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.872G>A (p.Cys291Tyr)

CA121527

11505 (ClinVar)

Gene: CDKL5
Condition: CDKL5 disorder
Inheritance Mode: X-linked inheritance
Link to MONDO
UUID: c8b52814-c9f3-44eb-962d-939b5420da52
Approved on: 2022-08-25
Published on: 2022-09-06

HGVS expressions

NM_001323289.2:c.872G>A
NM_001323289.2(CDKL5):c.872G>A (p.Cys291Tyr)
NC_000023.11:g.18598508G>A
CM000685.2:g.18598508G>A
NC_000023.10:g.18616628G>A
CM000685.1:g.18616628G>A
NC_000023.9:g.18526549G>A
NG_008475.1:g.177904G>A
ENST00000623535.2:c.872G>A
ENST00000635828.1:c.872G>A
ENST00000637881.1:c.872G>A
ENST00000674046.1:c.872G>A
ENST00000379989.6:c.872G>A
ENST00000379996.7:c.872G>A
ENST00000463994.4:c.872G>A
ENST00000623535.1:n.872G>A
NM_001037343.1:c.872G>A
NM_003159.2:c.872G>A
NM_001323289.1:c.872G>A
NM_001037343.2:c.872G>A
NM_003159.3:c.872G>A
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Uncertain Significance

Met criteria codes 3
PM6 PM2_Supporting PS4_Supporting
Not Met criteria codes 6
PM5 PM1 BS3 PS1 PS3 PP3

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.Cys291Tyr variant in CDKL5 has been reported as a de novo occurrence (biological parentage unconfirmed) in an individual with severe early-onset encephalopathy (PMID 18809835) (PM6). The p.Cys291Tyr variant in CDKL5 is absent from gnomAD (PM2_Supporting). The p.Cys291Tyr variant has been observed in at least 1 other individual with CDKL5-related disorder (PMID 18809835, PMID 25657822) (PS4_Supporting). In summary, the p.Cys291Tyr variant in CDKL5 is classified as a variant of unknown significance based on the ACMG/AMP criteria (PM6, PM2_Supporting, PS4_Supporting).
Met criteria codes
PM6
The p.Cys291Tyr variant in CDKL5 has been reported as a de novo occurrence (biological parentage unconfirmed) in an individual with severe early-onset encephalopathy (PMID 18809835)
PM2_Supporting
The p.Cys291Tyr variant in CDKL5 is absent from gnomAD
PS4_Supporting
The p.Cys291Tyr variant has been observed in at least 1 other individual with CDKL5-related disorder (PMID 18809835, PMID 25657822)
Not Met criteria codes
PM5
c.871T>C; p.C291R also reported but could not get higher than LPATH
PM1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PS3
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
PP3
REVEL score = 0.706
Curation History
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