ClinVar Miner

Submissions for variant NM_000194.3(HPRT1):c.22_27+28del

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Total submissions: 1
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV001045083 SCV001208913 pathogenic Partial hypoxanthine-guanine phosphoribosyltransferase deficiency; Lesch-Nyhan syndrome 2020-01-06 criteria provided, single submitter clinical testing This variant results in the deletion of part of exon 1 (c.22_27+28del) of the HPRT1 gene. It is expected to disrupt RNA splicing and likely results in an absent or disrupted protein product. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate insufficient coverage at this position in the ExAC database. This variant has not been reported in the literature in individuals with HPRT1-related conditions. 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. This variant disrupts the c.27+5 nucleotide in the HPRT1 gene. Other variant(s) that disrupt this nucleotide have been determined to be pathogenic (PMID: 17027311). This suggests that this nucleotide is clinically-significant, and that variants that disrupt this position are likely to be disease-causing. Loss-of-function variants in HPRT1 are known to be pathogenic (PMID: 15571220, 17027311, 22157001). For these reasons, this variant has been classified as Pathogenic.

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