2-39190455-C-G
Variant summary
Our verdict is Uncertain significance. Variant got 3 ACMG points: 3P and 0B. PM2PP3
The NM_001346911.1(CDKL4):c.502G>C(p.Ala168Pro) variant causes a missense change. The variant allele was found at a frequency of 0.0000062 in 1,613,994 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_001346911.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 3 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CDKL4 | NM_001346911.1 | c.502G>C | p.Ala168Pro | missense_variant | Exon 5 of 9 | NP_001333840.1 | ||
CDKL4 | NM_001397900.1 | c.502G>C | p.Ala168Pro | missense_variant | Exon 6 of 10 | NP_001384829.1 | ||
CDKL4 | NM_001009565.2 | c.502G>C | p.Ala168Pro | missense_variant | Exon 5 of 8 | NP_001009565.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000131 AC: 2AN: 152112Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.00000795 AC: 2AN: 251466Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135902
GnomAD4 exome AF: 0.00000547 AC: 8AN: 1461882Hom.: 0 Cov.: 31 AF XY: 0.00000688 AC XY: 5AN XY: 727244
GnomAD4 genome AF: 0.0000131 AC: 2AN: 152112Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.502G>C (p.A168P) alteration is located in exon 5 (coding exon 5) of the CDKL4 gene. This alteration results from a G to C substitution at nucleotide position 502, causing the alanine (A) at amino acid position 168 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at