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_001323289.2(CDKL5):c.93A>G (p.Arg31=)

CA171658

94115 (ClinVar)

Gene: CDKL5

Condition: CDKL5 disorder

Inheritance Mode: X-linked inheritance

Link to MONDO

UUID: 3a17ecd4-9313-4127-93cc-85046b3f66ae

Approved on: 2022-09-01

Published on: 2022-09-06

HGVS expressions

NM_001323289.2:c.93A>G

NM_001323289.2(CDKL5):c.93A>G (p.Arg31=)

NC_000023.11:g.18510848A>G

CM000685.2:g.18510848A>G

NC_000023.10:g.18528968A>G

CM000685.1:g.18528968A>G

NC_000023.9:g.18438889A>G

NG_008475.1:g.90244A>G

ENST00000623535.2:c.93A>G

ENST00000635828.1:c.93A>G

ENST00000637881.1:c.93A>G

ENST00000674046.1:c.93A>G

ENST00000379989.6:c.93A>G

ENST00000379996.7:c.93A>G

ENST00000463994.4:c.93A>G

ENST00000623364.3:c.93A>G

ENST00000623535.1:n.93A>G

ENST00000624700.3:c.93A>G

NM_001037343.1:c.93A>G

NM_003159.2:c.93A>G

NM_001323289.1:c.93A>G

NM_001037343.2:c.93A>G

NM_003159.3:c.93A>G

Likely Benign

BS2 BP7

PM2 BA1 BS1

Evidence Links 0

Expert Panel

Rett and Angelman-like Disorders VCEP

Criteria Specification Information

Criteria Specifications for this VCEP

Evidence submitted by expert panel

Rett and Angelman-like Disorders VCEP

The p.Arg31= variant in CDKL5 is present in 3 female and 2 male individuals in gnomAD (0.002%) (not sufficient to meet BS1 criteria). The p.Arg31= variant is observed in at least 2 unaffected individuals (internal database) (BS2). The silent p.Arg31= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide (BP7). In summary, the p.Arg31= variant in CDKL5 is classified as likely benign based on the ACMG/AMP criteria (BS2, BP7).

BS2

The p.Arg31= variant is observed in at least 2 unaffected individuals (internal database)

BP7

The silent p.Arg31= variant is not predicted to affect splicing using multiple computational tools and does not affect a highly conserved nucleotide

PM2

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

BA1

No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline

BS1

The p.Arg31= variant in CDKL5 is present in 5 female and male individuals in gnomAD (0.002%) (not sufficient to meet BS1 criteria).

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