ClinVar Miner

Submissions for variant NM_015662.3(IFT172):c.1313C>T (p.Pro438Leu)

gnomAD frequency: 0.00026  dbSNP: rs367930028
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001054271 SCV001218576 likely benign Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71 2024-12-18 criteria provided, single submitter clinical testing
GeneDx RCV002291713 SCV002584499 uncertain significance not provided 2023-04-12 criteria provided, single submitter clinical testing 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
New York Genome Center RCV002468131 SCV002764515 uncertain significance Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71; Bardet-Biedl syndrome 20 2022-01-14 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV002468131 SCV002797706 uncertain significance Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71; Bardet-Biedl syndrome 20 2024-03-29 criteria provided, single submitter clinical testing
Ambry Genetics RCV002553339 SCV003541922 uncertain significance Inborn genetic diseases 2021-08-13 criteria provided, single submitter clinical testing The c.1313C>T (p.P438L) alteration is located in exon 13 (coding exon 13) of the IFT172 gene. This alteration results from a C to T substitution at nucleotide position 1313, causing the proline (P) at amino acid position 438 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Genetic Services Laboratory, University of Chicago RCV003151274 SCV003839599 uncertain significance not specified 2022-07-20 no assertion criteria provided clinical testing DNA sequence analysis of the IFT172 gene demonstrated a sequence change, c.1313C>T, in exon 13 that results in an amino acid change, p.Pro438Leu. This sequence change has been described in the gnomAD database with a frequency of 0.096% in the African/African American subpopulation (dbSNP rs367930028). The p.Pro438Leu change affects a highly conserved amino acid residue located in a domain of the IFT172 protein that is known to be functional. In-silico pathogenicity prediction tools (SIFT, PolyPhen2, Align GVGD, REVEL) provide contradictory results for the p.Pro438Leu substitution. This sequence change does not appear to have been previously described in individuals with IFT172-related disorders. Due to insufficient evidences and the lack of functional studies, the clinical significance of the p.Pro438Leu change remains unknown at this time.
PreventionGenetics, part of Exact Sciences RCV004553596 SCV004106084 uncertain significance IFT172-related disorder 2024-03-01 no assertion criteria provided clinical testing The IFT172 c.1313C>T variant is predicted to result in the amino acid substitution p.Pro438Leu. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.096% of alleles in individuals of African descent in gnomAD. 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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