ClinVar Miner

Submissions for variant NM_001371279.1(REEP1):c.844G>A (p.Glu282Lys)

gnomAD frequency: 0.00041  dbSNP: rs189652973
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Total submissions: 7
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000415754 SCV000252191 benign not provided 2020-10-14 criteria provided, single submitter clinical testing This variant is associated with the following publications: (PMID: 16826527)
Illumina Laboratory Services, Illumina RCV000986787 SCV000432410 likely benign Hereditary spastic paraplegia 31 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 determine this variant is unlikely to cause disease. Therefore, this variant is classified as likely benign.
CeGaT Center for Human Genetics Tuebingen RCV000415754 SCV000493298 likely benign not provided 2022-06-01 criteria provided, single submitter clinical testing REEP1: PP3, BS1
Invitae RCV000986787 SCV001000638 likely benign Hereditary spastic paraplegia 31 2023-08-17 criteria provided, single submitter clinical testing
Mendelics RCV000986787 SCV001135911 uncertain significance Hereditary spastic paraplegia 31 2019-05-28 criteria provided, single submitter clinical testing
Ambry Genetics RCV003165456 SCV003865421 likely benign Inborn genetic diseases 2023-02-20 criteria provided, single submitter clinical testing This alteration is classified as likely benign based on a combination of the following: population frequency, intact protein function, lack of segregation with disease, co-occurrence, RNA analysis, in silico models, amino acid conservation, lack of disease association in case-control studies, and/or the mechanism of disease or impacted region is inconsistent with a known cause of pathogenicity.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV000415754 SCV004562123 uncertain significance not provided 2023-11-17 criteria provided, single submitter clinical testing The REEP1 c.*50G>A variant (rs189652973), also known as c.606+50G>A, is reported in the literature in an individual affected with spastic paraplegia with a family history of disease (Zuchner 2006). This variant was also observed in an unaffected relative of an affected individual, although no neurological examination information was provided (Zuchner 2006). The c.*50G>A variant is reported in ClinVar (Variation ID: 215087), and is observed in the non-Finnish European population with an allele frequency of 0.08% (101/126844 alleles) in the Genome Aggregation Database (v2.1.1). This variant occurs in the 3' untranslated region at a nucleotide that is moderately conserved and is predicted to alter a microRNA binding site and impact protein levels (Zuchner 2006), however this was not verified with functional studies. Given the lack of clinical and functional data, the significance of the c.*50G>A variant is uncertain at this time. References: Zuchner S et al. Mutations in the novel mitochondrial protein REEP1 cause hereditary spastic paraplegia type 31. Am J Hum Genet. 2006 Aug;79(2):365-9. PMID: 16826527.

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