ClinVar Miner

Submissions for variant NM_001301365.1(LYST):c.5719A>G (p.Ile1907Val)

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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000681453 SCV000819784 uncertain significance Chédiak-Higashi syndrome 2020-09-28 criteria provided, single submitter clinical testing This sequence change replaces isoleucine with valine at codon 1907 of the LYST protein (p.Ile1907Val). The isoleucine residue is weakly conserved and there is a small physicochemical difference between isoleucine and valine. This variant is present in population databases (rs370441301, ExAC 0.009%). This variant has been observed in individual(s) with Chediak Higashi-syndrome (PMID: 31906877). ClinVar contains an entry for this variant (Variation ID: 561992). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: Tolerated; PolyPhen-2: Benign; Align-GVGD: Class C0. The valine amino acid residue is found in multiple mammalian species, suggesting that this missense change does not adversely affect protein function. These predictions have not been confirmed by published functional studies and their clinical significance is uncertain. 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.
Fan Lab,Zhengzhou University RCV000681453 SCV000804754 likely pathogenic Chédiak-Higashi syndrome 2018-04-23 no assertion criteria provided clinical testing This missense variant was inherited from the patient's mother (c.5719A>G, p.Ile1907Val). Typical clinical features of Chediak-Higashi Syndrome were observed in the patient, including decreased pigmentation of skin and hair, neutropenia, peculiar malignant lymphoma. Functional prediction showed loss of protein function caused by the peptide change.

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