2-206162090-C-A
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_001959.4(EEF1B2):c.383C>A(p.Ser128*) variant causes a stop gained change. 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 Pathogenic (★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001959.4 stop_gained
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
EEF1B2 | NM_001959.4 | c.383C>A | p.Ser128* | stop_gained | Exon 4 of 6 | ENST00000392222.7 | NP_001950.1 |
Ensembl
Frequencies
GnomAD3 genomes Cov.: 33
GnomAD4 exome Cov.: 31
GnomAD4 genome Cov.: 33
ClinVar
Submissions by phenotype
Seizure;C2237142:Moderate global developmental delay;C3714756:Intellectual disability Pathogenic:1
A first LoF variant was reported in one family with autosomal recessive intellectual disabilities (Najmabadi et al, 2011). The NM_001959.3:c.383C>A, NP_001950.1:p.(Ser128*) variant segregates in the sibship, and is absent in general population alleles in gnomAD ascertained by July 2019. It is a LoF variant in a gene where another LoF variant has been supposed to induce similar symptoms. Moreover, there are multiple lines of computational evidence that support a deleterious effect on the gene or gene product. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at