Analysis of exome data for 4293 trios suggests GPI-anchor biogenesis defects are a rare cause of developmental disorders

Abstract

Over 150 different proteins attach to the plasma membrane using glycosylphosphatidylinositol (GPI) anchors. Mutations in 18 genes that encode components of GPI-anchor biogenesis result in a phenotypic spectrum that includes learning disability, epilepsy, microcephaly, congenital malformations and mild dysmorphic features. To determine the incidence of GPI-anchor defects, we analysed the exome data from 4293 parent–child trios recruited to the Deciphering Developmental Disorders (DDD) study. All probands recruited had a neurodevelopmental disorder. We searched for variants in 31 genes linked to GPI-anchor biogenesis and detected rare biallelic variants in PGAP3, PIGN, PIGT (n=2), PIGO and PIGL, providing a likely diagnosis for six families. In five families, the variants were in a compound heterozygous configuration while in a consanguineous Afghani kindred, a homozygous c.709G>C; p.(E237Q) variant in PIGT was identified within 10–12 Mb of autozygosity. Validation and segregation analysis was performed using Sanger sequencing. Across the six families, five siblings were available for testing and in all cases variants co-segregated consistent with them being causative. In four families, abnormal alkaline phosphatase results were observed in the direction expected. FACS analysis of knockout HEK293 cells that had been transfected with wild-type or mutant cDNA constructs demonstrated that the variants in PIGN, PIGT and PIGO all led to reduced activity. Splicing assays, performed using leucocyte RNA, showed that a c.336-2A>G variant in PIGL resulted in exon skipping and p.D113fs*2. Our results strengthen recently reported disease associations, suggest that defective GPI-anchor biogenesis may explain ~0.15% of individuals with developmental disorders and highlight the benefits of data sharing.

Clinical variability in inherited glycosylphosphatidylinositol deficiency disorders

“…The majority of these reported individuals are severely affected; ophthalmologic, brain anomalies, and skeletal findings were noted for the majority of these patients. A few also had anomalies in other organs, including nephrocalcinosis which appeared more frequently in this cohort compared to those with mutations in other IGD genes . Interestingly, patients with PIGT mutations had a decreased level of serum ALP.…”

“…A few also had anomalies in other organs, including nephrocalcinosis which appeared more frequently in this cohort compared to those with mutations in other IGD genes. [30][31][32][33][34][35] Interestingly, patients with PIGT mutations had a decreased level of serum ALP. This is striking as one of the diagnostic markers for inherited GPI-anchor deficiencies is usually an elevated ALP level.…”

A likely pathogenic variant putatively affecting splicing of PIGA identified in a multiple congenital anomalies hypotonia‐seizures syndrome 2 (MCAHS2) family pedigree via whole‐exome sequencing

“…Also, at least three splicing defective variants of PGAP1 (MIM 611655) have been reported in autosomal recessive mental retardation‐42 (MRT42, MIM 615802) and related syndromes with psychomotor retardation and brain atrophy as well as other features (Granzow et al., ; Kettwig et al., ; Novarino et al., ). More IGD cases with splicing defective variants include one variant of PGAP3 (MIM 611801) in hyperphosphatasia with mental retardation syndrome 4 (HPMRS4, MIM 615716) (Knaus et al., ), two variants of PIGL (MIM 605947) in Chime syndrome (MIM 280000) and related neurodevelopmental disorder (Ng et al., ; Pagnamenta et al., ), one variant of PIGO (MIM 614730) in HPMRS2 (MIM 614749) (Krawitz et al., ), and one variant of PIGG (MIM 616918) in autosomal recessive mental retardation‐53 (MRT53, MIM 616917) (Makrythanasis et al., ), etc . Therefore, it is not quite surprising that a putative splicing defective variant was uncovered in PIGA gene under a disease condition.…”

“…GPI anchoring is an evolutionarily conserved protein posttranslational modification mechanism, and at least 30 genes are involved in the GPI anchor biosynthesis process, including a family of phosphatidylinositol glycan anchor biosynthesis class ( PIG ) and post‐GPI attachment to proteins ( PGAP ) genes. Defects of GPI anchoring are detrimental, and at least 18 genes have been reported to be affected in the inherited GPI deficiency (IGD) diseases, which are associated with various neuronal and developmental abnormalities (Pagnamenta et al., ).…”

Complement- and inflammasome-mediated autoinflammation-paroxysmal nocturnal hemoglobinuria

“…In PIGT-defective cells, GPI is synthesized but is not transferred to precursor proteins, resulting in GPI-AP deficiency on the cell surface ( Figure 1A(c)). We showed recently that non-protein-linked, free GPI remaining in the ER of PIGT-defective Chinese hamster ovary (CHO) cells is transported to and displayed on the cell surface ( Figure 1A(c)) (10).…”