chr2-61017777-A-AC
Variant summary
Our verdict is Pathogenic. Variant got 12 ACMG points: 12P and 0B. PVS1PM2PP5_Moderate
The NM_002618.4(PEX13):c.20dup(p.Pro8SerfsTer27) variant causes a frameshift change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000000716 in 1,397,484 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Pathogenic (★). Synonymous variant affecting the same amino acid position (i.e. P6P) has been classified as Likely benign.
Frequency
Consequence
NM_002618.4 frameshift
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 12 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX13 | NM_002618.4 | c.20dup | p.Pro8SerfsTer27 | frameshift_variant | 1/4 | ENST00000295030.6 | |
PUS10 | NM_144709.4 | c.-16+230_-16+231insG | intron_variant | ENST00000316752.11 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX13 | ENST00000295030.6 | c.20dup | p.Pro8SerfsTer27 | frameshift_variant | 1/4 | 1 | NM_002618.4 | P1 | |
PUS10 | ENST00000316752.11 | c.-16+230_-16+231insG | intron_variant | 1 | NM_144709.4 | P1 |
Frequencies
GnomAD3 genomes ? Cov.: 32
GnomAD4 exome AF: 7.16e-7 AC: 1AN: 1397484Hom.: 0 Cov.: 31 AF XY: 0.00 AC XY: 0AN XY: 689168
GnomAD4 genome ? Cov.: 32
ClinVar
Submissions by phenotype
Peroxisome biogenesis disorder 11A (Zellweger) Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Apr 30, 2023 | For these reasons, this variant has been classified as Pathogenic. This variant has not been reported in the literature in individuals affected with PEX13-related conditions. This variant is not present in population databases (gnomAD no frequency). This sequence change creates a premature translational stop signal (p.Pro8Serfs*27) in the PEX13 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PEX13 are known to be pathogenic (PMID: 10332040, 21031596). - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at
Publications
No publications associated with this variant yet.