Is GLA p.Cys382Ter (c.1146C>A) pathogenic?

GLA p.Cys382Ter (c.1146C>A) is classified Pathogenic in GLA (ClinVar, Single submitter, 1 submitter; last evaluated 2026-09-08). Absent from gnomAD v4.1; Associated with Fabry disease.

What condition is associated with GLA p.Cys382Ter (c.1146C>A)?

GLA p.Cys382Ter (c.1146C>A) is associated with Fabry disease (ClinVar).

How common is GLA p.Cys382Ter (c.1146C>A) in the general population?

GLA p.Cys382Ter (c.1146C>A) is absent from gnomAD v4.1 (gnomAD).

How is Fabry disease inherited?

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

GLA p.Cys382Ter

c.1146C>A · VCV4087198

Pathogenic Single submitter

Classification

Pathogenic

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

Consequence

nonsense (stop-gain)

predicted LoF

gnomAD v4.1

Absent

absent from gnomAD v4.1

Conditions

Fabry disease

Computational evidence

Protein change
Missense predictors do not apply to this variant type; conservation carries the signal.
Consequence	nonsense (stop-gain)	predicted loss-of-function in a haploinsufficient gene (ClinGen)
NMD	escapes	premature termination codon in the last exon (7 of 7) — the truncated protein is likely expressed. PVS1 input, not an applied code
Splicing
SpliceAI	—	not assessed · no allele here is in the release
Constraint at this position
Conservation	phyloP 2.6	GERP 0.33, phastCons 1
Overall
CADD	35.0	PHRED · no single calibrated threshold — expert panels disagree

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

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.Cys382Ter
Coding: c.1146C>A
MANE Select: NM_000169
Type: single nucleotide variant
Location: chrX:101397953 (GRCh38)
Structure: AlphaFold pLDDT 94.45 · 31 PDB
Residue 382: a disulfide bond; a β-strand

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.Cys382Ser Likely pathogenic ★ same residue
GLA p.Cys382Trp Pathogenic ★ same residue
GLA p.Cys382Tyr Pathogenic ★ same residue
GLA p.Cys382_Phe383insAsnProAlaCys Likely pathogenic ★ same residue
GLA p.Cys382fs 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

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-cys382ter (accessed [today's date]).

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