ClinVar Miner

Submissions for variant NM_000444.6(PHEX):c.1080-1G>A (rs886041695)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000350821 SCV000330426 pathogenic not provided 2016-05-11 criteria provided, single submitter clinical testing The c.1080-1 G>A splice site variant in the PHEX gene destroys the canonical splice acceptor site in intron 9. It is predicted to cause abnormal gene splicing, either leading to an abnormal message that is subject to nonsense-mediated mRNA decay, or to an abnormal protein product if the message is used for protein translation. The variant was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Other splice acceptor site variants in intron 9 (c.1080-3C>A, c.1080-2A>G) have been reported in the Human Gene Mutation Database in association with X-linked hypophosphatemic rickets (Stenson et al., 2014), supporting the deleterious effect of this variant on the protein. Although this pathogenic variant has not been previously reported to our knowledge, its presence is consistent with a diagnosis of X-linked hypophosphatemic rickets.
Fulgent Genetics,Fulgent Genetics RCV000763206 SCV000893827 pathogenic Familial X-linked hypophosphatemic vitamin D refractory rickets 2018-10-31 criteria provided, single submitter clinical testing

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