ClinVar Miner

Submissions for variant NM_015915.5(ATL1):c.686C>G (p.Ala229Gly)

gnomAD frequency: 0.00002  dbSNP: rs1454376300
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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 RCV001219488 SCV001391431 uncertain significance Hereditary spastic paraplegia 3A 2024-09-17 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with glycine, which is neutral and non-polar, at codon 229 of the ATL1 protein (p.Ala229Gly). This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with ATL1-related conditions. ClinVar contains an entry for this variant (Variation ID: 948267). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt ATL1 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.
Athena Diagnostics RCV001288451 SCV001475556 uncertain significance not provided 2020-03-04 criteria provided, single submitter clinical testing
Ambry Genetics RCV002365992 SCV002665617 uncertain significance Inborn genetic diseases 2019-09-18 criteria provided, single submitter clinical testing The p.A229G variant (also known as c.686C>G), located in coding exon 7 of the ATL1 gene, results from a C to G substitution at nucleotide position 686. The alanine at codon 229 is replaced by glycine, an amino acid with similar properties. This amino acid position is poorly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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