rs137852818
Positions:
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM2PP2PP3PP5_Moderate
The NM_001367721.1(CASK):c.2129A>G(p.Asp710Gly) 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 Likely pathogenic (★).
Frequency
Genomes: not found (cov: 23)
Consequence
CASK
NM_001367721.1 missense
NM_001367721.1 missense
Scores
8
6
3
Clinical Significance
Conservation
PhyloP100: 7.61
Genes affected
CASK (HGNC:1497): (calcium/calmodulin dependent serine protein kinase) This gene encodes a calcium/calmodulin-dependent serine protein kinase. The encoded protein is a MAGUK (membrane-associated guanylate kinase) protein family member. These proteins are scaffold proteins and the encoded protein is located at synapses in the brain. Mutations in this gene are associated with FG syndrome 4, intellectual disability and microcephaly with pontine and cerebellar hypoplasia, and a form of X-linked intellectual disability. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2017]
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ACMG classification
Classification made for transcript
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
PM2
Very rare variant in population databases, with high coverage;
PP2
Missense variant in gene, where missense usually causes diseases (based on misZ statistic), CASK. . Gene score misZ 4.2502 (greater than the threshold 3.09). GenCC has associacion of gene with syndromic X-linked intellectual disability Najm type, X-linked syndromic intellectual disability, developmental and epileptic encephalopathy, FG syndrome 4.
PP3
MetaRNN computational evidence supports a deleterious effect, 0.758
PP5
Variant X-41542717-T-C is Pathogenic according to our data. Variant chrX-41542717-T-C is described in ClinVar as [Likely_pathogenic]. Clinvar id is 11534.Status of the report is criteria_provided_single_submitter, 1 stars.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CASK | NM_001367721.1 | c.2129A>G | p.Asp710Gly | missense_variant | 22/27 | ENST00000378163.7 | NP_001354650.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CASK | ENST00000378163.7 | c.2129A>G | p.Asp710Gly | missense_variant | 22/27 | 5 | NM_001367721.1 | ENSP00000367405 | A1 |
Frequencies
GnomAD3 genomes Cov.: 23
GnomAD3 genomes
Cov.:
23
GnomAD4 exome Cov.: 28
GnomAD4 exome
Cov.:
28
GnomAD4 genome Cov.: 23
GnomAD4 genome
Cov.:
23
ClinVar
Significance: Likely pathogenic
Submissions summary: Pathogenic:2
Revision: criteria provided, single submitter
LINK: link
Submissions by phenotype
FG syndrome 4 Pathogenic:1
Pathogenic, no assertion criteria provided | literature only | OMIM | May 01, 2009 | - - |
FG syndrome 4;C2677903:Syndromic X-linked intellectual disability Najm type Pathogenic:1
Likely pathogenic, criteria provided, single submitter | clinical testing | Génétique des Maladies du Développement, Hospices Civils de Lyon | Mar 08, 2017 | - - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
CADD
Pathogenic
DANN
Uncertain
DEOGEN2
Uncertain
.;.;.;.;.;.;.;D;.;.;.;.;.;.;.
FATHMM_MKL
Uncertain
D
LIST_S2
Uncertain
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D;D;D;D;D;D;D;D;D;D;D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
.;.;.;M;.;.;.;M;.;.;.;.;.;.;.
MutationTaster
Benign
A;A;A;A;A;A;A
PrimateAI
Pathogenic
D
PROVEAN
Pathogenic
.;.;.;.;.;D;.;D;.;.;.;.;.;.;.
REVEL
Pathogenic
Sift
Benign
.;.;.;.;.;T;.;T;.;.;.;.;.;.;.
Sift4G
Benign
.;.;.;.;.;T;.;T;.;.;.;.;.;.;.
Polyphen
D;P;.;B;.;B;.;B;.;.;.;.;.;.;.
Vest4
0.68
MutPred
0.28
.;.;.;Loss of ubiquitination at K715 (P = 0.0247);.;.;.;Loss of ubiquitination at K715 (P = 0.0247);.;.;.;.;.;.;.;
MVP
0.96
MPC
1.5
ClinPred
D
GERP RS
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
DS_DG_spliceai
Position offset: 1
DS_DL_spliceai
Position offset: -26
Find out detailed SpliceAI scores and Pangolin per-transcript scores at