GALNT3 p.Ser511=
c.1533C>T · rs770800462 · VCV2910848
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Rare
very rare (popmax 0.00834%, amr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | no splice effect predicted · four deltas, not one · how we know |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.004 | GERP -5.3 |
| Overall | ||
| CADD | 5.917 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.00834%
Admixed American · 5/59,938 alleles
Filtering AF
0.00487%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.00447%
Overall
0.00516%
83/1,610,048 alleles · very rare
exomes 81/1,458,120 · genomes 2/151,928 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| Admixed Americangrpmax | 0.00834% | 11,988 |
| European (non-Finnish) | 0.00603% | 16,587 |
| East Asian | 0.00447% | 22,380 |
| Remaining individualsnot grpmax-eligible | 0.00321% | 31,149 |
| African / African-American | 0.00267% | 37,387 |
| Finnishnot grpmax-eligible | 0.00157% | 63,652 |
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.Ser511=
- Coding
- c.1533C>T
- MANE Select
- NM_004482
- dbSNP
- rs770800462
- Type
- single nucleotide variant
- Location
- chr2:165754720 (GRCh38)
- Gene constraint
- LOEUF 0.804 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 89.88
- Residue 511
- a UniProt-annotated variant site (in hftc1); the ricin b-type lectin domain
Similar variants
- GALNT3 p.Ser511Arg 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
- GALNT3 c.689-2A>G Likely 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-ser511 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown