#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_Chromosome_hg18	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_End_position_hg18	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_NormalRefReads_WU	i_NormalVAF_WU	i_NormalVarReads_WU	i_ORegAnno_bin	i_RNARefReads_WU	i_RNAVAF_WU	i_RNAVarReads_WU	i_Start_position_hg18	i_TumorRefReads_WU	i_TumorVAF_WU	i_TumorVarReads_WU	i_UniProt_alt_uniprot_accessions	i_Variant_Classification	i_Variant_Type	i_all_domains	i_amino_acid_change	i_annotation_transcript	i_build	i_c_position	i_ccds_id	i_chromosome_name	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_deletion_substructures	i_domain	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_name	i_gene_type	i_havana_transcript	i_reference	i_refseq_mrna_id	i_secondary_variant_classification	i_stop	i_strand	i_transcript_error	i_transcript_name	i_transcript_source	i_transcript_species	i_transcript_status	i_transcript_version	i_trv_type	i_type	i_ucsc_cons	i_variant
LHCGR	3973	genome.wustl.edu	37	2	48936146	48936146	+	Silent	SNP	G	G	A			TCGA-AB-2950-03A-01W-0733-08	TCGA-AB-2950-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	dce07a7f-06d3-415f-a454-8ebdf7244d4f	87d2a3f8-e5bd-4b87-bde0-2c2b49f2b42e	g.chr2:48936146G>A	ENST00000294954.7	-	8	642	c.621C>T	c.(619-621)aaC>aaT	p.N207N	LHCGR_ENST00000403273.1_Silent_p.N207N|LHCGR_ENST00000344775.3_Silent_p.N207N|LHCGR_ENST00000405626.1_Silent_p.N207N|STON1-GTF2A1L_ENST00000402114.2_Intron|LHCGR_ENST00000401907.1_Silent_p.N207N	NM_000233.3	NP_000224.2	P22888	LSHR_HUMAN	luteinizing hormone/choriogonadotropin receptor	207					activation of adenylate cyclase activity (GO:0007190)|cellular response to gonadotropin stimulus (GO:0071371)|cognition (GO:0050890)|development of secondary male sexual characteristics (GO:0046544)|G-protein coupled receptor signaling pathway (GO:0007186)|G-protein coupled receptor signaling pathway, coupled to cyclic nucleotide second messenger (GO:0007187)|male genitalia development (GO:0030539)|male gonad development (GO:0008584)|ovarian follicle development (GO:0001541)|phospholipase C-activating G-protein coupled receptor signaling pathway (GO:0007200)|positive regulation of cAMP-mediated signaling (GO:0043950)|positive regulation of inositol trisphosphate biosynthetic process (GO:0032962)|regulation of steroid hormone biosynthetic process (GO:0090030)|seminiferous tubule development (GO:0072520)|spermatogenesis (GO:0007283)|uterus development (GO:0060065)	endosome (GO:0005768)|integral component of plasma membrane (GO:0005887)|plasma membrane (GO:0005886)	choriogonadotropin hormone binding (GO:0038106)|choriogonadotropin hormone receptor activity (GO:0035472)|luteinizing hormone receptor activity (GO:0004964)			NS(1)|breast(6)|central_nervous_system(1)|cervix(1)|endometrium(5)|kidney(1)|large_intestine(5)|liver(1)|lung(23)|ovary(3)|pancreas(2)|prostate(1)|skin(4)|upper_aerodigestive_tract(2)	56		all_hematologic(82;0.151)|Acute lymphoblastic leukemia(82;0.176)	Lung(47;0.101)|LUSC - Lung squamous cell carcinoma(58;0.151)		Buserelin(DB06719)|Cetrorelix(DB00050)|Choriogonadotropin alfa(DB00097)|Goserelin(DB00014)|Lutropin alfa(DB00044)|Menotropins(DB00032)	CCAGATGTACGTTTTCCTTTA	0.512																																						dbGAP											0			2											220.0	188.0	199.0					2																	48936146		2203	4300	6503	48789650	SO:0001819	synonymous_variant	0				CCDS1842.1	2p21	2012-08-10			ENSG00000138039	ENSG00000138039		"""GPCR / Class A : Gonadotropin and TSH receptors"""	6585	protein-coding gene	gene with protein product		152790	"""hypergonadotropic hypogonadism"""	HHG			Standard	NM_000233		Approved	LHR, LCGR, LGR2, ULG5	uc002rwu.4	P22888	OTTHUMG00000129257	ENST00000294954.7:c.621C>T	2.37:g.48936146G>A		137	2.14	3		NA	NA	NA	48789650	259	40.14	175	Q14751|Q15996|Q9UEW9	Silent	SNP	HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1,superfamily_L domain-like,superfamily_Family A G protein-coupled receptor-like	p.N207	ENST00000294954.7	37	c.621	CCDS1842.1	2																																																																																			-	superfamily_L domain-like		0.512	LHCGR-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LHCGR	protein_coding	OTTHUMT00000251364.4	G	NM_000233.3		48789650	-1	no_errors	NM_000233.3	genbank	human	reviewed	54_36p	silent	SNP	0.019	A
ACOXL	55289	genome.wustl.edu	37	2	111542370	111542370	+	Missense_Mutation	SNP	C	C	T	rs201574685		TCGA-AB-2950-03A-01W-0733-08	TCGA-AB-2950-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	dce07a7f-06d3-415f-a454-8ebdf7244d4f	87d2a3f8-e5bd-4b87-bde0-2c2b49f2b42e	g.chr2:111542370C>T	ENST00000389811.4	+	3	361	c.137C>T	c.(136-138)gCg>gTg	p.A46V	ACOXL_ENST00000340561.4_Missense_Mutation_p.A46V|ACOXL_ENST00000439055.1_Missense_Mutation_p.A46V			Q9NUZ1	ACOXL_HUMAN	acyl-CoA oxidase-like	46					fatty acid beta-oxidation (GO:0006635)	peroxisome (GO:0005777)	acyl-CoA dehydrogenase activity (GO:0003995)|acyl-CoA oxidase activity (GO:0003997)			kidney(1)|large_intestine(4)|lung(10)|pancreas(1)|prostate(2)|skin(2)|urinary_tract(1)	21						CTCTCCATGGCGGACATGGCC	0.488													C|||	1	0.000199681	0.0008	0.0	5008	,	,		15444	0.0		0.0	False		,,,				2504	0.0					dbGAP											0			2						C	VAL/ALA	1,3803		0,1,1901	57.0	60.0	59.0		137	1.9	0.0	2		59	0,8274		0,0,4137	yes	missense	ACOXL	NM_001142807.1	64	0,1,6038	TT,TC,CC		0.0,0.0263,0.0083	benign	46/581	111542370	1,12077	1902	4137	6039	111258841	SO:0001583	missense	0				CCDS46389.1	2q13	2010-06-30	2010-04-30		ENSG00000153093	ENSG00000153093			25621	protein-coding gene	gene with protein product			"""acyl-Coenzyme A oxidase-like"""				Standard	NM_001142807		Approved	FLJ11042	uc010yxk.1	Q9NUZ1	OTTHUMG00000131257	ENST00000389811.4:c.137C>T	2.37:g.111542370C>T	ENSP00000374461:p.Ala46Val	79	2.44	2		NA	NA	NA	111258841	93	42.94	70	A2RRB7|B7WPB3|B7WPP7|E9PB20|Q53R27|Q53R31|Q53SC6|Q8TCE7	Missense_Mutation	SNP	HMMPfam_Acyl-CoA_dh_1,HMMPfam_Acyl-CoA_dh_M,superfamily_Acyl-CoA dehydrogenase C-terminal domain-like,superfamily_Acyl-CoA dehydrogenase NM domain-like	p.A46V	ENST00000389811.4	37	c.137		2	1	4.578754578754579E-4	1	0.0020325203252032522	0	0.0	0	0.0	0	0.0	C	0.028	-1.355767	0.01245	2.63E-4	0.0	ENSG00000153093	ENST00000389811;ENST00000439055;ENST00000340561;ENST00000448863	D;D;D	0.98926	-5.24;-5.24;-5.24	5.43	1.91	0.25777	Acyl-CoA dehydrogenase/oxidase (1);	0.556675	0.13692	N	0.369469	D	0.94132	0.8118	N	0.17082	0.46	0.09310	N	1	B;B;B	0.22983	0.046;0.078;0.005	B;B;B	0.17979	0.013;0.02;0.001	D	0.87183	0.2229	10	0.16896	T	0.51	-1.5526	6.9407	0.24490	0.0:0.637:0.0:0.363	.	46;46;46	E9PB20;Q9NUZ1-2;Q9NUZ1	.;.;ACOXL_HUMAN	V	46	ENSP00000374461:A46V;ENSP00000407761:A46V;ENSP00000343717:A46V	ENSP00000343717:A46V	A	+	2	0	ACOXL	111258841	0.032000	0.19561	0.001000	0.08648	0.373000	0.29922	0.533000	0.23082	0.062000	0.16340	-0.251000	0.11542	GCG	-	superfamily_Acyl-CoA dehydrogenase NM domain-like		0.488	ACOXL-001	NOVEL	basic|appris_principal	protein_coding	ACOXL	protein_coding	OTTHUMT00000254024.2	C	NM_018308		111258841	+1	no_errors	NM_001105516.2	genbank	human	validated	54_36p	missense	SNP	0.187	T
NAALADL2	254827	genome.wustl.edu	37	3	175165096	175165096	+	Silent	SNP	G	G	A			TCGA-AB-2950-03A-01W-0733-08	TCGA-AB-2950-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	dce07a7f-06d3-415f-a454-8ebdf7244d4f	87d2a3f8-e5bd-4b87-bde0-2c2b49f2b42e	g.chr3:175165096G>A	ENST00000454872.1	+	6	1298	c.1170G>A	c.(1168-1170)ctG>ctA	p.L390L	NAALADL2_ENST00000473253.1_3'UTR	NM_207015.2	NP_996898.2	Q58DX5	NADL2_HUMAN	N-acetylated alpha-linked acidic dipeptidase-like 2	390						integral component of membrane (GO:0016021)				central_nervous_system(1)|cervix(1)|endometrium(6)|haematopoietic_and_lymphoid_tissue(2)|kidney(2)|large_intestine(5)|lung(20)|pancreas(1)|prostate(4)|skin(2)|stomach(1)|upper_aerodigestive_tract(4)	49	Ovarian(172;0.0102)	all_cancers(1;0.0272)|all_epithelial(1;0.0553)	OV - Ovarian serous cystadenocarcinoma(80;9.26e-28)	Colorectal(1;1.66e-10)|COAD - Colon adenocarcinoma(1;2.1e-07)|STAD - Stomach adenocarcinoma(1;0.00261)|READ - Rectum adenocarcinoma(3;0.0284)		TTGCAAAACTGATCTCTTCGC	0.398																																						dbGAP											0			3											66.0	63.0	64.0					3																	175165096		1877	4123	6000	176647790	SO:0001819	synonymous_variant	0				CCDS46960.1	3q26.3	2011-08-16			ENSG00000177694	ENSG00000177694			23219	protein-coding gene	gene with protein product	"""glutamate carboxypeptidase II-type non-peptidase homologue"""	608806				15168106	Standard	NM_207015		Approved		uc003fir.3	Q58DX5	OTTHUMG00000157120	ENST00000454872.1:c.1170G>A	3.37:g.175165096G>A		68	0.00	0		1	0.00	0	176647790	59	42.72	44	Q658X9|Q6H9J8|Q6H9J9|Q6PG38	Silent	SNP	superfamily_Transferrin receptor ectodomain C-terminal domain,PatternScan_GLYCOSYL_HYDROL_F5,superfamily_Transferrin receptor ectodomain apical domain,superfamily_Zn-dependent exopeptidases	p.L390	ENST00000454872.1	37	c.1170	CCDS46960.1	3																																																																																			-	superfamily_Transferrin receptor ectodomain apical domain,superfamily_Zn-dependent exopeptidases		0.398	NAALADL2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	NAALADL2	protein_coding	OTTHUMT00000347390.2	G	NM_207015		176647790	+1	no_errors	NM_207015.2	genbank	human	validated	54_36p	silent	SNP	0.953	A
KIAA1109	84162	genome.wustl.edu	37	4	123202879	123202879	+	Missense_Mutation	SNP	C	C	G			TCGA-AB-2950-03A-01W-0733-08	TCGA-AB-2950-11A-01W-0732-08	C	C	C	G	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	dce07a7f-06d3-415f-a454-8ebdf7244d4f	87d2a3f8-e5bd-4b87-bde0-2c2b49f2b42e	g.chr4:123202879C>G	ENST00000264501.4	+	52	9360	c.8987C>G	c.(8986-8988)tCt>tGt	p.S2996C	KIAA1109_ENST00000455637.1_Missense_Mutation_p.S2996C|KIAA1109_ENST00000388738.3_Missense_Mutation_p.S2996C			Q2LD37	K1109_HUMAN	KIAA1109	2996					regulation of cell growth (GO:0001558)|regulation of epithelial cell differentiation (GO:0030856)	integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)				breast(7)|central_nervous_system(1)|cervix(1)|endometrium(16)|kidney(6)|large_intestine(33)|liver(4)|lung(74)|ovary(9)|pancreas(1)|prostate(5)|skin(6)|upper_aerodigestive_tract(6)|urinary_tract(3)	172						CTTTTACCATCTCTGAAAGCA	0.363																																						dbGAP											0			4											103.0	98.0	100.0					4																	123202879		1842	4098	5940	123422329	SO:0001583	missense	0			AL137384	CCDS43267.1	4q28.1	2012-07-09			ENSG00000138688	ENSG00000138688			26953	protein-coding gene	gene with protein product	"""fragile site-associated"""	611565				16386706	Standard	NM_015312		Approved	FLJ21404, FSA, KIAA1371, Tweek	uc003ieh.3	Q2LD37	OTTHUMG00000150116	ENST00000264501.4:c.8987C>G	4.37:g.123202879C>G	ENSP00000264501:p.Ser2996Cys	69	1.43	1		20	54.55	24	123422329	52	49.02	50	Q4W598|Q5CZA9|Q6ZS70|Q6ZV75|Q86XA5|Q8WVD8|Q9H742|Q9NT48|Q9NTC3|Q9NTI4|Q9P2H6|Q9UPP3	Missense_Mutation	SNP	PatternScan_ASP_PROTEASE,HMMPfam_FSA_C	p.S2996C	ENST00000264501.4	37	c.8987	CCDS43267.1	4	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	23.9|23.9	4.471617|4.471617	0.84533|0.84533	.|.	.|.	ENSG00000138688|ENSG00000138688	ENST00000419325|ENST00000264501;ENST00000388738;ENST00000455637	.|T;T;T	.|0.38240	.|1.72;1.72;1.15	5.4|5.4	5.4|5.4	0.78164|0.78164	.|.	.|0.000000	.|0.64402	.|D	.|0.000001	T|T	0.60011|0.60011	0.2236|0.2236	M|M	0.61703|0.61703	1.905|1.905	0.58432|0.58432	D|D	0.999996|0.999996	.|D;D	.|0.76494	.|0.999;0.999	.|D;D	.|0.81914	.|0.995;0.99	T|T	0.62320|0.62320	-0.6879|-0.6879	5|10	.|0.87932	.|D	.|0	.|.	19.1675|19.1675	0.93562|0.93562	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	.|2996;2996	.|Q2LD37-6;Q2LD37	.|.;K1109_HUMAN	M|C	953|2996	.|ENSP00000264501:S2996C;ENSP00000373390:S2996C;ENSP00000389925:S2996C	.|ENSP00000264501:S2996C	I|S	+|+	3|2	3|0	KIAA1109|KIAA1109	123422329|123422329	1.000000|1.000000	0.71417|0.71417	0.443000|0.443000	0.26883|0.26883	0.965000|0.965000	0.64279|0.64279	7.678000|7.678000	0.84035|0.84035	2.537000|2.537000	0.85549|0.85549	0.591000|0.591000	0.81541|0.81541	ATC|TCT	-	NULL		0.363	KIAA1109-001	KNOWN	basic|appris_principal|CCDS	protein_coding	KIAA1109	protein_coding	OTTHUMT00000316415.1	C	NM_020797		123422329	+1	no_errors	NM_015312.2	genbank	human	validated	54_36p	missense	SNP	1.000	G
GRID1	2894	genome.wustl.edu	37	10	87407082	87407082	+	Nonsense_Mutation	SNP	G	G	T			TCGA-AB-2950-03A-01W-0733-08	TCGA-AB-2950-11A-01W-0732-08	G	G	G	T	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	dce07a7f-06d3-415f-a454-8ebdf7244d4f	87d2a3f8-e5bd-4b87-bde0-2c2b49f2b42e	g.chr10:87407082G>T	ENST00000327946.7	-	13	2155	c.2070C>A	c.(2068-2070)taC>taA	p.Y690*	RN7SKP238_ENST00000516483.1_RNA|RP11-93H12.4_ENST00000474115.2_RNA|GRID1_ENST00000536331.1_Nonsense_Mutation_p.Y261*	NM_017551.2	NP_060021.1	Q9ULK0	GRID1_HUMAN	glutamate receptor, ionotropic, delta 1	690					ion transmembrane transport (GO:0034220)|ionotropic glutamate receptor signaling pathway (GO:0035235)|social behavior (GO:0035176)|synaptic transmission, glutamatergic (GO:0035249)	cell junction (GO:0030054)|dendrite (GO:0030425)|extracellular vesicular exosome (GO:0070062)|ionotropic glutamate receptor complex (GO:0008328)|postsynaptic membrane (GO:0045211)	extracellular-glutamate-gated ion channel activity (GO:0005234)|ionotropic glutamate receptor activity (GO:0004970)			NS(1)|breast(1)|central_nervous_system(2)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(4)|large_intestine(24)|lung(46)|ovary(5)|prostate(4)|skin(5)|stomach(4)|upper_aerodigestive_tract(5)	106						TGGCTCGGAAGTACTCATATA	0.547										Multiple Myeloma(13;0.14)																												dbGAP											0			10											279.0	259.0	266.0					10																	87407082		2203	4300	6503	87397062	SO:0001587	stop_gained	0			AB033046	CCDS31236.1	10q22	2012-08-29			ENSG00000182771	ENSG00000182771		"""Ligand-gated ion channels / Glutamate receptors, ionotropic"", ""Glutamate receptors"""	4575	protein-coding gene	gene with protein product		610659					Standard	NM_017551		Approved	GluD1, KIAA1220	uc001kdl.1	Q9ULK0	OTTHUMG00000018650	ENST00000327946.7:c.2070C>A	10.37:g.87407082G>T	ENSP00000330148:p.Tyr690*	147	1.95	3		NA	NA	NA	87397062	209	25.09	70	B3KXD5|B7Z7L0|Q8IXT3	Nonsense_Mutation	SNP	HMMPfam_Lig_chan,HMMSmart_SM00079,HMMPfam_ANF_receptor,PatternScan_ALDEHYDE_DEHYDR_GLU,HMMPfam_Lig_chan-Glu_bd,superfamily_Periplasmic binding protein-like I,superfamily_Periplasmic binding protein-like II	p.Y690*	ENST00000327946.7	37	c.2070	CCDS31236.1	10	.	.	.	.	.	.	.	.	.	.	G	38	7.076775	0.98048	.	.	ENSG00000182771	ENST00000327946;ENST00000536331	.	.	.	5.7	4.77	0.60923	.	0.000000	0.85682	D	0.000000	.	.	.	.	.	.	0.80722	A	1	.	.	.	.	.	.	.	.	.	.	0.32370	T	0.25	.	8.5134	0.33231	0.1841:0.0:0.8159:0.0	.	.	.	.	X	690;261	.	ENSP00000330148:Y690X	Y	-	3	2	GRID1	87397062	1.000000	0.71417	1.000000	0.80357	0.988000	0.76386	2.109000	0.41863	1.315000	0.45114	0.650000	0.86243	TAC	-	HMMPfam_Lig_chan,HMMSmart_SM00079,superfamily_Periplasmic binding protein-like II		0.547	GRID1-002	KNOWN	basic|appris_principal|CCDS	protein_coding	GRID1	protein_coding	OTTHUMT00000049148.3	G	XM_043613		87397062	-1	no_errors	NM_017551.2	genbank	human	reviewed	54_36p	nonsense	SNP	1.000	T
SMC3	9126	genome.wustl.edu	37	10	112360890	112360890	+	Splice_Site	SNP	T	T	C			TCGA-AB-2950-03A-01W-0733-08	TCGA-AB-2950-11A-01W-0732-08	T	T	T	C	T	T	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	dce07a7f-06d3-415f-a454-8ebdf7244d4f	87d2a3f8-e5bd-4b87-bde0-2c2b49f2b42e	g.chr10:112360890T>C	ENST00000361804.4	+	23	2770		c.e23+2			NM_005445.3	NP_005436.1	Q9UQE7	SMC3_HUMAN	structural maintenance of chromosomes 3						DNA repair (GO:0006281)|meiotic nuclear division (GO:0007126)|mitotic cell cycle (GO:0000278)|mitotic nuclear division (GO:0007067)|mitotic sister chromatid cohesion (GO:0007064)|mitotic spindle organization (GO:0007052)|negative regulation of DNA endoreduplication (GO:0032876)|regulation of DNA replication (GO:0006275)|signal transduction (GO:0007165)|sister chromatid cohesion (GO:0007062)|stem cell maintenance (GO:0019827)	basement membrane (GO:0005604)|chromatin (GO:0000785)|chromosome (GO:0005694)|chromosome, centromeric region (GO:0000775)|cohesin complex (GO:0008278)|cohesin core heterodimer (GO:0008280)|cytoplasm (GO:0005737)|cytosol (GO:0005829)|lateral element (GO:0000800)|meiotic cohesin complex (GO:0030893)|nuclear matrix (GO:0016363)|nuclear meiotic cohesin complex (GO:0034991)|nucleoplasm (GO:0005654)|nucleus (GO:0005634)|spindle pole (GO:0000922)	ATP binding (GO:0005524)|chromatin binding (GO:0003682)|dynein binding (GO:0045502)|microtubule motor activity (GO:0003777)|protein heterodimerization activity (GO:0046982)			NS(1)|breast(1)|central_nervous_system(1)|endometrium(2)|haematopoietic_and_lymphoid_tissue(3)|kidney(7)|large_intestine(5)|lung(13)|ovary(1)|skin(2)|upper_aerodigestive_tract(2)|urinary_tract(1)	39		Breast(234;0.0848)|Lung NSC(174;0.238)		Epithelial(162;0.00206)|all cancers(201;0.0227)|BRCA - Breast invasive adenocarcinoma(275;0.127)		GATCAGAAGGTGAATTTTTAT	0.343																																						dbGAP											0			10											99.0	113.0	108.0					10																	112360890		2203	4300	6503	112350880	SO:0001630	splice_region_variant	0			AF020043	CCDS31285.1	10q25	2014-09-17	2006-07-06	2006-07-06	ENSG00000108055	ENSG00000108055		"""Structural maintenance of chromosomes proteins"", ""Proteoglycans / Extracellular Matrix : Other"""	2468	protein-coding gene	gene with protein product	"""bamacan proteoglycan"""	606062	"""chondroitin sulfate proteoglycan 6 (bamacan)"""	CSPG6		9506951, 10358101	Standard	NM_005445		Approved	HCAP, BAM, SMC3L1, bamacan	uc001kze.3	Q9UQE7	OTTHUMG00000019042	ENST00000361804.4:c.2644+2T>C	10.37:g.112360890T>C		31	5.71	2		1	98.25	56	112350880	26	48.00	24	A8K156|O60464|Q5T482	Splice_Site	SNP	-	e23+2	ENST00000361804.4	37	c.2644+2	CCDS31285.1	10	.	.	.	.	.	.	.	.	.	.	T	18.08	3.543532	0.65198	.	.	ENSG00000108055	ENST00000361804	.	.	.	5.32	5.32	0.75619	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.2944	0.73891	0.0:0.0:0.0:1.0	.	.	.	.	.	-1	.	.	.	+	.	.	SMC3	112350880	0.999000	0.42202	0.905000	0.35620	0.675000	0.39556	5.445000	0.66594	2.002000	0.58637	0.477000	0.44152	.	-	-		0.343	SMC3-001	KNOWN	non_canonical_conserved|basic|appris_principal|CCDS	protein_coding	SMC3	protein_coding	OTTHUMT00000050337.1	T	NM_005445	Intron	112350880	+1	no_errors	NM_005445.3	genbank	human	reviewed	54_36p	splice_site	SNP	0.991	C
EHD1	10938	genome.wustl.edu	37	11	64627708	64627708	+	Silent	SNP	C	C	T			TCGA-AB-2950-03A-01W-0733-08	TCGA-AB-2950-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	dce07a7f-06d3-415f-a454-8ebdf7244d4f	87d2a3f8-e5bd-4b87-bde0-2c2b49f2b42e	g.chr11:64627708C>T	ENST00000320631.3	-	3	857	c.603G>A	c.(601-603)tcG>tcA	p.S201S	EHD1_ENST00000359393.2_Silent_p.S201S	NM_001282445.1|NM_006795.2	NP_001269374.1|NP_006786.2	Q9H4M9	EHD1_HUMAN	EH-domain containing 1	201	Dynamin-type G.				blood coagulation (GO:0007596)|cellular response to nerve growth factor stimulus (GO:1990090)|cholesterol homeostasis (GO:0042632)|endocytic recycling (GO:0032456)|endocytosis (GO:0006897)|intracellular protein transport (GO:0006886)|low-density lipoprotein particle clearance (GO:0034383)|neuron projection development (GO:0031175)|positive regulation of cholesterol storage (GO:0010886)|positive regulation of endocytic recycling (GO:2001137)|positive regulation of myoblast fusion (GO:1901741)|protein homooligomerization (GO:0051260)	early endosome membrane (GO:0031901)|endocytic vesicle (GO:0030139)|endosome membrane (GO:0010008)|extracellular vesicular exosome (GO:0070062)|lipid particle (GO:0005811)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|plasma membrane (GO:0005886)|platelet dense tubular network membrane (GO:0031095)|recycling endosome membrane (GO:0055038)	ATP binding (GO:0005524)|calcium ion binding (GO:0005509)|GTP binding (GO:0005525)|GTPase activity (GO:0003924)|Rab GTPase binding (GO:0017137)			breast(1)|endometrium(2)|kidney(2)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)	12						TGATCACTTCCGAGAACTCAT	0.582																																						dbGAP											0			11											79.0	72.0	74.0					11																	64627708		2201	4297	6498	64384284	SO:0001819	synonymous_variant	0			AF099011	CCDS8084.1, CCDS73315.1	11q13	2013-01-10			ENSG00000110047	ENSG00000110047		"""EF-hand domain containing"""	3242	protein-coding gene	gene with protein product	"""testilin"""	605888		PAST1		10395801, 10673336	Standard	NM_001282444		Approved	H-PAST, HPAST1, FLJ42622, FLJ44618	uc001obu.1	Q9H4M9	OTTHUMG00000066832	ENST00000320631.3:c.603G>A	11.37:g.64627708C>T		35	2.78	1		58	36.96	34	64384284	68	30.61	30	O14611|Q2M3Q4|Q9UNR3	Silent	SNP	HMMSmart_SM00027,HMMPfam_Dynamin_N,PatternScan_EF_HAND_1,superfamily_EF-hand,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.S201	ENST00000320631.3	37	c.603	CCDS8084.1	11																																																																																			-	HMMPfam_Dynamin_N,superfamily_P-loop containing nucleoside triphosphate hydrolases		0.582	EHD1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	EHD1	protein_coding	OTTHUMT00000143229.2	C	NM_006795		64384284	-1	no_errors	NM_006795.2	genbank	human	reviewed	54_36p	silent	SNP	0.208	T
COPS2	9318	genome.wustl.edu	37	15	49447748	49447748	+	Missense_Mutation	SNP	A	A	C			TCGA-AB-2950-03A-01W-0733-08	TCGA-AB-2950-11A-01W-0732-08	A	A	A	C	A	A	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	dce07a7f-06d3-415f-a454-8ebdf7244d4f	87d2a3f8-e5bd-4b87-bde0-2c2b49f2b42e	g.chr15:49447748A>C	ENST00000388901.5	-	1	101	c.28T>G	c.(28-30)Tgc>Ggc	p.C10G	COPS2_ENST00000299259.6_Missense_Mutation_p.C10G|COPS2_ENST00000542928.1_Missense_Mutation_p.C10G|GALK2_ENST00000327171.3_5'Flank	NM_001143887.1|NM_004236.3	NP_001137359.1|NP_004227.1	P61201	CSN2_HUMAN	COP9 signalosome subunit 2	10					cell proliferation (GO:0008283)|cullin deneddylation (GO:0010388)|negative regulation of transcription from RNA polymerase II promoter (GO:0000122)|neuron differentiation (GO:0030182)|signal transduction (GO:0007165)|skeletal muscle cell differentiation (GO:0035914)|transcription from RNA polymerase II promoter (GO:0006366)	COP9 signalosome (GO:0008180)|cytoplasm (GO:0005737)	signal transducer activity (GO:0004871)|transcription corepressor activity (GO:0003714)			cervix(1)|endometrium(1)|kidney(3)|large_intestine(2)|lung(8)|prostate(1)|skin(2)	18		all_lung(180;0.0428)		all cancers(107;1.34e-07)|GBM - Glioblastoma multiforme(94;3.02e-05)		TCATCATCGCACATGAAATCA	0.607																																					NSCLC(36;322 1063 10349 30082 48062)|Esophageal Squamous(122;685 1633 15569 21293 52803)	dbGAP											0			15											147.0	137.0	140.0					15																	49447748		2196	4295	6491	47235040	SO:0001583	missense	0			AF212227	CCDS32235.1, CCDS45257.1	15q21.2	2013-03-14	2013-03-14						30747	protein-coding gene	gene with protein product		604508	"""COP9 constitutive photomorphogenic homolog subunit 2 (Arabidopsis)"""			7776974, 9535219	Standard	NM_004236		Approved	TRIP15, ALIEN, CSN2	uc001zxh.3	P61201		ENST00000388901.5:c.28T>G	15.37:g.49447748A>C	ENSP00000373553:p.Cys10Gly	59	3.28	2		46	41.77	33	47235040	76	38.71	48	O88950|Q15647|Q6FGP4|Q9BY54|Q9R249|Q9UNI2|Q9UNQ5	Missense_Mutation	SNP	"HMMPfam_PCI,HMMSmart_SM00088,HMMSmart_SM00753,superfamily_""Winged helix"" DNA-binding domain,superfamily_TPR-like"	p.C10G	ENST00000388901.5	37	c.28	CCDS32235.1	15	.	.	.	.	.	.	.	.	.	.	A	13.68	2.308242	0.40895	.	.	ENSG00000166200	ENST00000299259;ENST00000388901;ENST00000542928	.	.	.	5.02	5.02	0.67125	.	0.000000	0.85682	D	0.000000	T	0.52645	0.1747	M	0.68317	2.08	0.31527	N	0.661634	P;P;P	0.34662	0.462;0.462;0.462	B;B;B	0.36534	0.227;0.227;0.227	T	0.60172	-0.7315	9	0.25751	T	0.34	-4.5241	14.9277	0.70893	1.0:0.0:0.0:0.0	.	10;11;10	B4DIH5;Q59EL2;P61201	.;.;CSN2_HUMAN	G	10	.	ENSP00000299259:C10G	C	-	1	0	COPS2	47235040	1.000000	0.71417	1.000000	0.80357	0.999000	0.98932	5.701000	0.68325	2.105000	0.64084	0.533000	0.62120	TGC	-	NULL		0.607	COPS2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COPS2	protein_coding	OTTHUMT00000417840.1	A	NM_004236		47235040	-1	no_errors	NM_004236.1	genbank	human	validated	54_36p	missense	SNP	1.000	C
FCGBP	8857	genome.wustl.edu	37	19	40408297	40408297	+	Silent	SNP	C	C	T	rs368657008		TCGA-AB-2950-03A-01W-0733-08	TCGA-AB-2950-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	dce07a7f-06d3-415f-a454-8ebdf7244d4f	87d2a3f8-e5bd-4b87-bde0-2c2b49f2b42e	g.chr19:40408297C>T	ENST00000221347.6	-	8	4549	c.4542G>A	c.(4540-4542)gcG>gcA	p.A1514A		NM_003890.2	NP_003881.2	Q9Y6R7	FCGBP_HUMAN	Fc fragment of IgG binding protein	1514						extracellular vesicular exosome (GO:0070062)				NS(3)|autonomic_ganglia(1)|breast(7)|central_nervous_system(5)|endometrium(13)|kidney(9)|large_intestine(27)|lung(49)|ovary(8)|pancreas(3)|prostate(13)|skin(9)|stomach(9)|upper_aerodigestive_tract(6)|urinary_tract(3)	165	all_cancers(60;6.03e-06)|all_lung(34;5.58e-08)|Lung NSC(34;6.62e-08)|Ovarian(47;0.06)		Epithelial(26;6.25e-23)|all cancers(26;1.13e-20)			GGCCTCCAGCCGCCTGGCAAG	0.592																																						dbGAP											0			19						C		1,4405	2.1+/-5.4	0,1,2202	64.0	52.0	56.0		4542	-9.2	0.5	19		56	0,8586		0,0,4293	no	coding-synonymous	FCGBP	NM_003890.2		0,1,6495	TT,TC,CC		0.0,0.0227,0.0077		1514/5406	40408297	1,12991	2203	4293	6496	45100137	SO:0001819	synonymous_variant	0			D84239		19q13.2	2013-09-20			ENSG00000090920	ENSG00000275395			13572	protein-coding gene	gene with protein product	"""IgG Fc binding protein"", ""Human Fc gamma BP"""					9182547	Standard	NM_003890		Approved	FC(GAMMA)BP	uc002omp.4	Q9Y6R7	OTTHUMG00000182580	ENST00000221347.6:c.4542G>A	19.37:g.40408297C>T		68	2.86	2		1	0.00	0	45100137	42	65.57	80	O95784	Silent	SNP	HMMSmart_VWC,HMMPfam_VWD,HMMSmart_VWD,superfamily_Cysrich_TIL,HMMPfam_TIL_assoc,HMMSmart_FOLN,HMMPfam_C8,HMMPfam_TIL	p.A1514	ENST00000221347.6	37	c.4542	CCDS12546.1	19																																																																																			-	HMMPfam_C8		0.592	FCGBP-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FCGBP	protein_coding	OTTHUMT00000462507.1	C	NM_003890		45100137	-1	no_errors	NM_003890.2	genbank	human	validated	54_36p	silent	SNP	0.937	T
ARHGAP35	2909	genome.wustl.edu	37	19	47423101	47423101	+	Missense_Mutation	SNP	C	C	T			TCGA-AB-2950-03A-01W-0733-08	TCGA-AB-2950-11A-01W-0732-08	C	C	C	T	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	dce07a7f-06d3-415f-a454-8ebdf7244d4f	87d2a3f8-e5bd-4b87-bde0-2c2b49f2b42e	g.chr19:47423101C>T	ENST00000404338.3	+	1	1169	c.1169C>T	c.(1168-1170)gCc>gTc	p.A390V		NM_004491.4	NP_004482.4	Q9NRY4	RHG35_HUMAN	Rho GTPase activating protein 35	390	FF 2.				axon guidance (GO:0007411)|camera-type eye development (GO:0043010)|forebrain development (GO:0030900)|negative regulation of transcription, DNA-templated (GO:0045892)|negative regulation of vascular permeability (GO:0043116)|neural tube closure (GO:0001843)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of cell shape (GO:0008360)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)|transcription, DNA-templated (GO:0006351)	actin cytoskeleton (GO:0015629)|cytosol (GO:0005829)|nucleus (GO:0005634)	DNA binding (GO:0003677)|GTP binding (GO:0005525)|Rho GTPase activator activity (GO:0005100)|transcription corepressor activity (GO:0003714)										CCATGGGATGCCACCAGTCAC	0.458																																						dbGAP											0			19											110.0	103.0	106.0					19																	47423101		1906	4138	6044	52114941	SO:0001583	missense	0			M73077	CCDS46127.1	19q13.32	2011-06-29	2011-06-07	2011-06-07	ENSG00000160007	ENSG00000160007		"""Rho GTPase activating proteins"""	4591	protein-coding gene	gene with protein product		605277	"""glucocorticoid receptor DNA binding factor 1"""	GRLF1		1894621, 20675588	Standard	NM_004491		Approved	GRF-1, p190ARhoGAP, P190A, KIAA1722, p190RhoGAP	uc010ekv.3	Q9NRY4		ENST00000404338.3:c.1169C>T	19.37:g.47423101C>T	ENSP00000385720:p.Ala390Val	95	5.94	6		17	67.31	35	52114941	76	53.89	90	A7E2A4|Q14452|Q9C0E1	Missense_Mutation	SNP	HMMPfam_RhoGAP,HMMSmart_SM00324,HMMPfam_FF,HMMSmart_SM00441,superfamily_GTPase activation domain GAP,HMMPfam_Ras,superfamily_P-loop containing nucleoside triphosphate hydrolases	p.A390V	ENST00000404338.3	37	c.1169	CCDS46127.1	19	.	.	.	.	.	.	.	.	.	.	C	10.82	1.458626	0.26248	.	.	ENSG00000160007	ENST00000317082;ENST00000501576;ENST00000404338	T	0.07567	3.18	5.84	3.69	0.42338	.	0.498399	0.23519	N	0.047303	T	0.05135	0.0137	N	0.14661	0.345	0.33905	D	0.63895	B	0.28605	0.217	B	0.28139	0.086	T	0.19679	-1.0298	10	0.66056	D	0.02	-15.8083	6.6911	0.23171	0.1453:0.7059:0.0:0.1488	.	390	Q9NRY4-2	.	V	390	ENSP00000385720:A390V	ENSP00000324820:A390V	A	+	2	0	ARHGAP35	52114941	0.851000	0.29673	1.000000	0.80357	0.949000	0.60115	0.575000	0.23729	0.784000	0.33661	0.655000	0.94253	GCC	-	HMMSmart_SM00441		0.458	ARHGAP35-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GRLF1	protein_coding	OTTHUMT00000466652.1	C	NM_004491		52114941	+1	no_errors	NM_004491.4	genbank	human	reviewed	54_36p	missense	SNP	0.998	T
B3GALT5	10317	genome.wustl.edu	37	21	41033192	41033192	+	Missense_Mutation	SNP	G	G	A	rs369365169		TCGA-AB-2950-03A-01W-0733-08	TCGA-AB-2950-11A-01W-0732-08	G	G	G	A	G	G	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	dce07a7f-06d3-415f-a454-8ebdf7244d4f	87d2a3f8-e5bd-4b87-bde0-2c2b49f2b42e	g.chr21:41033192G>A	ENST00000380620.4	+	5	1298	c.706G>A	c.(706-708)Gtc>Atc	p.V236I	AF064860.5_ENST00000416555.1_RNA|B3GALT5_ENST00000380618.1_Missense_Mutation_p.V236I|B3GALT5_ENST00000343118.4_Missense_Mutation_p.V236I|B3GALT5_ENST00000398714.2_Missense_Mutation_p.V236I			Q9Y2C3	B3GT5_HUMAN	UDP-Gal:betaGlcNAc beta 1,3-galactosyltransferase, polypeptide 5	236					protein glycosylation (GO:0006486)	endoplasmic reticulum (GO:0005783)|Golgi apparatus (GO:0005794)|integral component of membrane (GO:0016021)	UDP-galactose:beta-N-acetylglucosamine beta-1,3-galactosyltransferase activity (GO:0008499)			breast(1)|central_nervous_system(1)|endometrium(1)|kidney(1)|large_intestine(5)|prostate(1)|skin(4)|stomach(1)|urinary_tract(1)	16		Prostate(19;2.55e-06)				CTCCAAGAGCGTCCCATACAT	0.542																																						dbGAP											0			21						G	ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL,ILE/VAL	0,4406		0,0,2203	92.0	92.0	92.0		706,706,706,706,706	3.6	0.1	21		92	1,8599	1.2+/-3.3	0,1,4299	no	missense,missense,missense,missense,missense	B3GALT5	NM_006057.1,NM_033170.1,NM_033171.1,NM_033172.1,NM_033173.1	29,29,29,29,29	0,1,6502	AA,AG,GG		0.0116,0.0,0.0077	possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging,possibly-damaging	236/311,236/311,236/311,236/311,236/311	41033192	1,13005	2203	4300	6503	39955062	SO:0001583	missense	0			AB020337	CCDS13667.1, CCDS74795.1	21q22.3	2013-02-19			ENSG00000183778	ENSG00000183778		"""Beta 3-glycosyltransferases"""	920	protein-coding gene	gene with protein product	"""homolog of C. elegans Bt toxin resistance gene bre-5"", ""GlcNAc-beta-1,3-galactosyltransferase 5"""	604066				10212226	Standard	NM_006057		Approved	beta3Gal-T5, B3GalT-V, GLCT5, B3T5	uc002yyj.1	Q9Y2C3	OTTHUMG00000086725	ENST00000380620.4:c.706G>A	21.37:g.41033192G>A	ENSP00000369994:p.Val236Ile	134	3.52	5		NA	NA	NA	39955062	303	41.62	216	A8KA86|D3DSI3|Q2M3L5|Q53Z19|Q9NY96|Q9P1X6|Q9P1X7	Missense_Mutation	SNP	HMMPfam_Galactosyl_T	p.V236I	ENST00000380620.4	37	c.706	CCDS13667.1	21	.	.	.	.	.	.	.	.	.	.	G	0.259	-1.000971	0.02128	0.0	1.16E-4	ENSG00000183778	ENST00000380620;ENST00000380618;ENST00000343118;ENST00000398714	T;T;T;T	0.42131	0.98;0.98;0.98;0.98	5.49	3.56	0.40772	.	0.245691	0.27759	N	0.017980	T	0.26955	0.0660	L	0.33189	0.99	0.26116	N	0.980614	P	0.35174	0.488	B	0.32624	0.149	T	0.11567	-1.0582	10	0.12766	T	0.61	.	10.1276	0.42658	0.2345:0.0:0.7655:0.0	.	236	Q9Y2C3	B3GT5_HUMAN	I	236	ENSP00000369994:V236I;ENSP00000369992:V236I;ENSP00000343318:V236I;ENSP00000381699:V236I	ENSP00000343318:V236I	V	+	1	0	B3GALT5	39955062	0.000000	0.05858	0.088000	0.20740	0.046000	0.14306	0.658000	0.24979	1.188000	0.43014	0.655000	0.94253	GTC	-	HMMPfam_Galactosyl_T		0.542	B3GALT5-001	KNOWN	basic|appris_principal|CCDS	protein_coding	B3GALT5	protein_coding	OTTHUMT00000195008.2	G	NM_033170		39955062	+1	no_errors	NM_006057.1	genbank	human	reviewed	54_36p	missense	SNP	0.292	A
ARHGEF6	9459	genome.wustl.edu	37	X	135772783	135772783	+	Frame_Shift_Del	DEL	C	C	-			TCGA-AB-2950-03A-01W-0733-08	TCGA-AB-2950-11A-01W-0732-08	C	C	C	-	C	C	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	dce07a7f-06d3-415f-a454-8ebdf7244d4f	87d2a3f8-e5bd-4b87-bde0-2c2b49f2b42e	g.chrX:135772783delC	ENST00000250617.6	-	10	2376	c.1171delG	c.(1171-1173)gaafs	p.E391fs	ARHGEF6_ENST00000370620.1_Frame_Shift_Del_p.E237fs|ARHGEF6_ENST00000535227.1_Frame_Shift_Del_p.E264fs|ARHGEF6_ENST00000370622.1_Frame_Shift_Del_p.E237fs	NM_004840.2	NP_004831.1	Q15052	ARHG6_HUMAN	Rac/Cdc42 guanine nucleotide exchange factor (GEF) 6	391	DH. {ECO:0000255|PROSITE- ProRule:PRU00062}.				apoptotic process (GO:0006915)|apoptotic signaling pathway (GO:0097190)|cell junction assembly (GO:0034329)|JNK cascade (GO:0007254)|lamellipodium assembly (GO:0030032)|neurotrophin TRK receptor signaling pathway (GO:0048011)|positive regulation of apoptotic process (GO:0043065)|positive regulation of GTPase activity (GO:0043547)|positive regulation of Rho GTPase activity (GO:0032321)|regulation of small GTPase mediated signal transduction (GO:0051056)|small GTPase mediated signal transduction (GO:0007264)	cell-cell junction (GO:0005911)|cytosol (GO:0005829)|intracellular (GO:0005622)|lamellipodium (GO:0030027)	GTPase activator activity (GO:0005096)|Rho guanyl-nucleotide exchange factor activity (GO:0005089)			cervix(1)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(12)|liver(1)|lung(14)|prostate(1)	38	Acute lymphoblastic leukemia(192;0.000127)					ATATGCCGTTCTAACTCTTGC	0.463																																						dbGAP											0			X											163.0	129.0	140.0					X																	135772783		2203	4300	6503	135600449	SO:0001589	frameshift_variant	0			D13631	CCDS14660.1	Xq26	2013-01-10	2002-05-23		ENSG00000129675	ENSG00000129675		"""Rho guanine nucleotide exchange factors"", ""Pleckstrin homology (PH) domain containing"""	685	protein-coding gene	gene with protein product	"""Rac/Cdc42 guanine exchange factor (GEF) 6"", ""PAK-interacting exchange factor, alpha"", ""rho guanine nucleotide exchange factor 6"""	300267	"""mental retardation, X-linked 46"""	MRX46		7584048, 9659915	Standard	NM_004840		Approved	alphaPIX, Cool-2, KIAA0006, alpha-PIX, Cool2	uc004fab.3	Q15052	OTTHUMG00000022518	ENST00000250617.6:c.1171delG	X.37:g.135772783delC	ENSP00000250617:p.Glu391fs	104	1.83	2		9	70.00	49	135600449	39	57.28	59	A6NMW9|A8K6S7|B1AL37|Q15396|Q5JQ66|Q7Z3W1|Q86XH0	Frame_Shift_Del	DEL	HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain),HMMPfam_SH3_1,HMMSmart_SM00326,superfamily_SH3-domain,HMMPfam_CH,HMMSmart_SM00033,HMMPfam_PH,HMMSmart_SM00233,superfamily_Calponin-homology domain CH-domain,superfamily_PH domain-like	p.E391fs	ENST00000250617.6	37	c.1171	CCDS14660.1	X																																																																																			-	HMMPfam_RhoGEF,HMMSmart_SM00325,superfamily_DBL homology domain (DH-domain)		0.463	ARHGEF6-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ARHGEF6	protein_coding	OTTHUMT00000058511.2	C	NM_004840		135600449	-1	no_errors	NM_004840.2	genbank	human	reviewed	54_36p	frame_shift_del	DEL	1.000	-
MGA	23269	genome.wustl.edu	37	15	42046641	42046642	+	Frame_Shift_Del	DEL	TG	TG	-			TCGA-AB-2950-03A-01W-0733-08	TCGA-AB-2950-11A-01W-0732-08	TG	TG	TG	-	TG	TG	Verified	Valid	Somatic	Phase_IV	WXS	Hybrid_Capture_Illumina_Seq	1		Illumina HiSeq	dce07a7f-06d3-415f-a454-8ebdf7244d4f	87d2a3f8-e5bd-4b87-bde0-2c2b49f2b42e	g.chr15:42046641_42046642delTG	ENST00000570161.1	+	17	7015_7016	c.7015_7016delTG	c.(7015-7017)tgtfs	p.C2339fs	MGA_ENST00000219905.7_Frame_Shift_Del_p.C2339fs|MGA_ENST00000545763.1_Frame_Shift_Del_p.C2130fs|MGA_ENST00000566586.1_Frame_Shift_Del_p.C2130fs|MGA_ENST00000389936.4_Frame_Shift_Del_p.C2300fs			O43451	MGA_HUMAN	MGA, MAX dimerization protein	0					carbohydrate metabolic process (GO:0005975)|polysaccharide digestion (GO:0044245)|small molecule metabolic process (GO:0044281)|starch catabolic process (GO:0005983)	extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	alpha-1,4-glucosidase activity (GO:0004558)|amylase activity (GO:0016160)|carbohydrate binding (GO:0030246)|catalytic activity (GO:0003824)|glucan 1,4-alpha-glucosidase activity (GO:0004339)|maltose alpha-glucosidase activity (GO:0032450)			NS(1)|breast(4)|central_nervous_system(3)|endometrium(16)|haematopoietic_and_lymphoid_tissue(1)|kidney(5)|large_intestine(18)|lung(33)|ovary(8)|prostate(1)|skin(1)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	95		all_cancers(109;0.00356)|all_epithelial(112;0.0413)|all_lung(180;0.18)|Ovarian(310;0.238)		OV - Ovarian serous cystadenocarcinoma(18;1.41e-18)|GBM - Glioblastoma multiforme(113;2.15e-06)|COAD - Colon adenocarcinoma(120;0.031)|Lung(196;0.0721)|BRCA - Breast invasive adenocarcinoma(123;0.0964)|Colorectal(105;0.0998)|LUSC - Lung squamous cell carcinoma(244;0.235)	Acarbose(DB00284)|Miglitol(DB00491)|Voglibose(DB04878)	TCAGAATAACTGTGTAGAATAC	0.381																																						dbGAP											0			15																																								39833934	SO:0001589	frameshift_variant	0			AB011090	CCDS55959.1, CCDS55960.1	15q15	2012-11-15	2012-11-15		ENSG00000174197	ENSG00000174197		"""MAX dimerization proteins"", ""T-boxes"""	14010	protein-coding gene	gene with protein product			"""MAX gene associated"""				Standard	NM_001080541		Approved	KIAA0518, MAD5, MXD5, FLJ12634	uc010ucy.2	Q8IWI9		ENST00000570161.1:c.7015_7016delTG	15.37:g.42046643_42046644delTG	ENSP00000457035:p.Cys2339fs	0	3.17	4		0	0.00	0	39833933	0	31.30	41	Q0VAX6|Q75ME7|Q86UM5	Frame_Shift_Del	DEL	HMMPfam_HLH,HMMSmart_SM00353,HMMPfam_T-box,HMMSmart_SM00425,superfamily_p53-like transcription factors,superfamily_HLH helix-loop-helix DNA-binding domain,PatternScan_TBOX_2	p.V2389fs	ENST00000570161.1	37	c.7162_7163	CCDS55959.1	15																																																																																			-	NULL		0.381	MGA-005	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	MGA	protein_coding	OTTHUMT00000420229.1	TG	NM_001164273.1		39833934	+1	no_errors	NM_001080541.1	genbank	human	provisional	54_36p	frame_shift_del	DEL	0.094:0.101	-
