ClinVar Miner

Submissions for variant NM_014363.6(SACS):c.10675C>G (p.Pro3559Ala)

gnomAD frequency: 0.00003  dbSNP: rs767704103
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Athena Diagnostics RCV003482271 SCV000614923 uncertain significance not provided 2022-12-23 criteria provided, single submitter clinical testing Available data are insufficient to determine the clinical significance of the variant at this time. The frequency of this variant in the general population is uninformative in assessment of its pathogenicity (http://gnomad.broadinstitute.org). Computational tools predict that this variant is not damaging.
Labcorp Genetics (formerly Invitae), Labcorp RCV000633011 SCV000754223 uncertain significance Spastic paraplegia 2024-10-24 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 3559 of the SACS protein (p.Pro3559Ala). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with SACS-related conditions. ClinVar contains an entry for this variant (Variation ID: 448186). 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 SACS 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.
Genome-Nilou Lab RCV001783014 SCV002026490 uncertain significance Charlevoix-Saguenay spastic ataxia 2021-09-05 criteria provided, single submitter clinical testing

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