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NM_001323289.2(CDKL5):c.37T>A (p.Phe13Ile) AND Developmental and epileptic encephalopathy, 2

Germline classification:
Uncertain significance (1 submission)
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:
RCV001823439.3

Allele description [Variation Report for NM_001323289.2(CDKL5):c.37T>A (p.Phe13Ile)]

NM_001323289.2(CDKL5):c.37T>A (p.Phe13Ile)

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.37T>A (p.Phe13Ile)
HGVS:
  • NC_000023.11:g.18507133T>A
  • NG_008475.1:g.86529T>A
  • NM_001037343.2:c.37T>A
  • NM_001323289.2:c.37T>AMANE SELECT
  • NM_003159.3:c.37T>A
  • NP_001032420.1:p.Phe13Ile
  • NP_001310218.1:p.Phe13Ile
  • NP_003150.1:p.Phe13Ile
  • NC_000023.10:g.18525253T>A
  • NM_003159.2:c.[37T>A]
Protein change:
F13I
Links:
dbSNP: rs2147092100
NCBI 1000 Genomes Browser:
rs2147092100
Molecular consequence:
  • NM_001037343.2:c.37T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_001323289.2:c.37T>A - missense variant - [Sequence Ontology: SO:0001583]
  • NM_003159.3:c.37T>A - missense variant - [Sequence Ontology: SO:0001583]

Condition(s)

Name:
Developmental and epileptic encephalopathy, 2 (DEE2)
Synonyms:
INFANTILE SPASM SYNDROME, X-LINKED 2; Early infantile epileptic encephalopathy 2
Identifiers:
MONDO: MONDO:0010396; MedGen: C4750718; Orphanet: 1934; Orphanet: 3451; OMIM: 300672

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Assertion and evidence details

Help
Submission AccessionSubmitterReview Status
(Assertion method)		Clinical Significance
(Last evaluated)		OriginMethodCitations
SCV002072876Neuberg Centre For Genomic Medicine, NCGM
criteria provided, single submitter

(ACMG Guidelines, 2015)		Uncertain significancegermlineclinical testing

PubMed (1)
[See all records that cite this PMID]

Help

Summary from all submissions

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

Citations

PubMed

Standards and guidelines for the interpretation of sequence variants: a joint consensus recommendation of the American College of Medical Genetics and Genomics and the Association for Molecular Pathology.

Richards S, Aziz N, Bale S, Bick D, Das S, Gastier-Foster J, Grody WW, Hegde M, Lyon E, Spector E, Voelkerding K, Rehm HL; ACMG Laboratory Quality Assurance Committee..

Genet Med. 2015 May;17(5):405-24. doi: 10.1038/gim.2015.30. Epub 2015 Mar 5.

PubMed [citation]
PMID:
25741868
PMCID:
PMC4544753

Details of each submission

From Neuberg Centre For Genomic Medicine, NCGM, SCV002072876.1

#EthnicityIndividualsChromosomes TestedFamily HistoryMethodCitations
1not providednot providednot providednot providedclinical testing PubMed (1)

Description

The missense variant p.F13I in CDKL5 (NM_003159.3) has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. Another missense variant affecting the same residue F13S has been classified as a variant of uncertain significance in the RettDatabase. The p.F13I variant is novel (not in any individuals) in gnomAD Exomes and is novel (not in any individuals) in 1000 Genomes. The p.F13I missense variant is predicted to be damaging by both SIFT and PolyPhen2. The phenylalanine residue at codon 13 of CDKL5 is conserved in all mammalian species. The nucleotide c.37 in CDKL5 is predicted conserved by GERP++ and PhyloP across 100 vertebrates. For these reasons, this variant has been classified as Uncertain Significance.

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

Last Updated: Apr 6, 2024