EN2

Inheritance Pattern: AD

Disease ID:MONDO:0100038

Submitter: ClinGen

The engrailed 2 (EN2) gene, encoding a homeodomain transcription factor, was first reported to be associated with autism spectrum disorder (ASD) in 2004, based on an association study of common intronic variants (PMID: 15024396). This study, as well as other association studies that followed, performed over a decade ago, analyzed very small samples and were thus underpowered. No association between EN2 and ASD was found when larger samples were analyzed in a genome-wide association meta-analysis (PMID: 30804558). Concerning rare variants in EN2, no clear evidence has emerged to implicate EN2 in complex neurodevelopmental disorder. In a study of 94 individuals with encephalic structural anomalies and neurodevelopmental disorders including intellectual disability (ID), ASD and epilepsy, 12 patients were reported to have deletions in EN2 identified by PCR analysis of DNA or cDNA from blood (PMID: 30147646). (Because the deletion coordinates were not defined, they cannot be entered into the curation interface.) The subjects had variable abnormalities on MRI, including cortico-subcortical atrophy, corpus callosum atrophy, microcephaly or macrocephaly. This very high prevalence of EN2 deletions, including in some individuals with deletions in genes involved in cortical dysplasia, questions the significance of these findings. The lack of validation with modern sequencing technologies and the fact that no other studies have reported EN2 deletions also make these findings difficult to interpret. Therefore, these variants were not scored. In addition, three heterozygous missense variants in EN2 have been reported in individuals with variable neurodevelopmental presentations, including ASD, ID, and ataxia. However, these variants were not scored because in one case, the variant as described in the publication could not be unambiguously identified (PMID: 24321989); in the others, the variants were inherited from unaffected parents and were observed multiple times in gnomAD (PMID: 27755371). Population data from gnomAD (v2.1.1) indicates that EN2 is not highly constrained for either protein truncating variants (pLI = 0.63, LOEUF = 0.63) or missense variation (Z score = 1.08). The relationship between EN2 and complex neurodevelopmental disorder is supported by animal models. En2 knockout mice exhibit changes in cerebellar patterning, reduction in Purkinje cell number, reduction in GABAergic interneurons in the hippocampus and cerebral cortex, and deficits in social behavior, learning and memory, and motor coordination (PMIDs: 1672471 9315908, 16935268, 22829897, 23360806). While the experimental data is compelling, the genetic evidence reported thus far does not support a role for EN2 in human neurodevelopmental disorders. Thus, the experimental evidence was not scored. In summary, there is no convincing genetic evidence to support the relationship between EN2 and complex neurodevelopmental disorder, including ASD, so this gene-disease relationship is disputed. This classification was approved by the ClinGen Intellectual disability and Autism Gene Curation Expert Panel on February 16, 2021 (SOP Version 8).