ClinVar Miner

Submissions for variant NM_003640.5(ELP1):c.520G>A (p.Glu174Lys)

gnomAD frequency: 0.00010  dbSNP: rs758924768
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001508264 SCV000626028 uncertain significance not provided 2022-04-18 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with lysine, which is basic and polar, at codon 174 of the ELP1 protein (p.Glu174Lys). This variant is present in population databases (rs758924768, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with ELP1-related conditions. ClinVar contains an entry for this variant (Variation ID: 455969). 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: "Tolerated"; PolyPhen-2: "Possibly Damaging"; 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.
Mayo Clinic Laboratories, Mayo Clinic RCV001508264 SCV001714306 uncertain significance not provided 2020-02-17 criteria provided, single submitter clinical testing
St. Jude Molecular Pathology, St. Jude Children's Research Hospital RCV002291654 SCV002584774 uncertain significance Medulloblastoma 2022-08-01 criteria provided, single submitter clinical testing The ELP1 c.520G>A (p.Glu174Lys) missense change has a maximum subpopulation frequency of 0.0070% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The in silico tool REVEL is inconclusive about a pathogenic or benign effect of this variant on protein function, and to our knowledge functional studies have not been performed. To our knowledge, this variant has not been reported in individuals with a personal or family history of medulloblastoma. In summary, the evidence currently available is insufficient to determine the clinical significance of this variant. It has therefore been classified as of uncertain significance.
Ambry Genetics RCV004023740 SCV002755215 uncertain significance not specified 2020-07-07 criteria provided, single submitter clinical testing The p.E174K variant (also known as c.520G>A), located in coding exon 5 of the IKBKAP gene, results from a G to A substitution at nucleotide position 520. The glutamic acid at codon 174 is replaced by lysine, an amino acid with similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, the in silico prediction for this alteration is inconclusive. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Natera, Inc. RCV000542595 SCV001452222 uncertain significance Familial dysautonomia 2020-01-17 no assertion criteria provided clinical testing

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