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Variant: NM_000156.6(GAMT):c.623G>A (p.Arg208His)

CA9043553

577478 (ClinVar)

Gene: GAMT
Condition: guanidinoacetate methyltransferase deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 0b112e8e-11e7-41d8-8188-3c18676a3ec3
Approved on: 2022-06-06
Published on: 2022-10-07

HGVS expressions

NM_000156.6:c.623G>A
NM_000156.6(GAMT):c.623G>A (p.Arg208His)
NC_000019.10:g.1397447C>T
CM000681.2:g.1397447C>T
NC_000019.9:g.1397446C>T
CM000681.1:g.1397446C>T
NC_000019.8:g.1348446C>T
NG_008283.1:g.18564C>T
NG_009785.1:g.9107G>A
ENST00000252288.8:c.623G>A
ENST00000640164.1:n.456G>A
ENST00000640762.1:c.554G>A
ENST00000252288.6:c.623G>A
NM_000156.5:c.623G>A
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Uncertain Significance

Met criteria codes 3
PM2_Supporting PM5_Supporting BP4

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

Criteria Specification Approval History
Criteria Specifications for this VCEP
Evidence submitted by expert panel
Cerebral Creatine Deficiency Syndromes VCEP
The NM_000156.6:c.623G>A variant in GAMT is a missense variant predicted to cause substitution of arginine by histidine at amino acid 208 (p.Arg208His). The highest population minor allele frequency in gnomAD v2.1.1 is 0.00012 (3/24752 alleles) in the African population, which is lower 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 0.279 which is below the threshold of 0.5, evidence that correlates with no impact to GAMT function (BP4). Two additional missense variants at this amino acid position have been reported - c.622C>T (p.Arg208Cys) (ClinVarID: 5442618) and c.623G>C (p.Arg208Pro) (PMID 24415674). The ClinGen CCDS VCEP has classified p.Arg208Pro as likely pathogenic, while p.Arg208Cys has been classified as a VUS (PM5_Supporting). To our knowledge, c.623G>A (p.Arg208His) has not been previously reported in the published literature, but has been noted in ClinVar (ClinVar ID 577478). In summary, this variant meets the criteria to be classified as a variant of uncertain significance for GAMT deficiency. GAMT-specific ACMG/AMP criteria applied, as specified by the ClinGen CCDS VCEP (Specifications Version 1.1.0: PM2_Supporting, PM5_Supporting, BP4. (Classification approved by the ClinGen CCDS VCEP on June 6, 2022).
Met criteria codes
PM2_Supporting
Ten heterozygotes and zero homozygotes for the p.Arg208His variant are present in gnomAD, corresponding to a global frequency of 0.00003588; the highest population-specific frequency in a continental population of >2,000 alleles is 0.0001212, less than the 0.0004 cutoff for use of PM2_Supporting (PM2_Supporting).
PM5_Supporting
Two additional missense variants at this amino acid position have been reported - c.622C>T (p.Arg208Cys) (ClinVarID: 5442618) and c.623G>C (p.Arg208Pro) (PMID 24415674). The ClinGen CCDS VCEP has classified p.Arg208Pro as likely pathogenic, while p.Arg208Cys has been classified as a VUS (PM5_Supporting).
BP4
The computational predictor REVEL gives a score of 0.279 which is below the threshold of 0.5, evidence that does not predict a damaging effect on GAMT function (BP4).
Curation History
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