	RNA	INS	-	-	AGCT	rs141324796|rs79472512	byFrequency	TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	-	-	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr1:17034125_17034126insAGCT	ENST00000492551.1	-	0	477_478					NR_026567.1				espin pseudogene																		CAGCAGCAGCCAGCTGAGCACC	0.718														1500	0.299521	0.1188	0.3444	5008	,	,		24180	0.4177		0.3101	False		,,,				2504	0.3793																0																																												284729			AL035288		1p36.13	2013-05-22			ENSG00000268869	ENSG00000268869			23285	pseudogene	pseudogene						15286153	Standard	NR_026567		Approved		uc001azn.1		OTTHUMG00000000803		1.37:g.17034126_17034129dupAGCT		Somatic		WXS	Illumina GAIIx	Phase_I		Frame_Shift_Ins	INS	ENST00000492551.1	37																																																																																					0.718	ESPNP-002	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000326311.1			
ZBTB18	10472	broad.mit.edu;hgsc.bcm.edu;ucsc.edu	37	1	244218338	244218338	+	Missense_Mutation	SNP	G	G	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr1:244218338G>T	ENST00000358704.4	+	2	1411	c.1262G>T	c.(1261-1263)tGc>tTc	p.C421F		NM_001278196.1|NM_006352.4|NM_205768.2	NP_001265125.1|NP_006343.2|NP_991331.1	Q99592	ZBT18_HUMAN	zinc finger and BTB domain containing 18	412	Interaction with DNMT3A.				cerebellum development (GO:0021549)|cerebral cortex development (GO:0021987)|hippocampus development (GO:0021766)|homeostasis of number of cells (GO:0048872)|in utero embryonic development (GO:0001701)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|negative regulation of transcription, DNA-templated (GO:0045892)|neuron development (GO:0048666)|regulation of cell division (GO:0051302)|skeletal muscle tissue development (GO:0007519)|transcription, DNA-templated (GO:0006351)	intercellular bridge (GO:0045171)|microtubule cytoskeleton (GO:0015630)|nuclear chromosome (GO:0000228)|nucleus (GO:0005634)	DNA binding (GO:0003677)|metal ion binding (GO:0046872)|sequence-specific DNA binding (GO:0043565)|sequence-specific DNA binding transcription factor activity (GO:0003700)	p.C412F(2)									GTGCCCACGTGCTCGCTGTGT	0.632																																																	2	Substitution - Missense(2)	kidney(2)											61.0	62.0	62.0					1																	244218338		2203	4300	6503	SO:0001583	missense	0			U38896	CCDS1622.1	1q44	2013-09-19	2013-01-09	2013-01-09	ENSG00000179456	ENSG00000179456		"""-"", ""BTB/POZ domain containing"", ""Zinc fingers, C2H2-type"""	13030	protein-coding gene	gene with protein product		608433	"""zinc finger protein 238"""	ZNF238		9568537, 9013868	Standard	NM_205768		Approved	C2H2-171, TAZ-1, RP58	uc031psv.1	Q99592	OTTHUMG00000040013	ENST00000358704.4:c.1262G>T	1.37:g.244218338G>T	ENSP00000351539:p.Cys421Phe	Somatic		WXS	Illumina HiSeq	Phase_I	A8K5U3|Q13397|Q5VU40|Q8N463|Q9UD99	Missense_Mutation	SNP	ENST00000358704.4	37	CCDS1622.1	.	.	.	.	.	.	.	.	.	.	G	17.48	3.399627	0.62177	.	.	ENSG00000179456	ENST00000366538;ENST00000358704	D	0.85411	-1.98	5.84	5.84	0.93424	Zinc finger, C2H2-like (1);Zinc finger, C2H2 (3);Zinc finger, C2H2-type/integrase, DNA-binding (1);	0.000000	0.85682	D	0.000000	D	0.89417	0.6709	L	0.34521	1.04	0.80722	D	1	D;D	0.69078	0.995;0.997	D;D	0.78314	0.979;0.991	D	0.89992	0.4108	10	0.87932	D	0	.	20.1379	0.98040	0.0:0.0:1.0:0.0	.	412;421	Q99592;Q99592-2	ZN238_HUMAN;.	F	421	ENSP00000351539:C421F	ENSP00000351539:C421F	C	+	2	0	ZNF238	242284961	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	9.869000	0.99810	2.779000	0.95612	0.655000	0.94253	TGC		0.632	ZBTB18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000096513.2		NM_205768	
