ClinVar Miner

Submissions for variant NM_001244008.2(KIF1A):c.4007G>A (p.Arg1336Gln)

gnomAD frequency: 0.00001  dbSNP: rs772545191
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001318243 SCV001508936 uncertain significance Hereditary spastic paraplegia 30; Neuropathy, hereditary sensory, type 2C; Intellectual disability, autosomal dominant 9 2023-04-26 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. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant  is likely to be tolerated. ClinVar contains an entry for this variant (Variation ID: 1018883). This variant has not been reported in the literature in individuals affected with KIF1A-related conditions. This variant is present in population databases (rs772545191, gnomAD 0.006%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 1235 of the KIF1A protein (p.Arg1235Gln). This variant also falls at the last nucleotide of exon 35, which is part of the consensus splice site for this exon.
Ambry Genetics RCV002375410 SCV002625370 uncertain significance Inborn genetic diseases 2020-10-29 criteria provided, single submitter clinical testing The p.R1336Q variant (also known as c.4007G>A), located in coding exon 37 of the KIF1A gene, results from a G to A substitution at nucleotide position 4007. The arginine at codon 1336 is replaced by glutamine, an amino acid with highly similar properties. This amino acid position is well conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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