BCL11A p.Pro98=
c.294C>T · rs201120802 · VCV3042356
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0156%, eas)
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 -1.6 | GERP -5.5 |
| Overall | ||
| CADD | 9.289 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0156%
East Asian · 7/44,902 alleles
Filtering AF
0.00726%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00514%
Overall
0.00409%
66/1,614,088 alleles · ultra-rare
exomes 59/1,461,884 · genomes 7/152,204 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.0156% | 6,415 |
| Admixed American | 0.0117% | 8,571 |
| South Asian | 0.00549% | 18,217 |
| European (non-Finnish) | 0.00373% | 26,819 |
| Ashkenazi Jewishnot grpmax-eligible | 0.00338% | 29,608 |
| Remaining individualsnot grpmax-eligible | 0.0032% | 31,243 |
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.Pro98=
- Coding
- c.294C>T
- MANE Select
- NM_022893
- dbSNP
- rs201120802
- Type
- single nucleotide variant
- Location
- chr2:60546062 (GRCh38)
- Gene constraint
- LOEUF 0.125 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.09 · 17 PDB
- Residue 98
- the 'required for nuclear body formation and for sumo1 recruitment' region
Similar variants
- 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
- BCL11A p.Gly610Ser 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-pro98 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown