rs61752138
Variant summary
Our verdict is Pathogenic. Variant got 20 ACMG points: 20P and 0B. PS1_Very_StrongPM2PP3_ModeratePP5_Very_Strong
The NM_001351132.2(PEX5):āc.1578T>Gā(p.Asn526Lys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.00000138 in 1,453,044 control chromosomes in the GnomAD database, with no homozygous occurrence. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (ā ā ). Another nucleotide change resulting in same amino acid change has been previously reported as Pathogenicin ClinVar.
Frequency
Consequence
NM_001351132.2 missense
Scores
Clinical Significance
Conservation
Genome browser will be placed here
ACMG classification
Verdict is Pathogenic. Variant got 20 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
PEX5 | NM_001351132.2 | c.1578T>G | p.Asn526Lys | missense_variant | 15/16 | ENST00000675855.1 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
PEX5 | ENST00000675855.1 | c.1578T>G | p.Asn526Lys | missense_variant | 15/16 | NM_001351132.2 | A1 |
Frequencies
GnomAD3 genomes Cov.: 34
GnomAD4 exome AF: 0.00000138 AC: 2AN: 1453044Hom.: 0 Cov.: 35 AF XY: 0.00 AC XY: 0AN XY: 722748
GnomAD4 genome Cov.: 34
ClinVar
Submissions by phenotype
Peroxisome biogenesis disorder 2A (Zellweger) Pathogenic:3
Pathogenic, no assertion criteria provided | clinical testing | Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City | Jun 26, 2018 | - - |
Pathogenic, criteria provided, single submitter | research | Center for Genomic Medicine, King Faisal Specialist Hospital and Research Center | May 08, 2023 | - - |
Pathogenic, criteria provided, single submitter | clinical testing | Baylor Genetics | May 15, 2020 | This variant was determined to be pathogenic according to ACMG Guidelines, 2015 [PMID:25741868]. - |
Peroxisome biogenesis disorder 2B Pathogenic:2
Pathogenic, no assertion criteria provided | clinical testing | Biochemical Molecular Genetic Laboratory, King Abdulaziz Medical City | Jun 26, 2018 | - - |
Pathogenic, no assertion criteria provided | literature only | OMIM | Feb 01, 1995 | - - |
not provided Pathogenic:2
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Mar 28, 2019 | Published functional studies demonstrate a damaging effect (Dodt et al., 1995; Shimozawa et al., 1999; Carvalho et al., 2007); Not observed in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 31130284, 11101887, 7719337, 10462504, 18712838, 17532062) - |
Likely pathogenic, criteria provided, single submitter | clinical testing | Revvity Omics, Revvity | Nov 19, 2021 | - - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at