ClinVar Miner

Submissions for variant NM_021828.5(HPSE2):c.1516C>T (p.Arg506Ter)

gnomAD frequency: 0.00001  dbSNP: rs267606866
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001061376 SCV001226116 pathogenic not provided 2023-01-25 criteria provided, single submitter clinical testing This variant is present in population databases (rs267606866, gnomAD 0.003%). This sequence change creates a premature translational stop signal (p.Arg506*) in the HPSE2 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in HPSE2 are known to be pathogenic (PMID: 20560210, 25510506). This premature translational stop signal has been observed in individual(s) with urofacial syndrome (PMID: 20560209). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. ClinVar contains an entry for this variant (Variation ID: 83).
Eurofins-Biomnis RCV000000103 SCV003935117 likely pathogenic Urofacial syndrome type 1 2022-12-13 criteria provided, single submitter clinical testing
OMIM RCV000000103 SCV000020246 pathogenic Urofacial syndrome type 1 2010-06-11 no assertion criteria provided literature only
GeneReviews RCV000000103 SCV000086987 not provided Urofacial syndrome type 1 no assertion provided literature only

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