Total submissions: 1
| Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
|---|---|---|---|---|---|---|---|---|
| Victorian Clinical Genetics Services, |
RCV004595233 | SCV005086038 | likely pathogenic | Catecholaminergic polymorphic ventricular tachycardia 1 | 2023-12-21 | criteria provided, single submitter | clinical testing | Based on the classification scheme VCGS_Germline_v1.3.4, this variant is classified as Likely pathogenic. Following criteria are met: 0103 - Dominant negative and gain of function are known mechanisms of disease in this gene and are associated with catecholaminergic polymorphic ventricular tachycardia 1 (MIM#604772) and left ventricular non-compaction (PMIDs: 12459180, 27646203, 29477366, 31875585, 33500567). Loss of function has been reported for ventricular arrhythmias due to cardiac ryanodine receptor calcium release deficiency syndrome (MIM#115000), however dominant negative mechanism has not been excluded (PMID: 33536282). (I) 0107 - This gene is associated with autosomal dominant disease. (I) 0112 - The condition associated with this gene has incomplete penetrance. Penetrance for CPVT is estimated to be 60-70% (PMID: 23549275). (I) 0200 - Variant is predicted to result in a missense amino acid change from serine to arginine. (I) 0251 - This variant is heterozygous. (I) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0501 - Missense variant consistently predicted to be damaging by multiple in silico tools or highly conserved with a major amino acid change. (SP) 0602 - Variant is located in a hotspot region or cluster of pathogenic variants (PMID: 30696458). (SP) 0710 - Other missense variants comparable to the one identified in this case have inconclusive previous evidence for pathogenicity. An alternative change to isoleucine, p.(Ser4153Ile), has been reported in an individual with CPVT (PMID: 26114861) and also as a VUS by a clinical testing laboratory (ClinVar). Additionally, a change to threonine, p.(Ser4153Thr), has been reported as a VUS by a clinical testing laboratory (ClinVar). (I) 0803 - This variant has limited previous evidence of pathogenicity in an unrelated individual. This variant has been reported in an individual with CPVT (PMID: 21652165). (SP) 0903 - This variant has limited evidence for segregation with disease. This variant is segregating with symptoms of CPVT in several members of a large family. However, some individuals with this variant are asymptomatic but have not had a cardiac assessment or stress test. All individuals without this variant are asymptomatic (VCGS internal data). (SP) 1002 - This variant has moderate functional evidence supporting abnormal protein function. Functional studies using HEK293 cells have demonstrated that this variant results in a gain-of-function and abnormal calcium ion handling (PMID: 23498838). (SP) 1205 - This variant has been shown to be maternally inherited (by segregation analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign |