Is GALT p.Phe93= (c.279C>T) pathogenic?

GALT p.Phe93= (c.279C>T) is classified Likely benign in GALT (ClinVar, Single submitter, 1 submitter; last evaluated 2021-05-07). Absent from gnomAD v4.1; Associated with classic galactosemia.

What condition is associated with GALT p.Phe93= (c.279C>T)?

GALT p.Phe93= (c.279C>T) is associated with classic galactosemia (ClinVar).

How common is GALT p.Phe93= (c.279C>T) in the general population?

GALT p.Phe93= (c.279C>T) 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.

GALT p.Phe93=

c.279C>T · rs1307903821 · VCV1557504

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

classic galactosemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation/SpliceAI carries the signal.
Splicing
SpliceAI	Δ0.28	donor loss, 49 bp away · masked 0 · deltas
Pangolin	Δ0.32	loss · gain 0.02 · agrees with SpliceAI · independent
Constraint at this position
Conservation	phyloP 0.34	GERP 0.64, phastCons 0.3
Overall
CADD	8.077	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.Phe93=
Coding: c.279C>T
MANE Select: NM_000155
dbSNP: rs1307903821
Type: single nucleotide variant
Location: chr9:34647518 (GRCh38)
Gene constraint: LOEUF 0.935 · pLI <0.01 · ClinGen HI gene assoc. with recessive phenotype (gnomAD)
Structure: AlphaFold pLDDT 92.08 · 2 PDB
Residue 93: a β-strand

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.Phe93Ser Uncertain significance ★ ⚠ same residue
GALT p.Phe93Ile Uncertain significance ★ ⚠ 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

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-phe93 (accessed [today's date]).

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