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NM_001323289.2(CDKL5):c.1768G>A (p.Glu590Lys) AND CDKL5 disorder

Germline classification:
Benign (1 submission)
Last evaluated:
Mar 17, 2023
Review status:
3 stars out of maximum of 4 stars
reviewed by expert panel
Somatic classification
of clinical impact:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Somatic classification
of oncogenicity:
None
Review status:
(0/4) 0 stars out of maximum of 4 stars
no assertion criteria provided
Record status:
current
Accession:
RCV003169069.2

Allele description [Variation Report for NM_001323289.2(CDKL5):c.1768G>A (p.Glu590Lys)]

NM_001323289.2(CDKL5):c.1768G>A (p.Glu590Lys)

Gene:
CDKL5:cyclin dependent kinase like 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Xp22.13
Genomic location:
Preferred name:
NM_001323289.2(CDKL5):c.1768G>A (p.Glu590Lys)
Other names:
NM_001323289.2(CDKL5):c.1768G>A; p.Glu590Lys
HGVS:
  • NC_000023.11:g.18604692G>A
  • NG_008475.1:g.184088G>A
  • NM_001037343.2:c.1768G>A
  • NM_001323289.2:c.1768G>AMANE SELECT
  • NM_003159.3:c.1768G>A
  • NP_001032420.1:p.Glu590Lys
  • NP_001310218.1:p.Glu590Lys
  • NP_003150.1:p.Glu590Lys
  • NP_003150.1:p.Glu590Lys
  • NC_000023.10:g.18622812G>A
  • NM_003159.2:c.1768G>A
Protein change:
E590K
Links:
dbSNP: rs372629988
NCBI 1000 Genomes Browser:
rs372629988
Molecular consequence:
  • NM_001037343.2:c.1768G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001323289.2:c.1768G>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003159.3:c.1768G>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
CDKL5 disorder
Identifiers:
MONDO: MONDO:0100039; MedGen: CN296942

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV003853567ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel
reviewed by expert panel

(ClinGen RettAS ACMG Specifications V2)		Benign
(Mar 17, 2023) 		germlinecuration

Citation Link

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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, SCV003853567.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The allele frequency of the p.Glu590Lys variant in CDKL5 is 0.015% in Latino 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). Additionally, the p.Glu590Lys variant is observed in at least 14 unaffected individuals (internal database - GeneDx) (BS2) and at least 4 patients with an alternate molecular basis of disease (internal database - Invitae, internal database - GeneDx) (BP5_strong). In summary, the p.Glu590Lys variant in CDKL5 is classified as Benign for CDKL5-associated disorder based on the ACMG/AMP criteria (BS1, BS2, BP5_Strong).

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

Last Updated: Aug 4, 2024