BCL11B p.Pro413=
c.1239C>T · rs931484413 · VCV2055526
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00179%, 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 -0.095 | GERP -3.2, phastCons 0.14 |
| Overall | ||
| CADD | 8.762 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00179%
Admixed American · 1/55,752 alleles
Overall
0.000127%
2/1,573,722 alleles · very rare
exomes 0/1,421,620 · genomes 2/152,102 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00179% | 55,752 |
| African / African-American | 0.00138% | 72,694 |
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.Pro413=
- Coding
- c.1239C>T
- MANE Select
- NM_138576
- dbSNP
- rs931484413
- Type
- single nucleotide variant
- Location
- chr14:99175597 (GRCh38)
- Gene constraint
- LOEUF 0.462 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 51.76 · 6 PDB
- Residue 413
- the 'disordered' region
Similar variants
- BCL11B p.Pro413Ala Uncertain significance ★ ⚠ same residue
- BCL11B p.Pro413fs Uncertain significance ★ same residue
- 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
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-pro413 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown