ClinVar Miner

Submissions for variant NM_024753.5(TTC21B):c.2758-2A>G

gnomAD frequency: 0.00003  dbSNP: rs766132877
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Center of Genomic medicine, Geneva, University Hospital of Geneva RCV000857220 SCV000999804 pathogenic Infantile nephronophthisis 2019-01-28 criteria provided, single submitter clinical testing This variant was identified in composite heterozygosity with another variant in the same gene in a female patient with nephronophtisis, retinopathy and suspected ciliopathy
Fulgent Genetics, Fulgent Genetics RCV001535927 SCV001752581 likely pathogenic Asphyxiating thoracic dystrophy 4; Nephronophthisis 12 2021-06-30 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001852034 SCV002196147 pathogenic Jeune thoracic dystrophy; Nephronophthisis 2023-08-07 criteria provided, single submitter clinical testing ClinVar contains an entry for this variant (Variation ID: 30937). For these reasons, this variant has been classified as Pathogenic. Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. Disruption of this splice site has been observed in individual(s) with nephronophthisis (PMID: 21258341). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. This variant is present in population databases (rs766132877, gnomAD 0.005%). This sequence change affects an acceptor splice site in intron 20 of the TTC21B 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 TTC21B are known to be pathogenic (PMID: 18327258, 21068128, 21258341, 23559409, 24876116, 25492405, 27491411, 29068549).
OMIM RCV000023926 SCV000045217 pathogenic Nephronophthisis 12 2011-03-01 no assertion criteria provided literature only

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