ZNF25

Chr 10

zinc finger protein 25

Also known as: KOX19, Zfp9

NCBI Gene: 219749ENSG00000175395UniProt: P17030

The protein is predicted to function as a DNA-binding transcription factor that regulates RNA polymerase II transcription in the nucleus. This gene is not highly constrained against loss-of-function variants and is not currently associated with any established Mendelian disease or inheritance pattern in clinical databases.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
2
Pubs (1 yr)
8
P/LP submissions
0%
P/LP missense
0.91
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— ZNF25
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
8 unique Pathogenic / Likely Pathogenic· 57 VUS of 74 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.91LOEUF
pLI 0.000
Z-score 1.87
OE 0.53 (0.33–0.91)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
-0.15Z-score
OE missense 1.03 (0.92–1.15)
237 obs / 230.5 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE0.53 (0.33–0.91)
0≤0.351.4
Missense OE1.03 (0.92–1.15)
0≤0.61.4
Synonymous OE0.97
0≤1.21.6
LoF obs/exp: 10 / 18.7Missense obs/exp: 237 / 230.5Syn Z: 0.22
DN
0.86top 5%
GOF
0.77top 25%
LOF
0.2583th %ile

This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.

DNprediction above median
GOFprediction above median

Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.

ClinVar Variant Classifications

74 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic7
Likely Pathogenic1
VUS57
Likely Benign3
Benign2
7
Pathogenic
1
Likely Pathogenic
57
VUS
3
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
7
0
7
Likely Pathogenic
0
0
1
0
1
VUS
0
54
3
0
57
Likely Benign
0
1
2
0
3
Benign
0
0
2
0
2
Total05515070

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

View in ClinVar →

Protein Context — Lollipop Plot

ZNF25 · protein map & ClinVar variants

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

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →
Clinical Literature
Open Research Assistant →
Full-Text Mentions
NLP-detected gene mentions in article bodies · via PubTator3
PubTator3
Top 5 full-text resultsSearch PubTator3 ↗
Key Publications
Landmark & review papers · by relevance
PubMed
Top 1 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

External Resources

Links to major genomics databases and tools

Franklin by Genoox
AI-powered variant curation and clinical analysis
DECIPHER
Genomic variants and phenotypes in rare disease patients