ClinVar Miner

Submissions for variant NM_000444.6(PHEX):c.2071-2A>G

dbSNP: rs1936359447
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV001268141 SCV001446825 pathogenic not provided 2020-10-23 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001268141 SCV001579962 pathogenic not provided 2024-05-23 criteria provided, single submitter clinical testing This sequence change affects an acceptor splice site in intron 20 of the PHEX gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in PHEX are known to be pathogenic (PMID: 9097956, 9106524, 19219621). This variant is not present in population databases (gnomAD no frequency). Disruption of this splice site has been observed in individuals with hypophosphatemic rickets (PMID: 10737991, 22695891). This variant is also known as IVS20-2A>G. ClinVar contains an entry for this variant (Variation ID: 986956). 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.
Athena Diagnostics RCV001268141 SCV002771796 pathogenic not provided 2021-11-05 criteria provided, single submitter clinical testing This variant is expected to severely impact normal RNA splicing, and consequently, protein structure and/or function. This variant has not been reported in large, multi-ethnic general populations (http://gnomad.broadinstitute.org). This variant has been identified in at least one individual with clinical features associated with this gene. In some published literature, this variant is referred to as IVS20-2A>G.

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