GALK1 p.Pro181=
c.543C>T · rs2545903504 · VCV2013751
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
galactokinase deficiency
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 3.4 | phastCons 1 |
| Overall | ||
| CADD | 10.35 | 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
- GALK1
- Protein
- p.Pro181=
- Coding
- c.543C>T
- MANE Select
- NM_000154
- dbSNP
- rs2545903504
- Type
- single nucleotide variant
- Location
- chr17:75763082 (GRCh38)
- Gene constraint
- LOEUF 1.198 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 97.31 · 20 PDB
Disease context
galactokinase deficiency — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsFor Galactokinase deficiency (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
Similar variants
- GALK1 c.355+1G>A Likely pathogenic ★★ same condition
- GALK1 c.611+1G>T Pathogenic/Likely pathogenic ★★ same condition
- GALK1 c.793+1G>T Pathogenic/Likely pathogenic ★★ same condition
- GALK1 c.793+2T>C Pathogenic/Likely pathogenic ★★ same condition
- GALK1 c.793+2T>G Pathogenic/Likely pathogenic ★★ same condition
- GALK1 p.Arg256Trp Pathogenic/Likely pathogenic ★★ same condition
- GALK1 p.Arg301Ter Pathogenic/Likely pathogenic ★★ same condition
- GALK1 p.Cys170Ter Pathogenic/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/galk1-p-pro181 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown