BCL11B p.Asp33=
c.99C>T · rs141214308 · VCV1617604
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0172%, mid)
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 -2.1 | GERP -3.4 |
| Overall | ||
| CADD | 3.706 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0172%
Middle Eastern · 1/5,800 alleles
Filtering AF
0.00334%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00301%
Overall
0.00397%
62/1,561,122 alleles · ultra-rare
exomes 53/1,408,806 · genomes 9/152,316 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 0.0172% | 5,800 |
| Remaining individualsnot grpmax-eligible | 0.005% | 19,987 |
| European (non-Finnish) | 0.00434% | 23,030 |
| African / African-American | 0.00409% | 24,455 |
| Admixed American | 0.00373% | 26,842 |
| South Asian | 0.00361% | 27,685 |
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.Asp33=
- Coding
- c.99C>T
- MANE Select
- NM_138576
- dbSNP
- rs141214308
- Type
- single nucleotide variant
- Location
- chr14:99257799 (GRCh38)
- Gene constraint
- LOEUF 0.462 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 51.76 · 6 PDB
Similar variants
- BCL11B p.Asp33Tyr 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
- BCL11B p.Ala424Asp 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-asp33 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown