ZNF287

Chr 17

zinc finger protein 287

Also known as: ZKSCAN13, ZSCAN45

NCBI Gene: 57336ENSG00000141040UniProt: Q9HBT7

This gene encodes a zinc finger transcription factor involved in transcriptional regulation. Mutations cause neurodevelopmental disorders with intellectual disability and developmental delay, inherited in an autosomal dominant pattern. The gene is highly constrained against loss-of-function variants, indicating that proper gene dosage is critical for normal development.

ResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 0.40
Clinical Summary— ZNF287
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.58) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
27 unique Pathogenic / Likely Pathogenic· 70 VUS of 109 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
0.40LOEUF
pLI 0.583
Z-score 4.22
OE 0.21 (0.12–0.40)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint
2.37Z-score
OE missense 0.67 (0.60–0.74)
268 obs / 402.0 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios
LoF OE0.21 (0.12–0.40)
0≤0.351.4
Missense OE0.67 (0.60–0.74)
0≤0.61.4
Synonymous OE0.94
0≤1.21.6
LoF obs/exp: 7 / 33.3Missense obs/exp: 268 / 402.0Syn Z: 0.52
DN
0.6551th %ile
GOF
0.6443th %ile
LOF
0.4825th %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

109 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic27
VUS70
Likely Benign6
27
Pathogenic
70
VUS
6
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
27
0
27
Likely Pathogenic
0
0
0
0
0
VUS
0
54
16
0
70
Likely Benign
0
5
1
0
6
Benign
0
0
0
0
0
Total059440103

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

View in ClinVar →

Protein Context — Lollipop Plot

ZNF287 · protein map & ClinVar variants

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

3D Protein StructureAlphaFold

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 ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC

No open access results found

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