ClinVar Miner

Submissions for variant NM_003764.4(STX11):c.799G>A (p.Val267Met)

gnomAD frequency: 0.00545  dbSNP: rs45574234
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Total submissions: 8
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
PreventionGenetics, part of Exact Sciences RCV000252800 SCV000309826 likely benign not specified criteria provided, single submitter clinical testing
Invitae RCV000551253 SCV000644901 benign Familial hemophagocytic lymphohistiocytosis 4 2024-01-31 criteria provided, single submitter clinical testing
Illumina Laboratory Services, Illumina RCV000551253 SCV001315059 benign Familial hemophagocytic lymphohistiocytosis 4 2017-04-27 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). Publications were found based on this search. The evidence from the literature, in combination with allele frequency data from public databases where available, was sufficient to rule this variant out of causing disease. Therefore, this variant is classified as benign.
CeGaT Center for Human Genetics Tuebingen RCV001172178 SCV001335156 likely benign not provided 2023-10-01 criteria provided, single submitter clinical testing STX11: BP4, BS2
GeneDx RCV001172178 SCV001815012 likely benign not provided 2020-07-28 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 24524345, 30290665, 28399723)
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000252800 SCV002500166 likely benign not specified 2022-03-07 criteria provided, single submitter clinical testing Variant summary: STX11 c.799G>A (p.Val267Met) results in a conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. The variant allele was found at a frequency of 0.0053 in 247122 control chromosomes in the gnomAD database, including 6 homozygotes. The observed variant frequency is approximately 10 fold of the estimated maximal expected allele frequency for a pathogenic variant in STX11 causing Familial Hemophagocytic Lymphohistiocytosis phenotype (0.0005), strongly suggesting that the variant is benign. Four clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 and classified the variant as benign (n=2) and likely benign (n=2). Based on the evidence outlined above, the variant was classified as likely benign.
Genome Diagnostics Laboratory, The Hospital for Sick Children RCV002262884 SCV002542971 likely benign Autoinflammatory syndrome 2021-08-17 criteria provided, single submitter clinical testing
Fulgent Genetics, Fulgent Genetics RCV000551253 SCV002804267 likely benign Familial hemophagocytic lymphohistiocytosis 4 2022-05-25 criteria provided, single submitter clinical testing

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