VPS25
Chr 17vacuolar protein sorting 25 homolog
Also known as: DERP9, EAP20, FAP20
This gene encodes a protein that is a subunit of the endosomal sorting complex required for transport II (ESCRT-II). This protein complex functions in sorting of ubiquitinated membrane proteins during endocytosis. A pseudogene of this gene is present on chromosome 1. [provided by RefSeq, Jul 2013]
Clinical Summary— VPS25
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Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.32) despite low pLI — interpret in context.
Some data sources returned errors (1)
ensembl: TimeoutError: The operation was aborted due to timeout
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Tolerant — LoF & missense variants common in population
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.
0.73LOEUF
pLI 0.078
Z-score 2.24
OE 0.32 (0.15–0.73)
Typical tolerance to LoF variation
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.
1.48Z-score
OE missense 0.58 (0.47–0.73)
59 obs / 100.9 exp
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.0.32 (0.15–0.73)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.58 (0.47–0.73)
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.1.10
0≤1.21.6
LoF obs/exp: 4 / 12.6Missense obs/exp: 59 / 100.9Syn Z: -0.52
ClinVar Variant Classifications
0 submitted variants in ClinVar
Protein Context — Lollipop Plot
VPS25 · 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
VACUOLAR PROTEIN SORTING 25 HOMOLOG; VPS25
MIM #610907 · *
External Resources
Links to major genomics databases and tools
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
VPS25 Promotes an Immunosuppressive Microenvironment in Head and Neck Squamous Cell Carcinoma.
Chen LG et al.·Biomolecules
2025
Hub gene associated with prognosis in bladder cancer is a novel therapeutic target.
Fang D et al.·PeerJ
2023
Loss of SR-BI Down-Regulates MITF and Suppresses Extracellular Vesicle Release in Human Melanoma.
Kinslechner K et al.·Int J Mol Sci
2019
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
VPS25 alleviates depression-like behavior in rats by inhibiting apoptosis in the hippocampus.
Yuan L et al.·Brain Res Bull
2026
Germline MYOF1::WNK4 and VPS25::MYOF1 Chimeras Generated by the Constitutional Translocation t(17;19)(q21;p13) in Two Siblings With Myelodysplastic Syndrome.
Panagopoulos I et al.·Cancer Genomics Proteomics
2024
Crosstalk between integrin/FAK and Crk/Vps25 governs invasion of bovine mammary epithelial cells by S. agalactiae.
Guo Z et al.·iScience
2023Open Access
YTHDC1-mediated VPS25 regulates cell cycle by targeting JAK-STAT signaling in human glioma cells.
Zhu X et al.·Cancer Cell Int
2021Open Access
Top 5 resultsSearch Europe PMC ↗
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
Enterovirus 71 non-structural protein 3A hijacks vacuolar protein sorting 25 to boost exosome biogenesis to facilitate viral replication
Ruan Z et al.·Front Microbiol
2022
ESCRT-dependent control of craniofacial morphogenesis with concomitant perturbation of NOTCH signaling.
Hermosilla Aguayo V et al.·Dev Biol
2023
Cellular ESCRT components are recruited to regulate the endocytic trafficking and RNA replication compartment assembly during classical swine fever virus infection
Liu CC et al.·PLoS Pathog
2022
Lack of cellular prion protein causes Amyloid beta accumulation, increased extracellular vesicle abundance, and changes to exosome biogenesis proteins
Johansson L et al.·Mol Cell Biochem
2024
Novel application of bergapten and quercetin with anti-bacterial, osteogenesis-potentiating, and anti-inflammation tri-effects.
Wei J et al.·Acta Biochim Biophys Sin (Shanghai)
2021
Top 6 full-text resultsSearch PubTator3 ↗
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →External Resources
Links to major genomics databases and tools