ClinVar Miner

Submissions for variant NM_015662.3(IFT172):c.2522C>T (p.Ala841Val)

gnomAD frequency: 0.00006  dbSNP: rs762431558
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001067301 SCV001232355 uncertain significance Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71 2022-08-31 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 841 of the IFT172 protein (p.Ala841Val). This variant is present in population databases (rs762431558, 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: 860905). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV002274134 SCV002559309 uncertain significance not provided 2022-02-08 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Has not been previously published as pathogenic or benign to our knowledge
Fulgent Genetics, Fulgent Genetics RCV002505648 SCV002816170 uncertain significance Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71; Bardet-Biedl syndrome 20 2024-05-09 criteria provided, single submitter clinical testing
Dept Of Ophthalmology, Nagoya University RCV003890220 SCV004705261 uncertain significance Retinal dystrophy 2023-10-01 criteria provided, single submitter research
PreventionGenetics, part of Exact Sciences RCV004738150 SCV005358596 uncertain significance IFT172-related disorder 2024-09-16 no assertion criteria provided clinical testing The IFT172 c.2522C>T variant is predicted to result in the amino acid substitution p.Ala841Val. This variant has been reported in an individual with retinitis pigmentosa (Table S5, Koyanagi et al. 2019. PubMed ID: 31213501). This variant is reported in 0.011% of alleles in individuals of Latino descent in gnomAD. At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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