ZNF202

Chr 11

zinc finger protein 202

Also known as: ZKSCAN10, ZSCAN42

NCBI Gene: 7753ENSG00000166261UniProt: O95125

Enables DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Located in chromosome; nuclear body; and nucleolus. [provided by Alliance of Genome Resources, Jul 2025]

Research Assistant →
0
Active trials
2
Pubs (1 yr)
52
P/LP submissions
0%
P/LP missense
0.42
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— ZNF202
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.53) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
52 unique Pathogenic / Likely Pathogenic· 75 VUS of 141 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint
0.42LOEUF
pLI 0.526
Z-score 3.88
OE 0.21 (0.12–0.42)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
1.69Z-score
OE missense 0.75 (0.68–0.83)
277 obs / 368.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.21 (0.12–0.42)
0≤0.351.4
Missense OE0.75 (0.68–0.83)
0≤0.61.4
Synonymous OE1.03
0≤1.21.6
LoF obs/exp: 6 / 28.3Missense obs/exp: 277 / 368.5Syn Z: -0.33
DN
0.6649th %ile
GOF
0.6638th %ile
LOF
0.4037th %ile

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

GOFprediction above median
DNprediction 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

141 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic50
Likely Pathogenic2
VUS75
Likely Benign4
Benign2
50
Pathogenic
2
Likely Pathogenic
75
VUS
4
Likely Benign
2
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
50
0
50
Likely Pathogenic
0
0
2
0
2
VUS
0
70
5
0
75
Likely Benign
0
4
0
0
4
Benign
0
0
0
2
2
Total074572133

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

View in ClinVar →

Protein Context — Lollipop Plot

ZNF202 · 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
Macrophage-activating lipopeptide-2 downregulates the expression of ATP-binding cassette transporter A1 by activating the TLR2/NF-кB/ZNF202 pathway in THP-1 macrophages.
Peng L et al.·Acta Biochim Biophys Sin (Shanghai)
2016
Znf202 affects high density lipoprotein cholesterol levels and promotes hepatosteatosis in hyperlipidemic mice.
Vrins CL et al.·PLoS One
2013Open Access
Population-Based Resequencing of LIPG and ZNF202 Genes in Subjects with Extreme HDL Levels.
Razzaghi H et al.·Front Genet
2012Open Access
Zinc finger protein ZNF202 structure and function in transcriptional control of HDL metabolism.
Schmitz G et al.·Curr Opin Lipidol
2004
ZNF202 is inversely regulated with its target genes ABCA1 and apoE during macrophage differentiation and foam cell formation.
Langmann T et al.·J Lipid Res
2003
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