ClinVar Miner

Submissions for variant NM_001793.6(CDH3):c.160+1G>A

gnomAD frequency: 0.00001  dbSNP: rs1474181679
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Revvity Omics, Revvity RCV001780469 SCV002016990 pathogenic not provided 2019-06-18 criteria provided, single submitter clinical testing
Medical Genetics UMG, Mater Domini University Hospital/ Magna Graecia University of Catanzaro RCV002300590 SCV002587811 pathogenic Congenital hypotrichosis with juvenile macular dystrophy criteria provided, single submitter clinical testing The c.160+1G>A variant results from a G to A substitution in intron 2 of the CDH3 gene, affecting a donor splice site. This splicing variant is predicted to cause a loss of function. The frequency of this variant in gnomAD database is 0.00001394. In our laboratory this variant was found in trans with a pathogenic variant in a patient affected by congenital hypotrichosis with juvenile macular dystrophy (HJMD).
Labcorp Genetics (formerly Invitae), Labcorp RCV001780469 SCV003443657 pathogenic not provided 2024-01-03 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 2 of the CDH3 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 CDH3 are known to be pathogenic (PMID: 15805154, 27386845, 29620724). This variant is present in population databases (no rsID available, gnomAD 0.004%). Disruption of this splice site has been observed in individuals with hypotrichosis and juvenile macular dystrophy (PMID: 17342797, 31696509). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 1322049). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. For these reasons, this variant has been classified as Pathogenic.
Institute of Human Genetics, Univ. Regensburg, Univ. Regensburg RCV004815631 SCV005069829 pathogenic Retinal dystrophy 2019-01-01 criteria provided, single submitter clinical testing

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