GALNT2 p.Pro353=
c.1059G>A · VCV4706659
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00439%, sas)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| REVEL | 0.078 | moderately benign-leaning |
|---|---|---|
| Splicing | ||
| SpliceAI | — | not assessed · no allele here is in the release |
| Constraint at this position | ||
| Conservation | phyloP -5.9 | GERP -3.9 |
| Overall | ||
| CADD | 8.495 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00439%
South Asian · 4/91,088 alleles
Filtering AF
0.00231%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00202%
Overall
0.00285%
46/1,614,110 alleles · very rare
exomes 42/1,461,892 · genomes 4/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.00439% | 22,772 |
| African / African-American | 0.004% | 24,979 |
| European (non-Finnish) | 0.00314% | 31,893 |
| Admixed American | 0.00167% | 60,004 |
| Remaining individualsnot grpmax-eligible | 0.0016% | 62,488 |
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.Pro353=
- Coding
- c.1059G>A
- MANE Select
- NM_004481
- Type
- single nucleotide variant
- Location
- chr1:230255267 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI 0.89 (gnomAD)
- Structure
- AlphaFold pLDDT 90.27 · 13 PDB
- Residue 353
- 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 'catalytic subdomain b' region; a β-strand
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-pro353 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown