CTU2

cytosolic thiouridylase subunit 2

Basic information

Region (hg38): 16:88706483-88715396

Previous symbols: [ "C16orf84" ]

Links

ENSG00000174177NCBI:348180OMIM:617057HGNC:28005Uniprot:Q2VPK5AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

  • microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome (Strong), mode of inheritance: AR
  • microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome (Limited), mode of inheritance: AR
  • microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome (Strong), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

ConditionInheritanceIntervention CategoriesIntervention/Rationale Manifestation CategoriesReferences
Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndromeARGeneralGenetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testingCraniofacial; Genitourinary; Musculoskeletal; Neurologic; Renal26633546; 27480277

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CTU2 gene.

  • Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome (4 variants)
  • not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CTU2 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type Pathogenic Likely pathogenic VUS Likely benign Benign Sum
synonymous
1
clinvar
21
clinvar
15
clinvar
37
missense
102
clinvar
9
clinvar
14
clinvar
125
nonsense
1
clinvar
2
clinvar
3
start loss
0
frameshift
2
clinvar
2
inframe indel
2
clinvar
2
splice donor/acceptor (+/-2bp)
2
clinvar
2
splice region
2
3
11
5
21
non coding
26
clinvar
18
clinvar
44
Total 3 2 107 56 47

Highest pathogenic variant AF is 0.000138

Variants in CTU2

This is a list of pathogenic ClinVar variants found in the CTU2 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position Type Phenotype Significance ClinVar
16-88706528-C-G CTU2-related disorder Likely benign (Jul 30, 2019)3035852
16-88706540-G-A not specified Uncertain significance (Feb 22, 2023)2486828
16-88706552-T-A Uncertain significance (Jul 19, 2022)2190088
16-88706555-G-A CTU2-related disorder Benign (Jan 22, 2024)1529311
16-88706566-G-A Likely benign (Jul 17, 2023)1668718
16-88706579-C-G not specified Uncertain significance (Jan 03, 2022)2210404
16-88706598-G-C Uncertain significance (Dec 15, 2023)3252804
16-88706610-C-T Likely benign (Nov 14, 2022)3004110
16-88706618-C-G Benign (Jul 06, 2023)3020373
16-88707117-C-T Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome Benign/Likely benign (Jan 08, 2024)1600007
16-88707120-C-A CTU2-related disorder Benign (Jan 29, 2024)1253335
16-88707137-C-T not specified Uncertain significance (Nov 21, 2022)2397667
16-88707140-G-A not specified Uncertain significance (Apr 01, 2024)3270265
16-88707141-A-C CTU2-related disorder Benign (Dec 09, 2023)2906481
16-88707144-A-G not specified Uncertain significance (Jan 23, 2023)2477044
16-88707153-T-C not specified Uncertain significance (Nov 01, 2022)2321721
16-88707176-G-C not specified Uncertain significance (Jan 26, 2022)2345114
16-88707186-T-A CTU2-related disorder Uncertain significance (Jul 26, 2022)2063448
16-88707188-C-G CTU2-related disorder Uncertain significance (Jul 26, 2022)2063449
16-88707191-G-A Uncertain significance (Dec 09, 2022)2504860
16-88707213-G-T Uncertain significance (Jan 15, 2022)1509109
16-88707228-C-A Likely benign (Sep 06, 2022)1921261
16-88709981-C-G Uncertain significance (May 08, 2022)2135711
16-88709982-T-C Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome • CTU2-related disorder Conflicting classifications of pathogenicity (Dec 07, 2023)635410
16-88709992-C-G not specified Uncertain significance (Mar 08, 2024)3078888

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CTU2protein_codingprotein_codingENST00000453996 158924
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
3.97e-220.000324299778910438051257120.846
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-3.955143161.620.00001983276
Missense in Polyphen13382.9671.603801
Synonymous-7.232431361.790.000009171051
Loss of Function-0.5333128.01.110.00000141311

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American1.741.67
Ashkenazi Jewish0.9840.892
East Asian0.9190.906
Finnish0.8990.814
European (Non-Finnish)0.9360.843
Middle Eastern0.9190.906
South Asian0.8660.855
Other0.9260.870

dbNSFP

Source: dbNSFP

Function
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 wobble position. {ECO:0000255|HAMAP-Rule:MF_03054, ECO:0000269|PubMed:19017811}.;
Pathway
Sulfur relay system - Homo sapiens (human);tRNA modification in the nucleus and cytosol;tRNA processing;Metabolism of RNA (Consensus)

Intolerance Scores

loftool
0.989
rvis_EVS
1.43
rvis_percentile_EVS
95.02

Haploinsufficiency Scores

pHI
0.280
hipred
N
hipred_score
0.197
ghis
0.536

Essentials

essential_gene_CRISPR
E
essential_gene_CRISPR2
E
essential_gene_gene_trap
E
gene_indispensability_pred
E
gene_indispensability_score
0.539

Gene Damage Prediction

AllRecessiveDominant
MendelianHighHighHigh
Primary ImmunodeficiencyHighHighHigh
CancerHighHighHigh

Mouse Genome Informatics

Gene name
Ctu2
Phenotype

Gene ontology

Biological process
tRNA wobble uridine modification;tRNA wobble position uridine thiolation;protein urmylation;tRNA thio-modification
Cellular component
cytosol;protein-containing complex
Molecular function
tRNA binding;protein binding;nucleotidyltransferase activity;sulfurtransferase activity