CTU2
Basic information
Region (hg38): 16:88706483-88715396
Previous symbols: [ "C16orf84" ]
Links
Phenotypes
GenCC
Source:
- 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:
Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
---|---|---|---|---|---|
Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome | AR | General | Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing | Craniofacial; Genitourinary; Musculoskeletal; Neurologic; Renal | 26633546; 27480277 |
ClinVar
This is a list of variants' phenotypes submitted to
- 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 | 21 | 15 | 37 | |||
missense | 102 | 14 | 125 | |||
nonsense | 3 | |||||
start loss | 0 | |||||
frameshift | 2 | |||||
inframe indel | 2 | |||||
splice donor/acceptor (+/-2bp) | 2 | |||||
splice region | 2 | 3 | 11 | 5 | 21 | |
non coding | 26 | 18 | 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) | ||
16-88706540-G-A | not specified | Uncertain significance (Feb 22, 2023) | ||
16-88706552-T-A | Uncertain significance (Jul 19, 2022) | |||
16-88706555-G-A | CTU2-related disorder | Benign (Jan 22, 2024) | ||
16-88706566-G-A | Likely benign (Jul 17, 2023) | |||
16-88706579-C-G | not specified | Uncertain significance (Jan 03, 2022) | ||
16-88706598-G-C | Uncertain significance (Dec 15, 2023) | |||
16-88706610-C-T | Likely benign (Nov 14, 2022) | |||
16-88706618-C-G | Benign (Jul 06, 2023) | |||
16-88707117-C-T | Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome | Benign/Likely benign (Jan 08, 2024) | ||
16-88707120-C-A | CTU2-related disorder | Benign (Jan 29, 2024) | ||
16-88707137-C-T | not specified | Uncertain significance (Nov 21, 2022) | ||
16-88707140-G-A | not specified | Uncertain significance (Apr 01, 2024) | ||
16-88707141-A-C | CTU2-related disorder | Benign (Dec 09, 2023) | ||
16-88707144-A-G | not specified | Uncertain significance (Jan 23, 2023) | ||
16-88707153-T-C | not specified | Uncertain significance (Nov 01, 2022) | ||
16-88707176-G-C | not specified | Uncertain significance (Jan 26, 2022) | ||
16-88707186-T-A | CTU2-related disorder | Uncertain significance (Jul 26, 2022) | ||
16-88707188-C-G | CTU2-related disorder | Uncertain significance (Jul 26, 2022) | ||
16-88707191-G-A | Uncertain significance (Dec 09, 2022) | |||
16-88707213-G-T | Uncertain significance (Jan 15, 2022) | |||
16-88707228-C-A | Likely benign (Sep 06, 2022) | |||
16-88709981-C-G | Uncertain significance (May 08, 2022) | |||
16-88709982-T-C | Microcephaly, facial dysmorphism, renal agenesis, and ambiguous genitalia syndrome • CTU2-related disorder | Conflicting classifications of pathogenicity (Dec 07, 2023) | ||
16-88709992-C-G | not specified | Uncertain significance (Mar 08, 2024) |
GnomAD
Source:
Gene | Type | Bio Type | Transcript | Coding Exons | Length |
---|---|---|---|---|---|
CTU2 | protein_coding | protein_coding | ENST00000453996 | 15 | 8924 |
pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
---|---|---|---|---|---|---|
3.97e-22 | 0.000324 | 2997 | 78910 | 43805 | 125712 | 0.846 |
Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
---|---|---|---|---|---|---|
Missense | -3.95 | 514 | 316 | 1.62 | 0.0000198 | 3276 |
Missense in Polyphen | 133 | 82.967 | 1.603 | 801 | ||
Synonymous | -7.23 | 243 | 136 | 1.79 | 0.00000917 | 1051 |
Loss of Function | -0.533 | 31 | 28.0 | 1.11 | 0.00000141 | 311 |
LoF frequencies by population
Ethnicity | Sum of pLOFs | p |
---|---|---|
African & African-American | 1.74 | 1.67 |
Ashkenazi Jewish | 0.984 | 0.892 |
East Asian | 0.919 | 0.906 |
Finnish | 0.899 | 0.814 |
European (Non-Finnish) | 0.936 | 0.843 |
Middle Eastern | 0.919 | 0.906 |
South Asian | 0.866 | 0.855 |
Other | 0.926 | 0.870 |
dbNSFP
Source:
- 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
All | Recessive | Dominant | |
---|---|---|---|
Mendelian | High | High | High |
Primary Immunodeficiency | High | High | High |
Cancer | High | High | High |
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