Bone Fragility and Fracture Panel

This panel includes the major genes associated with fragile bone conditions such as osteogenesis imperfecta, hypophosphatasia, inherited hypophosphatemic rickets,  inherited sclerosing bone dysplasias and Paget disease of bone.

Osteogenesis imperfecta (OI) is a clinically and genetically heterogeneous skeletal disorder characterized by frequent bone fractures with or without minimal trauma. Clinical signs of OI can range from mild to severe. In addition to bone fractures, patients may have scoliosis, bowing of long bones, short stature, blue sclera, hearing loss, dentin defects, muscle weakness or joint laxity. Bone fractures and bowing of long bones in osteogenesis imperfecta patients may occur prenatally in severe OI cases, and hearing loss may occur in ~50% of type I OI patients by 40-years of age (Genetics of Osteogenesis Imperfecta). The incidence is approximately 6/100,000 (van Dijk et al. 2012. PubMed ID: 21829228). Approximately 90% of clinically diagnosed OI is caused by pathogenic variants in the COL1A1 and COL1A2 genes, while ~10% is caused by pathogenic variants in the BMP1, CREB3L1, CRTAP, FKBP10, IFITM5, P3H1 (also called LEPRE1), PLOD2, PPIB, SEC24D, SERPINF1, SERPINH1, SP7, WNT1, TMEM38B, NTRK1 and other undefined genes (van Dijk and Sillence. 2014. PubMed ID: 24715559; Valadares et al. 2014. PubMed ID: 25046257; Moosa et al. 2015. PubMed ID: 26467156; Caparros-Martin et al. 2017. PubMed ID: 28116328).

Hypophosphatasia (HPP) is characterized by defective mineralization of bone and/or teeth in the presence of low activity of serum and bone alkaline phosphatase. Clinical features range from stillbirth without mineralized bone at the severe end to pathologic fractures of the lower extremities in later adulthood at the mild end. At least six clinical forms are currently recognized based on age at diagnosis and severity of features, including: (1) perinatal lethal HPP characterized by respiratory insufficiency and hypercalcemia; (2) perinatal benign HPP with prenatal skeletal manifestations that slowly resolve into the milder childhood or adult form; (3) infantile HPP with onset of rickets between birth and six months; (4) childhood HPP that ranges from low bone mineral density for age with unexplained fractures to rickets; (5) adult HPP characterized by early loss of adult dentition and stress fractures and pseudofractures of the lower extremities in middle age; and (6) odontohypophosphatasia characterized by premature exfoliation of primary teeth and/or severe dental caries as an isolated finding or as part of the above forms of HPP (Mornet and Nunes. 2016. PubMed ID: 20301329). HPP is caused by pathogenic variants in the ALPL gene.

Hypophosphatemic rickets is a condition of abnormal phosphate homeostasis characterized by renal phosphate wasting, hypophosphatemia, and rickets/osteomalacia. Patients usually manifest bone deformity such as bowed legs after 2 years old. Patients will also develop pain in the pelvis and legs with age (Bastepe and Jüppner. 2008. PubMed ID: 18365315).

Sclerosing bone dysplasias is an abnormal accumulation of bone caused by defect of osteoblast or osteoclast regulation. It is a clinically and genetically heterogeneous group of diseases including several conditions such as, but not limited to steopetrosis, pyknodysostosis, osteopoikilosis, osteopathia striata, progressive diaphyseal dysplasia, multiple diaphyseal sclerosis, and hyperostosis corticalis generalisata (Ihde et al. 2011. PubMed ID: 22084176; Boulet et al. 2016. PubMed ID: 26898950).

Osteopetrosis (also called Marble bone disease) is a disorder of increased bone density and bone mass caused by malfunction of bone resorption. Some clinical features can occur in infancy (Aker et al. 2012. PubMed ID: 22499339). Affected patients are at high risk of frequent bone fractures, delayed healing, hip osteoarthritis and osteomyelitis. Some patients have vision loss, hearing loss, paralysis of facial muscles, and bone marrow abnormalities caused by abnormal dense bone structure. Other features include short stature, development delay, dental abnormalities, hepatosplenomegaly, intellectual disability, and epilepsy (Tolar et al. 2004. PubMed ID: 15625335; Del Fattore et al. 2008. PubMed ID: 17936098; Sobacchi et al. 2013. PubMed ID: 23877423). The estimated incidence of this condition is 1:20,000 (autosomal dominant) to 1:250,000 (autosomal recessive) births (Palagano et al. 2018. PubMed ID: 29335834). It can be inherited in autosomal dominat, autosomal recessive and rarely in X-linked manners. The major genes involved are CLCN7, LRP5, TCIRG1, TNFSF11, CA2, OSTM1, SNX10 and TNFRSF11A.

Paget disease of bone (PDB) is the second most common metabolic bone disorder affecting ~2% of the population aged >40 years. It is chronic, non-inflammatory bone condition caused by increased bone resorption and new bone formation within lesion sites. The disorder is characterized by focal areas of increased and disorganized bone turnover, leading to bone pain, deformity, pathological fracture, neurological complications, and an increased risk of osteosarcoma (Laurin et.al. 2002. PubMed ID: 11992264; Wysiński and Krajewska-Włodarczyk. 2019. PubMed ID: 31462833; Nebot Valenzuela and Pietschmann. 2017. PubMed ID: 27600564). The axial skeleton is preferentially affected. Common sites of involvement include the pelvis (70% of cases), femur (55%), lumbar spine (53%), skull (42%), and tibia (32%) (Ralston et al. 2008. PubMed ID: 18620951). PDB can be inherited or sporadic, with the inherited form accounting for about one-third of patients with PDB (Michou. 2006. PubMed ID: 16574459).  The major genes are involved are SQSTM1 and TNFRSF11B. 

Molecular genetic testing is advantageous to establish an accurate diagnosis for individuals with weakened bone and bone fracture conditions.

Pathogenic variants in the COL1A1, COL1A2, and IFITM5 genes cause autosomal dominant OI. More than 95% of pathogenic variants in the COL1A1 and COL1A2 genes are nucleotide substitutions or small deletions or insertions, 1% -2% of COL1A1 and COL1A2 pathogenic variants are larger deletions or insertions (van Dijk and Sillence. 2014. PubMed ID: 24715559; Steiner and Basel. 2019. PubMed ID: 20301472). Almost all perinatal lethal OI are caused by de novo variants in COL1A1 and COL1A2 (Steiner and Basel. 2019. PubMed ID: 20301472).

Autosomal dominant and autosomal recessive Hypophosphatasia are caused by pathogenic variants in the ALPL gene. The majority of ALPL variants are inherited. In rare cases, de novo variants were reported (Mornet and Nunes. 2016. PubMed ID: 20301329; Taillandier et al. 2005. PubMed ID: 15671102).

X-linked Hypophosphatemic Rickets is mainly caused by deleterious variants in the PHEX gene and rarely caused by deleterious variants in CLCN5 (Hauer et al. 2018. PubMed ID: 29758562). Approximately 83% of female sporadic PHEX-related X-linked Hypophosphatemic ricket cases had a de novo variant (Durmaz et al. 2013. PubMed ID: 23079138).

Osteopetrosis are mainly caused by pathogenic variants in the following genes: CLCN7, LRP5, TCIRG1, TNFSF11, CA2, OSTM1, SNX10, and TNFRSF11A.

See individual gene summaries for more information about molecular biology of gene products and spectra of pathogenic variants.

Pathogenic variants in COL1A1 and COL1A2 were found in 90% of individuals with Osteogenesis Imperfecta (OI) types I, II, III, or IV (Steiner and Basel. 2019. PubMed ID: 20301472). A recent study reported that COL1A1 and COL1A2 pathogenic were identified in 56% (14/35) and 44% (11/35) of the OI cases, respectively (Stephen et al. 2014. PubMed ID: 24668929).

Sequencing of ALPL is predicted to detect pathogenic variants in 95% of cases with severe perinatal and infantile HPP. In milder forms, the detection rate is difficult to estimate. Overall, ~50% of cases with a clinical diagnosis of HPP have two ALPL pathogenic variants and 40%-45% have one pathogenic variant. The milder the disease, the higher the proportion in which only one ALPL pathogenic variant is detected (Mornet and Nunes. 2016. PubMed ID: 20301329).

In one study on hypophosphatemic rickets, PHEX pathogenic variants were identified 93 out of 118 probands (79%) (Gaucher et al. 2009. PubMed ID: 19219621). In another study, PHEX pathogenic variants were identified in 20 out of 24 unrelated probands (83%); three of these probands carried a large deletion or duplication detected by MLPA (Beck-Nielsen et al. 2012. PubMed ID: 22695891).

Pathogenic variants in the TCIRG1 and CLCN7 genes explain ~50% and 17% of autosomal recessive osteopetrosis, respectively (Palagano et al. 2018. PubMed ID: 29335834). In one study, SNX10 pathogenic variants were identified in 4% of 310 clinically diagnosed osteopetrosis cases (Pangrazio et al. 2013).

This test is performed using Next-Gen sequencing with additional Sanger sequencing as necessary.

This panel typically provides 97.8% coverage of all coding exons of the genes plus 10 bases of flanking noncoding DNA in all available transcripts along with other non-coding regions in which pathogenic variants have been identified at PreventionGenetics or reported elsewhere. We define coverage as ≥20X NGS reads or Sanger sequencing. PGnome panels typically provide slightly increased coverage over the PGxome equivalent. PGnome sequencing panels have the added benefit of additional analysis and reporting of deep intronic regions (where applicable).

Dependent on the sequencing backbone selected for this testing, discounted reflex testing to any other similar backbone-based test is available (i.e., PGxome panel to whole PGxome; PGnome panel to whole PGnome).