ClinVar Miner

Submissions for variant NM_000444.6(PHEX):c.1601C>T (p.Pro534Leu)

dbSNP: rs886041363
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000260839 SCV000329878 pathogenic not provided 2022-03-28 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 24660072, 11502829, 20688626, 30298486, 22261628, 16055933, 29707405, 29460029, 25042154, 10439971, 14564077, 16636593, 21050253, 9768674, 19219621, 22101457, 22713460, 9097956, 9199930, 22695891, 18162710, 30599486, 30682568, 32104046, 32253725, 29505567, 34434907, 33639975, 32329911, 34141703, 27535533)
Institute Of Human Genetics Munich, Klinikum Rechts Der Isar, Tu München RCV000505461 SCV000599609 pathogenic Familial X-linked hypophosphatemic vitamin D refractory rickets 2013-11-19 criteria provided, single submitter clinical testing
Mendelics RCV000505461 SCV001141539 pathogenic Familial X-linked hypophosphatemic vitamin D refractory rickets 2019-05-28 criteria provided, single submitter clinical testing
Invitae RCV000260839 SCV001206281 pathogenic not provided 2024-01-21 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 534 of the PHEX protein (p.Pro534Leu). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with PHEX-related conditions (PMID: 9097956, 18162710, 19219621, 22261628, 29460029, 29505567). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 280076). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt PHEX protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
Laboratory of Cyto-molecular Genetics, Department of Anatomy, All India Institute of Medical Sciences (AIIMS), New Delhi RCV001843504 SCV002102783 pathogenic Hypophosphatemic rickets 2022-03-07 criteria provided, single submitter clinical testing

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