#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_CGC_Cancer Germline Mut	i_CGC_Cancer Molecular Genetics	i_CGC_Cancer Somatic Mut	i_CGC_Cancer Syndrome	i_CGC_Chr	i_CGC_Chr Band	i_CGC_GeneID	i_CGC_Name	i_CGC_Other Germline Mut	i_CGC_Tissue Type	i_COSMIC_n_overlapping_mutations	i_COSMIC_overlapping_mutation_descriptions	i_COSMIC_overlapping_primary_sites	i_ClinVar_ASSEMBLY	i_ClinVar_HGMD_ID	i_ClinVar_SYM	i_ClinVar_TYPE	i_ClinVar_rs	i_ESP_AA	i_ESP_AAC	i_ESP_AA_AC	i_ESP_AA_AGE	i_ESP_AA_GTC	i_ESP_AvgAAsampleReadDepth	i_ESP_AvgEAsampleReadDepth	i_ESP_AvgSampleReadDepth	i_ESP_CA	i_ESP_CDP	i_ESP_CG	i_ESP_CP	i_ESP_Chromosome	i_ESP_DBSNP	i_ESP_DP	i_ESP_EA_AC	i_ESP_EA_AGE	i_ESP_EA_GTC	i_ESP_EXOME_CHIP	i_ESP_FG	i_ESP_GL	i_ESP_GM	i_ESP_GS	i_ESP_GTC	i_ESP_GTS	i_ESP_GWAS_PUBMED	i_ESP_MAF	i_ESP_PH	i_ESP_PP	i_ESP_Position	i_ESP_TAC	i_ESP_TotalAAsamplesCovered	i_ESP_TotalEAsamplesCovered	i_ESP_TotalSamplesCovered	i_Ensembl_so_accession	i_Ensembl_so_term	i_Entrez_Gene_Id	i_Familial_Cancer_Genes_Reference	i_Familial_Cancer_Genes_Synonym	i_HGNC_Accession Numbers	i_HGNC_CCDS IDs	i_HGNC_Chromosome	i_HGNC_Date Modified	i_HGNC_Date Name Changed	i_HGNC_Date Symbol Changed	i_HGNC_Ensembl Gene ID	i_HGNC_Ensembl ID(supplied by Ensembl)	i_HGNC_Enzyme IDs	i_HGNC_Gene family description	i_HGNC_HGNC ID	i_HGNC_Locus Group	i_HGNC_Locus Type	i_HGNC_Name Synonyms	i_HGNC_OMIM ID(supplied by NCBI)	i_HGNC_Previous Names	i_HGNC_Previous Symbols	i_HGNC_Primary IDs	i_HGNC_Pubmed IDs	i_HGNC_Record Type	i_HGNC_RefSeq(supplied by NCBI)	i_HGNC_Secondary IDs	i_HGNC_Status	i_HGNC_Synonyms	i_HGNC_UCSC ID(supplied by UCSC)	i_HGNC_UniProt ID(supplied by UniProt)	i_HGNC_VEGA IDs	i_HGVS_coding_DNA_change	i_HGVS_genomic_change	i_HGVS_protein_change	i_ORegAnno_bin	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_annotation_transcript	i_build	i_ccds_id	i_dbNSFP_1000Gp1_AC	i_dbNSFP_1000Gp1_AF	i_dbNSFP_1000Gp1_AFR_AC	i_dbNSFP_1000Gp1_AFR_AF	i_dbNSFP_1000Gp1_AMR_AC	i_dbNSFP_1000Gp1_AMR_AF	i_dbNSFP_1000Gp1_ASN_AC	i_dbNSFP_1000Gp1_ASN_AF	i_dbNSFP_1000Gp1_EUR_AC	i_dbNSFP_1000Gp1_EUR_AF	i_dbNSFP_Ancestral_allele	i_dbNSFP_CADD_phred	i_dbNSFP_CADD_raw	i_dbNSFP_CADD_raw_rankscore	i_dbNSFP_ESP6500_AA_AF	i_dbNSFP_ESP6500_EA_AF	i_dbNSFP_Ensembl_geneid	i_dbNSFP_Ensembl_transcriptid	i_dbNSFP_FATHMM_pred	i_dbNSFP_FATHMM_rankscore	i_dbNSFP_FATHMM_score	i_dbNSFP_GERP++_NR	i_dbNSFP_GERP++_RS	i_dbNSFP_GERP++_RS_rankscore	i_dbNSFP_Interpro_domain	i_dbNSFP_LRT_Omega	i_dbNSFP_LRT_converted_rankscore	i_dbNSFP_LRT_pred	i_dbNSFP_LRT_score	i_dbNSFP_LR_pred	i_dbNSFP_LR_rankscore	i_dbNSFP_LR_score	i_dbNSFP_MutationAssessor_pred	i_dbNSFP_MutationAssessor_rankscore	i_dbNSFP_MutationAssessor_score	i_dbNSFP_MutationTaster_converted_rankscore	i_dbNSFP_MutationTaster_pred	i_dbNSFP_MutationTaster_score	i_dbNSFP_Polyphen2_HDIV_pred	i_dbNSFP_Polyphen2_HDIV_rankscore	i_dbNSFP_Polyphen2_HDIV_score	i_dbNSFP_Polyphen2_HVAR_pred	i_dbNSFP_Polyphen2_HVAR_rankscore	i_dbNSFP_Polyphen2_HVAR_score	i_dbNSFP_RadialSVM_pred	i_dbNSFP_RadialSVM_rankscore	i_dbNSFP_RadialSVM_score	i_dbNSFP_Reliability_index	i_dbNSFP_SIFT_converted_rankscore	i_dbNSFP_SIFT_pred	i_dbNSFP_SIFT_score	i_dbNSFP_SLR_test_statistic	i_dbNSFP_SiPhy_29way_logOdds	i_dbNSFP_SiPhy_29way_logOdds_rankscore	i_dbNSFP_SiPhy_29way_pi	i_dbNSFP_UniSNP_ids	i_dbNSFP_Uniprot_aapos	i_dbNSFP_Uniprot_acc	i_dbNSFP_Uniprot_id	i_dbNSFP_aaalt	i_dbNSFP_aapos	i_dbNSFP_aapos_FATHMM	i_dbNSFP_aapos_SIFT	i_dbNSFP_aaref	i_dbNSFP_cds_strand	i_dbNSFP_codonpos	i_dbNSFP_fold-degenerate	i_dbNSFP_genename	i_dbNSFP_hg18_pos(1-coor)	i_dbNSFP_phastCons100way_vertebrate	i_dbNSFP_phastCons100way_vertebrate_rankscore	i_dbNSFP_phastCons46way_placental	i_dbNSFP_phastCons46way_placental_rankscore	i_dbNSFP_phastCons46way_primate	i_dbNSFP_phastCons46way_primate_rankscore	i_dbNSFP_phyloP100way_vertebrate	i_dbNSFP_phyloP100way_vertebrate_rankscore	i_dbNSFP_phyloP46way_placental	i_dbNSFP_phyloP46way_placental_rankscore	i_dbNSFP_phyloP46way_primate	i_dbNSFP_phyloP46way_primate_rankscore	i_dbNSFP_refcodon	i_entrez_gene_id	i_gc_content_full	i_gencode_transcript_name	i_gencode_transcript_status	i_gencode_transcript_tags	i_gencode_transcript_type	i_gene_type	i_havana_transcript	i_refseq_mrna_id	i_secondary_variant_classification	i_t_alt_count_full	i_t_ref_count_full	t_alt_count	t_ref_count
CTSG	1511	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	14	25043508	25043508	+	Silent	SNP	G	G	A			TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chr14:25043508G>A	ENST00000216336.2	-	4	573	c.537C>T	c.(535-537)taC>taT	p.Y179Y		NM_001911.2	NP_001902.1	P08311	CATG_HUMAN	cathepsin G	179	Peptidase S1. {ECO:0000255|PROSITE- ProRule:PRU00274}.				angiotensin maturation (GO:0002003)|cellular protein metabolic process (GO:0044267)|defense response to fungus (GO:0050832)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|immune response (GO:0006955)|negative regulation of growth of symbiont in host (GO:0044130)|neutrophil mediated killing of gram-positive bacterium (GO:0070946)|positive regulation of immune response (GO:0050778)|proteolysis (GO:0006508)|response to lipopolysaccharide (GO:0032496)	extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)	heparin binding (GO:0008201)|peptidase activity (GO:0008233)|serine-type endopeptidase activity (GO:0004252)	p.Y179Y(1)		autonomic_ganglia(1)|breast(2)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(4)|lung(12)|ovary(2)|skin(1)|urinary_tract(1)	25				GBM - Glioblastoma multiforme(265;0.0269)		TTCGGGGGTCGTAGGAACCGA	0.627																																																1	Substitution - coding silent(1)	kidney(1)											91.0	76.0	81.0					14																	25043508		2203	4300	6503	SO:0001819	synonymous_variant	1511			M16117	CCDS9631.1	14q12	2013-02-25			ENSG00000100448	ENSG00000100448		"""Cathepsins"", ""Endogenous ligands"""	2532	protein-coding gene	gene with protein product		116830				2569462	Standard	NM_001911		Approved	CG	uc001wpq.3	P08311	OTTHUMG00000140182	ENST00000216336.2:c.537C>T	14.37:g.25043508G>A			Q6IBJ6|Q9UCA5|Q9UCU6	Silent	SNP	ENST00000216336.2	37	CCDS9631.1																																																																																				0.627	CTSG-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000276536.2	NM_001911		19	20	19	20
FPR1	2357	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	19	52250087	52250087	+	Missense_Mutation	SNP	C	C	T	rs145808420		TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chr19:52250087C>T	ENST00000595042.1	-	3	302	c.161G>A	c.(160-162)cGg>cAg	p.R54Q	FPR1_ENST00000304748.4_Missense_Mutation_p.R54Q	NM_001193306.1	NP_001180235.1	P21462	FPR1_HUMAN	formyl peptide receptor 1	54					activation of MAPK activity (GO:0000187)|adenylate cyclase-modulating G-protein coupled receptor signaling pathway (GO:0007188)|cellular component movement (GO:0006928)|chemotaxis (GO:0006935)|G-protein coupled receptor signaling pathway (GO:0007186)|nitric oxide mediated signal transduction (GO:0007263)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|signal transduction (GO:0007165)	endosome (GO:0005768)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	N-formyl peptide receptor activity (GO:0004982)|receptor activity (GO:0004872)			endometrium(2)|kidney(2)|large_intestine(2)|lung(6)|ovary(1)|pancreas(1)|prostate(1)|skin(2)|stomach(3)	20		all_neural(266;0.0189)|Medulloblastoma(540;0.146)		GBM - Glioblastoma multiforme(134;0.00106)|OV - Ovarian serous cystadenocarcinoma(262;0.018)	Nedocromil(DB00716)	GTGTGTCATCCGGAATCCAGC	0.527																																																0								C	GLN/ARG,GLN/ARG	2,4404		0,2,2201	159.0	125.0	136.0		161,161	2.6	0.6	19	dbSNP_134	136	0,8600		0,0,4300	no	missense,missense	FPR1	NM_001193306.1,NM_002029.3	43,43	0,2,6501	TT,TC,CC		0.0,0.0454,0.0154	possibly-damaging,possibly-damaging	54/351,54/351	52250087	2,13004	2203	4300	6503	SO:0001583	missense	2357			M60627	CCDS12839.1	19q13.41	2014-09-17				ENSG00000171051		"""GPCR / Class A : Formyl peptide receptors"""	3826	protein-coding gene	gene with protein product		136537				2161213, 12595898	Standard	NM_001193306		Approved	FPR, FMLP	uc002pxq.3	P21462		ENST00000595042.1:c.161G>A	19.37:g.52250087C>T	ENSP00000471493:p.Arg54Gln		Q14939|Q7Z6A4|Q86U52|Q9NS48	Missense_Mutation	SNP	ENST00000595042.1	37	CCDS12839.1	.	.	.	.	.	.	.	.	.	.	.	16.78	3.217300	0.58560	4.54E-4	0.0	ENSG00000171051	ENST00000304748	T	0.40756	1.02	3.67	2.62	0.31277	GPCR, rhodopsin-like superfamily (1);	0.431779	0.22832	N	0.055096	T	0.36358	0.0964	L	0.46741	1.465	0.30025	N	0.813958	P	0.44659	0.84	P	0.45343	0.477	T	0.25047	-1.0143	10	0.35671	T	0.21	.	6.6407	0.22906	0.0:0.7667:0.0:0.2333	.	54	P21462	FPR1_HUMAN	Q	54	ENSP00000302707:R54Q	ENSP00000302707:R54Q	R	-	2	0	FPR1	56941899	0.982000	0.34865	0.578000	0.28575	0.877000	0.50540	1.505000	0.35736	0.834000	0.34852	-0.244000	0.11960	CGG		0.527	FPR1-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000466905.1	NM_002029		18	24	18	24
FMNL2	114793	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	2	153473700	153473700	+	Silent	SNP	C	C	T			TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chr2:153473700C>T	ENST00000288670.9	+	13	1675	c.1308C>T	c.(1306-1308)gtC>gtT	p.V436V	FMNL2_ENST00000475377.2_5'Flank	NM_052905.3	NP_443137.2	Q96PY5	FMNL2_HUMAN	formin-like 2	436	GBD/FH3. {ECO:0000255|PROSITE- ProRule:PRU00579}.				cortical actin cytoskeleton organization (GO:0030866)|cytoskeleton organization (GO:0007010)|regulation of cell morphogenesis (GO:0022604)	cytoplasm (GO:0005737)				central_nervous_system(2)|endometrium(3)|large_intestine(5)|liver(2)|lung(3)|ovary(3)|prostate(2)|skin(1)|upper_aerodigestive_tract(2)	23						AGCTGGATGTCGTTCGGGTAA	0.473																																																0													112.0	111.0	111.0					2																	153473700		1993	4178	6171	SO:0001819	synonymous_variant	114793			AB067489	CCDS46429.1	2q23.3	2008-02-05	2003-12-02	2003-12-03	ENSG00000157827	ENSG00000157827			18267	protein-coding gene	gene with protein product			"""formin homology 2 domain containing 2"""	FHOD2			Standard	XM_005246263		Approved	KIAA1902	uc002tye.3	Q96PY5	OTTHUMG00000154035	ENST00000288670.9:c.1308C>T	2.37:g.153473700C>T			B2RZH5|Q14CC9|Q4ZG52|Q8N3E0	Silent	SNP	ENST00000288670.9	37	CCDS46429.1																																																																																				0.473	FMNL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000333582.2	NM_052905		18	28	18	28
ACOX3	8310	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	8396382	8396382	+	Nonsense_Mutation	SNP	G	G	A	rs142042116		TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chr4:8396382G>A	ENST00000356406.5	-	10	1221	c.1144C>T	c.(1144-1146)Cga>Tga	p.R382*	ACOX3_ENST00000413009.2_Nonsense_Mutation_p.R382*|RNA5SP152_ENST00000365184.1_RNA|ACOX3_ENST00000503233.1_Nonsense_Mutation_p.R382*	NM_003501.2	NP_003492.2	O15254	ACOX3_HUMAN	acyl-CoA oxidase 3, pristanoyl	382					cellular lipid metabolic process (GO:0044255)|fatty acid beta-oxidation using acyl-CoA oxidase (GO:0033540)|small molecule metabolic process (GO:0044281)	membrane (GO:0016020)|mitochondrion (GO:0005739)|peroxisomal matrix (GO:0005782)|peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|flavin adenine dinucleotide binding (GO:0050660)|pristanoyl-CoA oxidase activity (GO:0016402)|receptor binding (GO:0005102)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(4)|large_intestine(9)|lung(17)|prostate(1)|skin(3)|stomach(1)	42						GCAAGTCCTCGCTGGAGCTCC	0.542													G|||	1	0.000199681	0.0	0.0	5008	,	,		20830	0.001		0.0	False		,,,				2504	0.0															0								G	stop/ARG,stop/ARG	1,4405	2.1+/-5.4	0,1,2202	62.0	59.0	60.0		1144,1144	3.5	0.2	4	dbSNP_134	60	0,8600		0,0,4300	yes	stop-gained,stop-gained	ACOX3	NM_001101667.1,NM_003501.2	,	0,1,6502	AA,AG,GG		0.0,0.0227,0.0077	,	382/625,382/701	8396382	1,13005	2203	4300	6503	SO:0001587	stop_gained	8310			Y11411	CCDS3401.1, CCDS47017.1	4p15.3	2010-04-30	2010-04-30		ENSG00000087008	ENSG00000087008	1.3.3.6		121	protein-coding gene	gene with protein product		603402	"""acyl-Coenzyme A oxidase 3, pristanoyl"""			9271077	Standard	NM_003501		Approved		uc003glc.4	O15254	OTTHUMG00000090509	ENST00000356406.5:c.1144C>T	4.37:g.8396382G>A	ENSP00000348775:p.Arg382*		Q96AJ8	Nonsense_Mutation	SNP	ENST00000356406.5	37	CCDS3401.1	1	4.578754578754579E-4	0	0.0	0	0.0	1	0.0017482517482517483	0	0.0	G	29.5	5.010135	0.93346	2.27E-4	0.0	ENSG00000087008	ENST00000413009;ENST00000356406;ENST00000503233	.	.	.	4.32	3.46	0.39613	.	0.901301	0.09605	N	0.779700	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.15952	T	0.53	-0.6378	10.504	0.44823	0.0:0.0:0.528:0.472	.	.	.	.	X	382	.	ENSP00000348775:R382X	R	-	1	2	ACOX3	8447282	0.046000	0.20272	0.212000	0.23672	0.021000	0.10359	0.772000	0.26647	1.141000	0.42275	0.655000	0.94253	CGA		0.542	ACOX3-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000206997.4			17	10	17	10
SPP1	6696	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	4	88901213	88901213	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chr4:88901213C>T	ENST00000395080.3	+	4	236	c.109C>T	c.(109-111)Cca>Tca	p.P37S	SPP1_ENST00000509659.1_3'UTR|SPP1_ENST00000360804.4_Intron|SPP1_ENST00000237623.7_Missense_Mutation_p.P37S	NM_001040058.1|NM_001251830.1	NP_001035147.1|NP_001238759.1	P10451	OSTP_HUMAN	secreted phosphoprotein 1	37					biomineral tissue development (GO:0031214)|cell adhesion (GO:0007155)|decidualization (GO:0046697)|embryo implantation (GO:0007566)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|inflammatory response (GO:0006954)|negative regulation of collateral sprouting of intact axon in response to injury (GO:0048685)|neutrophil chemotaxis (GO:0030593)|osteoblast differentiation (GO:0001649)|positive regulation of bone resorption (GO:0045780)|positive regulation of cell-substrate adhesion (GO:0010811)|response to steroid hormone (GO:0048545)|response to vitamin D (GO:0033280)	apical part of cell (GO:0045177)|cell projection (GO:0042995)|extracellular region (GO:0005576)|extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)|perinuclear region of cytoplasm (GO:0048471)	extracellular matrix binding (GO:0050840)			NS(1)|endometrium(1)|kidney(1)|large_intestine(1)|lung(4)|ovary(1)|prostate(3)|skin(1)	13		Hepatocellular(203;0.114)		OV - Ovarian serous cystadenocarcinoma(123;9.87e-05)		CAACAAATACCCAGATGCTGT	0.363																																																0													93.0	95.0	94.0					4																	88901213		2203	4300	6503	SO:0001583	missense	6696				CCDS3626.1, CCDS34027.1, CCDS43250.1	4q22.1	2014-01-30	2008-07-31		ENSG00000118785	ENSG00000118785		"""Endogenous ligands"""	11255	protein-coding gene	gene with protein product	"""early T-lymphocyte activation 1"""	166490	"""osteopontin"", ""bone sialoprotein I"""	BNSP, OPN		1575754	Standard	NM_001251829		Approved	BSPI, ETA-1	uc003hra.3	P10451	OTTHUMG00000130599	ENST00000395080.3:c.109C>T	4.37:g.88901213C>T	ENSP00000378517:p.Pro37Ser		B2RDA1|Q15681|Q15682|Q15683|Q4W597|Q567T5|Q8NBK2|Q96IZ1	Missense_Mutation	SNP	ENST00000395080.3	37	CCDS43250.1	.	.	.	.	.	.	.	.	.	.	C	15.87	2.959912	0.53400	.	.	ENSG00000118785	ENST00000359072;ENST00000237623;ENST00000395080	T;T	0.27890	1.64;1.64	5.62	2.97	0.34412	.	0.198829	0.35708	N	0.003039	T	0.19725	0.0474	N	0.19112	0.55	0.46185	D	0.998916	P;P;P	0.45827	0.717;0.867;0.867	B;B;B	0.43194	0.32;0.411;0.411	T	0.02075	-1.1218	10	0.36615	T	0.2	-1.4696	8.134	0.31043	0.0:0.7464:0.0:0.2536	.	50;37;37	B7Z351;B2RDA1;P10451	.;.;OSTP_HUMAN	S	37	ENSP00000237623:P37S;ENSP00000378517:P37S	ENSP00000237623:P37S	P	+	1	0	SPP1	89120237	0.482000	0.25948	0.124000	0.21820	0.974000	0.67602	0.084000	0.14891	0.324000	0.23333	0.643000	0.83706	CCA		0.363	SPP1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000253048.3			26	65	26	65
TRO	7216	hgsc.bcm.edu;broad.mit.edu;ucsc.edu	37	X	54953051	54953051	+	Missense_Mutation	SNP	C	C	T	rs377101973		TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chrX:54953051C>T	ENST00000173898.7	+	9	1805	c.1693C>T	c.(1693-1695)Cgc>Tgc	p.R565C	TRO_ENST00000375022.4_Missense_Mutation_p.R565C|TRO_ENST00000420798.2_Missense_Mutation_p.R96C|SNORA11_ENST00000408823.1_RNA|TRO_ENST00000319167.8_Missense_Mutation_p.R565C|TRO_ENST00000375041.2_Missense_Mutation_p.R168C|TRO_ENST00000399736.1_Missense_Mutation_p.R168C	NM_001039705.2	NP_001034794.1	Q12816	TROP_HUMAN	trophinin	565	MAGE. {ECO:0000255|PROSITE- ProRule:PRU00127}.				embryo implantation (GO:0007566)|homophilic cell adhesion (GO:0007156)|negative regulation of cell growth (GO:0030308)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)|nucleus (GO:0005634)|plasma membrane (GO:0005886)				breast(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|lung(19)|ovary(2)|skin(2)|urinary_tract(1)	37						GTTGGGGCTGCGCCCTGGGTA	0.577																																																0								C	CYS/ARG,CYS/ARG,CYS/ARG	0,3835		0,0,1632,571	137.0	126.0	130.0		1693,1693,1693	1.3	0.2	X		130	1,6727		0,1,2427,1872	no	missense,missense,missense	TRO	NM_177556.1,NM_016157.2,NM_001039705.1	180,180,180	0,1,4059,2443	TT,TC,CC,C		0.0149,0.0,0.0095	benign,benign,benign	565/707,565/707,565/1432	54953051	1,10562	2203	4300	6503	SO:0001583	missense	7216			U04811	CCDS43958.1, CCDS43959.1, CCDS59527.1, CCDS59528.1, CCDS59529.1	Xp11.22-p11.21	2008-02-05			ENSG00000067445	ENSG00000067445			12326	protein-coding gene	gene with protein product		300132				9533028, 11454705	Standard	NM_001039705		Approved	MAGE-D3, KIAA1114, MAGED3	uc004dtq.4	Q12816	OTTHUMG00000021640	ENST00000173898.7:c.1693C>T	X.37:g.54953051C>T	ENSP00000173898:p.Arg565Cys		B1AKE9|B1AKF1|F5GY27|Q96SX2|Q9NU89|Q9UPN8	Missense_Mutation	SNP	ENST00000173898.7	37	CCDS43959.1	.	.	.	.	.	.	.	.	.	.	C	5.668	0.307823	0.10733	0.0	1.49E-4	ENSG00000067445	ENST00000173898;ENST00000319167;ENST00000375022;ENST00000399736;ENST00000319179;ENST00000420798;ENST00000375041	T;T;T;T;T;T	0.05025	3.51;3.51;3.51;3.51;3.51;3.51	3.08	1.29	0.21616	.	.	.	.	.	T	0.11281	0.0275	L	0.32530	0.975	0.09310	N	0.999994	B;B;D;B	0.76494	0.008;0.262;0.999;0.008	B;B;D;B	0.64877	0.004;0.105;0.93;0.002	T	0.21518	-1.0243	9	0.62326	D	0.03	.	5.1005	0.14756	0.0:0.5705:0.0:0.4295	.	168;168;565;565	B1AKE9;B1AKF1;Q96SX2;Q12816	.;.;.;TROP_HUMAN	C	565;565;565;168;168;96;168	ENSP00000173898:R565C;ENSP00000318278:R565C;ENSP00000364162:R565C;ENSP00000382641:R168C;ENSP00000405126:R96C;ENSP00000364181:R168C	ENSP00000173898:R565C	R	+	1	0	TRO	54969776	0.032000	0.19561	0.190000	0.23270	0.530000	0.34684	0.173000	0.16724	0.211000	0.20683	0.513000	0.50165	CGC		0.577	TRO-008	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	protein_coding	OTTHUMT00000056837.3	NM_016157		55	83	55	83
GDPD2	54857	hgsc.bcm.edu;broad.mit.edu	37	X	69652187	69652187	+	Missense_Mutation	SNP	C	C	A			TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chrX:69652187C>A	ENST00000374382.3	+	13	1589	c.1338C>A	c.(1336-1338)aaC>aaA	p.N446K	GDPD2_ENST00000536730.1_Missense_Mutation_p.N367K|GDPD2_ENST00000538649.1_Missense_Mutation_p.N367K|GDPD2_ENST00000472623.1_3'UTR|GDPD2_ENST00000453994.2_Missense_Mutation_p.N497K	NM_017711.3	NP_060181.2	Q9HCC8	GDPD2_HUMAN	glycerophosphodiester phosphodiesterase domain containing 2	446	GP-PDE.				glycerol metabolic process (GO:0006071)|lipid metabolic process (GO:0006629)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	glycerophosphodiester phosphodiesterase activity (GO:0008889)|glycerophosphoinositol inositolphosphodiesterase activity (GO:0047394)|metal ion binding (GO:0046872)			NS(1)|breast(1)|cervix(1)|endometrium(6)|large_intestine(8)|lung(3)|ovary(2)	22	Renal(35;0.156)					TCTCGGTGAACCTATTTGTAG	0.527																																																0													219.0	187.0	198.0					X																	69652187		2203	4300	6503	SO:0001583	missense	54857			AK000214	CCDS14402.1, CCDS55437.1, CCDS55438.1	Xq13.1	2011-01-25			ENSG00000130055	ENSG00000130055			25974	protein-coding gene	gene with protein product	"""osteoblast differentiation promoting factor"""					12975309	Standard	NM_017711		Approved	OBDPF, FLJ20207, GDE3	uc011mpk.2	Q9HCC8	OTTHUMG00000021776	ENST00000374382.3:c.1338C>A	X.37:g.69652187C>A	ENSP00000363503:p.Asn446Lys		B4DRH4|B4DVC9|Q9NXJ6	Missense_Mutation	SNP	ENST00000374382.3	37	CCDS14402.1	.	.	.	.	.	.	.	.	.	.	C	14.75	2.628770	0.46944	.	.	ENSG00000130055	ENST00000453994;ENST00000536730;ENST00000538649;ENST00000374382	T;T;T;T	0.71461	-0.57;-0.57;-0.57;-0.57	4.77	4.77	0.60923	PLC-like phosphodiesterase, TIM beta/alpha-barrel domain (2);	0.056113	0.64402	D	0.000001	T	0.82204	0.4986	M	0.81341	2.54	0.41095	D	0.985625	D;P	0.89917	1.0;0.651	D;B	0.80764	0.994;0.343	D	0.83511	0.0080	9	.	.	.	-15.8013	9.3242	0.37982	0.0:0.8987:0.0:0.1013	.	497;446	B4DVC9;Q9HCC8	.;GDPD2_HUMAN	K	497;367;367;446	ENSP00000414019:N497K;ENSP00000445982:N367K;ENSP00000444601:N367K;ENSP00000363503:N446K	.	N	+	3	2	GDPD2	69568912	1.000000	0.71417	1.000000	0.80357	0.960000	0.62799	1.666000	0.37460	2.214000	0.71695	0.468000	0.43344	AAC		0.527	GDPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000057070.1	NM_017711		12	148	12	148
TRBV11-1	28582	broad.mit.edu;ucsc.edu	37	7	142224222	142224222	+	RNA	SNP	C	C	A			TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chr7:142224222C>A	ENST00000390367.3	-	0	62									T cell receptor beta variable 11-1																		GACACACCTGCCCCCAGGAGA	0.498																																																0													53.0	54.0	54.0					7																	142224222		1949	4153	6102			28582			M33233		7q34	2012-02-07			ENSG00000211720	ENSG00000211720		"""T cell receptors / TRB locus"""	12180	other	T cell receptor gene						8650574	Standard	NG_001333		Approved	TRBV111, TCRBV11S1, TCRBV21S1			OTTHUMG00000158505		7.37:g.142224222C>A				RNA	SNP	ENST00000390367.3	37																																																																																					0.498	TRBV11-1-001	KNOWN	mRNA_end_NF|cds_end_NF|basic|appris_principal	TR_V_gene	TR_V_gene	OTTHUMT00000351211.1	NG_001333		20	32	20	32
G6PD	2539	broad.mit.edu;ucsc.edu	37	X	153761826	153761826	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chrX:153761826C>T	ENST00000393564.2	-	8	941	c.829G>A	c.(829-831)Gcc>Acc	p.A277T	G6PD_ENST00000497281.1_5'Flank|G6PD_ENST00000393562.2_Missense_Mutation_p.A307T|G6PD_ENST00000369620.2_Missense_Mutation_p.A323T	NM_001042351.1	NP_001035810.1	P11413	G6PD_HUMAN	glucose-6-phosphate dehydrogenase	277					carbohydrate metabolic process (GO:0005975)|cellular response to oxidative stress (GO:0034599)|cholesterol biosynthetic process (GO:0006695)|cytokine production (GO:0001816)|erythrocyte maturation (GO:0043249)|glucose 6-phosphate metabolic process (GO:0051156)|glutathione metabolic process (GO:0006749)|lipid metabolic process (GO:0006629)|NADP metabolic process (GO:0006739)|NADPH regeneration (GO:0006740)|negative regulation of protein glutathionylation (GO:0010734)|oxidation-reduction process (GO:0055114)|pentose biosynthetic process (GO:0019322)|pentose-phosphate shunt (GO:0006098)|pentose-phosphate shunt, oxidative branch (GO:0009051)|regulation of neuron apoptotic process (GO:0043523)|response to ethanol (GO:0045471)|response to food (GO:0032094)|response to organic cyclic compound (GO:0014070)|ribose phosphate biosynthetic process (GO:0046390)|small molecule metabolic process (GO:0044281)|substantia nigra development (GO:0021762)	cytoplasm (GO:0005737)|cytoplasmic side of plasma membrane (GO:0009898)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)|membrane (GO:0016020)|nucleus (GO:0005634)	glucose binding (GO:0005536)|glucose-6-phosphate dehydrogenase activity (GO:0004345)|NADP binding (GO:0050661)|protein homodimerization activity (GO:0042803)			breast(2)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(3)|lung(3)|ovary(4)	18	all_cancers(53;5.05e-16)|all_epithelial(53;1.87e-10)|all_lung(58;1.84e-07)|Lung NSC(58;5.84e-07)|all_hematologic(71;2.45e-06)|Acute lymphoblastic leukemia(192;6.56e-05)|Breast(217;0.176)					TTGGTGGAGGCGGGCTTCTCC	0.637																																																0													114.0	91.0	99.0					X																	153761826		2203	4300	6503	SO:0001583	missense	2539			X03674	CCDS14756.2, CCDS44023.1	Xq28	2014-09-17			ENSG00000160211	ENSG00000160211	1.1.1.49		4057	protein-coding gene	gene with protein product		305900				3012556, 2428611	Standard	NM_000402		Approved	G6PD1	uc004flx.1	P11413	OTTHUMG00000024237	ENST00000393564.2:c.829G>A	X.37:g.153761826C>T	ENSP00000377194:p.Ala277Thr		D3DWX9|Q16000|Q16765|Q8IU70|Q8IU88|Q8IUA6|Q96PQ2	Missense_Mutation	SNP	ENST00000393564.2	37	CCDS44023.1	.	.	.	.	.	.	.	.	.	.	C	14.30	2.493024	0.44352	.	.	ENSG00000160211	ENST00000393562;ENST00000291567;ENST00000393564;ENST00000369620;ENST00000439227;ENST00000440967	D;D;D;D;D	0.99816	-6.91;-6.91;-6.91;-6.91;-6.91	5.67	3.91	0.45181	Glucose-6-phosphate dehydrogenase, C-terminal (1);	0.055174	0.64402	N	0.000001	D	0.99007	0.9661	L	0.53780	1.695	0.51767	D	0.999932	B;B	0.30021	0.195;0.265	B;B	0.20955	0.024;0.032	D	0.98667	1.0686	10	0.56958	D	0.05	.	9.4636	0.38800	0.0:0.8231:0.0:0.1769	.	277;307	P11413;P11413-3	G6PD_HUMAN;.	T	307;277;277;323;278;278	ENSP00000377192:A307T;ENSP00000377194:A277T;ENSP00000358633:A323T;ENSP00000395599:A278T;ENSP00000400648:A278T	ENSP00000291567:A277T	A	-	1	0	G6PD	153415020	0.554000	0.26522	0.824000	0.32777	0.420000	0.31355	1.117000	0.31234	0.554000	0.29061	0.422000	0.28245	GCC		0.637	G6PD-006	KNOWN	basic|appris_candidate|CCDS	protein_coding	protein_coding	OTTHUMT00000061170.3	NM_000402		4	34	4	34
SLC25A19	60386	broad.mit.edu;ucsc.edu	37	17	73282427	73282427	+	Silent	SNP	G	G	A	rs535476833		TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chr17:73282427G>A	ENST00000402418.3	-	2	1155	c.246C>T	c.(244-246)caC>caT	p.H82H	SLC25A19_ENST00000580994.1_Silent_p.H82H|SLC25A19_ENST00000416858.2_Silent_p.H82H|SLC25A19_ENST00000375261.4_Silent_p.H82H|SLC25A19_ENST00000320362.3_Silent_p.H82H|SLC25A19_ENST00000442286.2_Silent_p.H82H			Q9HC21	TPC_HUMAN	solute carrier family 25 (mitochondrial thiamine pyrophosphate carrier), member 19	82					deoxynucleotide transport (GO:0030302)	integral component of membrane (GO:0016021)|mitochondrial inner membrane (GO:0005743)|nucleus (GO:0005634)	deoxynucleotide transmembrane transporter activity (GO:0030233)			breast(1)|endometrium(3)|kidney(1)|large_intestine(1)|lung(1)|ovary(1)|skin(1)	9	all_cancers(13;5.98e-08)|all_epithelial(9;1.16e-08)|Breast(9;3.1e-08)		all cancers(21;6.82e-07)|Epithelial(20;6.86e-06)			GAGCTGGGACGTGTCCTTTCC	0.592													g|||	1	0.000199681	0.0	0.0	5008	,	,		20110	0.0		0.0	False		,,,				2504	0.001															0													120.0	120.0	120.0					17																	73282427		2203	4300	6503	SO:0001819	synonymous_variant	60386				CCDS11720.1	17q25.1	2013-05-22	2007-03-08		ENSG00000125454	ENSG00000125454		"""Solute carriers"""	14409	protein-coding gene	gene with protein product		606521	"""solute carrier family 25 (mitochondrial deoxynucleotide carrier), member 19"", ""microcephaly, Amish"""	MCPHA		11474176, 11226231, 19798730	Standard	NM_021734		Approved	DNC, MUP1, TPC	uc002jnw.4	Q9HC21		ENST00000402418.3:c.246C>T	17.37:g.73282427G>A			E9PF74|Q6V9R7	Silent	SNP	ENST00000402418.3	37	CCDS11720.1																																																																																				0.592	SLC25A19-005	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000447282.1	NM_021734		40	80	40	80
ATG5	9474	broad.mit.edu;ucsc.edu	37	6	106764059	106764059	+	Nonsense_Mutation	SNP	G	G	A			TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chr6:106764059G>A	ENST00000369076.3	-	2	348	c.25C>T	c.(25-27)Cga>Tga	p.R9*	ATG5_ENST00000343245.3_Nonsense_Mutation_p.R9*|ATG5_ENST00000369070.1_5'UTR|ATG5_ENST00000360666.4_Nonsense_Mutation_p.R9*	NM_004849.2	NP_004840.1	Q9H1Y0	ATG5_HUMAN	autophagy related 5	9					apoptotic process (GO:0006915)|autophagic vacuole assembly (GO:0000045)|autophagy (GO:0006914)|blood vessel remodeling (GO:0001974)|heart contraction (GO:0060047)|innate immune response (GO:0045087)|negative regulation of apoptotic process (GO:0043066)|negative regulation of protein ubiquitination (GO:0031397)|negative regulation of type I interferon production (GO:0032480)|negative stranded viral RNA replication (GO:0039689)|otolith development (GO:0048840)|post-translational protein modification (GO:0043687)|regulation of cilium assembly (GO:1902017)|regulation of cytokine secretion involved in immune response (GO:0002739)|response to drug (GO:0042493)|response to fungus (GO:0009620)|vasodilation (GO:0042311)|ventricular cardiac muscle cell development (GO:0055015)	autophagic vacuole (GO:0005776)|axoneme (GO:0005930)|cytoplasm (GO:0005737)|membrane (GO:0016020)|pre-autophagosomal structure membrane (GO:0034045)				endometrium(1)|large_intestine(5)|lung(1)|prostate(1)	8	Breast(9;0.0296)	all_cancers(87;0.000301)|Acute lymphoblastic leukemia(125;2.15e-07)|all_hematologic(75;5.28e-06)|all_epithelial(87;0.0612)|Lung NSC(302;0.216)	BRCA - Breast invasive adenocarcinoma(8;0.00802)	OV - Ovarian serous cystadenocarcinoma(136;0.128)|Epithelial(106;0.159)|all cancers(137;0.18)		CACACATCTCGAAGCACATCT	0.368																																																0													212.0	192.0	199.0					6																	106764059		2203	4300	6503	SO:0001587	stop_gained	9474			Y11588	CCDS5055.1, CCDS69159.1, CCDS75498.1	6q21	2014-02-12	2012-06-06	2005-09-11	ENSG00000057663	ENSG00000057663			589	protein-coding gene	gene with protein product		604261	"""APG5 (autophagy 5, S. cerevisiae)-like"", ""APG5 autophagy 5-like (S. cerevisiae)"", ""ATG5 autophagy related 5 homolog (S. cerevisiae)"""	APG5L		9563500, 11349150, 15778222	Standard	NM_001286111		Approved	ASP, APG5, hAPG5	uc003prf.3	Q9H1Y0	OTTHUMG00000016193	ENST00000369076.3:c.25C>T	6.37:g.106764059G>A	ENSP00000358072:p.Arg9*		O60875|Q5JVR2|Q68DI4|Q9H2B8|Q9HCZ7	Nonsense_Mutation	SNP	ENST00000369076.3	37	CCDS5055.1	.	.	.	.	.	.	.	.	.	.	G	38	6.888696	0.97912	.	.	ENSG00000057663	ENST00000369076;ENST00000343245;ENST00000360666	.	.	.	5.15	3.27	0.37495	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.02654	T	1	-1.9696	7.0972	0.25317	0.1538:0.0:0.7123:0.1339	.	.	.	.	X	9	.	ENSP00000343313:R9X	R	-	1	2	ATG5	106870752	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	4.884000	0.63135	1.088000	0.41272	0.655000	0.94253	CGA		0.368	ATG5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	protein_coding	OTTHUMT00000043476.1	NM_004849		43	72	43	72
