RNF138
Basic information
Region (hg38): 18:32091874-32131561
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the RNF138 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 | 0 | |||||
| missense | 4 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 4 | 0 | 0 |
Variants in RNF138
This is a list of pathogenic ClinVar variants found in the RNF138 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 18-32092829-G-A | not specified | Uncertain significance (Apr 22, 2024) | ||
| 18-32092831-C-T | not specified | Uncertain significance (Nov 15, 2024) | ||
| 18-32092843-G-A | not specified | Uncertain significance (Feb 07, 2023) | ||
| 18-32111832-A-C | not specified | Uncertain significance (Jan 21, 2025) | ||
| 18-32111863-G-A | not specified | Uncertain significance (Sep 17, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| RNF138 | protein_coding | protein_coding | ENST00000261593 | 7 | 39707 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.675 | 0.324 | 125687 | 0 | 8 | 125695 | 0.0000318 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.12 | 60 | 127 | 0.472 | 0.00000622 | 1622 |
| Missense in Polyphen | 4 | 37.172 | 0.10761 | 489 | ||
| Synonymous | 0.879 | 35 | 42.3 | 0.828 | 0.00000199 | 425 |
| Loss of Function | 2.73 | 2 | 12.3 | 0.162 | 5.18e-7 | 167 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000316 | 0.0000316 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.000262 | 0.000229 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: E3 ubiquitin-protein ligase involved in DNA damage response by promoting DNA resection and homologous recombination (PubMed:26502055, PubMed:26502057). Recruited to sites of double- strand breaks following DNA damage and specifically promotes double-strand break repair via homologous recombination (PubMed:26502055, PubMed:26502057). Two different, non-exclusive, mechanisms have been proposed. According to a report, regulates the choice of double-strand break repair by favoring homologous recombination over non-homologous end joining (NHEJ): acts by mediating ubiquitination of XRCC5/Ku80, leading to remove the Ku complex from DNA breaks, thereby promoting homologous recombination (PubMed:26502055). According to another report, cooperates with UBE2Ds E2 ubiquitin ligases (UBE2D1, UBE2D2, UBE2D3 or UBE2D4) to promote homologous recombination by mediating ubiquitination of RBBP8/CtIP (PubMed:26502057). Together with NLK, involved in the ubiquitination and degradation of TCF/LEF (PubMed:16714285). Also exhibits auto-ubiquitination activity in combination with UBE2K (PubMed:16714285). May act as a negative regulator in the Wnt/beta-catenin-mediated signaling pathway (PubMed:16714285). {ECO:0000269|PubMed:16714285, ECO:0000269|PubMed:26502055, ECO:0000269|PubMed:26502057}.;
- Pathway
- Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation
(Consensus)
Recessive Scores
- pRec
- 0.114
Intolerance Scores
- loftool
- 0.217
- rvis_EVS
- 0.48
- rvis_percentile_EVS
- 78.95
Haploinsufficiency Scores
- pHI
- 0.368
- hipred
- Y
- hipred_score
- 0.693
- ghis
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.988
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Rnf138
- Phenotype
Gene ontology
- Biological process
- double-strand break repair via homologous recombination;DNA double-strand break processing involved in repair via single-strand annealing;Wnt signaling pathway;protein ubiquitination;cellular response to leukemia inhibitory factor
- Cellular component
- nucleus;site of double-strand break
- Molecular function
- single-stranded DNA binding;protein binding;protein kinase binding;metal ion binding;ubiquitin protein ligase activity