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]
  • See Evidence submitted by expert panel for details.

Variant: NM_003159.2(CDKL5):c.2927C>T (p.Pro976Leu)

CA171640

156694 (ClinVar)

Gene: CDKL5
Condition: CDKL5 disorder
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 68b2dec4-9be9-413d-8245-733323b08447
Approved on: 2021-03-26
Published on: 2021-05-17

HGVS expressions

NM_003159.2:c.2927C>T
NM_003159.2(CDKL5):c.2927C>T (p.Pro976Leu)
ENST00000379984.4:c.185-3207G>A
ENST00000673617.1:n.199C>T
ENST00000379984.3:c.185-3207G>A
ENST00000379989.6:c.2927C>T
ENST00000379996.7:c.2927C>T
NM_000330.3:c.185-3207G>A
NM_001037343.1:c.2927C>T
NM_000330.4:c.185-3207G>A
NM_001037343.2:c.2927C>T
NM_003159.3:c.2927C>T
NC_000023.11:g.18650539C>T
CM000685.2:g.18650539C>T
NC_000023.10:g.18668659C>T
CM000685.1:g.18668659C>T
NC_000023.9:g.18578580C>T
NG_008475.1:g.229935C>T
NG_008659.3:g.31910G>A
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Likely Benign

Met criteria codes 3
BP2 BP4 BS1

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 allele frequency of the p.Pro976Leu variant in CDKL5 is 0.01% in South Asian sub population in gnomAD, which is high enough to be classified as likely benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). The p.Pro976Leu variant is observed in the CDKL5 gene where a second pathogenic variant in the same gene is present in the patient (internal database) (BP2). Computational analysis prediction tools suggest that the p.Pro976Leu variant does not have a deleterious impact; however this information does not predict clinical significance on its own (BP4). In summary, the p.Pro976Leu variant in CDKL5 is classified as likely benign based on the ACMG/AMP criteria (BS1, BP2, BP4).
Met criteria codes
BP2
The p.Pro976Leu variant is observed in the CDKL5 gene where a second pathogenic variant in the same gene is present in the patient (internal database)
BP4
Computational analysis prediction tools suggest that the p.Pro976Leu variant does not have a deleterious impact; however this information does not predict clinical significance on its own
BS1
The allele frequency of the p.Pro976Leu variant in CDKL5 is 0.01% in South Asian sub population in gnomAD, which is high enough to be classified as likely benign based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions.
Curation History
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