GOLGA6L10	647042	broad.mit.edu	37	15	82635117	82635117	+	IGR	SNP	T	T	C	rs201663151	byFrequency	TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	T	T	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr15:82635117T>C	ENST00000439287.4	-	0	1540					NM_001164465.1	NP_001157937.1	A6NI86	GG6LA_HUMAN	golgin A6 family-like 10											endometrium(1)|kidney(4)	5						TTTTTCAATTTCTTGACCCGC	0.403																																																	0																																										SO:0001628	intergenic_variant	647042				CCDS45325.1	15q25.2	2014-08-13	2010-02-12		ENSG00000278662				37228	protein-coding gene	gene with protein product			"""golgi autoantigen, golgin subfamily a, 6-like 10"", ""golgin A6 family-like 18"""	GOLGA6L18			Standard	XM_006720643		Approved		uc021ssn.1	A6NI86	OTTHUMG00000172580		15.37:g.82635117T>C		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000439287.4	37	CCDS45325.1																																																																																				0.403	GOLGA6L10-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000419403.2		NM_001164465	
KIF1A	547	broad.mit.edu	37	2	241660401	241660401	+	Missense_Mutation	SNP	C	C	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr2:241660401C>A	ENST00000320389.7	-	43	4653	c.4495G>T	c.(4495-4497)Gtg>Ttg	p.V1499L	KIF1A_ENST00000498729.2_Missense_Mutation_p.V1600L	NM_004321.6	NP_004312.2	Q12756	KIF1A_HUMAN	kinesin family member 1A	1499					anterograde axon cargo transport (GO:0008089)|ATP catabolic process (GO:0006200)|cell death (GO:0008219)|cytoskeleton-dependent intracellular transport (GO:0030705)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|vesicle-mediated transport (GO:0016192)	cytoplasm (GO:0005737)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|neuron projection (GO:0043005)|neuronal cell body (GO:0043025)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|motor activity (GO:0003774)|plus-end-directed microtubule motor activity (GO:0008574)	p.V1499L(1)		NS(1)|central_nervous_system(2)|endometrium(14)|haematopoietic_and_lymphoid_tissue(1)|kidney(6)|large_intestine(8)|lung(25)|ovary(1)|prostate(5)|skin(2)|urinary_tract(1)	66		all_epithelial(40;1.35e-15)|Breast(86;2.14e-05)|Renal(207;0.00183)|Ovarian(221;0.0228)|all_lung(227;0.0295)|all_neural(83;0.0459)|Lung NSC(271;0.0942)|all_hematologic(139;0.158)|Melanoma(123;0.16)|Hepatocellular(293;0.244)		Epithelial(32;6.12e-30)|all cancers(36;3.46e-27)|OV - Ovarian serous cystadenocarcinoma(60;1.38e-14)|Kidney(56;5e-09)|KIRC - Kidney renal clear cell carcinoma(57;5e-08)|BRCA - Breast invasive adenocarcinoma(100;5.87e-06)|Lung(119;0.00209)|LUSC - Lung squamous cell carcinoma(224;0.00902)|Colorectal(34;0.0282)|COAD - Colon adenocarcinoma(134;0.176)		AGAGTGGCCACCCCTAGAGGG	