ClinVar Miner

Submissions for variant NM_014714.4(IFT140):c.1009+1G>T

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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 RCV002695487 SCV002990625 likely pathogenic Saldino-Mainzer syndrome 2024-12-05 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 9 of the IFT140 gene. It is expected to disrupt RNA splicing. Variants that disrupt the donor or acceptor splice site typically lead to a loss of protein function (PMID: 16199547), and loss-of-function variants in IFT140 are known to be pathogenic (PMID: 22503633, 23418020, 24009529, 26216056). This variant is present in population databases (no rsID available, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with IFT140-related conditions. ClinVar contains an entry for this variant (Variation ID: 1955567). 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 currently available evidence indicates that the variant is pathogenic, but additional data are needed to prove that conclusively. Therefore, this variant has been classified as Likely Pathogenic.
PreventionGenetics, part of Exact Sciences RCV003409908 SCV004114341 likely pathogenic IFT140-related disorder 2022-10-07 criteria provided, single submitter clinical testing The IFT140 c.1009+1G>T variant is predicted to disrupt the GT donor site and interfere with normal splicing. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.011% of alleles in individuals of African descent in gnomAD (http://gnomad.broadinstitute.org/variant/16-1637198-C-A). Variants that disrupt the consensus splice donor site in IFT140 are expected to be pathogenic. This variant is interpreted as likely pathogenic.
Fulgent Genetics, Fulgent Genetics RCV005008700 SCV005638735 likely pathogenic Saldino-Mainzer syndrome; Retinitis pigmentosa 80 2024-01-14 criteria provided, single submitter clinical testing

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