CTU2 (cytosolic thiouridylase subunit 2)

Gene

• Entrez ID: 348180
• Gene name: Cytosolic thiouridylase subunit 2
• Gene symbol: CTU2
• Synonyms (NCBI Gene): C16orf84, MFRG, NCS2, UPF0432
• Chromosome: 16
• Chromosome location: 16q24.3
• Summary: This gene encodes a protein which is involved in the post-transcriptional modification of transfer RNAs (tRNAs). The encoded protein plays a role in thiolation of uridine residue present at the wobble position in a subset of tRNAs, resulting in enhanced c

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs147948789	T>C	Pathogenic	Coding sequence variant, 5 prime UTR variant, intron variant, missense variant
rs769481947	G>A,T	Pathogenic	Coding sequence variant, synonymous variant
rs1351549465	G>A,T	Pathogenic	Intron variant
rs1597434884	->T	Pathogenic	Coding sequence variant, frameshift variant

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000049	Function	TRNA binding	IEA
GO:0002098	Process	TRNA wobble uridine modification	IEA
GO:0002098	Process	TRNA wobble uridine modification	NAS	19017811
GO:0002143	Process	TRNA wobble position uridine thiolation	IBA
GO:0005515	Function	Protein binding	IPI	19017811
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	IBA
GO:0005829	Component	Cytosol	TAS
GO:0008033	Process	TRNA processing	IEA
GO:0016779	Function	Nucleotidyltransferase activity	IEA
GO:0016783	Function	Sulfurtransferase activity	IBA
GO:0032447	Process	Protein urmylation	IEA
GO:0032991	Component	Protein-containing complex	IDA	19017811
GO:0034227	Process	TRNA thio-modification	IEA
GO:0034227	Process	TRNA thio-modification	NAS	19017811

Other IDs

• MIM: 617057
• HGNC: 28005
• e!Ensembl: ENSG00000174177

Protein

• UniProt ID: Q2VPK5
• Protein name: Cytoplasmic tRNA 2-thiolation protein 2 (Cytosolic thiouridylase subunit 2)
• Protein function: Plays a central role in 2-thiolation of mcm(5)S(2)U at tRNA wobble positions of tRNA(Lys), tRNA(Glu) and tRNA(Gln). May act by forming a heterodimer with CTU1/ATPBD3 that ligates sulfur from thiocarboxylated URM1 onto the uridine of tRNAs at wob
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF10288	CTU2	341 → 468	Cytoplasmic tRNA 2-thiolation protein 2	Family

• Sequence:

  MCQVGEDYGEPAPEEPPPAPRPSREQKCVKCKEAQPVVVIRAGDAFCRDCFKAFYVHKFR
  AMLGKNRLIFPGEKVLLAWSGGPSSSSMVWQVLEGLSQDSAKRLRFVAGVIFVDEGAACG
  QSLEERSKTLAEVKPILQATGFPWHVVALEEVFSLPPSVLWCSAQELVGSEGAYKAAVDS
  FLQQQHVLGAGGGPGPTQGEEQPPQPPLDPQNLARPPAPAQTEALSQLFCSVRTLTAKEE
  LLQTLRTHLILHMARAHGYSKVMTGDSCTRLAIKLMTNLALGRGAFLAWDTGFSDERHGD
  VVVVRPMRDHTLKEVAFYNRLFSVPSVFTPAVDTKAPEKASIHRLMEAFILRLQTQFPST
  VSTVYRTSEKLVKGPRDGPAAGDSGPRCLLCMCALDVDAADSATAFGAQTSSRLSQMQSP
  IPLTETRTPPGPCCSPGVGWAQRCGQGACRREDPQACIEEQLCYSCRVNMKDLPSLDPLP
  PYILAEAQLRTQRAWGLQEIRDCLIEDSDDEAGQS

• Sequence length: 515

Pathways

KEGG:

Sulfur relay system

Reactome:

tRNA modification in the nucleus and cytosol

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
Microcephaly	Pathogenic	rs769481947	RCV004798859	★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome	Likely pathogenic; Pathogenic	rs201104411, rs769481947, rs1597434884, rs779980669, rs1351549465	RCV005412150 RCV000709622 RCV000984614 RCV000984616 RCV000984617	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
Acute myeloid leukemia	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
AUTISM SPECTRUM DISORDER	—	GWAS catalog	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
BREAST NEOPLASMS	—	CTD	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CAKUT	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital anomaly of kidney and urinary tract	Benign; Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CTU2-related disorder	Conflicting classifications of pathogenicity; Benign; Likely benign; Uncertain significance	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Differences in sex development	Conflicting classifications of pathogenicity	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Ambiguous Genitalia	Ambiguous Genitalia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Atrial Septal Defects	Atrial Septal Defect	HPO_DG			★☆☆☆☆ Found in Text Mining only
Brachycephaly	Brachycephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Breast Carcinoma	Breast Carcinoma	CTD_human_DG	27811057		★☆☆☆☆ Found in Text Mining only
Byzanthine arch palate	High palate	HPO_DG			★☆☆☆☆ Found in Text Mining only
Congenital Abnormalities	Congenital abnormalities	Pubtator	32604767	Associate	★☆☆☆☆ Found in Text Mining only
Congenital malformation syndrome	Congenital Malformation Syndrome	BEFREE	31301155		★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Intellectual developmental disorder	Pubtator	32604767	Associate	★☆☆☆☆ Found in Text Mining only
Language Development Disorders	Language development disorders	Pubtator	32604767	Associate	★☆☆☆☆ Found in Text Mining only
Lissencephaly	Lissencephaly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Macrotia	Macrotia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Malignant neoplasm of breast	Breast Cancer	CTD_human_DG	27811057		★☆☆☆☆ Found in Text Mining only
Mammary Carcinoma, Human	Marfan Syndrome	CTD_human_DG	27811057		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms	Mammary Neoplasms	CTD_human_DG	27811057		★☆☆☆☆ Found in Text Mining only
Mammary Neoplasms, Human	Mammary Neoplasms	CTD_human_DG	27811057		★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
MICROCEPHALY, FACIAL DYSMORPHISM, RENAL AGENESIS, AND AMBIGUOUS GENITALIA SYNDROME	MICROCEPHALY, FACIAL DYSMORPHISM, RENAL AGENESIS, AND AMBIGUOUS GENITALIA SYNDROME	GENOMICS_ENGLAND_DG	26633546, 31301155		★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
MICROCEPHALY, FACIAL DYSMORPHISM, RENAL AGENESIS, AND AMBIGUOUS GENITALIA SYNDROME	MICROCEPHALY, FACIAL DYSMORPHISM, RENAL AGENESIS, AND AMBIGUOUS GENITALIA SYNDROME	CLINVAR_DG			★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Micrognathism	Micrognathism	HPO_DG			★☆☆☆☆ Found in Text Mining only
Patent ductus arteriosus	Patent ductus arteriosus	HPO_DG			★☆☆☆☆ Found in Text Mining only
Penis agenesis	Penis Agenesis	HPO_DG			★☆☆☆☆ Found in Text Mining only
POLYDACTYLY, POSTAXIAL	Polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Pulmonary Disease Chronic Obstructive	Chronic obstructive pulmonary disease	Pubtator	28621160	Associate	★☆☆☆☆ Found in Text Mining only
Radial polydactyly	Radial Polydactyly	HPO_DG			★☆☆☆☆ Found in Text Mining only
Unilateral agenesis of kidney	Renal aplasia	HPO_DG			★☆☆☆☆ Found in Text Mining only
Ventricular Septal Defects	Ventricular septal defect	HPO_DG			★☆☆☆☆ Found in Text Mining only