ClinVar Miner

Submissions for variant NM_000414.4(HSD17B4):c.1210-11C>G

gnomAD frequency: 0.00001  dbSNP: rs779466683
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000676080 SCV000859249 uncertain significance not provided 2018-01-22 criteria provided, single submitter clinical testing
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV003317335 SCV004020604 likely pathogenic Bifunctional peroxisomal enzyme deficiency 2023-06-12 criteria provided, single submitter clinical testing Variant summary: HSD17B4 c.1210-11C>G alters a non-conserved nucleotide located close to a canonical splice site and therefore could affect mRNA splicing, leading to a significantly altered protein sequence. Several computational tools predict a significant impact on normal splicing: Two predict the variant abolishes a 3' acceptor site. One predicts the variant creates a 3' acceptor site. At least one publication reports experimental evidence that this variant affects mRNA splicing resulting in exon 14 skipping, predicted to cause a frameshift resulting in premature termination of three amino acids downstream (p.Val404Glufs*3) (example: Werner_2022). The variant allele was found at a frequency of 1.2e-05 in 250824 control chromosomes. c.1210-11C>G has been reported in the literature in compound heterozygous individuals affected with D-Bifunctional Protein Deficiency (examples: Meng_2017, Werner_2022). The following publications have been ascertained in the context of this evaluation (PMID: 28973083, 34623748). Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation, classifying the variant as likely pathogenic (n=1), uncertain significance (n=1), or likely benign (n=1). Based on the evidence outlined above, the variant was classified as likely pathogenic.
Baylor Genetics RCV003317335 SCV004192380 likely pathogenic Bifunctional peroxisomal enzyme deficiency 2023-09-22 criteria provided, single submitter clinical testing
Mayo Clinic Laboratories, Mayo Clinic RCV000676080 SCV000801816 likely benign not provided 2016-10-14 no assertion criteria provided clinical testing
Elsea Laboratory, Baylor College of Medicine RCV001250119 SCV001424305 likely pathogenic Bifunctional peroxisomal enzyme deficiency; Perrault syndrome 1 2020-04-01 no assertion criteria provided clinical testing

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