A novel splice variant in EMC1 is associated with cerebellar atrophy, visual impairment, psychomotor retardation with epilepsy

Abstract

Background: Several genes have been implicated in a highly variable presentation of developmental delay with psychomotor retardation. Mutations in EMC1 gene have recently been reported. Herein, we describe a proband born of a consanguineous marriage, who presented with early infantile onset epilepsy, scaphocephaly, developmental delay, central hypotonia, muscle wasting, and severe cerebellar and brainstem atrophy.

Methods: Genetic testing in the proband was performed using custom clinical exome and targeted next-generation sequencing. This was followed by segregation analysis of the variant in the parents by Sanger sequencing and evaluation of the splice variant by RNA sequencing.

Results: Clinical exome sequencing identified a novel homozygous intronic splice variant in the EMC1 gene (chr1:19564510C>T, c.1212 + 1G>A, NM_015047.2). Neither population databases (ExAC and 1000 genomes) nor our internal database (n = 1,500) had reported this rare variant, predicted to affect the splicing. RNA sequencing data from the proband confirmed aberrant splicing with intron 11 retention, thereby introducing a stop codon in the resultant mRNA. This nonsense mutation is predicted to result in the premature termination of protein synthesis leading to loss of function of the EMC1 protein.

Conclusion: We report, for the first time the role of aberrant EMC1RNA splicing as a potential cause of disease pathogenesis. The severe epilepsy observed in our study expands the disease-associated phenotype and also emphasizes the need for comprehensive screening of intronic splice mutations.

Keywords: EMC1; Indian population; South Asian; clinical exome; developmental delay; epilepsy; psychomotor retardation; splice variant.

Figure 1

(A) Schematic representation of the consanguineous partial pedigree of the family: circles indicate female and squares indicate male, filled‐in squares indicate affected; circles/squares with dots are obligate carriers; arrow indicates the consultand. The Sanger sequencing chromatogram of the splice variant (c.1212 + 1G>A; NM_015047.2; NG_032948.1) detected in the parents (III‐5, III‐6) and proband (IV‐1) are represented as “+” for variant/mutant allele and “−” for wild‐type allele. The nucleotide numbering reflects cDNA numbering; the initiation codon is codon 1 according to the journal guidelines (http://www.hgvs.org/mutnomen); (B) Side profile photograph of the affected proband showing scaphocephaly; (C, D) MRI Brain Sections of the proband (C) T1 axial view showing supratentorial cerebral atrophy (D) T2 sagittal view showing cerebellar and brainstem atrophy; (E) Schematic representation from Integrative Genomics Viewer showing exome and RNA sequencing data reads encompassing exon 11 and exon 12. The RNA reads show intron 11 retention in the aligned data (F) This peptide sequence represents partial exon 11 (in blue) followed by retained intron 11 sequence (in red); translated upstream (frame 1) till the first stop codon; (G) Schematic representation of the domains of EMC1, where PQQ_2 represents the quinoprotein alcohol dehydrogenase‐like domain and DUF1620 represents an uncharacterized domain of unknown function 1,620 with the two variants identified in this study (p.Arg401Trp and c.1212 + 1G>A; NM_015047.2; NG_032948.1). The dotted line indicates protein domains which may be lost due to the mutation detected