ClinVar Miner

Submissions for variant NM_001301365.1(LYST):c.3311G>A (p.Arg1104Gln) (rs148299757)

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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000520552 SCV000618976 uncertain significance not provided 2017-07-19 criteria provided, single submitter clinical testing The R1104Q variant in the LYST gene has not been reported previously as a pathogenic variant, nor as a benign variant, to our knowledge. The R1104Q variant is observed in 35/66666 (0.05%) alleles from individuals of non-Finnish European background, in the ExAC dataset (Lek et al., 2016). The R1104Q variant is a semi-conservative amino acid substitution, which may impact secondary protein structure as these residues differ in some properties. This substitution occurs at a position that is conserved across species. In silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. We interpret R1104Q as a variant of uncertain significance.
Invitae RCV000629208 SCV000750126 uncertain significance Chédiak-Higashi syndrome 2017-12-04 criteria provided, single submitter clinical testing This sequence change replaces arginine with glutamine at codon 1104 of the LYST protein (p.Arg1104Gln). The arginine residue is moderately conserved and there is a small physicochemical difference between arginine and glutamine. This variant is present in population databases (rs148299757, ExAC 0.05%). This variant has not been reported in the literature in individuals with LYST-related disease. Algorithms developed to predict the effect of missense changes on protein structure and function do not agree on the potential impact of this missense change (SIFT: "Tolerated"; 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.
Fulgent Genetics,Fulgent Genetics RCV000629208 SCV000896289 uncertain significance Chédiak-Higashi syndrome 2018-10-31 criteria provided, single submitter clinical testing
Illumina Clinical Services Laboratory,Illumina RCV000629208 SCV001258775 uncertain significance Chédiak-Higashi syndrome 2017-04-28 criteria provided, single submitter clinical testing This variant was observed as part of a predisposition screen in an ostensibly healthy population. A literature search was performed for the gene, cDNA change, and amino acid change (where applicable). No publications were found based on this search. Allele frequency data from public databases did not allow this variant to be ruled in or out of causing disease. Therefore, this variant is classified as a variant of unknown significance.

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