ClinVar Miner

Submissions for variant NM_001244008.2(KIF1A):c.7G>A (p.Gly3Arg)

gnomAD frequency: 0.00005  dbSNP: rs751960710
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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 RCV001062622 SCV001227436 uncertain significance Hereditary spastic paraplegia 30; Neuropathy, hereditary sensory, type 2C; Intellectual disability, autosomal dominant 9 2025-01-13 criteria provided, single submitter clinical testing This sequence change replaces glycine, which is neutral and non-polar, with arginine, which is basic and polar, at codon 3 of the KIF1A protein (p.Gly3Arg). This variant is present in population databases (rs751960710, gnomAD 0.005%). This variant has not been reported in the literature in individuals affected with KIF1A-related conditions. ClinVar contains an entry for this variant (Variation ID: 857025). 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 expected to disrupt KIF1A protein function with a positive 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.
Ambry Genetics RCV002418528 SCV002679432 uncertain significance Inborn genetic diseases 2021-07-28 criteria provided, single submitter clinical testing The p.G3R variant (also known as c.7G>A), located in coding exon 1 of the KIF1A gene, results from a G to A substitution at nucleotide position 7. The glycine at codon 3 is replaced by arginine, an amino acid with dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
GeneDx RCV004590071 SCV005079268 uncertain significance not provided 2023-12-22 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge; This variant is associated with the following publications: (PMID: 21376300, 21820098, 26125038)

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