UBE2W

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

Basic information

Region (hg38): 8:73780097-73878910

Links

ENSG00000104343

∙ NCBI:55284 ∙ OMIM:614277 ∙ HGNC:25616 ∙ Uniprot:Q96B02 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the UBE2W gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2W 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			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in UBE2W

This is a list of pathogenic ClinVar variants found in the UBE2W region.

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

Position	Type	Phenotype	Significance	ClinVar
8-73810557-G-C		not specified	Uncertain significance (Jan 29, 2024)	3185579
8-73810626-T-C		not specified	Uncertain significance (Dec 27, 2023)	3185578

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE2W	protein_coding	protein_coding	ENST00000419880	7	98814

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0924	0.900	117288	179	7155	124622	0.0299

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.81	43	91.8	0.468	0.00000416	1225
Missense in Polyphen		7	31.657	0.22112		418
Synonymous	-0.111	32	31.2	1.03	0.00000151	349
Loss of Function	2.33	4	13.1	0.305	7.86e-7	145

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0305	0.0304
Ashkenazi Jewish	0.0580	0.0579
East Asian	0.0000559	0.0000556
Finnish	0.0292	0.0288
European (Non-Finnish)	0.0460	0.0455
Middle Eastern	0.0000559	0.0000556
South Asian	0.00178	0.00177
Other	0.0345	0.0340

dbNSFP

Source: dbNSFP

Function: FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins (PubMed:20061386, PubMed:21229326). Specifically monoubiquitinates the N-terminus of various substrates, including ATXN3, MAPT/TAU, POLR2H/RPB8 and STUB1/CHIP, by recognizing backbone atoms of disordered N-termini (PubMed:23560854, PubMed:23696636, PubMed:25436519). Involved in degradation of misfolded chaperone substrates by mediating monoubiquitination of STUB1/CHIP, leading to recruitment of ATXN3 to monoubiquitinated STUB1/CHIP, and restriction of the length of ubiquitin chain attached to STUB1/CHIP substrates by ATXN3. After UV irradiation, but not after mitomycin-C (MMC) treatment, acts as a specific E2 ubiquitin-conjugating enzyme for the Fanconi anemia complex by associating with E3 ubiquitin-protein ligase FANCL and catalyzing monoubiquitination of FANCD2, a key step in the DNA damage pathway (PubMed:19111657, PubMed:21229326). In vitro catalyzes 'Lys-11'-linked polyubiquitination. UBE2W-catalyzed ubiquitination occurs also in the presence of inactive RING/U-box type E3s, i.e. lacking the active site cysteine residues to form thioester bonds with ubiquitin, or even in the absence of E3, albeit at a slower rate (PubMed:25436519). {ECO:0000269|PubMed:19111657, ECO:0000269|PubMed:20061386, ECO:0000269|PubMed:21229326, ECO:0000269|PubMed:23560854, ECO:0000269|PubMed:23696636, ECO:0000269|PubMed:25436519}.;
Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Post-translational protein modification;protein ubiquitylation;Metabolism of proteins;Synthesis of active ubiquitin: roles of E1 and E2 enzymes;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation;Protein ubiquitination (Consensus)

Recessive Scores

pRec: 0.0945

Intolerance Scores

loftool
rvis_EVS: 0.12
rvis_percentile_EVS: 62.38

Haploinsufficiency Scores

pHI: 0.634
hipred: Y
hipred_score: 0.712
ghis

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap
gene_indispensability_pred: N
gene_indispensability_score: 0.443

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

Gene name: Ube2w
Phenotype: endocrine/exocrine gland phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype; immune system phenotype; 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); reproductive system phenotype; hematopoietic system phenotype; hearing/vestibular/ear phenotype;

Gene ontology

Biological process: DNA repair;protein monoubiquitination;protein quality control for misfolded or incompletely synthesized proteins;protein ubiquitination;proteasome-mediated ubiquitin-dependent protein catabolic process;protein K11-linked ubiquitination;cellular response to misfolded protein
Cellular component: nucleus;nucleoplasm
Molecular function: ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin protein ligase binding;ubiquitin conjugating enzyme activity