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NM_001323289.2(CDKL5):c.13A>G (p.Asn5Asp) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jul 15, 2016
Review status:
1 star out of maximum of 4 stars
criteria provided, single submitter
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:
RCV000482464.1

Allele description [Variation Report for NM_001323289.2(CDKL5):c.13A>G (p.Asn5Asp)]

NM_001323289.2(CDKL5):c.13A>G (p.Asn5Asp)

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.13A>G (p.Asn5Asp)
HGVS:
  • NC_000023.11:g.18507109A>G
  • NG_008475.1:g.86505A>G
  • NM_001037343.2:c.13A>G
  • NM_001323289.2:c.13A>GMANE SELECT
  • NM_003159.3:c.13A>G
  • NP_001032420.1:p.Asn5Asp
  • NP_001310218.1:p.Asn5Asp
  • NP_003150.1:p.Asn5Asp
  • NP_003150.1:p.Asn5Asp
  • NC_000023.10:g.18525229A>G
  • NM_003159.2:c.13A>G
Protein change:
N5D
Links:
dbSNP: rs767844474
NCBI 1000 Genomes Browser:
rs767844474
Molecular consequence:
  • NM_001037343.2:c.13A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001323289.2:c.13A>G - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003159.3:c.13A>G - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Synonyms:
none provided
Identifiers:
MedGen: C3661900

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Assertion and evidence details

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Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV000570981GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jul 15, 2016) 		germlineclinical testing

Citation Link

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Summary from all submissions

EthnicityOriginAffectedIndividualsFamiliesChromosomes testedNumber TestedFamily historyMethod
not providedgermlineyesnot providednot providednot providednot providednot providedclinical testing

Details of each submission

From GeneDx, SCV000570981.3

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

Description

A variant of uncertain significance has been identified in the CDKL5 gene. The N5D variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations and it was not observed with any significant frequency in the 1000 Genomes Project. The N5D variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species. However, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.

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

Last Updated: Sep 29, 2024