UBE2D4

ubiquitin conjugating enzyme E2 D4 (putative), the group of Ubiquitin conjugating enzymes E2

Basic information

Region (hg38): 7:43926436-43956136

Links

ENSG00000078967 ∙ NCBI:51619 ∙ ∙ HGNC:21647 ∙ Uniprot:Q9Y2X8 ∙ 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 UBE2D4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE2D4 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			6			6
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	6	0	0

Variants in UBE2D4

This is a list of pathogenic ClinVar variants found in the UBE2D4 region.

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

Position	Type	Phenotype	Significance	ClinVar
7-43926537-C-T		not specified	Uncertain significance (Nov 11, 2024)
7-43942850-T-C		not specified	Uncertain significance (Mar 22, 2023)
7-43948645-C-T		not specified	Uncertain significance (Dec 18, 2023)
7-43948652-T-G		not specified	Uncertain significance (Feb 07, 2023)
7-43948675-A-G		not specified	Uncertain significance (Oct 11, 2024)
7-43948702-G-A		not specified	Uncertain significance (Aug 12, 2022)
7-43950601-C-G		not specified	Uncertain significance (Sep 26, 2022)
7-43950667-C-T		not specified	Uncertain significance (May 09, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE2D4	protein_coding	protein_coding	ENST00000222402	7	29699

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000186	0.471	125718	0	28	125746	0.000111

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.924	59	82.7	0.714	0.00000430	959
Missense in Polyphen		22	27.447	0.80156		360
Synonymous	0.629	30	34.7	0.864	0.00000219	274
Loss of Function	0.511	8	9.72	0.823	4.13e-7	114

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000145	0.000145
Ashkenazi Jewish	0.00	0.00
East Asian	0.000272	0.000272
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.0000967	0.0000967
Middle Eastern	0.000272	0.000272
South Asian	0.000131	0.000131
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Accepts ubiquitin from the E1 complex and catalyzes its covalent attachment to other proteins. In vitro able to promote polyubiquitination using all 7 ubiquitin Lys residues, but may prefer 'Lys-11' and 'Lys-48'-linked polyubiquitination. {ECO:0000269|PubMed:20061386}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);protein ubiquitylation;Immune System;Adaptive Immune System;Antigen processing: Ubiquitination & Proteasome degradation;Class I MHC mediated antigen processing & presentation (Consensus)

Recessive Scores

• pRec: 0.113

Intolerance Scores

• loftool: 0.733
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.179
• hipred: Y
• hipred_score: 0.761
• ghis: 0.502

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.903

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ube2d2b

Gene ontology

• Biological process: ubiquitin-dependent protein catabolic process;protein ubiquitination;protein K29-linked ubiquitination;protein K27-linked ubiquitination;protein K63-linked ubiquitination;protein K48-linked ubiquitination;protein K11-linked ubiquitination;protein K6-linked ubiquitination
• Cellular component: ubiquitin ligase complex
• Molecular function: ubiquitin-protein transferase activity;protein binding;ATP binding;ubiquitin protein ligase binding;ubiquitin conjugating enzyme activity