•Detecting pathogenic variants in VNTRs is challenging due to poor read mappability•VNtyper detects VNTR the MUC1 gene using Kestrel algorithm•VNtyper improves ADTKD-MUC1 diagnosis by accurate genotyping of coding VNTR•Integration VNtyper with SRS panel testing identified new overlooked patients The human genome comprises approximately 3% tandem repeats variable length (VNTR), a few which have ...