ClinVar Miner

Submissions for variant NM_001482.3(GATM):c.-1G>A

gnomAD frequency: 0.00010  dbSNP: rs778453861
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000497975 SCV000589332 uncertain significance not provided 2017-06-16 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the GATM gene. The c.-1 G>A sequence change in the 5' untranslated region of GATM has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The c.-1 G>A variant is not observed in large population cohorts; however, limited data are available (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). This substitution occurs at a position in the Kozak sequence that is not conserved, and it is not expected to alter the ATG initiation codon. Additionally, other regulatory variants have not been reported in the GATM gene in association with AGAT deficiency (Stenson et al., 2014). However, in the absence of RNA/functional studies, the actual effect of this sequence change in this individual is unknown. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Ambry Genetics RCV002318601 SCV000850388 uncertain significance Inborn genetic diseases 2024-01-17 criteria provided, single submitter clinical testing The c.-1G>A variant is located in the 5' untranslated region (5’ UTR) of the GATM gene. This variant results from a G to A substitution 1 bases upstream from the first translated codon. This nucleotide position is not well conserved in available vertebrate species. Since supporting evidence is limited at this time, the clinical significance of this variant remains unclear.
Fulgent Genetics, Fulgent Genetics RCV002475983 SCV002792513 uncertain significance Arginine:glycine amidinotransferase deficiency; Fanconi renotubular syndrome 1 2022-04-28 criteria provided, single submitter clinical testing

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