GALNT2 p.Pro164=
c.492G>A · rs34897003 · VCV769555
Benign
Multiple submitters
Classification
Benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 5 submitters
gnomAD v4.1
Rare
low-frequency (popmax 2.1%, mid)
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 -12 | GERP -3.8 |
| Overall | ||
| CADD | 0.331 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
2.1%
Middle Eastern · 127/6,060 alleles
Filtering AF
1.8%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.69%
Overall
0.999%
16,118/1,613,692 alleles · low-frequency
exomes 14,451/1,461,568 · genomes 1,667/152,124 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Middle Easterngrpmax | 2.1% | 48 |
| Ashkenazi Jewishnot grpmax-eligible | 1.77% | 56 |
| Finnishnot grpmax-eligible | 1.61% | 62 |
| African / African-American | 1.49% | 67 |
| European (non-Finnish) | 1.01% | 99 |
| Remaining individualsnot grpmax-eligible | 0.936% | 107 |
| Admixed American | 0.659% | 152 |
| South Asian | 0.484% | 206 |
| East Asian | 0.0201% | 4,987 |
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.Pro164=
- Coding
- c.492G>A
- MANE Select
- NM_004481
- dbSNP
- rs34897003
- Type
- single nucleotide variant
- Location
- chr1:230236371 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI 0.89 (gnomAD)
- Structure
- AlphaFold pLDDT 90.27 · 13 PDB
- Residue 164
- the 'catalytic subdomain a' region
Similar variants
- GALNT2 p.Pro164Arg 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-pro164 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown