Amelogenesis Imperfecta Panel

Amelogenesis imperfecta (AI) is a heterogeneous condition of enamel defects affecting both primary and permanent dentitions. Affected teeth are usually small, discolored, pitted or grooved, and prone to rapid wear and breakage. Based on clinical and radiographic features of the enamel defects as well as on the mode of inheritance pattern, AI has been divided into 14 different subtypes, which can be grouped into four major forms: hypoplastic, hypomaturation, hypocalcified, and hypomaturation-hypoplastic with taurodontism (Witkop et al. 1988). Hypoplastic AI shows reduced enamel volume with pits or grooves, but enamel is usually hard and translucent. Hypomaturation and hypocalcified AI have hypomineralized enamel with nearly normal matrix volume. Hypomaturation enamel is hard, but brittle and prone to breaking off. Hypocalcified AI may present soft enamel which can be easily scraped away by attrition. Hypomaturation-hypoplastic with taurodontism shows reduced, hypomineralized enamel with pits; in addition, molars or other teeth may present enlarged pulp chambers (Witkop et al. 1988; Crawford et al. 2007).

AI and AI-related syndrome are currently known to be caused by pathogenic variants in the following genes: AMELX (Aldred et al. 1992), DLX3 (Price et al. 1998), ENAM (Mårdh et al. 2002), KLK4 (Hart et al. 2004), MMP20 (Kim et al. 2005), FAM83H (Lee et al. 2008; Kim et al. 2008), WDR72 (El-Sayed et al. 2009), FAM20A (O'Sullivan et al. 2011), ODAPH (C4orf26) (Parry et al. 2012), ROGDI (Schossig et al. 2012), SLC24A4 (Parry et al. 2013), ITGB6 (Poulter et al. 2014; Wang et al. 2014), LAMB3 (Kim et al. 2013), CNNM4 (Parry et al. 2009), NHS (Burdon et al. 2003), GPR68 (Parry et al. 2016), SLC24A4 (Parry et al. 2013), LTBP3 (Huckert et al. 2015) and SMOC2 (Bloch-Zupan et al. 2011).

Enamel defects can also occur as syndromic disorders. For example, Kohlschütter–Tönz syndrome features enamel defects, psychomotor delay or regression and seizures caused by ROGDI pathogenic variants (Tucci et al. 2013); Nance-Horan syndrome (NHS) is characterized by congenital cataracts, dental anomalies, dysmorphic features and mental retardation caused by pathogenic variants in the NHS gene (Burdon et al. 2003); Jalili Syndrome features autosomal-Recessive Cone-Rod dystrophy and amelogenesis Imperfecta caused by pathogenic variants in the CNNM4 gene (Parry et al. 2009); pathogenic variants in the FAM20A gene cause amelogenesis imperfecta and gingival hyperplasia syndrome as well as amelogenesis imperfecta and renal syndrome (O’Sullivan et al. 2011; Wang et al. 2013), and pathogenic variants in the LTBP3 gene cause Dental anomalies and short stature (Huckert et al. 2015).

Amelogenesis imperfecta is a highly heterogeneous condition. Pathogenic variants in AMELX are responsible for X-linked AI, FAM83H is the major gene currently known responsible for dominant AI, pathogenic variants in ENAM cause both dominant (mainly) and recessive AI (a few cases). Heterozygous carriers of LAMA3 pathogenic variants in a family affected with epidermolysis Bullosa were found to have enamel defects (Yuen et al. 2012). Autosomal recessive AI is caused by pathogenic variants in the ODAPH, KLK4, MMP20, WDR72, FAM20A, LAMB3, ITGB6, GPR68, SLC24A4 and SMOC2 genes. Pathogenic variants in DLX3 are responsible for dominant AI with trichodentoosseous syndrome. Pathogenic variants in ROGDI, CNNM4, FAM20A and LTBP3 are reported to cause autosomal recessive syndromic amelogenesis imperfecta. See individual gene test descriptions for information on molecular biology of gene products.

As reported, six genes (AMELX, ENAM, MMP20, KLK4, FAM83H, and WDR72) can explain roughly half of clinical diagnosed Amelogenesis Imperfecta (AI) cases. For reported pathogenic variants identified among only these six genes, pathogenic variants in FAM83H, AMELX and ENAM account for ~46%, ~23% and 11%, respectively, and MMP20, KLK4, and WDR72 together account for ~20% (Chan et al. 2011). In addition, FAM20A is the major gene for AI with gingival fibromatosis and nephrocalcinosis (O'Sullivan et al. 2011; Wang et al. 2013). In one study, pathogenic variants in CNNM4 were found in all affected patients with Jalili syndrome from 7 ethnically diverse families (Parry et al. 2009). Therefore, this entire panel is expected to explain more than 50% of clinically diagnosed AI.

Six gross deletions/duplications greater than 100 bp have been reported in AMELX (Hobson et al. 2009; HU et al. 2012; Human Gene Mutation Database). One large deletion involving DLX3 was identified in a family affected with osteogenesis imperfecta, tricho-dento-osseous syndrome and intellectual disability (Harbuz et al. 2013). One or two large deletions were reported in the CNNM4, FAM20A, LAMB3 and WDR72 (Human Gene Mutation Database). No gross deletions/duplications have been reported in ENAM, FAM83H, KLK4, LAMB3, MMP20, WDR72 and ROGDI (Human Gene Mutation Database).

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

This panel typically provides at least 99.7% 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).