BCL11B p.Pro552=
c.1656C>T · rs749263941 · VCV1545113
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.00538%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -1.2 | GERP -2.8 |
| Overall | ||
| CADD | 9.304 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00538%
Admixed American · 3/55,774 alleles
Filtering AF
0.00143%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000727%
Overall
0.00139%
22/1,577,444 alleles · very rare
exomes 17/1,425,794 · genomes 5/151,650 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00538% | 18,591 |
| Remaining individualsnot grpmax-eligible | 0.00327% | 30,602 |
| European (non-Finnish) | 0.00146% | 68,468 |
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
- BCL11B
- Protein
- p.Pro552=
- Coding
- c.1656C>T
- MANE Select
- NM_138576
- dbSNP
- rs749263941
- Type
- single nucleotide variant
- Location
- chr14:99175180 (GRCh38)
- Gene constraint
- LOEUF 0.462 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 51.76 · 6 PDB
- Residue 552
- a UniProt-annotated variant site (in iddsfta); the 'disordered' region
Similar variants
- BCL11B p.Asn807Lys Pathogenic/Likely pathogenic ★★ ⚠ same type
- BCL11B p.Cys808Arg Likely pathogenic ★★ same type
- BCL11B p.Tyr824Ter Likely pathogenic ★★ same type
- BCL11B p.Ala152Val Uncertain significance ★★ ⚠ same type
- BCL11B p.Ala188Thr Uncertain significance ★★ ⚠ same type
- BCL11B p.Ala339Val Uncertain significance ★★ ⚠ same type
- BCL11B p.Ala424Asp Uncertain significance ★★ ⚠ same type
- BCL11B p.Ala579Thr 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/bcl11b-p-pro552 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown