Performance of the ACMG‐AMP criteria in a large familial renal glucosuria cohort with identified SLC5A2 sequence variants

• Published in: Clinical genetics Vol. 104; no. 5; pp. 582 - 586
• Main Authors: Barata, Rui, Fila, Marc, Dalla‐Vale, Fabienne, Bogarin, Roberto, Nunes, Paula, Ramalho, José, Rueff, José, Calado, Joaquim
• Format: Journal Article
• Language: English
• Published: Oxford, UK Blackwell Publishing Ltd 01-11-2023; Wiley
• Subjects: Alleles; glycosuria; Human health and pathology; Life Sciences; Na+/glucose cotransporter; Pathogenicity; proximal tubule; renal; sodium glucose transporter 2; Urology and Nephrology; renal; sodium glucose transporter 2; proximal tubule; glycosuria
• ISSN: 0009-9163; 1399-0004
• DOI: 10.1111/cge.14395

Familial Renal Glucosuria (FRG) is a co‐dominantly inherited trait characterized by orthoglycaemic glucosuria. From 2003 to 2015 we have reported several cohorts validating SLC5A2 (16p11.2), encoding SGLT2 (Na+/glucose cotransporter family member 2), as the gene responsible for FRG. The aim of this work was to validate the variants identified in our extended FRG cohort of published, as well more recent unreported cases, according to the ACMG‐AMP 2015 criteria. Forty‐six variants were evaluated, including 16 novel alleles first described in this study. All are rare, ultra‐rare or absent from population databases and most are missense changes. According to the ACMG‐AMP standards, only 74% of the variants were classified as P/LP. The lack of descriptions of unrelated patients with similar variants or failing to test additional affected family members, averted a conclusion for pathogenicity in the alleles that scored VUS, highlighting the importance of both family testing and variant reporting. Finally, the cryo‐EM structure of the hSGLT2–MAP17 complex in the empagliflozin‐bound state improved the ACMG‐AMP pathogenicity score by identifying critical/functional protein domains.
The gene SLC5A2 (16p11.2) encodes the Na+/glucose cotransporter family member 2 (SGLT2) and is responsible for Familial Renal Glucosuria (FRG). The aim of this work was to validate the SLC5A2 variants identified in our FRG extended cohort according to the ACMG‐AMP 2015 criteria.