ClinVar Miner

Submissions for variant NM_177550.5(SLC13A5):c.338C>T (p.Thr113Met)

gnomAD frequency: 0.00004  dbSNP: rs759069275
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000521962 SCV000620614 uncertain significance not provided 2018-10-15 criteria provided, single submitter clinical testing A variant of uncertain significance has been identified in the SLC13A5 gene. The T113M variant has not been published as a pathogenic variant, nor has it been reported as a benign variant to our knowledge. The T113M variant is observed in 9/30668 (0.03%) alleles from individuals of South Asian background (Lek et al., 2016). In-silico analyses, including protein predictors and evolutionary conservation, support that this variant does not alter protein structure/function. However, the T113M variant is a non-conservative amino acid substitution, which is likely to impact secondary protein structure as these residues differ in polarity, charge, size and/or other properties. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic variant or a rare benign variant.
Labcorp Genetics (formerly Invitae), Labcorp RCV000687384 SCV000814948 uncertain significance Developmental and epileptic encephalopathy, 25 2024-12-02 criteria provided, single submitter clinical testing This sequence change replaces threonine, which is neutral and polar, with methionine, which is neutral and non-polar, at codon 113 of the SLC13A5 protein (p.Thr113Met). This variant is present in population databases (rs759069275, gnomAD 0.03%). This variant has not been reported in the literature in individuals affected with SLC13A5-related conditions. ClinVar contains an entry for this variant (Variation ID: 451860). 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 SLC13A5 protein function with a negative predictive value of 80%. 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.
Genome-Nilou Lab RCV000687384 SCV002055679 uncertain significance Developmental and epileptic encephalopathy, 25 2021-07-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV002528257 SCV003548529 uncertain significance Inborn genetic diseases 2024-08-05 criteria provided, single submitter clinical testing The c.338C>T (p.T113M) alteration is located in exon 3 (coding exon 3) of the SLC13A5 gene. This alteration results from a C to T substitution at nucleotide position 338, causing the threonine (T) at amino acid position 113 to be replaced by a methionine (M). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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