ClinVar Miner

Submissions for variant NM_001165963.4(SCN1A):c.1790C>A (p.Thr597Asn) (rs149715258)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000725552 SCV000242510 uncertain significance not provided 2018-08-09 criteria provided, single submitter clinical testing c.1790 C>A in exon 11 in the SCN1A gene (NM_001165963.1). The T597N variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. The T597N variant was not observed at any significant frequency in approximately 6,500 individuals of European and African American ancestry by the NHLBI Exome Sequencing Project. The T597N variant is a conservative amino acid substitution that alters a position in the intracellular loop between the first and second transmembrane domains. This substitution occurs at a position that is well conserved through mammals. In silico analysis predicts this variant is probably damaging to protein structure/function. We interpret T597N as a variant of unknown significance. This variant has been observed to be maternally inherited.The variant is found in EPILEPSY panel(s).
EGL Genetic Diagnostics, Eurofins Clinical Diagnostics RCV000725552 SCV000337710 uncertain significance not provided 2016-12-27 criteria provided, single submitter clinical testing
Invitae RCV000691458 SCV000819237 uncertain significance Early infantile epileptic encephalopathy with suppression bursts 2020-10-07 criteria provided, single submitter clinical testing This sequence change replaces threonine with asparagine at codon 597 of the SCN1A protein (p.Thr597Asn). The threonine residue is highly conserved and there is a small physicochemical difference between threonine and asparagine. This variant is present in population databases (rs149715258, ExAC 0.05%). This variant has not been reported in the literature in individuals with SCN1A-related conditions. ClinVar contains an entry for this variant (Variation ID: 206774). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: Deleterious; PolyPhen-2: Probably Damaging; Align-GVGD: Class C0). 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.
Athena Diagnostics Inc RCV000725552 SCV001475466 likely benign not provided 2020-05-29 criteria provided, single submitter clinical testing

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