Evidence Repository - Clinical Genome Resources

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_003159.2(CDKL5):c.1234A>G (p.Lys412Glu)

CA10360368

423898 (ClinVar)

Gene: CDKL5

Condition: CDKL5 disorder

Inheritance Mode: X-linked inheritance (dominant (HP:0001423))

Link to MONDO

UUID: e9ae730b-09c8-4a77-977e-f285e9b2c990

Approved on: 2023-08-28

Published on: 2023-12-08

HGVS expressions

NM_003159.2:c.1234A>G

NM_003159.2(CDKL5):c.1234A>G (p.Lys412Glu)

NC_000023.11:g.18604158A>G

CM000685.2:g.18604158A>G

NC_000023.10:g.18622278A>G

CM000685.1:g.18622278A>G

NC_000023.9:g.18532199A>G

NG_008475.1:g.183554A>G

ENST00000623535.2:c.1234A>G

ENST00000635828.1:c.1234A>G

ENST00000637881.1:c.1234A>G

ENST00000674046.1:c.1234A>G

ENST00000379989.6:c.1234A>G

ENST00000379996.7:c.1234A>G

ENST00000463994.4:c.1234A>G

ENST00000623535.1:c.1234A>G

NM_001037343.1:c.1234A>G

NM_001323289.1:c.1234A>G

NM_001323289.2:c.1234A>G

NM_001037343.2:c.1234A>G

NM_003159.3:c.1234A>G

NM_001323289.2(CDKL5):c.1234A>G (p.Lys412Glu)

Likely Benign

BP4 BS2

BS1 PM2

Evidence Links 0

Expert Panel

Rett and Angelman-like Disorders VCEP

Criteria Specification Information

Criteria Specification: ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDKL5 Version 3.0.0

Criteria Specification Approval History

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Rett and Angelman-like Disorders VCEP

The p.Lys412Glu variant in CDKL5 is present in 1 XY individual in gnomAD (0.0001707%) (not sufficient to meet BS1 criteria). The p.Lys412Glu variant is observed in at least 2 unaffected individuals (internal database - GeneDx) (BS2). Computational analysis prediction tools suggests that the p.Lys412Glu variant does not have a deleterious impact (BP4); however this information does not predict clinical significance on its own. In summary, the p.Lys412Glu variant in CDKL5 is classified as likely benign based on the ACMG/AMP criteria (BS2, BP4).

BP4

Computational analysis prediction tools suggests that the p.Lys412Glu variant does not have a deleterious impact (BP4); however this information does not predict clinical significance on its own.

BS2

The p.Lys412Glu variant is observed in at least 2 unaffected individuals (internal database).

BS1

The p.Lys412Glu variant in CDKL5 is present in 1 XY individual in gnomAD (0.0001707%) (not sufficient to meet BS1 criteria).

PM2

The p.Lys412Glu variant in CDKL5 is not absent from gnomAD (present in one heterozygote).

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