SALL3
Chr 18spalt like transcription factor 3
Also known as: ZNF796
The protein is a zinc-finger transcription factor that regulates DNA methylation by binding to and inhibiting DNA methyltransferase 3 alpha (DNMT3A). Mutations cause autosomal dominant intellectual disability with developmental delay and distinctive facial features. The gene shows significant constraint against loss-of-function variants (LOEUF 0.44), reflecting its important role in embryonic development.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% 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
199 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 | 62 | 0 | 62 |
Likely Pathogenic | 0 | 0 | 6 | 0 | 6 |
VUS | 0 | 102 | 12 | 0 | 114 |
Likely Benign | 0 | 6 | 3 | 2 | 11 |
Benign | 0 | 0 | 0 | 1 | 1 |
| Total | 0 | 108 | 83 | 3 | 194 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
SALL3 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
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 →External Resources
Links to major genomics databases and tools