NM_001367721.1:c.1922G>A
Variant summary
Our verdict is Benign. Variant got -12 ACMG points: 1P and 13B. PP2BP4_StrongBP6BS1BS2
The NM_001367721.1(CASK):c.1922G>A(p.Arg641Lys) variant causes a missense change. The variant allele was found at a frequency of 0.000167 in 1,203,462 control chromosomes in the GnomAD database, including 1 homozygotes. There are 74 hemizygotes in GnomAD. In-silico tool predicts a benign outcome for this variant. Variant has been reported in ClinVar as Conflicting classifications of pathogenicity (no stars).
Frequency
Consequence
NM_001367721.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CASK | NM_001367721.1 | c.1922G>A | p.Arg641Lys | missense_variant | Exon 21 of 27 | ENST00000378163.7 | NP_001354650.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.000116 AC: 13AN: 111669Hom.: 1 Cov.: 23 AF XY: 0.000118 AC XY: 4AN XY: 33849
GnomAD3 exomes AF: 0.000224 AC: 41AN: 183137Hom.: 1 AF XY: 0.000251 AC XY: 17AN XY: 67623
GnomAD4 exome AF: 0.000172 AC: 188AN: 1091739Hom.: 0 Cov.: 28 AF XY: 0.000196 AC XY: 70AN XY: 357275
GnomAD4 genome AF: 0.000116 AC: 13AN: 111723Hom.: 1 Cov.: 23 AF XY: 0.000118 AC XY: 4AN XY: 33913
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:2
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CASK: PP2, BS1, BS2 -
This variant is associated with the following publications: (PMID: 31139143) -
Inborn genetic diseases Benign:1
This alteration is classified as 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. -
Intellectual disability, CASK-related, X-linked Benign:1
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Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at