Is GALT p.Pro87Arg (c.260C>G) pathogenic?

GALT p.Pro87Arg (c.260C>G) is classified Pathogenic in GALT (ClinVar, Multiple submitters, 2 submitters; last evaluated 2026-02-09). AlphaMissense: likely benign (0.1987); Absent from gnomAD v4.1; Associated with classic galactosemia.

What condition is associated with GALT p.Pro87Arg (c.260C>G)?

GALT p.Pro87Arg (c.260C>G) is associated with classic galactosemia (ClinVar).

How common is GALT p.Pro87Arg (c.260C>G) in the general population?

GALT p.Pro87Arg (c.260C>G) is absent from gnomAD v4.1 (gnomAD).

How is Classic galactosemia inherited?

Typically Autosomal recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about GALT p.Pro87Arg (c.260C>G)?

AlphaMissense predicts likely benign (score 0.1987) — an in-silico prediction, not a clinical call.

GALT p.Pro87Arg

c.260C>G · rs2492863998 · VCV2732172

Pathogenic Multiple submitters

Classification

Pathogenic

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.1987 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

classic galactosemia

Computational evidence

Protein change
AlphaMissense	0.1987	likely benign ⚠ discordant with ClinVar
REVEL	0.799	moderately pathogenic-leaning
SaProt	LLR -11.59	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	Δ0.22	acceptor gain · deltas
Pangolin	Δ0.24	gain · loss 0.00 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 7.7	GERP 1.7, phastCons 1
Regional constraint	o/e 0.82	unconstrained · MANE · 3,741 bp · p 6.8e-05 · regional, not allelic
Overall
CADD	27.6	PHRED · no single calibrated threshold — expert panels disagree

AlphaMissense carries the ACMG weight for missense; REVEL and SaProt are independent agreement signals.

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.Pro87Arg
Coding: c.260C>G
MANE Select: NM_000155
dbSNP: rs2492863998
Type: single nucleotide variant
Location: chr9:34647499 (GRCh38)
Gene constraint: LOEUF 0.935 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 92.08 · 2 PDB

Full GALT gene report on Sugi Atlas → Gene function, pathways, protein structure, interactions & more

Disease context

classic galactosemia — disease report on Sugi Atlas → Associated genes, phenotypes, clinical trials & treatments

For Classic galactosemia (Orphanet):

Inheritance: Autosomal recessive
Onset: Infancy, Neonatal
Prevalence: 1-9 / 100 000 (Europe)

Similar variants

GALT p.Pro87Leu Likely pathogenic ★ ⚠ same residue
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

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-pro87arg (accessed [today's date]).

Preprint & method: sugi.bio/variant/method Machine-readable: this page as Markdown