rs369792621
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 3P and 1B. PP2PP3_ModerateBP6
The NM_001367721.1(CASK):c.2470C>T(p.Arg824Trp) variant causes a missense change. The variant allele was found at a frequency of 0.0000479 in 1,209,912 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 19 hemizygotes in GnomAD. In-silico tool predicts a pathogenic 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. R824Q) has been classified as Likely benign.
Frequency
Consequence
NM_001367721.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASK | NM_001367721.1 | c.2470C>T | p.Arg824Trp | missense_variant | 25/27 | ENST00000378163.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASK | ENST00000378163.7 | c.2470C>T | p.Arg824Trp | missense_variant | 25/27 | 5 | NM_001367721.1 | A1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000357 AC: 4AN: 111960Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34130
GnomAD3 exomes AF: 0.0000382 AC: 7AN: 183463Hom.: 0 AF XY: 0.0000147 AC XY: 1AN XY: 67895
GnomAD4 exome AF: 0.0000492 AC: 54AN: 1097952Hom.: 0 Cov.: 31 AF XY: 0.0000495 AC XY: 18AN XY: 363308
GnomAD4 genome ? AF: 0.0000357 AC: 4AN: 111960Hom.: 0 Cov.: 23 AF XY: 0.0000293 AC XY: 1AN XY: 34130
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Mar 26, 2020 | In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; Has not been previously published as pathogenic or benign to our knowledge; Observed in 0.004% (8/200477 alleles) in large population cohorts (Lek et al., 2016); This variant is associated with the following publications: (PMID: 24893065) - |
Uncertain significance, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Oct 10, 2019 | - - |
Inborn genetic diseases Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Ambry Genetics | Apr 18, 2017 | The p.R819W variant (also known as c.2455C>T), located in coding exon 25 of the CASK gene, results from a C to T substitution at nucleotide position 2455. The arginine at codon 819 is replaced by tryptophan, an amino acid with dissimilar properties. This variant was observed in the unaffected father of a female proband tested by our laboratory. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear. - |
Intellectual disability, CASK-related, X-linked Benign:1
Likely benign, criteria provided, single submitter | clinical testing | Invitae | Aug 17, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at