*This poster was also presented at the 2024 Curating the Clinical Genome Conference by Jenny Goldstein.
SHORT SUMMARY
ClinGen’s Cereberal Creatine Deficiency Syndromes Variant Curation Expert Panel (CCDS VCEP) has been diligently working to classify variants in the three CCDS associated genes, GATM, GAMT, and SLC6A8 for upload into the publicly available database ClinVar. In collaboration with the Association for Creatine Deficiencies (ACD) and CreatineINFO, the CCDS VCEP has requested de-identified biochemical and genetic data on some CCDS variants, which has enabled the reclassification of 50% (n=3) variants, two of which were reclassified from a Variant of Uncertain Significance to Likely Pathogenic, and one reclassified from Likely Pathogenic to Pathogenic. Ongoing collaboration between the ACD, CreatineINFO, and the CCDS VCEP is critical for accurate variant interpretation for families as well as the genetic community and serves as a model for other organizations to further the goal of improving patient care through genomic medicine.
ABSTRACT
Background/Objectives: Understanding the clinical significance of variants within the genes causing cerebral creatine deficiency syndromes (CCDS) is important to ensure timely diagnosis and initiation of treatment for these neurological disorders. The Association for Creatine Deficiencies (ACD), a patient advocacy organization, collaborates with the NIHfunded Clinical Genome resource (ClinGen) to share data and assist in robust variant classification.
Methods: Via collaboration with ClinGen’s GenomeConnect, ACD registry participants provide their genetic testing reports for submission to the public variant database, ClinVar. Data is also shared with the ClinGen CCDS Variant Curation Expert Panel (VCEP), which has developed guidelines for classification of variants in the genes causing CCDS (GAMT, GATM, SLC6A8) and submits those classifications to ClinVar as part of an FDA-approved process. Results: Using published data, the ClinGen CCDS VCEP has classified 43 variants from ACD registry participants; 15 were classified by the VCEP as pathogenic (8 SLC6A8, 7 GAMT), 7 likely pathogenic (LP) (5 SLC6A8, 2 GAMT), 2 benign (1 SLC6A8, 1 GAMT), and 19 were variants of uncertain significance (VUS) (15 SLC6A8, 4 GAMT). 12 VUS were identified as tending towards LP by the VCEP based on the strength of evidence already available; ACD participants with these variants were recontacted to request additional case-level data (biochemical testing, magnetic resonance spectroscopy, family history, genetic testing of parents) with the goal of reclassifying these variants as LP or pathogenic.
Conclusions: Collaboration between the ACD and ClinGen increases understanding of the clinical significance of variants in the gene causing CCDS and may serve as a model for collaboration between other ClinGen VCEPs and patient advocacy organizations.
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