ClinVar Miner

Submissions for variant NM_015662.3(IFT172):c.2365C>T (p.Arg789Ter)

gnomAD frequency: 0.00001  dbSNP: rs202024173
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001008014 SCV001167746 likely pathogenic not provided 2019-02-20 criteria provided, single submitter clinical testing The R789X variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The R789X variant is observed in 2/15302 (0.01%) alleles from individuals of African background in large population cohorts (Lek et al., 2016). The R789X nonsense variant is predicted to cause loss of normal protein function either through protein truncation or nonsense-mediated mRNA decay. Therefore, this variant is likely pathogenic; however, the possibility that it is benign cannot be excluded.
Labcorp Genetics (formerly Invitae), Labcorp RCV001213870 SCV001385522 pathogenic Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71 2024-03-19 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Arg789*) in the IFT172 gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in IFT172 are known to be pathogenic (PMID: 24140113). This variant is present in population databases (rs202024173, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with IFT172-related conditions. ClinVar contains an entry for this variant (Variation ID: 816981). For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV001008014 SCV002016691 likely pathogenic not provided 2019-06-28 criteria provided, single submitter clinical testing
Baylor Genetics RCV003458171 SCV004183451 likely pathogenic Short-rib thoracic dysplasia 10 with or without polydactyly 2023-10-26 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV005021316 SCV005651417 likely pathogenic Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71; Bardet-Biedl syndrome 20 2024-05-18 criteria provided, single submitter clinical testing

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