ClinVar Miner

Submissions for variant NM_000444.6(PHEX):c.1543C>T (p.Gln515Ter) (rs886041361)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000333172 SCV000329876 pathogenic not provided 2017-04-19 criteria provided, single submitter clinical testing The Q515X nonsense variant in the PHEX gene has been reported as a de novo finding in patients with X-linked hypophosphatemic rickets (Morey et al., 2011; Durmaz et al., 2013; Zhang et al., 2015). This pathogenic variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. In addition, the Q515X variant was not observed in approximately 6,500 individuals of European and African American ancestry by the NHLBI Exome Sequencing Project. Therefore, we interpret the Q515X variant to be pathogenic.
Institute of Human Genetics, Klinikum rechts der Isar RCV000505394 SCV000599619 pathogenic Familial X-linked hypophosphatemic vitamin D refractory rickets 2013-10-31 criteria provided, single submitter clinical testing
Invitae RCV000333172 SCV001402417 pathogenic not provided 2019-10-08 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Gln515*) in the PHEX gene. It is expected to result in an absent or disrupted protein product. This variant is not present in population databases (ExAC no frequency). This variant has been observed in an individual affected with hypophosphatemic rickets (PMID: 21902834, 30682568). ClinVar contains an entry for this variant (Variation ID: 280074). Loss-of-function variants in PHEX are known to be pathogenic (PMID: 9097956, 9106524, 19219621). For these reasons, this variant has been classified as Pathogenic.

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