ZNF7

Chr 8

zinc finger protein 7

Also known as: HF.16, KOX4, zf30

NCBI Gene: 7553ENSG00000147789UniProt: P17097

ZNF7 encodes a zinc finger transcription factor that regulates gene expression by binding to specific DNA sequences and modulating RNA polymerase II transcription. The gene is not loss-of-function intolerant (pLI near 0, LOEUF 0.867), suggesting it may tolerate some degree of functional variation. Currently, no definitive disease associations have been established for ZNF7 mutations in clinical practice.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
1
Pubs (1 yr)
54
P/LP submissions
0%
P/LP missense
0.87
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— ZNF7
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
54 unique Pathogenic / Likely Pathogenic· 107 VUS of 174 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
0.87LOEUF
pLI 0.000
Z-score 2.09
OE 0.56 (0.38–0.87)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.23Z-score
OE missense 0.97 (0.89–1.05)
364 obs / 376.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.56 (0.38–0.87)
0≤0.351.4
Missense OE0.97 (0.89–1.05)
0≤0.61.4
Synonymous OE1.15
0≤1.21.6
LoF obs/exp: 15 / 26.7Missense obs/exp: 364 / 376.4Syn Z: -1.38
DN
0.91top 5%
GOF
0.83top 10%
LOF
0.1994th %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

174 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic49
Likely Pathogenic5
VUS107
Likely Benign3
49
Pathogenic
5
Likely Pathogenic
107
VUS
3
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
49
0
49
Likely Pathogenic
0
0
5
0
5
VUS
0
97
10
0
107
Likely Benign
0
3
0
0
3
Benign
0
0
0
0
0
Total0100640164

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

View in ClinVar →

Protein Context — Lollipop Plot

ZNF7 · 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