UBE2M
Basic information
Region (hg38): 19:58555712-58558954
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 UBE2M 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 | 5 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 5 | 0 | 0 |
Variants in UBE2M
This is a list of pathogenic ClinVar variants found in the UBE2M region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 19-58556146-C-A | not specified | Uncertain significance (Jun 12, 2023) | ||
| 19-58556899-C-G | not specified | Uncertain significance (Feb 17, 2022) | ||
| 19-58557107-G-T | not specified | Uncertain significance (Oct 14, 2023) | ||
| 19-58558348-T-C | not specified | Uncertain significance (Dec 19, 2022) | ||
| 19-58558351-T-G | not specified | Uncertain significance (Jul 14, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| UBE2M | protein_coding | protein_coding | ENST00000253023 | 6 | 3249 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.798 | 0.201 | 113661 | 0 | 6 | 113667 | 0.0000264 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.29 | 40 | 107 | 0.375 | 0.00000604 | 1202 |
| Missense in Polyphen | 6 | 44.05 | 0.13621 | 506 | ||
| Synonymous | -0.487 | 50 | 45.8 | 1.09 | 0.00000282 | 330 |
| Loss of Function | 2.58 | 1 | 9.64 | 0.104 | 4.09e-7 | 120 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.0000637 | 0.0000637 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000296 | 0.0000296 |
| Middle Eastern | 0.0000637 | 0.0000637 |
| South Asian | 0.0000683 | 0.0000683 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Accepts the ubiquitin-like protein NEDD8 from the UBA3- NAE1 E1 complex and catalyzes its covalent attachment to other proteins. The specific interaction with the E3 ubiquitin ligase RBX1, but not RBX2, suggests that the RBX1-UBE2M complex neddylates specific target proteins, such as CUL1, CUL2, CUL3 and CUL4. Involved in cell proliferation. {ECO:0000269|PubMed:10207026, ECO:0000269|PubMed:15361859}.;
- Pathway
- Ubiquitin mediated proteolysis - Homo sapiens (human);regulation of p27 phosphorylation during cell cycle progression;Signal Transduction;Post-translational protein modification;protein ubiquitylation;Metabolism of proteins;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Neddylation;Signaling by TGF-beta Receptor Complex;Signaling by TGF-beta family members;TGF-beta receptor signaling activates SMADs;Validated nuclear estrogen receptor alpha network;Validated nuclear estrogen receptor beta network
(Consensus)
Recessive Scores
- pRec
- 0.142
Intolerance Scores
- loftool
- 0.361
- rvis_EVS
- 0.13
- rvis_percentile_EVS
- 62.74
Haploinsufficiency Scores
- pHI
- 0.321
- hipred
- Y
- hipred_score
- 0.754
- ghis
- 0.445
Essentials
- essential_gene_CRISPR
- E
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.781
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Ube2m
- Phenotype
- growth/size/body region phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span);
Gene ontology
- Biological process
- cellular protein modification process;protein ubiquitination;positive regulation of neuron apoptotic process;post-translational protein modification;protein neddylation
- Cellular component
- nucleoplasm;cytosol
- Molecular function
- ubiquitin-protein transferase activity;protein binding;ATP binding;NEDD8 transferase activity