rs1572996700
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PM2PP5BP4
The NM_001135651.3(EIF2AK2):c.1382C>G(p.Ser461Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. 15/21 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001135651.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 exome Cov.: 30
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
Leukoencephalopathy, developmental delay, and episodic neurologic regression syndrome Pathogenic:2Uncertain:1
The EIF2AK2 c.1382C>G (p.Ser461Cys) variant is a missense variant that is located in the protein-kinase domain of the EIF2AK2 protein (Mao et al. 2020). The p.Ser461Cys variant has been reported in a de novo state in one individual with leukoencephalopathy, developmental delay, and episodic neurologic regression syndrome (Mao et al. 2020). The p.Ser461Cys variant is not found in version 2.1.1 or version 3.1.1 of the Genome Aggregation Database in a region of good sequence coverage, which suggests the variant is rare. Functional studies in patient fibroblasts for the p.Ser461Cys variant demonstrated impaired kinase activity with consistent reduction in p-EIF2S1 levels and decrease in ATF4 levels, a downstream target of p-EIF2S1 (Mao et al. 2020). Based on the collective evidence and identification of this variant in a de novo state, the p.Ser461Cys variant is classified as likely pathogenic for leukoencephalopathy, developmental delay, and episodic neurologic regression syndrome. -
This variant is interpreted as a variant of uncertain significance for Leukoencephalopathy, developmental delay, and episodic neurologic regression syndrome, autosomal dominant The following ACMG Tag(s) were applied: Absent from controls (or at extremely low frequency if recessive) in Exome Sequencing Project, 1000 Genomes Project, or Exome Aggregation Consortium (PM2); de novo variant (PS2 downgraded to moderate); Well-established functional studies show a deleterious effect (PS3 downgraded to supporting). -
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Leukoencephalopathy;C0557874:Global developmental delay;C1836830:Developmental regression Uncertain:1
The heterozygous c.1382C>G (p.Ser461Cys) variant in EIF2AK2 was identified by our study in 1 individual with developmental regression, leukoencephalopathy, and global developmental delay. Trio exome analysis showed this variant to be de novo with confirmed paternity and maternity. The c.1382C>G (p.Ser461Cys) variant in EIF2AK2 has not been previously reported in individuals with developmental regression, leukoencephalopathy, and global developmental delay and this variant was absent from large population studies. The EIF2AK2 gene has no established gene-disease association. However, this gene has a role in the EIF2B pathway, which has been associated with vanishing white matter leukoencephalopathies. Unpublished cohort data has identified other unrelated patients with similar neurologic phenotypes and suggest that de novo missense variants are implicated in disease. Functional studies demonstrate this variant impairs kinase activity of EIF2AK2 (publication pending). It is of note that computational prediction tools, including splice predictors, suggest that this variant may not impact the protein. Additionally, the serine (Ser) at position 461 is not highly conserved in mammals and evolutionary distant species, and 2 mammals (dolphins and killer whales) carry a cystine (Cys), raising the possibility that this change at this position may be tolerated. In summary, the clinical significance of the Ser461Cys variant is uncertain. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at