chrX-41520523-G-T
Variant summary
Our verdict is Uncertain significance. Variant got 4 ACMG points: 4P and 0B. PM2PP2PP3
The NM_001367721.1(CASK):c.2678C>A(p.Thr893Lys) variant causes a missense change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Uncertain significance (★). Synonymous variant affecting the same amino acid position (i.e. T893T) has been classified as Likely benign.
Frequency
Consequence
NM_001367721.1 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Uncertain_significance. Variant got 4 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
CASK | NM_001367721.1 | c.2678C>A | p.Thr893Lys | missense_variant | 27/27 | ENST00000378163.7 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
CASK | ENST00000378163.7 | c.2678C>A | p.Thr893Lys | missense_variant | 27/27 | 5 | NM_001367721.1 | A1 | |
CASK-AS1 | ENST00000451126.1 | n.331+157G>T | intron_variant, non_coding_transcript_variant | 2 |
Frequencies
GnomAD3 genomes ? Cov.: 22
GnomAD4 exome Data not reliable, filtered out with message: AS_VQSR AF: 0.00000183 AC: 2AN: 1090726Hom.: 0 Cov.: 28 AF XY: 0.00000281 AC XY: 1AN XY: 356392
GnomAD4 genome ? Cov.: 22
ClinVar
Submissions by phenotype
Global developmental delay Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Human Genetics Bochum, Ruhr University Bochum | Dec 06, 2022 | ACMG criteria used to clasify this variant: PP3_MOD, PM2_SUP - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.