Variant: NM_000156.6(GAMT):c.59G>T (p.Trp20Leu)

CA402998326

588631 (ClinVar)

Gene: GAMT

Condition: guanidinoacetate methyltransferase deficiency

Inheritance Mode: Autosomal recessive inheritance

UUID: c9c80575-0e97-4d8a-bd94-486ed947d032

Approved on: 2023-09-13

Published on: 2023-09-13

HGVS expressions

NM_000156.6:c.59G>T
NM_000156.6(GAMT):c.59G>T (p.Trp20Leu)
NC_000019.10:g.1401418C>A
CM000681.2:g.1401418C>A
NC_000019.9:g.1401417C>A
CM000681.1:g.1401417C>A
NC_000019.8:g.1352417C>A
NG_009785.1:g.5136G>T
ENST00000252288.8:c.59G>T
ENST00000447102.8:c.59G>T
ENST00000640762.1:c.59G>T
ENST00000252288.6:c.59G>T
ENST00000447102.7:c.59G>T
NM_000156.5:c.59G>T
NM_138924.2:c.59G>T
NM_138924.3:c.59G>T

Uncertain Significance

• Met criteria codes: PP3 PM5 PM2_Supporting

Expert Panel

Cerebral Creatine Deficiency Syndromes VCEP

Criteria Specification Information

Criteria Specification: ClinGen Cerebral Creatine Deficiency Syndromes Expert Panel Specifications to the ACMG/AMP Variant Interpretation Guidelines for GAMT Version 1.1.0

Evidence submitted by expert panel

Cerebral Creatine Deficiency Syndromes VCEP

The NM_000156.6:c.59G>T variant in GAMT is a missense variant that is predicted to result in the substitution of tryptophan by leucine at amino acid 20 (p.Trp20Leu). To our knowledge, this variant has not been reported in individuals with GAMT deficiency and the result of functional studies are not available. The computational predictor REVEL gives a score of 0.804 which is above the threshold of 0.75, evidence that correlates with impact to GAMT function (PP3). Another missense variant, c.59G>C (p.Trp20Ser) (ClinVar Variation ID: 8303)) has been reported at the same amino acid position and has been classified as pathogenic for GAMT deficiency by the ClinGen CCDS VCEP (PM5). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). There is a ClinVar entry for this variant (Variation ID: 588631, 1 star review status). In summary, this variant meets the criteria to be classified as uncertain significance 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): PM2_Supporting, PM5, PP3. (Classification approved by the ClinGen CCDS VCEP, Sept 12, 2023)

Met criteria codes

• PP3: The computational predictor REVEL gives a score of 0.804 which is above the threshold of 0.75, evidence that correlates with impact to GAMT function (PP3).
• PM5: Other missense variants at the same amino acid residue have been reported pathogenic (Trp20Ser - ClinVar ID 8303, Pathogenic)
• PM2_Supporting: Absent in gnomAD v2.1.1 (PM2_Supporting).