ZCCHC18

Chr X

zinc finger CCHC-type containing 18

Also known as: PNMA7B, SIZN2

NCBI Gene: 644353ENSG00000166707UniProt: P0CG32

The ZCCHC18 protein is predicted to bind zinc ions and function in the nucleus. No established human disease associations have been reported for mutations in this gene based on the available information.

Summary from RefSeq
Research Assistant →
0
Active trials
1
Pubs (1 yr)
73
P/LP submissions
0%
P/LP missense
0.92
LOEUF
Multiple*
Mechanism· predicted
Clinical Summary— ZCCHC18
⚡
Population Constraint (gnomAD)
Constrained for loss-of-function variants (OE-LoF 0.19) despite low pLI — interpret in context.
📋
ClinVar Variants
68 unique Pathogenic / Likely Pathogenic· 45 VUS of 131 total submissions
Explore recent and relevant literature in Research Assistant →

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Tolerant — LoF & missense variants common in population
LoF Constraint
0.92LOEUF
pLI 0.413
Z-score 1.70
OE 0.19 (0.07–0.92)
Tolerant

Typical tolerance to LoF variation

Missense Constraint
0.75Z-score
OE missense 0.83 (0.72–0.96)
132 obs / 158.5 exp
Tolerant

Mild missense constraint

Observed / Expected Ratios
LoF OE0.19 (0.07–0.92)
0≤0.351.4
Missense OE0.83 (0.72–0.96)
0≤0.61.4
Synonymous OE0.83
0≤1.21.6
LoF obs/exp: 1 / 5.2Missense obs/exp: 132 / 158.5Syn Z: 1.01
DN
0.6552th %ile
GOF
0.6541th %ile
LOF
0.3260th %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

131 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic67
Likely Pathogenic1
VUS45
Likely Benign5
67
Pathogenic
1
Likely Pathogenic
45
VUS
5
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
67
0
67
Likely Pathogenic
0
0
1
0
1
VUS
0
42
3
0
45
Likely Benign
0
4
0
1
5
Benign
0
0
0
0
0
Total046711118

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

View in ClinVar →

Protein Context — Lollipop Plot

ZCCHC18 · 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 ↗
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

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