ClinVar Miner

Submissions for variant NM_003119.4(SPG7):c.1172G>A (p.Arg391Gln)

gnomAD frequency: 0.00004  dbSNP: rs778409451
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Illumina Laboratory Services, Illumina RCV001118113 SCV001276376 uncertain significance Hereditary spastic paraplegia 7 2017-04-27 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.
Centre for Mendelian Genomics, University Medical Centre Ljubljana RCV001118113 SCV001367695 uncertain significance Hereditary spastic paraplegia 7 2018-11-21 criteria provided, single submitter clinical testing This variant was classified as: Uncertain significance. The available evidence on this variant's pathogenicity is insufficient or conflicting. The following ACMG criteria were applied in classifying this variant: PM2,PP3.
Labcorp Genetics (formerly Invitae), Labcorp RCV001118113 SCV003205121 uncertain significance Hereditary spastic paraplegia 7 2022-08-20 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 391 of the SPG7 protein (p.Arg391Gln). This variant is present in population databases (rs778409451, gnomAD 0.006%). This variant has not been reported in the literature in individuals affected with SPG7-related conditions. ClinVar contains an entry for this variant (Variation ID: 886110). 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 expected to disrupt SPG7 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.
Revvity Omics, Revvity RCV001118113 SCV003820055 uncertain significance Hereditary spastic paraplegia 7 2022-12-22 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004753210 SCV005359037 uncertain significance SPG7-related disorder 2024-04-03 no assertion criteria provided clinical testing The SPG7 c.1172G>A variant is predicted to result in the amino acid substitution p.Arg391Gln. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0065% of alleles in individuals of South Asian descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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