ClinVar Miner

Submissions for variant NM_019892.6(INPP5E):c.1162G>T (p.Val388Leu)

gnomAD frequency: 0.00003  dbSNP: rs863225201
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
UW Hindbrain Malformation Research Program, University of Washington RCV000201647 SCV000256424 pathogenic Familial aplasia of the vermis 2015-02-23 criteria provided, single submitter research
GeneDx RCV001753604 SCV002007369 uncertain significance not provided 2019-12-30 criteria provided, single submitter clinical testing Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports that this variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 26092869)
Invitae RCV000201647 SCV003013735 uncertain significance Familial aplasia of the vermis 2022-04-16 criteria provided, single submitter clinical testing 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. Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. This sequence change replaces valine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 388 of the INPP5E protein (p.Val388Leu). This variant is present in population databases (no rsID available, gnomAD 0.002%). This missense change has been observed in individual(s) with Joubert syndrome and related disorders and/or retinitis pigmentosa (PMID: 26092869; Invitae). In at least one individual the data is consistent with being in trans (on the opposite chromosome) from a pathogenic variant. ClinVar contains an entry for this variant (Variation ID: 217663).

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