ClinVar Miner

Submissions for variant NM_015340.4(LARS2):c.880G>A (p.Glu294Lys)

gnomAD frequency: 0.00001  dbSNP: rs749627411
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001587314 SCV001826221 likely pathogenic not provided 2024-03-19 criteria provided, single submitter clinical testing Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant does not alter protein structure/function; This variant is associated with the following publications: (PMID: 29205794, 30737337, 32369273, 32767731, 28000701, 35750896, 35982127, 36515421)
Labcorp Genetics (formerly Invitae), Labcorp RCV001587314 SCV005834408 pathogenic not provided 2024-12-24 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 294 of the LARS2 protein (p.Glu294Lys). This variant is present in population databases (rs749627411, gnomAD 0.003%). This missense change has been observed in individuals with clinical features of Perrault syndrome or deafness (PMID: 29205794, 30737337, 32767731, 35982127). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 992952). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is not expected to disrupt LARS2 protein function with a negative predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV001283750 SCV001469096 pathogenic Perrault syndrome 4 2021-01-15 no assertion criteria provided literature only
GeneReviews RCV002542964 SCV003525953 not provided Perrault syndrome no assertion provided literature only

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