Introduction: Pseudoachondroplasia (PSACH) and multiple epiphyseal dysplasia (MED) are allelic and caused by mutations in the COMP gene. Other mutations in the genes MMP13, AIFM1, B3GALT6, MATN3, COL9A1, COL9A2, COL9A3, and SLC26A2 have also been associated with evidence of dysplasia in the epiphysis, metaphysis, and spine. Case Presentation: We report on the first Mexican patient diagnosed with PSACH. The diagnosis was confirmed by identifying a recurrent heterozygous mutation c.2153G>C (p.Arg718Pro) in the COMP gene using whole-exome sequencing. Discussion: The anterior spindle-shaped vertebral bodies and severe short stature are not observed in patients carrying p.Arg718Pro, identifying another amino acid site associated with clinical heterogeneity. Reporting new cases with clinical heterogeneity in terms of phenotype plays a crucial role in understanding PSACH and MED pathogenesis. The most important aspect of this presentation is providing a new perspective on a recognized clinical scenario, thus setting the standard for better genetic counseling.

Established Facts

  • Pseudoachondroplasia presents with anterior spindle-shaped vertebral bodies and metaphyseal dysplasia. Severe short stature is most associated with mutations in the eight calmodulin-like repeats of the COMP gene.

  • Mutation p.Arg718Pro in the COMP gene has been associated with multiple epiphyseal dysplasia (MED), but MED can also be associated with other mutated genes.

Novel Insights

  • The severe short-stature phenotype observed in our case is not consistent with the mutation located outside the eight calmodulin-like repeats of the COMP gene.

  • The recurrent mutation p.Arg718Pro in the COMP gene adds another amino acid site, with clinical heterogeneity regarding pseudoachondroplasia with anterior spindle-shaped vertebral bodies and severe short stature.

Pseudoachondroplasia (PSACH; OMIM 177170) is an autosomal dominant osteochondrodysplasia that is allelic to multiple epiphyseal dysplasia-1 (MED1; 132400), which can be autosomal dominant or recessive due to a mutation in the cartilage oligomeric matrix protein (COMP; 600310) gene. PSACH is characterized by brachydactyly, ligamentous laxity, and short stature with bony dysplasia deformity in the long bones. The anterior peak of the vertebral bodies, present in childhood, usually resolves with age, but osteoarthritis is severe and progressive, while MED is characterized by early-onset osteoarthritis and range-of-motion issues in the major joints. Spinal abnormalities are subtle or completely absent. The genotype-phenotype relationship has been observed between the type and site of the mutation and shorter stature [Mabuchi et al., 2003]. Mutations in the MMP13, AIFM1, B3GALT6, MATN3, COL9A1, COL9A2, COL9A3, and SLC26A2 genes have also been observed in patients with evidence of dysplasia in the epiphysis, metaphysis, or spine [Mabuchi et al., 2003; Kennedy et al., 2005; Jackson et al., 2011], making the clinical-molecular genetic diagnosis of PSACH and MED difficult. The COMP gene is located in chromosome region 19p13 and comprises 19 exons. More than 180 mutations have been found in the COMP gene, predominantly point mutations and small insertions/deletions based on the Human Genome Mutation Database Professional (HGMDpro) (URL: https://portal.biobase-international.com/cgi-bin/portal/login.cgi). The COMP gene encodes the COMP glycoprotein (P49747), which belongs to the thrombospondin family and localizes to the extracellular matrix of cartilage [Hedbom et al., 1992], ligament, and tendon [DiCesare et al., 1994]. The COMP protein consists of an N-terminal domain that participates in the pentamer assembly, four epidermal growth factor-like repeats, eight calmodulin-like repeats (CLRs), and a C-terminal globular domain [Oldberg et al., 1992; Efimov et al., 1994; Newton et al., 1994]. The amino acid sequence in the CLRs is highly conserved and thought to play a role in binding calcium ions. Most mutations in the COMP gene have been identified within these repeats [Unger and Hecht, 2001; Briggs and Chapman, 2002]. In the present report, we describe the case of a boy who carries the recurrent mutation (p.Arg718Pro) in the COMP gene with clinical heterogeneity in the form of PSACH, setting the standard for better genetic counseling.

