ClinVar Miner

Submissions for variant NM_015662.3(IFT172):c.3178G>A (p.Ala1060Thr)

gnomAD frequency: 0.00001  dbSNP: rs560379580
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001308721 SCV001498190 uncertain significance Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71 2023-07-07 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 1060 of the IFT172 protein (p.Ala1060Thr). This variant is present in population databases (rs560379580, gnomAD 0.09%). 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: 1010990). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt IFT172 protein function. 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 RCV002493618 SCV002785046 uncertain significance Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71; Bardet-Biedl syndrome 20 2021-12-06 criteria provided, single submitter clinical testing
Ambry Genetics RCV002543247 SCV003741328 uncertain significance Inborn genetic diseases 2021-11-30 criteria provided, single submitter clinical testing The c.3178G>A (p.A1060T) alteration is located in exon 29 (coding exon 29) of the IFT172 gene. This alteration results from a G to A substitution at nucleotide position 3178, causing the alanine (A) at amino acid position 1060 to be replaced by a threonine (T). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
PreventionGenetics, part of Exact Sciences RCV004548151 SCV004759704 uncertain significance IFT172-related disorder 2024-01-02 no assertion criteria provided clinical testing The IFT172 c.3178G>A variant is predicted to result in the amino acid substitution p.Ala1060Thr. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.091% of alleles in individuals of South Asian descent in gnomAD, which may be too common to be an undocumented disease causing variant. Although we suspect that this variant may be benign, 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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