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Systematic Literature Review of GLA Variants Uncovers Additional Fabry Disease-Causing Variants

Clinical Genetics and Therapeutics
  • Primary Categories:
    • Clinical Genetics
  • Secondary Categories:
    • Clinical Genetics
Introduction:
Fabry disease is a rare X-linked metabolic disorder resulting from deficiency of the lysosomal enzyme alpha-galactosidase A (GLA) leading to accumulation of glycolipids and cellular dysfunction in numerous tissues. If left untreated, lethal cardiac disease, stroke, and renal failure may result. A complete understanding of disease-associated GLA variants can help with timely and accurate identification of affected individuals. Moreover, comprehensive cataloging and characterization of such variants can provide valuable context for a better mechanistic understanding of disease pathobiology.

Methods:
We developed a comprehensive variant database from a systematic literature review using the Mastermind Genomic Search Engine and ClinVar followed by detailed manual evidence curation according to standard ACMG variant interpretation guidelines. In total, 1634 references were curated with detailed annotation and documentation of clinical and functional evidence from the primary literature as well as assessment of relevant information for allele frequencies from population databases and in silico predictions of pathogenicity. For the assessment of functional consequences, we developed a novel approach for establishing GLA enzyme activity threshold to assess results for both in vitro and in vivo assays.

Results:


Our investigation uncovered a total of 1677 unique GLA variants including 1093 (65%) missense, 206 (12%) frameshift, 111 (6.6%) nonsense, 55 (3.3%) deletions/insertions, and 45 (2.6%) splice variants. 

Of the 1677 total variants, 511 variants (30.5%) were both cited in literature and also found in ClinVar. Among these 511 variants, comparison of variant interpretation results revealed high concordance with 385 out of 511 variants (75.3%) showing consistent classifications. These 385 variants included 306 pathogenic variants, 69 VUS, and 10 benign variants. An additional 126 variants out of 511 total (24.7%) had discordant classifications. These 126 variants included 49 variants deemed pathogenic by expert review but listed as VUS or conflicting in ClinVar; 73 variants for which expert review failed to demonstrate conclusive evidence for a definitive call; and 4 variants deemed benign by expert review.

Importantly, of the 1677 total variants, 802 (47.8%) were found only through this systematic literature review and were not previously aggregated in public databases like ClinVar. Among these 802 variants, 512 (63.8%) were associated with clinical cases and/or functional studies and were deemed pathogenic according to ACMG guidelines. An additional 278 variants were associated with clinical cases and/or functional studies but lacked sufficient evidence for a definitive call (34.7%; VUS). The remaining 12 variants (1.5%) were benign.

Finally, of the 1677 total variants, 364 (21.7%) were represented in ClinVar but lacked any citing clinical or functional evidence for detailed assessment. 

This database of GLA variants and clinical and functional information was used to establish cutoffs for functional assays of GLA enzyme activity systematically. For a total of 305 variants, results from enzyme studies on patient-derived samples were available from citing literature. Functional studies conducted on known pathogenic variants associated with Fabry disease were used as positive controls to establish enzyme activity threshold values of <5.5% for in vitro and <3.0% for in vivo studies. Using these cutoffs to define thresholds for deleterious functional consequences to protein function, 71 out of 126 VUS variants associated with Fabry patient cases and with published functional studies were promoted from VUS to pathogenic classification.

Conclusion:
This study resulted in a uniquely comprehensive database of disease-causing GLA variants and a complete characterization of the nature of their role in GLA enzyme disruption leading to clinical disease. Alongside clinically reported GLA variants provided in ClinVar, it will provide a useful resource to the medical community diagnosing and treating Fabry patients. 

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