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Variant: NM_000156.6(GAMT):c.22C>A (p.Pro8Thr)

CA314840

205598 (ClinVar)

Gene: GAMT
Condition: guanidinoacetate methyltransferase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 88895225-665c-4e9b-bf17-ca9fe729cf9c
Approved on: 2023-02-23
Published on: 2023-03-09

HGVS expressions

NM_000156.6:c.22C>A
NM_000156.6(GAMT):c.22C>A (p.Pro8Thr)
NC_000019.10:g.1401455G>T
CM000681.2:g.1401455G>T
NC_000019.9:g.1401454G>T
CM000681.1:g.1401454G>T
NC_000019.8:g.1352454G>T
NG_009785.1:g.5099C>A
ENST00000252288.8:c.22C>A
ENST00000447102.8:c.22C>A
ENST00000640762.1:c.22C>A
ENST00000252288.6:c.22C>A
ENST00000447102.7:c.22C>A
NM_000156.5:c.22C>A
NM_138924.2:c.22C>A
NM_138924.3:c.22C>A

Uncertain Significance

Met criteria codes 3
PM2_Supporting BS3_Supporting BP4
Not Met criteria codes 3
PP4 PP3 PM3

Evidence Links 1

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.22C>A variant in GAMT is a missense variant that is predicted to result in the substitution of proline by threonine at amino acid 8 (p.Pro8Thr). One patient, who is heterozygous for the variant, has been reported. This individual, who presented with severe global develpomental delay, hypotonia, and intractable seizures, died at 11 months of age. Urine and plasma guanidinoacetate were elevated 2.5 and 1.8 times, respectively. However, on 1H-MRS, creatine peak was about 90% of normal, marginally low, which was not suggestive of GAMT deficiency(PMID: 24415674) (PP4 not applied). GAA-deficient fibroblasts overexpressing the c.22C>A (p.Pro8Thr) variant showed similar GAMT enzyme activity as those transfected with wild-type cDNA (PMID: 24415674) (BS3_Supporting). The computational predictor REVEL gives a score of 0.479 which is below the threshold of 0.5, evidence that does not predict a damaging effect on GAMT function (BP4). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00023 (7/30820 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). There is a ClinVar entry for this variant (Variation ID: 205598). In summary, this variant meets the criteria to be classified as a variant of uncertain significance for GAMT deficiency. GAMT-specific ACMG/AMP criteria met, based on the specifications of the ClinGen Cerebral Creatine Deficiencies VCEP (Specifications Version 1.1.0): BS3_Supporting, BP4, PM2_Supporting. Although this variant meets criteria for a classification of Variant of Uncertain Significance, the ClinGen Cerebral Creatine Deficiencies VCEP considers this variant suspicious for Likely Benign. Future literature may warrant a reclassification of this variant.
Met criteria codes
PM2_Supporting
The highest population minor allele frequency in gnomAD v2.1.1 is 0.00023 (7/30820 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).
BS3_Supporting
Fibroblasts overexpressing cells the c.22C>A (p.Pro8Thr) variant showed similar GAMT enzyme activity as those transfected with wild-type enzyme (PMID: 24415674).

BP4
The computational predictor REVEL gives a score of 0.479 which is below the threshold of 0.5, evidence that does not predict a damaging effect on GAMT function (BP4).
Not Met criteria codes
PP4
One patient, heterozygous for the variant, with urine guanidinoacetate elevated 2.5 times and plasma guanidinoacetate 1.8 times above the upper limit of reference range. However, on 1H-MRS, creatine peak was about 90% of normal, marginally low, which was not suggestive of GAMT deficiency (Note: 1H-MRS data overrides biochemical findings) (PMID: 24415674).
PP3
REVEL score 0.479 (>0.75 cutoff for PP3).
PM3
PMID: 24415674: Found as a single heterozygous variant in one patient, no second variant identified
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