ClinVar Miner

Submissions for variant NM_002047.4(GARS1):c.59T>C (p.Leu20Pro)

gnomAD frequency: 0.00004  dbSNP: rs756664556
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001570172 SCV001794403 uncertain significance not provided 2024-08-21 criteria provided, single submitter clinical testing In silico analysis indicates that this missense variant does not alter protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV002241378 SCV002508762 likely benign Charcot-Marie-Tooth disease type 2 2025-01-29 criteria provided, single submitter clinical testing
Ambry Genetics RCV003987879 SCV002755855 uncertain significance not specified 2024-04-01 criteria provided, single submitter clinical testing The c.59T>C (p.L20P) alteration is located in exon 1 (coding exon 1) of the GARS gene. This alteration results from a T to C substitution at nucleotide position 59, causing the leucine (L) at amino acid position 20 to be replaced by a proline (P). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003987879 SCV004804135 uncertain significance not specified 2024-01-04 criteria provided, single submitter clinical testing Variant summary: GARS1 c.59T>C (p.Leu20Pro) results in a non-conservative amino acid change in the encoded protein sequence. Four of five in-silico tools predict a benign effect of the variant on protein function. The variant allele was found at a frequency of 9.4e-06 in 1594000 control chromosomes. This frequency is not significantly higher than estimated for a pathogenic variant in GARS1 causing GARS1-Related Disorders, allowing no conclusion about variant significance. To our knowledge, no occurrence of c.59T>C in individuals affected with GARS1-Related Disorders and no experimental evidence demonstrating its impact on protein function have been reported. ClinVar contains an entry for this variant (Variation ID: 1203950). Based on the evidence outlined above, the variant was classified as uncertain significance.

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