ClinVar Miner

Submissions for variant NM_001173990.3(TMEM216):c.34+2T>C

gnomAD frequency: 0.00001  dbSNP: rs1057517498
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000409881 SCV000487607 likely pathogenic Meckel syndrome, type 2 2016-05-19 criteria provided, single submitter clinical testing
Counsyl RCV000411402 SCV000487608 likely pathogenic Joubert syndrome 2 2016-05-19 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001053497 SCV001217763 likely pathogenic Familial aplasia of the vermis 2024-11-19 criteria provided, single submitter clinical testing This sequence change affects a donor splice site in intron 1 of the TMEM216 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 TMEM216 are known to be pathogenic (PMID: 20512146). This variant is present in population databases (no rsID available, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with TMEM216-related conditions. ClinVar contains an entry for this variant (Variation ID: 371740). 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.
Fulgent Genetics, Fulgent Genetics RCV002502435 SCV002813927 likely pathogenic Joubert syndrome 2; Meckel syndrome, type 2 2022-03-04 criteria provided, single submitter clinical testing
Baylor Genetics RCV000411402 SCV005054316 likely pathogenic Joubert syndrome 2 2024-03-30 criteria provided, single submitter clinical testing

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