The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • Gene obtained from curated document aligns with the Allele Registry but not with ClinVar data
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Variant: NM_000156.6(GAMT):c.575C>T (p.Thr192Met)

CA314808

205582 (ClinVar)

Gene: GAMT
Condition: guanidinoacetate methyltransferase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 216adac0-8b20-40b4-9ae0-8611e8e299fb
Approved on: 2024-09-11
Published on: 2024-09-12

HGVS expressions

NM_000156.6:c.575C>T
NM_000156.6(GAMT):c.575C>T (p.Thr192Met)
NC_000019.10:g.1397495G>A
CM000681.2:g.1397495G>A
NC_000019.9:g.1397494G>A
CM000681.1:g.1397494G>A
NC_000019.8:g.1348494G>A
NG_008283.1:g.18612G>A
NG_009785.1:g.9059C>T
ENST00000252288.8:c.575C>T
ENST00000640164.1:n.408C>T
ENST00000640762.1:c.506C>T
ENST00000252288.6:c.575C>T
NM_000156.5:c.575C>T
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Uncertain Significance

Met criteria codes 2
PM2_Supporting PP3
Not Met criteria codes 1
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 2.0.0

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_000156.6:c.575C>T variant in GAMT is a missense variant that is predicted to cause the substitution of a threonine by a methionine at amino acid position 192 (p.Thr192Met). To our knowledge, this variant has not been reported in the literature and results of functional studies are unavailable. The highest continental population minor allele frequency in gnomAD v4.1.0. is 0.0002665 (20/75058 alleles; no homozygotes) in the African/African American population, which is lower than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.0004), meeting this criterion (PM2_Supporting). Although the allele frequency in the Ashkenazi Jewish population in gnomAD v4.1.0. is higher at 0.002467 (73/29588 alleles; no homozygotes) (meeting BS1, >0.001) this frequency is not counted because it was found in a non-continental population (Ghosh et al, 2018, PMID: 30311383). The computational predictor REVEL gives a score of 0.677 which is above the threshold of 0.644, evidence that correlates with impact to GAMT function (PP3). There is a ClinVar entry for this variant (Variation ID: 205582). In summary, this variant meets the criteria to be classified as a variant of uncertain significance for GAMT deficiency. GAMT-specific ACMG/AMP codes met, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes VCEP (Specifications Version 2.0.0): PM2_Supporting, PP3. (Classification approved by the ClinGen Creatine Deficiency Syndromes Variant Curation Expert Panel on September 11, 2024).
Met criteria codes
PM2_Supporting
The highest continental population minor allele frequency in gnomAD v4.1.0. is 0.0002665 (20/75058 alleles; no homozygotes) in the African/African American population, which is lower than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.0004), meeting this criterion (PM2_Supporting). Although the allele frequency in the Ashkenazi Jewish population in gnomAD v4.1.0. is higher at 0.002467 (73/29588 alleles; no homozygotes) (meeting BS1, >0.001) this frequency is not counted because it was found in a non-continental population (Ghosh et al, 2018, PMID: 30311383).
PP3
The computational predictor REVEL gives a score of 0.677 which is above the threshold of 0.644, evidence that correlates with impact to GAMT function (PP3).
Not Met criteria codes
BS1
See explanation for PM2.
Curation History
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