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NM_001323289.2(CDKL5):c.1196A>C (p.Asn399Thr) AND not provided

Germline classification:
Uncertain significance (1 submission)
Last evaluated:
Jan 7, 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:
RCV000479280.2

Allele description [Variation Report for NM_001323289.2(CDKL5):c.1196A>C (p.Asn399Thr)]

NM_001323289.2(CDKL5):c.1196A>C (p.Asn399Thr)

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.1196A>C (p.Asn399Thr)
Other names:
NM_001323289.2(CDKL5):c.1196A>C
HGVS:
  • NC_000023.11:g.18604120A>C
  • NG_008475.1:g.183516A>C
  • NM_001037343.2:c.1196A>C
  • NM_001323289.2:c.1196A>CMANE SELECT
  • NM_003159.3:c.1196A>C
  • NP_001032420.1:p.Asn399Thr
  • NP_001310218.1:p.Asn399Thr
  • NP_003150.1:p.Asn399Thr
  • NP_003150.1:p.Asn399Thr
  • NC_000023.10:g.18622240A>C
  • NM_003159.2(CDKL5):c.1196A>C
  • NM_003159.2:c.1196A>C
  • O76039:p.Asn399Thr
Protein change:
N399T
Links:
RettBASE (CDKL5): 85; UniProtKB: O76039#VAR_058030; dbSNP: rs267608611
NCBI 1000 Genomes Browser:
rs267608611
Molecular consequence:
  • NM_001037343.2:c.1196A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001323289.2:c.1196A>C - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003159.3:c.1196A>C - 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
SCV000568364GeneDx
criteria provided, single submitter

(GeneDx Variant Classification (06012015))		Uncertain significance
(Jan 7, 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, SCV000568364.3

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

Description

The N399T variant in the CDKL5 gene has been reported previously in a female with Rett syndrome, whose mother did not carry the variant and her father was unavailable for testing (Sprovieri et al., 2009). The N399T variant 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. The N399T variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This substitution occurs at a position where amino acids with similar properties to Asparagine are tolerated across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret N399T as a variant of uncertain significance

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

Last Updated: Oct 8, 2024