#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_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_ORegAnno_bin	i_Start_position_hg18	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
CPNE9	151835	genome.wustl.edu	37	3	9767736	9767736	+	Splice_Site	SNP	G	G	A			TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr3:9767736G>A	ENST00000383832.3	+	18	1534		c.e18+1		CPNE9_ENST00000383831.3_Splice_Site	NM_153635.2	NP_705899.2	Q8IYJ1	CPNE9_HUMAN	copine family member IX							extracellular space (GO:0005615)|extracellular vesicular exosome (GO:0070062)				breast(1)|central_nervous_system(1)|endometrium(4)|kidney(1)|large_intestine(2)|lung(2)|ovary(2)|prostate(1)|skin(1)|urinary_tract(1)	16	Medulloblastoma(99;0.227)					CATCGTCAGCGTGAGTCTGAG	0.512																																																0			3											85.0	95.0	91.0					3																	9767736		2202	4300	6502	9742736	SO:0001630	splice_region_variant	151835				CCDS2574.2	3p25.3	2008-10-30			ENSG00000144550	ENSG00000144550			24336	protein-coding gene	gene with protein product						9430674	Standard	XM_006712990		Approved	KIAA4217	uc003bsd.3	Q8IYJ1	OTTHUMG00000128418	ENST00000383832.3:c.1344+1G>A	3.37:g.9767736G>A			9742736	A1L430|A6NDX6|A8MSP8	Splice_Site	SNP	-	e18+1	ENST00000383832.3	37	c.1344+1	CCDS2574.2	3	.	.	.	.	.	.	.	.	.	.	G	18.98	3.737013	0.69304	.	.	ENSG00000144550	ENST00000383832;ENST00000383831;ENST00000273027	.	.	.	5.41	4.54	0.55810	.	.	.	.	.	.	.	.	.	.	.	0.80722	D	1	.	.	.	.	.	.	.	.	.	.	.	.	.	.	15.3655	0.74519	0.0:0.0:0.8591:0.1409	.	.	.	.	.	-1	.	.	.	+	.	.	CPNE9	9742736	1.000000	0.71417	1.000000	0.80357	0.778000	0.44026	7.595000	0.82710	1.286000	0.44565	-0.196000	0.12772	.	-	-		0.512	CPNE9-001	KNOWN	basic|appris_principal|CCDS	protein_coding	CPNE9	protein_coding	OTTHUMT00000250205.4	G	NM_001033755	Intron	9742736	+1	no_errors	NM_153635	genbank	human	validated	54_36p	splice_site	SNP	1.000	A
RDH8	50700	genome.wustl.edu	37	19	10129569	10129569	+	Missense_Mutation	SNP	G	G	T			TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr19:10129569G>T	ENST00000171214.1	+	3	674	c.425G>T	c.(424-426)aGt>aTt	p.S142I	RDH8_ENST00000591589.1_Missense_Mutation_p.S162I	NM_015725.2	NP_056540.2	Q9NYR8	RDH8_HUMAN	retinol dehydrogenase 8 (all-trans)	142					estrogen biosynthetic process (GO:0006703)|phototransduction, visible light (GO:0007603)|retinoid metabolic process (GO:0001523)|steroid biosynthetic process (GO:0006694)|visual perception (GO:0007601)	cytoplasm (GO:0005737)|integral component of plasma membrane (GO:0005887)	estradiol 17-beta-dehydrogenase activity (GO:0004303)|NADP-retinol dehydrogenase activity (GO:0052650)|retinol dehydrogenase activity (GO:0004745)			endometrium(3)|large_intestine(3)|lung(10)|ovary(3)|pancreas(1)|prostate(1)	21			Epithelial(33;4.24e-05)		Vitamin A(DB00162)	GTGATCAGCAGTGTCATGGGC	0.562																																																0			19											72.0	71.0	71.0					19																	10129569		2203	4300	6503	9990569	SO:0001583	missense	50700			AF229845	CCDS12223.1, CCDS12223.2	19p13.2	2011-09-14				ENSG00000080511	1.1.1.-	"""Short chain dehydrogenase/reductase superfamily / Classical SDR fold cluster 2"""	14423	protein-coding gene	gene with protein product	"""short chain dehydrogenase/reductase family 28C, member 2"""	608575				10753906, 19027726	Standard	NM_015725		Approved	PRRDH, SDR28C2	uc002mmr.4	Q9NYR8		ENST00000171214.1:c.425G>T	19.37:g.10129569G>T	ENSP00000171214:p.Ser142Ile		9990569	Q9H838	Missense_Mutation	SNP	superfamily_NAD(P)-bd,HMMPfam_adh_short,PatternScan_ADH_SHORT	p.S142I	ENST00000171214.1	37	c.425		19	.	.	.	.	.	.	.	.	.	.	G	21.6	4.167591	0.78339	.	.	ENSG00000080511	ENST00000171214	D	0.96802	-4.13	5.34	5.34	0.76211	Short-chain dehydrogenase/reductase, conserved site (1);NAD(P)-binding domain (1);	0.000000	0.85682	D	0.000000	D	0.98912	0.9631	H	0.98256	4.185	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	D	0.99474	1.0946	10	0.87932	D	0	.	16.5222	0.84320	0.0:0.0:1.0:0.0	.	142	Q9NYR8	RDH8_HUMAN	I	142	ENSP00000171214:S142I	ENSP00000171214:S142I	S	+	2	0	RDH8	9990569	1.000000	0.71417	0.998000	0.56505	0.705000	0.40729	9.422000	0.97458	2.492000	0.84095	0.491000	0.48974	AGT	-	superfamily_NAD(P)-bd,HMMPfam_adh_short,PatternScan_ADH_SHORT		0.562	RDH8-201	KNOWN	basic|appris_principal	protein_coding	RDH8	protein_coding		G			9990569	+1	no_errors	NM_015725	genbank	human	validated	54_36p	missense	SNP	1.000	T
Unknown	0	genome.wustl.edu	37	21	14529341	14529341	+	IGR	SNP	G	G	A	rs189587437	byFrequency	TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr21:14529341G>A								RNU6-614P (109331 upstream) : AL050302.1 (212589 downstream)																							CTAATGTCACGTTGATGTCTG	0.328													a|||	256	0.0511182	0.0008	0.0072	5008	,	,		15170	0.1389		0.0169	False		,,,				2504	0.0951															0			21																																								13451212	SO:0001628	intergenic_variant	727867																															21.37:g.14529341G>A			13451212		RNA	SNP	-	NULL		37	NULL		21																																																																																			-	-	0	0.328					LOC727867			G			13451212	-1	pseudogene	XR_036978	genbank	human	model	54_36p	rna	SNP	0.000	A
KIF13A	63971	genome.wustl.edu	37	6	17762801	17762801	+	IGR	SNP	C	C	G	rs77465094	byFrequency	TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr6:17762801C>G	ENST00000259711.6	-	0	5941				KIF13A_ENST00000378814.5_Intron	NM_022113.5	NP_071396.4	Q9H1H9	KI13A_HUMAN	kinesin family member 13A						ATP catabolic process (GO:0006200)|cargo loading into vesicle (GO:0035459)|cytokinesis (GO:0000910)|endosome to lysosome transport (GO:0008333)|Golgi to plasma membrane protein transport (GO:0043001)|intracellular protein transport (GO:0006886)|melanosome organization (GO:0032438)|metabolic process (GO:0008152)|microtubule-based movement (GO:0007018)|plus-end-directed vesicle transport along microtubule (GO:0072383)	centrosome (GO:0005813)|endosome membrane (GO:0010008)|kinesin complex (GO:0005871)|microtubule (GO:0005874)|midbody (GO:0030496)|trans-Golgi network membrane (GO:0032588)	ATP binding (GO:0005524)|ATPase activity (GO:0016887)|microtubule motor activity (GO:0003777)			breast(3)|cervix(2)|endometrium(7)|haematopoietic_and_lymphoid_tissue(1)|kidney(7)|large_intestine(19)|lung(16)|ovary(2)|prostate(1)|skin(3)|upper_aerodigestive_tract(1)|urinary_tract(2)	64	Breast(50;0.0107)|Ovarian(93;0.016)	all_hematologic(90;0.125)	all cancers(50;0.0865)|Epithelial(50;0.0974)			GTTTGTAGCACCTTTAGGTTT	0.438													C|||	50	0.00998403	0.0	0.013	5008	,	,		18300	0.0		0.0358	False		,,,				2504	0.0051															0			6																																								17870780	SO:0001628	intergenic_variant	63971			AJ291578	CCDS47380.1, CCDS47381.1, CCDS54967.1, CCDS54968.1, CCDS58998.1	6p23	2008-10-21			ENSG00000137177	ENSG00000137177		"""Kinesins"""	14566	protein-coding gene	gene with protein product		605433				11106728	Standard	NM_022113		Approved	bA500C11.2	uc003ncg.4	Q9H1H9	OTTHUMG00000014313		6.37:g.17762801C>G			17870780	A0JP21|A0JP22|F2Z382|Q5THQ2|Q5THQ3|Q9H193|Q9H194|Q9H1H8	Missense_Mutation	SNP	HMMSmart_SM00129,superfamily_P-loop containing nucleoside triphosphate hydrolases,HMMPfam_Kinesin,PatternScan_KINESIN_MOTOR_DOMAIN1,superfamily_SMAD/FHA domain,HMMPfam_FHA	p.G1744A	ENST00000259711.6	37	c.5231	CCDS47381.1	6																																																																																			-	NULL		0.438	KIF13A-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	KIF13A	protein_coding	OTTHUMT00000039954.4	C			17870780	-1	no_stop_codon	ENST00000378814	ensembl	human	known	54_36p	missense	SNP	0.245	G
Unknown	0	genome.wustl.edu	37	18	19812487	19812487	+	IGR	SNP	C	C	A	rs111174224		TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr18:19812487C>A								RP11-627G18.4 (4495 upstream) : snoU13 (28051 downstream)																							atccatccatccatacataca	0.383																																																0			18																																								18066485	SO:0001628	intergenic_variant	0																															18.37:g.19812487C>A			18066485		Missense_Mutation	SNP	NULL	p.P211T		37	c.631		18																																																																																			-	NULL	0	0.383					LOC100131966			C			18066485	+1	no_errors	XM_001714344	genbank	human	model	54_36p	missense	SNP	0.000	A
Unknown	0	genome.wustl.edu	37	14	19758286	19758286	+	IGR	SNP	A	A	G	rs200435800	byFrequency	TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	A	A					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr14:19758286A>G								RP11-496I2.2 (15542 upstream) : RP11-146E13.4 (53889 downstream)																							ATTCCCCTCCAGGGACAGCGC	0.597													.|||	180	0.0359425	0.0605	0.0187	5008	,	,		16477	0.0456		0.0209	False		,,,				2504	0.0204															0			14																																								18828286	SO:0001628	intergenic_variant	642669																															14.37:g.19758286A>G			18828286		Silent	SNP	NULL	p.P37		37	c.111		14																																																																																			-	NULL	0	0.597					LOC642669			A			18828286	+1	no_errors	XM_926123	genbank	human	model	54_36p	silent	SNP	0.983	G
OR4L1	122742	genome.wustl.edu	37	14	20528941	20528941	+	Silent	SNP	G	G	T			TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr14:20528941G>T	ENST00000315683.1	+	1	738	c.738G>T	c.(736-738)gtG>gtT	p.V246V		NM_001004717.1	NP_001004717.1	Q8NH43	OR4L1_HUMAN	olfactory receptor, family 4, subfamily L, member 1	246						integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	G-protein coupled receptor activity (GO:0004930)|olfactory receptor activity (GO:0004984)			central_nervous_system(1)|endometrium(3)|large_intestine(4)|lung(16)|ovary(2)|pancreas(2)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	34	all_cancers(95;0.00108)		Epithelial(56;4.65e-07)|all cancers(55;2.9e-06)	GBM - Glioblastoma multiforme(265;0.0064)		ACATCATTGTGGTCACTCTGT	0.408																																																0			14											164.0	148.0	153.0					14																	20528941		2203	4300	6503	19598781	SO:0001819	synonymous_variant	122742				CCDS32029.1	14q11.2	2013-09-23			ENSG00000176246	ENSG00000176246		"""GPCR / Class A : Olfactory receptors"""	15356	protein-coding gene	gene with protein product				OR4L2P			Standard	NM_001004717		Approved		uc001vwn.1	Q8NH43	OTTHUMG00000169492	ENST00000315683.1:c.738G>T	14.37:g.20528941G>T			19598781	Q6IEZ5	Silent	SNP	superfamily_SSF81321,HMMPfam_7tm_1,PatternScan_G_PROTEIN_RECEP_F1_1	p.V246	ENST00000315683.1	37	c.738	CCDS32029.1	14																																																																																			-	superfamily_SSF81321,HMMPfam_7tm_1		0.408	OR4L1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	OR4L1	protein_coding	OTTHUMT00000404381.1	G			19598781	+1	no_errors	NM_001004717	genbank	human	provisional	54_36p	silent	SNP	0.998	T
GUSBP1	728411	genome.wustl.edu	37	5	21484081	21484081	+	RNA	SNP	G	G	C	rs200910368	byFrequency	TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr5:21484081G>C	ENST00000607545.1	+	0	179					NR_027026.1		Q15486	GUSP1_HUMAN	glucuronidase, beta pseudogene 1						carbohydrate metabolic process (GO:0005975)|nervous system development (GO:0007399)|skeletal system development (GO:0001501)		hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)										TGATCAGCAGGATTTTCTTGG	0.607													.|||	49	0.00978435	0.0015	0.0115	5008	,	,		67139	0.0		0.0199	False		,,,				2504	0.0194															0			5																																								21519838			728401			BC064850, X75940		5p14.3	2012-10-04			ENSG00000183666	ENSG00000183666			13670	pseudogene	pseudogene						8565635	Standard	NR_027026		Approved		uc010iub.3	Q15486	OTTHUMG00000162474		5.37:g.21484081G>C			21519838	A6NLY8|A8K1B7|Q969T8|Q9BUH2	Missense_Mutation	SNP	NULL	p.P14A	ENST00000607545.1	37	c.40		5																																																																																			-	NULL		0.607	GUSBP1-006	KNOWN	basic	processed_transcript	LOC728401	pseudogene	OTTHUMT00000470546.1	G	NG_008324		21519838	-1	no_errors	XM_001128001	genbank	human	model	54_36p	missense	SNP	0.010	C
SLC2A11	66035	genome.wustl.edu	37	22	24224737	24224737	+	Silent	SNP	G	G	A			TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr22:24224737G>A	ENST00000345044.6	+	7	1045	c.777G>A	c.(775-777)cgG>cgA	p.R259R	RN7SL268P_ENST00000491172.2_RNA|SLC2A11_ENST00000398356.2_Silent_p.R266R|AP000350.10_ENST00000433835.3_Intron|SLC2A11_ENST00000316185.8_Silent_p.R262R|SLC2A11_ENST00000467660.1_3'UTR			Q9BYW1	GTR11_HUMAN	solute carrier family 2 (facilitated glucose transporter), member 11	259					carbohydrate transport (GO:0008643)|transmembrane transport (GO:0055085)	integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)	substrate-specific transmembrane transporter activity (GO:0022891)			endometrium(2)|kidney(1)|large_intestine(2)|lung(3)|ovary(1)|prostate(1)|skin(2)	12						GCCGTGCCCGGCGCCCATGGG	0.692																																																0			22											13.0	14.0	14.0					22																	24224737		2203	4290	6493	22554737	SO:0001819	synonymous_variant	66035			AJ271290	CCDS13818.1, CCDS33616.1, CCDS46673.1, CCDS74828.1	22q11.23	2013-05-22			ENSG00000133460	ENSG00000133460		"""Solute carriers"""	14239	protein-coding gene	gene with protein product		610367					Standard	NM_001024938		Approved	GLUT11, GLUT10	uc002zyp.4	Q9BYW1	OTTHUMG00000166469	ENST00000345044.6:c.777G>A	22.37:g.24224737G>A			22554737	E9PH55|Q542Y4|Q6ICJ5|Q8WXF9|Q8WYM4	Splice_Site	SNP	-	e6-1	ENST00000345044.6	37	c.538-1	CCDS46673.1	22	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	G|G	15.80|15.80	2.940627|2.940627	0.52972|0.52972	.|.	.|.	ENSG00000133460|ENSG00000251357	ENST00000398363|ENST00000502845	.|.	.|.	.|.	4.12|4.12	3.05|3.05	0.35203|0.35203	.|.	.|.	.|.	.|.	.|.	.|T	.|0.61874	.|0.2382	.|.	.|.	.|.	0.80722|0.80722	D|D	1|1	.|.	.|.	.|.	.|.	.|.	.|.	.|T	.|0.59144	.|-0.7509	.|4	.|.	.|.	.|.	.|.	11.3125|11.3125	0.49372|0.49372	0.0:0.0:0.8158:0.1842|0.0:0.0:0.8158:0.1842	.|.	.|.	.|.	.|.	.|D	-1|31	.|.	.|.	.|G	+|+	.|2	.|0	SLC2A11|AP000350.10	22554737|22554737	1.000000|1.000000	0.71417|0.71417	0.880000|0.880000	0.34516|0.34516	0.450000|0.450000	0.32258|0.32258	5.346000|5.346000	0.65992|0.65992	0.980000|0.980000	0.38523|0.38523	0.597000|0.597000	0.82753|0.82753	.|GGC	-	-		0.692	SLC2A11-001	KNOWN	basic|appris_principal|CCDS	protein_coding	SLC2A11	protein_coding	OTTHUMT00000319889.3	G	NM_030807		22554737	+1	no_start_codon	ENST00000398363	ensembl	human	known	54_36p	splice_site	SNP	0.101	A
LOC100996413	100996413	genome.wustl.edu	37	15	32777142	32777142	+	Silent	SNP	C	C	T			TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr15:32777142C>T	ENST00000593303.1	+	1	2321	c.261C>T	c.(259-261)tcC>tcT	p.S87S																								CCATCCGCTCCCCTGACCCAG	0.607																																																0			15																																								30564434	SO:0001819	synonymous_variant	0																														ENST00000593303.1:c.261C>T	15.37:g.32777142C>T			30564434		Silent	SNP	NULL	p.S248	ENST00000593303.1	37	c.744		15																																																																																			-	NULL		0.607	AC135983.2-201	NOVEL	basic|appris_principal	protein_coding	LOC100129979	protein_coding		C			30564434	+1	no_errors	XM_001718810	genbank	human	model	54_36p	silent	SNP	0.000	T
LARGE	9215	genome.wustl.edu	37	22	33712103	33712103	+	Missense_Mutation	SNP	G	G	C	rs370668049		TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr22:33712103G>C	ENST00000354992.2	-	12	1990	c.1419C>G	c.(1417-1419)gaC>gaG	p.D473E	LARGE_ENST00000397394.2_Missense_Mutation_p.D473E|LARGE_ENST00000452586.2_Missense_Mutation_p.D272E|LARGE_ENST00000402320.1_Missense_Mutation_p.D421E|LARGE_ENST00000437602.2_Missense_Mutation_p.D473E|LARGE_ENST00000337431.2_Missense_Mutation_p.D421E	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	473					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				CCAGGGTGACGTCCGTGCTGT	0.597																																					Colon(70;397 1175 4573 19089 45288)											0			22											137.0	100.0	113.0					22																	33712103		2203	4300	6503	32042103	SO:0001583	missense	9215			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"""Glycosyltransferase family 8 domain containing"""	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.1419C>G	22.37:g.33712103G>C	ENSP00000347088:p.Asp473Glu		32042103	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Missense_Mutation	SNP	superfamily_Nucleotide-diphospho-sugar transferases,HMMPfam_Glyco_transf_8	p.D473E	ENST00000354992.2	37	c.1419	CCDS13912.1	22	.	.	.	.	.	.	.	.	.	.	G	16.78	3.218891	0.58560	.	.	ENSG00000133424	ENST00000443693;ENST00000429788;ENST00000445431;ENST00000354992;ENST00000337431;ENST00000397394;ENST00000402320;ENST00000452586;ENST00000437602	T;T;T;T;T;T	0.57436	0.81;0.85;0.81;0.85;0.4;2.0	5.26	-6.73	0.01749	.	0.000000	0.85682	D	0.000000	T	0.61739	0.2371	M	0.64260	1.97	0.53688	D	0.999978	D;B;P;D	0.76494	0.999;0.272;0.818;0.973	D;B;P;P	0.74348	0.983;0.181;0.638;0.866	T	0.69176	-0.5214	10	0.46703	T	0.11	-6.143	14.996	0.71431	0.6499:0.0:0.3501:0.0	.	473;272;421;473	B7Z2I9;E9PH73;O95461-2;O95461	.;.;.;LARGE_HUMAN	E	150;150;150;473;421;473;421;272;473	ENSP00000347088:D473E;ENSP00000336636:D421E;ENSP00000380549:D473E;ENSP00000385223:D421E;ENSP00000407917:D272E;ENSP00000388544:D473E	ENSP00000336636:D421E	D	-	3	2	LARGE	32042103	0.004000	0.15560	0.511000	0.27724	0.343000	0.28985	-1.102000	0.03332	-1.014000	0.03379	-0.749000	0.03505	GAC	-	NULL		0.597	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LARGE	protein_coding	OTTHUMT00000320515.2	G	NM_133642		32042103	-1	no_errors	NM_004737	genbank	human	reviewed	54_36p	missense	SNP	0.976	C
LARGE	9215	genome.wustl.edu	37	22	33777919	33777919	+	Missense_Mutation	SNP	C	C	A			TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr22:33777919C>A	ENST00000354992.2	-	10	1688	c.1117G>T	c.(1117-1119)Gtg>Ttg	p.V373L	LARGE_ENST00000397394.2_Missense_Mutation_p.V373L|LARGE_ENST00000452586.2_Missense_Mutation_p.V172L|LARGE_ENST00000402320.1_Missense_Mutation_p.V373L|LARGE_ENST00000437602.2_Missense_Mutation_p.V373L|LARGE_ENST00000337431.2_Missense_Mutation_p.V373L	NM_004737.4	NP_004728.1	O95461	LARGE_HUMAN	like-glycosyltransferase	373					glycoprotein biosynthetic process (GO:0009101)|glycosphingolipid biosynthetic process (GO:0006688)|muscle cell cellular homeostasis (GO:0046716)|N-acetylglucosamine metabolic process (GO:0006044)|protein glycosylation (GO:0006486)	integral component of Golgi membrane (GO:0030173)	acetylglucosaminyltransferase activity (GO:0008375)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(2)|central_nervous_system(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(1)|large_intestine(13)|lung(23)|ovary(1)|skin(4)|upper_aerodigestive_tract(1)|urinary_tract(1)	51		Lung NSC(1;0.219)				AGATCAGACACGTCTCTGTAG	0.567																																					Colon(70;397 1175 4573 19089 45288)											0			22											142.0	137.0	139.0					22																	33777919		2203	4300	6503	32107919	SO:0001583	missense	9215			AJ007583	CCDS13912.1	22q12.3	2013-02-22			ENSG00000133424	ENSG00000133424		"""Glycosyltransferase family 8 domain containing"""	6511	protein-coding gene	gene with protein product		603590				9892679, 10591208, 12966029	Standard	NM_004737		Approved	KIAA0609	uc003ane.4	O95461	OTTHUMG00000150914	ENST00000354992.2:c.1117G>T	22.37:g.33777919C>A	ENSP00000347088:p.Val373Leu		32107919	B0QXZ7|O60348|Q17R80|Q9UGD1|Q9UGE7|Q9UGG3|Q9UGZ8|Q9UH22	Missense_Mutation	SNP	HMMPfam_Glyco_transf_8,superfamily_Nucleotide-diphospho-sugar transferases	p.V373L	ENST00000354992.2	37	c.1117	CCDS13912.1	22	.	.	.	.	.	.	.	.	.	.	C	18.34	3.602022	0.66445	.	.	ENSG00000133424	ENST00000443693;ENST00000429788;ENST00000445431;ENST00000354992;ENST00000337431;ENST00000397394;ENST00000402320;ENST00000452586;ENST00000437602;ENST00000421768	T;T;T;T;T;T;T	0.42513	0.97;2.14;0.97;2.14;0.97;0.97;0.97	4.94	4.94	0.65067	.	0.000000	0.85682	D	0.000000	T	0.36991	0.0987	L	0.44542	1.39	0.80722	D	1	B;B;B;B	0.10296	0.003;0.001;0.002;0.001	B;B;B;B	0.18871	0.023;0.004;0.009;0.015	T	0.20405	-1.0276	10	0.12103	T	0.63	-4.1187	18.5375	0.91015	0.0:1.0:0.0:0.0	.	373;172;373;373	B7Z2I9;E9PH73;O95461-2;O95461	.;.;.;LARGE_HUMAN	L	50;50;50;373;373;373;373;172;373;172	ENSP00000347088:V373L;ENSP00000336636:V373L;ENSP00000380549:V373L;ENSP00000385223:V373L;ENSP00000407917:V172L;ENSP00000388544:V373L;ENSP00000403841:V172L	ENSP00000336636:V373L	V	-	1	0	LARGE	32107919	1.000000	0.71417	0.999000	0.59377	0.992000	0.81027	5.587000	0.67510	2.444000	0.82710	0.563000	0.77884	GTG	-	HMMPfam_Glyco_transf_8,superfamily_Nucleotide-diphospho-sugar transferases		0.567	LARGE-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LARGE	protein_coding	OTTHUMT00000320515.2	C	NM_133642		32107919	-1	no_errors	NM_004737	genbank	human	reviewed	54_36p	missense	SNP	1.000	A
RPN2	6185	genome.wustl.edu	37	20	35858445	35858445	+	Missense_Mutation	SNP	C	C	A			TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr20:35858445C>A	ENST00000237530.6	+	13	1875	c.1564C>A	c.(1564-1566)Cca>Aca	p.P522T	RPN2_ENST00000470352.1_3'UTR|RPN2_ENST00000373622.5_Missense_Mutation_p.P490T	NM_002951.3	NP_002942.2	P04844	RPN2_HUMAN	ribophorin II	522					aging (GO:0007568)|cellular protein metabolic process (GO:0044267)|cellular protein modification process (GO:0006464)|gene expression (GO:0010467)|post-translational protein modification (GO:0043687)|protein N-linked glycosylation via asparagine (GO:0018279)|response to drug (GO:0042493)|SRP-dependent cotranslational protein targeting to membrane (GO:0006614)|translation (GO:0006412)	autophagic vacuole membrane (GO:0000421)|endoplasmic reticulum (GO:0005783)|endoplasmic reticulum membrane (GO:0005789)|integral component of membrane (GO:0016021)|membrane (GO:0016020)|nucleus (GO:0005634)|oligosaccharyltransferase complex (GO:0008250)|rough endoplasmic reticulum (GO:0005791)	ribosome binding (GO:0043022)|transferase activity, transferring glycosyl groups (GO:0016757)			breast(1)|cervix(1)|endometrium(3)|haematopoietic_and_lymphoid_tissue(1)|kidney(3)|large_intestine(2)|lung(7)|ovary(2)|pancreas(1)|skin(2)|stomach(1)	24		Myeloproliferative disorder(115;0.00878)				CCTTTTCACTCCAAAACAGGA	0.478																																																0			20											112.0	109.0	110.0					20																	35858445		2203	4300	6503	35291859	SO:0001583	missense	6185			Y00282	CCDS13291.1, CCDS46599.1	20q12-q13.1	2013-03-06			ENSG00000118705	ENSG00000118705			10382	protein-coding gene	gene with protein product	"""oligosaccharyltransferase complex subunit (non-catalytic)"""	180490					Standard	NM_002951		Approved	SWP1, RPNII, RIBIIR, RPN-II	uc002xgp.3	P04844	OTTHUMG00000032409	ENST00000237530.6:c.1564C>A	20.37:g.35858445C>A	ENSP00000237530:p.Pro522Thr		35291859	Q5JYR6|Q6IBA5|Q96E21|Q9BUQ3|Q9UBE1	Missense_Mutation	SNP	HMMPfam_Ribophorin_II	p.P522T	ENST00000237530.6	37	c.1564	CCDS13291.1	20	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	.|.	C|C	19.91|19.91	3.915431|3.915431	0.73098|0.73098	.|.	.|.	ENSG00000118705|ENSG00000118705	ENST00000237530;ENST00000373622;ENST00000397161;ENST00000373623;ENST00000437329|ENST00000456400	T;T;T|.	0.73897|.	-0.79;-0.79;-0.79|.	5.65|5.65	5.65|5.65	0.86999|0.86999	.|.	0.000000|.	0.85682|.	D|.	0.000000|.	T|T	0.72755|0.72755	0.3500|0.3500	L|L	0.61036|0.61036	1.89|1.89	0.80722|0.80722	D|D	1|1	P;B|.	0.47677|.	0.899;0.181|.	P;B|.	0.54210|.	0.745;0.36|.	T|T	0.69083|0.69083	-0.5239|-0.5239	10|5	0.27082|.	T|.	0.32|.	-17.7359|-17.7359	17.2626|17.2626	0.87075|0.87075	0.0:1.0:0.0:0.0|0.0:1.0:0.0:0.0	.|.	490;522|.	Q5JYR6;P04844|.	.;RPN2_HUMAN|.	T|Y	522;490;61;46;61|46	ENSP00000237530:P522T;ENSP00000362724:P490T;ENSP00000409580:P61T|.	ENSP00000237530:P522T|.	P|S	+|+	1|2	0|0	RPN2|RPN2	35291859|35291859	1.000000|1.000000	0.71417|0.71417	0.988000|0.988000	0.46212|0.46212	0.947000|0.947000	0.59692|0.59692	4.305000|4.305000	0.59110|0.59110	2.941000|2.941000	0.99782|0.99782	0.655000|0.655000	0.94253|0.94253	CCA|TCC	-	HMMPfam_Ribophorin_II		0.478	RPN2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	RPN2	protein_coding	OTTHUMT00000079076.2	C	NM_002951		35291859	+1	no_errors	NM_002951	genbank	human	reviewed	54_36p	missense	SNP	0.996	A
YAE1D1	57002	genome.wustl.edu	37	7	39606022	39606022	+	Missense_Mutation	SNP	C	C	G			TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr7:39606022C>G	ENST00000223273.2	+	1	48	c.5C>G	c.(4-6)tCg>tGg	p.S2W	AC011290.4_ENST00000439751.2_RNA|YAE1D1_ENST00000448268.1_Missense_Mutation_p.S2W|YAE1D1_ENST00000432096.2_Missense_Mutation_p.S2W	NM_020192.3	NP_064577.1	Q9NRH1	YAED1_HUMAN	Yae1 domain containing 1	2																	TCGGTGATGTCGTGGGTTCAA	0.642																																																0			7											83.0	72.0	76.0					7																	39606022		2203	4300	6503	39572547	SO:0001583	missense	57002			AF226046	CCDS5459.1, CCDS64630.1	7p14.1	2011-11-24	2011-11-24	2011-11-24	ENSG00000241127	ENSG00000241127			24857	protein-coding gene	gene with protein product			"""chromosome 7 open reading frame 36"""	C7orf36		12477932	Standard	NM_020192		Approved	GK003	uc003thc.4	Q9NRH1	OTTHUMG00000128689	ENST00000223273.2:c.5C>G	7.37:g.39606022C>G	ENSP00000223273:p.Ser2Trp		39572547	A4D1W4|B4DE83|Q6IAF7|Q8WVZ5	Missense_Mutation	SNP	HMMPfam_Yae1_N	p.S2W	ENST00000223273.2	37	c.5	CCDS5459.1	7	.	.	.	.	.	.	.	.	.	.	C	22.2	4.258462	0.80246	.	.	ENSG00000241127	ENST00000223273;ENST00000448268;ENST00000432096	T;T;T	0.60797	0.16;0.51;0.33	5.65	5.65	0.86999	.	0.063903	0.64402	D	0.000004	T	0.75339	0.3836	M	0.66939	2.045	0.80722	D	1	D	0.89917	1.0	D	0.91635	0.999	T	0.77140	-0.2697	10	0.87932	D	0	-11.2996	17.5154	0.87771	0.0:1.0:0.0:0.0	.	2	Q9NRH1	CG036_HUMAN	W	2	ENSP00000223273:S2W;ENSP00000400511:S2W;ENSP00000395777:S2W	ENSP00000223273:S2W	S	+	2	0	C7orf36	39572547	1.000000	0.71417	1.000000	0.80357	0.623000	0.37688	4.925000	0.63425	2.646000	0.89796	0.655000	0.94253	TCG	-	NULL		0.642	YAE1D1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	C7orf36	protein_coding	OTTHUMT00000250586.1	C	NM_020192		39572547	+1	no_errors	NM_020192	genbank	human	predicted	54_36p	missense	SNP	1.000	G
FRMPD2	143162	genome.wustl.edu	37	10	49430388	49430388	+	Missense_Mutation	SNP	A	A	C			TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	A	A					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr10:49430388A>C	ENST00000374201.3	-	12	1725	c.1423T>G	c.(1423-1425)Ttg>Gtg	p.L475V	FRMPD2_ENST00000305531.3_Missense_Mutation_p.L451V|FRMPD2_ENST00000407470.4_Missense_Mutation_p.L444V	NM_001018071.3|NM_001042512.2	NP_001018081|NP_001035977.2	Q68DX3	FRPD2_HUMAN	FERM and PDZ domain containing 2	475	FERM. {ECO:0000255|PROSITE- ProRule:PRU00084}.				tight junction assembly (GO:0070830)	basolateral plasma membrane (GO:0016323)|cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|tight junction (GO:0005923)	1-phosphatidylinositol binding (GO:0005545)			NS(2)|autonomic_ganglia(2)|breast(5)|cervix(1)|endometrium(3)|kidney(7)|large_intestine(15)|lung(24)|ovary(2)|prostate(1)|skin(3)|urinary_tract(1)	66				Kidney(211;0.201)		TCAGCCTGCAAGGCAAGGACC	0.532																																																0			10											149.0	138.0	142.0					10																	49430388		2203	4300	6503	49100394	SO:0001583	missense	143162			AK123038	CCDS31195.1	10q11	2010-10-13			ENSG00000170324	ENSG00000170324			28572	protein-coding gene	gene with protein product		613323	"""PDZ domain containing 5C"""	PDZD5C, PDZK5C			Standard	NM_001018071		Approved	MGC35285	uc001jdv.3	Q68DX3	OTTHUMG00000018171	ENST00000374201.3:c.1423T>G	10.37:g.49430388A>C	ENSP00000363317:p.Leu475Val		49100394	B7WNW0|B7ZML5|Q2VY07|Q6GMQ9|Q6ZN38|Q6ZWI2|Q8N5T9	Missense_Mutation	SNP	HMMSmart_SM00750,superfamily_Ubiquitin-like,HMMSmart_SM00295,HMMPfam_FERM_N,superfamily_Second domain of FERM,HMMPfam_FERM_M,superfamily_PH domain-like,HMMPfam_FERM_C,superfamily_PDZ domain-like,HMMPfam_PDZ,HMMSmart_SM00228	p.L475V	ENST00000374201.3	37	c.1423	CCDS31195.1	10	.	.	.	.	.	.	.	.	.	.	A	14.53	2.562780	0.45694	.	.	ENSG00000170324	ENST00000374201;ENST00000305531;ENST00000407470	T;T;T	0.80033	-1.33;-1.33;-1.33	5.24	-1.55	0.08558	Band 4.1 domain (1);FERM central domain (2);FERM domain (1);FERM/acyl-CoA-binding protein, 3-helical bundle (1);	.	.	.	.	T	0.81870	0.4914	L	0.39898	1.24	0.37307	D	0.908979	D;D;D	0.89917	1.0;1.0;1.0	D;D;D	0.97110	0.996;1.0;0.996	T	0.77321	-0.2631	9	0.26408	T	0.33	.	11.051	0.47889	0.444:0.0:0.556:0.0	.	451;475;444	Q68DX3-2;Q68DX3;F8WCT2	.;FRPD2_HUMAN;.	V	475;451;444	ENSP00000363317:L475V;ENSP00000307079:L451V;ENSP00000384339:L444V	ENSP00000307079:L451V	L	-	1	2	FRMPD2	49100394	0.893000	0.30496	0.859000	0.33776	0.280000	0.26924	0.512000	0.22755	-0.546000	0.06216	-0.388000	0.06559	TTG	-	HMMSmart_SM00295,superfamily_Second domain of FERM,HMMPfam_FERM_M		0.532	FRMPD2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	FRMPD2	protein_coding	OTTHUMT00000047923.3	A	NM_152428		49100394	-1	no_errors	NM_001018071	genbank	human	reviewed	54_36p	missense	SNP	0.959	C
LAMB2	3913	genome.wustl.edu	37	3	49168829	49168829	+	Missense_Mutation	SNP	T	T	C			TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	T	T					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr3:49168829T>C	ENST00000418109.1	-	7	859	c.695A>G	c.(694-696)tAc>tGc	p.Y232C	LAMB2_ENST00000305544.4_Missense_Mutation_p.Y232C	NM_002292.3	NP_002283.3	P55268	LAMB2_HUMAN	laminin, beta 2 (laminin S)	232	Laminin N-terminal. {ECO:0000255|PROSITE- ProRule:PRU00466}.				astrocyte development (GO:0014002)|axon extension involved in regeneration (GO:0048677)|axon guidance (GO:0007411)|cell adhesion (GO:0007155)|extracellular matrix organization (GO:0030198)|metanephric glomerular basement membrane development (GO:0072274)|metanephric glomerular visceral epithelial cell development (GO:0072249)|neuromuscular junction development (GO:0007528)|retina development in camera-type eye (GO:0060041)|Schwann cell development (GO:0014044)|visual perception (GO:0007601)	basal lamina (GO:0005605)|basement membrane (GO:0005604)|extracellular region (GO:0005576)|extracellular vesicular exosome (GO:0070062)|laminin-11 complex (GO:0043260)|laminin-3 complex (GO:0005608)|synapse (GO:0045202)	structural molecule activity (GO:0005198)			NS(1)|breast(1)|endometrium(15)|kidney(3)|large_intestine(6)|lung(21)|ovary(4)|prostate(2)|skin(4)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	61				BRCA - Breast invasive adenocarcinoma(193;8.01e-05)|Kidney(197;0.00219)|KIRC - Kidney renal clear cell carcinoma(197;0.00245)		CCGTGAGCTGTAGGGGTCTGG	0.552																																																0			3											95.0	88.0	90.0					3																	49168829		2203	4300	6503	49143833	SO:0001583	missense	3913				CCDS2789.1	3p21.3-p21.2	2013-03-01			ENSG00000172037	ENSG00000172037		"""Laminins"""	6487	protein-coding gene	gene with protein product	"""laminin S"""	150325		LAMS		2922051, 10393422	Standard	NM_002292		Approved		uc003cwe.3	P55268	OTTHUMG00000156807	ENST00000418109.1:c.695A>G	3.37:g.49168829T>C	ENSP00000388325:p.Tyr232Cys		49143833	Q16321	Missense_Mutation	SNP	HMMSmart_LamNT,HMMPfam_Laminin_N,HMMPfam_Laminin_EGF,HMMSmart_EGF_Lam,superfamily_SSF57196,PatternScan_EGF_1,PatternScan_EGF_LAM_1,PatternScan_EGF_2	p.Y232C	ENST00000418109.1	37	c.695	CCDS2789.1	3	.	.	.	.	.	.	.	.	.	.	t	19.05	3.752499	0.69533	.	.	ENSG00000172037	ENST00000418109;ENST00000305544;ENST00000494831	T;T;T	0.61040	1.07;1.07;0.14	4.88	4.88	0.63580	Laminin, N-terminal (3);	0.000000	0.85682	D	0.000000	D	0.82375	0.5023	H	0.95151	3.63	0.80722	D	1	D	0.89917	1.0	D	0.97110	1.0	D	0.87443	0.2396	10	0.62326	D	0.03	.	14.3226	0.66496	0.0:0.0:0.0:1.0	.	232	P55268	LAMB2_HUMAN	C	232;232;83	ENSP00000388325:Y232C;ENSP00000307156:Y232C;ENSP00000444751:Y83C	ENSP00000307156:Y232C	Y	-	2	0	LAMB2	49143833	1.000000	0.71417	0.997000	0.53966	0.979000	0.70002	6.125000	0.71627	2.055000	0.61198	0.529000	0.55759	TAC	-	HMMSmart_LamNT,HMMPfam_Laminin_N		0.552	LAMB2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	LAMB2	protein_coding	OTTHUMT00000345939.1	T	NM_002292		49143833	-1	no_errors	NM_002292	genbank	human	reviewed	54_36p	missense	SNP	1.000	C
NUP62	23636	genome.wustl.edu	37	19	50412217	50412217	+	Missense_Mutation	SNP	C	C	G	rs1062798	byFrequency	TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr19:50412217C>G	ENST00000596217.1	-	2	2735	c.848G>C	c.(847-849)aGc>aCc	p.S283T	NUP62_ENST00000600583.1_5'Flank|IL4I1_ENST00000341114.3_Intron|NUP62_ENST00000597723.1_Intron|NUP62_ENST00000413454.1_Missense_Mutation_p.S283T|NUP62_ENST00000422090.2_Missense_Mutation_p.S283T|NUP62_ENST00000352066.3_Missense_Mutation_p.S283T|NUP62_ENST00000597029.1_Missense_Mutation_p.S283T|IL4I1_ENST00000595948.1_Intron			P37198	NUP62_HUMAN	nucleoporin 62kDa	283	15 X 9 AA approximate repeats.|Ala-rich.|Thr-rich.		S -> T (in dbSNP:rs1062798). {ECO:0000269|PubMed:15489334, ECO:0000269|PubMed:17974005, ECO:0000269|PubMed:1915414}.		carbohydrate metabolic process (GO:0005975)|cell aging (GO:0007569)|cell death (GO:0008219)|cell surface receptor signaling pathway (GO:0007166)|cytokine-mediated signaling pathway (GO:0019221)|glucose transport (GO:0015758)|hexose transport (GO:0008645)|hormone-mediated signaling pathway (GO:0009755)|mitotic cell cycle (GO:0000278)|mitotic nuclear envelope disassembly (GO:0007077)|mRNA transport (GO:0051028)|negative regulation of apoptotic process (GO:0043066)|negative regulation of cell proliferation (GO:0008285)|negative regulation of epidermal growth factor receptor signaling pathway (GO:0042059)|negative regulation of MAP kinase activity (GO:0043407)|negative regulation of programmed cell death (GO:0043069)|negative regulation of Ras protein signal transduction (GO:0046580)|nucleocytoplasmic transport (GO:0006913)|positive regulation of epidermal growth factor receptor signaling pathway (GO:0045742)|positive regulation of I-kappaB kinase/NF-kappaB signaling (GO:0043123)|positive regulation of transcription, DNA-templated (GO:0045893)|protein transport (GO:0015031)|regulation of glucose transport (GO:0010827)|regulation of Ras protein signal transduction (GO:0046578)|regulation of signal transduction (GO:0009966)|small molecule metabolic process (GO:0044281)|transcription, DNA-templated (GO:0006351)|transmembrane transport (GO:0055085)|viral process (GO:0016032)	cytoplasm (GO:0005737)|cytoskeleton (GO:0005856)|intracellular membrane-bounded organelle (GO:0043231)|nuclear envelope (GO:0005635)|nuclear membrane (GO:0031965)|nuclear pore (GO:0005643)|nucleocytoplasmic shuttling complex (GO:0031074)|pore complex (GO:0046930)|ribonucleoprotein complex (GO:0030529)	chromatin binding (GO:0003682)|receptor signaling complex scaffold activity (GO:0030159)|SH2 domain binding (GO:0042169)|structural constituent of nuclear pore (GO:0017056)|thyroid hormone receptor binding (GO:0046966)|ubiquitin binding (GO:0043130)			breast(2)|endometrium(1)|kidney(1)|large_intestine(4)|lung(8)|stomach(1)|urinary_tract(2)	19		all_lung(116;1.47e-05)|all_neural(266;0.0459)|Ovarian(192;0.0481)		GBM - Glioblastoma multiforme(134;0.00242)|OV - Ovarian serous cystadenocarcinoma(262;0.0177)		gctgctgctgctggtggtggt	0.627													C|||	1584	0.316294	0.2383	0.379	5008	,	,		15105	0.3938		0.3827	False		,,,				2504	0.229															0			19						C	THR/SER,THR/SER,THR/SER,THR/SER,THR/SER,	997,3405		118,761,1322	31.0	29.0	30.0		848,848,848,848,848,	0.8	0.0	19	dbSNP_86	30	3113,5481		577,1959,1761	yes	missense,missense,missense,missense,missense,intron	NUP62,IL4I1	NM_001193357.1,NM_012346.4,NM_016553.4,NM_153718.3,NM_153719.3,NM_172374.1	58,58,58,58,58,	695,2720,3083	GG,GC,CC		36.2229,22.6488,31.6251	benign,benign,benign,benign,benign,	283/523,283/523,283/523,283/523,283/523,	50412217	4110,8886	2201	4297	6498	55104029	SO:0001583	missense	23636			X58521	CCDS12788.1	19q13.33	2013-09-20	2002-08-29		ENSG00000213024	ENSG00000213024			8066	protein-coding gene	gene with protein product	"""nuclear pore glycoprotein p62"""	605815	"""nucleoporin 62kD"""			1915414	Standard	NM_016553		Approved	p62, DKFZp547L134, IBSN, SNDI, MGC841, FLJ20822, FLJ43869	uc002pqx.3	P37198	OTTHUMG00000183077	ENST00000596217.1:c.848G>C	19.37:g.50412217C>G	ENSP00000471191:p.Ser283Thr		55104029	B3KWU5|Q503A4|Q6GTM2|Q96C43|Q9NSL1	Missense_Mutation	SNP	HMMPfam_Nsp1_C	p.S283T	ENST00000596217.1	37	c.848	CCDS12788.1	19	763	0.34935897435897434	103	0.20934959349593496	134	0.3701657458563536	230	0.4020979020979021	296	0.39050131926121373	C	0.016	-1.533751	0.00951	0.226488	0.362229	ENSG00000213024	ENST00000352066;ENST00000422090;ENST00000413454	T;T;T	0.36157	1.27;1.27;1.27	4.24	0.801	0.18679	Nucleoporin, NSP1-like, C-terminal (1);	1.330530	0.05670	N	0.588508	T	0.00012	0.0000	N	0.14661	0.345	0.80722	P	0.0	B	0.02656	0.0	B	0.01281	0.0	T	0.45366	-0.9266	8	.	.	.	-2.1099	13.4683	0.61268	0.0:0.2452:0.7548:0.0	rs1062798;rs3203778;rs3745497;rs4009638;rs5828420;rs17844993;rs17857752;rs52814004	283	P37198	NUP62_HUMAN	T	283	ENSP00000305503:S283T;ENSP00000407331:S283T;ENSP00000387991:S283T	.	S	-	2	0	NUP62	55104029	0.050000	0.20438	0.000000	0.03702	0.004000	0.04260	1.221000	0.32503	0.190000	0.20209	-1.162000	0.01777	AGC	-	NULL		0.627	NUP62-003	KNOWN	alternative_5_UTR|basic|appris_principal|CCDS	protein_coding	NUP62	protein_coding	OTTHUMT00000464991.1	C	NM_153719		55104029	-1	no_errors	NM_012346	genbank	human	reviewed	54_36p	missense	SNP	0.018	G
FCHO2	115548	genome.wustl.edu	37	5	72333731	72333731	+	Intron	SNP	G	G	A	rs139361956	byFrequency	TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr5:72333731G>A	ENST00000430046.2	+	10	1030				FCHO2_ENST00000341845.6_Intron|FCHO2_ENST00000512348.1_Intron|FCHO2_ENST00000287761.6_Missense_Mutation_p.A348T	NM_001146032.1|NM_138782.2	NP_001139504.1|NP_620137.2	Q0JRZ9	FCHO2_HUMAN	FCH domain only 2						clathrin coat assembly (GO:0048268)|clathrin-mediated endocytosis (GO:0072583)|membrane invagination (GO:0010324)|protein localization to plasma membrane (GO:0072659)	clathrin-coated vesicle (GO:0030136)|coated pit (GO:0005905)|plasma membrane (GO:0005886)	phosphatidylinositol binding (GO:0035091)|phosphatidylinositol-4,5-bisphosphate binding (GO:0005546)|phosphatidylserine binding (GO:0001786)			cervix(1)|endometrium(2)|kidney(2)|large_intestine(6)|lung(4)|ovary(1)|prostate(1)	17		Lung NSC(167;0.0465)|Ovarian(174;0.0908)|Prostate(461;0.165)		OV - Ovarian serous cystadenocarcinoma(47;4.6e-53)		gaattacggcgcccaccacca	0.517													G|||	20	0.00399361	0.0008	0.0086	5008	,	,		13889	0.001		0.0119	False		,,,				2504	0.0															0			5																																								72369487	SO:0001627	intron_variant	115548			AL831971	CCDS47230.1, CCDS54868.1	5q13.2	2005-08-15			ENSG00000157107	ENSG00000157107			25180	protein-coding gene	gene with protein product		613438				15254787	Standard	NM_138782		Approved		uc003kcl.3	Q0JRZ9	OTTHUMG00000162413	ENST00000430046.2:c.914+689G>A	5.37:g.72333731G>A			72369487	A8K6W7|B2RNQ9|B4DHK0|E9PG79|Q0JTJ3|Q96CF5	Missense_Mutation	SNP	HMMPfam_FCH,HMMSmart_FCH	p.A348T	ENST00000430046.2	37	c.1042	CCDS47230.1	5	12	0.005494505494505495	0	0.0	5	0.013812154696132596	0	0.0	7	0.009234828496042216	G	2.532	-0.308202	0.05458	.	.	ENSG00000157107	ENST00000287761	T	0.42131	0.98	0.14	0.14	0.14804	.	.	.	.	.	T	0.18299	0.0439	.	.	.	0.09310	N	1	B	0.29671	0.254	B	0.17098	0.017	T	0.11275	-1.0594	7	0.42905	T	0.14	.	.	.	.	.	348	Q0JRZ9-2	.	T	348	ENSP00000287761:A348T	ENSP00000287761:A348T	A	+	1	0	FCHO2	72369487	0.000000	0.05858	0.022000	0.16811	0.111000	0.19643	-0.382000	0.07408	0.182000	0.20032	0.185000	0.17295	GCC	-	NULL		0.517	FCHO2-001	KNOWN	basic|appris_candidate_longest|CCDS	protein_coding	FCHO2	protein_coding	OTTHUMT00000368795.3	G	XM_291142		72369487	+1	no_stop_codon	ENST00000287761	ensembl	human	known	54_36p	missense	SNP	0.022	A
FRG2C	100288801	genome.wustl.edu	37	3	75718087	75718087	+	IGR	SNP	C	C	T	rs201117282		TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr3:75718087C>T	ENST00000308062.3	+	0	2078					NM_001124759.1	NP_001118231.1	A6NGY1	FRG2C_HUMAN	FSHD region gene 2 family, member C							nucleus (GO:0005634)				breast(2)|ovary(1)	3						ccgcgatggccctcccgacac	0.716																																																0			3																																								75800777	SO:0001628	intergenic_variant	0				CCDS43108.1	3p12.3	2009-11-25			ENSG00000172969	ENSG00000172969			33626	protein-coding gene	gene with protein product							Standard	NM_001124759		Approved			A6NGY1	OTTHUMG00000158963		3.37:g.75718087C>T			75800777		RNA	SNP	-	NULL	ENST00000308062.3	37	NULL	CCDS43108.1	3																																																																																			-	-		0.716	FRG2C-001	KNOWN	NAGNAG_splice_site|not_best_in_genome_evidence|basic|appris_candidate_longest|CCDS	protein_coding	LOC440015	protein_coding	OTTHUMT00000352694.1	C	NM_001124759.1		75800777	+1	no_errors	XR_015234	genbank	human	model	54_36p	rna	SNP	0.001	T
Unknown	0	genome.wustl.edu	37	12	94534899	94534899	+	IGR	SNP	C	C	T	rs146567211	byFrequency	TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	C	C					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr12:94534899C>T								RN7SKP263 (132076 upstream) : PLXNC1 (7599 downstream)																							GCACCACCCCCGTTCCACCTC	0.637													C|||	29	0.00579073	0.0015	0.0144	5008	,	,		14875	0.0		0.0159	False		,,,				2504	0.001															0			12																																								93059030	SO:0001628	intergenic_variant	0																															12.37:g.94534899C>T			93059030		Silent	SNP	HMMPfam_ELM2	p.P258		37	c.774		12																																																																																			-	NULL	0	0.637					LOC441644			C			93059030	+1	no_errors	XM_001714973	genbank	human	model	54_36p	silent	SNP	0.987	T
ROBO4	54538	genome.wustl.edu	37	11	124756990	124756990	+	Missense_Mutation	SNP	G	G	T			TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr11:124756990G>T	ENST00000306534.3	-	15	2803	c.2318C>A	c.(2317-2319)gCt>gAt	p.A773D	RP11-664I21.5_ENST00000524453.1_RNA|ROBO4_ENST00000533054.1_Missense_Mutation_p.A628D	NM_019055.5	NP_061928.4	Q8WZ75	ROBO4_HUMAN	roundabout, axon guidance receptor, homolog 4 (Drosophila)	773	Pro/Ser-rich.				angiogenesis (GO:0001525)|cell differentiation (GO:0030154)|negative regulation of cell migration (GO:0030336)|regulation of cell migration (GO:0030334)	external side of plasma membrane (GO:0009897)|extracellular vesicular exosome (GO:0070062)|integral component of membrane (GO:0016021)	receptor activity (GO:0004872)			NS(2)|breast(1)|cervix(1)|endometrium(5)|haematopoietic_and_lymphoid_tissue(1)|large_intestine(11)|lung(42)|ovary(1)|prostate(4)|skin(5)|urinary_tract(3)	76	all_hematologic(175;0.215)	Medulloblastoma(222;0.0523)|Lung NSC(97;0.118)|all_lung(97;0.126)|Breast(109;0.171)|all_neural(223;0.224)		BRCA - Breast invasive adenocarcinoma(274;1.5e-06)|OV - Ovarian serous cystadenocarcinoma(99;0.0301)		GCGACTGGAAGCTGGGCTGGG	0.652																																																0			11											33.0	36.0	35.0					11																	124756990		2201	4299	6500	124262200	SO:0001583	missense	54538			AF361473	CCDS8455.1, CCDS73409.1	11q24.2	2013-02-11	2011-12-09		ENSG00000154133	ENSG00000154133		"""Immunoglobulin superfamily / I-set domain containing"", ""Fibronectin type III domain containing"""	17985	protein-coding gene	gene with protein product	"""magic roundabout"""	607528	"""roundabout homolog 4 (Drosophila)"""			11076864	Standard	NM_019055		Approved	FLJ20798, MRB, ECSM4	uc001qbg.3	Q8WZ75	OTTHUMG00000165936	ENST00000306534.3:c.2318C>A	11.37:g.124756990G>T	ENSP00000304945:p.Ala773Asp		124262200	A8K154|Q14DU7|Q8TEG1|Q96JV6|Q9H718|Q9NWJ8	Missense_Mutation	SNP	superfamily_Immunoglobulin,HMMPfam_I-set,HMMSmart_SM00409,HMMSmart_SM00408,HMMSmart_SM00060,HMMPfam_fn3,superfamily_Fibronectin type III	p.A773D	ENST00000306534.3	37	c.2318	CCDS8455.1	11	.	.	.	.	.	.	.	.	.	.	g	14.62	2.590972	0.46214	.	.	ENSG00000154133	ENST00000306534;ENST00000374963;ENST00000533054	T;T	0.64991	-0.13;0.25	4.61	1.54	0.23209	.	45.921700	0.00166	N	0.000014	T	0.57577	0.2063	L	0.44542	1.39	0.09310	N	1	B;B;B	0.29646	0.253;0.16;0.099	B;B;B	0.28232	0.06;0.087;0.04	T	0.46638	-0.9177	10	0.59425	D	0.04	.	8.7539	0.34635	0.0:0.3097:0.5301:0.1602	.	773;663;773	Q8WZ75-2;Q8WZ75-3;Q8WZ75	.;.;ROBO4_HUMAN	D	773;663;628	ENSP00000304945:A773D;ENSP00000437129:A628D	ENSP00000304945:A773D	A	-	2	0	ROBO4	124262200	0.002000	0.14202	0.185000	0.23176	0.994000	0.84299	1.021000	0.30040	0.033000	0.15463	0.552000	0.68991	GCT	-	NULL		0.652	ROBO4-001	KNOWN	basic|appris_principal|CCDS	protein_coding	ROBO4	protein_coding	OTTHUMT00000387111.1	G	NM_019055		124262200	-1	no_errors	NM_019055	genbank	human	validated	54_36p	missense	SNP	0.152	T
GOLGA1	2800	genome.wustl.edu	37	9	127651513	127651513	+	Missense_Mutation	SNP	G	G	A	rs142814558		TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	G	G					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr9:127651513G>A	ENST00000373555.4	-	18	2003	c.1670C>T	c.(1669-1671)gCg>gTg	p.A557V	RNU4-82P_ENST00000362443.1_RNA	NM_002077.3	NP_002068	Q92805	GOGA1_HUMAN	golgin A1	557					protein targeting to Golgi (GO:0000042)	Golgi apparatus (GO:0005794)|intracellular membrane-bounded organelle (GO:0043231)|membrane (GO:0016020)|perinuclear region of cytoplasm (GO:0048471)|trans-Golgi network (GO:0005802)				NS(1)|endometrium(5)|kidney(2)|large_intestine(3)|lung(7)|ovary(1)|stomach(1)	20						AGCCTCCTCCGCCTTGAGGGT	0.657													G|||	1	0.000199681	0.0	0.0	5008	,	,		19114	0.0		0.0	False		,,,				2504	0.001															0			9						G	VAL/ALA	0,4406		0,0,2203	42.0	40.0	41.0		1670	1.0	0.0	9	dbSNP_134	41	3,8597	2.2+/-6.3	0,3,4297	no	missense	GOLGA1	NM_002077.3	64	0,3,6500	AA,AG,GG		0.0349,0.0,0.0231	benign	557/768	127651513	3,13003	2203	4300	6503	126691334	SO:0001583	missense	2800			U51587	CCDS6860.1	9q34.11	2010-02-12	2010-02-12		ENSG00000136935	ENSG00000136935			4424	protein-coding gene	gene with protein product		602502	"""golgi autoantigen, golgin subfamily a, 1"""			9324025	Standard	NM_002077		Approved	golgin-97, MGC33154	uc004bpc.3	Q92805	OTTHUMG00000020665	ENST00000373555.4:c.1670C>T	9.37:g.127651513G>A	ENSP00000362656:p.Ala557Val		126691334	Q5T164|Q8IYZ9	Missense_Mutation	SNP	superfamily_Prefoldin,HMMPfam_GRIP,HMMSmart_SM00755	p.A557V	ENST00000373555.4	37	c.1670	CCDS6860.1	9	.	.	.	.	.	.	.	.	.	.	G	11.02	1.517117	0.27123	0.0	3.49E-4	ENSG00000136935	ENST00000373555	T	0.24538	1.85	5.22	1.05	0.20165	.	0.800351	0.10325	N	0.688277	T	0.16938	0.0407	L	0.33485	1.01	0.09310	N	1	B	0.17268	0.021	B	0.13407	0.009	T	0.27706	-1.0066	10	0.32370	T	0.25	1.4528	5.3824	0.16199	0.2445:0.2757:0.4797:0.0	.	557	Q92805	GOGA1_HUMAN	V	557	ENSP00000362656:A557V	ENSP00000362656:A557V	A	-	2	0	GOLGA1	126691334	0.914000	0.31030	0.002000	0.10522	0.005000	0.04900	2.982000	0.49337	0.298000	0.22638	-0.717000	0.03617	GCG	-	NULL		0.657	GOLGA1-001	KNOWN	basic|appris_principal|CCDS	protein_coding	GOLGA1	protein_coding	OTTHUMT00000054049.1	G	NM_002077		126691334	-1	no_errors	NM_002077	genbank	human	reviewed	54_36p	missense	SNP	0.003	A
COL5A2	1290	genome.wustl.edu	37	2	189901351	189901351	+	Silent	SNP	T	T	C			TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	T	T					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr2:189901351T>C	ENST00000374866.3	-	52	4378	c.4104A>G	c.(4102-4104)agA>agG	p.R1368R		NM_000393.3	NP_000384.2	P05997	CO5A2_HUMAN	collagen, type V, alpha 2	1368	Fibrillar collagen NC1. {ECO:0000255|PROSITE-ProRule:PRU00793}.				axon guidance (GO:0007411)|cellular response to amino acid stimulus (GO:0071230)|collagen catabolic process (GO:0030574)|collagen fibril organization (GO:0030199)|extracellular matrix disassembly (GO:0022617)|extracellular matrix organization (GO:0030198)|eye morphogenesis (GO:0048592)|negative regulation of endodermal cell differentiation (GO:1903225)|skeletal system development (GO:0001501)|skin development (GO:0043588)	collagen type V trimer (GO:0005588)|endoplasmic reticulum lumen (GO:0005788)|extracellular matrix (GO:0031012)|extracellular region (GO:0005576)	extracellular matrix structural constituent (GO:0005201)|metal ion binding (GO:0046872)			NS(3)|breast(2)|central_nervous_system(1)|endometrium(2)|kidney(4)|large_intestine(16)|lung(53)|ovary(3)|prostate(2)|skin(6)|urinary_tract(3)	95			OV - Ovarian serous cystadenocarcinoma(117;0.0106)|Epithelial(96;0.127)			CCTGAGACCCTCTGTTCATAT	0.318																																																0			2											72.0	66.0	68.0					2																	189901351		2203	4300	6503	189609596	SO:0001819	synonymous_variant	1290			Y14690	CCDS33350.1	2q14-q32	2014-09-17			ENSG00000204262	ENSG00000204262		"""Collagens"""	2210	protein-coding gene	gene with protein product	"""AB collagen"""	120190				1572660	Standard	NM_000393		Approved		uc002uqk.3	P05997	OTTHUMG00000149842	ENST00000374866.3:c.4104A>G	2.37:g.189901351T>C			189609596	P78440|Q13908|Q53WR4|Q59GR4|Q6LDJ5|Q7KZ55|Q86XF6|Q96QB0|Q96QB3	Silent	SNP	HMMPfam_VWC,HMMSmart_VWC,PatternScan_VWFC_1,HMMPfam_Collagen,HMMSmart_COLFI,HMMPfam_COLFI	p.R1368	ENST00000374866.3	37	c.4104	CCDS33350.1	2																																																																																			-	HMMSmart_COLFI,HMMPfam_COLFI		0.318	COL5A2-001	KNOWN	basic|appris_principal|CCDS	protein_coding	COL5A2	protein_coding	OTTHUMT00000313523.1	T	NM_000393		189609596	-1	no_errors	NM_000393	genbank	human	reviewed	54_36p	silent	SNP	1.000	C
HCG22	285834	genome.wustl.edu	37	6	31023092	31023099	+	lincRNA	DEL	AAGGAAGG	AAGGAAGG	-	rs147716681|rs113623983|rs113015259		TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	AAGGAAGG	AAGGAAGG					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr6:31023092_31023099delAAGGAAGG	ENST00000426185.1	+	0	310					NR_003948.2		E2RYF7	PBMU2_HUMAN	HLA complex group 22							extracellular region (GO:0005576)											GAGAGAGGGAaaggaaggaaggaaggaa	0.457																																																0			6																																								31131078			285834			AK094433		6p21.32	2013-12-20	2013-12-20		ENSG00000228789	ENSG00000228789		"""Long non-coding RNAs"""	27780	protein-coding gene	gene with protein product	"""panbronchiolitis related mucin-like 2"""	613918	"""HLA complex group 22 (non-protein coding)"""			14702039	Standard	NR_003948		Approved	FLJ37114, PBMUCL2	uc003nsj.2	E2RYF7	OTTHUMG00000031179		6.37:g.31023100_31023107delAAGGAAGG			31131071		RNA	DEL	-	NULL	ENST00000426185.1	37	NULL		6																																																																																			(deletion:rna[31129963,31135632])	-		0.457	HCG22-001	KNOWN	basic|exp_conf	lincRNA	HCG22	lincRNA	OTTHUMT00000076351.4	AAGGAAGG	NR_003948		31131078	+1	pseudogene	NR_003948	genbank	human	provisional	54_36p	rna	DEL	0.000:0.000:0.000:0.000:0.000:0.000:0.000:0.000	-
AK9	221264	genome.wustl.edu	37	6	109906330	109906332	+	In_Frame_Del	DEL	CTT	CTT	-	rs71770197|rs73519211|rs568921203|rs141134529	byFrequency	TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	CTT	CTT					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr6:109906330_109906332delCTT	ENST00000424296.2	-	19	2184_2186	c.2108_2110delAAG	c.(2107-2112)gaagca>gca	p.E703del	AK9_ENST00000341338.6_5'UTR|AK9_ENST00000368948.2_In_Frame_Del_p.E703del	NM_001145128.2	NP_001138600.2	Q5TCS8	KAD9_HUMAN	adenylate kinase 9	703					ADP phosphorylation (GO:0006757)|AMP phosphorylation (GO:0006756)|CDP phosphorylation (GO:0061508)|CMP phosphorylation (GO:0061566)|dADP phosphorylation (GO:0006174)|dAMP phosphorylation (GO:0061565)|dCDP phosphorylation (GO:0061570)|dCMP phosphorylation (GO:0061567)|dGDP phosphorylation (GO:0006186)|GDP phosphorylation (GO:0061568)|TDP phosphorylation (GO:0061571)|UDP phosphorylation (GO:0061569)	cytoplasm (GO:0005737)|nuclear membrane (GO:0031965)|nucleolus (GO:0005730)|nucleus (GO:0005634)	ATP binding (GO:0005524)|nucleoside diphosphate kinase activity (GO:0004550)|nucleoside phosphate kinase activity (GO:0050145)										TTTTACCTTGCTTCTTCTTCTTC	0.227														1863	0.372005	0.2542	0.4092	5008	,	,		14640	0.377		0.4095	False		,,,				2504	0.4611															0			6								396,1116		113,170,473						-0.1	0.2		dbSNP_130	6	1116,1910		355,406,752	no	coding	AKD1	NM_001145128.2		468,576,1225	A1A1,A1R,RR		36.8804,26.1905,33.3186				1512,3026				110013025	SO:0001651	inframe_deletion	0			AK131244, BC146443, BC087860	CCDS5077.1, CCDS55048.1	6q21	2013-04-29	2013-04-29	2013-04-29			2.7.4.3		33814	protein-coding gene	gene with protein product		615358	"""chromosome 6 open reading frame 224"", ""adenylate kinase domain containing 2"", ""chromosome 6 open reading frame 199"", ""adenylate kinase domain containing 1"""	C6orf224, AKD2, C6orf199, AKD1		23416111	Standard	NM_145025		Approved	FLJ42177, FLJ25791, dJ70A9.1, MGC26954		Q5TCS8		ENST00000424296.2:c.2108_2110delAAG	6.37:g.109906339_109906341delCTT	ENSP00000410186:p.Glu703del		110013023	A6NL75|B2RDJ0|B6ZDM7|Q3MIS4|Q5I0W8|Q6ZNF1|Q6ZVR7|Q8N7C6|Q8WW00|Q96NF4	Splice_Site	DEL	-	e19-1	ENST00000424296.2	37	c.2109+3_2109+1	CCDS55048.1	6																																																																																			(deletion:intron[110007523,110013023], cds_exon[110013024,110013133])	-		0.227	AK9-202	KNOWN	basic|appris_principal|CCDS	protein_coding	AKD2	protein_coding		CTT	NM_001145128		110013025	-1	no_errors	ENST00000341338	ensembl	human	known	54_36p	splice_site_del	DEL	0.003:0.003:0.001	-
MED13L	23389	genome.wustl.edu	37	12	116586415	116586418	+	Intron	DEL	TATA	TATA	-	rs375659860|rs556083996|rs10549054|rs3043743|rs140957424|rs199554727|rs113328518	byFrequency	TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	TATA	TATA					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr12:116586415_116586418delTATA	ENST00000281928.3	-	3	517				MIR620_ENST00000385232.1_RNA|MED13L_ENST00000551197.1_Intron	NM_015335.4	NP_056150.1	Q71F56	MD13L_HUMAN	mediator complex subunit 13-like							mediator complex (GO:0016592)	RNA polymerase II transcription cofactor activity (GO:0001104)			NS(2)|breast(1)|endometrium(9)|kidney(3)|large_intestine(18)|lung(34)|ovary(4)|prostate(4)|skin(6)|stomach(1)|upper_aerodigestive_tract(1)|urinary_tract(2)	85	all_neural(191;0.117)|Medulloblastoma(191;0.163)			BRCA - Breast invasive adenocarcinoma(302;0.0407)		tggagatatctatatatatatata	0.255																																																0			12																																								115070801	SO:0001627	intron_variant	0			AB028948	CCDS9177.1	12q24.22	2010-07-29	2007-07-30	2007-07-30	ENSG00000123066	ENSG00000123066			22962	protein-coding gene	gene with protein product		608771	"""thyroid hormone receptor associated protein 2"""	THRAP2			Standard	NM_015335		Approved	KIAA1025, TRAP240L	uc001tvw.3	Q71F56	OTTHUMG00000169404	ENST00000281928.3:c.311-37098TATA>-	12.37:g.116586423_116586426delTATA			115070798	A1L469|Q68DN4|Q9H8C0|Q9NSY9|Q9UFD8|Q9UPX5	RNA	DEL	-	NULL	ENST00000281928.3	37	NULL	CCDS9177.1	12																																																																																			(deletion:rna[115070748,115070842])	-		0.255	MED13L-001	KNOWN	basic|appris_principal|CCDS	protein_coding	MIRN620	protein_coding	OTTHUMT00000403879.3	TATA			115070801	-1	no_errors	ENST00000385232	ensembl	human	known	54_36p	rna	DEL	0.006:0.005:0.001:0.001	-
SLC30A8	169026	genome.wustl.edu	37	8	118030489	118030492	+	Intron	DEL	ATAA	ATAA	-	rs140340202	byFrequency	TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	ATAA	ATAA					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr8:118030489_118030492delATAA	ENST00000521243.1	+	2	214				RN7SL228P_ENST00000470060.2_RNA|SLC30A8_ENST00000427715.2_Intron|SLC30A8_ENST00000521035.1_Intron	NM_001172811.1	NP_001166282.1	Q8IWU4	ZNT8_HUMAN	solute carrier family 30 (zinc transporter), member 8						cellular zinc ion homeostasis (GO:0006882)|insulin secretion (GO:0030073)|positive regulation of insulin secretion (GO:0032024)|regulation of sequestering of zinc ion (GO:0061088)|regulation of vesicle-mediated transport (GO:0060627)|response to glucose (GO:0009749)|response to interferon-gamma (GO:0034341)|response to interleukin-1 (GO:0070555)|sequestering of zinc ion (GO:0032119)|transmembrane transport (GO:0055085)|zinc ion transmembrane transport (GO:0071577)|zinc ion transport (GO:0006829)	cytoplasmic membrane-bounded vesicle (GO:0016023)|integral component of membrane (GO:0016021)|plasma membrane (GO:0005886)|secretory granule (GO:0030141)|secretory granule membrane (GO:0030667)	protein homodimerization activity (GO:0042803)|zinc ion binding (GO:0008270)|zinc ion transmembrane transporter activity (GO:0005385)			breast(1)|endometrium(2)|large_intestine(9)|liver(2)|lung(18)|ovary(2)|pancreas(2)|skin(5)	41	all_cancers(13;2.11e-22)|Lung NSC(37;6.08e-05)|Ovarian(258;0.0173)		STAD - Stomach adenocarcinoma(47;0.203)			cttgtctcttataaataaatacat	0.304														406	0.0810703	0.0129	0.062	5008	,	,		18930	0.1776		0.1352	False		,,,				2504	0.0317				Ovarian(162;1202 1922 6011 16223 52092)											0			8																																								118099673	SO:0001627	intron_variant	0				CCDS6322.1, CCDS55272.1	8q24.11	2014-08-12			ENSG00000164756			"""Solute carriers"""	20303	protein-coding gene	gene with protein product		611145					Standard	NM_001172811		Approved		uc003yoh.3	Q8IWU4	OTTHUMG00000164962	ENST00000521243.1:c.-107+67131ATAA>-	8.37:g.118030493_118030496delATAA			118099670	A0AVP9|A5YM39|B4DPE0|Q8TCL3	RNA	DEL	-	NULL	ENST00000521243.1	37	NULL	CCDS55272.1	8																																																																																			(deletion:rna[118099366,118099672], flank[118099673,118149672])	-		0.304	SLC30A8-003	PUTATIVE	alternative_5_UTR|basic|CCDS	protein_coding	ENSG00000222183	protein_coding	OTTHUMT00000381197.1	ATAA	NM_173851		118099673	+1	no_errors	ENST00000410251	ensembl	human	novel	54_36p	rna	DEL	0.515:0.455:0.256:0.163	-
EMX2OS	196047	genome.wustl.edu	37	10	119248457	119248458	+	RNA	DEL	TG	TG	-	rs529062361|rs397834340|rs369963513	byFrequency	TCGA-57-1586-01A-02W-0633-09	TCGA-57-1586-11A-01W-0633-09	TG	TG					Unknown	Unknown	Somatic	4	Capture	none	1	dbGAP	Illumina GAIIx	28f5e4a4-de41-4c6e-9d8b-a2526743ac79	746ffb07-3eab-4c11-81f5-00cd3717bb53	g.chr10:119248457_119248458delTG	ENST00000424371.2	-	0	0				EMX2OS_ENST00000551288.1_RNA|EMX2OS_ENST00000440007.1_RNA|EMX2OS_ENST00000423419.1_RNA|CTA-109P11.4_ENST00000549104.1_lincRNA|EMX2OS_ENST00000450314.2_RNA					EMX2 opposite strand/antisense RNA																		CCATCAGAACtgtgtgtgtgtg	0.446																																																0			10																																								119238448			196047			AY117034		10q26.11	2012-10-19	2012-08-15	2011-11-14	ENSG00000229847	ENSG00000229847		"""Long non-coding RNAs"", ""-"""	18511	non-coding RNA	RNA, long non-coding	"""non-protein coding RNA 45"""	607637	"""empty spiracles homeobox 2 opposite strand"", ""EMX2 opposite strand (non-protein coding)"", ""EMX2 opposite strand/antisense RNA (non-protein coding)"""			12573261	Standard	NR_002791		Approved	NCRNA00045, EMX2-AS1	uc001ldg.3		OTTHUMG00000019125		10.37:g.119248467_119248468delTG			119238447		RNA	DEL	-	NULL	ENST00000424371.2	37	NULL		10																																																																																			(deletion:rna[119233794,119240412])	-		0.446	EMX2OS-004	KNOWN	basic|exp_conf	antisense	EMX2OS	antisense	OTTHUMT00000050574.2	TG	NR_002791		119238448	-1	no_errors	NR_002791	genbank	human	provisional	54_36p	rna	DEL	0.002:0.003	-
