# A novel de novo ATP2B1 variant causes autosomal dominant intellectual developmental disorder 66 by disrupting calcium homeostasis via impaired membrane trafficking

## TL;DR

A new ATP2B1 gene variant causes a developmental disorder by disrupting calcium balance in cells, leading to severe neurological symptoms in an infant.

## Contribution

A novel de novo ATP2B1 variant is identified and functionally characterized as pathogenic in MRD66.

## Key findings

- The p.Thr714Pro ATP2B1 variant causes cytoplasmic mislocalization of the PMCA1 protein.
- The mutant variant leads to a 2.07-fold increase in basal intracellular calcium levels.
- This expands the known ATP2B1 variant spectrum in MRD66 and highlights calcium dyshomeostasis as a key mechanism.

## Abstract

Heterozygous pathogenic variants in ATP2B1 (encoding PMCA1) cause autosomal dominant intellectual developmental disorder 66 (MRD66; OMIM #619910). To date, only 12 pathogenic de novo ATP2B1 variants have been reported in MRD66. This study aimed to identify the genetic etiology in a Chinese infant with a neurodevelopmental disorder characterized by early-onset seizures and global developmental delay (GDD) and functionally characterize a novel ATP2B1 missense variant. Trio-based whole-exome sequencing revealed a heterozygous de novo ATP2B1 variant (c.2140A>C, p.Thr714Pro) in the proband. The proband presented with infantile spasms, GDD (Gesell Developmental Quotient: 65–74), and severe growth restriction (height/weight <−2 SD). To investigate the variant’s pathogenicity, the wild-type (WT) and mutant ATP2B1 constructs, N-terminally tagged with mScarlet, were transfected into HEK293T cells. Confocal imaging demonstrated profound cytoplasmic mislocalization of the p.Thr714Pro mutant protein, contrasting sharply with the characteristic plasma membrane localization of WT ATP2B1. Measurement of intracellular Ca2+ levels using Fluo-4 AM showed a significant 2.07-fold increase in basal Ca2+ levels in cells expressing the mutant compared to WT. This finding expands the spectrum of ATP2B1 variants associated with MRD66 and confirms calcium dyshomeostasis as the core pathomechanism. This case of MRD66 demonstrates a very early onset of seizures, consistent with the recognized phenotypic variability and the critical role of PMCA1 in early neurodevelopment.