GTF2IRD1
Chr 7GTF2I repeat domain containing 1
Also known as: BEN, CREAM1, GTF3, MUSTRD1, RBAP2, WBS, WBSCR11, WBSCR12
This protein functions as a transcription regulator involved in craniofacial and cognitive development, cell-cycle progression, and skeletal muscle differentiation. Mutations cause Williams-Beuren syndrome, a multisystem developmental disorder with craniofacial abnormalities and intellectual disability that follows an autosomal dominant inheritance pattern due to deletions at 7q11.23. The gene is highly constrained against loss-of-function variants (pLI 0.90, LOEUF 0.33), indicating that complete loss of protein function is likely deleterious.
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Highly LoF-intolerant (top ~10% of genes)
Moderately missense-constrained (top ~2.5%)
Predictions shown for reference only — model trained on dominant genes, not applicable to AR conditions.
The Badonyi & Marsh prediction model was trained exclusively on dominant disease genes. Predictions are not reliable for genes with autosomal recessive inheritance and are shown at reduced opacity for reference only.
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
408 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 | 160 | 0 | 160 |
Likely Pathogenic | 0 | 1 | 6 | 0 | 7 |
VUS | 3 | 124 | 10 | 0 | 137 |
Likely Benign | 0 | 10 | 5 | 40 | 55 |
Benign | 0 | 1 | 3 | 13 | 17 |
Conflicting | — | 1 | |||
| Total | 3 | 136 | 184 | 53 | 377 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →Protein Context — Lollipop Plot
GTF2IRD1 · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
3D Protein StructureAlphaFold
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