ClinVar Miner

Submissions for variant NM_001323289.2(CDKL5):c.1400A>G (p.His467Arg)

gnomAD frequency: 0.00001  dbSNP: rs267608631
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000145518 SCV000192606 benign not specified 2013-02-08 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV001531130 SCV001746108 likely benign not provided 2021-04-01 criteria provided, single submitter clinical testing
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV002470772 SCV002767285 likely benign Developmental and epileptic encephalopathy, 2 2019-08-28 criteria provided, single submitter clinical testing A heterozygous missense variant, NM_003159.2(CDKL5):c.1400A>G, has been identified in exon 12 of 21 of the CDKL5 gene. The variant is predicted to result in a minor amino acid change from His to Arg at position 467 of the protein (NP_003150.1(CDKL5):p.(His467Arg)). The His residue at this position has high conservation (100 vertebrates, UCSC), but is not located within a well established functional domain. In-silico predictions for this variant are consistently pathogenic (Polyphen, SIFT, CADD, Mutation Taster). The variant is present in the gnomAD database at a frequency of 0.0005% (1 heterozyogte, 0 homozygotes, 0 hemizygoutes). The variant has been previously described as benign and segregated with disease in one family with disease (ClinVar, RettBASE, Evans et al 2005)). A different variant in the same codon resulting in a change to proline has also been reported as VUS (ClinVar, RettBASE, Liang et al 2011)). Based on the information available at the time of curation, this variant has been classified as LIKELY BENIGN.
RettBASE RCV000145518 SCV000222277 likely benign not specified 2014-05-09 no assertion criteria provided curation Likely benign variation, found in normal female carrier; reported as c.1399A>G, but should be c.1400A>G; in silico predictions: SIFT = deleterious, MutationTaster = disease-causing, PolyPhen2 = probably damaging, AlignGVGD = C25

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