ClinVar Miner

Submissions for variant NM_006517.5(SLC16A2):c.1204A>T (p.Met402Leu)

gnomAD frequency: 0.00003  dbSNP: rs773263889
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV001568128 SCV001791947 likely pathogenic not provided 2020-08-06 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; Has not been previously published as pathogenic or benign to our knowledge
Labcorp Genetics (formerly Invitae), Labcorp RCV002569042 SCV003520508 uncertain significance Spastic paraplegia 2024-03-05 criteria provided, single submitter clinical testing This sequence change replaces methionine, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 402 of the SLC16A2 protein (p.Met402Leu). This variant is present in population databases (rs773263889, gnomAD 0.001%). This variant has not been reported in the literature in individuals affected with SLC16A2-related conditions. ClinVar contains an entry for this variant (Variation ID: 1202449). 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) has been performed at Invitae for this missense variant, however the output from this modeling did not meet the statistical confidence thresholds required to predict the impact of this variant on SLC16A2 protein function. 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.
Ambry Genetics RCV003346618 SCV004066970 uncertain significance Inborn genetic diseases 2023-08-20 criteria provided, single submitter clinical testing The c.1426A>T (p.M476L) alteration is located in exon 5 (coding exon 5) of the SLC16A2 gene. This alteration results from a A to T substitution at nucleotide position 1426, causing the methionine (M) at amino acid position 476 to be replaced by a leucine (L). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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