A novel variant in GATM causes idiopathic renal Fanconi syndrome and predicts progression to end‐stage kidney disease

Abstract

Renal Fanconi syndrome (RFS) is a generalised disorder of the proximal convoluted tubule. Many genes have been associated with RFS including those that cause systemic disorders such as cystinosis, as well as isolated RFS. We discuss the case of a 10‐year‐old female who presented with leg pain and raised creatinine on a screening blood test. Her mother has RFS and required a kidney transplant in her thirties. Further investigations confirmed RFS in the daughter. Exome sequencing was performed on the affected mother, child, and unaffected father. We identified a novel variant in GATM; c.965G>C p.(Arg322Pro) segregating dominantly in the mother and daughter. We validated our finding with molecular dynamics simulations and demonstrated a dynamic signature that differentiates our variant and two previously identified pathogenic variants in GATM from wildtype. Genetic testing has uncovered a novel pathogenic variant that predicts progression to end stage kidney failure and has important implications for family planning and cascade testing. We recommend that GATM is screened for in children presenting with RFS, in addition to adults, particularly with kidney failure, who may have had previous negative gene testing.

Review of childhood genetic nephrolithiasis and nephrocalcinosis

“…GATM encodes for glycine amidinotransferase, which is expressed in the PT mitochondria ( Reichold et al, 2018 ). An inactivating variant in GATM leads to Fanconi renotubular syndrome 1 (OMIM phenotype number 134600 ), an AD condition associated with decreased solute and water reabsorption in the PT with polydipsia, polyuria, phosphaturia, glycosuria, aminoaciduria, uricosuria, hypophosphatemic rickets, metabolic acidosis, progressive kidney insufficiency, and NC in 1 definitive case, and at least 1 case of AD Fanconi syndrome suspected to be secondary a variant in GATM , although genetic testing was not performed ( Wen et al, 1989 ; Reichold et al, 2018 ; Seaby et al, 2023 ).…”