ClinVar Miner

Submissions for variant NM_000444.6(PHEX):c.1586+3_1586+6del (rs886042234)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
EGL Genetic Diagnostics,Eurofins Clinical Diagnostics RCV000316107 SCV000332746 uncertain significance not provided 2015-07-28 criteria provided, single submitter clinical testing
Institute of Human Genetics,Klinikum rechts der Isar RCV000505446 SCV000599666 pathogenic Familial X-linked hypophosphatemic vitamin D refractory rickets 2013-11-06 criteria provided, single submitter clinical testing
Mendelics RCV000505446 SCV001141537 likely pathogenic Familial X-linked hypophosphatemic vitamin D refractory rickets 2019-05-28 criteria provided, single submitter clinical testing
Invitae RCV000316107 SCV001387148 pathogenic not provided 2019-10-29 criteria provided, single submitter clinical testing This sequence change falls in intron 14 of the PHEX gene. It does not directly change the encoded amino acid sequence of the PHEX protein, but it affects a nucleotide within the consensus splice site of the intron. This variant is not present in population databases (ExAC no frequency). This variant has been observed in individuals affected with hypophosphatemia (PMID: 9106524, 18625346, Invitae). This variant is also known in the literature as del gagt and 4bp deletion. ClinVar contains an entry for this variant (Variation ID: 281773). Nucleotide substitutions within the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site, but this prediction has not been confirmed by published transcriptional studies. For these reasons, this variant has been classified as Pathogenic.

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