Submissions for variant NM_015662.3(IFT172):c.4519C>T (p.Arg1507Ter)

gnomAD frequency: 0.00001  dbSNP: rs150246251

Total submissions: 3

Submitter	RCV	SCV	Clinical significance	Condition	Last evaluated	Review status	Method	Comment
Labcorp Genetics (formerly Invitae), Labcorp	RCV001900954	SCV002158503	pathogenic	Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71	2023-08-30	criteria provided, single submitter	clinical testing	This sequence change creates a premature translational stop signal (p.Arg1507*) 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 (rs150246251, 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: 1394651). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may create or strengthen a splice site. For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics	RCV002490161	SCV002796891	likely pathogenic	Short-rib thoracic dysplasia 10 with or without polydactyly; Retinitis pigmentosa 71; Bardet-Biedl syndrome 20	2022-01-10	criteria provided, single submitter	clinical testing
PreventionGenetics, part of Exact Sciences	RCV004738423	SCV005357928	likely pathogenic	IFT172-related disorder	2024-08-08	no assertion criteria provided	clinical testing	The IFT172 c.4519C>T variant is predicted to result in premature protein termination (p.Arg1507*). To our knowledge, this variant has not been reported in the literature in patients with IFT172-related disorders. This variant is reported in 0.012% of alleles in individuals of African descent in gnomAD. Nonsense variants in IFT172 are expected to be pathogenic. This variant is interpreted as likely pathogenic.