GALNT2 p.Asp183=
c.549C>T · rs752133091 · VCV1987541
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00446%, eas)
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 -6.4 | GERP -1.8 |
| Overall | ||
| CADD | 6.081 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00446%
East Asian · 2/44,888 alleles
Filtering AF
0.000763%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000605%
Overall
0.0013%
21/1,612,530 alleles · very rare
exomes 18/1,460,394 · genomes 3/152,136 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00446% | 22,444 |
| Admixed American | 0.00336% | 29,800 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,420 |
| African / African-American | 0.00134% | 74,734 |
| European (non-Finnish) | 0.00127% | 78,642 |
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
- GALNT2
- Protein
- p.Asp183=
- Coding
- c.549C>T
- MANE Select
- NM_004481
- dbSNP
- rs752133091
- Type
- single nucleotide variant
- Location
- chr1:230236667 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI 0.89 (gnomAD)
- Structure
- AlphaFold pLDDT 90.27 · 13 PDB
- Residue 183
- an α-helix; the 'catalytic subdomain a' region
Similar variants
- GALNT2 p.Arg200Ter Pathogenic ★★ same type
- GALNT2 c.1560+4C>T Uncertain significance ★★ same type
- GALNT2 p.Ala299Thr Uncertain significance ★★ ⚠ same type
- GALNT2 p.Ala30Val Uncertain significance ★★ ⚠ same type
- GALNT2 p.Ala35Thr Uncertain significance ★★ ⚠ same type
- GALNT2 p.Arg128Gln Uncertain significance ★★ ⚠ same type
- GALNT2 p.Arg404Ile Uncertain significance ★★ ⚠ same type
- GALNT2 p.Arg502Gln 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/galnt2-p-asp183 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown