DDX39A
Chr 19DExD-box helicase 39A
Also known as: BAT1, BAT1L, DDX39, DDXL, URH49
This DEAD-box helicase regulates nuclear mRNA export to the cytoplasm and plays essential roles in RNA splicing and spliceosomal RNA processing. Mutations cause autosomal dominant neurodevelopmental disorder with variable intellectual disability, behavioral abnormalities, and dysmorphic features. The gene is highly constrained against loss-of-function variants, indicating intolerance to protein-disrupting mutations.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
More LoF-intolerant than ~75% of genes
Moderately missense-constrained (top ~2.5%)
The highest-scoring mechanism for this gene is dominant-negative.
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
70 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 | 13 | 0 | 13 |
Likely Pathogenic | 0 | 1 | 1 | 0 | 2 |
VUS | 0 | 34 | 4 | 0 | 38 |
Likely Benign | 0 | 0 | 0 | 0 | 0 |
Benign | 0 | 0 | 0 | 1 | 1 |
| Total | 0 | 35 | 18 | 1 | 54 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
DDX39A · 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