B3GLCT p.Ser461=
c.1383G>A · VCV3666854
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00212%, nfe)
Conditions
1
Peters plus syndrome
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 -9.3 | GERP -4.3 |
| Overall | ||
| CADD | 1.535 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00212%
European (non-Finnish) · 25/1,180,034 alleles
Filtering AF
0.00145%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00123%
Overall
0.00161%
26/1,614,032 alleles · very rare
exomes 24/1,461,880 · genomes 2/152,152 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| European (non-Finnish)grpmax | 0.00212% | 47,201 |
| Admixed American | 0.00167% | 59,990 |
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
- B3GLCT
- Protein
- p.Ser461=
- Coding
- c.1383G>A
- MANE Select
- NM_194318
- Type
- single nucleotide variant
- Location
- chr13:31329554 (GRCh38)
- Gene constraint
- LOEUF 1.109 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.94 · 1 PDB
Similar variants
- B3GLCT c.459+1G>A Pathogenic/Likely pathogenic ★★ same condition
- B3GLCT c.660+1G>A Pathogenic ★★ same condition
- B3GLCT p.Tyr380Ter Pathogenic/Likely pathogenic ★★ same condition
- B3GLCT c.*1752C>T Uncertain significance ★★ same condition
- B3GLCT p.Arg377His Uncertain significance ★★ same condition
- B3GLCT p.Asn243Ser Uncertain significance ★★ ⚠ same condition
- B3GLCT p.Asp469Asn Uncertain significance ★★ ⚠ same condition
- B3GLCT p.Asp469Tyr 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/b3glct-p-ser461 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown