Is GLA p.Ser126Ile (c.377G>T) pathogenic?

GLA p.Ser126Ile (c.377G>T) is classified Uncertain significance in GLA (ClinVar, Single submitter, 1 submitter; last evaluated 2023-11-02). AlphaMissense: likely benign (0.2486); Very rare (popmax 0.00176%, sas); Associated with Fabry disease.

What condition is associated with GLA p.Ser126Ile (c.377G>T)?

GLA p.Ser126Ile (c.377G>T) is associated with Fabry disease (ClinVar).

How common is GLA p.Ser126Ile (c.377G>T) in the general population?

GLA p.Ser126Ile (c.377G>T) is very rare (popmax 0.00176%, sas) (gnomAD).

How is Fabry disease inherited?

Typically X-linked dominant, X-linked recessive (Orphanet). A genetic counselor can assess individual risk for a family.

What do computational predictors say about GLA p.Ser126Ile (c.377G>T)?

AlphaMissense predicts likely benign (score 0.2486) — an in-silico prediction, not a clinical call.

GLA p.Ser126Ile

c.377G>T · rs782336447 · VCV3074286

Uncertain significance Single submitter

Classification

Uncertain significance

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

AlphaMissense

likely benign

0.2486 · ACMG-weighted

gnomAD v4.1

Rare

very rare (popmax 0.00176%, sas)

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

Fabry disease

Computational evidence

Protein change
AlphaMissense	0.2486	likely benign
REVEL	0.9	moderately pathogenic-leaning
SaProt	LLR -12.99	damaging
⇒ REVEL and SaProt call this damaging; AlphaMissense does not.
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.3	GERP 2.5, phastCons 1
Regional constraint	o/e 0.66	unconstrained · MANE · 6,067 bp · p 6.6e-08 · regional, not allelic
Overall
CADD	23.9	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

Grpmax group 0.00176% South Asian · 1/56,919 alleles

Overall 8.27e-05% 1/1,208,533 alleles · very rare exomes 1/1,094,745 · genomes 0/113,788 · joint denominator

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: GLA
Protein: p.Ser126Ile
Coding: c.377G>T
MANE Select: NM_000169
dbSNP: rs782336447
Type: single nucleotide variant
Location: chrX:101401802 (GRCh38)
Structure: AlphaFold pLDDT 94.45 · 31 PDB
Residue 126: an α-helix

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

Disease context

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

For Fabry disease (Orphanet):

Inheritance: X-linked dominant, X-linked recessive
Onset: Adolescent, Adult, Childhood
Prevalence: 1-9 / 1 000 000 (Worldwide)

Similar variants

GLA p.Ser126Cys Likely pathogenic ★ ⚠ same residue
GLA p.Ser126= Likely benign ★ same residue
GLA p.Ser126Arg Uncertain significance ⚠ same residue
GLA c.1000-10G>A Likely pathogenic ★★ same condition
GLA c.1000-1G>A Pathogenic ★★ same condition
GLA c.1000-1G>C Pathogenic ★★ same condition
GLA c.1023A>C Pathogenic/Likely pathogenic ★★ ⚠ same condition
GLA c.194+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/gla-p-ser126ile (accessed [today's date]).

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