Identification of a novel homozygous mutation in the DDR2 gene from a patient with spondylo-meta-epiphyseal dysplasia by whole exome sequencing

Document Type : Original Article


1 Department of Animal Biology, Faculty of Natural Sciences, University of Tabriz, Tabriz, Iran

2 Ariagene Medical Genetics Laboratory, Mahmoudnejad Ave, Qom, Iran

3 Immunology Research Center, Tabriz University of Medical Sciences, Tabriz, Iran

4 Advanced Diagnostic and Interventional Radiology Research Center (ADIR), Tehran University of Medical Sciences (TUMS), Tehran, Iran

5 Department of Medical Genetics, Tehran University of Medical Sciences (TUMS), Tehran, Iran


Objective(s): The spondylo-meta-epiphyseal dysplasia (SMED) short limbs-hand type is a rare autosomal recessive disease, which is characterized by premature calcification leading to severe disproportionate short stature and various skeletal changes. Defective function of a conserved region encoding discoidin domain receptor tyrosine kinase 2 (DDR2 protein) by the discoidin domain-containing receptor 2 (DDR2 gene) is cause of this disease. The purpose of present study was to investigate disease-causing mutations on DDR2 gene in an Iranian family with SMED, and predict the DDR2 protein molecular mechanism in development of SMED.
Materials and Methods: In the present study, we evaluated a 2-year-old male with SMED. Detection of genetic changes in the studied patient was performed using Whole-Exome Sequencing (WES). PCR direct sequencing was performed for analysis of co-segregation of variants with the disease in family. Finally, in silico study was performed for further identification of molecular function of the identified genetic variant.
Results: We detected a novel splice-site mutation (NM_001014796: exon9: c.855+1G>A; NM_006182: exon8: c.855+1G>A) in DDR2 gene of the studied patient using WES. This mutation was exclusively detected in patients with homozygous SMED, not in healthy people. The effects of detected mutation on functions of DDR2 protein was predicted using in silico study.
Conclusion: The causative mutation in studied patient with SMED was identified using Next-generation sequencing (NGS), successfully. The identified novel mutation in DDR2 gene can be useful in prenatal diagnosis (PND) of SMED, preimplantation genetic diagnosis (PGD), and genetic counseling.


1. Smithson SF, Grier D, Hall CM. Spondylo-meta-epiphyseal dysplasia, short limb-abnormal calcification type. Clin Dysmorphol 2009; 18:31-35.
2. Al-Gazali LI, Bakalinova D, Sztriha L. Spondylo-meta-epiphyseal dysplasia, short limb, abnormal calcification type. Clin Dysmorphol 1996; 5:197-206.
3. Dias C, Cairns R, Patel MS. Sudden death in spondylo-meta-epiphyseal dysplasia, short limb-abnormal calcification type. Clin Dysmorphol 2009; 18:25-29.
4. Bargal R, Cormier-Daire V, Ben-Neriah Z, Le Merrer M, Sosna J, Melki J, et al. Mutations in DDR2 gene cause SMED with short limbs and abnormal calcifications. Am J Hum Genet 2009; 84:80-84.
5. Ali BR, Xu H, Akawi NA, John A, Karuvantevida NS, Langer R, et al. Trafficking defects and loss of ligand binding are the underlying causes of all reported DDR2 missense mutations found in SMED-SL patients. Hum Mol Genet 2010; 19:2239-2250.
6. Shrivastava A, Radziejewski C, Campbell E, Kovac L, McGlynn M, Ryan TE, et al. An orphan receptor tyrosine kinase family whose members serve as nonintegrin collagen receptors. Mol Cell 1997; 1:25-34.
7. Vogel WF, Abdulhussein R, Ford CE. Sensing extracellular matrix: an update on discoid in domain receptor function. Cell Signal 2006; 18:1108-1116.
8. Leitinger B. Transmembrane collagen receptors. Annu Rev Cell Dev Biol 2011; 27:265-290.
9. Valiathan RR, Marco M, Leitinger B, Kleer CG, Fridman R. Discoidin domain receptor tyrosine kinases: new players in cancer progression. Cancer Metastasis Rev 2012; 31:295-321.
10. Leitinger B, Kwan AP. The discoidin domain receptor DDR2 is a receptor for type X collagen. Matrix Biol 2006; 25:355-364.
11. Flynn LA, Blissett AR, Calomeni EP, Agarwal G. Inhibition of collagen fibrillogenesis by cells expressing soluble extracellular domains of DDR1 and DDR2. J MolBiol 2010; 395:533-543.
12. Labrador JP, Azcoitia V, Tuckermann J, Lin C, Olaso E, Mañes S, et al. The collagen receptor DDR2 regulates proliferation and its elimination leads to dwarfism. EMBO Rep 2001; 2:446-452.
13. Carafoli F, Mayer MC, Shiraishi K, Pecheva MA, Chan LY, Nan R, et al. Structure of the discoidin domain receptor 1 extracellular region bound to an inhibitory Fab fragment reveals features important for signaling. Structure 2012; 20:688-697.
14. Mihai C, Chotani M, Elton TS, Agarwal G. Mapping of DDR1 distribution and oligomerization on the cell surface by FRET microscopy. J Mol Biol 2009; 385:432-445.
15. Carafoli F, Bihan D, Stathopoulos S, Konitsiotis AD, Kvansakul M, Farndale RW, et al. Crystallographic insight into collagen recognition by discoidin domain receptor 2. Structure 2009; 17:1573-1581.
16. Heidari M, Soleyman-Nejad M, Taskhiri MH, Isazadeh A, Bolhassani M, Shahpouri J, et al. A Heterozygous STXBP1 gene de novo mutation in an Iranian child with epileptic encephalopathy: Case Report. Acta Med Iran 2019; 57:518-521.
17. Ahmadi M, Dehghanifard A, Isazadeh A, Hajazimian S, Mehdizadeh M, Rahaei S, et al. A Novel Homozygous MYO7A Mutation: Case Report. Acta Med Iran 2018; 56:348-350.
18. Heidari M, Soleyman-Nejad M, Taskhiri MH, Shahpouri J, Isazadeh A, Ahangari R, et al. Identification of two novel mutations in the ATM gene from patients with ataxia-telangiectasia by whole exome sequencing. Curr Genomics 2019; 20:531-534.
19. Al-Kindi A, Kizhakkedath P, Xu H, John A, Al Sayegh A, Ganesh A, et al. A novel mutation in DDR2 causing spondylo-meta-epiphyseal dysplasia with short limbs and abnormal calcifications (SMED-SL) results in defective intra-cellular trafficking. BMC Med Genet 2014; 15:42-52.
20. Leitinger B. Discoidin domain receptor functions in physiological and pathological conditions. Int Rev Cell Mol Biol 2014; 310:39-87.
21. Phan TN, Wong EL, Sun X, Kim G, Jung SH, Yoon CN, et al. Low stability and a conserved N-glycosylation site are associated with regulation of the discoidin domain receptor family by glucose via post-translational N-glycosylation. Biosci Biotechnol Biochem 2013;77:1907-1916.
22. Chen Y, Bellamy WP, Seabra MC, Field MC, Ali BR. ER-associated protein degradation is a common mechanism underpinning numerous monogenic diseases including Robinow syndrome. Hum Mol Genet 2005; 14:2559-2569.
23. Langer Jr LO, Wolfson BJ, Scott Jr CI, Reid CS, Schidlow DV, Millar EA, et al. Further delineation of spondylo‐meta‐epiphyseal dysplasia, short limb‐abnormal calcification type, with emphasis on diagnostic features. Am J Med Genet 1993; 45:488-500.
24. Borochowitz Z, Langer Jr LO, Gruber HE, Lachman R, Katznelson MB, Rimoin DL. Spondylo‐meta‐epiphyseal dysplasia (SMED), short limb‐hand type: A congenital familial skeletal dysplasia with distinctive features and histopathology. Am J Med Genet 1993; 45:320-326.
25. Rozovsky K, Sosna J, Le Merrer M, Simanovsky N, Koplewitz BZ, Bar-Ziv J, et al. Spondyloepimetaphyseal dysplasia, short limb-abnormal calcifications type: progressive radiological findings from fetal age to adolescence. Pediatr Radiol 2011; 41:1298-1307.