ClinVar Miner

Submissions for variant NM_000466.3(PEX1):c.2922del (p.Leu974fs)

dbSNP: rs762324548
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000478887 SCV000572331 pathogenic not provided 2020-10-05 criteria provided, single submitter clinical testing 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 a significant frequency in large population cohorts (Lek et al., 2016); Has not been previously published as pathogenic or benign to our knowledge
Invitae RCV001376561 SCV001222508 pathogenic Zellweger spectrum disorders 2023-10-22 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Leu974Phefs*15) in the PEX1 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PEX1 are known to be pathogenic (PMID: 21031596, 26387595, 31831025). This variant is present in population databases (rs762324548, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with PEX1-related conditions. ClinVar contains an entry for this variant (Variation ID: 371696). For these reasons, this variant has been classified as Pathogenic.
Preventiongenetics, part of Exact Sciences RCV003418086 SCV004113961 likely pathogenic PEX1-related condition 2023-07-18 criteria provided, single submitter clinical testing The PEX1 c.2922delA variant is predicted to result in a frameshift and premature protein termination (p.Leu974Phefs*15). To our knowledge, this variant has not been previously reported in the literature. This variant is reported in 0.00088% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/7-92123804-GT-G). Frameshift variants in PEX1 are expected to be pathogenic. This variant is interpreted as likely pathogenic.
Counsyl RCV000411605 SCV000487468 likely pathogenic Peroxisome biogenesis disorder 1A (Zellweger) 2015-12-22 no assertion criteria provided clinical testing
Counsyl RCV000409154 SCV000487469 likely pathogenic Heimler syndrome 1 2015-12-22 no assertion criteria provided clinical testing

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