ZC3H7A

Chr 16

zinc finger CCCH-type containing 7A

Also known as: HSPC055, ZC3H7, ZC3HDC7

NCBI Gene: 29066ENSG00000122299UniProt: Q8IWR0OMIM: 619819

The protein binds to specific microRNA hairpins and regulates microRNA biogenesis, recognizing the 3'-ATA(A/T)-5' motif in apical loops. Mutations cause autosomal dominant neurodevelopmental disorders with intellectual disability and developmental delay. This gene is highly constrained against loss-of-function variants (pLI=1.00, LOEUF=0.115), indicating intolerance to protein-truncating mutations.

OMIMResearchSummary from RefSeq, UniProt
LOFmechanismLOEUF 0.12
Clinical Summary— ZC3H7A
⚡
Population Constraint (gnomAD)
Highly constrained gene — heterozygous loss-of-function variants are very rare in the population (pLI 1.00). One damaged copy is likely sufficient to cause disease.
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Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
LoF intolerant — likely haploinsufficient
LoF Constraint
0.12LOEUF
pLI 1.000
Z-score 6.62
OE 0.04 (0.01–0.12)
Highly constrained

Among the most LoF-intolerant genes (~top 3%)

Missense Constraint
1.75Z-score
OE missense 0.78 (0.72–0.85)
406 obs / 518.0 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.04 (0.01–0.12)
0≤0.351.4
Missense OE0.78 (0.72–0.85)
0≤0.61.4
Synonymous OE1.06
0≤1.21.6
LoF obs/exp: 2 / 54.9Missense obs/exp: 406 / 518.0Syn Z: -0.64
DN
0.2897th %ile
GOF
0.3094th %ile
LOF
0.67top 25%

The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).

LOFprediction above median · LOEUF 0.12

Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312. Mechanism ranking also informed by gnomAD constraint, ClinVar, and ClinGen data.

ClinVar Variant Classifications

0 submitted variants in ClinVar

ClinVar

Protein Context — Lollipop Plot

ZC3H7A · 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.

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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