ClinVar Miner

Submissions for variant NM_005097.4(LGI1):c.310G>A (p.Asp104Asn)

gnomAD frequency: 0.00005  dbSNP: rs145675377
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV002230816 SCV000548368 uncertain significance Autosomal dominant epilepsy with auditory features 2024-01-15 criteria provided, single submitter clinical testing This sequence change replaces aspartic acid, which is acidic and polar, with asparagine, which is neutral and polar, at codon 104 of the LGI1 protein (p.Asp104Asn). This variant is present in population databases (rs145675377, gnomAD 0.01%). This variant has not been reported in the literature in individuals affected with LGI1-related conditions. ClinVar contains an entry for this variant (Variation ID: 408589). 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 not expected to disrupt LGI1 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.
Fulgent Genetics, Fulgent Genetics RCV000458976 SCV000896091 uncertain significance Epilepsy, familial temporal lobe, 1 2018-10-31 criteria provided, single submitter clinical testing
New York Genome Center RCV000458976 SCV002548940 uncertain significance Epilepsy, familial temporal lobe, 1 2021-08-26 criteria provided, single submitter clinical testing
Ambry Genetics RCV002323715 SCV002608443 likely benign Inborn genetic diseases 2018-02-14 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.

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