Is GLA p.Pro259Ser (c.775C>T) pathogenic?

GLA p.Pro259Ser (c.775C>T) is classified Conflicting classifications of pathogenicity in GLA (ClinVar, Conflicting submitters, 2 submitters; last evaluated 2026-09-08). AlphaMissense: likely benign (0.3274); Absent from gnomAD v4.1; Associated with GLA-related disorder.

What condition is associated with GLA p.Pro259Ser (c.775C>T)?

GLA p.Pro259Ser (c.775C>T) is associated with GLA-related disorder, Fabry disease (ClinVar).

How common is GLA p.Pro259Ser (c.775C>T) in the general population?

GLA p.Pro259Ser (c.775C>T) is absent from gnomAD v4.1 (gnomAD).

What do computational predictors say about GLA p.Pro259Ser (c.775C>T)?

AlphaMissense predicts likely benign (score 0.3274) — an in-silico prediction, not a clinical call.

GLA p.Pro259Ser

c.775C>T · VCV4087507

Conflicting classifications of pathogenicity Conflicting submitters

Classification

Conflicting classifications of pathogenicity

ClinVar

Review

Conflicting submitters ★☆☆☆

ClinVar · 2 submitters

AlphaMissense

likely benign

0.3274 · ACMG-weighted

gnomAD v4.1

Absent

absent from gnomAD v4.1

Missense predictors

2/3 damaging

AlphaMissense, REVEL, SaProt

Conditions

GLA-related disorder

Computational evidence

Protein change
AlphaMissense	0.3274	likely benign
REVEL	0.853	moderately pathogenic-leaning
SaProt	LLR -11.86	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 9.9	GERP 3.4, phastCons 1
Regional constraint	o/e 0.66	unconstrained · MANE · 6,067 bp · p 6.6e-08 · regional, not allelic
Overall
CADD	27.1	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

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: GLA
Protein: p.Pro259Ser
Coding: c.775C>T
MANE Select: NM_000169
Type: single nucleotide variant
Location: chrX:101398811 (GRCh38)
Structure: AlphaFold pLDDT 94.45 · 31 PDB
Residue 259: a UniProt-annotated variant site (in fabryd); a UniProt-annotated variant site (in fabryd; decreased enzyme activity)

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

Disease context

GLA-related disorder

Also linked: Fabry disease

Similar variants

GLA p.Pro259Arg Pathogenic ★★ ⚠ same residue
GLA p.Pro259Leu Likely pathogenic ★ ⚠ same residue
GLA p.Pro259fs Pathogenic ★ 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-pro259ser (accessed [today's date]).

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