ClinVar Miner

Submissions for variant NM_004817.4(TJP2):c.1056+2T>C

dbSNP: rs1278244243
Minimum review status: Collection method:
Minimum conflict level:
ClinVar version:
Total submissions: 4
Download table as spreadsheet
Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000579219 SCV000681216 uncertain significance not provided 2025-03-13 criteria provided, single submitter clinical testing Canonical splice site variant predicted to result in a null allele in a gene for which loss of function is a known mechanism of disease; Has not been previously published as pathogenic or benign to our knowledge
Fulgent Genetics, Fulgent Genetics RCV000763622 SCV000894479 likely pathogenic Hypercholanemia, familial 1; Cholestasis, progressive familial intrahepatic, 4 2018-10-31 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000579219 SCV005847631 likely pathogenic not provided 2024-05-09 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 6 of the TJP2 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 TJP2 are known to be pathogenic (PMID: 24614073, 25921221, 28039895). This variant is present in population databases (no rsID available, gnomAD 0.009%). This variant has not been reported in the literature in individuals affected with TJP2-related conditions. ClinVar contains an entry for this variant (Variation ID: 489223). 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 RCV003900292 SCV004714564 likely pathogenic TJP2-related disorder 2024-01-03 no assertion criteria provided clinical testing The TJP2 c.1056+2T>C 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 0.0087% of alleles in individuals of Latino descent in gnomAD. Variants that disrupt the consensus splice donor site in TJP2 are expected to be pathogenic. This variant is interpreted as likely pathogenic.

The information on this website is not intended for direct diagnostic use or medical decision-making without review by a genetics professional. Individuals should not change their health behavior solely on the basis of information contained on this website. Neither the University of Utah nor the National Institutes of Health independently verfies the submitted information. If you have questions about the information contained on this website, please see a health care professional.