Is GALT p.Phe290fs (c.870del) pathogenic?

GALT p.Phe290fs (c.870del) is classified Likely pathogenic in GALT (ClinVar, Single submitter, 1 submitter; last evaluated 2025-04-25). Associated with galactosemia.

What condition is associated with GALT p.Phe290fs (c.870del)?

GALT p.Phe290fs (c.870del) is associated with galactosemia (ClinVar).

GALT p.Phe290fs

c.870del · VCV4068277

Likely pathogenic Single submitter

Classification

Likely pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

frameshift

predicted LoF

gnomAD v4.1

Rare

Conditions

galactosemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	frameshift	predicted loss-of-function
NMD	predicted	premature termination codon in exon 9 of 11
Splicing
SpliceAI	—	not assessed · substitutions only
Constraint at this position
Conservation	phyloP -4.3	GERP -3.6

Predicted loss-of-function is descriptive, not an applied PVS1 code.

Variant & gene context

Gene: GALT
Protein: p.Phe290fs
Coding: c.870del
MANE Select: NM_000155
Type: Deletion
Location: chr9:34649045 (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

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

Similar variants

GALT p.Arg272fs Pathogenic/Likely pathogenic ★★ same condition
GALT p.Arg67fs Pathogenic ★★ same condition
GALT p.Asn97del Pathogenic/Likely pathogenic ★★ same condition
GALT p.Asp7fs Pathogenic ★★ same condition
GALT p.Gln200fs Pathogenic/Likely pathogenic ★★ same condition
GALT p.His184fs Pathogenic/Likely pathogenic ★★ same condition
GALT p.His186fs Likely pathogenic ★★ same condition
GALT p.Leu217_Leu218insTer 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/galt-p-phe290fs (accessed [today's date]).

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