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_001323289.2(CDKL5):c.1564T>G (p.Leu522Val)

CA10360394

434664 (ClinVar)

Gene: CDKL5
Condition: CDKL5 disorder
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: 32174cab-38f2-4ca9-816b-e98c24809005
Approved on: 2023-02-20
Published on: 2023-03-31

HGVS expressions

NM_001323289.2:c.1564T>G
NM_001323289.2(CDKL5):c.1564T>G (p.Leu522Val)
NC_000023.11:g.18604488T>G
CM000685.2:g.18604488T>G
NC_000023.10:g.18622608T>G
CM000685.1:g.18622608T>G
NC_000023.9:g.18532529T>G
NG_008475.1:g.183884T>G
ENST00000623535.2:c.1564T>G
ENST00000635828.1:c.1564T>G
ENST00000674046.1:c.1564T>G
ENST00000379989.6:c.1564T>G
ENST00000379996.7:c.1564T>G
ENST00000463994.4:c.1564T>G
ENST00000623535.1:n.1564T>G
NM_001037343.1:c.1564T>G
NM_003159.2:c.1564T>G
NM_001323289.1:c.1564T>G
NM_001037343.2:c.1564T>G
NM_003159.3:c.1564T>G

Benign

Met criteria codes 3
BS1 BS2 BP5
Not Met criteria codes 5
BP4 PS4 PP3 PM2 PM1

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.Leu522Val variant in CDKL5 is 0.011% in European Non-Finnish sub population in gnomAD, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1). Additionally, the p.Leu522Val variant is observed in at least 2 unaffected individuals (internal database - GeneDx, internal database - Ambry Genetics) (BS2) and is found in a patient with an alternate molecular basis of disease (internal database - GeneDx) (BP5). In summary, the p.Leu522Val variant in CDKL5 is classified as Benign for CDKL5-associated disorder according to ACMG/AMP criteria (BS1, BS2, BP5).
Met criteria codes
BS1
The allele frequency of the p.Leu522Val variant in CDKL5 is 0.011% in European Non-Finnish sub population in gnomAD, which is high enough to meet the BS1 criteria based on thresholds defined by the ClinGen Rett/Angelman-like Expert Panel for Rett/AS-like conditions (BS1).
BS2
The p.Leu522Val variant is observed in at least 2 unaffected individuals (internal database - GeneDx, internal database - Ambry Genetics).
BP5
The p.Leu522Val variant is found in a patient with an alternate molecular basis of disease (internal database - GeneDx).
Not Met criteria codes
BP4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS4
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM2
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
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