ClinVar Miner

Submissions for variant NM_199242.3(UNC13D):c.2588G>A (p.Gly863Asp)

gnomAD frequency: 0.00013  dbSNP: rs140184929
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Soonchunhyang University Bucheon Hospital, Soonchunhyang University Medical Center RCV000490335 SCV000267550 uncertain significance Familial hemophagocytic lymphohistiocytosis 3 2016-03-18 criteria provided, single submitter reference population
Invitae RCV000490335 SCV001047674 likely benign Familial hemophagocytic lymphohistiocytosis 3 2024-01-29 criteria provided, single submitter clinical testing
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002262801 SCV002543163 uncertain significance Autoinflammatory syndrome 2016-12-12 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV002509306 SCV002819883 uncertain significance not specified 2022-12-28 criteria provided, single submitter clinical testing Variant summary: UNC13D c.2588G>A (p.Gly863Asp) results in a non-conservative amino acid change located in the MUN domain (IPR010439) of the encoded protein sequence. Five of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0003 in 250652 control chromosomes, predominantly at a frequency of 0.0036 within the East Asian subpopulation in the gnomAD database. The observed variant frequency within East Asian control individuals in the gnomAD database is approximately 1.3 fold of the estimated maximal expected allele frequency for a pathogenic variant in UNC13D causing Familial Hemophagocytic Lymphohistiocytosis phenotype (0.0027), strongly suggesting that the variant is a benign polymorphism found primarily in populations of East Asian origin. c.2588G>A has been reported in the literature as homozygous and/or presumably compound heterozygous genotypes predominantly in East Asian individuals affected with features resembling or with a reported diagnosis of Familial Hemophagocytic Lymphohistiocytosis (example, PMID: 32638196, 29113160, 29415165, 30899265, 32375849). These data indicate that the variant may be associated with disease. To our knowledge, no experimental evidence demonstrating an impact on protein function has been reported. Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation (VUS, n=2, LB, n=1). Based on the evidence outlined above, the variant was classified as VUS-possibly benign.

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