Deleterious de novo variants of X-linked ZC4H2 in females cause a variable phenotype with neurogenic arthrogryposis multiplex congenita

Abstract

Pathogenic variants in the X-linked gene ZC4H2, which encodes a zinc-finger protein, cause an infrequently described syndromic form of arthrogryposis multiplex congenita (AMC) with central and peripheral nervous system involvement. We present genetic and detailed phenotypic information on 23 newly identified families and simplex cases that include 19 affected females from 18 families and 14 affected males from nine families. Of note, the 15 females with deleterious de novo ZC4H2 variants presented with phenotypes ranging from mild to severe, and their clinical features overlapped with those seen in affected males. By contrast, of the nine carrier females with inherited ZC4H2 missense variants that were deleterious in affected male relatives, four were symptomatic. We also compared clinical phenotypes with previously published cases of both sexes and provide an overview on 48 males and 57 females from 42 families. The spectrum of ZC4H2 defects comprises novel and recurrent mostly inherited missense variants in affected males, and de novo splicing, frameshift, nonsense, and partial ZC4H2 deletions in affected females. Pathogenicity of two newly identified missense variants was further supported by studies in zebrafish. We propose ZC4H2 as a good candidate for early genetic testing of males and females with a clinical suspicion of fetal hypo-/akinesia and/or (neurogenic) AMC.

Keywords: Xq11.2 microdeletion; ZC4H2; ZC4H2-Associated Rare Disorders (ZARD); club foot/-feet; complicated spastic paraplegia/ spasticity; fetal hypo-/akinesia.

Figure 1. Pedigrees of the families with pathogenic ZC4H2 variants discovered by candidate gene approach, whole exome/genome sequencing and array-CGH.

Families 1, 4–6, 8, 9, 15, 18, 19 and 24 with likely pathogenic ZC4H2 missense variants, famillies 2, 3, 13, 14, 16, 17, 21, and 22 with splicing, frameshift and stop codon variants and families 10–12, 20, and 23 with a microdeletion removing the 5’ part of ZC4H2, Fam, family; *, variant present; wt, wild-type. For family7 see Supp. Figure S2.

Figure 2. Overview of genetic results in ZARD affected males and females.

An overview of newly identified likely pathogenic variants of ZC4H2 described here and previously reported in the literature. (a) Schematic view of the Xchromosome with the location of ZC4H2 and the five known RNA isoforms. Horizontal bars indicate the de novo complete ZC4H2 deletions in affected females published previously (Hirata et al., 2013; Okubo et al., 2018; Zanzottera et al., 2017), DECIPHER case 323746 and the newly identified de novo ZC4H2 microdeletions removing part of ZC4H2 identified in this study (families 10–12, 20, and 23). All deletions removed ZC4H2 exon 1 but no other known gene. (b) The structure of human ZC4H2 (Isoform 1; NM_018684.3) with non-translated sequences grey-striped, exons encoding the coiled-coil domain in grey and exons encoding the zinc finger domain in white. Newly identified pathogenic ZC4H2 variants identified in this study are depicted above the gene with de novo variants in affected females underlined. Likely pathogenic variants from the literature are depicted below the gene and protein. (c) Schematic representation of ZC4H2 protein isoform 1 (NP_061154.1) with its functional domains (CC domain: Coiled coil domain; ZNF: zinc finger domain). ZC4H2 variants newly identified in this study are depicted above the protein with de novo variants in females underlined and variants from the literature are depicted below the protein. (d) Multiple sequence alignment of ZC4H2 protein sequences in five species showing 100% conservation of the newly identified mutated amino acids (boxed). Amino acids of the ZC4H2 zinc-finger domain in the C-terminal part of the protein are underlined.