0.647																																																	1	Substitution - Missense(1)	kidney(1)											21.0	27.0	25.0					2																	241660401		2000	4165	6165	SO:0001583	missense	547			AF004425	CCDS46561.1, CCDS58757.1	2q37.2	2014-09-17	2004-01-09	2004-01-14	ENSG00000130294	ENSG00000130294		"""Kinesins"", ""Pleckstrin homology (PH) domain containing"""	888	protein-coding gene	gene with protein product		601255	"""axonal transport of synaptic vesicles"", ""chromosome 2 open reading frame 20"", ""spastic paraplegia 30 (autosomal recessive)"""	ATSV, C2orf20, SPG30		7539720, 10323250, 22258533	Standard	NM_001244008		Approved	UNC104	uc010fzk.3	Q12756	OTTHUMG00000151940	ENST00000320389.7:c.4495G>T	2.37:g.241660401C>A	ENSP00000322791:p.Val1499Leu	Somatic		WXS	Illumina GAIIx	Phase_I	B0I1S5|F5H045|O95068|Q13355|Q14752|Q2NKJ6|Q4LE42|Q53T78|Q59GH1|Q63Z40|Q6P1R9|Q7KZ57	Missense_Mutation	SNP	ENST00000320389.7	37	CCDS46561.1	.	.	.	.	.	.	.	.	.	.	C	7.745	0.702152	0.15172	.	.	ENSG00000130294	ENST00000320389;ENST00000498729;ENST00000373308	T;T	0.71341	-0.48;-0.56	4.02	2.17	0.27698	.	0.403999	0.22033	U	0.065565	T	0.52980	0.1768	L	0.29908	0.895	0.09310	N	1	B;B	0.06786	0.0;0.001	B;B	0.06405	0.002;0.002	T	0.33752	-0.9856	10	0.23891	T	0.37	.	8.1737	0.31270	0.0:0.7492:0.1603:0.0904	.	1600;1499	F5H045;Q12756	.;KIF1A_HUMAN	L	1499;1600;1608	ENSP00000322791:V1499L;ENSP00000438388:V1600L	ENSP00000322791:V1499L	V	-	1	0	KIF1A	241309074	0.000000	0.05858	0.346000	0.25655	0.642000	0.38348	-0.005000	0.12855	0.681000	0.31386	-0.150000	0.13652	GTG		0.647	KIF1A-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000324536.3		NM_138483	
PCDHGA8	9708	broad.mit.edu	37	5	140774176	140774176	+	Missense_Mutation	SNP	G	G	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr5:140774176G>T	ENST00000398604.2	+	1	1796	c.1796G>T	c.(1795-1797)gGc>gTc	p.G599V	PCDHGA6_ENST00000517434.1_Intron|PCDHGB3_ENST00000576222.1_Intron|PCDHGB4_ENST00000519479.1_Intron|PCDHGA7_ENST00000518325.1_Intron|PCDHGA2_ENST00000394576.2_Intron|PCDHGB1_ENST00000523390.1_Intron|PCDHGA4_ENST00000571252.1_Intron|PCDHGB2_ENST00000522605.1_Intron|PCDHGA3_ENST00000253812.6_Intron|PCDHGA1_ENST00000517417.1_Intron|PCDHGA5_ENST00000518069.1_Intron	NM_032088.1	NP_114477.1	Q9Y5G5	PCDG8_HUMAN	protocadherin gamma subfamily A, 8	599	Cadherin 6. {ECO:0000255|PROSITE- ProRule:PRU00043}.				homophilic cell adhesion (GO:0007156)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	calcium ion binding (GO:0005509)	p.G599V(3)		endometrium(6)|kidney(6)|large_intestine(6)|lung(30)|ovary(1)|stomach(1)|upper_aerodigestive_tract(1)	51			KIRC - Kidney renal clear cell carcinoma(527;0.00112)|Kidney(363;0.00191)			AGAGACTCGGGCCAGAACGCC	0.706																																																	3	Substitution - Missense(3)	kidney(3)																																								SO:0001583	missense	9708			AF152515	CCDS47291.1, CCDS75338.1	5q31	2010-01-26			ENSG00000253767	ENSG00000253767		"""Cadherins / Protocadherins : Clustered"""	8706	other	protocadherin		606295				10380929	Standard	NM_014004		Approved	KIAA0327, PCDH-GAMMA-A8		Q9Y5G5	OTTHUMG00000164053	ENST00000398604.2:c.1796G>T	5.37:g.140774176G>T	ENSP00000381605:p.Gly599Val	Somatic		WXS	Illumina GAIIx	Phase_I	A7MCZ4|O15039	Missense_Mutation	SNP	ENST00000398604.2	37	CCDS47291.1	.	.	.	.	.	.	.	.	.	.	.	18.62	3.662262	0.67700	.	.	ENSG00000253767	ENST00000398604	T	0.21361	2.01	4.96	4.96	0.65561	Cadherin (4);Cadherin-like (1);	0.000000	0.31624	U	0.007336	T	0.68751	0.3035	H	0.99697	4.71	0.80722	D	1	D;D	0.89917	1.0;1.0	D;D	0.97110	1.0;1.0	D	0.85054	0.0930	10	0.87932	D	0	.	17.843	0.88720	0.0:0.0:1.0:0.0	.	599;599	Q9Y5G5;Q9Y5G5-2	PCDG8_HUMAN;.	V	599	ENSP00000381605:G599V	ENSP00000381605:G599V	G	+	2	0	PCDHGA8	140754360	1.000000	0.71417	0.974000	0.42286	0.997000	0.91878	7.609000	0.82925	2.308000	0.77769	0.655000	0.94253	GGC		0.706	PCDHGA8-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000376972.1		NM_032088	
PF4	5196	broad.mit.edu	37	4	74847209	74847209	+	Missense_Mutation	SNP	G	G	A			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	G	G	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr4:74847209G>A	ENST00000296029.3	-	2	313	c.143C>T	c.(142-144)tCc>tTc	p.S48F		NM_002619.3	NP_002610.1	P02776	PLF4_HUMAN	platelet factor 4	48					blood coagulation (GO:0007596)|cytokine-mediated signaling pathway (GO:0019221)|immune response (GO:0006955)|leukocyte chemotaxis (GO:0030595)|negative regulation of angiogenesis (GO:0016525)|negative regulation of cytolysis (GO:0045918)|negative regulation of extrinsic apoptotic signaling pathway in absence of ligand (GO:2001240)|negative regulation of megakaryocyte differentiation (GO:0045653)|negative regulation of MHC class II biosynthetic process (GO:0045347)|platelet activation (GO:0030168)|platelet degranulation (GO:0002576)|positive regulation of cAMP metabolic process (GO:0030816)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of gene expression (GO:0010628)|positive regulation of macrophage derived foam cell differentiation (GO:0010744)|positive regulation of macrophage differentiation (GO:0045651)|positive regulation of transcription from RNA polymerase II promoter (GO:0045944)|positive regulation of tumor necrosis factor production (GO:0032760)|regulation of cell proliferation (GO:0042127)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|platelet alpha granule lumen (GO:0031093)	chemokine activity (GO:0008009)|CXCR3 chemokine receptor binding (GO:0048248)|heparin binding (GO:0008201)	p.S48F(1)		kidney(1)|lung(1)	2	Breast(15;0.00136)		all cancers(17;0.0034)|Lung(101;0.196)		Drotrecogin alfa(DB00055)	ACGGACCTGGGAGGTGGTCTT	0.602																																																	1	Substitution - Missense(1)	kidney(1)											68.0	62.0	64.0					4																	74847209		2203	4296	6499	SO:0001583	missense	5196			M25897	CCDS3562.1	4q12-q21	2012-10-02	2008-08-29		ENSG00000163737	ENSG00000163737			8861	protein-coding gene	gene with protein product	"""chemokine (C-X-C motif) ligand 4"""	173460	"""platelet factor 4"""			3622011	Standard	NM_002619		Approved	SCYB4, CXCL4	uc003hhi.3	P02776	OTTHUMG00000130009	ENST00000296029.3:c.143C>T	4.37:g.74847209G>A	ENSP00000296029:p.Ser48Phe	Somatic		WXS	Illumina GAIIx	Phase_I	Q53X61|Q9UC64|Q9UC65	Missense_Mutation	SNP	ENST00000296029.3	37	CCDS3562.1	.	.	.	.	.	.	.	.	.	.	G	17.89	3.500403	0.64298	.	.	ENSG00000163737	ENST00000296029	T	0.06068	3.35	2.63	1.63	0.23807	CXC chemokine, conserved site (1);Chemokine interleukin-8-like domain (3);	0.576564	0.18332	N	0.144449	T	0.24470	0.0593	M	0.89904	3.07	0.09310	N	1	D	0.89917	1.0	D	0.79108	0.992	T	0.01795	-1.1272	10	0.87932	D	0	.	5.9293	0.19130	0.0:0.0:0.69:0.31	.	48	P02776	PLF4_HUMAN	F	48	ENSP00000296029:S48F	ENSP00000296029:S48F	S	-	2	0	PF4	75066073	0.001000	0.12720	0.002000	0.10522	0.978000	0.69477	0.727000	0.25999	1.472000	0.48140	0.305000	0.20034	TCC		0.602	PF4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000252282.1			
POM121L9P	29774	broad.mit.edu	37	22	24659591	24659591	+	RNA	SNP	A	A	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	A	A	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr22:24659591A>G	ENST00000414583.2	+	0	3116					NR_003714.1				POM121 transmembrane nucleoporin-like 9, pseudogene																		ACTCACTGACATCGAAGGCTG	0.632																																																	0																																												29774			AL040062, AL117401		22q11.22	2012-03-13	2012-03-13		ENSG00000128262	ENSG00000128262			30080	pseudogene	pseudogene			"""POM121 membrane glycoprotein-like 9, pseudogene"""				Standard	NR_003714		Approved				OTTHUMG00000150763		22.37:g.24659591A>G		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000414583.2	37																																																																																					0.632	POM121L9P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000319991.1		NM_014549	
POM121L9P	29774	broad.mit.edu	37	22	24659593	24659593	+	RNA	SNP	C	C	T			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr22:24659593C>T	ENST00000414583.2	+	0	3118					NR_003714.1				POM121 transmembrane nucleoporin-like 9, pseudogene																		TCACTGACATCGAAGGCTGCC	0.632																																																	0																																												29774			AL040062, AL117401		22q11.22	2012-03-13	2012-03-13		ENSG00000128262	ENSG00000128262			30080	pseudogene	pseudogene			"""POM121 membrane glycoprotein-like 9, pseudogene"""				Standard	NR_003714		Approved				OTTHUMG00000150763		22.37:g.24659593C>T		Somatic		WXS	Illumina GAIIx	Phase_I		RNA	SNP	ENST00000414583.2	37																																																																																					0.632	POM121L9P-001	KNOWN	basic	processed_transcript	pseudogene	OTTHUMT00000319991.1		NM_014549	
PTPN18	26469	broad.mit.edu	37	2	131129929	131129934	+	In_Frame_Del	DEL	GACGGG	GACGGG	-	rs112040677	byFrequency	TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	GACGGG	GACGGG	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr2:131129929_131129934delGACGGG	ENST00000175756.5	+	13	1214_1219	c.1113_1118delGACGGG	c.(1111-1119)cagacgggg>cag	p.TG378del	PTPN18_ENST00000347849.3_In_Frame_Del_p.TG271del	NM_014369.3	NP_055184.2	Q99952	PTN18_HUMAN	protein tyrosine phosphatase, non-receptor type 18 (brain-derived)	378				Missing (in Ref. 1; CAA56105). {ECO:0000305}.	peptidyl-tyrosine dephosphorylation (GO:0035335)|protein dephosphorylation (GO:0006470)	cytoplasm (GO:0005737)|nucleus (GO:0005634)	non-membrane spanning protein tyrosine phosphatase activity (GO:0004726)	p.T378_G379delTG(1)		endometrium(1)|kidney(3)|large_intestine(2)|lung(5)|ovary(3)|prostate(1)	15	Colorectal(110;0.1)					gtgggacgcagacggggacggggacg	0.777														1724	0.344249	0.6324	0.2349	5008	,	,		12983	0.3214		0.2008	False		,,,				2504	0.2035																1	Deletion - In frame(1)	prostate(1)							,	1068,966		446,176,395					,	-3.8	0.0		dbSNP_132	3	951,4205		280,391,1907	no	coding,coding	PTPN18	NM_014369.3,NM_001142370.1	,	726,567,2302	A1A1,A1R,RR		18.4445,47.4926,28.0807	,	,		2019,5171				SO:0001651	inframe_deletion	26469			X79568	CCDS2161.1, CCDS46410.1	2q21	2011-06-09			ENSG00000072135	ENSG00000072135		"""Protein tyrosine phosphatases / Class I Cys-based PTPs : Non-receptor"""	9649	protein-coding gene	gene with protein product		606587				8950995	Standard	NM_014369		Approved	BDP1	uc002trc.3	Q99952	OTTHUMG00000131630	ENST00000175756.5:c.1113_1118delGACGGG	2.37:g.131129935_131129940delGACGGG	ENSP00000175756:p.Thr378_Gly379del	Somatic		WXS	Illumina GAIIx	Phase_I	B4E1E6|Q53P42	In_Frame_Del	DEL	ENST00000175756.5	37	CCDS2161.1																																																																																				0.777	PTPN18-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000254523.2			
PYCR1	5831	broad.mit.edu	37	17	79894640	79894640	+	Missense_Mutation	SNP	C	C	G			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	C	C	.	.	.	.	Unknown	Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr17:79894640C>G	ENST00000329875.8	-	1	115	c.51G>C	c.(49-51)aaG>aaC	p.K17N	PYCR1_ENST00000403172.4_Missense_Mutation_p.K17N|PYCR1_ENST00000402252.2_Missense_Mutation_p.K44N|PYCR1_ENST00000577756.1_Missense_Mutation_p.K17N|PYCR1_ENST00000337943.5_Missense_Mutation_p.K17N	NM_001282280.1|NM_001282281.1|NM_006907.2	NP_001269209.1|NP_001269210.1|NP_008838.2	P32322	P5CR1_HUMAN	pyrroline-5-carboxylate reductase 1	17					cellular amino acid biosynthetic process (GO:0008652)|cellular nitrogen compound metabolic process (GO:0034641)|cellular response to oxidative stress (GO:0034599)|L-proline biosynthetic process (GO:0055129)|negative regulation of hydrogen peroxide-induced cell death (GO:1903206)|proline biosynthetic process (GO:0006561)|regulation of mitochondrial membrane potential (GO:0051881)|small molecule metabolic process (GO:0044281)	mitochondrial matrix (GO:0005759)|mitochondrion (GO:0005739)	identical protein binding (GO:0042802)|pyrroline-5-carboxylate reductase activity (GO:0004735)	p.K17N(2)		endometrium(2)|kidney(1)|lung(1)|prostate(1)	5	all_neural(118;0.0878)|Ovarian(332;0.12)		BRCA - Breast invasive adenocarcinoma(99;0.0165)|OV - Ovarian serous cystadenocarcinoma(97;0.0382)		L-Proline(DB00172)	CTGTGAAGCCCTTGGCCAGGG	0.672																																																	2	Substitution - Missense(2)	kidney(2)											24.0	28.0	27.0					17																	79894640		2199	4292	6491	SO:0001583	missense	5831				CCDS11794.1, CCDS11795.1, CCDS62365.1, CCDS62366.1	17q25.3	2013-09-23			ENSG00000183010	ENSG00000183010	1.5.1.2		9721	protein-coding gene	gene with protein product		179035				1730675	Standard	XM_005256381		Approved	P5C	uc002kcr.1	P32322	OTTHUMG00000178436	ENST00000329875.8:c.51G>C	17.37:g.79894640C>G	ENSP00000328858:p.Lys17Asn	Somatic		WXS	Illumina GAIIx	Phase_I	A6NFM2|B4DMU0|Q6FHI4|Q96DI6|Q9HBQ4	Missense_Mutation	SNP	ENST00000329875.8	37	CCDS11795.1	.	