The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]


Variant: NM_000156.6(GAMT):c.134G>A (p.Trp45Ter)

CA402998096

2419155 (ClinVar)

Gene: GAMT
Condition: guanidinoacetate methyltransferase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 683bc758-d93c-4fd6-a8f9-f9c5cd7a5bfa

HGVS expressions

NM_000156.6:c.134G>A
NM_000156.6(GAMT):c.134G>A (p.Trp45Ter)
NC_000019.10:g.1401343C>T
CM000681.2:g.1401343C>T
NC_000019.9:g.1401342C>T
CM000681.1:g.1401342C>T
NC_000019.8:g.1352342C>T
NG_009785.1:g.5211G>A
ENST00000252288.8:c.134G>A
ENST00000447102.8:c.134G>A
ENST00000640762.1:c.112+22G>A
ENST00000252288.6:c.134G>A
ENST00000447102.7:c.134G>A
NM_000156.5:c.134G>A
NM_138924.2:c.134G>A
NM_138924.3:c.134G>A

Pathogenic

Met criteria codes 4
PP4 PVS1 PM2_Supporting PM3
Not Met criteria codes 2
BA1 BS1

Evidence Links 0

Expert Panel

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_000156.6:c.134G>A (p.Trp45Ter) variant in GAMT is a nonsense variant predicted to cause a premature stop codon in biologically relevant exon 1/6 leading to nonsense mediated decay in a gene in which loss-of-function is an established disease mechanism (PVS1). This variant has been detected in at least two probands with GAMT deficiency. Of those probands, both were homozygous for the variant (PMIDs 31222513, 33996490) (PM3). At least one proband (two siblings) with this variant had elevated GAA and low creatine in plasma (PP4). This variant is absent in gnomAD v2.1.1 (PM2_Supporting). There is a ClinVar entry for this variant (Variation ID: 2419155). In summary, this variant meets the criteria to be classified as 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, PM3, PP4, PM2_Supporting. (Classification approved by the ClinGen CCDS VCEP on Oct 12, 2023)
Met criteria codes
PP4
Variant found homozygous in two affected siblings with elevated plasma GAA and low creatine levels.
PVS1
Nonsense variant in exon 1
PM2_Supporting
Absent from gnomAD
PM3
Variant observed in the homozygous state in two probands with clinical features of GAMT deficiency
Not Met criteria codes
BA1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
BS1
No code specific comments provided, please refer to the summary above or general recommendations provided in the guideline
Approved on: 2023-10-12
Published on: 2023-11-08
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