Biallelic loss-of-function variants of SLC12A9 cause lysosome dysfunction and a syndromic neurodevelopmental disorder

Purpose: Pathogenic variants of FIG4 generate enlarged lysosomes and neurological and developmental disorders. To identify additional genes regulating lysosomal volume, we carried out a genome-wide activation screen to detect suppression of enlarged lysosomes in FIG4-/- cells. Methods: The CRISPR-a gene activation screen utilized sgRNAs from the promoters of protein coding genes. Fluorescence-activated cell sorting separated cells with correction of the enlarged lysosomes from uncorrected cells. Patient variants of SLC12A9 were identified by exome or genome sequencing and studied by segregation analysis and clinical characterization. Results: Overexpression of SLC12A9, a solute co-transporter, corrected lysosomal swelling in FIG4-/- cells. SLC12A9 (NP_064631.2) co-localized with LAMP2 at the lysosome membrane. Biallelic variants of SLC12A9 were identified in three unrelated probands with neurodevelopmental disorders. Common features included intellectual disability, skeletal and brain structural abnormalities, congenital heart defects and hypopigmented hair. Patient 1 was homozygous for nonsense variant p.(Arg615*); patient 2 was compound heterozygous for p.(Ser109Lysfs*20) and a large deletion, and proband 3 was compound heterozygous for p.(Glu290Glyfs*36) and p.(Asn552Lys). Fibroblasts from proband 1 contained enlarged lysosomes that were corrected by wildtype SLC12A9 cDNA. Patient variant p.(Asn552Lys) failed to correct the lysosomal defect. Conclusions: Impaired function of SLC12A9 results in enlarged lysosomes and a recessive disorder with a recognizable neurodevelopmental phenotype.