GALNT2 p.Ser489=
c.1467G>A · rs16851310 · VCV1601567
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Common
common (popmax 10.5%, afr) — too common for a highly-penetrant pathogenic allele
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 -3.7 | GERP -3.1 |
| Overall | ||
| CADD | 4.843 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
10.5%
African / African-American · 7,880/74,976 alleles
Filtering AF
10.3%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 10.2%
Overall
0.66%
10,646/1,613,630 alleles · common
exomes 6,043/1,461,340 · genomes 4,603/152,290 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 10.5% | 10 |
| Middle Eastern | 2.44% | 41 |
| Remaining individualsnot grpmax-eligible | 0.922% | 108 |
| Admixed American | 0.847% | 118 |
| South Asian | 0.429% | 233 |
| Ashkenazi Jewishnot grpmax-eligible | 0.23% | 435 |
| European (non-Finnish) | 0.0905% | 1,105 |
| East Asian | 0.0156% | 6,412 |
| Finnishnot grpmax-eligible | 0.00156% | 64,036 |
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.Ser489=
- Coding
- c.1467G>A
- MANE Select
- NM_004481
- dbSNP
- rs16851310
- Type
- single nucleotide variant
- Location
- chr1:230274471 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI 0.89 (gnomAD)
- Structure
- AlphaFold pLDDT 90.27 · 13 PDB
- Residue 489
- a UniProt-annotated variant site (in cdg2t; loss of apoc-iii glycosylation); a UniProt-annotated variant site (in cdg2t; loss-of-function variant resulting in lack of apoc-iii glycosylation); the ricin b-type lectin domain
Similar variants
- GALNT2 p.Ser489Leu Uncertain significance ★ ⚠ same residue
- 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
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-ser489 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown