OSGEP (O-sialoglycoprotein endopeptidase)

Gene

• Entrez ID: 55644
• Gene name: O-sialoglycoprotein endopeptidase
• Gene symbol: OSGEP
• Synonyms (NCBI Gene): GAMOS3, GCPL1, KAE1, OSGEP1, PRSMG1, TCS3
• Chromosome: 14
• Chromosome location: 14q11.2

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs140076803	A>G	Pathogenic	Missense variant, coding sequence variant
rs140583554	C>T	Likely-pathogenic	Missense variant, coding sequence variant
rs144732839	C>A,G,T	Pathogenic	Coding sequence variant, missense variant
rs147548960	G>A	Conflicting-interpretations-of-pathogenicity	Coding sequence variant, missense variant
rs200347983	T>C	Likely-pathogenic	Coding sequence variant, missense variant
rs374322839	G>A	Pathogenic	Coding sequence variant, missense variant
rs753237335	C>T	Pathogenic	Missense variant, coding sequence variant
rs761839638	G>A,C	Likely-pathogenic	Missense variant, coding sequence variant
rs773173317	C>T	Pathogenic	Coding sequence variant, missense variant
rs778931753	C>G	Pathogenic	Coding sequence variant, missense variant
rs1443735811	A>G	Pathogenic	Missense variant, coding sequence variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT1206590	hsa-miR-1273e	CLIP-seq
MIRT1206591	hsa-miR-1289	CLIP-seq
MIRT1206592	hsa-miR-1343	CLIP-seq
MIRT1206593	hsa-miR-137	CLIP-seq
MIRT1206594	hsa-miR-3170	CLIP-seq
MIRT1206595	hsa-miR-3198	CLIP-seq
MIRT1206596	hsa-miR-4294	CLIP-seq
MIRT1206597	hsa-miR-4309	CLIP-seq
MIRT1206598	hsa-miR-432	CLIP-seq
MIRT1206599	hsa-miR-4663	CLIP-seq
MIRT1206600	hsa-miR-4793-5p	CLIP-seq
MIRT1206601	hsa-miR-4796-5p	CLIP-seq
MIRT1206602	hsa-miR-587	CLIP-seq
MIRT1206603	hsa-miR-628-5p	CLIP-seq
MIRT1206592	hsa-miR-1343	CLIP-seq
MIRT1206593	hsa-miR-137	CLIP-seq
MIRT1206594	hsa-miR-3170	CLIP-seq
MIRT1206599	hsa-miR-4663	CLIP-seq
MIRT1206600	hsa-miR-4793-5p	CLIP-seq
MIRT1206603	hsa-miR-628-5p	CLIP-seq
MIRT1206592	hsa-miR-1343	CLIP-seq
MIRT1206593	hsa-miR-137	CLIP-seq
MIRT1206594	hsa-miR-3170	CLIP-seq
MIRT1206599	hsa-miR-4663	CLIP-seq
MIRT1206600	hsa-miR-4793-5p	CLIP-seq
MIRT1206603	hsa-miR-628-5p	CLIP-seq
MIRT2585978	hsa-miR-1267	CLIP-seq
MIRT2585979	hsa-miR-3664-5p	CLIP-seq
MIRT2585980	hsa-miR-3920	CLIP-seq
MIRT2585981	hsa-miR-4652-3p	CLIP-seq
MIRT2585982	hsa-miR-4714-5p	CLIP-seq
MIRT2585983	hsa-miR-4778-5p	CLIP-seq
MIRT2585978	hsa-miR-1267	CLIP-seq
MIRT2585979	hsa-miR-3664-5p	CLIP-seq
MIRT2585980	hsa-miR-3920	CLIP-seq
MIRT2585981	hsa-miR-4652-3p	CLIP-seq
MIRT2585982	hsa-miR-4714-5p	CLIP-seq
MIRT2585983	hsa-miR-4778-5p	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000408	Component	EKC/KEOPS complex	IBA
GO:0000408	Component	EKC/KEOPS complex	IDA	27903914, 28805828, 31481669
GO:0000408	Component	EKC/KEOPS complex	IEA
GO:0002949	Process	TRNA threonylcarbamoyladenosine modification	IDA	28805828
GO:0002949	Process	TRNA threonylcarbamoyladenosine modification	IEA
GO:0002949	Process	TRNA threonylcarbamoyladenosine modification	IMP	31481669
GO:0005515	Function	Protein binding	IPI	23414517, 23455922, 27903914, 28514442, 32296183, 32707033, 33961781
GO:0005634	Component	Nucleus	IDA	27903914, 28805828
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IBA
GO:0005737	Component	Cytoplasm	IDA	28805828
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IDA
GO:0006400	Process	TRNA modification	IDA	34268557
GO:0006400	Process	TRNA modification	IDA	28805828
GO:0008033	Process	TRNA processing	IEA
GO:0016740	Function	Transferase activity	IEA
GO:0016746	Function	Acyltransferase activity	IEA
GO:0016747	Function	Acyltransferase activity, transferring groups other than amino-acyl groups	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0061711	Function	TRNA N(6)-L-threonylcarbamoyladenine synthase activity	IDA	28805828
GO:0061711	Function	TRNA N(6)-L-threonylcarbamoyladenine synthase activity	IEA

Other IDs

• MIM: 610107
• HGNC: 18028
• e!Ensembl: ENSG00000092094

Protein

• UniProt ID: Q9NPF4
• Protein name: tRNA N6-adenosine threonylcarbamoyltransferase (EC 2.3.1.234) (N6-L-threonylcarbamoyladenine synthase) (t(6)A synthase) (O-sialoglycoprotein endopeptidase) (hOSGEP) (t(6)A37 threonylcarbamoyladenosine biosynthesis protein OSGEP) (tRNA threonylcarbamoylade
• Protein function: Component of the EKC/KEOPS complex that is required for the formation of a threonylcarbamoyl group on adenosine at position 37 (t(6)A37) in tRNAs that read codons beginning with adenine. The complex is probably involved in the transfer of the th
• PDB: 6GWJ
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00814	TsaD	23 → 301	tRNA N6-adenosine threonylcarbamoyltransferase	Family

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed at low level. Expressed in heart, placenta, liver, kidney, lung, brain, skeletal muscle and pancreas. {ECO:0000269|PubMed:12039036}.
• Sequence:

  MPAVLGFEGSANKIGVGVVRDGKVLANPRRTYVTPPGTGFLPGDTARHHRAVILDLLQEA
  LTESGLTSQDIDCIAYTKGPGMGAPLVSVAVVARTVAQLWNKPLVGVNHCIGHIEMGRLI
  TGATSPTVLYVSGGNTQVIAYSEHRYRIFGETIDIAVGNCLDRFARVLKISNDPSPGYNI
  EQMAKRGKKLVELPYTVKGMDVSFSGILSFIEDVAHRMLATGECTPEDLCFSLQETVFAM
  LVEITERAMAHCGSQEALIVGGVGCNVRLQEMMATMCQERGARLFATDERFCIDNGAMIA
  QAGWEMFRAGHRTPLSDSGVTQRYRTDEVEVTWRD

• Sequence length: 335

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Galloway-Mowat syndrome	Pathogenic	rs753237335	RCV002274049	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Galloway-Mowat syndrome 3	Likely pathogenic; Pathogenic	rs2139289899, rs144732839, rs1166790792, rs1417690595, rs2501756695, rs753237335, rs140076803, rs1555331969, rs1443735811, rs374322839, rs773173317, rs140583554, rs1566507605, rs780944919, rs1881216647, rs140696201	RCV001619764 RCV001619765 RCV002222273 RCV002244557 RCV003444166 RCV000513377 RCV000512715 RCV000513299 RCV000512749 RCV000513079 RCV000513428 RCV000512759 RCV002221565 RCV000735761 RCV001281254 RCV001281255 RCV002471079	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Nephrotic syndrome	Pathogenic	rs1555331969, rs773173317	RCV001849392 RCV001849393	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
OSGEP-related disorder	Likely pathogenic; Pathogenic	rs140076803	RCV004757241	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Radioulnar synostosis with amegakaryocytic thrombocytopenia 2	Likely pathogenic	rs1566507605	RCV005860135	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Adrenocortical carcinoma, hereditary	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GALLOWAY MOWAT SYNDROME	—	CTD, Disgenet CTD, Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Sarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Allergic rhinitis (disorder)	Allergic rhinitis	BEFREE	30479078		★☆☆☆☆ Found in Text Mining only
Aqueductal Stenosis	Aqueductal Stenosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Arachnodactyly	Arachnodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Autosomal Recessive Primary Microcephaly	Primary microcephaly	Pubtator	30558655	Associate	★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Carcinoma Renal Cell	Renal cell carcinoma	Pubtator	35373928	Associate	★☆☆☆☆ Found in Text Mining only
Cerebellar atrophy	Cerebellar atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Cerebral atrophy	Cerebral Atrophy	HPO_DG			★☆☆☆☆ Found in Text Mining only
Chronic kidney disease stage 5	Kidney Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Camptodactyly	Congenital Camptodactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Epicanthus	Congenital Epicanthus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Coronary heart disease	Coronary Heart Disease	BEFREE	26033827		★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Developmental disability	Pubtator	28272532	Associate	★☆☆☆☆ Found in Text Mining only
Diffuse mesangial sclerosis (disorder)	Mesangial sclerosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Distal Renal Tubular Acidosis	Distal Renal Tubular Acidosis	BEFREE	11934690, 12227829, 15252044, 16107207, 16420521, 16849697, 17027918, 20151848, 27767102, 28638614, 28646128		★☆☆☆☆ Found in Text Mining only
Dwarfism	Dwarfism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Dysmorphic features	Dysmorphic Features	CLINVAR_DG	28272532, 28805828		★☆☆☆☆ Found in Text Mining only
Dysmorphism	Dysmorphism	BEFREE	30558655		★☆☆☆☆ Found in Text Mining only
Galloway Mowat syndrome	Galloway-Mowat Syndrome	ORPHANET_DG	28805828		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Galloway Mowat syndrome	Galloway-Mowat Syndrome	CTD_human_DG	28805828		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Galloway Mowat syndrome	Galloway-Mowat Syndrome	BEFREE	30141175, 30558655, 30975089		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Galloway Mowat syndrome	Galloway-mowat syndrome	Pubtator	30558655, 33980730, 36856752	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Galloway-Mowat syndrome	Galloway-Mowat Syndrome	Orphanet			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
GALLOWAY-MOWAT SYNDROME 3	Galloway-Mowat Syndrome	UNIPROT_DG	28272532, 28805828		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
GALLOWAY-MOWAT SYNDROME 3	Galloway-Mowat Syndrome	GENOMICS_ENGLAND_DG	28805828		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
GALLOWAY-MOWAT SYNDROME 3	Galloway-Mowat Syndrome	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Global developmental delay	Developmental Delay	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glomerulonephritis	Glomerulonephritis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Glomerulosclerosis (disorder)	Glomerulosclerosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Heart Defects Congenital	Congenital heart defect	Pubtator	26033827	Associate	★☆☆☆☆ Found in Text Mining only
Hemiplegia/hemiparesis	Hemiplegia/hemiparesis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hiatal Hernia	Hiatal Hernia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypertensive disease	Hypertension	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoalbuminemia	Hypoalbuminemia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hypoplasia of corpus callosum	Hypoplasia Of Corpus Callosum	HPO_DG			★☆☆☆☆ Found in Text Mining only
Impaired cognition	Impaired Cognition	HPO_DG			★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	GENOMICS_ENGLAND_DG	28805828		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Mental retardation	HPO_DG			★☆☆☆☆ Found in Text Mining only
Kidney Diseases	Kidney Disease	HPO_DG			★☆☆☆☆ Found in Text Mining only
Lissencephaly	Lissencephaly	Pubtator	30558655	Associate	★☆☆☆☆ Found in Text Mining only
Macrotia	Macrotia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Mandibulofacial dysostosis, Treacher Collins type, autosomal recessive	Mandibulofacial Dysostosis	BEFREE	28272532		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	BEFREE	30141175		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microphthalmos	Microphthalmos	HPO_DG			★☆☆☆☆ Found in Text Mining only
Microstomia	Microstomia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Nephrosis congenital	Nephrotic syndrome	Pubtator	37845138	Associate	★☆☆☆☆ Found in Text Mining only
Nephrotic Syndrome	Nephrotic Syndrome	BEFREE	28805828, 30141175, 30558655, 30975089		★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Nephrotic Syndrome	Nephrotic syndrome	Pubtator	30558655	Associate	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Nephrotic Syndrome	Nephrotic Syndrome	HPO_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
nervous system disorder	Nervous System Disorder	BEFREE	28272532		★☆☆☆☆ Found in Text Mining only
Neurodegenerative Diseases	Neurodegenerative disorder	Pubtator	28272532	Associate	★☆☆☆☆ Found in Text Mining only
Ovalocytosis, Malaysian-Melanesian-Filipino Type	Ovalocytosis	BEFREE	17027918, 21039340		★☆☆☆☆ Found in Text Mining only
Pachygyria	Pachygyria	HPO_DG			★☆☆☆☆ Found in Text Mining only
Primary microcephaly	Microcephaly	BEFREE	30558655		★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	21824498	Associate	★☆☆☆☆ Found in Text Mining only
Proteinuria	Proteinuria	Pubtator	28272532	Associate	★☆☆☆☆ Found in Text Mining only
Renal tubular acidosis distal autosomal recessive	Distal renal tubular acidosis	Pubtator	15252044	Associate	★☆☆☆☆ Found in Text Mining only
RENAL TUBULAR ACIDOSIS, DISTAL, AUTOSOMAL RECESSIVE	Renal Tubular Acidosis	BEFREE	15252044		★☆☆☆☆ Found in Text Mining only
Steroid resistant nephrotic syndrome of childhood	Steroid resistant nephrotic syndrome	BEFREE	30141175		★☆☆☆☆ Found in Text Mining only
Strabismus	Strabismus	HPO_DG			★☆☆☆☆ Found in Text Mining only