NM_001323289.2(CDKL5):c.99+5G>A AND not provided

Clinical significance:Pathogenic (Last evaluated: Feb 29, 2012)

Review status:1 star out of maximum of 4 stars

criteria provided, single submitter

Based on:
1 submission [Details]
Record status:

Allele description [Variation Report for NM_001323289.2(CDKL5):c.99+5G>A]


CDKL5:cyclin dependent kinase like 5 [Gene - OMIM - HGNC]
Variant type:
single nucleotide variant
Cytogenetic location:
Genomic location:
Preferred name:
Other names:
  • NC_000023.11:g.18510859G>A
  • NG_008475.1:g.90255G>A
  • NM_001037343.1:c.99+5G>A
  • NM_001323289.2:c.99+5G>AMANE SELECT
  • NM_003159.2:c.99+5G>A
  • NC_000023.10:g.18528979G>A
RettBASE (CDKL5): 89; dbSNP: rs587783131
NCBI 1000 Genomes Browser:
Molecular consequence:
  • NM_001037343.1:c.99+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_001323289.2:c.99+5G>A - intron variant - [Sequence Ontology: SO:0001627]
  • NM_003159.2:c.99+5G>A - intron variant - [Sequence Ontology: SO:0001627]


MedGen: CN517202

Recent activity

Your browsing activity is empty.

Activity recording is turned off.

Turn recording back on

See more...

Assertion and evidence details

Submission AccessionSubmitterReview Status
(Assertion method)
Clinical Significance
(Last evaluated)
SCV000191029GeneDxcriteria provided, single submitter
(Feb 29, 2012)
germlineclinical testing

Citation Link

Summary from all submissions

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

Details of each submission

From GeneDx, SCV000191029.10

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


The c.99+5 G>A mutation in the CDKL5 gene has been previously reported in two individuals with early onset epilepsy. A male with early onset intractable seizures, infantile spasms, and severe intellectual disability had somatic mosaicism for the c.99+5 G>A mutation (Masilah Plachon et al., 2010). Additionally, a female with intractable epilepsy, severe intellectual disability, hypotonia, and spastic tetraparesis was reported to harbor a de novo c.99+5 G>A mutation (Stalpers et al., 2012). The c.99+5 G>A mutation damages the native splice donor site at the exon 3/intron 3 junction of the CDKL5 gene. In vitro mRNA studies indicate that it leads to skipping of exon 3, which is predicted to lead to loss of function due to protein truncation (Masilah Plachon et al., 2010). The variant is found in INFANT-EPI panel(s).

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

Last Updated: Feb 27, 2021

Support Center