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Early onset or syndromic epilepsy v8.105 CRNKL1 Ida Ertmanska Phenotypes for gene: CRNKL1 were changed from Microcephaly, progressive, with simplified gyral pattern and cerebellar hypoplasia, OMIM:621436 to Microcephaly, progressive, with simplified gyral pattern and cerebellar hypoplasia, OMIM:621436; complex neurodevelopmental disorder, MONDO:0100038
Early onset or syndromic epilepsy v8.104 CRNKL1 Ida Ertmanska Publications for gene: CRNKL1 were set to https://doi.org/10.1016/j.ajhg.2025.05.013
Early onset or syndromic epilepsy v8.103 CRNKL1 Ida Ertmanska Added comment: Comment on phenotypes: OMIM phenotype added 30th Jan 2026.
Early onset or syndromic epilepsy v8.103 CRNKL1 Ida Ertmanska Phenotypes for gene: CRNKL1 were changed from complex neurodevelopmental disorder, MONDO:0100038 to Microcephaly, progressive, with simplified gyral pattern and cerebellar hypoplasia, OMIM:621436
Early onset or syndromic epilepsy v8.93 CRNKL1 John Taylor reviewed gene: CRNKL1: Rating: GREEN; Mode of pathogenicity: Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments; Publications: 40857589; Phenotypes: microcephaly, pontocerebellar hypoplasia, seizures; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Early onset or syndromic epilepsy v8.10 CRNKL1 Achchuthan Shanmugasundram Tag dd_review tag was added to gene: CRNKL1.
Early onset or syndromic epilepsy v8.9 CRNKL1 Achchuthan Shanmugasundram Classified gene: CRNKL1 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v8.9 CRNKL1 Achchuthan Shanmugasundram Added comment: Comment on list classification: There is sufficient evidence available for the promotion of this gene to green rating in the next GMS update.
Early onset or syndromic epilepsy v8.9 CRNKL1 Achchuthan Shanmugasundram Gene: crnkl1 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v8.8 CRNKL1 Achchuthan Shanmugasundram Tag Q3_25_promote_green tag was added to gene: CRNKL1.
Early onset or syndromic epilepsy v8.8 CRNKL1 Achchuthan Shanmugasundram gene: CRNKL1 was added
gene: CRNKL1 was added to Early onset or syndromic epilepsy. Sources: Literature
Mode of inheritance for gene: CRNKL1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Publications for gene: CRNKL1 were set to https://doi.org/10.1016/j.ajhg.2025.05.013
Phenotypes for gene: CRNKL1 were set to complex neurodevelopmental disorder, MONDO:0100038
Review for gene: CRNKL1 was set to GREEN
Added comment: There are 10 unrelated patents identified with de novo missense variants in the spliceosomal component CRNKL1, where nine of them harboured one of the two missense variants affecting the same amino acid residue, Arg 267 (p.Arg267Cys & p.Arg267His), while the tenth patient harboured a different variant (p.Arg301Gly). All affected individuals share a common and specific phenotype: profound pre- and post-natal microcephaly (8 of 10 patients), with pontocerebellar hypoplasia (9 patients), seizures (8 patients), and severe intellectual disability (8 patients).

Microinjection of mRNA encoding Crnkl1 variant into a zebrafish model caused a severe lack of brain development accompanied by a significant reduction in proliferating cells and widespread cellular stress, as indicated by p53 staining. RNA sequencing analysis of injected zebrafish embryos showed broad transcriptomic changes, with altered expression of neuronal and cell cycle genes.

This gene has not yet been associated with relevant phenotypes in OMIM or in Gene2Phenotype.
Sources: Literature