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NM_001323289.2(CDKL5):c.1579C>T (p.Pro527Ser) AND CDKL5 disorder

Germline classification:
Likely benign (1 submission)
Last evaluated:
Feb 20, 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:
RCV003448340.2

Allele description [Variation Report for NM_001323289.2(CDKL5):c.1579C>T (p.Pro527Ser)]

NM_001323289.2(CDKL5):c.1579C>T (p.Pro527Ser)

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.1579C>T (p.Pro527Ser)
Other names:
NM_001323289.2(CDKL5):c.1579C>T; p.Pro527Ser
HGVS:
  • NC_000023.11:g.18604503C>T
  • NG_008475.1:g.183899C>T
  • NM_001037343.2:c.1579C>T
  • NM_001323289.2:c.1579C>TMANE SELECT
  • NM_003159.3:c.1579C>T
  • NP_001032420.1:p.Pro527Ser
  • NP_001310218.1:p.Pro527Ser
  • NP_003150.1:p.Pro527Ser
  • NP_003150.1:p.Pro527Ser
  • NC_000023.10:g.18622623C>T
  • NM_003159.2:c.1579C>T
Protein change:
P527S
Links:
dbSNP: rs1275389347
NCBI 1000 Genomes Browser:
rs1275389347
Molecular consequence:
  • NM_001037343.2:c.1579C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001323289.2:c.1579C>T - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003159.3:c.1579C>T - 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
SCV004176030ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel
reviewed by expert panel

(ClinGen RettAS ACMG Specifications V2)		Likely benign
(Feb 20, 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, SCV004176030.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The allele frequency of the p.Pro527Ser variant in CDKL5 is 0.017% in African sub population in gnomAD, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). The p.Pro527Ser variant is observed in at least 1 unaffected individual (internal database - Invitae) (BS2_supporting). In summary, the p.Pro527Ser variant in CDKL5 is classified as a Likely Benign based on the ACMG/AMP criteria (BS1, BS2_supporting).

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

Last Updated: Nov 10, 2024