ClinVar Miner

Submissions for variant NM_000286.3(PEX12):c.334C>T (p.Gln112Ter) (rs776731688)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000675037 SCV000800467 likely pathogenic Peroxisome biogenesis disorder type 3B; Peroxisome biogenesis disorder 3A 2018-06-07 criteria provided, single submitter clinical testing
Baylor Genetics RCV000679868 SCV000807239 pathogenic Peroxisome biogenesis disorder 3A 2017-09-01 criteria provided, single submitter clinical testing This nonsense variant is categorized as deleterious according to ACMG guidelines (PMID:18414213) and was found once in our laboratory homozygous in a deceased 1.5-month-old female with Zellweger syndrome (abnormal VLCFAs), epilepsy, polymicrogyria, Dandy-Walker malformation, heart defect, hydronephrosis, hypothyroidism; family history of infant deaths in multiple sibs and double first cousins
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego RCV000679868 SCV000996241 pathogenic Peroxisome biogenesis disorder 3A 2019-01-31 criteria provided, single submitter clinical testing This nonsense variant found in exon 2 of 3 encodes for a premature stop codon and is predicted to result in loss of normal protein function. This variant has been previously reported as a homozygous change in association with intellectual disability and inborn error of metabolism (PMID: 27124789). It is absent from the gnomAD population database and is present in the heterozygous state in the ExAC population database at a frequency of 0.001% (1/120740) and thus is presumed to be rare. This variant has been classified in ClinVar as a pathogenic and likely pathogenic variant (Variation ID: 191074). In silico analyses support a deleterious effect of the c.334C>T (p.Gln112Ter) variant on protein function. Based on the available evidence, the c.334C>T (p.Gln112Ter) variant is classified as pathogenic.
Invitae RCV000679868 SCV001592170 pathogenic Peroxisome biogenesis disorder 3A 2020-09-07 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln112*) in the PEX12 gene. It is expected to result in an absent or disrupted protein product. This variant is present in population databases (rs776731688, ExAC 0.009%). This variant has not been reported in the literature in individuals with PEX12-related conditions. ClinVar contains an entry for this variant (Variation ID: 191074). Loss-of-function variants in PEX12 are known to be pathogenic (PMID: 9090384, 9632816, 21031596). For these reasons, this variant has been classified as Pathogenic.
Developmental Genetics Unit,King Faisal Specialist Hospital & Research Centre RCV000171254 SCV000221451 likely pathogenic not provided no assertion criteria provided research

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