ClinVar Miner

Submissions for variant NM_020320.5(RARS2):c.1679G>A (p.Arg560His)

gnomAD frequency: 0.00003  dbSNP: rs756502974
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000197761 SCV000252174 likely pathogenic not provided 2024-06-26 criteria provided, single submitter clinical testing In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 31665838, 33120460, 31618753, 35068129, 35468344)
Fulgent Genetics, Fulgent Genetics RCV000765895 SCV000897315 uncertain significance Pontocerebellar hypoplasia type 6 2018-10-31 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV000197761 SCV003269650 pathogenic not provided 2023-11-20 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 560 of the RARS2 protein (p.Arg560His). This variant is present in population databases (rs756502974, gnomAD 0.02%). This missense change has been observed in individual(s) with clinical features of RARS2-related conditions (PMID: 31618753, 31665838, 35068129; 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: 215071). 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 RARS2 protein function with a negative predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
Revvity Omics, Revvity RCV000765895 SCV003813858 uncertain significance Pontocerebellar hypoplasia type 6 2023-11-02 criteria provided, single submitter clinical testing
Baylor Genetics RCV000765895 SCV004206137 likely pathogenic Pontocerebellar hypoplasia type 6 2024-03-27 criteria provided, single submitter clinical testing

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