rs141840001
Variant summary
Our verdict is Benign. Variant got -9 ACMG points: 1P and 10B. PP2BP4BP6BS1BS2
The NM_001367721.1(CASK):c.1718C>T(p.Thr573Ile) variant causes a missense change. The variant allele was found at a frequency of 0.000145 in 1,209,115 control chromosomes in the GnomAD database, with no homozygous occurrence. There are 53 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). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. T573S) has been classified as Uncertain significance.
Frequency
Consequence
NM_001367721.1 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Benign. Variant got -9 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASK | NM_001367721.1 | c.1718C>T | p.Thr573Ile | missense_variant | 18/27 | ENST00000378163.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASK | ENST00000378163.7 | c.1718C>T | p.Thr573Ile | missense_variant | 18/27 | 5 | NM_001367721.1 | A1 |
Frequencies
GnomAD3 genomes AF: 0.0000711 AC: 8AN: 112534Hom.: 0 Cov.: 23 AF XY: 0.0000577 AC XY: 2AN XY: 34678
GnomAD3 exomes AF: 0.0000660 AC: 12AN: 181937Hom.: 0 AF XY: 0.000105 AC XY: 7AN XY: 66467
GnomAD4 exome AF: 0.000152 AC: 167AN: 1096581Hom.: 0 Cov.: 28 AF XY: 0.000141 AC XY: 51AN XY: 361987
GnomAD4 genome AF: 0.0000711 AC: 8AN: 112534Hom.: 0 Cov.: 23 AF XY: 0.0000577 AC XY: 2AN XY: 34678
ClinVar
Submissions by phenotype
not provided Uncertain:1Benign:1
Uncertain significance, criteria provided, single submitter | clinical testing | Eurofins Ntd Llc (ga) | Aug 24, 2016 | - - |
Likely benign, criteria provided, single submitter | clinical testing | GeneDx | Sep 01, 2020 | - - |
Intellectual disability, CASK-related, X-linked Benign:1
Benign, criteria provided, single submitter | clinical testing | Invitae | Oct 28, 2023 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at