GALNT2 p.Ser150=
c.450G>A · rs138909324 · VCV1565342
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.147%, afr)
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.67 | donor gain · deltas |
|---|---|---|
| Pangolin | Δ0.36 | gain · loss 0.08 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP -2.1 | GERP -4.1 |
| Overall | ||
| CADD | 17.6 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.147%
African / African-American · 110/75,016 alleles
Filtering AF
0.124%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.116%
Overall
0.00867%
140/1,614,018 alleles · rare
exomes 72/1,461,790 · genomes 68/152,228 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| African / African-Americangrpmax | 0.147% | 682 |
| Remaining individualsnot grpmax-eligible | 0.0192% | 5,209 |
| Admixed American | 0.0117% | 8,575 |
| South Asian | 0.0011% | 91,068 |
| European (non-Finnish) | 0.000847% | 118,001 |
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.Ser150=
- Coding
- c.450G>A
- MANE Select
- NM_004481
- dbSNP
- rs138909324
- Type
- single nucleotide variant
- Location
- chr1:230236089 (GRCh38)
- Gene constraint
- LOEUF 0.515 · pLI 0.89 (gnomAD)
- Structure
- AlphaFold pLDDT 90.27 · 13 PDB
- Residue 150
- an α-helix; the 'catalytic subdomain a' region
Similar variants
- GALNT2 p.Ser150Leu 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-ser150 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown