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Variant: NM_000156.6(GAMT):c.526del (p.Glu176fs)

CA2499225402

1067935 (ClinVar)

Gene: GAMT
Condition: guanidinoacetate methyltransferase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: df780bbd-6d93-4670-9d0e-121f7e0c44d9
Approved on: 2023-05-25
Published on: 2023-05-25

HGVS expressions

NM_000156.6:c.526del
NM_000156.6(GAMT):c.526del (p.Glu176fs)
NC_000019.10:g.1398965del
CM000681.2:g.1398965del
NC_000019.9:g.1398964del
CM000681.1:g.1398964del
NC_000019.8:g.1349964del
NG_009785.1:g.7594del
ENST00000252288.8:c.526del
ENST00000447102.8:c.526del
ENST00000591788.3:n.209del
ENST00000640164.1:n.359del
ENST00000640762.1:c.457del
ENST00000252288.6:c.526del
ENST00000447102.7:c.526del
ENST00000591788.2:n.211del
NM_000156.5:c.526del
NM_138924.2:c.526del
NM_138924.3:c.526del

Likely Pathogenic

Met criteria codes 3
PVS1_Strong PP4_Moderate PM2_Supporting
Not Met criteria codes 1
PM3

Evidence Links 0

Expert Panel

Criteria Specification Information

Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_000156.6:c.526del (p.Glu176SerfsTer2) variant in GAMT is a frameshift variant predicted to cause a premature stop codon in the last 50 nucleotides of the penultimate exon/the last exon of the gene and therefore to escape nonsense mediated decay. More than 10% of the protein is predicted to be removed (PVS1_Strong). This variant in not in gnomAD v2.1.1 (PM2_Supporting). This variant has been reported in one individual with GAMT deficiency who had elevated GAA and low creatine in plasma and in urine (PMID: 19288536) (PP4_Moderate). There is a ClinVar entry for this variant (Variation ID: 1067935, 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): PVS1_Strong, PM2_Supporting, PP4_Moderate. (Classification approved by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel on April 13, 2023)
Met criteria codes
PVS1_Strong
Frameshift variant in exon 5/6 in the last 50bp of the penultimate exon (c.526), such that NMD is not predicted. Predicted to result in frameshift at amino acid position 176 and premature termination at amino acid position 178/236, resulting in removal of 58 amino acids (24.5% of the protein, >10% of the protein), such that PVS1_Strong applies per CCDS specifications.
PP4_Moderate
PMID: 19288536: identified in one patient with elevated plasma GAA with low creatine and elevated urine GAA with low creatine (3pts total, PP4_Mod)
PM2_Supporting
Absent in population databases
Not Met criteria codes
PM3
Patient 3: comp het for c.590T>C (p.L197P)/c.526delG (p.E176SfsX2); did not count for PM3 here because this occurrence was counted for PM3 for the p.L197P variant, thereby preventing circularity in use of PM3
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