rs376341076
Variant summary
Our verdict is Benign. Variant got -8 ACMG points: 2P and 10B. PM2BP4_ModerateBP6_Very_Strong
The NM_001323289.2(CDKL5):c.1684A>G(p.Thr562Ala) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000033 in 1,210,493 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 1 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 15/20 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★★).
Frequency
Consequence
NM_001323289.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Benign. Variant got -8 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CDKL5 | NM_001323289.2 | c.1684A>G | p.Thr562Ala | missense_variant | 12/18 | ENST00000623535.2 | |
CDKL5 | NM_001037343.2 | c.1684A>G | p.Thr562Ala | missense_variant | 13/22 | ||
CDKL5 | NM_003159.3 | c.1684A>G | p.Thr562Ala | missense_variant | 12/21 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CDKL5 | ENST00000623535.2 | c.1684A>G | p.Thr562Ala | missense_variant | 12/18 | 1 | NM_001323289.2 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.00000891 AC: 1AN: 112279Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34443
GnomAD4 exome AF: 0.00000273 AC: 3AN: 1098214Hom.: 0 Cov.: 32 AF XY: 0.00000275 AC XY: 1AN XY: 363570
GnomAD4 genome ? AF: 0.00000891 AC: 1AN: 112279Hom.: 0 Cov.: 23 AF XY: 0.00 AC XY: 0AN XY: 34443
ClinVar
Submissions by phenotype
not specified Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Genetic Services Laboratory, University of Chicago | Aug 16, 2016 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | May 02, 2016 | The p.T562A variant (also known as c.1684A>G), located in coding exon 11 of the CDKL5 gene, results from an A to G substitution at nucleotide position 1684. The threonine at codon 562 is replaced by alanine, an amino acid with similar properties. This variant was previously reported in the SNPDatabase as rs376341076. Based on data from the NHLBI Exome Sequencing Project (ESP), the G allele was absent out of 2443 total male alleles studied. This amino acid position is not well conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
CDKL5 disorder Benign:1
Likely benign, reviewed by expert panel | curation | ClinGen Rett and Angelman-like Disorders Variant Curation Expert Panel | Mar 17, 2023 | The p.Thr562Ala variant in CDKL5 is present in 1 female individual in gnomAD (0.001879%) (not sufficient to meet BS1 criteria). Computational analysis prediction tools suggest that the p.Thr562Ala variant does not have a deleterious impact; however this information does not predict clinical significance on its own (BP4). The p.Thr562Ala variant is observed in at least 2 unaffected individuals (internal database - Ambry Genetics, internal database - Invitae) (BS2). In summary, the p.Thr562Ala variant in CDKL5 is classified as Likely Benign for CDKL5-associated disorder based on the ACMG/AMP criteria (BP4, BS2). - |
Developmental and epileptic encephalopathy, 2;CN128785:Angelman syndrome-like Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Dec 09, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at