ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.5707G>A (p.Asp1903Asn)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001224228 SCV001396412 uncertain significance Chédiak-Higashi syndrome 2024-10-07 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 1903 of the LYST protein (p.Asp1903Asn). This variant is present in population databases (no rsID available, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with LYST-related conditions. ClinVar contains an entry for this variant (Variation ID: 952170). 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 LYST 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.
Ambry Genetics RCV004986970 SCV005619005 uncertain significance Inborn genetic diseases 2024-12-04 criteria provided, single submitter clinical testing The c.5707G>A (p.D1903N) alteration is located in exon 19 (coding exon 17) of the LYST gene. This alteration results from a G to A substitution at nucleotide position 5707, causing the aspartic acid (D) at amino acid position 1903 to be replaced by an asparagine (N). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.

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