The 6-year-old Mexican male proband is the first child of healthy, unrelated parents who were aged 31 and 33 years at delivery. No history of prenatal exposure to teratogens or maternal illness was recorded. After an uneventful pregnancy, he was born by vaginal delivery at 42 weeks gestation with a weight of 4,150 g (25th percentile), a length of 57 cm (50–75th percentile), and occipito-frontal circumference of 35.5 cm (25–50th percentile). Apgar scores were 81 and 95. The neonatal period proceeded without issue. His language and motor development have been normal. His family history was negative for bone defects and other malformations. At 1 year 7 months old, the parents noticed that their son was exhibiting stunted growth.

At the last physical examination, at 6 years old, his weight was 20.100 kg (50th percentile), his length was 99 cm (<3rd percentile; −17 standard deviations), and his occipito-frontal circumference was 51 cm (50–25th percentile). He had shortening of all four limbs with painful and enlarged joints, as well as lumbar lordosis. No further dysmorphic changes were observed at the craniofacial, neck, or chest levels. His genitalia were normal for a male.

X-rays showed thoraco-lumbar scoliosis with a left concavity and lumbar lordosis, and the vertebral bodies were observed to be anteriorly spindle-shaped. At the level of the metaphysis and epiphysis of the femur, tibia, and fibula, they were observed to be widened and dysplastic (shown in Fig. 1a). Abdominal ultrasound and skull X-rays were normal in appearance. Electrolyte, vitamin D, calcitonin, and parathyroid hormone levels were normal. According to the above, a multiple spondylo-epi-metaphyseal dysplasia was suspected due to the heterogeneous genetic origin of the disease. A total exome sequencing study of the proband was recommended.

Fig. 1.

a X-rays of our proband at 3 years and 10 months old. A lumbar lordosis with spindle-shaped vertebral bodies, abnormal alignment of the epiphysis, widening and fraying metaphysis of the tibia and fibula at the ankle and knee, and dysplasia of the femoral head. b Pedigree of examined family with phenotype/genotype information; circle represents female, squares indicate males, and filled symbol shows affected individual. Arrow indicates proband. Partial electropherograms show the wild type homozygous state in the father and the mother; and the heterozygous mutation c.2153 G>C (p.Arg718Pro) in the COMPgene in the proband.

Fig. 1.

a X-rays of our proband at 3 years and 10 months old. A lumbar lordosis with spindle-shaped vertebral bodies, abnormal alignment of the epiphysis, widening and fraying metaphysis of the tibia and fibula at the ankle and knee, and dysplasia of the femoral head. b Pedigree of examined family with phenotype/genotype information; circle represents female, squares indicate males, and filled symbol shows affected individual. Arrow indicates proband. Partial electropherograms show the wild type homozygous state in the father and the mother; and the heterozygous mutation c.2153 G>C (p.Arg718Pro) in the COMPgene in the proband.

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Exome Sequencing Analysis

Genomic DNA was analyzed using whole-exome sequencing (WES) in the proband. To capture the exonic regions of interest, the SureSelectXT Human All Exon V5 (Agilent Technologies) kit was used. The paired-end libraries were generated. For the massive sequencing of these libraries (2 × 150 bp), the Illumina HiSeq 2000 Sequencer (Illumina Inc., San Diego, CA, USA) was used. Next, the bioinformatic analysis of the obtained data was carried out for quality control and mapping of the reads. Subsequently, for identification purposes, the pathogenic variants were compared with the HGMDpro (URL: https://portal.biobase-international.com/cgi-bin/portal/login.cgi), NCBI ClinVar database (URL: http://www.ncbi.nlm.nih.gov/clinvar/), Gene Reviews database (URL: https://www.ncbi.nlm.nih.gov/books/NBK1123/#edm-ad.Molecular_Genetics), and SNP database (URL: https://www.ncbi.nlm.nih.gov/projects/SNP/). The prediction of the effect of the variant at the protein level was carried out with PolyPhen-2 (http://genetics.bwh.harvard.edu/pph2/), SIFT (https://sift.bii.a-star.edu.sg/www/sift_seq_submit2), and MutationTaster (https://www.mutationtaster.org/). The allelic frequency of the variants was determined with Exome Aggregation Consortium (ExAC) and Exome Sequencing Project (ESP) (URL: http://evs.gs.washington.edu/EVS/). The confirmation of the variant was performed via the Sanger sequencing of the proband and those of the parents using an automated sequencer (ABI3500; PE Biosystems, Foster City, CA). The primers for amplifying the COMP gene were forward 5′-CTGAAGCTCTGAGAGGGAAG-3′ and reverse 5′-CAGCTGATGGGTCTCATAGTC-3′ for exon 18.

The WES analysis showed a heterozygous variant, c.2153G>C (p.Arg718Pro) in exon 18 of the COMP gene (Chr19 [GRCh38]: g.18783128C>G, NM_000095.2). Targeted Sanger sequencing analysis confirmed the mutation in the proband, but it was not found in either of the healthy parents, confirming that the origin of the mutation was de novo (shown in Fig. 1b). The p.Arg718Pro variant has been described in the literature and appears in the HGMDpro database (CM051440) as a pathogenic variant associated with MED [Kennedy et al., 2005]. In the ClinVar database (65,557) and Gene Reviews database p.Arg718Pro has been classified as a pathogenic variant. This variant is recorded in the dbSNP database with reference number rs149551600 and minor allele frequencies of T = 0.00002/2 in (ExAC) and T = 0.00008/1 in ESP. In silico prediction algorithms have described the p.Arg718Pro change as probably damaging (score 1.0) in Polyphen, tolerated in SIFT, and having a deleterious effect in MutationTaster. The nucleotide variant c.2153G>C is a transversion, which produces a change of the amino acid arginine to proline at position 718 of the polypeptide chain (p.Arg718Pro). The amino acids arginine and proline have moderate physicochemical differences (Grantham distance: 103 [0–215]). The p.Arg718Pro change is found in a highly conserved residue and is part of the globular C-terminal domain.

In this study, according to the clinical, radiological, and genetic data, our case was diagnosed as severe, sporadic PSACH. Overall, 42.8% of PSACH cases are diagnosed as severe, and 85.8% are diagnosed as sporadic [Kennedy et al., 2005]. The main difference between our severe PSACH case and the previous MED case with the c.2153G>C (p.Arg718Pro) mutation was the radiological observation of spindle-shaped vertebrae at the lumbar level in our case, which was not described in the previously reported MED case [Kennedy et al., 2005]. The severe short stature of our patient is in apparent disagreement with the point mutation located in the C-terminal globular region, outside the CLR site, which has been most related to severe short stature [Mabuchi et al., 2003]. Point mutations predominate with 53% on the COMP gene, and 85% of the time these are located in the 10, 13, and 14 exons of the PSACH cases. The remainder of the mutations were deletion-insertions [Kennedy et al., 2005]. Other mutations, such as the c.2152C>T (p.Arg718Trp) contiguous to the point mutation in our case, were related to a family exhibiting Fairbank-type MED (case MED001) [Mabuchi et al., 2003], while the c.2155G>A (p.Gly719Ser) [Kennedy et al., 2005] and c.2156G>A (p.Gly719Asp) [Mabuchi et al., 2001] mutations were observed in a family with PSACH no specified and a patient with PSACH no specified, respectively. Interestingly, these adjacent mutations in exon 18 have produced different phenotypes (shown in Table 1). The function of the region encoded by exon 18 and other 16 sites in other exons (p.292Cys, p.326Asp, p.348Cys, p.371Cys, p.376Asp, p.378Asp, p.397Asp, p.407Cys, p.427Gly, p.453Asp, p.454ser, 479Asp, p.507Asp, p.518Asp, p.585Thr, and p719Gly) regarding the clinical heterogeneity of MED and PSACH based in HGMDpro 2021 remains to be determined. We note that the wild-type amino acid sites that underwent changes and that are related to clinical heterogeneity of MED and PSACH are located in the CLR domains; these were Asp at 64% and Cys at 28% (Fig. 2), which could partially explain their relationship with clinical heterogeneity, while the amino acid changes (mutations) are heterogeneous to show relationship with clinical heterogeneity. On the other hand, the p.Arg718Pro mutation in our case and the previous Ser454Arg mutation showing both PSACH and MED or the study of Kennedy et al. [2005], where they observed that the type I polymorphism (Asn386Asp) was not disease causing in a highly conserved residue, and mutations in neighboring residues (Asp385Asn and Cys387Gly) were shown to cause MED and PSACH, respectively, could be more explained by epigenetic factors, the variation in each allele’s expression, or the different protein concentrations, that could play a role in determining the phenotype of patients with PSACH or MED. It is noteworthy that, in the study of Kennedy et al. [2005], 22% of the families with clinical suspicion of PSACH did not have a mutation in the COMP gene, which confirms the genetic and clinical heterogeneity of bone dysplasia that includes the spine, epiphysis, and metaphysis, emphasizing the need for the application of genomic techniques to maximize the efficiency of mutation detection, as was carried out in this case.

Table 1.

Mutations detected in exon 18 of the COMP gene

 Mutations detected in exon 18 of the COMP gene
 Mutations detected in exon 18 of the COMP gene
Fig. 2.

Shows the exons of the cartilage oligomeric matrix protein gene (red squares), the N-terminal domain (blue), four epidermal growth factor-like repeats (yellow), eight calmodulin-like repeats (CLR) (purple), and C-terminal domains (orange) of the COMP protein. The ubication sites of fifteen wild-type amino acids are shown (black); black lines indicate the connection of the changed amino acid sites with the CLRs or C-terminal domains. The continuous green and blue lines below the amino acid changes (red in parenthesis) are related to the clinical presentation of MED and PSACH. The amino acid change in blue indicates the recurrent mutation and purple indicates the change found in the 18 exon and C-terminal domain.

Fig. 2.

Shows the exons of the cartilage oligomeric matrix protein gene (red squares), the N-terminal domain (blue), four epidermal growth factor-like repeats (yellow), eight calmodulin-like repeats (CLR) (purple), and C-terminal domains (orange) of the COMP protein. The ubication sites of fifteen wild-type amino acids are shown (black); black lines indicate the connection of the changed amino acid sites with the CLRs or C-terminal domains. The continuous green and blue lines below the amino acid changes (red in parenthesis) are related to the clinical presentation of MED and PSACH. The amino acid change in blue indicates the recurrent mutation and purple indicates the change found in the 18 exon and C-terminal domain.

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In conclusion, the recurrent mutation p.Arg718Pro in the COMP gene adds another amino acid site with clinical heterogeneity regarding PSACH with anterior spindle-shaped vertebral bodies and severe short stature. The severe short-stature phenotype observed in our case is not consistent with the mutation located outside the eight CLRs of the COMP gene. The rapid detection of the mutation by means of WES allowed a specific diagnosis to be established. This result had implications for the family and helped set a better standard for genetic counseling.

We thank the patient and his family.

Written informed consent for performing genetic tests and other medical diagnostic procedures as well as publication of this case report, including any accompanying images was obtained from the patient’s guardians and all participants in compliance with the Helsinki Declaration. This study protocol was reviewed and approved by the Ethics and Health Research Committee of the ISSEMYM Ecatepec Medical Center, approval number PICME 2022/06.

The authors have no conflicts of interest to declare.

The authors have no funding sources to declare.

Jaime Toral López took care of the patient and collected the data, created the concept and designed the case report, took the lead in writing the manuscript, and planned and supervised the work. Luz Maria Gonzalez Huerta and Jaime Toral López carried out the genetic examination using WES and interpretation of the results, review and editing of the manuscript.

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

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