B3GLCT p.Asp244=
c.732C>T · rs778364563 · VCV2498576
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00445%, eas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP -5.6 | GERP -3.1 |
| Overall | ||
| CADD | 0.2 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00445%
East Asian · 2/44,894 alleles
Filtering AF
0.000738%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000276%
Overall
0.000682%
11/1,614,060 alleles · very rare
exomes 10/1,461,862 · genomes 1/152,198 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00445% | 22,447 |
| Admixed American | 0.00167% | 59,994 |
| European (non-Finnish) | 0.000678% | 147,503 |
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.Asp244=
- Coding
- c.732C>T
- MANE Select
- NM_194318
- dbSNP
- rs778364563
- Type
- single nucleotide variant
- Location
- chr13:31274580 (GRCh38)
- Gene constraint
- LOEUF 1.109 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 86.94 · 1 PDB
Similar variants
- B3GLCT c.1065-1G>A Pathogenic ★★ same type
- B3GLCT c.459+1G>A Pathogenic/Likely pathogenic ★★ same type
- B3GLCT c.660+1G>A Pathogenic ★★ same type
- B3GLCT p.Asp349Asn Likely pathogenic ★★ same type
- B3GLCT p.Tyr380Ter Pathogenic/Likely pathogenic ★★ same type
- B3GLCT c.*1752C>T Uncertain significance ★★ same type
- B3GLCT p.Arg377His Uncertain significance ★★ same type
- B3GLCT p.Asn243Ser 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/b3glct-p-asp244 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown