ClinVar Miner

Submissions for variant NM_003640.5(ELP1):c.2578G>A (p.Glu860Lys)

gnomAD frequency: 0.00007  dbSNP: rs137983175
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Ambry Genetics RCV004035444 SCV002755923 uncertain significance not specified 2025-01-22 criteria provided, single submitter clinical testing The c.2578G>A (p.E860K) alteration is located in exon 24 (coding exon 23) of the IKBKAP gene. This alteration results from a G to A substitution at nucleotide position 2578, causing the glutamic acid (E) at amino acid position 860 to be replaced by a lysine (K). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear.
Labcorp Genetics (formerly Invitae), Labcorp RCV002537749 SCV003248397 uncertain significance not provided 2022-02-18 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 860 of the ELP1 protein (p.Glu860Lys). This variant is present in population databases (rs137983175, gnomAD 0.004%). 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: 989529). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Tolerated"; PolyPhen-2: "Benign"; Align-GVGD: "Class C0". The lysine amino acid residue is found in multiple mammalian species, which suggests that this missense change does not adversely affect protein function. 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.
St. Jude Molecular Pathology, St. Jude Children's Research Hospital RCV003230281 SCV003928048 uncertain significance Medulloblastoma 2023-05-16 criteria provided, single submitter clinical testing The ELP1 c.2578G>A (p.Glu860Lys) missense change has a maximum subpopulation frequency of 0.0044% in gnomAD v2.1.1 (https://gnomad.broadinstitute.org/). The in silico tool REVEL predicts a benign effect on protein function, but to our knowledge this prediction has not been confirmed by functional studies. 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.
Natera, Inc. RCV001277381 SCV001464329 uncertain significance Familial dysautonomia 2020-08-24 no assertion criteria provided clinical testing

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