STAG1
Chr 3ADSTAG1 cohesin complex component
Also known as: MRD47, SA1, SCC3A
Encodes a component of the cohesin complex that maintains sister chromatid cohesion during cell division. Mutations cause autosomal dominant intellectual developmental disorder with onset in early childhood. The gene is highly constrained against loss-of-function variants, indicating that such variants are likely pathogenic when they occur.
Primary Disease Associations & Inheritance
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Among the most LoF-intolerant genes (~top 3%)
Highly missense-constrained (top ~0.1%)
The highest-scoring mechanism for this gene is loss-of-function (haploinsufficiency).
Literature Evidence
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
300 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 | 5 | 0 | 7 | 0 | 12 |
Likely Pathogenic | 3 | 2 | 1 | 0 | 6 |
VUS | 3 | 134 | 11 | 3 | 151 |
Likely Benign | 0 | 5 | 44 | 42 | 91 |
Benign | 0 | 1 | 2 | 0 | 3 |
Conflicting | — | 3 | |||
| Total | 11 | 142 | 65 | 45 | 266 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
STAG1 · 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
External Resources
Links to major genomics databases and tools