BSCL2 p.Ala262=
c.786G>A · rs780533531 · VCV1628745
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
ultra-rare (popmax 0.0117%, amr)
Conditions
1
Charcot-Marie-Tooth disease type 2
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 -5.1 | GERP -4.7 |
| Overall | ||
| CADD | 7.89 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0117%
Admixed American · 7/59,996 alleles
Filtering AF
0.00543%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0038%
Overall
0.0013%
21/1,613,890 alleles · ultra-rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0117% | 8,571 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,486 |
| South Asian | 0.0011% | 91,086 |
| European (non-Finnish) | 0.00102% | 98,337 |
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
- BSCL2
- Protein
- p.Ala262=
- Coding
- c.786G>A
- MANE Select
- NM_001122955
- dbSNP
- rs780533531
- Type
- single nucleotide variant
- Location
- chr11:62692453 (GRCh38)
- Gene constraint
- LOEUF 0.869 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 75.09 · 1 PDB
Similar variants
- BSCL2 c.1006-2A>C Likely pathogenic ★★ same condition
- BSCL2 c.486+1G>A Pathogenic/Likely pathogenic ★★ same condition
- BSCL2 p.Ala276Pro Pathogenic ★★ same condition
- BSCL2 p.Arg329Ter Pathogenic ★★ same condition
- BSCL2 p.Asn152Ser Pathogenic ★★ ⚠ same condition
- BSCL2 p.Glu253Ter Pathogenic ★★ same condition
- BSCL2 p.Ser154Leu Pathogenic/Likely pathogenic ★★ ⚠ same condition
- BSCL2 p.Ser154Trp Pathogenic ★★ same condition
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/bscl2-p-ala262 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown