ClinVar Miner

Submissions for variant NM_024580.6(EFL1):c.787C>G (p.Leu263Val)

gnomAD frequency: 0.00001  dbSNP: rs751006899
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001957197 SCV002199318 uncertain significance not provided 2022-07-05 criteria provided, single submitter clinical testing This sequence change replaces leucine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 263 of the EFL1 protein (p.Leu263Val). This variant is present in population databases (rs751006899, gnomAD 0.0009%). This variant has not been reported in the literature in individuals affected with EFL1-related conditions. ClinVar contains an entry for this variant (Variation ID: 1424546). Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Deleterious"; PolyPhen-2: "Not Available"; Align-GVGD: "Class C0"). In summary, the available evidence is currently insufficient to determine the role of this variant in disease. Therefore, it has been classified as a Variant of Uncertain Significance.
Victorian Clinical Genetics Services, Murdoch Childrens Research Institute RCV002471187 SCV002767103 uncertain significance Shwachman-Diamond syndrome 2 2020-05-21 criteria provided, single submitter clinical testing A heterozygous missense variant was identified, NM_024580.5(EFL1):c.787C>G in exon 8 of 20 of the EFL1gene (NB: This variant is non-coding in one alternative transcript). This substitution is predicted to create a minor amino acid change from leucine to valine at position 263 of the protein, NP_078856.4(EFL1): p.(Leu263Val). The leucine at this position has very high conservation (100 vertebrates, UCSC), and is located within the elongation factor Tu GTP binding domain. In silico software predicts this variant to be damaging (Polyphen, SIFT, CADD, Mutation Taster). The variant is not present in the gnomAD population database. The variant has not been previously reported in clinical cases. Based on information available at the time of curation, this variant has been classified as a VARIANT of UNCERTAIN SIGNIFICANCE (VUS).

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