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NM_001323289.2(CDKL5):c.1002T>C (p.Ala334=) AND CDKL5 disorder

Germline classification:
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:
RCV003165430.9

Allele description [Variation Report for NM_001323289.2(CDKL5):c.1002T>C (p.Ala334=)]

NM_001323289.2(CDKL5):c.1002T>C (p.Ala334=)

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.1002T>C (p.Ala334=)
Other names:
NM_001323289.2(CDKL5):c.1002T>C; p.Ala334=
HGVS:
  • NC_000023.11:g.18603926T>C
  • NG_008475.1:g.183322T>C
  • NM_001037343.2:c.1002T>C
  • NM_001323289.2:c.1002T>CMANE SELECT
  • NM_003159.3:c.1002T>C
  • NP_001032420.1:p.Ala334=
  • NP_001310218.1:p.Ala334=
  • NP_003150.1:p.Ala334=
  • NP_003150.1:p.Ala334=
  • NC_000023.10:g.18622046T>C
  • NM_003159.2:c.1002T>C
Links:
dbSNP: rs756986206
NCBI 1000 Genomes Browser:
rs756986206
Molecular consequence:
  • NM_001037343.2:c.1002T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_001323289.2:c.1002T>C - synonymous variant - [Sequence Ontology: SO:0001819]
  • NM_003159.3:c.1002T>C - synonymous variant - [Sequence Ontology: SO:0001819]

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
SCV003853563ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel
reviewed by expert panel

(ClinGen RettAS ACMG Specifications V2)		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, SCV003853563.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedcurationnot provided

Description

The allele frequency of the p.Ala334= variant in CDKL5 is 0.07448% in South Asian sub population in gnomAD, which is high enough to be classified as benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BA1). The p.Ala334= variant is observed in at least 1 unaffected individual (Clinvar 210642) (BS2_supporting). The silent p.Ala334= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP7). In summary, the p.Ala334= variant in CDKL5 is classified as Benign based on the ACMG/AMP criteria (BA1, BA2_supporting, BP7).

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

Last Updated: Oct 13, 2024