ClinVar Miner

Submissions for variant NM_001365951.3(KIF1B):c.2839G>T (p.Ala947Ser)

gnomAD frequency: 0.00001  dbSNP: rs748284088
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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 RCV001930625 SCV002193531 uncertain significance Charcot-Marie-Tooth disease type 2 2023-09-11 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. 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: 1414744). This variant has not been reported in the literature in individuals affected with KIF1B-related conditions. This variant is present in population databases (rs748284088, gnomAD 0.004%). This sequence change replaces alanine, which is neutral and non-polar, with serine, which is neutral and polar, at codon 901 of the KIF1B protein (p.Ala901Ser).
Ambry Genetics RCV004043454 SCV002741738 uncertain significance not specified 2024-03-30 criteria provided, single submitter clinical testing The p.A901S variant (also known as c.2701G>T), located in coding exon 24 of the KIF1B gene, results from a G to T substitution at nucleotide position 2701. The alanine at codon 901 is replaced by serine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
St. Jude Molecular Pathology, St. Jude Children's Research Hospital RCV005055180 SCV005689105 uncertain significance Pheochromocytoma 2025-02-05 criteria provided, single submitter clinical testing The KIF1B c.2701G>T p.(Ala901Ser) missense change has a maximum subpopulation frequency of 0.004% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org). The in silico tool REVEL predicts a benign effect on protein function, but to our knowledge this prediction has not been confirmed by functional studies. To our knowledge, this variant has not been reported in individuals with pheochromocytoma or neuroblastoma. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.

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