ClinVar Miner

Submissions for variant NM_005055.5(RAPSN):c.484G>A (p.Glu162Lys)

gnomAD frequency: 0.00001  dbSNP: rs121909255
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001231489 SCV001404015 pathogenic Fetal akinesia deformation sequence 1; Congenital myasthenic syndrome 11 2023-11-24 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 162 of the RAPSN protein (p.Glu162Lys). This variant is present in population databases (rs121909255, gnomAD 0.02%). This missense change has been observed in individual(s) with fetal akinesia deformation sequence, arthrogryposis multiplex congenita, and congenital myasthenic syndrome (PMID: 17594401, 26147564, 26910802, 28495245). 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: 8056). Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is not expected to disrupt RAPSN protein function with a negative predictive value of 80%. Experimental studies have shown that this missense change affects RAPSN function (PMID: 17594401). For these reasons, this variant has been classified as Pathogenic.
Baylor Genetics RCV003460443 SCV004206119 pathogenic Fetal akinesia deformation sequence 2 2024-03-01 criteria provided, single submitter clinical testing
OMIM RCV000008522 SCV000028730 pathogenic Congenital myasthenic syndrome 11 2007-07-01 no assertion criteria provided literature only

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