BCL11A p.Ser201=
c.603C>T · VCV4515092
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
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 7.7 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 14.74 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,068 alleles
Overall
6.2e-05%
1/1,614,136 alleles · very rare
exomes 1/1,461,878 · genomes 0/152,258 · joint denominator
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.Ser201=
- Coding
- c.603C>T
- MANE Select
- NM_022893
- Type
- single nucleotide variant
- Location
- chr2:60462309 (GRCh38)
- Gene constraint
- LOEUF 0.125 · pLI 1.00 · ClinGen HI 3/3 (gnomAD)
- Structure
- AlphaFold pLDDT 53.09 · 17 PDB
- Residue 201
- 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-ser201 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown