ClinVar Miner

Submissions for variant NM_000532.5(PCCB):c.1173dup (p.Val392fs)

dbSNP: rs587776758
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000012794 SCV000697265 pathogenic Propionic acidemia 2017-03-02 criteria provided, single submitter clinical testing Variant summary: The PCCB c.1173dupT (p.Val392Cysfs) variant results in a premature termination codon, predicted to cause a truncated or absent PCCB protein due to nonsense mediated decay, which are commonly known mechanisms for disease. Truncations downstream of this position have been classified as pathogenic by our laboratory (e.g.p.Gly407fs). One in silico tool predicts a damaging outcome for this variant. This variant is one of the most common pathogenic variant in Spanish patients with propionic acidemia and is absent in 121400 control chromosomes. Functional studies showed that the protein levels and PCC activity were extremely low in patients carrying this variant. Taken together, this variant is classified as pathogenic.
Invitae RCV000012794 SCV000961041 pathogenic Propionic acidemia 2023-12-31 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Val392Cysfs*2) in the PCCB gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in PCCB are known to be pathogenic (PMID: 15464417). This variant is present in population databases (rs753064211, gnomAD 0.02%). This premature translational stop signal has been observed in individuals with propionic acidemia (PMID: 9452096, 9683601, 20549364). ClinVar contains an entry for this variant (Variation ID: 12014). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
GeneDx RCV001576958 SCV001804251 pathogenic not provided 2022-10-13 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; This variant is associated with the following publications: (PMID: 9683601, 10780784, 9452096, 20549364, 25865301, 32778825)
Fulgent Genetics, Fulgent Genetics RCV000012794 SCV002812012 pathogenic Propionic acidemia 2022-03-14 criteria provided, single submitter clinical testing
Baylor Genetics RCV000012794 SCV004205195 pathogenic Propionic acidemia 2023-09-09 criteria provided, single submitter clinical testing
OMIM RCV000012794 SCV000033034 pathogenic Propionic acidemia 1998-08-01 no assertion criteria provided literature only
Counsyl RCV000012794 SCV001132453 pathogenic Propionic acidemia 2017-06-30 no assertion criteria provided clinical testing
Natera, Inc. RCV000012794 SCV001454525 pathogenic Propionic acidemia 2020-09-16 no assertion criteria provided clinical testing

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