Is GALT p.Ser2= (c.6G>A) pathogenic?

GALT p.Ser2= (c.6G>A) is classified Likely benign in GALT (ClinVar, Single submitter, 1 submitter; last evaluated 2024-02-07). Ultra-rare (popmax 0.0267%, eas); Associated with classic galactosemia.

What condition is associated with GALT p.Ser2= (c.6G>A)?

GALT p.Ser2= (c.6G>A) is associated with classic galactosemia (ClinVar).

How common is GALT p.Ser2= (c.6G>A) in the general population?

GALT p.Ser2= (c.6G>A) is ultra-rare (popmax 0.0267%, eas) (gnomAD).

How is Classic galactosemia inherited?

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

GALT p.Ser2=

c.6G>A · rs1410764100 · VCV1145631

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Rare

ultra-rare (popmax 0.0267%, eas)

Conditions

classic galactosemia

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 0.49	GERP 2, phastCons 0.001
Overall
CADD	11.58	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

Grpmax group 0.0267% East Asian · 12/44,870 alleles

Filtering AF 0.0154% ClinGen BA1/BS1 input FAF95, joint · FAF99 0.0121%

Overall 0.000806% 13/1,613,776 alleles · ultra-rare exomes 12/1,461,450 · genomes 1/152,326 · joint denominator

Ancestry group	Frequency	1 in
East Asiangrpmax	0.0267%	3,739
Remaining individualsnot grpmax-eligible	0.0016%	62,496

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.Ser2=
Coding: c.6G>A
MANE Select: NM_000155
dbSNP: rs1410764100
Type: single nucleotide variant
Location: chr9:34646710 (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 2: the 'disordered' region

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 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-ser2 (accessed [today's date]).

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