The NM_000156.6:c.497T>C variant in GAMT is a missense variant predicted to cause substitution of leucine by proline at amino acid 166 (p.Leu166Pro). This variant has been detected in one individual with GAMT deficiency, who was homozygous for the variant (0.5pts, PM3_Supporting) (PMID: 24268530, PMID: 17466557, PMID: 17186272). This individual had elevated GAA and low creatine in urine, absent creatine peak on brain MRS, and deficient (<5% normal) GAMT activity in cultured fibroblasts with full GAMT gene sequencing (PMID: 24268530, PMID: 17466557, PMID: 17186272) (PP4_Strong). The highest population minor allele frequency in gnomAD v2.1.1 is 0.000009 (1/113320 alleles) in the European (non-Finnish) population, which is lower than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.0004), meeting this criterion (PM2_Supporting). Expression of the variant in GAMT-deficient human fibroblast cell line resulted in <5% wild type GAMT activity indicating that this variant may impact protein function (PMID: 24415674) (PS3_Supporting). The computational predictor REVEL gives a score of 0.953 which is above the threshold of 0.75, evidence that correlates with impact to GAMT function (PP3). There is a ClinVar entry for this variant (Variation ID: 1312506, 1 star review status) with 1 submitter classifying the variant as likely pathogenic. In summary, this variant meets the criteria to be classified as likely pathogenic for GAMT deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 1.1.0): PS3_Supporting, PM2_Supporting, PM3_Supporting, PP4_Strong, PP3. (Classification approved by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel on May 25, 2023)