ClinVar Miner

Submissions for variant NM_001323289.2(CDKL5):c.291C>T (p.Leu97=)

gnomAD frequency: 0.00004  dbSNP: rs138125282
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel RCV002281143 SCV002569950 benign CDKL5 disorder 2022-09-01 reviewed by expert panel curation The allele frequency of the p.Leu97= variant in CDKL5 is 0.011% in African sub population in gnomAD, which is high enough to be classified as likely benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). The p.Leu97= variant is observed in at least 2 unaffected individuals (internal database) (BS2). The silent p.Leu97= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP7). The p.Leu97= variant in CDKL5 has been reported apparently homozygous in an individual with infantile epileptic encephalopathy (PMID 28454995); no criteria were applied for this case. In summary, the p.Leu97= variant in CDKL5 is classified as benign based on the ACMG/AMP criteria (BS1, BS2, BP7).
Labcorp Genetics (formerly Invitae), Labcorp RCV000925502 SCV001071040 likely benign Developmental and epileptic encephalopathy, 2; Angelman syndrome-like 2023-10-13 criteria provided, single submitter clinical testing
GeneDx RCV002225768 SCV002504358 likely benign not provided 2020-09-22 criteria provided, single submitter clinical testing See Variant Classification Assertion Criteria.
Ambry Genetics RCV004609567 SCV005105222 likely benign Inborn genetic diseases 2024-06-17 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City RCV000985112 SCV001133083 likely pathogenic Developmental and epileptic encephalopathy, 2 2019-09-26 no assertion criteria provided clinical testing

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