KLHL13	90293	broad.mit.edu;ucsc.edu	37	X	117043975	117043975	+	Missense_Mutation	SNP	C	C	T			TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chrX:117043975C>T	ENST00000262820.3	-	5	1564	c.655G>A	c.(655-657)Gtc>Atc	p.V219I	KLHL13_ENST00000469946.1_Missense_Mutation_p.V168I|KLHL13_ENST00000545703.1_Missense_Mutation_p.V177I|KLHL13_ENST00000371878.1_Missense_Mutation_p.V168I|KLHL13_ENST00000541812.1_Missense_Mutation_p.V203I|KLHL13_ENST00000371882.1_Missense_Mutation_p.V168I|KLHL13_ENST00000540167.1_Missense_Mutation_p.V203I|KLHL13_ENST00000539496.1_Missense_Mutation_p.V222I|KLHL13_ENST00000371876.1_Missense_Mutation_p.V168I	NM_033495.3	NP_277030.2	Q9P2N7	KLH13_HUMAN	kelch-like family member 13	219	BACK.				cytokinesis (GO:0000910)|mitotic nuclear division (GO:0007067)|protein ubiquitination (GO:0016567)	Cul3-RING ubiquitin ligase complex (GO:0031463)				NS(1)|breast(3)|cervix(1)|endometrium(6)|kidney(1)|large_intestine(6)|lung(9)|prostate(2)|skin(3)|stomach(1)|urinary_tract(1)	34						TTCTTCAAGACGAAACTGTTA	0.423																																																0													85.0	79.0	81.0					X																	117043975		2201	4299	6500	SO:0001583	missense	90293			AB037730	CCDS14571.1, CCDS55479.1, CCDS55480.1, CCDS55481.1	Xq23-q24	2013-01-30	2013-01-30	2004-02-18	ENSG00000003096	ENSG00000003096		"""Kelch-like"", ""BTB/POZ domain containing"""	22931	protein-coding gene	gene with protein product		300655	"""BTB and kelch domain containing 2, KIAA1309"", ""kelch-like 13 (Drosophila)"""	BKLHD2, KIAA1309		10718198	Standard	NM_033495		Approved	FLJ10262	uc011mtp.2	Q9P2N7	OTTHUMG00000022252	ENST00000262820.3:c.655G>A	X.37:g.117043975C>T	ENSP00000262820:p.Val219Ile		B3KV78|B3KWM7|B7Z3S9|B7Z5P2|B7Z802|D3DWH6|Q6P2E3|Q96QI7|Q9UDN9	Missense_Mutation	SNP	ENST00000262820.3	37	CCDS14571.1	.	.	.	.	.	.	.	.	.	.	C	3.121	-0.180617	0.06380	.	.	ENSG00000003096	ENST00000371882;ENST00000371876;ENST00000371878;ENST00000447671;ENST00000541812;ENST00000540167;ENST00000539496;ENST00000262820;ENST00000545703;ENST00000469946	T;T;T;T;T;T;T;T;T;T	0.64618	-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11;-0.11	4.7	3.75	0.43078	BTB/Kelch-associated (2);	0.175650	0.48286	D	0.000189	T	0.21962	0.0529	N	0.00960	-1.095	0.31356	N	0.68195	B;B;B;B	0.09022	0.001;0.002;0.0;0.0	B;B;B;B	0.09377	0.001;0.002;0.001;0.004	T	0.35425	-0.9789	10	0.05833	T	0.94	.	3.3037	0.06992	0.0:0.5791:0.0:0.4209	.	203;222;213;219	Q9P2N7-3;Q9P2N7-5;Q9P2N7-4;Q9P2N7	.;.;.;KLH13_HUMAN	I	168;168;168;168;203;203;222;219;177;168	ENSP00000360949:V168I;ENSP00000360943:V168I;ENSP00000360945:V168I;ENSP00000412640:V168I;ENSP00000444450:V203I;ENSP00000441029:V203I;ENSP00000443191:V222I;ENSP00000262820:V219I;ENSP00000440707:V177I;ENSP00000419803:V168I	ENSP00000262820:V219I	V	-	1	0	KLHL13	116928003	1.000000	0.71417	0.949000	0.38748	0.997000	0.91878	6.033000	0.70925	2.150000	0.67090	0.594000	0.82650	GTC		0.423	KLHL13-201	KNOWN	basic|CCDS	protein_coding	protein_coding		NM_033495		20	120	20	120
KALRN	8997	broad.mit.edu;ucsc.edu	37	3	124053129	124053129	+	Missense_Mutation	SNP	A	A	C			TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chr3:124053129A>C	ENST00000240874.3	+	9	1585	c.1428A>C	c.(1426-1428)aaA>aaC	p.K476N	KALRN_ENST00000460856.1_Missense_Mutation_p.K476N|KALRN_ENST00000360013.3_Missense_Mutation_p.K476N	NM_003947.4	NP_003938.1	O60229	KALRN_HUMAN	kalirin, RhoGEF kinase	476					apoptotic signaling pathway (GO:0097190)|intracellular signal transduction (GO:0035556)|nervous system development (GO:0007399)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|protein phosphorylation (GO:0006468)|regulation of small GTPase mediated signal transduction (GO:0051056)|signal transduction (GO:0007165)|small GTPase mediated signal transduction (GO:0007264)|vesicle-mediated transport (GO:0016192)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|extracellular vesicular exosome (GO:0070062)	ATP binding (GO:0005524)|guanyl-nucleotide exchange factor activity (GO:0005085)|metal ion binding (GO:0046872)|protein serine/threonine kinase activity (GO:0004674)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			NS(1)|breast(1)|central_nervous_system(1)|cervix(2)|endometrium(6)|haematopoietic_and_lymphoid_tissue(1)|kidney(2)|large_intestine(21)|lung(28)|ovary(4)|prostate(5)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(3)	83						AGGATGGCAAAGCACTACTTG	0.572																																																0													96.0	99.0	98.0					3																	124053129		2203	