UBE4B

ubiquitination factor E4B, the group of U-box domain containing

Basic information

Region (hg38): 1:10032831-10181239

Links

ENSG00000130939 ∙ NCBI:10277 ∙ OMIM:613565 ∙ HGNC:12500 ∙ Uniprot:O95155 ∙ 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 UBE4B gene.

• Inborn genetic diseases (30 variants)
• not provided (11 variants)
• Developmental disorder (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the UBE4B 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				1	2	3
missense			30		2	32
nonsense			1			1
start loss						0
frameshift			1			1
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding				3	1	4
Total	0	0	32	4	5

Variants in UBE4B

This is a list of pathogenic ClinVar variants found in the UBE4B region.

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

Position	Type	Phenotype	Significance	ClinVar
1-10033703-G-T			Likely benign (Mar 28, 2018)
1-10072095-C-T		not specified	Uncertain significance (Jan 08, 2024)
1-10072145-G-A		not specified	Uncertain significance (Sep 26, 2023)
1-10072183-G-A		not specified	Uncertain significance (Aug 12, 2021)
1-10095464-T-G		not specified	Uncertain significance (Nov 12, 2021)
1-10095509-G-C		not specified	Uncertain significance (Dec 22, 2023)
1-10101105-A-C			Benign (Dec 31, 2019)
1-10101206-G-A			Likely benign (Jan 01, 2023)
1-10101207-A-G			Likely benign (Jan 01, 2023)
1-10102980-G-C		not specified	Uncertain significance (Oct 20, 2023)
1-10103090-A-G		not specified	Uncertain significance (Aug 16, 2021)
1-10105522-C-G		not specified	Uncertain significance (Jun 07, 2023)
1-10105554-A-T		not specified	Uncertain significance (Oct 20, 2023)
1-10105569-A-T		not specified	Uncertain significance (Jun 18, 2021)
1-10105570-T-C		not specified	Uncertain significance (Oct 04, 2022)
1-10105726-G-T		not specified	Uncertain significance (Oct 17, 2023)
1-10106259-C-T		not specified	Uncertain significance (May 23, 2023)
1-10106280-G-A		not specified	Uncertain significance (Oct 26, 2021)
1-10106318-A-G		not specified	Uncertain significance (May 24, 2023)
1-10106370-C-T		not specified	Uncertain significance (May 27, 2022)
1-10106409-C-T		not specified	Uncertain significance (Nov 22, 2021)
1-10106438-C-T		not specified	Uncertain significance (Jun 21, 2021)
1-10106444-C-A		not specified	Uncertain significance (Apr 26, 2023)
1-10106447-C-G		not specified	Uncertain significance (Dec 02, 2022)
1-10106459-A-G		not specified	Uncertain significance (Jun 07, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
UBE4B	protein_coding	protein_coding	ENST00000343090	28	148408

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	9.02e-8	125597	0	150	125747	0.000597

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.73	488	781	0.625	0.0000471	8556
Missense in Polyphen		68	197.64	0.34406		2086
Synonymous	0.677	284	299	0.950	0.0000188	2554
Loss of Function	7.02	5	67.0	0.0747	0.00000358	763

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000152	0.000151
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.000264	0.000231
European (Non-Finnish)	0.00127	0.00119
Middle Eastern	0.00	0.00
South Asian	0.0000327	0.0000327
Other	0.000880	0.000815

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Ubiquitin-protein ligase that probably functions as an E3 ligase in conjunction with specific E1 and E2 ligases (By similarity). May also function as an E4 ligase mediating the assembly of polyubiquitin chains on substrates ubiquitinated by another E3 ubiquitin ligase (By similarity). May regulate myosin assembly in striated muscles together with STUB1 and VCP/p97 by targeting myosin chaperone UNC45B for proteasomal degradation (PubMed:17369820). {ECO:0000250|UniProtKB:P54860, ECO:0000250|UniProtKB:Q9ES00, ECO:0000269|PubMed:17369820}.
• Pathway: Ubiquitin mediated proteolysis - Homo sapiens (human);Protein processing in endoplasmic reticulum - Homo sapiens (human);p73 transcription factor network (Consensus)

Recessive Scores

• pRec: 0.133

Intolerance Scores

• loftool: 0.283
• rvis_EVS: -1.39
• rvis_percentile_EVS: 4.31

Haploinsufficiency Scores

• pHI: 0.388
• hipred: Y
• hipred_score: 0.706
• ghis: 0.614

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.788

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Ube4b
• Phenotype: cellular phenotype; homeostasis/metabolism phenotype; muscle 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); 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); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan)

Gene ontology

• Biological process: protein polyubiquitination;ventricular trabecula myocardium morphogenesis;ubiquitin-dependent protein catabolic process;protein monoubiquitination;granzyme-mediated apoptotic signaling pathway;response to UV;ubiquitin-dependent ERAD pathway;neuron projection development;proteasome-mediated ubiquitin-dependent protein catabolic process;protein autoubiquitination
• Cellular component: ubiquitin ligase complex;nucleus;cytoplasm
• Molecular function: ATP binding;enzyme binding;ubiquitin-ubiquitin ligase activity;ATPase binding