ClinVar Miner

Submissions for variant NR_003051.3(RMRP):n.-22_-4dup

gnomAD frequency: 0.00001  dbSNP: rs1554651427
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Counsyl RCV000671238 SCV000796193 likely pathogenic Metaphyseal chondrodysplasia, McKusick type 2017-12-07 criteria provided, single submitter clinical testing
Invitae RCV001242503 SCV001415595 pathogenic Anauxetic dysplasia 2023-10-20 criteria provided, single submitter clinical testing This variant occurs in the RMRP gene, which encodes an RNA molecule that does not result in a protein product. This variant is present in population databases (no rsID available, gnomAD 0.002%). While this particular variant has not been reported in the literature, it is located in the promoter region between the TATA box and the transcription initiation site, and other insertions and duplications immediately upstream of the coding sequence have been reported in individuals affected with cartilage-hair hypoplasia-anauxetic dysplasia (CHH-AD) spectrum disorders (PMID: 16244706, 11207361, 12107819). ClinVar contains an entry for this variant (Variation ID: 555417). While functional studies for this variant have not been reported, experimental analyses using patient derived cells, as well as in vitro transfection studies, have shown that promoter insertions result in silencing of RMRP transcription and reduced expression of the gene product (PMID: 11207361, 16254002). For these reasons, this variant has been classified as Pathogenic.
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000671238 SCV002600804 likely pathogenic Metaphyseal chondrodysplasia, McKusick type 2022-10-28 criteria provided, single submitter clinical testing Variant summary: RMRP n.-22_-4dup19 is located in the promoter region of the RMRP gene. Other insertions or duplications in the promoter region of RMRP have been classified as pathogenic (internally and in ClinVar). The variant was absent in 127922 control chromosomes (gnomAD). The available data on variant occurrences in the general population are insufficient to allow any conclusion about variant significance. To our knowledge, no occurrence of n.-22_-4dup19 in individuals affected with Cartilage-Hair Hypoplasia and no experimental evidence demonstrating its impact on protein function have been reported. Many other insertions or duplications in the promoter region of RMRP have been reported in affected individuals in the literature (e.g. PMIDs: 21956908, 21396580) and have been demonstrated through functional studies to lead to reduced RMRP transcription (e.g. PMIDs: 11207361, 16254002). Three clinical diagnostic laboratories have submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evaluation. All laboratories classified the variant as likely pathogenic. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Natera, Inc. RCV000671238 SCV002075578 likely pathogenic Metaphyseal chondrodysplasia, McKusick type 2021-10-16 no assertion criteria provided clinical testing

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