BCL11A p.Pro264=
c.792C>T · VCV4955283
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00679%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 9.8 | GERP 2.7, phastCons 1 |
| Overall | ||
| CADD | 12.83 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00679%
East Asian · 3/44,204 alleles
Filtering AF
0.0018%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000995%
Overall
0.00168%
26/1,551,746 alleles · very rare
exomes 25/1,405,044 · genomes 1/146,702 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00679% | 14,735 |
| Admixed American | 0.00193% | 51,808 |
| European (non-Finnish) | 0.00182% | 54,797 |
| Remaining individualsnot grpmax-eligible | 0.00167% | 59,840 |
Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.
Variant & gene context
- Gene
- BCL11A
- Protein
- p.Pro264=
- Coding
- c.792C>T
- MANE Select
- NM_022893
- Type
- single nucleotide variant
- Location
- chr2:60462120 (GRCh38)
- Gene constraint
- LOEUF 0.125 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.09 · 17 PDB
Similar variants
- BCL11A p.Pro264Arg Uncertain significance ★ ⚠ same residue
- BCL11A c.385+2T>C Pathogenic ★★ same type
- BCL11A c.488-1G>A Pathogenic/Likely pathogenic ★★ same type
- BCL11A p.Gln124Ter Pathogenic/Likely pathogenic ★★ same type
- BCL11A p.Glu473Ter Pathogenic/Likely pathogenic ★★ same type
- BCL11A p.Met1Val Pathogenic/Likely pathogenic ★★ same type
- BCL11A p.Arg713His Uncertain significance ★★ ⚠ same type
- BCL11A p.Cys48Arg Uncertain significance ★★ ⚠ same type
Built on 18 open, versioned datasets — ClinVar, gnomAD, AlphaMissense, REVEL, ClinGen & more — plus Sugi Variant's own cross-source analysis. Source data 2026-01–2026-10, ClinVar 2026-10. Full sources & versions →
Cite Sugi Variant
Gür T. Sugi Variant: A Deterministic Per-Variant Germline Reference from a Knowledge Graph for Humans and AI Agents. 2026. doi:10.5281/zenodo.21509445. This variant: https://sugi.bio/variant/bcl11a-p-pro264 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown