ClinVar Miner

Submissions for variant NM_007214.5(SEC63):c.292C>T (p.Arg98Ter)

gnomAD frequency: 0.00001  dbSNP: rs768568123
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV002471134 SCV002769159 pathogenic Polycystic liver disease 2 2022-02-02 criteria provided, single submitter clinical testing Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Pathogenic. Following criteria are met: 0102 - Loss of function is a known mechanism of disease in this gene and is associated with polycystic liver disease 2 (MIM#617004). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0115 - Variants in this gene are known to have variable expressivity. Different individuals with the same variant can show a marked variation in disease phenotype from having hepatomegaly and more than 20 cysts to only having a few small cysts (PMID: 20095989). (I) 0201 - Variant is predicted to cause nonsense-mediated decay (NMD) and loss of protein (premature termination codon is located at least 54 nucleotides upstream of the final exon-exon junction). (SP) 0251 - This variant is heterozygous. (I) 0302 - Variant is present in gnomAD (v2) <0.001 for a dominant condition (3 heterozygotes, 0 homozygotes). (SP) 0701 - Other NMD predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. Other NMD predicted variants have been reported as pathogenic in individuals with polycystic liver disease (ClinVar, PMID: 20095989). (SP) 0803 - This variant has limited previous evidence of pathogenicity in an unrelated individual. This variant has been reported in an individual with polycystic liver disease (PMID: 20095989). (SP) 1208 - Inheritance information for this variant is not currently available in this individual. (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign
Laboratory of Gastroenterology and Hepatology, Radboud University Medical Center RCV001844962 SCV001876894 pathogenic Autosomal dominant polycystic liver disease 2021-09-01 no assertion criteria provided research
Genomics And Bioinformatics Analysis Resource, Columbia University RCV002471134 SCV004024079 likely pathogenic Polycystic liver disease 2 no assertion criteria provided research

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