ZNF22

Chr 10

zinc finger protein 22

Also known as: HKR-T1, KOX15, ZNF422, Zfp422

NCBI Gene: 7570ENSG00000165512UniProt: P17026

ZNF22 encodes a zinc finger transcription factor that binds DNA through the consensus sequence 5'-CAATG-3' and regulates gene expression, with predicted involvement in tooth formation. The gene shows low constraint to loss-of-function variation (pLI 0.002, LOEUF 1.34), and no definitive disease associations have been established in humans.

Summary from RefSeq, UniProt
Research Assistant →
0
Active trials
0
Pubs (1 yr)
13
P/LP submissions
0%
P/LP missense
1.33
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— ZNF22
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
13 unique Pathogenic / Likely Pathogenic· 22 VUS of 42 total submissions
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
1.33LOEUF
pLI 0.002
Z-score 0.94
OE 0.64 (0.33–1.33)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
0.54Z-score
OE missense 0.87 (0.74–1.01)
112 obs / 129.4 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.64 (0.33–1.33)
0≤0.351.4
Missense OE0.87 (0.74–1.01)
0≤0.61.4
Synonymous OE0.91
0≤1.21.6
LoF obs/exp: 5 / 7.8Missense obs/exp: 112 / 129.4Syn Z: 0.47
DN
0.74top 25%
GOF
0.6542th %ile
LOF
0.4134th %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

42 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic11
Likely Pathogenic2
VUS22
Likely Benign1
Benign1
11
Pathogenic
2
Likely Pathogenic
22
VUS
1
Likely Benign
1
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
11
0
11
Likely Pathogenic
0
0
2
0
2
VUS
0
22
0
0
22
Likely Benign
0
1
0
0
1
Benign
0
0
1
0
1
Total02314037

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

View in ClinVar →

Protein Context — Lollipop Plot

ZNF22 · 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 3 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