ClinVar Miner

Submissions for variant NM_030962.3(SBF2):c.5017_5019GAA[1] (p.Glu1674del) (rs572571832)

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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000198474 SCV000255137 uncertain significance Charcot-Marie-Tooth disease type 4 2019-12-27 criteria provided, single submitter clinical testing This sequence change deletes 3 nucleotides from exon 36 of the SBF2 mRNA (c.5020_5022delGAA). This leads to the deletion of 1 amino acid residue in the SBF2 protein (p.Glu1674del) but otherwise preserves the integrity of the reading frame. This variant is present in population databases (rs572571832, ExAC 0.2%), including at least one homozygous individual. This variant has been reported in two individuals affected with Charcot-Marie-Tooth disease (PMID: 25025039). ClinVar contains an entry for this variant (Variation ID: 216777). Experimental studies and prediction algorithms are not available for this variant, and the functional significance of the deleted amino acid is currently unknown. In summary, this variant is a rare in-frame deletion with uncertain impact on protein function. Because it is found in the population at an appreciable frequency, this variant is not anticipated to cause disease. However, the available evidence is currently insufficient to prove that conclusively. Therefore, it has been classified as a Variant of Uncertain Significance.
GeneDx RCV000236239 SCV000293045 uncertain significance not provided 2017-10-19 criteria provided, single submitter clinical testing The c.5020_5022delGAA variant has been reported previously in the heterozygous state in an individual with CMT2, who also had a variant in a different geneloosely associated with neuropathy (Hoyer at al., 2014). No conclusions regarding the pathogenicity of thec.5020_5022delGAA variant can be made from the Hoyer et al. report. The c.5020_5022delGAA variant is observed in 45/25790 (0.2%) alleles from individuals of European background, including one homozygous individual, in largepopulation cohorts (Lek et al., 2016). This variant results in an in-frame deletion of a single Glutamic acid residue, denoted p.E1674del. However, this deletion occurs at a position that is not conserved. Based on the currentlyavailable information, it is unclear whether the c.5020_5022delGAA variant is a pathogenic variant or a rare benign variant.
Athena Diagnostics Inc RCV000236239 SCV001145368 uncertain significance not provided 2019-06-17 criteria provided, single submitter clinical testing
ARUP Laboratories, Molecular Genetics and Genomics,ARUP Laboratories RCV001000984 SCV001158086 likely benign Charcot-Marie-Tooth disease, type 4B2 2018-08-05 criteria provided, single submitter clinical testing
Molecular Genetics Laboratory,London Health Sciences Centre RCV001172790 SCV001335859 uncertain significance Charcot-Marie-Tooth disease criteria provided, single submitter clinical testing

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