Is GLA p.Ala190= (c.570C>A) pathogenic?

GLA p.Ala190= (c.570C>A) is classified Likely benign in GLA (ClinVar, Single submitter, 1 submitter; last evaluated 2023-02-09). No allele count reported in gnomAD v4.1 (AN 1,169,811); Associated with Fabry disease.

What condition is associated with GLA p.Ala190= (c.570C>A)?

GLA p.Ala190= (c.570C>A) is associated with Fabry disease (ClinVar).

How common is GLA p.Ala190= (c.570C>A) in the general population?

GLA p.Ala190= (c.570C>A) is no allele count reported in gnomAD v4.1 (AN 1,169,811) (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.Ala190=

c.570C>A · rs2520887338 · VCV2835796

Likely benign Single submitter

Classification

Likely benign

ClinVar

Review

Single submitter ★☆☆☆

ClinVar · 1 submitter

gnomAD v4.1

Not reported

no allele count reported in gnomAD v4.1 (AN 1,169,811)

Conditions

Fabry disease

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 2.5	GERP -1.2, phastCons 1
Overall
CADD	8.128	PHRED · no single calibrated threshold — expert panels disagree

Population frequency

gnomAD v4.1 · exomes + genomes

No allele count reported in gnomAD v4.1 (AN 1,169,811). This is missing data, not an absence: the variant may or may not be present in gnomAD. Rarity (ACMG PM2) and BA1/BS1 cannot be assessed for it.

Variant & gene context

Gene: GLA
Protein: p.Ala190=
Coding: c.570C>A
MANE Select: NM_000169
dbSNP: rs2520887338
Type: single nucleotide variant
Location: chrX:101400735 (GRCh38)
Structure: AlphaFold pLDDT 94.45 · 31 PDB
Residue 190: 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.Ala190Val Uncertain significance ★★ ⚠ same residue
GLA p.Ala190Gly Uncertain significance ★ ⚠ same residue
GLA p.Ala190fs 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-ala190 (accessed [today's date]).

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