ClinVar Miner

Submissions for variant NM_015915.5(ATL1):c.922G>A (p.Glu308Lys)

gnomAD frequency: 0.00001  dbSNP: rs773401705
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
CeGaT Center for Human Genetics Tuebingen RCV000488307 SCV000574973 likely benign not provided 2022-07-01 criteria provided, single submitter clinical testing ATL1: BP4
Baylor Genetics RCV001334885 SCV001527868 uncertain significance Neuropathy, hereditary sensory, type 1D 2018-01-16 criteria provided, single submitter clinical testing This variant was determined to be of uncertain significance according to ACMG Guidelines, 2015 [PMID:25741868].
Labcorp Genetics (formerly Invitae), Labcorp RCV001856884 SCV002187912 uncertain significance Hereditary spastic paraplegia 3A 2024-02-23 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 308 of the ATL1 protein (p.Glu308Lys). This variant is present in population databases (rs773401705, gnomAD 0.003%). 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: 425042). 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 95%. 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.

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