Biallelic variants in Plexin B2 (PLXNB2) cause amelogenesis imperfecta, hearing loss and intellectual disability

Abstract

Background: Plexins are large transmembrane receptors for the semaphorin family of signalling proteins. Semaphorin-plexin signalling controls cellular interactions that are critical during development as well as in adult life stages. Nine plexin genes have been identified in humans, but despite the apparent importance of plexins in development, only biallelic PLXND1 and PLXNA1 variants have so far been associated with Mendelian genetic disease.

Methods: Eight individuals from six families presented with a recessively inherited variable clinical condition, with core features of amelogenesis imperfecta (AI) and sensorineural hearing loss (SNHL), with variable intellectual disability. Probands were investigated by exome or genome sequencing. Common variants and those unlikely to affect function were excluded. Variants consistent with autosomal recessive inheritance were prioritised. Variant segregation analysis was performed by Sanger sequencing. RNA expression analysis was conducted in C57Bl6 mice.

Results: Rare biallelic pathogenic variants in plexin B2 (PLXNB2), a large transmembrane semaphorin receptor protein, were found to segregate with disease in all six families. The variants identified include missense, nonsense, splicing changes and a multiexon deletion. Plxnb2 expression was detected in differentiating ameloblasts.

Conclusion: We identify rare biallelic pathogenic variants in PLXNB2 as a cause of a new autosomal recessive, phenotypically diverse syndrome with AI and SNHL as core features. Intellectual disability, ocular disease, ear developmental abnormalities and lymphoedema were also present in multiple cases. The variable syndromic human phenotype overlaps with that seen in Plxnb2 knockout mice, and, together with the rarity of human PLXNB2 variants, may explain why pathogenic variants in PLXNB2 have not been reported previously.

Keywords: Dentistry; Genetic Research; Genetics; Genetics, Medical.

Figure 1

Pedigrees, Sanger sequencing and schematic diagram of the PLXNB2 protein. (A) DNA was available for all labelled individuals on each pedigree. Arrows indicate the individuals whose DNA was exome or genome sequenced. Affected status is as reported by the families for individuals for which DNA was not available. Sanger sequencing traces showing the segregation of each variant with disease in each family, except for Family 5, for which this is shown in online supplemental figure 9. The schematic diagram shows (B) the PLXNB2 transcript (ENST00000359337.9, NM_012401.4; 6409 bp) and (C) the PLXNB2 protein (ENSP00000352288.4, NP_036533.2; 1838 amino acids), with the positions marked for the pathogenic variants identified in this study. IPT, immunoglobulin, plexin and transcription factor; PSI, plexin, semaphorin and integrin; TIG, transcription factor immunoglobin.

Figure 2

Clinical images that are illustrative of the shared and variable clinical features for affected individuals. (A) The anterior clinical photograph showing primary teeth, the posterior teeth have changes consistent with loss of enamel (arrowheads) due to fracturing, whereas the enamel of the anterior teeth is developmentally thin and optically abnormal (Family 3 II:1). (B) Panoramic radiograph of the adult permanent dentition illustrates that the enamel is more radiodense than the supporting dentine, but with a variably reduced enamel volume and irregular occlusal cusp morphology (arrowhead) consistent with amelogenesis imperfecta (AI) characterised by enamel that is hypomineralised with variable hypoplasia (Family 4 II:2). (C) Sensorineural hearing loss (SNHL) was typical, with provision of hearing aids in childhood (Family 4 II:2). Blind-end skin tracts involving the skin of the ears or adjacent tissues (arrowhead) were observed in at least 3/6 families. (D) Lower limb lymphoedema was observed in two families (Families 4 and 5, with Family 4 illustrated). (E) Fundus autofluorescence images (Family 3 II:1) illustrate a developmental macular abnormality with pale fundus and attenuated blood vessels. The individual also has high myopia, nystagmus and microcornea.

Figure 3

Analysis of mouse Plxnb2 transcript distribution by in situ hybridisation. Selected sections illustrating Plxnb2 expression features in the developing skull bone, sensorial organs and viscera are shown in the left side panels (A–F), whereas right side panels focus on incisor (G, I and K) and molar (H, J and L) tooth development. Developmental stages and section planes are: E14.5 frontal (A, B, G and H), E16.5 sagittal (C, D, E, I and J); E19.5 sagittal (F, K and L) sections. Scale bars: 25 µm (J); 40 µm (H and I); 50 µm (C and K); 60 µm (F and H), 80 µm (A, D, E and L); 150 µm (B and G). Am, ameloblasts; Co, cochlea; DP, dental papilla; EL, epithelial loop; Gu, gubernaculum; IDE, inner dental epithelium; In, intestine; Ki, kidney; LI, lower incisor; Lu, lung; Od, odontoblasts; ODE, outer dental epithelium; OE, olfactory epithelium; Re, retina; SB, skull bone; SR, stellate reticulum.