.	.	.	.	.	.	.	.	.	C	11.63	1.696832	0.30142	.	.	ENSG00000183010	ENST00000337943;ENST00000329875;ENST00000403172;ENST00000402252;ENST00000405481	T;T;T;T;T	0.46063	0.88;0.88;0.88;0.88;0.88	4.42	3.43	0.39272	NAD(P)-binding domain (1);	0.223955	0.43747	D	0.000537	T	0.50650	0.1628	L	0.50993	1.605	0.58432	D	0.999997	D;D;D;D;B;D	0.69078	0.972;0.966;0.997;0.966;0.274;0.992	P;P;D;P;B;D	0.65773	0.899;0.818;0.938;0.818;0.202;0.934	T	0.48080	-0.9066	10	0.46703	T	0.11	.	7.4882	0.27445	0.0:0.7059:0.1387:0.1554	.	44;17;17;17;17;17	B4DMU0;E7D7X9;Q9HBQ4;P32322;E7D7Y0;A6NFM2	.;.;.;P5CR1_HUMAN;.;.	N	17;17;17;44;17	ENSP00000336579:K17N;ENSP00000328858:K17N;ENSP00000385483:K17N;ENSP00000384949:K44N;ENSP00000386002:K17N	ENSP00000328858:K17N	K	-	3	2	PYCR1	77487931	0.906000	0.30813	1.000000	0.80357	0.929000	0.56500	0.557000	0.23454	2.009000	0.58944	0.561000	0.74099	AAG		0.672	PYCR1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000441953.1			
LRRC7	57554	broad.mit.edu	37	1	70502282	70502282	+	Missense_Mutation	SNP	G	G	C			TCGA-B2-4099-01A-02D-1458-08	TCGA-B2-4099-10A-01D-1458-08	G	G	G	C	G	G	Unknown	Valid	Somatic	Phase_I	WXS	454	.		Illumina GAIIx	01c54f7c-84b9-4f5b-ae44-2ac1f661fd29	54cf60f2-947e-4eb0-b5a7-1e644ca10dba	g.chr1:70502282G>C	ENST00000035383.5	+	18	2179	c.2149G>C	c.(2149-2151)Gta>Cta	p.V717L	LRRC7_ENST00000310961.5_Missense_Mutation_p.V722L|LRRC7_ENST00000415775.2_Intron	NM_020794.2	NP_065845.1	Q96NW7	LRRC7_HUMAN	leucine rich repeat containing 7	717						cell junction (GO:0030054)|cytoplasm (GO:0005737)|postsynaptic membrane (GO:0045211)		p.V717L(2)		breast(11)|central_nervous_system(3)|cervix(1)|endometrium(9)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(25)|liver(3)|lung(81)|ovary(9)|pancreas(1)|prostate(2)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)|urinary_tract(2)	162						TAAAGATGCAGTACATAATTC	0.423																																						.											2	Substitution - Missense(2)	kidney(2)											141.0	153.0	149.0					1																	70502282		2203	4300	6503	SO:0001583	missense	57554				CCDS645.1	1p31.1	2008-02-05			ENSG00000033122	ENSG00000033122			18531	protein-coding gene	gene with protein product		614453				12525888	Standard	NM_020794		Approved	KIAA1365, densin-180	uc001dep.3	Q96NW7	OTTHUMG00000059194	ENST00000035383.5:c.2149G>C	1.37:g.70502282G>C	ENSP00000035383:p.Val717Leu	Somatic		WXS	Illumina GAIIx	Phase_I	Q5VXC2|Q5VXC3|Q68D07|Q86VE8|Q8WX20|Q9P2I2	Missense_Mutation	SNP	ENST00000035383.5	37	CCDS645.1	.	.	.	.	.	.	.	.	.	.	G	15.05	2.718215	0.48622	.	.	ENSG00000033122	ENST00000310961;ENST00000035383;ENST00000370957	T;T	0.36699	1.24;1.31	5.77	5.77	0.91146	.	0.457883	0.21756	N	0.069590	T	0.22820	0.0551	L	0.44542	1.39	0.80722	D	1	B	0.02656	0.0	B	0.01281	0.0	T	0.01500	-1.1339	10	0.38643	T	0.18	.	19.335	0.94312	0.0:0.0:1.0:0.0	.	717	Q96NW7	LRRC7_HUMAN	L	722;717;540	ENSP00000309245:V722L;ENSP00000035383:V717L	ENSP00000035383:V717L	V	+	1	0	LRRC7	70274870	1.000000	0.71417	1.000000	0.80357	0.991000	0.79684	4.680000	0.61656	2.890000	0.99128	0.650000	0.86243	GTA		0.423	LRRC7-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000131261.1		NM_020794	
