rs202153551
Variant summary
Our verdict is Uncertain significance. Variant got 0 ACMG points: 8P and 8B. PVS1BS1BS2
The ENST00000379989.6(CDKL5):c.2854C>T(p.Arg952Ter) variant causes a stop gained change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000496 in 1,210,305 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 17 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Likely benign (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
ENST00000379989.6 stop_gained
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 0 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
RS1 | NM_000330.4 | c.185-3134G>A | intron_variant | ENST00000379984.4 | |||
CDKL5 | NM_001037343.2 | c.2854C>T | p.Arg952Ter | stop_gained | 21/22 | ||
CDKL5 | NM_003159.3 | c.2854C>T | p.Arg952Ter | stop_gained | 20/21 | ||
RS1 | XM_047442337.1 | c.-83G>A | 5_prime_UTR_variant | 1/4 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
RS1 | ENST00000379984.4 | c.185-3134G>A | intron_variant | 1 | NM_000330.4 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000624 AC: 7AN: 112257Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34407
GnomAD3 exomes AF: 0.000196 AC: 36AN: 183500Hom.: 0 AF XY: 0.000162 AC XY: 11AN XY: 67930
GnomAD4 exome AF: 0.0000483 AC: 53AN: 1098048Hom.: 0 Cov.: 30 AF XY: 0.0000468 AC XY: 17AN XY: 363404
GnomAD4 genome ? AF: 0.0000624 AC: 7AN: 112257Hom.: 0 Cov.: 24 AF XY: 0.00 AC XY: 0AN XY: 34407
ClinVar
Submissions by phenotype
not specified Benign:1
Benign, no assertion criteria provided | curation | RettBASE | May 09, 2014 | In exon 20, affecting only the transcript lowly expressed; found in multiple normal females in control population and normal family members - |
Inborn genetic diseases Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Ambry Genetics | Aug 02, 2017 | This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity. - |
not provided Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Nov 07, 2019 | This variant is associated with the following publications: (PMID: 26112015, 23756444, 22779007, 21775177, 25525159, 27824329, 30564305, 29933521, 30405208, 30763456) - |
Developmental and epileptic encephalopathy, 2;CN128785:Angelman syndrome-like Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Dec 23, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at