ZNF706

Chr 8

zinc finger protein 706

Also known as: HSPC038, PNAS-106, PNAS-113

NCBI Gene: 51123 ENSG00000120963 UniProt: Q9Y5V0 OMIM: 619526

ZNF706 encodes a transcription repressor that binds zinc ions and negatively regulates DNA transcription, specifically repressing KLF4 expression to control embryonic stem cell exit from self-renewal. Mutations cause autosomal recessive developmental and epileptic encephalopathy with severe intellectual disability and early-onset seizures. The gene shows moderate constraint against loss-of-function variants (LOEUF 0.75), suggesting some tolerance to complete gene loss.

OMIM ResearchSummary from RefSeq, UniProt

Predicted to enable zinc ion binding activity. Predicted to be involved in negative regulation of DNA-templated transcription and negative regulation of stem cell population maintenance. Predicted to be located in cytoplasm and nucleus. [provided by Alliance of Genome Resources, Jul 2025]

OMIM ResearchGenerating clinical summary…

LOEUF 0.75

Clinical Summary— ZNF706

⚡

Population Constraint (gnomAD)

Moderately constrained gene (pLI 0.70) — some intolerance to loss-of-function variants.

📋

ClinVar Variants

9 total variants — no pathogenic classifications of 9 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?

0.75LOEUF

pLI 0.702

Z-score 1.85

OE 0.00 (0.00–0.75)

Moderately constrained

Typical tolerance to LoF variation

Missense Constraint?

1.76Z-score

OE missense 0.21 (0.12–0.37)

8 obs / 38.9 exp

Tolerant

Mild missense constraint

Observed / Expected Ratios?

LoF OE?0.00 (0.00–0.75)

0≤0.351.4

Missense OE?0.21 (0.12–0.37)

0≤0.61.4

Synonymous OE?1.08

0≤1.21.6

LoF obs/exp: 0 / 4.0Missense obs/exp: 8 / 38.9Syn Z: -0.22

ClinVar Variant Classifications

9 submitted variants in ClinVar

ClinVar

Classification Summary

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories· variant type breakdown unavailable

Classification	LoF	Missense + Inframe	Non-coding	Synonymous
Pathogenic	—	—	—	—
Likely Pathogenic	—	—	—	—
VUS	—	—	—	—
Likely Benign	—	—	—	—
Benign	—	—	—	—
Total	—

Counts from ClinVar esearch · Updated hourly

View in ClinVar →

38 pathogenic / likely-pathogenic (of 43) ClinVar copy-number / structural variants overlap ZNF706 — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →