ClinVar Miner

Submissions for variant NM_001365951.3(KIF1B):c.3131G>A (p.Ser1044Asn)

gnomAD frequency: 0.00016  dbSNP: rs769602520
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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 RCV001980653 SCV002273726 uncertain significance Charcot-Marie-Tooth disease type 2 2023-11-29 criteria provided, single submitter clinical testing This sequence change replaces serine, which is neutral and polar, with asparagine, which is neutral and polar, at codon 998 of the KIF1B protein (p.Ser998Asn). This variant is present in population databases (rs769602520, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with KIF1B-related conditions. ClinVar contains an entry for this variant (Variation ID: 1489493). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The asparagine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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 RCV004045297 SCV002746932 likely benign not specified 2021-02-12 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: seen in unaffected individuals, population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
PreventionGenetics, part of Exact Sciences RCV003408052 SCV004116100 uncertain significance KIF1B-related disorder 2023-05-30 criteria provided, single submitter clinical testing The KIF1B c.2993G>A variant is predicted to result in the amino acid substitution p.Ser998Asn. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.024% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/1-10397133-G-A) and has conflicting interpretations regarding it pathogenicity in ClinVar, ranging from uncertain significance to likely benign (https://www.ncbi.nlm.nih.gov/clinvar/variation/1489493/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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