ClinVar Miner

Submissions for variant NM_006579.3(EBP):c.440G>A (p.Arg147His)

dbSNP: rs28935174
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Genetic Services Laboratory, University of Chicago RCV000012247 SCV000193078 pathogenic Chondrodysplasia punctata 2 X-linked dominant 2013-02-08 criteria provided, single submitter clinical testing
Kasturba Medical College, Manipal, Kasturba Medical College, Manipal, Manipal Academy of Higher Education, Manipal, India RCV000012247 SCV002053793 pathogenic Chondrodysplasia punctata 2 X-linked dominant criteria provided, single submitter clinical testing
3billion RCV000012247 SCV002521099 pathogenic Chondrodysplasia punctata 2 X-linked dominant 2022-05-22 criteria provided, single submitter clinical testing The variant is observed at an extremely low frequency in the gnomAD v2.1.1 dataset (total allele frequency: <0.001%). In silico tool predictions suggest damaging effect of the variant on gene or gene product (REVEL: 0.95; 3Cnet: 0.96). Same nucleotide change resulting in same amino acid change has been previously reported as pathogenic/likely pathogenic with strong evidence (ClinVar ID: VCV000011492). The variant has been observed in multiple (>3) similarly affected unrelated individuals (PMID:10942423, 12483303, 1355069, 24726177, 7677157). Different missense changes at the same codon (p.Arg147Cys, p.Arg147Gly) have been reported to be associated with EBP related disorder (ClinVar ID: VCV000265110 / PMID: 11493318, 26075358). Therefore, this variant is classified as pathogenic according to the recommendation of ACMG/AMP guideline.
GeneDx RCV003329229 SCV004036915 pathogenic not provided 2023-09-22 criteria provided, single submitter clinical testing Female patient witth this variant showed accumulation of 8(9)-cholesterol and 8-dehydrocholesterol by GC/MS, suggestive of a defect of sterol-delta8-isomerase, and subsequent functional studies showed that this variant partially impairs enzyme activity (Braverman et al., 1999); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; This variant is associated with the following publications: (PMID: 11982764, 22121851, 10391219, 7677157, 1355069, 11493318, 25814754, 22229330, 12824059, 12509714, 27276700, 14632217, 12483303, 11038443, 17625999, 19416264, 31299979, 30608402, 10942423, 34450268, SunMA2023[Article])
OMIM RCV000012247 SCV000032481 pathogenic Chondrodysplasia punctata 2 X-linked dominant 2003-01-01 no assertion criteria provided literature only

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