Prenatal diagnosis of SMPD4 loss ‐ A neurodevelopmental disorder with microcephaly, arthrogryposis and structural brain anomalies

SMPD4 loss is a rare neurodevelopmental disorder that leads to severe mental and physical disability and early death in infancy. Most cases of this genetic condition have been diagnosed postnatally. This article focuses on the prenatal findings of affected fetuses. The phenotypes can include growth restriction, arthrogryposis (clenched hands, foot deformity), as well as cerebral abnormalities (simplified gyral pattern/lissencephaly, cerebellar hypoplasia, corpus callosum deformity). SMPD4 loss is detectable via exome sequencing. Here, two fetuses displayed a homozygotic pathogen variant in the SMPD4 gene, encoding for the enzyme Sphingomyelinase‐4. Both parents were heterozygous carriers of the pathogenic variant. On detection of the above mentioned signs exome sequencing is indicated, with focus on the SMPD4 gene.


| FETAL PHENOTYPE
wileyonlinelibrary.com/journal/pd normal. Of note, the parents had a previous child that was affected by an unknown severe neurodevelopmental delay who died at age 5due to a viral respiratory infection. An MRI of the first affected child at the age of 3 months showed delayed myelination, cerebellar hypoplasia, hypoplasia of the corpus callosum, as well as simplified gyral pattern. Furthermore, he did not achieve any motor or cognitive developmental milestones, displayed visual inattention, and lacked any speech development.

| DIAGNOSTIC METHOD
Trio exome sequencing of our own cohort DNA quantity and quality were determined using Qubit®uFluorometer and NanoDrop ND-8000 (Thermo Fisher Scientific, Dreieich, Germany). Enrichment of the coding DNA sections of the test persons was carried out with one of the following enrichment methods: SureSelect Human All Exon 50Mb V6 Kit, SureSelect Human All Exon 50Mb V7 Kit (Agilent, Santa Clara, CA, USA), the Twist Human Core + the Reference Sequence database exome (Twist Bioscience, San Fransisco, CA, USA) or the CeGaT Exome Xtra V1 (CeGaT GmbH, Tübingen, Germany).
For Agilent enrichment kits, sequencing libraries were prepared using the SureSelectXT workflow. Library preparation and capture for all samples was performed according to the respective manufacturer's instructions. Paired-end sequencing was performed using the Nova-seq6000 system (Illumina, San Diego, CA) with 2x100 base pairs (bp) read length. Sequence data were processed with Illumina bcl2fastq2.
Adapter sequences were removed with Skewer and the sequences obtained were aligned to the human reference genome (hg19) with the Burrows Wheeler aligner (BWA mem). Sequences that could not be clearly assigned to a genomic position were removed, as were sequence duplicates that were probably due to amplification (internal software). The average coverage was 170x. Sequence variants (single nucleotide exchanges and short insertions/deletions) were determined from the remaining high-quality sequences (CeGaT StrataCall).
Copy number variations were computed on uniquely mapping, nonduplicate, high quality reads using an internally developed method based on sequencing coverage depth. Briefly, we used reference samples to create a model of the expected coverage that represents wet-lab biases as well as inter-sample variation.

| DIAGNOSTIC RESULTS AND INTERPRETATION
Cytogenetic testing revealed a normal karyotype. Trio exome analysis detected SMPD4 loss, due to the homozygous pathogenic SMPD4 -285 fibroblasts and the nervous system during fetal development.
Dysfunction of SMPD4 can lead to proliferation defects of the developing fetal brain.

| PREGNANCY OUTCOME
The parents opted to terminate the pregnancy at 23 gestational weeks. The prenatal findings of rocker bottom feet, clenched fists and small size for the gestational age were confirmed postnatally ( Figure 1). The patents decided against a post-mortem examination of the fetus.  Table 1). [1][2][3][4][5] The outcome of the affected children is described as unfavorable: one third die before the age of 1 year. If Open Access funding enabled and organized by Projekt DEAL.

CONFLICT OF INTEREST STATEMENT
There is no conflict of interest.

DATA AVAILABILITY STATEMENT
The data supporting the findings of this study are available upon request. has been granted a waiver of informed consent, as all clinical data contained in this report have been anonymized.