ClinVar Miner

Submissions for variant NM_001365951.3(KIF1B):c.3259+3A>C

gnomAD frequency: 0.00004  dbSNP: rs1388178227
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Molecular Genetics Laboratory, London Health Sciences Centre RCV001173586 SCV001336685 uncertain significance Charcot-Marie-Tooth disease criteria provided, single submitter clinical testing
Invitae RCV001367392 SCV001563740 uncertain significance Charcot-Marie-Tooth disease type 2 2023-12-31 criteria provided, single submitter clinical testing This sequence change falls in intron 28 of the KIF1B gene. It does not directly change the encoded amino acid sequence of the KIF1B protein. It affects a nucleotide within the consensus splice site. This variant is present in population databases (no rsID available, gnomAD 0.005%). This variant has been observed in individual(s) with clinical features of Charcot-Marie-Tooth disease (PMID: 32376792). ClinVar contains an entry for this variant (Variation ID: 917103). 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 disrupt the consensus splice site. 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 RCV002320388 SCV002607354 uncertain significance Hereditary cancer-predisposing syndrome 2023-02-09 criteria provided, single submitter clinical testing The c.3121+3A>C intronic variant results from an A to C substitution 3 nucleotides after coding exon 27 in the KIF1B gene. This nucleotide position is poorly conserved in available vertebrate species. In silico splice site analysis predicts that this alteration will weaken the native splice donor site. The evidence for this gene-disease relationship is limited; therefore, the clinical significance of this alteration is unclear.

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