ClinVar Miner

Submissions for variant NM_003193.5(TBCE):c.464T>A (p.Ile155Asn)

dbSNP: rs780472451
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001569082 SCV001793071 pathogenic not provided 2021-02-17 criteria provided, single submitter clinical testing Not observed at a significant frequency in GeneDX; 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: 27666369)
Revvity Omics, Revvity RCV001569082 SCV002016851 likely pathogenic not provided 2021-05-12 criteria provided, single submitter clinical testing
Labcorp Genetics (formerly Invitae), Labcorp RCV001569082 SCV004292995 pathogenic not provided 2024-02-24 criteria provided, single submitter clinical testing This sequence change replaces isoleucine, which is neutral and non-polar, with asparagine, which is neutral and polar, at codon 155 of the TBCE protein (p.Ile155Asn). This variant is present in population databases (rs780472451, gnomAD 0.0009%). This missense change has been observed in individual(s) with clinical features of progressive encephalopathy with amyotrophy and optic atrophy (PMID: 27666369). 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: 372201). 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 expected to disrupt TBCE protein function with a positive predictive value of 80%. For these reasons, this variant has been classified as Pathogenic.
OMIM RCV000412509 SCV000490274 pathogenic Encephalopathy, progressive, with amyotrophy and optic atrophy 2016-11-29 no assertion criteria provided literature only

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