ClinVar Miner

Submissions for variant NM_015662.3(IFT172):c.1829G>A (p.Arg610Gln)

gnomAD frequency: 0.00008  dbSNP: rs144890293
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001228957 SCV001401387 uncertain significance Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71 2022-10-24 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 610 of the IFT172 protein (p.Arg610Gln). This variant also falls at the last nucleotide of exon 17, which is part of the consensus splice site for this exon. This variant is present in population databases (rs144890293, 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: 956199). 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"). Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). 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.
Fulgent Genetics, Fulgent Genetics RCV002484248 SCV002789316 uncertain significance Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71; Bardet-Biedl syndrome 20 2021-12-14 criteria provided, single submitter clinical testing
PreventionGenetics, part of Exact Sciences RCV004738204 SCV005359115 uncertain significance IFT172-related disorder 2024-07-24 no assertion criteria provided clinical testing The IFT172 c.1829G>A variant is predicted to result in the amino acid substitution p.Arg610Gln. This variant occurs at the last nucleotide position of exon 17 and is predicted to alter splicing based on available splicing prediction programs (Alamut Visual Plus v1.6.1). To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.016% of alleles in individuals of African 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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