ClinVar Miner

Submissions for variant NM_001128228.3(TPRN):c.1725+5G>A

gnomAD frequency: 0.00004  dbSNP: rs373827566
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001564643 SCV001787840 uncertain significance not provided 2019-04-17 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes splice predictors and evolutionary conservation, suggests this variant may impact gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 26969326)
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV001803363 SCV002048902 uncertain significance Autosomal recessive nonsyndromic hearing loss 79 2021-11-30 criteria provided, single submitter clinical testing The c.1725+5G>A variant has been previously reported in an individual with propound congenital hearing loss who also carried an additional pathogenic variant in TPRN. However, segregation, allele phase, and other evidence of causality was not presented. This is an intronic variant in a moderately conserved nucleotide in intron 1, and computational analyses (Alamut v.2.11) predict that this variant may impact splicing. However, in the absence of functional data, such predictions are not sufficient to assign pathogenicity. Due to limited information, the clinical significance of this variant is uncertain at this time. References: Sloan-Heggen et al. Comprehensive genetic testing in the clinical evaluation of 1119 patients with hearing loss. Hum Genet. 2016 Apr;135(4):441-450. PMID: 26969326

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