A distinctive oral phenotype points to FAM20A mutations not identified by Sanger sequencing

Abstract

Biallelic FAM20A mutations cause two conditions where Amelogenesis Imperfecta (AI) is the presenting feature: Amelogenesis Imperfecta and Gingival Fibromatosis Syndrome; and Enamel Renal Syndrome. A distinctive oral phenotype is shared in both conditions. On Sanger sequencing of FAM20A in cases with that phenotype, we identified two probands with single, likely pathogenic heterozygous mutations. Given the recessive inheritance pattern seen in all previous FAM20A mutation‐positive families and the potential for renal disease, further screening was carried out to look for a second pathogenic allele. Reverse transcriptase‐PCR on cDNA was used to determine transcript levels. CNVseq was used to screen for genomic insertions and deletions. In one family, FAM20A cDNA screening revealed only a single mutated FAM20A allele with the wild‐type allele not transcribed. In the second family, CNV detection by whole genome sequencing (CNVseq) revealed a heterozygous 54.7 kb duplication encompassing exons 1 to 4 of FAM20A. This study confirms the link between biallelic FAM20A mutations and the characteristic oral phenotype. It highlights for the first time examples of FAM20A mutations missed by the most commonly used mutation screening techniques. This information informed renal assessment and ongoing clinical care.

Amelogenesis Imperfecta; Genes, Proteins, and Pathways

“…As costs continue to fall, whole genome sequencing is also facilitating the discovery of mutations that cannot be found by conventional WES analysis (Poulter et al, 2015). For many human conditions, greater awareness of the importance of non-coding mutations is leading to an increase in the study of patient mRNA.…”

“…WES has expedited the identification of new genetic variants that cause AI (O'Sullivan et al, 2011 ; Jaureguiberry et al, 2012 ; Poulter et al, 2014a , b ) but it is likely that more genes, not currently known to be critical for enamel formation, remain to be identified. As costs continue to fall, whole genome sequencing is also facilitating the discovery of mutations that cannot be found by conventional WES analysis (Poulter et al, 2015 ). For many human conditions, greater awareness of the importance of non-coding mutations is leading to an increase in the study of patient mRNA.…”

“…Calcification of other organs, most frequently nephrocalcinosis, is variably reported. This may be due to a combination of age, genetic modifiers, and exposure to Ca 2+ channel blocking drugs (Poulter et al, 2015 ).…”

“…This suggests that additional AI genes remain to be identified and/or that variants in known AI genes, such as intronic, regulatory, and larger structural alterations, are being missed by current analysis pipelines. For example, particular variant types, such as heterozygous copy number changes larger than an exon, are likely to be under-represented in reports since they would not have been identified by Sanger sequencing or WES data without specific downstream analysis (Poulter et al, 2015 ; Smith et al, 2016 ).…”

Nephrocalcinosis in Amelogenesis Imperfecta Caused by the <b><i>FAM20A</i></b> Mutation

“…Two patients with FAM20A mutations had AI but a normal nephrology workup, including normal urinary ultrasound [40]. These patients were 15 and 17 years old, so it is possible that in these patients, nephrocalcinosis will take longer to develop or be visible on ultrasound.…”