Evidence Repository
The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
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Variant: NM_001323289.1:c.59G>T

CA412489610

918032 (ClinVar)

Gene: CDKL5
Condition: CDKL5 disorder
Inheritance Mode: X-linked inheritance (dominant (HP:0001423))
Link to MONDO
UUID: b09d88a5-341c-4085-be46-89ee10c7cf6f
Approved on: 2021-03-26
Published on: 2021-05-17

HGVS expressions

NM_001323289.1:c.59G>T
ENST00000623535.2:c.59G>T
ENST00000635828.1:c.59G>T
ENST00000637881.1:c.59G>T
ENST00000674046.1:c.59G>T
ENST00000379989.6:c.59G>T
ENST00000379996.7:c.59G>T
ENST00000463994.4:c.59G>T
ENST00000623364.3:c.59G>T
ENST00000623535.1:n.59G>T
ENST00000624700.3:c.59G>T
NM_001037343.1:c.59G>T
NM_003159.2:c.59G>T
NM_001323289.2:c.59G>T
NM_001037343.2:c.59G>T
NM_003159.3:c.59G>T
NC_000023.11:g.18507155G>T
CM000685.2:g.18507155G>T
NC_000023.10:g.18525275G>T
CM000685.1:g.18525275G>T
NC_000023.9:g.18435196G>T
NG_008475.1:g.86551G>T

Pathogenic

Met criteria codes 5
PP3 PS2 PM1 PM5_Strong PM2_Supporting

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The p.Gly20Val variant in CDKL5 occurs in the de novo state (biological parentage confirmed) in this individual (PS2). Multiple pathogenic missense variants have been previously identified within this codon which indicates that this residue is critical to the function of the protein (PMID 23064044, 20397747) (PM5_Strong). The p.Gly20Val variant in CDKL5 is absent from gnomAD (PM2_Supporting). Computational prediction analysis tools suggests a deleterious impact; however, this information does not predict clinical significance on its own (PP3). In summary, the p.Gly20Val variant in CDKL5 is classified as pathogenic for CDKL5-associated disorder based on the ACMG/AMP criteria (PS2, PM5_strong, PM2_supporting, PP3).
Met criteria codes
PP3
Computational prediction analysis tools suggests a deleterious impact; however, this information does not predict clinical significance on its own
PS2
The p.Gly20Val variant in CDKL5 occurs in the de novo state (biological parentage confirmed) in this individual
PM1
The p.Gly20Val variant occurs in the well-characterized ATP binding region functional domain of the CDKL5 gene.
PM5_Strong
Multiple pathogenic missense variants have been previously identified within this codon which indicates that this residue is critical to the function of the protein (PMID 23064044, 20397747)
PM2_Supporting
The p.Gly20Val variant in CDKL5 is absent from gnomAD.
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