ClinVar Miner

Submissions for variant NM_000081.4(LYST):c.4322_4325del (p.Glu1441fs)

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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Diagnostics Services (NGS), CSIR - Centre For Cellular And Molecular Biology RCV001527403 SCV001738396 pathogenic Chédiak-Higashi syndrome 2021-05-13 criteria provided, single submitter clinical testing The c.4322_4325del variant is not present in publicly available population databases like1000 Genomes,Exome Variant Server (EVS), Exome Aggregation Consortium (ExAC), Genome Aggregation Database (gnomAD) or in the Indian Exome Database [Kausthubham et al. Hum Mutat, 2021] and our in-house exome database. The variant has never been previosuly reported to ClinVar, Human Genome Mutation Database (HGMD) or OMIM databases in affected individuals. In-silico pathogenicity prediction programs like MutationTaster2, CADD, Varsome etc. predicted this variant to be likely disease causing.The variant causes frameshift at 1441 amino acid of the wild-type transcript,leading to a premature stop codon at the 1452 amino acid of the altered transcript, resulting either in a truncated protein or nonsense mediated decay of the mRNA. The variant qualifies all the criteria of ACMG guidelines to be classified as pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV001527403 SCV004311577 pathogenic Chédiak-Higashi syndrome 2023-12-30 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Glu1441Valfs*12) in the LYST gene. It is expected to result in an absent or disrupted protein product. Loss-of-function variants in LYST are known to be pathogenic (PMID: 9215679, 11857544). This variant is not present in population databases (gnomAD no frequency). This variant has not been reported in the literature in individuals affected with LYST-related conditions. For these reasons, this variant has been classified as Pathogenic.
Fulgent Genetics, Fulgent Genetics RCV001527403 SCV005646625 pathogenic Chédiak-Higashi syndrome 2024-06-22 criteria provided, single submitter clinical testing

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