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
  • No CSPEC computed assertion could be determined for this classification!


Variant: NM_001482.3(GATM):c.*104A>G

CA10642026

316208 (ClinVar)

Gene: GATM
Condition: AGAT deficiency
Inheritance Mode: Autosomal recessive inheritance
UUID: 13677f0c-6e6f-4a05-ab23-d7f129ded13b
Approved on: 2025-10-07
Published on: 2025-10-07

HGVS expressions

NM_001482.3:c.*104A>G
NM_001482.3(GATM):c.*104A>G
NC_000015.10:g.45362005T>C
CM000677.2:g.45362005T>C
NC_000015.9:g.45654203T>C
CM000677.1:g.45654203T>C
NC_000015.8:g.43441495T>C
NG_011674.1:g.21778A>G
NG_011674.2:g.45313A>G
ENST00000396659.8:c.*104A>G
ENST00000674905.1:c.*338A>G
ENST00000675158.1:c.*276A>G
ENST00000675323.1:c.*1878A>G
ENST00000675701.1:c.*104A>G
ENST00000675974.1:n.3925A>G
ENST00000676090.1:c.*2107A>G
ENST00000396659.7:c.*104A>G
ENST00000558362.5:n.3032A>G
NM_001482.2:c.*104A>G
NM_001321015.1:c.*104A>G
NM_001321015.2:c.*104A>G
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Uncertain Significance

Met criteria codes 1
PM2_Supporting

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 GATM 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_001482.3:c.*104A>G variant is a single nucleotide substitution in the 3'UTR of GATM. To our knowledge, this variant has not been reported in the literature in an individual with features of AGAT deficiency. Because the variant is located in the 3'UTR, it is not expected to alter the amino acid sequence, and SpliceAI predicts no impact on splicing. The highest population minor allele frequency in gnomAD v4.1.0. is 0.000004811 (2/415744 alleles) in the European non-Finnish population. This is below the ClinGen CCDS VCEP's threshold for PM2_Supporting (<0.000055), meeting this criterion (PM2_Supporting). There is a ClinVar entry for this variant (Variation ID: 316208). In summary, this variant meets the criteria to be classified as uncertain significance for AGAT deficiency based on the ACMG/AMP criteria applied, as specified by the ClinGen Cerebral Creatine Deficiency Syndromes Variant Curation Expert Panel (Specifications Version 2.0.0): PM2_Supporting. (Classification approved by the ClinGen CCDS VCEP on October 7, 2025).
Met criteria codes
PM2_Supporting
The highest population minor allele frequency in gnomAD v4.1.0. is 0.000004811 (2/415744 alleles) in the European non-Finnish population. This is below the ClinGen CCDS VCEP's threshold for PM2_Supporting (<0.000055), meeting this criterion (PM2_Supporting).
Curation History
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