X-48902390-CAGAG-CAGAGAG
Variant summary
Our verdict is Pathogenic. Variant got 18 ACMG points: 18P and 0B. PVS1PM2PP5_Very_Strong
The NM_001032382.2(PQBP1):c.461_462dupAG(p.Arg155SerfsTer41) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000183 in 1,095,228 control chromosomes in the GnomAD database, with no homozygous occurrence. There are no hemizygote samples in GnomAD. Variant has been reported in ClinVar as Pathogenic (★★). Variant results in nonsense mediated mRNA decay.
Frequency
Consequence
NM_001032382.2 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 18 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | Exon rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
PQBP1 | NM_001032382.2 | c.461_462dupAG | p.Arg155SerfsTer41 | frameshift_variant | Exon 5 of 7 | ENST00000447146.7 | NP_001027554.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.00 AC: 0AN: 110939Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33237 FAILED QC
GnomAD4 exome AF: 0.00000183 AC: 2AN: 1095228Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 360906
GnomAD4 genome Data not reliable, filtered out with message: AC0;AS_VQSR AF: 0.00 AC: 0AN: 110992Hom.: 0 Cov.: 22 AF XY: 0.00 AC XY: 0AN XY: 33300
ClinVar
Submissions by phenotype
Renpenning syndrome Pathogenic:4
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not provided Pathogenic:1
The c.461_462dupAG variant, denoted as 3898_3899dupAG due to alternative nomenclature, in the PQBP1 gene has been reported previously to segregate in affected males from two families with X-linked mental retardation, including one family with Sutherland-Haan syndrome (Kalscheuer et al., 2003). Functional studies of the variant, denoted as 3898_3899dupAG due to alternative nomenclature, demonstrate the abnormal PQBP1 protein is not properly localized in the nucleus (Kalscheuer et al., 2003). In addition, functional studies of the variant, denoted as c.463_464dupAG due to alternative nomenclature, demonstrate the abnormal PQBP1 protein affects fragile X mental retardation protein (FMRP) degradation leading to FMRP-dependent synaptic defects (Zhang et al., 2017). The c.461_462dupAG variant causes a frameshift starting with codon Arginine 155, changes this amino acid to a Serine residue, and creates a premature Stop codon at position 41 of the new reading frame, denoted p.Arg155SerfsX41. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.461_462dupAG variant is not observed in large population cohorts (Lek et al., 2016). We interpret c.461_462dupAG as a pathogenic variant. -
PQBP1-related disorder Pathogenic:1
The PQBP1 c.461_462dupAG variant is predicted to result in a frameshift and premature protein termination (p.Arg155Serfs*41). This variant has been reported to segregate with disease in two families with X-linked intellectual disability (families with AG duplication in Kalscheuer et al. 2003. PubMed ID: 14634649). In vitro experimental studies indicate this variant impacts protein function (reported as c.463_464dupAG in Mizuguchi et al. 2014. PubMed ID: 24781215 and Zhang et al. 2017. PubMed ID: 28073926). This variant is reported in 0.0014% of alleles in individuals of European (Non-Finnish) descent in gnomAD. Frameshift variants in PQBP1 are expected to be pathogenic. This variant is interpreted as pathogenic. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at