B3GAT3 p.Asp32=
c.96C>T · rs1473116963 · VCV2913540
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.0011%, sas)
Conditions
1
Larsen-like syndrome, B3GAT3 type
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · G>C here scores Δ0.25 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 5.6 | GERP 1.8, phastCons 1 |
| Overall | ||
| CADD | 11.54 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0011%
South Asian · 1/90,802 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000186%
3/1,611,334 alleles · very rare
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.0011% | 90,802 |
| European (non-Finnish) | 0.00017% | 589,102 |
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
- B3GAT3
- Protein
- p.Asp32=
- Coding
- c.96C>T
- MANE Select
- NM_012200
- dbSNP
- rs1473116963
- Type
- single nucleotide variant
- Location
- chr11:62620658 (GRCh38)
- Gene constraint
- LOEUF 0.825 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 92.67 · 3 PDB
Similar variants
- B3GAT3 p.Asp32Gly Uncertain significance ★ ⚠ same residue
- B3GAT3 c.619-1G>A Likely pathogenic ★★ same condition
- B3GAT3 p.Arg169Trp Pathogenic/Likely pathogenic ★★ ⚠ same condition
- B3GAT3 p.Arg225Ter Pathogenic/Likely pathogenic ★★ same condition
- B3GAT3 p.Arg277Gln Pathogenic/Likely pathogenic ★★ ⚠ same condition
- B3GAT3 p.Arg59Ter Pathogenic/Likely pathogenic ★★ same condition
- B3GAT3 p.Arg95Ter Pathogenic/Likely pathogenic ★★ same condition
- B3GAT3 p.Gln29Ter Pathogenic/Likely 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/b3gat3-p-asp32 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown