Evidence Repository - Clinical Genome Resources

The ClinGen Evidence Repository is an FDA-recognized human genetic variant database containing expert-curated assertions regarding variants' pathogenicity and supporting evidence summaries. [Disclaimer]

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

CA10642026

316208 (ClinVar)

Gene: GATM

Condition: AGAT deficiency

Inheritance Mode: Autosomal recessive inheritance

Link to MONDO

UUID: 13677f0c-6e6f-4a05-ab23-d7f129ded13b

Approved on: 2022-06-06

Published on: 2022-10-06

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

Uncertain Significance

PM2_Supporting

Evidence Links 0

Expert Panel

Cerebral Creatine Deficiency Syndromes VCEP

Criteria Specification Information

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. 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. This variant is absent in gnomAD v2.1.1 (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 1.1.0): PM2_Supporting. (Classification approved by the ClinGen CCDS VCEP on June 6, 2022).

PM2_Supporting

Absent from gnomAD v2.1.1 (PM2_Supporting).

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