Is GALT p.Ser293= (c.879C>T) pathogenic?

GALT p.Ser293= (c.879C>T) is classified Benign/Likely benign in GALT (ClinVar, Multiple submitters, 7 submitters; last evaluated 2026-01-28). Low-frequency (popmax 1.34%, afr); Associated with classic galactosemia.

What condition is associated with GALT p.Ser293= (c.879C>T)?

GALT p.Ser293= (c.879C>T) is associated with classic galactosemia, galactosemia (ClinVar).

How common is GALT p.Ser293= (c.879C>T) in the general population?

GALT p.Ser293= (c.879C>T) is low-frequency (popmax 1.34%, afr) (gnomAD).

How is Classic galactosemia inherited?

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

GALT p.Ser293=

c.879C>T · rs115527942 · VCV38553

Benign/Likely benign Multiple submitters

Classification

Benign/Likely benign

ClinVar

Review

Multiple submitters ★★☆☆

ClinVar · 7 submitters

gnomAD v4.1

Rare

low-frequency (popmax 1.34%, afr)

Conditions

classic galactosemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	<0.2	no splice effect predicted · four deltas, not one · how we know
Constraint at this position
Conservation	phyloP 0.11	GERP -1.6, phastCons 0.93
Overall
CADD	6.025	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 1.34% African / African-American · 1,006/75,024 alleles

Filtering AF 1.27% ClinGen BA1/BS1 input FAF95, joint · FAF99 1.24%

Overall 0.0745% 1,203/1,614,128 alleles · low-frequency exomes 628/1,461,860 · genomes 575/152,268 · joint denominator

Ancestry group	Frequency	1 in
African / African-Americangrpmax	1.34%	75
Remaining individualsnot grpmax-eligible	0.139%	719
Admixed American	0.11%	909
Middle Eastern	0.033%	3,031
South Asian	0.00549%	18,216
European (non-Finnish)	0.00305%	32,778
East Asian	0.00223%	44,886

Rarity supports pathogenicity (ACMG PM2); frequency above a disease-specific BA1/BS1 threshold argues against it. A variant frequent in one ancestry group can be near-absent in others, so a single global figure can mislead.

Variant & gene context

Gene: GALT
Protein: p.Ser293=
Coding: c.879C>T
MANE Select: NM_000155
dbSNP: rs115527942
Type: single nucleotide variant
Location: chr9:34649056 (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

Also 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-ser293 (accessed [today's date]).

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