ClinVar Miner

Submissions for variant NM_001130438.3(SPTAN1):c.5545C>T (p.Arg1849Trp)

gnomAD frequency: 0.00006  dbSNP: rs148402616
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000189551 SCV000243194 likely benign not provided 2020-12-31 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 31873310)
Labcorp Genetics (formerly Invitae), Labcorp RCV000464908 SCV000553140 uncertain significance Early infantile epileptic encephalopathy with suppression bursts 2023-11-18 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with tryptophan, which is neutral and slightly polar, at codon 1849 of the SPTAN1 protein (p.Arg1849Trp). This variant is present in population databases (rs148402616, gnomAD 0.02%). This variant has not been reported in the literature in individuals affected with SPTAN1-related conditions. ClinVar contains an entry for this variant (Variation ID: 207376). 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 SPTAN1 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.
Genome-Nilou Lab RCV001808528 SCV002056601 likely benign Developmental and epileptic encephalopathy, 5 2021-07-15 criteria provided, single submitter clinical testing
Ambry Genetics RCV002345681 SCV002648150 uncertain significance Inborn genetic diseases 2018-06-12 criteria provided, single submitter clinical testing The p.R1849W variant (also known as c.5545C>T), located in coding exon 42 of the SPTAN1 gene, results from a C to T substitution at nucleotide position 5545. The arginine at codon 1849 is replaced by tryptophan, an amino acid with dissimilar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.

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