ClinVar Miner

Submissions for variant NM_000444.6(PHEX):c.2078G>A (p.Cys693Tyr)

dbSNP: rs1556200989
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute Of Human Genetics Munich, Klinikum Rechts Der Isar, Tu München RCV000505399 SCV000599642 pathogenic Familial X-linked hypophosphatemic vitamin D refractory rickets 2013-10-31 criteria provided, single submitter clinical testing
Invitae RCV001064981 SCV001229919 pathogenic not provided 2023-07-22 criteria provided, single submitter clinical testing 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. ClinVar contains an entry for this variant (Variation ID: 438513). This missense change has been observed in individuals with hypophosphatemic rickets (PMID: 10737991, 30682568; Invitae). This variant is not present in population databases (gnomAD no frequency). This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 693 of the PHEX protein (p.Cys693Tyr). For these reasons, this variant has been classified as Pathogenic. This variant disrupts the p.Cys693 amino acid residue in PHEX. Other variant(s) that disrupt this residue have been observed in individuals with PHEX-related conditions (PMID: 23079138, 30682568), which suggests that this may be a clinically significant amino acid residue.

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