ClinVar Miner

Submissions for variant NM_015559.3(SETBP1):c.1568del (p.His523fs) (rs886041469)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000355861 SCV000330123 pathogenic not provided 2016-10-04 criteria provided, single submitter clinical testing The c.1568delA pathogenic variant in the SETBP1 gene has not been reported previously as a pathogenic variant nor as a benign variant, to our knowledge. The c.1568delA variant causes a frameshift starting with codon Histidine 523, changes this amino acid to a Leucine residue, and creates a premature Stop codon at position 32 of the new reading frame, denoted p.His523LeufsX32. This variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. The c.1568delA variant was not observed in approximately 6500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. Protein truncating pathogenic variants downstream of this variant have been reported in the Human Gene Mutation Database in association with SETBP1-related disorders (Stenson et al., 2014), supporting the pathogenicity of more upstream truncating variants. We interpret c.1568delA as a pathogenic variant.
GenomeConnect, ClinGen RCV000509457 SCV000606938 not provided SETBP1-Related Disorder no assertion provided phenotyping only GenomeConnect assertions are reported exactly as they appear on the patient-provided report from the testing laboratory. GenomeConnect staff make no attempt to reinterpret the clinical significance of the variant.

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