ZC3H13
Chr 13zinc finger CCCH-type containing 13
Also known as: KIAA0853, Xio
ZC3H13 encodes a protein that regulates RNA N6-methyladenosine (m6A) methylation by anchoring components of the methyltransferase complex and bridging WTAP to RNA-binding proteins, playing a critical role in mRNA processing and splicing. The gene is extremely constrained against loss-of-function variants (pLI 1.0, LOEUF 0.21), indicating that mutations are likely to cause severe developmental phenotypes. Clinical reports of pathogenic ZC3H13 variants are limited, but given its essential role in RNA metabolism and embryonic development, mutations would be expected to cause neurodevelopmental disorders with autosomal recessive inheritance.
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Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Mild missense constraint
The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).
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
276 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 0 | 0 | 54 | 0 | 54 |
Likely Pathogenic | 0 | 0 | 1 | 0 | 1 |
VUS | 0 | 193 | 1 | 0 | 194 |
Likely Benign | 0 | 6 | 0 | 4 | 10 |
Benign | 0 | 0 | 0 | 0 | 0 |
| Total | 0 | 199 | 56 | 4 | 259 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
ZC3H13 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
No active trials found for this gene.
Search ClinicalTrials.gov →No open access results found
External Resources
Links to major genomics databases and tools