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

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Galloway-Mowat syndrome	Pathogenic	rs753237335	RCV002274049
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
Nephrotic syndrome	Pathogenic	rs1555331969, rs773173317	RCV001849392 RCV001849393
OSGEP-related disorder	Likely pathogenic; Pathogenic	rs140076803	RCV004757241
Radioulnar synostosis with amegakaryocytic thrombocytopenia 2	Likely pathogenic	rs1566507605	RCV005860135
See cases	Likely pathogenic; Pathogenic	rs140076803	RCV002252146

Unknown
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession
Adrenocortical carcinoma, hereditary	Benign	rs61278338	RCV005906671
Cervical cancer	Benign	rs58136957, rs61278338	RCV005914606 RCV005906672
Familial cancer of breast	Benign	rs938881	RCV005913019
Gastric cancer	Benign	rs58136957, rs61278338	RCV005914607 RCV005906674
Lung cancer	Benign	rs58136957, rs61278338	RCV005914608 RCV005906678
Malignant tumor of esophagus	Benign	rs61278338	RCV005906669
Nonpapillary renal cell carcinoma	Benign	rs61278338	RCV005906670
Ovarian serous cystadenocarcinoma	Benign	rs61278338	RCV005906675
Sarcoma	Benign	rs61278338	RCV005906673
Thymoma	Benign	rs61278338	RCV005906677
Uterine carcinosarcoma	Benign	rs61278338	RCV005906676
Uterine corpus endometrial carcinoma	Benign; Likely benign	rs58136957, rs1594408916, rs61278338	RCV005914609 RCV005926552 RCV005906679

Associations from Text Mining
Disease Name	Relationship Type	References
Acidosis Renal Tubular	Associate	15252044, 27767102
Autosomal Recessive Primary Microcephaly	Associate	30558655
Carcinoma Renal Cell	Associate	35373928
Death	Associate	30558655
Developmental Disabilities	Associate	28272532
Galloway Mowat syndrome	Associate	30558655, 33980730, 36856752
Heart Defects Congenital	Associate	26033827
Hypokalemia Familial	Associate	28272532
Lissencephaly	Associate	30558655
Nephrosis congenital	Associate	37845138
Nephrotic Syndrome	Associate	30558655
Neurodegenerative Diseases	Associate	28272532
Neurologic Manifestations	Associate	28272532
Plagiocephaly and X linked mental retardation	Associate	30558655
Prostatic Neoplasms	Associate	21824498
Proteinuria	Associate	28272532
Renal dysplasia limb defects syndrome	Associate	28272532
Renal tubular acidosis distal autosomal recessive	Associate	15252044