GALM p.Ser130=
c.390G>A · rs575533020 · VCV1608525
Benign/Likely benign
Multiple submitters
Classification
Benign/Likely benign
ClinVar
Review
Multiple submitters ★★☆☆
ClinVar · 2 submitters
gnomAD v4.1
Rare
rare (popmax 0.418%, sas)
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 -9.9 | GERP -4.3 |
| Overall | ||
| CADD | 0.071 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Grpmax group
0.418%
South Asian · 381/91,056 alleles
Filtering AF
0.384%
ClinGen BA1/BS1 input
FAF95, joint · FAF99 0.37%
Overall
0.0312%
503/1,613,824 alleles · rare
exomes 476/1,461,600 · genomes 27/152,224 · joint denominator
| Ancestry group | Frequency | 1 in |
|---|---|---|
| South Asiangrpmax | 0.418% | 239 |
| Middle Eastern | 0.206% | 486 |
| Remaining individualsnot grpmax-eligible | 0.0368% | 2,717 |
| European (non-Finnish) | 0.00678% | 14,750 |
| East Asian | 0.00668% | 14,961 |
| Admixed American | 0.005% | 20,003 |
| African / African-American | 0.00133% | 75,020 |
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
- GALM
- Protein
- p.Ser130=
- Coding
- c.390G>A
- MANE Select
- NM_138801
- dbSNP
- rs575533020
- Type
- single nucleotide variant
- Location
- chr2:38681324 (GRCh38)
- Gene constraint
- LOEUF 1.421 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 97.83 · 2 PDB
- Residue 130
- a UniProt-annotated variant site (in galac4; loss of protein accumulation); a β-strand
Similar variants
- GALM p.Ser130Leu Uncertain significance ★ ⚠ same residue
- GALM p.Arg131Cys Uncertain significance ★★ ⚠ same type
- GALM p.Gly155Arg Uncertain significance ★★ ⚠ same type
- GALM p.His333Arg Uncertain significance ★★ ⚠ same type
- GALM p.Val8Met Uncertain significance ★★ ⚠ same type
- GALM c.191-100G>T Benign ★★ same type
- GALM c.191-128T>C Benign ★★ same type
- GALM c.191-32T>A Benign ★★ 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/galm-p-ser130 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown