UBE2M

ubiquitin conjugating enzyme E2 M, the group of Ubiquitin conjugating enzymes E2

Basic information

Region (hg38): 19:58555712-58558954

Links

ENSG00000130725NCBI:9040OMIM:603173HGNC:12491Uniprot:P61081AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UBE2M gene.

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
clinvar
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)2512439
19-58556899-C-G not specified Uncertain significance (Feb 17, 2022)2277650
19-58557107-G-T not specified Uncertain significance (Oct 14, 2023)3185533
19-58558348-T-C not specified Uncertain significance (Dec 19, 2022)3185534
19-58558351-T-G not specified Uncertain significance (Jul 14, 2024)3465079

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
UBE2Mprotein_codingprotein_codingENST00000253023 63249
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
0.7980.201113661061136670.0000264
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense2.29401070.3750.000006041202
Missense in Polyphen644.050.13621506
Synonymous-0.4875045.81.090.00000282330
Loss of Function2.5819.640.1044.09e-7120

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00006370.0000637
Finnish0.000.00
European (Non-Finnish)0.00002960.0000296
Middle Eastern0.00006370.0000637
South Asian0.00006830.0000683
Other0.000.00

dbNSFP

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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