SBF2 p.Arg487=
c.1459C>A · rs120074139 · VCV543491
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Conditions
1
Charcot-Marie-Tooth disease type 4
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| REVEL | 0.205 | benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | Δ0.25 | acceptor gain · deltas |
| Constraint at this position | ||
| Conservation | phyloP 3.1 | GERP 1.1, phastCons 1 |
| Overall | ||
| CADD | 14.42 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/91,072 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000186%
3/1,613,860 alleles · very rare
exomes 2/1,461,786 · genomes 1/152,074 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 91,072 |
| European (non-Finnish) | 0.00017% | 589,960 |
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
- SBF2
- Protein
- p.Arg487=
- Coding
- c.1459C>A
- MANE Select
- NM_030962
- dbSNP
- rs120074139
- Type
- single nucleotide variant
- Location
- chr11:9968482 (GRCh38)
- Gene constraint
- LOEUF 0.591 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 73.74
Similar variants
- SBF2 p.Arg487Ter Pathogenic ★★ same residue
- SBF2 p.Arg487Gln Uncertain significance ★★ ⚠ same residue
- SBF2 c.3653-1G>A Likely pathogenic ★★ same condition
- SBF2 p.Arg342Ter Pathogenic/Likely pathogenic ★★ same condition
- SBF2 p.Arg356Ter Pathogenic ★★ same condition
- SBF2 p.Arg77Ter Pathogenic ★★ same condition
- SBF2 c.1601-3T>G Uncertain significance ★★ same condition
- SBF2 c.3111-3T>C Uncertain significance ★★ 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/sbf2-p-arg487 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown