Total submissions: 1
Submitter | RCV | SCV | Clinical significance | Condition | Last evaluated | Review status | Method | Comment |
---|---|---|---|---|---|---|---|---|
Victorian Clinical Genetics Services, |
RCV004788388 | SCV005400234 | pathogenic | Lymphatic malformation 6 | 2023-07-16 | 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: 0103 - Loss of function and gain of function are known mechanisms of disease in this gene and are associated with lymphatic malformation 6 (LMPHM6; MIM#616843), and dehydrated hereditary stomatocytosis with or without pseudohyperkalemia and/or perinatal edema (DHS; MIM#194380), respectively (OMIM). (I) 0108 - This gene is associated with both recessive and dominant disease. LMPHM6 has been reported in individuals with biallelic variants, while DHS has only been reported in individuals with heterozygous missense variants or inframe duplication variants with a gain of function mechanism (OMIM). (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) 0301 - Variant is absent from gnomAD (both v2 and v3). (SP) 0701 - Other NMD-predicted variants comparable to the one identified in this case have very strong previous evidence for pathogenicity. These variants have been reported many times as pathogenic, and in individuals with lymphatic malformation (DECIPHER, PMID: 26333996). (SP) 0803 - This variant has limited previous evidence of pathogenicity in an unrelated individual. This variant was observed in a compound heterozygous individual with recurrent cystic hydroma (VCGS). (SP) 0905 - No published segregation evidence has been identified for this variant. (I) 1007 - No published functional evidence has been identified for this variant. (I) 1205 - This variant has been shown to be maternally inherited (by trio analysis). (I) Legend: (SP) - Supporting pathogenic, (I) - Information, (SB) - Supporting benign |