ClinVar Miner

Submissions for variant NM_000187.4(HGD):c.342+1G>T

gnomAD frequency: 0.00002  dbSNP: rs397515518
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000169542 SCV000221029 likely pathogenic Alkaptonuria 2015-01-15 criteria provided, single submitter literature only
Invitae RCV000169542 SCV002237055 pathogenic Alkaptonuria 2023-08-25 criteria provided, single submitter clinical testing 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: 189127). This variant is also known as c.509+1G>T. Disruption of this splice site has been observed in individuals with alkaptonuria (PMID: 9529363, 10482952, 25681086). This variant is present in population databases (rs397515518, gnomAD 0.003%). This sequence change affects a donor splice site in intron 5 of the HGD 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 HGD are known to be pathogenic (PMID: 12501223, 19862842).
Fulgent Genetics, Fulgent Genetics RCV000169542 SCV002796090 pathogenic Alkaptonuria 2022-01-25 criteria provided, single submitter clinical testing
Department Of Human Genetics, Institute Of Clinical And Translational Research, Biomedical Research Center, Slovak Academy Of Sciences RCV000169542 SCV004098961 pathogenic Alkaptonuria no assertion criteria provided research The variant was originally described in AKU patient in PMID:9529363. It has been submitted to the HGD gene mutation database (, DB-ID: AKU_00024).

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