ClinVar Miner

Submissions for variant NM_001173990.3(TMEM216):c.7C>A (p.Pro3Thr)

dbSNP: rs1554972409
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000523528 SCV000621494 uncertain significance not provided 2017-10-12 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the TMEM216 gene. The P3T variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The P3T variant is not observed in large population cohorts (Lek et al., 2016). The P3T variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. This substitution occurs at a position that is conserved across species; and in silico analysis predicts this variant is probably damaging to the protein structure/function. Based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV001858034 SCV002257850 uncertain significance Familial aplasia of the vermis 2022-06-27 criteria provided, single submitter clinical testing This sequence change replaces proline, which is neutral and non-polar, with threonine, which is neutral and polar, at codon 3 of the TMEM216 protein (p.Pro3Thr). This variant is not present in population databases (gnomAD no frequency). 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: 452672). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Fulgent Genetics, Fulgent Genetics RCV005049587 SCV005683831 uncertain significance Joubert syndrome 2; Meckel syndrome, type 2 2024-05-18 criteria provided, single submitter clinical testing
Natera, Inc. RCV001275256 SCV001460229 uncertain significance Joubert syndrome 2 2020-09-16 no assertion criteria provided clinical testing

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