The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]
  • No ClinVar Id was directly found from the curated document
  • ClinVar Id was derived from the Allele Registry.


Variant: NM_138924.3:c.522G>C

CA402994365

2421360 (ClinVar)

Gene: GAMT
Condition: guanidinoacetate methyltransferase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: dc7ae64a-de29-424f-88bd-3984d1cf1a01
Approved on: 2023-12-12
Published on: 2023-12-12

HGVS expressions

NM_138924.3:c.522G>C
NC_000019.10:g.1398964C>G
CM000681.2:g.1398964C>G
NC_000019.9:g.1398963C>G
CM000681.1:g.1398963C>G
NC_000019.8:g.1349963C>G
NG_009785.1:g.7590G>C
ENST00000252288.8:c.522G>C
ENST00000447102.8:c.522G>C
ENST00000591788.3:c.205G>C
ENST00000640164.1:n.355G>C
ENST00000640762.1:c.453G>C
ENST00000252288.6:c.522G>C
ENST00000447102.7:c.522G>C
ENST00000591788.2:c.207G>C
NM_000156.5:c.522G>C
NM_138924.2:c.522G>C
NM_000156.6:c.522G>C
NM_000156.6(GAMT):c.522G>C (p.Trp174Cys)
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Uncertain Significance

Met criteria codes 2
PP3 PM2
Not Met criteria codes 1
PM5

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.522G>C variant in GAMT is a missense variant predicted to cause substitution of a tryptophan by cysteine at amino acid 174 (p.Trp174Cys). To our knowledge, this variant has not been reported in the literature and results of functional studies are unavailable. The highest population minor allele frequency in gnomAD v4.0. is 0.00002227 (1/44900 alleles) in the East Asian population, which lower is than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.0004), meeting this criterion (PM2_Supporting). The computational predictor REVEL gives a score of 0.813 which is above the threshold of 0.75, evidence that correlates with impact to GAMT function (PP3). There is a ClinVar entry for this variant (Variation ID: 2421360. In summary, this variant meets the criteria to be classified as a variant of 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): PP3, PM2_Supporting. (Classification approved by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel on December 12, 2023).
Met criteria codes
PP3
The computational predictor REVEL gives a score of 0.813 which is above the threshold of 0.75, evidence that correlates with impact to GAMT function (PP3).
PM2
The highest population minor allele frequency in gnomAD v4.0. is 0.00002227 (1/44900 alleles) in the East Asian population, which lower is than the ClinGen CCDS VCEP’s threshold for PM2_Supporting (<0.0004), meeting this criterion (PM2_Supporting).
Not Met criteria codes
PM5
Two different missense variants at the same codon, p.Trp174Arg (ClinVar ID: 1420866) and p.Trp174Leu (ClinVar ID: 966083), have been reported as VUS in ClinVar
Curation History
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