ClinVar Miner

Submissions for variant NM_001482.3(GATM):c.625A>G (p.Lys209Glu)

gnomAD frequency: 0.00001  dbSNP: rs1393968087
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000687853 SCV000815442 uncertain significance Arginine:glycine amidinotransferase deficiency 2023-11-20 criteria provided, single submitter clinical testing This sequence change replaces lysine, which is basic and polar, with glutamic acid, which is acidic and polar, at codon 209 of the GATM protein (p.Lys209Glu). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with GATM-related conditions. ClinVar contains an entry for this variant (Variation ID: 567693). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt GATM protein function with a negative predictive value of 80%. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Fulgent Genetics, Fulgent Genetics RCV002477533 SCV002789904 uncertain significance Arginine:glycine amidinotransferase deficiency; Fanconi renotubular syndrome 1 2022-04-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV002544787 SCV003555874 uncertain significance Inborn genetic diseases 2021-05-05 criteria provided, single submitter clinical testing The c.625A>G (p.K209E) alteration is located in exon 4 (coding exon 4) of the GATM gene. This alteration results from a A to G substitution at nucleotide position 625, causing the lysine (K) at amino acid position 209 to be replaced by a glutamic acid (E). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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