GALT p.Pro109=
c.327A>G · VCV4695073
Conflicting classifications of pathogenicity
Conflicting submitters
Classification
Conflicting classifications of pathogenicity
ClinVar
Review
Conflicting submitters ★☆☆☆
ClinVar · 2 submitters
gnomAD v4.1
Absent
absent from gnomAD v4.1
Conditions
2
classic galactosemia
Computational evidence
| Protein change | ||
| Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal. | ||
| Splicing | ||
| SpliceAI | Δ0.71 | donor loss · deltas |
|---|---|---|
| Pangolin | Δ0.57 | loss · gain 0.00 · agrees with SpliceAI · independent |
| Constraint at this position | ||
| Conservation | phyloP 5 | GERP 0.69, phastCons 1 |
| Overall | ||
| CADD | 19.26 | 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
- GALT
- Protein
- p.Pro109=
- Coding
- c.327A>G
- MANE Select
- NM_000155
- Type
- single nucleotide variant
- Location
- chr9:34647566 (GRCh38)
- Gene constraint
- LOEUF 0.935 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
- Structure
- AlphaFold pLDDT 92.08 · 2 PDB
Disease context
classic galactosemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatmentsAlso linked: galactosemia
For Classic galactosemia (Orphanet):
- Inheritance
- Autosomal recessive
- Onset
- Infancy, Neonatal
- Prevalence
- 1-9 / 100 000 (Europe)
Similar variants
- GALT c.1060-1G>A Pathogenic/Likely pathogenic ★★ same condition
- GALT c.252+1G>A Pathogenic ★★ same condition
- GALT c.253-1G>A Pathogenic/Likely pathogenic ★★ same condition
- GALT c.253-2A>G Pathogenic ★★ same condition
- GALT c.328+2T>G Pathogenic/Likely pathogenic ★★ same condition
- GALT c.329-2A>C Pathogenic ★★ same condition
- GALT c.377+1G>A Pathogenic ★★ same condition
- GALT c.377+1G>T 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/galt-p-pro109 (accessed [today's date]).
Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown