ClinVar Miner

Submissions for variant NM_015915.5(ATL1):c.688G>A (p.Asp230Asn)

gnomAD frequency: 0.00002  dbSNP: rs768367744
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000513662 SCV000608700 uncertain significance not provided 2020-07-01 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001346950 SCV001541188 uncertain significance Hereditary spastic paraplegia 3A 2023-12-27 criteria provided, single submitter clinical testing This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 230 of the ATL1 protein (p.Asp230Asn). This variant is present in population databases (rs768367744, gnomAD 0.006%). 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: 444328). 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 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.
Institute of Human Genetics, University of Leipzig Medical Center RCV001706655 SCV001934337 uncertain significance Neuropathy, hereditary sensory, type 1D 2020-11-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV002367703 SCV002666158 uncertain significance Inborn genetic diseases 2021-10-12 criteria provided, single submitter clinical testing The p.D230N variant (also known as c.688G>A), located in coding exon 7 of the ATL1 gene, results from a G to A substitution at nucleotide position 688. The aspartic acid at codon 230 is replaced by asparagine, an amino acid with highly similar properties. This amino acid position is not well 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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