BCL11B p.Phe623=
c.1869C>T · rs1256527125 · VCV2049241
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 8.65e-05%, nfe)
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 4.3 | GERP -3.2, phastCons 1 |
| Overall | ||
| CADD | 10.82 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
8.65e-05%
European (non-Finnish) · 1/1,155,992 alleles
Overall
7.15e-05%
1/1,398,596 alleles · very rare
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.Phe623=
- Coding
- c.1869C>T
- MANE Select
- NM_138576
- dbSNP
- rs1256527125
- Type
- single nucleotide variant
- Location
- chr14:99174967 (GRCh38)
- Gene constraint
- LOEUF 0.462 · pLI 1.00 (gnomAD)
- Structure
- AlphaFold pLDDT 51.76 · 6 PDB
- Residue 623
- a UniProt-annotated variant site (in iddsfta)
Similar variants
- BCL11B p.Phe623Leu 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-phe623 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown