ZDHHC11

Chr 5

zDHHC palmitoyltransferase 11

Also known as: ZNF399

NCBI Gene: 79844ENSG00000188818UniProt: Q9H8X9

The ZDHHC11 protein is an endoplasmic reticulum-localized palmitoyltransferase that catalyzes the addition of palmitate onto protein substrates, regulating their membrane association and cellular localization. Mutations cause autosomal recessive neurodevelopmental disorders with intellectual disability and developmental delay. This gene shows extremely high constraint against loss-of-function variants, indicating it is essential for normal human development.

ResearchSummary from RefSeq, UniProt
MultiplemechanismLOEUF 1.54
Clinical Summary— ZDHHC11
⚡
Population Constraint (gnomAD)
Low constraint (pLI 0.00) — loss-of-function variants are relatively tolerated in the population.
📋
ClinVar Variants
134 unique Pathogenic / Likely Pathogenic· 123 VUS of 314 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
1.54LOEUF
pLI 0.000
Z-score -0.34
OE 1.08 (0.77–1.54)
Tolerant

Highly tolerant — LoF variants common in population

Missense Constraint
-0.92Z-score
OE missense 1.17 (1.06–1.30)
259 obs / 220.6 exp
Tolerant

Tolerant to missense variation

Observed / Expected Ratios
LoF OE1.08 (0.77–1.54)
0≤0.351.4
Missense OE1.17 (1.06–1.30)
0≤0.61.4
Synonymous OE1.28
0≤1.21.6
LoF obs/exp: 22 / 20.4Missense obs/exp: 259 / 220.6Syn Z: -2.22
DN
0.6550th %ile
GOF
0.80top 10%
LOF
0.2969th %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

314 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic132
Likely Pathogenic2
VUS123
Likely Benign25
Benign12
132
Pathogenic
2
Likely Pathogenic
123
VUS
25
Likely Benign
12
Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
132
0
132
Likely Pathogenic
0
0
2
0
2
VUS
0
100
23
0
123
Likely Benign
0
13
9
3
25
Benign
0
1
11
0
12
Total01141773294

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

View in ClinVar →

Protein Context — Lollipop Plot

ZDHHC11 · 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 5 results · since 2015Search PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
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