TPRKB (TP53RK binding protein)

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Gene SNPs miRNA Gene ontology Other IDs Protein Associated diseases Related genes Diseases linked via similar genes

Gene

• Entrez ID: 51002
• Gene name: TP53RK binding protein
• Gene symbol: TPRKB
• Synonyms (NCBI Gene): CGI-121, CGI121, GAMOS5
• Chromosome: 2
• Chromosome location: 2p13.1

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs1233885358	T>C	Pathogenic	Coding sequence variant, missense variant
rs1553433412	A>G	Pathogenic	Coding sequence variant, missense variant

miRNA Show/Hide all (23)

miRTarBase ID	miRNA	Experiments	Reference
MIRT020915	hsa-miR-155-5p	Proteomics	18668040
MIRT029846	hsa-miR-26b-5p	Microarray	19088304
MIRT036857	hsa-miR-877-3p	CLASH	23622248
MIRT551897	hsa-miR-5700	PAR-CLIP	21572407
MIRT551896	hsa-miR-5003-3p	PAR-CLIP	21572407
MIRT551895	hsa-miR-873-5p	PAR-CLIP	21572407
MIRT551894	hsa-miR-627-3p	PAR-CLIP	21572407
MIRT551893	hsa-miR-7159-3p	PAR-CLIP	21572407
MIRT551892	hsa-miR-4482-3p	PAR-CLIP	21572407
MIRT020915	hsa-miR-155-5p	HITS-CLIP	22473208
MIRT020915	hsa-miR-155-5p	HITS-CLIP	22473208
MIRT551897	hsa-miR-5700	PAR-CLIP	21572407
MIRT551896	hsa-miR-5003-3p	PAR-CLIP	21572407
MIRT551895	hsa-miR-873-5p	PAR-CLIP	21572407
MIRT551894	hsa-miR-627-3p	PAR-CLIP	21572407
MIRT551893	hsa-miR-7159-3p	PAR-CLIP	21572407
MIRT551892	hsa-miR-4482-3p	PAR-CLIP	21572407
MIRT2134616	hsa-miR-155	CLIP-seq
MIRT2134617	hsa-miR-4251	CLIP-seq
MIRT2134618	hsa-miR-4307	CLIP-seq
MIRT2134619	hsa-miR-4663	CLIP-seq
MIRT2134620	hsa-miR-4728-3p	CLIP-seq
MIRT2134621	hsa-miR-580	CLIP-seq

Gene ontology (GO) Show/Hide all (15)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000408	Component	EKC/KEOPS complex	IBA
GO:0000408	Component	EKC/KEOPS complex	IDA	27903914, 28805828
GO:0002949	Process	TRNA threonylcarbamoyladenosine modification	IBA
GO:0002949	Process	TRNA threonylcarbamoyladenosine modification	IDA	28805828
GO:0005515	Function	Protein binding	IPI	16189514, 23414517, 23455922, 25416956, 27903914, 28805828, 31515488, 32707033, 33961781
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	12659830, 28805828
GO:0005634	Component	Nucleus	IEA
GO:0005737	Component	Cytoplasm	IDA	28805828
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	IDA	12659830
GO:0005829	Component	Cytosol	IEA
GO:0008033	Process	TRNA processing	IEA
GO:0019901	Function	Protein kinase binding	IPI	12659830

Other IDs

• MIM: 608680
• HGNC: 24259
• e!Ensembl: ENSG00000144034

Protein

• UniProt ID: Q9Y3C4
• Protein name: EKC/KEOPS complex subunit TPRKB (PRPK-binding protein) (TP53RK-binding protein)
• 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 (PubMed:22912744, PubMed:28805828). The complex is probably
• PDB: 3ENP , 6WQX , 7SZA , 7SZB , 7SZC , 7SZD
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF08617	CGI-121	20 → 172	Kinase binding protein CGI-121	Domain

• Tissue specificity: TISSUE SPECIFICITY: Widely expressed. {ECO:0000269|PubMed:12659830}.
• Sequence:

  MQLTHQLDLFPECRVTLLLFKDVKNAGDLRRKAMEGTIDGSLINPTVIVDPFQILVAANK
  AVHLYKLGKMKTRTLSTEIIFNLSPNNNISEALKKFGISANDTSILIVYIEEGEKQINQE
  YLISQVEGHQVSLKNLPEIMNITEVKKIYKLSSQEESIGTLLDAIICRMSTKDVL

• Sequence length: 175

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 5	Likely pathogenic; Pathogenic	rs754783287, rs1233885358	RCV003990530 RCV000512903	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Unknown / Other Associations Show/Hide Unknown Diseases (6)
Phenotype Name	Clinical Significance	Source	Reference	Evidence Score
GALLOWAY MOWAT SYNDROME	—	CTD, Disgenet CTD, Disgenet	28805828	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
GALLOWAY-MOWAT SYNDROME	—	GWAS catalog, Orphanet GWAS catalog, Orphanet	28805828, 28805828	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nephrotic syndrome	Conflicting classifications of pathogenicity	ClinVar Disgenet	—	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Nonpapillary renal cell carcinoma	Conflicting classifications of pathogenicity	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
THYROIDITIS	—	GWAS catalog	39024449	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
TPRKB-related disorder	Uncertain significance; Likely benign	ClinVar	—	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Related Genes

Sort by: Blended Diseases Pathways Evidence source

OSGEP 2 shared diseasesGalloway-mowat syndrome, Nephrotic syndrome 7 shared evidence sourcesDisgenet (Galloway-mowat syndrome), CTD (Galloway-mowat syndrome), Orphanet (Galloway-mowat syndrome), GWAS catalog (Galloway-mowat syndrome), ClinVar (Galloway-mowat syndrome), HPO (Galloway-mowat syndrome), Disgenet (Nephrotic syndrome) Related via 2 shared diseases including Galloway-mowat syndrome, Nephrotic syndrome — evidence mostly Disgenet. WDR73 2 shared diseasesGalloway-mowat syndrome, Nephrotic syndrome 7 shared evidence sourcesDisgenet (Galloway-mowat syndrome), CTD (Galloway-mowat syndrome), Orphanet (Galloway-mowat syndrome), GWAS catalog (Galloway-mowat syndrome), ClinVar (Galloway-mowat syndrome), HPO (Galloway-mowat syndrome), Disgenet (Nephrotic syndrome) Related via 2 shared diseases including Galloway-mowat syndrome, Nephrotic syndrome — evidence mostly Disgenet. TP53RK 1 shared diseaseGalloway-mowat syndrome 6 shared evidence sourcesDisgenet (Galloway-mowat syndrome), CTD (Galloway-mowat syndrome), Orphanet (Galloway-mowat syndrome), GWAS catalog (Galloway-mowat syndrome), ClinVar (Galloway-mowat syndrome), HPO (Galloway-mowat syndrome) Related via 1 shared disease including Galloway-mowat syndrome — evidence mostly Disgenet. NUP133 2 shared diseasesGalloway-mowat syndrome, Nephrotic syndrome 7 shared evidence sourcesDisgenet (Galloway-mowat syndrome), CTD (Galloway-mowat syndrome), Orphanet (Galloway-mowat syndrome), GWAS catalog (Galloway-mowat syndrome), ClinVar (Galloway-mowat syndrome), HPO (Galloway-mowat syndrome), Disgenet (Nephrotic syndrome) Related via 2 shared diseases including Galloway-mowat syndrome, Nephrotic syndrome — evidence mostly Disgenet. LAGE3 1 shared diseaseGalloway-mowat syndrome 5 shared evidence sourcesDisgenet (Galloway-mowat syndrome), CTD (Galloway-mowat syndrome), Orphanet (Galloway-mowat syndrome), ClinVar (Galloway-mowat syndrome), HPO (Galloway-mowat syndrome) Related via 1 shared disease including Galloway-mowat syndrome — evidence mostly Disgenet.

Related Gene	Shared Diseases	Shared Disease Names	Shared Pathways	Shared Pathway Names	Shared Evidence Sources	Shared Evidence Names
OSGEP	2	["Galloway-mowat syndrome","Nephrotic syndrome"]	0	[]	7	["Disgenet (Galloway-mowat syndrome)","CTD (Galloway-mowat syndrome)","Orphanet (Galloway-mowat syndrome)","GWAS catalog (Galloway-mowat syndrome)","ClinVar (Galloway-mowat syndrome)","HPO (Galloway-mowat syndrome)","Disgenet (Nephrotic syndrome)"]
WDR73	2	["Galloway-mowat syndrome","Nephrotic syndrome"]	0	[]	7	["Disgenet (Galloway-mowat syndrome)","CTD (Galloway-mowat syndrome)","Orphanet (Galloway-mowat syndrome)","GWAS catalog (Galloway-mowat syndrome)","ClinVar (Galloway-mowat syndrome)","HPO (Galloway-mowat syndrome)","Disgenet (Nephrotic syndrome)"]
TP53RK	1	["Galloway-mowat syndrome"]	0	[]	6	["Disgenet (Galloway-mowat syndrome)","CTD (Galloway-mowat syndrome)","Orphanet (Galloway-mowat syndrome)","GWAS catalog (Galloway-mowat syndrome)","ClinVar (Galloway-mowat syndrome)","HPO (Galloway-mowat syndrome)"]
NUP133	2	["Galloway-mowat syndrome","Nephrotic syndrome"]	0	[]	7	["Disgenet (Galloway-mowat syndrome)","CTD (Galloway-mowat syndrome)","Orphanet (Galloway-mowat syndrome)","GWAS catalog (Galloway-mowat syndrome)","ClinVar (Galloway-mowat syndrome)","HPO (Galloway-mowat syndrome)","Disgenet (Nephrotic syndrome)"]
LAGE3	1	["Galloway-mowat syndrome"]	0	[]	5	["Disgenet (Galloway-mowat syndrome)","CTD (Galloway-mowat syndrome)","Orphanet (Galloway-mowat syndrome)","ClinVar (Galloway-mowat syndrome)","HPO (Galloway-mowat syndrome)"]

Diseases Linked via Similar Genes

Camos syndrome Linked via 1 of 5 related genesWDR73 Color vision deficiency Linked via 1 of 5 related genesWDR73 Congenital neurologic anomalies Linked via 1 of 5 related genesWDR73 Dyskinesia Linked via 1 of 5 related genesWDR73 Periodontitis Linked via 1 of 5 related genesWDR73

Disease	Linked Via (Gene Count)	Linked Via (Gene Names)
Camos syndrome	1	["WDR73"]
Color vision deficiency	1	["WDR73"]
Congenital neurologic anomalies	1	["WDR73"]
Dyskinesia	1	["WDR73"]
Periodontitis	1	["WDR73"]