UBXN1

Chr 11

UBX domain protein 1

Also known as: 2B28, SAKS1, UBXD10

NCBI Gene: 51035ENSG00000162191UniProt: Q04323

Enables several functions, including enzyme binding activity; polyubiquitin modification-dependent protein binding activity; and proteasome regulatory particle binding activity. Involved in negative regulation of protein metabolic process. Located in cytosol; endoplasmic reticulum; and nucleoplasm. Part of VCP-NPL4-UFD1 AAA ATPase complex. [provided by Alliance of Genome Resources, Jul 2025]

63
ClinVar variants
11
Pathogenic / LP
0.73
pLI score
0
Active trials
Clinical Summary— UBXN1
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.73) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
11 Pathogenic / Likely Pathogenic· 48 VUS of 63 total submissions

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.45LOEUF
pLI 0.728
Z-score 3.20
OE 0.17 (0.08–0.45)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
0.84Z-score
OE missense 0.83 (0.73–0.95)
160 obs / 192.7 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.17 (0.08–0.45)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.83 (0.73–0.95)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.1.19
0≤1.21.6
LoF obs/exp: 3 / 17.4Missense obs/exp: 160 / 192.7Syn Z: -1.25

ClinVar Variant Classifications

63 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic8
Likely Pathogenic3
VUS48
Likely Benign4
8
Pathogenic
3
Likely Pathogenic
48
VUS
4
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
8
0
8
Likely Pathogenic
0
0
3
0
3
VUS
0
42
6
0
48
Likely Benign
0
1
1
2
4
Benign
0
0
0
0
0
Total04318263

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

UBXN1 · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
Therapeutic targeting of the USP2-E2F4 axis inhibits autophagic machinery essential for zinc homeostasis in cancer progression.
Xiao W et al.·Autophagy
2022
The Oncogenic Role of UBXN1 in Gastric Cancer Is Attributed to the METTL16-Mediated m6A Methylation and Histone Modifications.
Shi K et al.·Cancer Med
2025
ResiDUBs: A deubiquitinating enzyme-based prognostic model identifies UBXN1 driving sorafenib resistance in liver cancer.
Li M et al.·Int Immunopharmacol
2026Functional
Possible role of the Nipah virus V protein in the regulation of the interferon beta induction by interacting with UBX domain-containing protein1.
Uchida S et al.·Sci Rep
2018
HOTAIR Up-Regulation Activates NF-κB to Induce Immunoescape in Gliomas.
Wang Y et al.·Front Immunol
2021
Papillary Thyroid Cancer Remodels the Genetic Information Processing Pathways.
Iacobas DA et al.·Genes (Basel)
2024Functional
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools