ClinVar Miner

Submissions for variant NM_003119.4(SPG7):c.1601G>A (p.Arg534Gln)

gnomAD frequency: 0.00004  dbSNP: rs757160836
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001035268 SCV001198591 uncertain significance Hereditary spastic paraplegia 7 2022-06-04 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. 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. ClinVar contains an entry for this variant (Variation ID: 834557). This variant has not been reported in the literature in individuals affected with SPG7-related conditions. This variant is present in population databases (rs757160836, gnomAD 0.06%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 534 of the SPG7 protein (p.Arg534Gln).
GeneDx RCV004720041 SCV005325876 uncertain significance not provided 2023-11-15 criteria provided, single submitter clinical testing Has not been previously published as pathogenic or benign to our knowledge; In silico analysis supports that this missense variant has a deleterious effect on protein structure/function
Ambry Genetics RCV004962998 SCV005504107 uncertain significance Inborn genetic diseases 2024-10-20 criteria provided, single submitter clinical testing The c.1601G>A (p.R534Q) alteration is located in exon 12 (coding exon 12) of the SPG7 gene. This alteration results from a G to A substitution at nucleotide position 1601, causing the arginine (R) at amino acid position 534 to be replaced by a glutamine (Q). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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