ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.4688G>A (p.Arg1563His)

dbSNP: rs80338657
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV000055735 SCV003524127 uncertain significance Chédiak-Higashi syndrome 2022-04-20 criteria provided, single submitter clinical testing This sequence change replaces arginine, which is basic and polar, with histidine, which is basic and polar, at codon 1563 of the LYST protein (p.Arg1563His). This variant also falls at the last nucleotide of exon 13, which is part of the consensus splice site for this exon. This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with Chediak-Higashi syndrome (PMID: 22883044). ClinVar contains an entry for this variant (Variation ID: 3816). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. Variants that disrupt the consensus splice site are a relatively common cause of aberrant splicing (PMID: 17576681, 9536098). Algorithms developed to predict the effect of sequence changes on RNA splicing suggest that this variant may disrupt the consensus splice site. 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.
OMIM RCV000004020 SCV000024186 pathogenic Chediak-Higashi syndrome, adult type 2002-02-15 no assertion criteria provided literature only
GeneReviews RCV000055735 SCV000086673 not provided Chédiak-Higashi syndrome no assertion provided literature only

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