ClinVar Miner

Submissions for variant NM_004321.7(KIF1A):c.1829C>T (p.Ala610Val) (rs765812659)

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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000219370 SCV000279871 uncertain significance not provided 2018-11-23 criteria provided, single submitter clinical testing The A610V variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The A610V variant is observed in 7/14514 (0.05%) alleles from individuals of African background (Lek et al., 2016). The A610V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. This amino acid substitution does not occur within the predicted motor domain of the protein, where all pathogenic missense KIF1A pathogenic variants have been identified to-date (Lee et al., 2015). In-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function. Based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Illumina Clinical Services Laboratory,Illumina RCV000261830 SCV000429283 uncertain significance Hereditary sensory and autonomic neuropathy type II 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000319089 SCV000429284 uncertain significance Intellectual Disability, Dominant 2016-06-14 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000352933 SCV000429285 uncertain significance Spastic Paraplegia, Recessive 2016-06-14 criteria provided, single submitter clinical testing
Invitae RCV000639800 SCV000761381 uncertain significance Spastic paraplegia 30, autosomal recessive; Hereditary sensory and autonomic neuropathy type IIC; Mental retardation, autosomal dominant 9 2018-02-07 criteria provided, single submitter clinical testing This sequence change replaces alanine with valine at codon 610 of the KIF1A protein (p.Ala610Val). The alanine residue is highly conserved and there is a small physicochemical difference between alanine and valine. This variant is present in population databases (rs765812659, ExAC 0.06%). This variant has not been reported in the literature in individuals with KIF1A-related disease. ClinVar contains an entry for this variant (Variation ID: 234824). Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0"). 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.
GenomeConnect, ClinGen RCV000509269 SCV000606983 not provided Spastic paraplegia 30, autosomal recessive; Hereditary sensory and autonomic neuropathy type IIC no assertion provided phenotyping only GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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