GALNT3 p.Phe153=
c.459C>T · rs371366884 · VCV1119685
Likely benign
Multiple submitters
Classification
Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 3 submitters
gnomAD v4.1
Rare
ultra-rare (popmax 0.0267%, amr)
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 3.2 | GERP -4.4, phastCons 1 |
| Overall | ||
| CADD | 11.14 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.0267%
Admixed American · 16/60,024 alleles
Filtering AF
0.0195%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.0186%
Overall
0.0178%
288/1,614,094 alleles · ultra-rare
exomes 265/1,461,876 · genomes 23/152,218 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.0267% | 3,752 |
| European (non-Finnish) | 0.0217% | 4,609 |
| Middle Eastern | 0.0165% | 6,062 |
| Remaining individualsnot grpmax-eligible | 0.0144% | 6,945 |
| East Asian | 0.00891% | 11,218 |
| African / African-American | 0.00267% | 37,510 |
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.Phe153=
- Coding
- c.459C>T
- MANE Select
- NM_004482
- dbSNP
- rs371366884
- Type
- single nucleotide variant
- Location
- chr2:165770242 (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-phe153 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown