GALNT3 p.Phe28=
c.84T>C · rs2467890101 · VCV2882400
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00017%, nfe)
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 5.2 | GERP 4.1, phastCons 1 |
| Overall | ||
| CADD | 8.84 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00017%
European (non-Finnish) · 2/1,175,692 alleles
Filtering AF
2.8e-05%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 1.1e-05%
Overall
0.000138%
2/1,449,842 alleles · very rare
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.Phe28=
- Coding
- c.84T>C
- MANE Select
- NM_004482
- dbSNP
- rs2467890101
- Type
- single nucleotide variant
- Location
- chr2:165770617 (GRCh38)
- Gene constraint
- LOEUF 0.804 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.88
Similar variants
- 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
- GALNT3 c.689-2A>G Likely pathogenic ★★ same type
- GALNT3 p.Arg162Ter 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-phe28 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown