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NM_001323289.2(CDKL5):c.872G>A (p.Cys291Tyr) AND CDKL5 disorder

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Aug 25, 2022
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:

Allele description [Variation Report for NM_001323289.2(CDKL5):c.872G>A (p.Cys291Tyr)]

NM_001323289.2(CDKL5):c.872G>A (p.Cys291Tyr)

CDKL5:cyclin dependent kinase like 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
NM_001323289.2(CDKL5):c.872G>A (p.Cys291Tyr)
Other names:
  • NC_000023.11:g.18598508G>A
  • NG_008475.1:g.177904G>A
  • NM_001037343.2:c.872G>A
  • NM_001323289.2:c.872G>AMANE SELECT
  • NM_003159.3:c.872G>A
  • NP_001032420.1:p.Cys291Tyr
  • NP_001310218.1:p.Cys291Tyr
  • NP_003150.1:p.Cys291Tyr
  • NP_003150.1:p.Cys291Tyr
  • NC_000023.10:g.18616628G>A
  • NM_003159.2:c.872G>A
  • O76039:p.Cys291Tyr
Protein change:
C291Y; CYS291TYR
RettBASE (CDKL5): 62; UniProtKB: O76039#VAR_058029; OMIM: 300203.0012; dbSNP: rs267606714
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001037343.2:c.872G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001323289.2:c.872G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003159.3:c.872G>A - missense variant - [Sequence Ontology: SO:0001583]


CDKL5 disorder
MONDO: MONDO:0100039; MedGen: CN296942

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Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV002569928ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel
reviewed by expert panel

(ClinGen RettAS ACMG Specifications V2)
Uncertain significance
(Aug 25, 2022)

Citation Link

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineunknownnot providednot providednot providednot providednot providedcuration

Details of each submission

From ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel, SCV002569928.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided


The p.Cys291Tyr variant in CDKL5 has been reported as a de novo occurrence (biological parentage unconfirmed) in an individual with severe early-onset encephalopathy (PMID 18809835) (PM6). The p.Cys291Tyr variant in CDKL5 is absent from gnomAD (PM2_Supporting). The p.Cys291Tyr variant has been observed in at least 1 other individual with CDKL5-related disorder (PMID 18809835, PMID 25657822) (PS4_Supporting). In summary, the p.Cys291Tyr variant in CDKL5 is classified as a variant of unknown significance based on the ACMG/AMP criteria (PM6, PM2_Supporting, PS4_Supporting).

OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineunknownnot providednot providednot providednot providednot providednot providednot provided

Last Updated: Feb 28, 2024