4300	6503	SO:0001583	missense	8997			U94190	CCDS3027.1, CCDS3028.1	3q21.2	2013-02-11	2005-03-11	2005-03-12	ENSG00000160145	ENSG00000160145		"""Rho guanine nucleotide exchange factors"", ""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	4814	protein-coding gene	gene with protein product	"""serine/threonine kinase with Dbl and pleckstrin homology domains"""	604605	"""huntingtin-associated protein interacting protein (duo)"""	HAPIP		9285789, 10023074	Standard	NM_001024660		Approved	duo, Hs.8004, TRAD, DUET, Kalirin, ARHGEF24	uc003ehd.3	O60229	OTTHUMG00000125545	ENST00000240874.3:c.1428A>C	3.37:g.124053129A>C	ENSP00000240874:p.Lys476Asn		A8MSI4|C9JQ37|Q6ZN45|Q8TBQ5|Q9NSZ4|Q9Y2A5	Missense_Mutation	SNP	ENST00000240874.3	37	CCDS3027.1	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	A|A	16.50|16.50	3.140406|3.140406	0.56936|0.56936	.|.	.|.	ENSG00000160145|ENSG00000160145	ENST00000460856;ENST00000240874;ENST00000360013|ENST00000354186	T;T;T|T	0.43294|0.42513	0.95;0.95;0.95|0.97	4.86|4.86	2.34|2.34	0.29019|0.29019	.|.	0.000000|0.000000	0.85682|0.85682	D|D	0.000000|0.000000	T|T	0.53351|0.53351	0.1791|0.1791	M|M	0.77103|0.77103	2.36|2.36	0.80722|0.80722	D|D	1|1	D;D;D|.	0.89917|.	1.0;0.998;1.0|.	D;D;D|.	0.91635|.	0.998;0.987;0.999|.	T|T	0.52946|0.52946	-0.8507|-0.8507	10|8	0.54805|0.72032	T|D	0.06|0.01	.|.	7.7915|7.7915	0.29123|0.29123	0.6094:0.0:0.3906:0.0|0.6094:0.0:0.3906:0.0	.|.	476;476;476|.	C9IZQ6;O60229;O60229-2|.	.;KALRN_HUMAN;.|.	N|T	476|454	ENSP00000418611:K476N;ENSP00000240874:K476N;ENSP00000353109:K476N|ENSP00000346122:K454T	ENSP00000240874:K476N|ENSP00000346122:K454T	K|K	+|+	3|2	2|0	KALRN|KALRN	125535819|125535819	1.000000|1.000000	0.71417|0.71417	0.998000|0.998000	0.56505|0.56505	0.763000|0.763000	0.43281|0.43281	1.210000|1.210000	0.32370|0.32370	0.379000|0.379000	0.24794|0.24794	0.533000|0.533000	0.62120|0.62120	AAA|AAG		0.572	KALRN-005	KNOWN	basic|CCDS	protein_coding	protein_coding	OTTHUMT00000258843.4	NM_003947		38	75	38	75
MAGI3	260425	broad.mit.edu;ucsc.edu	37	1	114123223	114123223	+	Missense_Mutation	SNP	G	G	A			TCGA-DU-6404-01A-11D-1705-08	TCGA-DU-6404-10A-01D-1705-08								Untested	Somatic	Phase_I	WXS	none			Illumina GAIIx	c2b5382c-99ce-4fe0-aafb-4dc893198379	1895ec32-d356-44f2-94e4-7e43bf8ea156	g.chr1:114123223G>A	ENST00000307546.9	+	3	568	c.493G>A	c.(493-495)Gtt>Att	p.V165I	MAGI3_ENST00000486456.1_3'UTR|MAGI3_ENST00000369617.4_Missense_Mutation_p.V165I|MAGI3_ENST00000369615.1_Missense_Mutation_p.V165I|MAGI3_ENST00000369611.4_Missense_Mutation_p.V165I	NM_001142782.1	NP_001136254.1	Q5TCQ9	MAGI3_HUMAN	membrane associated guanylate kinase, WW and PDZ domain containing 3	165	Guanylate kinase-like. {ECO:0000255|PROSITE-ProRule:PRU00100}.				apoptotic process (GO:0006915)|intracellular signal transduction (GO:0035556)|nucleotide phosphorylation (GO:0046939)|positive regulation of JUN kinase activity (GO:0043507)|viral process (GO:0016032)	membrane (GO:0016020)|nucleus (GO:0005634)|plasma membrane (GO:0005886)|tight junction (GO:0005923)	ATP binding (GO:0005524)|guanylate kinase activity (GO:0004385)			NS(1)|central_nervous_system(1)|cervix(1)|endometrium(3)|kidney(3)|large_intestine(8)|lung(9)|ovary(3)|prostate(7)|skin(2)|upper_aerodigestive_tract(1)|urinary_tract(2)	41	Lung SC(450;0.184)	all_cancers(81;2.34e-09)|all_epithelial(167;7.41e-09)|all_lung(203;7.13e-06)|Lung NSC(69;1.2e-05)		Lung(183;0.0234)|Colorectal(144;0.0686)|all cancers(265;0.0792)|Epithelial(280;0.0866)|COAD - Colon adenocarcinoma(174;0.111)|LUSC - Lung squamous cell carcinoma(189;0.133)		TTTCATTTCCGTTGAACAGTT	0.393																																																0													114.0	115.0	114.0					1																	114123223		2203	4300	6503	SO:0001583	missense	260425			AF213259	CCDS860.1, CCDS44196.1	1p12-p11.2	2008-02-05			ENSG00000081026	ENSG00000081026			29647	protein-coding gene	gene with protein product		615943				10997877, 10748157	Standard	NM_152900		Approved	MAGI-3	uc001edk.3	Q5TCQ9	OTTHUMG00000011737	ENST00000307546.9:c.493G>A	1.37:g.114123223G>A	ENSP00000304604:p.Val165Ile		Q5TCQ8|Q5TCR0|Q9H2V6|Q9H5Y8|Q9HBC4|Q9HCD8	Missense_Mutation	SNP	ENST00000307546.9	37	CCDS44196.1	.	.	.	.	.	.	.	.	.	.	G	30	5.050588	0.93740	.	.	ENSG00000081026	ENST00000369617;ENST00000307546;ENST00000369615;ENST00000369611	T;T;T;T	0.17370	2.28;2.28;2.28;2.28	5.38	5.38	0.77491	.	0.124429	0.53938	D	0.000057	T	0.28300	0.0699	L	0.49571	1.57	0.58432	D	0.999998	D;D;D	0.76494	0.999;0.984;0.987	D;P;P	0.62955	0.909;0.482;0.697	T	0.01440	-1.1354	10	0.72032	D	0.01	-26.7631	19.5007	0.95093	0.0:0.0:1.0:0.0	.	165;165;165	Q5TCQ9-4;Q5TCQ9-3;Q5TCQ9-2	.;.;.	I	165	ENSP00000358630:V165I;ENSP00000304604:V165I;ENSP00000358628:V165I;ENSP00000358624:V165I	ENSP00000304604:V165I	V	+	1	0	MAGI3	113924746	1.000000	0.71417	1.000000	0.80357	0.987000	0.75469	6.325000	0.72901	2.673000	0.90976	0.650000	0.86243	GTT		0.393	MAGI3-004	NOVEL	basic|exp_conf|CCDS	protein_coding	protein_coding	OTTHUMT00000032429.1	NM_152900		20	77	20	77
