ClinVar Miner

Submissions for variant NM_001378452.1(ITPR1):c.4333G>A (p.Val1445Met)

dbSNP: rs1559718601
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Institute of Human Genetics, University of Goettingen RCV002268270 SCV002550877 likely pathogenic Spinocerebellar ataxia type 29 2022-07-26 criteria provided, single submitter clinical testing The variant c.4261G>A (p.(Val1421Met)) in exon 33 of the ITPR1-gene is not found in the gnomAD database, it affects a highly conserved nucleotide, a highly conserved amino acid and there is a small physicochemical difference between Val and Met. This variant has a pathogenic computational verdict based on in silico predictions algorithms. It was found to be de novo in our patient. ACMG criteria used for classification: PM2, PM6, PP2, BP4.
Rady Children's Institute for Genomic Medicine, Rady Children's Hospital San Diego RCV005250102 SCV005900715 likely pathogenic ITPR1-related disorders 2024-02-15 criteria provided, single submitter clinical testing The ITPR1 gene is highly constrained (Z-score= 6.2 and pLI = 1), which suggests it is intolerant to variation. The c.4288G>A (p.Val1430Met) variant affects a highly conserved amino acid and is predicted by multiple in silico tools to have a deleterious effect on protein function. This variant has not been previously reported or functionally characterized in the literature to our knowledge. The c.4288G>A (p.Val1430Met) variant is absent from the gnomAD population database and thus is presumed to be rare. Analysis of the parental samples was negative for the variant, indicating this variant likely occurred as a de novo event. Based on the available evidence, c.4288G>A (p.Val1430Met) is classified as Likely Pathogenic.
GenomeConnect, ClinGen RCV002311994 SCV000840339 not provided Spinocerebellar ataxia type 29; Spinocerebellar ataxia type 15/16; Gillespie syndrome 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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