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]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
  • No CSPEC computed assertion could be determined for this classification!

Variant: NM_001323289.2(CDKL5):c.38T>C (p.Phe13Ser)

CA412489564

929426 (ClinVar)

Gene: CDKL5 (HGNC:6792)
Condition: CDKL5 disorder (MONDO:0100039)
Inheritance Mode: X-linked inheritance
UUID: 00757f98-adba-4f7e-a510-520b9680a772
Approved on: 2025-06-25
Published on: 2025-12-23

HGVS expressions

NM_001323289.2(CDKL5):c.38T>C (p.Phe13Ser)
NM_001323289.2:c.38T>C
NC_000023.11:g.18507134T>C
CM000685.2:g.18507134T>C
NC_000023.10:g.18525254T>C
CM000685.1:g.18525254T>C
NC_000023.9:g.18435175T>C
NG_008475.1:g.86530T>C
ENST00000623535.2:c.38T>C
ENST00000635828.1:c.38T>C
ENST00000637881.1:c.38T>C
ENST00000674046.1:c.38T>C
ENST00000379989.6:c.38T>C
ENST00000379996.7:c.38T>C
ENST00000463994.4:c.38T>C
ENST00000623364.3:c.38T>C
ENST00000623535.1:c.38T>C
ENST00000624700.3:c.38T>C
ENST00000624953.1:c.38T>C
NM_001037343.1:c.38T>C
NM_003159.2:c.38T>C
NM_001323289.1:c.38T>C
NM_001037343.2:c.38T>C
NM_003159.3:c.38T>C
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Likely Pathogenic

Met criteria codes 3
PS2 PP4 PM2_Supporting
Not Met criteria codes 8
PS1 BP4 PP3 PM5 PM1 PM6 BA1 BS1

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specification: ClinGen Rett and Angelman-like Disorders Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for CDKL5 Version 4.1.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Rett and Angelman-like Disorders VCEP
The p.Phe13Ser variant in CDKL5 has been reported as a de novo occurrence (biological parentage confirmed) in an individual with CDKL5 disorder (internal database) and as a de novo occurrence (biological parentage unconfirmed) in an individual with CDKL5 disorder (PMID 31313283) (PS2). The p.Phe13Ser variant in CDKL5 is present in an individual with a clinical phenotype suggestive of CDKL5 disorder (internal database - Labcorp Genetics (formerly Invitae)) (PP4). The p.Phe13Ser variant in CDKL5 is absent from gnomAD v4.1 (PM2_Supporting). In summary, the p.Phe13Ser variant in CDKL5 is classified as likely pathogenic for CDKL5 disorder based on the ACMG/AMP criteria (PS2, PP4, PM2_Supporting). (CDKL5 Specifications v.4.1; curation approved on 06/25/2025)
Met criteria codes
PS2
The p.Phe13Ser variant in CDKL5 has been reported as a de novo occurrence (biological parentage confirmed) in an individual with CDKL5 disorder (internal database) and as a de novo occurrence (biological parentage unconfirmed) in an individual with CDKL5 disorder (PMID 31313283) (PS2).
PP4
The p.Phe13Ser variant in CDKL5 is present in an individual with a clinical phenotype suggestive of CDKL5 disorder (internal database - Labcorp Genetics (formerly Invitae)) (PP4).
PM2_Supporting
The p.Phe13Ser variant in CDKL5 is absent from gnomAD v4.1.
Not Met criteria codes
PS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BP4
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
PM5
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
PM6
The p.Phe13Ser variant in CDKL5 has been reported as a de novo occurrence (biological parentage unconfirmed) in an individual with CDKL5 disorder (PMID 31313283) - combined with PS2
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Curation History
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