Pathogenic EFHC1 mutations are tolerated in healthy individuals dependent on reported ancestry

Abstract

Objective: Screening for specific coding mutations in the EFHC1 gene has been proposed as a means of assessing susceptibility to juvenile myoclonic epilepsy (JME). To clarify the role of these mutations, especially those reported to be highly penetrant, we sought to measure the frequency of exonic EFHC1 mutations across multiple population samples.

Methods: To find and test variants of large effect, we sequenced all EFHC1 exons in 23 JME and 23 non-JME idiopathic generalized epilepsy (IGE) Hispanic patients, and 60 matched controls. We also genotyped specific EFHC1 variants in IGE cases and controls from multiple ethnic backgrounds, including 17 African American IGE patients, with 24 matched controls, and 92 Caucasian JME patients with 103 matched controls. These variants are reported to be pathogenic, but are also found among unphenotyped individuals in public databases. All subjects were from the New York City metro area and all controls were required to have no family history of seizures.

Results: We found the reportedly pathogenic EFHC1 P77T-R221H (rs149055334-rs79761183) JME haplotype in one Hispanic control and in two African American controls. Public databases also show that the EFHC1 P77T-R221H JME haplotype is present in unphenotyped West African ancestry populations, and we show that it can be found at appreciable frequency in healthy individuals with no family history of epilepsy. We also found a novel splice-site mutation in a single Hispanic JME patient, the effect of which is unknown.

Significance: Our findings raise questions about the effect of reportedly pathogenic EFHC1 mutations on JME. One intriguing possibility is that some EFHC1 mutations may be pathogenic only when introduced into specific genetic backgrounds. By focusing on data from multiple populations, including the understudied Hispanic and Black/African American populations, our study highlights that for complex traits like JME, the body of evidence necessary to infer causality is high.

Keywords: Ancestry-specific effects; Causative genetic variants; Complex genetic disorders; Disease prediction; Exonic variants; Idiopathic epilepsy.

Figure 1

Multidimensional scaling (MDS) of our Hispanics from the New York Metro area (HNYC) and of the Mexicans (MXL) of the 1,000 Genomes Project data. The MDS is based on genotypes at 39 ancestry-informative markers (AIMs) of chromosome 6, and is equivalent to the first two principal components of variation. Clearly, there is considerable overlap between HNYC (blue) and MXL (red).

Figure 2

Multidimensional scaling (MDS) of three super groups: African, Asian, and European. The genotypes at 39 ancestry-informative markers (AIMs) along chromosome 6 were extracted from the 1,000 Genomes Project data. Based on the first two principal components, there is a clear separation between Africans (AFR: black), Asians (ASN: red), and Europeans (EUR: blue).