GALC p.Ser502=
c.1506T>C · rs2139951654 · VCV1094859
Likely benign
Single submitter
Classification
Likely benign
ClinVar
Review
Single submitter ★☆☆☆
ClinVar · 1 submitter
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
1
Krabbe disease
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation carries the signal. | ||
| Splicing | ||
| SpliceAI | <0.2 | all four deltas below 0.2 · A>C here scores Δ0.63 · evaluated, not missing |
|---|---|---|
| Constraint at this position | ||
| Conservation | phyloP 0.5 | GERP -1.5, phastCons 0.75 |
| Overall | ||
| CADD | 7.5 | PHRED · no single calibrated threshold — expert panels disagree |
Population frequency
gnomAD v4.1 · exomes + genomes
Absent from gnomAD v4.1. Not observed in any sequenced alleles — a rarity signal (ACMG PM2-supporting), not evidence of pathogenicity on its own.
Variant & gene context
- Gene
- GALC
- Protein
- p.Ser502=
- Coding
- c.1506T>C
- MANE Select
- NM_000153
- dbSNP
- rs2139951654
- Type
- single nucleotide variant
- Location
- chr14:87945717 (GRCh38)
- Gene constraint
- LOEUF 1.019 · pLI <0.01 (gnomAD)
- Structure
- AlphaFold pLDDT 94.56
Disease context
Krabbe disease — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Krabbe disease (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Adolescent, Adult, Childhood, Infancy, Neonatal
- Prevalence
- 1-9 / 1 000 000 (United States)
Similar variants
- GALC p.Ser502Arg Uncertain significance ⚠ same residue
- GALC c.1033+1G>A Likely pathogenic ★★ same condition
- GALC c.1034-1G>C Pathogenic/Likely pathogenic ★★ same condition
- GALC c.1034-2A>G Pathogenic/Likely pathogenic ★★ same condition
- GALC c.1161+2T>A Likely pathogenic ★★ same condition
- GALC c.1251+1G>C Pathogenic/Likely pathogenic ★★ same condition
- GALC c.1252-1G>C Pathogenic/Likely pathogenic ★★ same condition
- GALC c.1338+1G>C Likely pathogenic ★★ same condition
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/galc-p-ser502 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown