chrX-18650553-C-G
Variant summary
Our verdict is Benign. Variant got -7 ACMG points: 0P and 7B. BP4_ModerateBP6BS2
The ENST00000379989.6(CDKL5):āc.2941C>Gā(p.Arg981Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000644 in 1,210,840 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 28 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. 13/19 in silico tools predict a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R981Q) has been classified as Uncertain significance.
Frequency
Consequence
ENST00000379989.6 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -7 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RS1 | NM_000330.4 | c.185-3221G>C | intron_variant | ENST00000379984.4 | |||
CDKL5 | NM_001037343.2 | c.2941C>G | p.Arg981Gly | missense_variant | 21/22 | ||
CDKL5 | NM_003159.3 | c.2941C>G | p.Arg981Gly | missense_variant | 20/21 | ||
RS1 | XM_047442337.1 | c.-170G>C | 5_prime_UTR_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RS1 | ENST00000379984.4 | c.185-3221G>C | intron_variant | 1 | NM_000330.4 | P1 |
Frequencies
GnomAD3 genomes AF: 0.0000355 AC: 4AN: 112685Hom.: 0 Cov.: 24 AF XY: 0.0000287 AC XY: 1AN XY: 34831
GnomAD3 exomes AF: 0.0000109 AC: 2AN: 183367Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 67803
GnomAD4 exome AF: 0.0000674 AC: 74AN: 1098155Hom.: 0 Cov.: 30 AF XY: 0.0000743 AC XY: 27AN XY: 363509
GnomAD4 genome AF: 0.0000355 AC: 4AN: 112685Hom.: 0 Cov.: 24 AF XY: 0.0000287 AC XY: 1AN XY: 34831
ClinVar
Submissions by phenotype
not provided Benign:2
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Dec 20, 2018 | - - |
Likely benign, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Feb 01, 2023 | CDKL5: BP4 - |
Developmental and epileptic encephalopathy, 2 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Nov 05, 2021 | - - |
Developmental and epileptic encephalopathy, 2;CN128785:Angelman syndrome-like Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Oct 29, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at