Regions of homozygosity and a novel variant in Steel syndrome: An added dilemma to diagnosisS Thakur1, P Paliwal2, KK Saxena3
1 Department of Genetics and Fetal Diagnosis, Fortis Hospital, New Delhi, India
2 Cytogenetics Lab, Institute of Medical Genetics and Genomics, Sir Ganga Ram Hospital, New Delhi, India
3 Radiology, Sir Ganga Ram Hospital, New Delhi, India
Correspondence Address: Source of Support: None, Conflict of Interest: None DOI: 10.4103/jpgm.jpgm_1153_21
Source of Support: None, Conflict of Interest: None
Keywords: Autosomal recessive, COL27A1, Steel syndrome, whole exome sequencing
Steel syndrome (OMIM #615155) is a rare autosomal recessive (AR) genetic disorder that is characterized by skeletal system abnormalities. The affected individuals present with features such as congenital bilateral hip and radial head dislocations, carpal coalitions, scoliosis, short stature, pes cavus, and facial dysmorphism., Mutations in COL27A1 gene were implicated in the etiology of the characteristic features of Steel syndrome. COL27A1 gene is located on chromosome 9q32. Proalpha1 (XXVII) is the major protein product of COL27A1 gene. Proalpha1 is an essential component of the extracellular matrices of cartilage and other tissues, and it plays an important structural role in the pericellular extracellular matrix of the proliferative zone in the growth plate and is required for the organization of the proliferative zone for chondrocytes. Majority of patients described with mutation in COL27A1 gene are of Puerto Rican origin. In the present study, we describe a patient from India carrying a novel homozygous mutation in COL27A1 gene.
A 4-year-old girl born of a non-consanguineous marriage presented with clinical indications of short stature, speech delay, kyphosis, mild dorsolumbar scoliosis, bilateral patellar dislocation, bilateral developmental dysplasia of the hip (DDH) with bilateral congenital talipes equinovarus with proximal femoral focal deficiency (PFFD).
Clinical history at the time of presentation revealed that she was delivered at eight months by lower segment cesarean section. Her birth weight was 2.5 kg. She cried immediately at birth. Club foot and bilateral hip dysplasia were noted at birth. Her developmental mile stones were mildly delayed. She achieved head control at four to five months of age, started sitting at one year and started standing at 1.5 years. She was able to walk when was she two years old. She had speech delay, and her fine motor skills and social skills were within normal limits.
Later at seven months of age, her left upper limb and lower limb were observed to be short as compared to the right side and PFFD0 was diagnosed. She had bilateral genu valgum since birth and had a lurching gait. Her bilateral medial femoral condyles were prominent. Bilateral patellar dislocation was also reported. For clubfoot she was provided casting 10–12 times but with no relief. She underwent bilateral distal femoral epiphysiodesis (at knee) with bone staples at the age of three.
On examination, the child had a prominent forehead, depressed nose, long philtrum, and thin lips. Growth standards were assessed with normative data for age using World Health Organization (WHO) child growth standards. The height was 80 cm (-3SD), arm span of 82 cm, head circumference was 48 cm (3rd–50th centile). Bilateral genu valgum was noted. Her speech was delayed, and she just started to combine words. BERA test done showed 50% hearing loss. Since then, she is on hearing aids [Figure 1]a, [Figure 1]b, [Figure 1]c, [Figure 1]d, [Figure 1]e.
Genomic DNA was extracted from lymphocytes from the child and parents. Whole exome sequencing was performed as reported earlier. A splice site homozygous change c. 4044 + 2T>C (ENST00000356083.8) was noted in the COL27A1 gene. This variant was not present in the 1000 Genomes project, GnomAD browser, and in-house exome dataset. Further in silico prediction of the variant was found to be damaging by MutationTaster2, and the reference base is conserved across species and is classified as pathogenic as per American College of Medical Genetics (ACMG) guidelines. The presence of this variant was confirmed by Sanger sequencing. Sequencing of parents for similar change revealed absence of this change in the father, and mother was found to be heterozygous for this change. Further investigation of proband to ascertain the cause of homozygosity revealed stretches of homozygosity (6.59% of genome) for the region containing COL27A1 gene as revealed by microarray analysis. [Figure 1]f The presence of the region of homozygosity (ROH) containing COL27A1 gene in this patient resulted in both copies of these genes harboring same variation (c.4044 +2T >C) and a rare possibility of inheriting the AR disease from only one parent who is a heterozygous carrier.
The parents presented to us for posttest counselling after two years of genetic testing; in the meanwhile, the child had undergone a repeat bilateral distal femoral epiphysiodesis at 4.5 years of age. Surgery for congenital hip dislocation was done at five years of age at a gap of one month and consisted of open reduction with varus derotation osteotomy plus staples. After one year of using hearing aid, she started to speak simple sentences, though speech was not clear at the last visit, and the patient is presently undergoing speech therapy.
Steel syndrome has a characteristic presentation for patients harboring the c.2089G>C; p. (Gly697Arg) variant in COL27A1 and has been reviewed earlier. Some atypical features, including sensorineural deafness, atypical facies, DDH, and the presence of the COL27A1 variant helped us with the differential diagnosis of the present case as Steel syndrome. However, there are several overlapping features of other skeletal developmental disorders such as Larsen syndrome, arthrogryposis multiplex congenital, or auriculo-osteodysplasia. Larsen syndrome in particular has multiple overlapping features such as the presence of multiple congenital dislocations, and unusual facial anomalies, with a depressed nasal bridge, wide-spaced eyes, and a prominent forehead; however, one distinguishing feature of Larsen syndrome is dislocation of the knees which is a nearly constant feature and can help with the differential diagnosis.
The presence of PFFD as noted in the present case has not been described previously in cases of Steel syndrome which can be unique presentation of this disorder leading to secondary hip dysplasia. In view of short stature, high forehead, frontal bossing, hypertelorism, we first suspected achondroplasia, hypochondroplasia, pseudoachondroplasia and because of severe joint deformities we planned to do the whole exome rather than FGFR3 gene analysis.
AR disorders are caused by mutations in both copies of the gene resulting in complete loss of functional protein. Splice site point mutations occurring at the consensus sequences can cause improper exon and intron recognition and may result in the formation of an aberrant transcript of the mutated gene, thus altering the open reading frame. The mutation c. 4044 +2T>C was categorized as pathogenic using the bioinformatics tools; however, further studies such as generation of mouse models are needed to assess the consequences of this mutation and its effect on the phenotype. A previously reported mouse model of Col27A1 deficiency exhibited severe skeletal abnormalities with chondrodysplasia and perinatal death due to lung defects and another study with orthologous variant equivalent to the most prevalent function altering variant and human disorder associated with this gene showed short stature and some of the skeletal abnormalities observed in the human subjects.
With technological advancements, we are gaining better insights into causation of these AR disorders. Consanguinity is usually associated with a higher prevalence of these disorders particularly at the population level. However, several studies have now indicated that ROHs may be present because of parental relatedness, chromosomal recombination, or rearrangements and can result in AR disorders. In the present case, the father was not harboring a similar mutation and microarray analysis identified region of homozygosity in the proband. Therefore, in this patient, the recombination has to be postzygotic (mitotic). This could be due to recombination in a trisomic cell, followed by trisomy rescue or loss of paternal chromosome 9q followed by reduplication of maternal chromosome 9q. Postzygotic recombination in a diploid cell can result in mosaicism with partial isodisomy.
Such studies further signify the importance of segregation analysis of rare homozygous variants where clinical suspicion is high and sequencing studies identify a variant of uncertain significance. The structure and characteristic of each population is unique and a genetic diagnosis in the absence of protein-based studies of mutations in rare disorders requires clinical acumen to help the patients. In the present case, the phenotype and the genetic correlation of the identified homozygous variant in COL27A1 gene led us to classify this to be a case of Steel syndrome. This helped in further management of the patient as it has been shown that surgeries of the skeletal changes are not beneficial to the patients and at times can result in other associated problems. Identification of mutation also helps in genetic counselling of these families where this needs to be emphasized that the recurrence risk is 1% despite this being an AR disorder. Studies such as these can help in determining the frequency of mutation in the gene in population worldwide.
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