ClinVar Miner

Submissions for variant NM_015915.5(ATL1):c.33G>C (p.Trp11Cys)

gnomAD frequency: 0.00002  dbSNP: rs765421231
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001935822 SCV002189455 uncertain significance Hereditary spastic paraplegia 3A 2024-10-22 criteria provided, single submitter clinical testing This sequence change replaces tryptophan, which is neutral and slightly polar, with cysteine, which is neutral and slightly polar, at codon 11 of the ATL1 protein (p.Trp11Cys). This variant is present in population databases (rs765421231, gnomAD 0.005%). 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: 1416672). 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) has been performed for this missense variant. However, the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on ATL1 protein function. 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.
Ambry Genetics RCV002458798 SCV002617092 uncertain significance Inborn genetic diseases 2021-11-02 criteria provided, single submitter clinical testing The p.W11C variant (also known as c.33G>C), located in coding exon 1 of the ATL1 gene, results from a G to C substitution at nucleotide position 33. The tryptophan at codon 11 is replaced by cysteine, an amino acid with highly dissimilar properties. This amino acid position is highly 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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