A Mild Skeletal Dysplasia Caused by a Biallelic Missense Variant in the SLC35D1 Gene

Abstract

Introduction

Biallelic variants in the SCL35D1 gene have been originally associated with a severe skeletal dysplasia called “Schneckenbecken dysplasia” because of the resemblance of the pelvic shape to a snail. More recently, SLC35D1 variants have been associated with much milder phenotypes of skeletal dysplasia. Our report describes one such individual with a novel SLC35D1 variant.

Case Presentation

A 17-year-old male with a coarse face and short stature was referred to our clinic. On his radiographic imaging, shortness of the long bones and metaphyseal flaring were detected. Using a clinical exome panel, we discovered a novel homozygous missense variant in the SLC35D1 gene, c.899G>T (p.Gly300Val).

Conclusions

We identified a biallelic variant that was causative for a mild skeletal dysplasia and showed its phenotypic effects. Our observation confirms the existence of nonlethal skeletal dysplasias associated with biallelic SLC35D1 variants and suggests the existence of a phenotypic spectrum.

Established Facts

• •Schneckenbecken dysplasia (SBD) is a rare skeletal dysplasia with only a few reported cases.
• •SBD has severe skeletal findings and results in death in the prenatal and early postnatal periods.

Novel Insights

• •A novel pathogenic variant in the SLC35D1 gene is described, causing a nonlethal phenotype.
• •The recently published study has shown for the first time that homozygous pathogenic variants of SLC35D1 can lead to mild phenotypic features in a patient, and the case we report is the second study to show this phenotype.

Introduction

Schneckenbecken dysplasia (SBD) (OMIM: 269250) is a rare autosomal recessive lethal skeletal dysplasia [Borochowitz et al., 1986; Nikkels et al., 2001]. “Schneckenbecken,” the German term, refers to the snail-like appearance of the hypoplastic ilia, and due to the classical radiological signs, it is named like this. In the international nosology for skeletal dysplasias, “SBD, SLC35D1-related” is classified into the “Severe Spondylodysplastic Dysplasias (SSDD)” group, which includes achondrogenesis type 1A (OMIM: 200600), spondylometaphyseal dysplasia Sedaghatian type (OMIM: 250220), spondylometaphyseal dysplasia Sedaghatian-like (OMIM: 260400), opsismodysplasia (OMIM: 258480), and MAGMAS-related skeletal dysplasia (OMIM: 613320) [Unger et al., 2023].

In the pathogenesis of SBD, the solute carrier (SLC) gene family, which encodes membrane transport proteins, is critical. The solute carrier-35 (SLC35) is a subgroup of this gene family and encodes nucleotide sugar transporters. A total of 31 human SLC35 members have been identified in the human genome, and solute carrier-35D1 (SLC35D1) is one of them. It is expressed in the endoplasmic reticulum and transports UDP-GalNAc, UDP-GlcUA, and UDP-N-acetylglucosamine from the cytoplasm into the endoplasmic reticulum lumen, which are the substrates for chondroitin sulfate and dermatan sulfate [Hiraoka et al., 2007; Ishida and Kawakita, 2004; Muraoka et al., 2001]. Chondroitin sulfate is an essential component of cartilage proteoglycans, and variants causing disruption of chondroitin sulfate synthesis may result in skeletal dysplasia.

The common clinical features of individuals with pathogenic variants in the SLC35D1 gene included lethal outcomes and severe skeletal dysplasia. Even in the most recent classification by Unger et al. [2023], nonlethal SLC35D1 dysplasias have not yet been defined; in 2022, Özer et al. [2022] reported a family with two affected siblings carrying a pathogenic mutation in the SLC35D1 gene who presented a mild clinical phenotype. This study showed that individuals with pathogenic variations in the SLC35D1 gene may exhibit mild clinical features. Our goal with this second reported case is to further support this notion.

Case Report

The department of pediatric metabolism referred a 17-year-old Syrian male patient with a coarse face and short stature to our clinic with findings suggestive of mucopolysaccharidosis. The parents were consanguineous, and the other five siblings were all healthy; one sibling died as a result of a neonatal infection, and there is no known person in the family pedigree with similar complaints (Fig. 1).

Fig. 1.

a The pedigree of the family: the proband is indicated with an arrow. Parents with heterozygous variants are indicated by the red dot. b Confirmation of the p.Gly300Val variant by Sanger sequencing of the proband and his parents. c The SLC35D1 gene, which is located on chromosome 1p31.3, is depicted schematically.

The patient had a macrocephalic appearance: a coarse face, a tall chin, mandibular prognathism, a short neck, and a narrow chest. All extremities were short, brachydactyly in the hands and feet, genu valgum in the left knee, and hallux valgus deformities in the right foot. The index patient’s developmental parameters were as follows: height: 139 cm (−5.12 SDS), weight: 45 kg (−3.35 SDS), BMI: 24.3 (0.28 SDS), head circumference: 54 cm, upper-to-lower segment ratio: 1, fathom distance: 141, right upper arm: 31 cm, right forearm: 23, left upper arm: 31 cm, left forearm: 23 cm, total arm: 54 cm, right hand: 18 cm, left hand: 18 cm, right upper leg: 34 cm, right lower leg: 35 cm, left upper leg: 34 cm, left lower leg: 30 cm, total leg: 69 cm, right foot: 24 cm, left foot: 24 cm (Fig. 2).

Fig. 2.

Examination photos of our patient. a In the front view, the genu valgum in the knees can be seen. b Scoliotic posture from behind. c Patient’s right lateral side. d Patient’s left lateral side. e Hand image of the patient. f Hallux valgus deformities in the right foot. g–o Radiographs of the patient. g, h Shortening of the metatarsal and metacarpal bones. i Shortening of the forearm bone. j Shortening of the humerus. k Scoliosis with a double curve. m–o Shortening of the tibia-fibula with a large metaphysis.

The radiographs of the patient revealed the upper chest was narrow, the ribs were mildly short and curved forward, and the clavicles were abnormally bowed. Double major scoliosis was present. In the lower body, there was no characteristic snail-like appearance in the ilia, but the right femoral head and acetabular zone had a degenerative appearance. The long bones were short and flared at both ends without significant metaphyseal irregularity (Fig. 2).

Materials and Methods

DNA was extracted from the peripheral blood samples using the QIAsymphony^® DNA Mini Kit (QIAGEN GmbH, Hilden, Germany). Clinical exome sequencing (Illumina TruSight1 Expanded) was performed on the DNA sample of the patient, and the number of variants was limited from 17,306 to 1,631 during the analytic process. All identified variants were evaluated for their pathogenicity and causality and categorized into classes according to the American College of Medical Genetics and Genomics (ACMG) Standards and Guidelines [Richards et al., 2015]. Of these, 671 variants had predicted deleterious effects. Based on pedigree analysis, 26 homozygous variants were identified, and one of these variants was found to be associated with skeletal dysplasia. Sanger confirmation of the detected pathogenic variant was performed on the individual and his parents. Primers were designed to cover the variant. DNA sequencing was performed using a model 3500 Genetic Analyzer (Applied Biosystems, Foster City, CA, USA), and sequence analysis was performed using SeqScape (Thermo Fisher Scientific, Waltham, MA, USA). All patients provided their written consent prior to participating in the study.

Results

The SLC35D1 gene was the only one related to skeletal disease. NM_015139.3:c.899G>T (p.Gly300Val) variant was found to be homozygous in the 11th exon of the SLC35D1 gene. The missense variant that we detected in our patient is in a conserved region and has not been reported in healthy individuals. It causes a p.Gly300Val change in the protein structure and is located in the region containing three functional domains (RhaT, VRG4, and TPT-triose-phosphate transporter) mainly involved in nucleotide sugar and phosphate transport mechanisms. The frequency of this variant was reported in the Genome Aggregation Database (gnomAD) as 0. In silico analyses have a CADD score (Phred-like rank score) of 33, and most of the other prediction tools (Sorting Intolerant from Tolerant [SIFT], Polymorphism Phenotyping v2 [PolyPhen2], Protein Variation Effect Analyzer [PROVEAN], MutPred2, MetaRNN, and Rare Exome Variant Ensemble Learner [REVEL]) indicate that it damages the protein structure. The detected variant is classified as a likely pathogenic variant (PP3: multiple lines of computational evidence support a deleterious effect on the gene or gene product, PM2: extremely low frequency in gnomAD population databases, PM1: located in a well-established functional domain), according to ACMG variant interpretation guidelines. It was observed that the parents were heterozygous after Sanger sequencing was performed on family members for this variant. Due to the inaccessibility of the siblings, genetic testing could not be performed.

Discussion

The SLC35D1 gene plays a crucial role in cartilage proteoglycan synthesis. SBD is caused by disruption of the SLC35D1 function. Although SBD has severe skeletal findings, additional clinical findings in the prenatal period may accompany it, such as polyhydramnios at the beginning of the third trimester [Camera et al., 1991; Giedion et al., 1991; Varkey and Jones, 2004] and hydrops at the beginning of the second trimester [Nikkels et al., 2001]. Due to our patient’s atypical clinical findings, such as dysmorphic facial features (coarse face), mild skeletal malformations (short stature), and lack of prenatal screening, we initially considered some MPS types in the differential diagnosis. Then, as a result of the clinical exome sequencing study, we detected the homozygous SLC35D1 c.899G>T (p.Gly300Val) variant. Short stature, a narrow chest, an abnormally shaped clavicle, shortness, and a large metaphysis of long bones are compatible with SBD, but typical radiographic findings “platyspondyly and snail-like ilia” were not observed (Fig. 1). Our findings suggest that the detected variant may be associated with a milder form of SBD, which is characterized by mild phenotypic and radiological features, or an unclassified mild form of skeletal dysplasia associated with the SLC35D1 gene.

In a literature review, four different studies have so far described nine different variants. All variants are shown in the SLC35D1 exon graphic [Furuichi et al., 2009; Hiraoka et al., 2007; Özer et al., 2022; Rautengarten et al., 2019] (Fig. 3). The first variant was discovered in a 22-week-old male fetus with severe hydrops, a small thorax, and extremely short extremities, as clinically described by Nikkels et al., [2001]. A homozygous 1-bp deletion (125delA) in exon 1 of the SLC35D1 gene that produced a premature stop codon (Ser42fsTer9) was reported by Hiraoka et al. [2007]. In the same study, two more variants were shown in different patients; one was a female infant who died in the neonatal period who had a hydropic narrow chest, a hypoplastic midface, very short limbs, and ilia had snail-like appearance in radiographs. The c.932G>A (p.W311X) variant in exon 11 was compound heterozygous with the c.636+1G>T (IVS7+1G-T) variant, which causes a premature stop codon. Then Furuichi reported four loss-of-function variants in three families [Furuichi et al., 2009]. The first patient was suspected of a skeletal malformation at 16 weeks of prenatal USG and terminated at 18 weeks. On radiographic examination, he had severe short limbs and a snail-like appearance. Compound heterozygosity was detected by genetic testing and c.319C>T, a nonsense variant with c.392+3A>G splice site variant caused by exon 4 skipping and a frameshift that results in a truncated protein. The second patient was diagnosed at 22 weeks gestation and showed similar signs to the first patient. The patient had a 4959-bp deletion causing the complete removal of exon 7 (p.R178fsX15), resulting in a premature stop codon (p.R178fsX15).

Fig. 3.

A schematic representation of the identified pathogenic SLC35D1 gene (NM_015139.3) variants. Coloration indicates different studies. Boxes marked with a red triangle show compound heterozygous variants.

The third and the last one was also diagnosed at 18 weeks of gestation and terminated at 20 weeks. The fetus had similar findings as the others and additionally had hydrops. Although the clinical findings are compatible with SBD due to the lack of biologic material from a fetus c.193A>C (p.T65P), a heterozygous missense variant was shown in consanguineous parents and an unaffected sister. In 2019, c.398C>T p.(Pro133Leu) in the 5th exon of the SLC35D1 was identified in the index’s parents due to a lack of biologic material [Rautengarten et al., 2019]. The patients’ parents were heterozygous for this variant. Radiological features were milder than previously reported SBD cases, and the “Schneckenbecken-like dysplasia” term was first used in this report. All these cases had lethal and severe skeletal malformations. But recently, a homozygous c.401T>C (p.Met134Thr) variant that causes a milder form of SBD has been first identified in 5 patients of one family [Özer et al., 2022]. The mild clinical findings of these patients were very similar to those of our patient. Even if it is not possible to define a mild phenotype in a single patient, it is known in the literature that mild and severe variants have different phenotypic effects. This situation can be seen in skeletal dysplasias such as acromesomelic dysplasia [Zeb et al., 2018] and syndromes with skeletal findings caused by enzyme deficiency. The pathogenic variant that we have identified has not been reported in the literature before. However, our study supports the term “Schneckenbecken-like dysplasia” proposed by Rautengarten and represents the second case study demonstrating that pathogenic variants in SLC35D1 can be compatible with mild clinical features.

Conclusion

In this report, we present a patient with pathogenic SLC35D1 variant who had milder phenotypic findings in contrast to most cases with severe clinical signs and perinatal deaths that have been previously reported. This is the second report of SLC35D1 gene variants with a mild phenotype after Özer et al. [2022]. This case will contribute to the expansion of the SLC35D1 variant database and to a better understanding and classification of skeletal dysplasias associated with SLC35D1 in nosology. In this way, the phenotypic spectrum of the SLC35D1 gene can be enhanced, and it can contribute more effectively to the genetic counseling and management of affected individuals.

Statement of Ethics

This study was performed in accordance with the Declaration of Helsinki principles. Written informed consent was obtained from the patient through an interpreter for the publication of this case report and accompanying images. The paper is exempt from ethical committee approval. Ethical approval was not required for this study in accordance with national guidelines.

Conflict of Interest Statement

The authors declare not conflict of interest.

Funding Sources

No funding was received for this study.

Author Contributions

Tuna Eren Esen and Ahmet Cevdet Ceylan: genetic diagnosis, follow-up, data collection, and drafting the manuscript. Ozlem Unal Uzun: clinical evaluation and interpretation of metabolic investigations. All authors have read, reviewed, and approved the final manuscript.

Funding Statement

No funding was received for this study.

Data Availability Statement

All data generated or analyzed during this study are included in this article. Further inquiries can be directed to the corresponding author.