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NM_001323289.2(CDKL5):c.1500C>A (p.Asn500Lys) AND not provided

Germline classification:
Uncertain significance (2 submissions)
Last evaluated:
Apr 1, 2023
Review status:
2 stars out of maximum of 4 stars
criteria provided, multiple submitters, no conflicts
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:
RCV000144828.12

Allele description [Variation Report for NM_001323289.2(CDKL5):c.1500C>A (p.Asn500Lys)]

NM_001323289.2(CDKL5):c.1500C>A (p.Asn500Lys)

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.1500C>A (p.Asn500Lys)
Other names:
p.N500K:AAC>AAA
HGVS:
  • NC_000023.11:g.18604424C>A
  • NG_008475.1:g.183820C>A
  • NM_001037343.2:c.1500C>A
  • NM_001323289.2:c.1500C>AMANE SELECT
  • NM_003159.3:c.1500C>A
  • NP_001032420.1:p.Asn500Lys
  • NP_001310218.1:p.Asn500Lys
  • NP_003150.1:p.Asn500Lys
  • NP_003150.1:p.Asn500Lys
  • NC_000023.10:g.18622544C>A
  • NM_003159.2:c.1500C>A
Protein change:
N500K
Links:
dbSNP: rs587783152
NCBI 1000 Genomes Browser:
rs587783152
Molecular consequence:
  • NM_001037343.2:c.1500C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001323289.2:c.1500C>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003159.3:c.1500C>A - missense variant - [Sequence Ontology: SO:0001583]
Observations:
1

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000191063GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Oct 22, 2018) 		germlineclinical testing

Citation Link,

SCV004166649CeGaT Center for Human Genetics Tuebingen
criteria provided, single submitter

(CeGaT Center For Human Genetics Tuebingen Variant Classification Criteria Version 2)		Uncertain significance
(Apr 1, 2023) 		germlineclinical testing

Citation Link

Help

Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyes1not providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000191063.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testingnot provided

Description

A variant of uncertain significance has been identified in the CDKL5 gene. The N500K variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. This variant is not observed in large population cohorts (Lek et al., 2016). The N500K variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. In-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function. Therefore, based on the currently available information, it is unclear whether the N500K variant is a pathogenic variant or a rare benign variant.

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

From CeGaT Center for Human Genetics Tuebingen, SCV004166649.10

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not provided1not providednot providedclinical testingnot provided

Description

CDKL5: PM2

#SampleMethodObservation
OriginAffectedNumber testedTissuePurposeMethodIndividualsAllele frequencyFamiliesCo-occurrences
1germlineyesnot providednot providednot provided1not providednot providednot provided

Last Updated: Oct 20, 2024