Identification of rare coding EFEMP1 variants in three families with JOAG.
Whole exome sequencing was completed for selected affected and unaffected family members, and exome data was filtered to retain rare variants (MAF < 0.1%) that were protein altering and predicted to be pathogenic using in silico programs. Mutations were identified in known disease-causing genes in 4 families, three withMYOC mutations (p.Ter505Trpext*42; p.Gln337Arg; p.Thr438Ile) and one with a PAX6 mutation (p.Tyr296*). Novel variants of interest (Table S2) were further evaluated for co-segregation with disease in each pedigree using Sanger sequencing. Rare EFEMP1 (MIM: 601548) coding variants (GenBank: NM_001039348.3) were identified in all affected individuals of 3 of the remaining families as follows: (c.238A>T, p. Asn80Tyr) in 16 affected individuals of Family A and not in 18 unaffected family members older than age 18; (c.1480T>C, p. Ter494Glnext*29) was identified in 17 affected family members in family B and not in any family members older than age 18. One Family A member (age 13) and 4 Family B members (ages 7-12) were identified as mutation carriers, but are likely to be too young to manifest disease. Additionally, a third variant (c.1429C>T, p.Arg477Cys) was identified in a single case (Family C) (Figure 1A).
Patients with EFEMP1 variants (N= 34 in total for all three families) exhibited severe disease with average age of disease onset of 16 years (range 3-43). Affected individuals had much higher than average IOP (28mmHg) and 76% were blind in at least one eye (Table 1). The majority of patients required surgical treatment for IOP elevation, however not all patients had access to clinical care. Retinal examination did not reveal evidence of subretinal deposits (drusen) characteristic of MLVT/DHRD in affected individuals (Figure 2).
The three variants p.Asn80Tyr, p.Ter494Glnext*29, and p.Arg477Cys, identified in affected individuals are not present in population databases including gnomAD and TOPMed and have not been previously reported (the stop loss variant, p.Ter494Glnext*29 is not the same variant as reported in a small Chinese adult onset glaucoma family) (Liu et al., 2020). All three variants are predicted to be deleterious by in silico programs SIFT and Polyphen2 (Table S3). p.Asn80Tyr is located within the first EGF-domain, while p.Arg477Cys and p.Ter494GLNext*29 are within the terminal fibulin-like carboxy terminal domain. p.Ter494GLNext*29 results from replacement of the wild type stop codon with a glutamine residue and the addition of 29 amino acid residues to the polypeptide before a stop codon is encountered (Figure 1B).