ClinVar Miner

Submissions for variant NM_000444.6(PHEX):c.1899+1G>A

dbSNP: rs1556138769
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV000516827 SCV000614446 pathogenic not provided 2017-01-17 criteria provided, single submitter clinical testing
Mendelics RCV000990540 SCV001141551 pathogenic Familial X-linked hypophosphatemic vitamin D refractory rickets 2019-05-28 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000516827 SCV002123169 pathogenic not provided 2023-03-01 criteria provided, single submitter clinical testing For these reasons, this variant has been classified as Pathogenic. Studies have shown that disruption of this splice site results in skipping of exon 18 and introduces a premature termination codon (PMID: 31102713). The resulting mRNA is expected to undergo nonsense-mediated decay. ClinVar contains an entry for this variant (Variation ID: 447937). Disruption of this splice site has been observed in individuals with hypophosphatemia (PMID: 19219621, 21050253). This variant is not present in population databases (gnomAD no frequency). This sequence change affects a donor splice site in intron 18 of the PHEX gene. RNA analysis indicates that disruption of this splice site induces altered splicing and may result in an absent or disrupted protein product.

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