NM_001904.4:c.1925_1926delAG
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_001904.4(CTNNB1):c.1925_1926delAG(p.Glu642ValfsTer5) variant causes a frameshift change involving the alteration of a conserved nucleotide. The variant was absent in control chromosomes in GnomAD project. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001904.4 frameshift
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
CTNNB1 | NM_001904.4 | c.1925_1926delAG | p.Glu642ValfsTer5 | frameshift_variant | Exon 12 of 15 | ENST00000349496.11 | NP_001895.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | TSL | MANE | Protein | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|---|
CTNNB1 | ENST00000349496.11 | c.1925_1926delAG | p.Glu642ValfsTer5 | frameshift_variant | Exon 12 of 15 | 1 | NM_001904.4 | ENSP00000344456.5 | ||
CTNNB1 | ENST00000645982.1 | c.1925_1926delAG | p.Glu642ValfsTer5 | frameshift_variant | Exon 12 of 16 | ENSP00000494845.1 |
Frequencies
GnomAD3 genomes Cov.: 32
GnomAD4 genome Cov.: 32
ClinVar
Submissions by phenotype
not provided Pathogenic:4
- -
Frameshift variant predicted to result in protein truncation or nonsense mediated decay in a gene for which loss of function is a known mechanism of disease; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 25326669, 26845106, 28191889, 33004838, 33994118) -
- -
This sequence change creates a premature translational stop signal (p.Glu642Valfs*5) in the CTNNB1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in CTNNB1 are known to be pathogenic (PMID: 23033978, 24614104, 25326669, 26350204, 28575650). This variant is not present in population databases (gnomAD no frequency). This premature translational stop signal has been observed in individual(s) with microcephaly, developmental delay, intellectual disability, and severe hypotonia (PMID: 25326669, 26845106). In at least one individual the variant was observed to be de novo. ClinVar contains an entry for this variant (Variation ID: 503703). For these reasons, this variant has been classified as Pathogenic. -
Severe intellectual disability-progressive spastic diplegia syndrome Pathogenic:3
Submission from Simons Searchlight facilitated by GenomeConnect. Variant interpreted by the Simons Searchlight team most recently on 2018-12-10 and interpreted as Pathogenic. The reporting laboratory might also submit to ClinVar. This variant was identified in multiple probands enrolled in Simons Searchlight. -
- -
The de novo c.1925_1926del (p.Glu642ValfsTer5) variant identified in the CTNNB1 gene is the deletion of two nucleotides resulting in a frameshift of the protein at amino acid 642/782 (exon 12/15), and is predicted to lead to the premature termination of the protein 5 amino acids downstream. This variant is absent from gnomAD(v3.0) suggesting it is not a common benign variant in the populations represented in that database. This variant is reported in ClinVar as Pathogenic (VarID:503703) and has been reported in multiple affected individuals in the literature [PMID:25326669,PMID:26845106]. Given its deleterious nature, presence de novo in this individual, absence in population databases, and observation in multiple affected individuals in the literature, the c.1925_1926del (p.Glu642ValfsTer5) variant identified in the CTNNB1 gene is reported as Pathogenic. -
Inborn genetic diseases Pathogenic:1
- -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at