GALNT3 p.Ser341=
c.1023G>A · rs764115801 · VCV2910722
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00223%, 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 -1.3 | GERP -5.6, phastCons 0.001 |
| Overall | ||
| CADD | 7.369 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00223%
East Asian · 1/44,872 alleles
Filtering AF
0.00114%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.000971%
Overall
0.00149%
24/1,613,848 alleles · very rare
exomes 20/1,461,728 · genomes 4/152,120 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| East Asiangrpmax | 0.00223% | 44,872 |
| European (non-Finnish) | 0.00178% | 56,189 |
| Finnishnot grpmax-eligible | 0.00156% | 64,022 |
| South Asian | 0.0011% | 91,072 |
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
- GALNT3
- Protein
- p.Ser341=
- Coding
- c.1023G>A
- MANE Select
- NM_004482
- dbSNP
- rs764115801
- Type
- single nucleotide variant
- Location
- chr2:165759386 (GRCh38)
- Gene constraint
- LOEUF 0.804 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.88
- Residue 341
- a UniProt-annotated variant site (in hftc1)
Similar variants
- GALNT3 p.Ser341Pro Uncertain significance ★ ⚠ same residue
- GALNT3 p.Ser341Leu Uncertain significance ⚠ same residue
- GALNT3 c.1074-1G>C Likely pathogenic ★★ same type
- GALNT3 c.1524+1G>A Pathogenic ★★ same type
- GALNT3 c.1524+5G>A Pathogenic ★★ same type
- GALNT3 c.1626+1G>A Pathogenic ★★ same type
- GALNT3 c.516-2A>G Pathogenic/Likely pathogenic ★★ same type
- GALNT3 c.516-2A>T Pathogenic ★★ 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/galnt3-p-ser341 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown