A variant of uncertain significance has been identified in the LAMP2 gene. The E334Q variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. This variant was not observed in approximately 6,500 individuals of European and African American ancestry in an external variant database, indicating it is not a common benign variant in these populations. The E334Q variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. In addition, this substitution occurs at a position that is conserved across species and in silico analysis predicts this variant is probably damaging to the protein structure/function. However, no missense variants in nearby residues have been reported in the Human Gene Mutation Database (Stenson et al., 2014). Furthermore, although this variant was previously identified in one other unrelated individual referred for cardiomyopathy genetic testing at GeneDx, family studies were not performed to discern whether this variant co-segregates with disease.Therefore, based on the currently available information, it is unclear whether this variant is pathogenic or benign.

This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score and internal cut-off values, a variant classified as benign is not then subjected to further curation. The score for this variant resulted in a classification of benign for this disease.

The p.E334Q variant (also known as c.1000G>C), located in coding exon 8 of the LAMP2 gene, results from a G to C substitution at nucleotide position 1000. The glutamic acid at codon 334 is replaced by glutamine, an amino acid with highly similar properties. Based on data from gnomAD, the C allele has an overall frequency of 0.002% (4/205486) total alleles studied. The highest observed frequency was 0.026% (2/7667) of Ashkenazi Jewish alleles, including 4 hemizygotes. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.