UBXN2B

protein-coding

UBX domain protein 2B, the group of UBX domain containing

Gene summary

Predicted to enable ubiquitin binding activity. Involved in several processes, including negative regulation of protein localization to centrosome; positive regulation of mitotic centrosome separation; and protein unfolding. Predicted to be located in Golgi apparatus; endoplasmic reticulum; and spindle pole centrosome. Predicted to be active in cytosol and nucleus. [provided by Alliance of Genome Resources, Jun 2026]

MANE transcript

NM_001077619.2

Inheritance

—

ClinVar variants

U:51B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.3

Max pathogenic AF

—

Genomic locus

chr8:58,411,359-58,451,501

External References & Databases

Ensembl (ENSG00000215114)

Transcript & Mutation Effects

hg38 • Region Span ~40.1 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to UBXN2B variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 48

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001077619.2. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous			1 clinvar			1
missense			49 clinvar	2 clinvar		51
nonsense						0
start loss						0
frameshift			1 clinvar			1
splice donor/acceptor (+/-2bp)						0
Total	0	0	51	2	0	53

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001077619.2	RefSeq	NP_001071087.1	8	MANE Select
ENST00000399598.7	Ensembl	ENSP00000382507.2	8	MANE Select
NM_001330535.2	RefSeq	NP_001317464.1	6	Standard
NM_001363181.1	RefSeq	NP_001350110.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

autophagosome assembly
establishment of mitotic spindle orientation
Golgi organization
nuclear envelope reassembly
proteasome-mediated ubiquitin-dependent protein catabolic process

Molecular Function

protein binding
ubiquitin binding

Cellular Component

nucleus
endoplasmic reticulum
Golgi apparatus
cytosol
spindle pole centrosome

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000399598
Coding exons: 8
Length: 40238
Individuals with no LoFs: 124765
Homozygous LoFs: 0
Heterozygous LoFs: 13
Defined: 124778
p: 0.0000521

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.268	148	157	0.940	0.00000811	2141
Missense (PolyPhen)		53	60.537	0.8755		787
Synonymous	0.703	49	55.7	0.880	0.00000255	646
Loss of Function	2.38	4	13.4	0.298	5.61e-7	212

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000065	0.000065	rare
Latino/Admixed American	0	0.0	absent
Ashkenazi Jewish	0	0.0	absent
East Asian	0	0.0	absent
Finnish	0.00023	0.00023	rare
European (Non-Finnish)	0.000054	0.000053	rare
South Asian	0.000044	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Adapter protein required for Golgi and endoplasmic reticulum biogenesis (PubMed:17141156). Involved in Golgi and endoplasmic reticulum maintenance during interphase and in their reassembly at the end of mitosis (PubMed:17141156). The complex formed with VCP has membrane fusion activity; membrane fusion activity requires USO1-GOLGA2 tethering and BET1L (PubMed:17141156). VCPIP1 is also required, but not its deubiquitinating activity (PubMed:17141156). Together with NSFL1C/p47, regulates the centrosomal levels of kinase AURKA/Aurora A during mitotic progression by promoting AURKA removal from centrosomes in prophase (PubMed:23649807). Also, regulates spindle orientation during mitosis (PubMed:23649807). {ECO:0000269|PubMed:17141156, ECO:0000269|PubMed:23649807}.;

Recessive Scores

pRec: 0.105

Intolerance Scores

LoFtool: 0.507
RVIS EVS: -0.07
RVIS percentile EVS: 48.12

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.677

Gene Damage Prediction

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