A New Class of Pathogenic Non-Coding Variants in GLA

TL;DR

This study identifies new non-coding genetic variants in the GLA gene linked to Fabry disease, using long-read sequencing to uncover previously undetected mutations.

Contribution

The study introduces a new class of pathogenic non-coding variants in GLA, detected through long-read sequencing in patients with unresolved Fabry disease.

Findings

Long-read sequencing identified a ~1.7 kb insertion in intron 4 of GLA in one patient, associated with new GLA transcripts.

A ~2.5 kb insertion in the 5′-untranslated region of GLA was found in another patient, leading to reduced normal transcript expression.

These findings suggest non-coding variants contribute to missing heritability in Fabry disease and highlight the value of LRS in diagnosis.

Abstract

Fabry disease (FD) exhibits a spectrum of clinical manifestations ranging from mild to severe, posing a diagnostic challenge, particularly in non-classic subtypes. Genetic testing remains a gold standard for a precise diagnosis of FD and is pivotal in genetic counseling. Although conventional approaches such as Sanger sequencing and short-read next-generation sequencing (NGS) have been successfully used to diagnose FD, they often fail to detect deep intronic variants, complex rearrangements, or large deletions or duplications. In contrast, long-read sequencing (LRS) enables comprehensive coverage of intronic and repetitive regions, facilitating precise identification of atypical variants missed by conventional methods. This case series reports two unrelated male patients with clinical, enzymatic, and pathological features consistent with FD, who tested negative for pathogenic variants in the alpha-galactosidase A (GLA) via Sanger sequencing and NGS. LRS identified novel non-coding variants in both patients. Patient 1 carried a ~1.7 kb insertion within intron 4, corresponding to part of a long interspersed nuclear element-1, while RNA sequencing revealed two new GLA transcripts. Patient 2 harbored a ~2.5 kb insertion within a SINE-VNTR-Alu retroposon element located in the 5′-untranslated region, with quantitative real-time PCR showing significantly reduced expression of normal GLA transcripts. These findings reveal non-coding variants that contribute to the missing heritability in FD, highlight this genomic region as a priority for future investigation, and demonstrate the potential utility of LRS in diagnostic workflows for unresolved FD cases.

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