A novel mutation in COL2A1 leading to spondyloepiphyseal dysplasia congenita in a three-generation family

Clinical-genetic analysis of selected genes involved in the development of the human skeleton in 128 Czech patients with suspected congenital skeletal abnormalities

BACKGROUND

Congenital skeletal abnormalities are a heterogeneous group of diseases most commonly associated with small or disproportionate growth, cranial and facial dysmorphisms, delayed bone maturation, etc. Nonetheless, no detailed genotype-phenotype correlation in patients with specific genetic variants is readily available. Ergo, this study focuses on the analysis of patient phenotypes with candidate variants in genes involved in bone growth as detected by molecular genetic analysis.

METHODS

In this study we used molecular genetic methods to analyse the ACAN, COL2A1, FGFR3, IGFALS, IGF1, IGF1R, GHR, NPR2, STAT5B and SHOX genes in 128 Czech children with suspected congenital skeletal abnormalities. Pathogenic variants and variants of unclear clinical significance were identified and we compared their frequency in this study cohort to the European non-Finnish population. Furthermore, a prediction tool was utilised to determine their possible impact on the final protein. All clinical patient data was obtained during pre-test genetic counselling.

RESULTS

Pathogenic variants were identified in the FGFR3, GHR, COL2A1 and SHOX genes in a total of six patients. Furthermore, we identified 23 variants with unclear clinical significance and high allelic frequency in this cohort of patients with skeletal abnormalities. Five of them have not yet been reported in the scientific literature.

CONCLUSION

Congenital skeletal abnormalities may lead to a number of musculoskeletal, neurological, cardiovascular problems. Knowledge of specific pathogenic variants may help us in therapeutic procedures.

Rgp1 contributes to craniofacial cartilage development and Rab8a-mediated collagen II secretion

Rgp1 was previously identified as a component of a guanine nucleotide exchange factor (GEF) complex to activate Rab6a-mediated trafficking events in and around the Golgi. While the role of Rgp1 in protein trafficking has been examined in vitro and in yeast, the role of Rgp1 during vertebrate embryogenesis and protein trafficking in vivo is unknown. Using genetic, CRISPR-induced zebrafish mutants for Rgp1 loss-of-function, we found that Rgp1 is required for craniofacial cartilage development. Within live rgp1-/- craniofacial chondrocytes, we observed altered movements of Rab6a+ vesicular compartments, consistent with a conserved mechanism described in vitro. Using transmission electron microscopy (TEM) and immunofluorescence analyses, we show that Rgp1 plays a role in the secretion of collagen II, the most abundant protein in cartilage. Our overexpression experiments revealed that Rab8a is a part of the post-Golgi collagen II trafficking pathway. Following loss of Rgp1, chondrocytes activate an Arf4b-mediated stress response and subsequently respond with nuclear DNA fragmentation and cell death. We propose that an Rgp1-regulated Rab6a-Rab8a pathway directs secretion of ECM cargoes such as collagen II, a pathway that may also be utilized in other tissues where coordinated trafficking and secretion of collagens and other large cargoes is required for normal development and tissue function.

Discovery of sensorineural hearing loss and ossicle deformity in a Chinese Li nationality family with spondyloepiphyseal dysplasia congenita caused by p.G504S mutation of COL2A1

Background

Spondyloepiphyseal dysplasia congenita (SEDC) is an autosomal dominant chondrodysplasia characterized by disproportionate short stature, abnormal epiphyses, and flattened vertebral bodies. COL2A1 has been confirmed as the pathogenic gene. Hearing loss represents an infrequent manifestation for 25–30% of patients with SEDC. The characteristics of the hearing impairment were rarely documented.

Methods

Audiological, ophthalmic, imaging examinations were conducted on the family members. The whole exome sequencing (WES) was performed to detect the candidate gene, and the Sanger sequencing was used to confirm the causative variation.

Results

COL2A1 c.1510G>A (p.G504S), a hot spot variation, was identified as the disease-causing mutation of the Chinese Li nationality family with SEDC. This variation was co-segregated with the SEDC phenotype in the family and was absent in the 1000 Genomes Project, ESP and ExAC. Clinically, several manifestations were first demonstrated in SEDC patients caused by p.G504S, including sensorineural hearing loss, auditory ossicles deformity, retinal detachment, sacrum cracked and elbow and wrist joints deformity. Other classical SEDC manifestations such as bones and joints pain, midfacial dysplasia, disproportionate short stature, spinal deformity, thoracocyllosis, coxa arthropathy, myopia and waddling gait were also showed in the family patients.

Conclusion

We first identified the mutation p.G504S in COL2A1 gene as the pathogenesis in a Chinese Li nationality family and reported the correlation between p.G504S and atypical clinical phenotypes including sensorineural hearing loss, auditory ossicles deformity, retinal detachment, sacrum cracked and elbow and wrist joints deformity. Our findings would extend the phenotypic spectrum of SEDC and deepen clinicians' understanding of genotype–phenotype correlation of the disease.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-021-01020-y.

Targeted Deletion of Loxl3 by Col2a1-Cre Leads to Progressive Hearing Loss

Collagens are major constituents of the extracellular matrix (ECM) that play an essential role in the structure of the inner ear and provide elasticity and rigidity when the signals of sound are received and transformed into electrical signals. LOXL3 is a member of the lysyl oxidase (LOX) family that are copper-dependent amine oxidases, generating covalent cross-links to stabilize polymeric elastin and collagen fibers in the ECM. Biallelic missense variant of LOXL3 was found in Stickler syndrome with mild conductive hearing loss. However, available information regarding the specific roles of LOXL3 in auditory function is limited. In this study, we showed that the Col2a1-Cre-mediated ablation of Loxl3 in the inner ear can cause progressive hearing loss, degeneration of hair cells and secondary degeneration of spiral ganglion neurons. The abnormal distribution of type II collagen in the spiral ligament and increased inflammatory responses were also found in Col2a1–Loxl3^–/– mice. Amino oxidase activity exerts an effect on collagen; thus, Loxl3 deficiency was expected to result in the instability of collagen in the spiral ligament and the basilar membrane, which may interfere with the mechanical properties of the organ of Corti and induce the inflammatory responses that are responsible for the hearing loss. Overall, our findings suggest that Loxl3 may play an essential role in maintaining hearing function.

Novel variants in COL2A1 causing rare spondyloepiphyseal dysplasia congenita

Background

Spondyloepiphyseal dysplasia congenita (SEDC) is an extremely rare inherited chondrodysplasia characterized by abnormal epiphyses, short stature, and flattened vertebral bodies. We investigate the phenotypes and the disease‐associated variants of SEDC in two unrelated Chinese families.

Methods

We identified disease‐associated variants in two nonconsanguineous families with SEDC using targeted next‐generation sequencing and confirmed the variants using Sanger sequencing. We investigated the phenotypes of the patients, including clinical manifestations, bone turnover biomarkers, bone mineral density and skeletal radiographic features.

Results

Two probands were diagnosed as SEDC according to the phenotypes of disproportionately short‐trunk stature, kyphosis, lumbar lordosis and adduction deformity of hips. Radiographs revealed kyphosis and lumbar lordosis, flattened vertebral bodies, compressed femoral heads and shortening of the femurs. Bone mineral density of the probands was lower than that of age‐ and gender‐matched normal children, but bone turnover biomarker levels were within normal range. Two novel heterozygous missense variants (NM_001844.5: c.1654 G>A, NP_001835.3: p.Gly552Arg; NM_001844.5: c.3518G>T, NP_001835.3: p.Gly1173Val) in collagen type II alpha 1 chain (COL2A1) were detected in the two families, which would impair the formation of stable triple‐helical type II collagen.

Conclusions

We identified two novel disease‐associated variants in COL2A1, which led to severe SEDC. Our findings expanded the gene variant spectrum and phenotypic spectrum of extremely rare type II collagenopathies.

COL2A1 Gene Mutations: Mechanisms of Spondyloepiphyseal Dysplasia Congenita

The COL2A1 gene consists of 54 exons spanning over 31.5 kb and encodes for type II collagen. Type II collagen is the main component of hyaline cartilage extracellular matrix, nucleus pulposus of intervertebral discus, vitreous humor of the eye and inner ear structure. Molecular defects in COL2A1 gene cause a wide variety of rare autosomal-dominant conditions known as type II collagenopathies. A clear genotype-phenotype relationship is not yet known. However, some correlations are described. Spondyloephyseal dysplasia congenita was suggested for a short-trunk dwarfing condition affecting primarily the vertebrae and the proximal epiphyses of the long bones.

A Heterozygous Mutation in the Triple Helical Region of the Alpha 1 (II) Chain of the COL2A1 Protein Causes Non-Lethal Spondyloepiphyseal Dysplasia Congenita

Objective:Heterozygous pathogenic variants in the COL2A1 gene result in several clinical features including impaired skeletal growth, ocular and otolaryngological abnormalities. Missense mutations in the triple helical region of the COL2A1 protein have been associated with lethal spondyloepiphyseal dysplasia (SED). In this study, we aimed to identify the underlying cause of a case of SED congenita (SEDC) in a 27-month-old child. Materials and Methods: A patient who was diagnosed initially with osteochondrodysplasia underwent a detailed clinical and radiological examination to obtain a conclusive diagnosis. The patient did not show any clinical features of hypochondrogenesis. Whole exome sequencing of the COL2A1 gene was carried out to identify the underlying genetic cause of the disorder. Results: Variant annotation and filtration detected a heterozygous missense mutation c.1357G>A (p.G453S) in the exon 21 of the COL2A1 gene of the proband which was confirmed by Sanger sequencing. Neither parent carried the mvariant suggesting this was a new mutation. Conclusion: The COL2A1 mutation (c.1357G>A), identified in this case, results in more mild phenotype than other missense mutations in exon 21 which are known to cause lethal hypochondrogenesis. We showed, for the first time, that a missense mutation (p.G453S) in the triple helical region of the alpha 1 (II) chain of the COL2A1 protein underlies SEDC and is not always lethal.

Identification of an Autosomal Dominant Mutation in the COL2A1 Gene Leading to Spondyloepiphyseal Dysplasia Congenita in a Greek Family

A boy and his father with severe short stature, progressively evolving body asymmetry, and skeletal abnormalities are presented. A next-generation sequencing exome study was performed, and the patient was found heterozygous for the c.1609G>A (p.Gly537Ser) mutation in the COL2A1 gene. This mutation is considered a pathogenic variant and has been previously registered in the Human Gene Mutation Database (HGMD) in association with spondyloepiphyseal dysplasia (accession: CM052184). It has been described in a patient as a sporadic case and resulted in a severe phenotype. Segregation studies, in order to determine the inheritance pattern, identified the same mutation in our patient's father. The variant was transmitted in an autosomal dominant pattern. In conclusion, we describe a patient with hereditary spondyloepiphyseal dysplasia congenita, caused by a c.1609G_A (p.Gly537Ser) mutation in the COL2A1 gene, which resulted in a milder phenotype.

Recurrent c.G1636A (p.G546S) mutation of COL2A1 in a Chinese family with skeletal dysplasia and different metaphyseal changes: a case report

Background

Mutations in the COL2A1 gene cause type II collagenopathies characterized by skeletal dysplasia with a wide spectrum of phenotypic severity. Most COL2A1 mutations located in the triple-helical region, and the glycine to bulky amino acid substitutions (e.g., glycine to serine) in the Gly-X-Y repeat were identified frequently. However, the same COL2A1 mutations are associated with different phenotypes and the genotype-phenotype relationship is still poorly understood. Therefore, the studies of more patients about the recurrent mutations in COL2A1 will be needed for further research to provide more comprehensive clinical and genetic data. In this paper, we report a rare recurrent c.G1636A (p.G546S) mutation in COL2A1 associated with different metaphyseal changes in a Chinese family.

Case presentation

The proband (III-3) was the second child of the family with skeletal dysplasia. She was 2 years and 3 months old with disproportional short stature, short neck, pectus carinatum, genu varum, bilateral pes planus, and obvious waddling gait. Notably, she displayed severe metaphyseal lesions, especially typical “dappling” and “corner fracture” appearance, whereas no particular metaphyseal involvement was detected in the proband’s mother (II-3) and elder sister (III-2) in the family. We identified a heterozygous mutation (c.1636G > A) in COL2A1 in the three patients, causing the substitution of glycine to serine in codon 546. Although the same mutation has been reported in two previous studies, the phenotypes of the previous patients were different from those of our patients, and the characteristic “dappling” and “corner fracture” metaphyseal abnormalities were not reported previously.

Conclusions

In this study, we identified a c.G1636A (p.G546S) mutation in the COL2A1 associated with different metaphyseal changes, which was never reported in the literature. Our findings revealed a different causative amino acid substitution (glycine to serine) associated with the “dappling” and “corner fracture” metaphyseal abnormalities, and may provide a useful reference for evaluating the phenotypic spectrum and variability of type II collagenopathies.

Molecular genetics of the COL2A1-related disorders

Type II collagen, comprised of three identical alpha-1(II) chains, is the major collagen synthesized by chondrocytes, and is found in articular cartilage, vitreous humour, inner ear and nucleus pulposus. Mutations in the collagen type II alpha-1 gene (COL2A1) have been reported to be responsible for a series of abnormalities, known as type II collagenopathies. To date, 16 definite disorders, inherited in an autosomal dominant or recessive pattern, have been described to be associated with the COL2A1 mutations, and at least 405 mutations ranging from point mutations to complex rearrangements have been reported, though the underlying pathogenesis remains unclear. Significant clinical heterogeneity has been reported in COL2A1-associated type II collagenopathies. In this review, we highlight current knowledge of known mutations in the COL2A1 gene for these disorders, as well as genetic animal models related to the COL2A1 gene, which may help us understand the nature of complex phenotypes and underlying pathogenesis of these conditions.

Mutation Update for COL2A1 Gene Variants Associated with Type II Collagenopathies

Mutations in the COL2A1 gene cause a spectrum of rare autosomal-dominant conditions characterized by skeletal dysplasia, short stature, and sensorial defects. An early diagnosis is critical to providing relevant patient care and follow-up, and genetic counseling to affected families. There are no recent exhaustive descriptions of the causal mutations in the literature. Here, we provide a review of COL2A1 mutations extracted from the Leiden Open Variation Database (LOVD) that we updated with data from PubMed and our own patients. Over 700 patients were recorded, harboring 415 different mutations. One-third of the mutations are dominant-negative mutations that affect the glycine residue in the G-X-Y repeats of the alpha 1 chain. These mutations disrupt the collagen triple helix and are common in achondrogenesis type II and hypochondrogenesis. The mutations resulting in a premature stop codon are found in less severe phenotypes such as Stickler syndrome. The p.(Arg275Cys) substitution is found in all patients with COL2A1-associated Czech dysplasia. LOVD-COL2A1 provides support and potential collaborative material for scientific and clinical projects aimed at elucidating phenotype-genotype correlation and differential diagnosis in patients with type II collagenopathies.

Identification of a Novel Mutation in the COL2A1 Gene in a Chinese Family with Spondyloepiphyseal Dysplasia Congenita

Spondyloepiphyseal dysplasia congenita (SEDC) is an autosomal dominant chondrodysplasia characterized by disproportionate short-trunk dwarfism, skeletal and vertebral deformities. Exome sequencing and Sanger sequencing were performed in a Chinese Han family with typical SEDC, and a novel mutation, c.620G>A (p.Gly207Glu), in the collagen type II alpha-1 gene (COL2A1) was identified. The mutation may impair protein stability, and lead to dysfunction of type II collagen. Family-based study suggested that the mutation is a de novo mutation. Our study extends the mutation spectrum of SEDC and confirms genotype-phenotype relationship between mutations at glycine in the triple helix of the alpha-1(II) chains of the COL2A1 and clinical findings of SEDC, which may be helpful in the genetic counseling of patients with SEDC.

Identification of a novel mutation of the COL2A1 gene in a Chinese family with spondyloepiphyseal dysplasia congenita

PURPOSE

To identify potential disease-causing mutation in the COL2A1 gene in a Chinese family with autosomal dominant spondyloepiphyseal dysplasia congenita (SEDC) and to analyze the phenotype-genotype correlation.

METHODS

Complete physical and radiographic examinations of four affected individuals from SEDC family were conducted. Genomic DNA were isolated from peripheral blood leukocytes. All 54 exons and exon-intron boundaries of the COL2A1 gene were amplified by polymerase chain reaction (PCR) and bidirectionally sequenced.

RESULTS

All four affected individuals were found carried a novel missense mutation of c.2224G>A (p.Gly687Ser) in COL2A1, while normal members of the family and 50 healthy controls did not have this mutation. Protein prediction of missense mutation by polyphen-2 and SIFT software and mutation taster indicated severe damage to the function.

CONCLUSIONS

c.2224G>A (p.Gly687Ser) is a novel mutation of COL2A1 associated with spondyloepiphyseal dysplasia congenital. There are heterozygous of phenotype for the mutation in members of the pedigree analyzed. Onset becomes more earlier and severe with each successive generation.