A novel frameshift deletion variant of ARSL associated with X-linked recessive chondrodysplasia punctata 1: a case report and literature review of prenatal, confirmed cases

Abstract

Background

X-linked recessive chondrodysplasia punctata 1 (CDPX1) is a rare congenital skeletal dysplasia characterized by stippled epiphyses, nasal hypoplasia, and brachytelephalangy. ARSL (formerly known as ARSE), a member of the sulfatase gene family located on Xp22.3, has been identified as the causative gene for CDPX1. The high clinical and genetic heterogeneity of CDPX1 presents a challenge to prenatal diagnosis.

Case presentation

A G1P0 woman in her 30s with an unremarkable prenatal course presented in the second trimester. Maternal diseases, tobacco, alcohol, and drug history during pregnancy were denied. Obstetrical ultrasound examination revealed a flattened nose and a flattened midface with echogenic alterations of lumbar spinous process in the fetus. Amniocentesis was performed for genetic testing. A normal karyotype and a negative result of CNV-seq were obtained. However, Whole exome sequencing (WES) in trios revealed a hemizygous ARSL variant [NM_000047.3:c.1108del p.(Trp370Glyfs*35)] in the fetus, which was maternally inherited as confirmed by Sanger sequencing. This variant was absent from the genomAD and HGMD databases. According to the ACMG guidelines, this variant was interpreted as likely pathogenic (PVS1 + PM2_Supporting). The couple decided to terminate the pregnancy. After induction of labour, a severe nasal hypoplasia was noted; and brachytelephalangy was not remarkable. Postmortem digital X-ray imaging revealed symmetrical stippled epiphyses of the vertebrae in all spine regions and enlargement of spinous process of L1-L4 vertebrae.

Conclusion

A novel frameshift deletion variant of ARSL and the associated fetal phenotype have been identified. This study provides useful information for prenatal diagnosis and genetic counseling of CDPX1.

Introduction

X-linked recessive chondrodysplasia punctata 1 (CDPX1, OMIM #302950) is a rare congenital skeletal dysplasia exhibiting both clinical and genetic heterogeneity [1]. The condition is characterized by stippled epiphyses, nasal hypoplasia, and hypoplasia of distal phalanges with various degrees of presentation of short stature, respiratory abnormalities, hearing loss, cervical spine abnormalities, cognitive impairment and/or other abnormalities.The vast majority of affected individuals are males; and as expected for an X-linked recessive disorder, females are less affected [2,3,4]. Most affected males have minimal morbidity; however, some suffer from severe conditions in need of treatment, such as airway stenosis and cervical spine instability [5].

In addition to maternal etiological factors such as maternal autoimmune disorders or use of warfarin during pregnancy, ARSL (formerly known as ARSE), a member of the sulfatase gene family located on Xp22.3, has been identified as the genetic cause for CDPX1 [6, 7]. The Human Gene Mutation Database (HGMD) Professional (2023.4) currently has a collection of 57 ARSL pathogenic / likely pathogenic variants, with a spectrum of mutation including 35 missense, 2 frameshift, 2 inframe, 2 nonsense, 2 splice, 1 synonymous, 6 single or multiple exons deletion, 4 null deletion, and 1 chromosomal rearrangement change. To date, there are no definitive genotype-phenotype correlations established regarding the disease [7]. Prenatal diagnosis of CDPX1 mainly relies on ultrasound examination and genetic testing [8].

In this study, we have identified a novel frameshift deletion variant of ARSL in a male fetus with facial dysmorphism detected by ultrasound. The radiographic skeletal features of the fetus after induction of labour were described. Further, a review of prenatal cases of CDPX1 with a molecular diagnosis depicted in literature and the present study was conducted to summarize the pre- and postnatal findings of the condition.

Case presentation

A G1P0 woman in her 30s with an unremarkable prenatal course presented during the second trimester. Maternal diseases, tobacco, alcohol, and drug history during pregnancy were denied. Obstetrical ultrasound examination revealed fetal anomalies including a flattened nose and an increased nasofrontal angle (145°) with echogenic alterations of lumbar spinous process (Fig. 1). After obtaining written informed consent, amniocentesis was performed for genetic testing. A normal karyotype and a negative result of CNV-seq were obtained. However, WES in trios revealed a hemizygous ARSL variant [NM_000047.3:c.1108del p.(Trp370Glyfs*35)] in the fetus, which was maternally inherited. This finding was further confirmed by Sanger sequencing (Fig. 2). The full-length mature acrylsulfatase L (ARSL) consists of 589 amino acid residues. The c.1108del variant causes a translational frameshift at codon 370 and premature polypeptide termination, resulting in significant C-terminal truncation of ARSL. This variant was absent from the genomAD and HGMD professional (2023.4) databases. According to the ACMG guidelines [9], this variant is classified as likely pathogenic (PVS1 + PM2_Supporting). With a thorough genetic counseling, the woman and her husband decided to proceed to termination of the pregnancy. After induction of labour, a severe nasal hypoplasia was noted, which was in line with the ultrasound finding (Fig. 3A). Brachytelephalangy (shortening of the distal phalanges) was not remarkable (Fig. 3B). Postmortem digital X-ray imaging revealed symmetrical stippled epiphyses of the vertebrae in all spine regions, and enlargement of spinous process of L1-L4 vertebrae (Fig. 4).

Fig. 1

Prenatal ultrasound examination revealed a flattened nose (indicated with a white arrow) and a flattened midface (A) and echogenic alterations of lumbar spinous process in the fetus (B)

Fig. 2

Sanger sequencing confirmed the hemizygous ARSL NM_000047.3 c.1108del p.(Trp370Glyfs*35) variant in the fetus. The mother was a heterozygous carrier of the c.1108del variant

Fig. 3

Facial features and a picture of the fetus after induction of labor. (A) The fetus had flattened nasal bridge and midface; (B) Brachytelephalangy (shortening of the distal phalanges) was not remarkable

Fig. 4

Radiographic features of the fetus after induction of labor. (A) Symmetrical punctate calcification spots around the vertebrae in all spine regions. Red arrows indicate the typical spots. (B) Enlargement of spinous process of L1-L4 vertebrae (indicated with arrows)

Discussion and conclusion

Chondrodysplasia punctata (CDP) is a heterogeneous group of skeletal dysplasia with characteristic radiographic stippling in multiple epiphyses. CDP contains rhizomelic chondrodysplasia punctata (RCDP, a peroxisome biogenesis disorder), X-linked dominant CDP (CDPX2, also known as Conradi-Hnermann syndrome OMIM #302960, impaired cholesterol biosynthesis), brachytelephalangic chondrodysplasia punctata (BCDP) / X-linked chondrodysplasia punctata 1 (CDPX1), and other disorders resulting from chromosomal abnormalities, maternal autoimmune diseases, use of warfarin during pregnancy, or maternal alcohol consumption [10]. Though there is partial overlap in ultrasound features, distinct causative genes are known to underlie different types of CDP, highlighting a diagnostic value of genetic testing in prenatal cases. In this study, the ultrasound findings at 24 weeks of gestation were insufficient to establish a definitive diagnosis. Identification of the ARSL c.1108del variant led to a final diagnosis of CDPX1.

A review of prenatal cases of CDPX1 with a molecular diagnosis published in literature and this study gives implications for perinatal management of this condition (Table 1). Of the 10 cases reviewed, prenatal ultrasound (MRI/CT) scan detected midface hypoplasia to various degrees in eight cases (80%), epiphyseal stippling in four cases (40%), brachytelephalangy in two cases (20%), with two cases (20%) presenting with all the three features concurrently. Other structural ultrasound anomalies that were recurrently detected include spine abnormality (5/10, 50%) and short limbs (4/10, 40%). The mutation spectrum of the cases includes one frameshift, one nonsense, two deletion (partial or contiguous), and six missense mutations. However, no clear genotype-phenotype correlation has been established [7]. Because of the variability of clinical manifestation, prenatal counseling of the condition is quite challenging [11]. One individual harboring a partial deletion of the ARSL gene had severe respiratory distress, which resulted in neonatal death on day 2 after birth [12], whereas another individual carrying a contiguous deletion on Xp22.33 region that affects multiple genes including ARSL displayed mild respiratory problem and survived postnatally [13] (Table 1). Of note, the 8.33 Mb contiguous deletion involving other genes (SHOX, CSF2RA, XG, NLGN4 and STS) along with the ARSL gene caused additional clinical manifestations, such as X-linked ichthyosis associated with a deletion of the STS gene [13]. Furthermore, another previous study has described a contiguous gene syndrome in two brothers from a Moroccan family who had short stature, hypertelorism, midface hypoplasia, sensorineural hearing loss, brachytelephalangy, and normal intelligence. The probands were carriers of a maternally inherited 3.1-Mb deletion on Xp22.33 covering the short stature homeobox (SHOX) and ARSL genes [14]. Therefore, both previous and present studies remind clinicians that a comprehensive postnatal examination is necessary for the newborns with CDPX1 to detect other malformations and complications for receiving timely medical care.

Table 1 Comparison of prenatal cases of CDPX1with a molecular diagnosis

ARSL encodes an acrylsulfatase that is localized to the Golgi apparatus membrane [15]. Reportedly, 60-75% of patients with CDPX1 carried ARSL point mutations; and Xp22.3 deletion or chromosomal rearrangement accounted for the further 25% of patients [16]. Therefore, a sequential karyotyping, CNV-seq and exome sequencing strategy is recommended for prenatal diagnosis of CDPX1. In this study, following a finding of normal karyotype and a negative result of CNV-seq, exomse sequencing identified a single nucleotide frameshift deletion variant of ARSL as the underlying genetic cause for the fetal anomalies. To date, the identified ARSL point mutations are predominantly missense mutations, whereas frameshift and nonsense mutations are relatively infrequent. This study provides useful information on the clinical phenotype of the ARSL c.1108del variant. Because of the developmental stage, the clinical presentation of the c.1108del variant may not be fully evocative in the fetus. Thus, it is difficult to evaluate the prognosis of this variant in the study.

In conclusion, a novel frameshift deletion variant of ARSL and the associated fetal phenotype have been identified. This study provides useful information for prenatal diagnosis and genetic counseling.