Biallelic ZNF407 mutations in a neurodevelopmental disorder with ID, short stature and variable microcephaly, hypotonia, ocular anomalies and facial dysmorphism

Novel Compound Heterozygous Variants in ZNF526 Causing Dentici-Novelli Neurodevelopmental Syndrome: A Case Report and Literature Review

BACKGROUND

The ZNF526 gene encodes a ubiquitously expressed Kruppel-type zinc finger protein crucial in transcriptional regulation. Recent studies suggest that biallelic pathogenic variants in ZNF526 may lead to Dentici-Novelli neurodevelopmental syndrome, characterized by microcephaly, developmental delay, epilepsy, and ocular anomalies. To date, phenotypic details have been reported for only six patients with ZNF526 variants.

METHODS

This study gathered clinical information and genetic data from a child with neurodevelopmental disorders. A three-dimensional protein model was employed to predict variant effects on protein structure. A literature review was conducted to compare this case with previously reported cases, analyzing clinical features and genetic findings.

RESULTS

The proband, a 7-month-old girl, exhibited developmental delay, microcephaly, limb hypotonia, abnormal brain imaging, and seizures. Chromosomal karyotype analysis and copy number variation analyses were normal. Whole exome sequencing revealed two heterozygous variants in the ZNF526 gene (NM_133444.3): c.1426del (p.Val476Phefs*9), a de novo frameshift variant, and c.1513T;> C (p.Cys505Arg), inherited from her mother. These previously unreported variants are on separate alleles, forming a compound heterozygous state correlated with the clinical presentation. Ocular anomalies were absent, while café-au-lait spots may represent a novel feature. Among 12 cases of Dentici-Novelli neurodevelopmental syndrome, 11 unique ZNF526 variants have been identified, with loss-of-function variants possibly linked to seizures.

CONCLUSION

This study describes the youngest patient with Dentici-Novelli neurodevelopmental syndrome, broadening the ZNF526 mutation spectrum and detailing the associated clinical profile. These findings are valuable for genetic diagnosis and family counseling in cases of this syndrome.

The genetics of autism spectrum disorder in an East African familial cohort

Autism spectrum disorder (ASD) is a group of complex neurodevelopmental conditions affecting communication and social interaction in 2.3% of children. Studies that demonstrated its complex genetic architecture have been mainly performed in populations of European ancestry. We investigate the genetics of ASD in an East African cohort (129 individuals) from a population with higher prevalence (5%). Whole-genome sequencing identified 2.13 million private variants in the cohort and potentially pathogenic variants in known ASD genes (including CACNA1C, CHD7, FMR1, and TCF7L2). Admixture analysis demonstrated that the cohort comprises two ancestral populations, African and Eurasian. Admixture mapping discovered 10 regions that confer ASD risk on the African haplotypes, containing several known ASD genes. The increased ASD prevalence in this population suggests decreased heterogeneity in the underlying genetic etiology, enabling risk allele identification. Our approach emphasizes the power of African genetic variation and admixture analysis to inform the architecture of complex disorders.

Assessment of burden and segregation profiles of CNVs in patients with epilepsy

Objective

Microdeletions are associated with different forms of epilepsy but show incomplete penetrance, which is not well understood. We aimed to assess whether unmasked variants or double CNVs could explain incomplete penetrance.

Methods

We analyzed copy number variants (CNVs) in 603 patients with four different subgroups of epilepsy and 945 controls. CNVs were called from genotypes and validated on whole‐genome (WGS) or whole‐exome sequences (WES). CNV burden difference between patients and controls was obtained by fitting a logistic regression. CNV burden was assessed for small and large (>1 Mb) deletions and duplications and for deletions overlapping different gene sets.

Results

Large deletions were enriched in genetic generalized epilepsies (GGE) compared to controls. We also found enrichment of deletions in epilepsy genes and hotspots for GGE. We did not find truncating or functional variants that could have been unmasked by the deletions. We observed a double CNV hit in two patients. One patient also carried a de novo deletion in the 22q11.2 hotspot.

Interpretation

We could corroborate previous findings of an enrichment of large microdeletions and deletions in epilepsy genes in GGE. We could also replicate that microdeletions show incomplete penetrance. However, we could not validate the hypothesis of unmasked variants nor the hypothesis of double CNVs to explain the incomplete penetrance. We found a de novo CNV on 22q11.2 that could be of interest. We also observed GGE families carrying a deletion on 15q13.3 hotspot that could be investigated in the Quebec founder population.

Biallelic truncation variants in ATP9A are associated with a novel autosomal recessive neurodevelopmental disorder

Intellectual disability (ID) is a highly heterogeneous disorder with hundreds of associated genes. Despite progress in the identification of the genetic causes of ID following the introduction of high-throughput sequencing, about half of affected individuals still remain without a molecular diagnosis. Consanguineous families with affected individuals provide a unique opportunity to identify novel recessive causative genes. In this report, we describe a novel autosomal recessive neurodevelopmental disorder. We identified two consanguineous families with homozygous variants predicted to alter the splicing of ATP9A which encodes a transmembrane lipid flippase of the class II P4-ATPases. The three individuals homozygous for these putatively truncating variants presented with severe ID, motor and speech impairment, and behavioral anomalies. Consistent with a causative role of ATP9A in these patients, a previously described Atp9a−/− mouse model showed behavioral changes.