Expanding the <em>CASR</em> variant landscape: integrated <em>in silico</em> and structural triage of previously unreported germline variants — ASN Events
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  2. CaSR-5 Session-4: Oral Posters
  3. Expanding the CASR variant landscape: integrated in silico and structural triage of previously unreported germline variants

Expanding the CASR variant landscape: integrated in silico and structural triage of previously unreported germline variants (#172)

Sarah C Brennan 1 2 , Catherine Luxford 3 , Roderick J Clifton-Bligh 1 2 3
  1. Department of Diabetes & Endocrinology,, Royal North Shore Hospital, Sydney, NSW, Australia
  2. Faculty of Medicine & Health, University of Sydney, Camperdown, NSW, Australia
  3. Cancer Genetics Lab, Kolling Institute, St Leonards, NSW, Australia

The calcium-sensing receptor (CaSR) governs systemic calcium homeostasis, and germline CASR variants cause inherited disorders including familial hypocalciuric hypercalcaemia (FHH1), autosomal dominant hypocalcaemia (ADH1) and neonatal severe hyperparathyroidism (NSHPT)(1).

Existing repositories – ClinVar and the dedicated CaSRdb(2) – capture only part of the mutational landscape, leaving many clinically encountered variants uncharacterised. Here we characterise 124 germline CASR variants from a single diagnostic cohort, focusing on 29 absent from both databases.

Variants were reclassified under ACMG/AMP criteria, scored with in silico predictors (REVEL, AlphaMissense), and mapped onto experimentally derived and AlphaFold CaSR structures in PyMOL(3, 4). Variants spanned the full receptor but distributed by phenotype: FHH1 variants predominated in the extracellular Venus flytrap domain (VFT), with additional cysteine-rich and transmembrane contributions, whereas ADH1 variants - exclusively missense - included a seven-transmembrane subset consistent with gain-of-function signalling.

The 29 novel variants form the principal focus. Mostly missense (22/29) but including nonsense, frameshift and start-loss changes, 13/29 already met likely-pathogenic or pathogenic criteria despite being absent from databases, and in silico tools supported their pathogenicity (median REVEL 0.73, AlphaMissense 0.85; 18/22 missense predicted pathogenic). Structurally, novel variants concentrated in the VFT (approximately 17/29), frequently at dimer-interface, agonist-contact and calcium-coordinating residues; a cysteine-rich cluster at Gly557 coordinates the inter-subunit LB2–CRD calcium site, and one novel variant (c.1670_1671delinsAA) is a previously unreported nucleotide change that recreates the functionally validated pathogenic substitution p.Gly557Glu. Transmembrane novel variants were more often mechanistically unresolved. All mechanistic inferences remain unconfirmed pending functional testing.

Taken together, these novel variants substantially expand the described CASR landscape, show phenotype-linked structural clustering, and demonstrate that integrated in-silico and structural triage can prioritise previously unreported variants for functional validation.

  1. Hannan FM, Kallay E, Chang W, Brandi ML, Thakker RV. The calcium-sensing receptor in physiology and in calcitropic and noncalcitropic diseases. Nat Rev Endocrinol. 2018;15(1):33-51.
  2. Charoenngam N, Wattanachayakul P, Mannstadt M. CASRdb: A Publicly Accessible Comprehensive Database for Disease-Associated Calcium-Sensing Receptor Variants. J Clin Endocrinol Metab. 2025;110(2):297-302.
  3. Chen X, Wang L, Cui Q, Ding Z, Han L, Kou Y, et al. Structural insights into the activation of human calcium-sensing receptor. Elife. 2021;10.
  4. Geng Y, Mosyak L, Kurinov I, Zuo H, Sturchler E, Cheng TC, et al. Structural mechanism of ligand activation in human calcium-sensing receptor. Elife. 2016;5.