X-18425684-G-A
Variant summary
Our verdict is Likely benign. The variant received -2 ACMG points: 2P and 4B. PM2BP4_Strong
The NM_001323289.2(CDKL5):c.-174G>A variant causes a 5 prime UTR change involving the alteration of a non-conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a benign outcome for this variant. No clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar.
Frequency
Consequence
NM_001323289.2 5_prime_UTR
Scores
Clinical Significance
Conservation
Publications
- CDKL5 disorderInheritance: XL Classification: DEFINITIVE Submitted by: ClinGen
- developmental and epileptic encephalopathy, 2Inheritance: XL Classification: DEFINITIVE, STRONG, SUPPORTIVE Submitted by: Orphanet, G2P, Labcorp Genetics (formerly Invitae), Ambry Genetics
- atypical Rett syndromeInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- genetic developmental and epileptic encephalopathyInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- infantile spasmsInheritance: AD Classification: SUPPORTIVE Submitted by: Orphanet
- precocious pubertyInheritance: XL Classification: LIMITED Submitted by: Ambry Genetics
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ACMG classification
Our verdict: Likely_benign. The variant received -2 ACMG points.
Transcripts
RefSeq
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CDKL5 | ENST00000623535.2 | c.-174G>A | 5_prime_UTR_variant | Exon 1 of 18 | 1 | NM_001323289.2 | ENSP00000485244.1 | |||
CDKL5 | ENST00000379996.7 | c.-174G>A | 5_prime_UTR_variant | Exon 1 of 21 | 1 | ENSP00000369332.3 | ||||
CDKL5 | ENST00000674046.1 | c.-174G>A | 5_prime_UTR_variant | Exon 1 of 19 | ENSP00000501174.1 |
Frequencies
GnomAD3 genomes Cov.: 24
GnomAD4 exome Cov.: 0
GnomAD4 genome Cov.: 24
ClinVar
Submissions by phenotype
not specified Benign:1
This variant is considered likely benign or benign based on one or more of the following criteria: it is a conservative change, it occurs at a poorly conserved position in the protein, it is predicted to be benign by multiple in silico algorithms, and/or has population frequency not consistent with disease. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at