ClinVar Miner

Submissions for variant NM_004304.5(ALK):c.1376A>G (p.Gln459Arg)

gnomAD frequency: 0.00002  dbSNP: rs773380015
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000231007 SCV000288317 uncertain significance Neuroblastoma, susceptibility to, 3 2024-01-10 criteria provided, single submitter clinical testing This sequence change replaces glutamine, which is neutral and polar, with arginine, which is basic and polar, at codon 459 of the ALK protein (p.Gln459Arg). This variant is present in population databases (rs773380015, gnomAD 0.007%). This variant has not been reported in the literature in individuals affected with ALK-related conditions. ClinVar contains an entry for this variant (Variation ID: 239795). Algorithms developed to predict the effect of missense changes on protein structure and function output the following: SIFT: "Not Available"; PolyPhen-2: "Benign"; Align-GVGD: "Not Available". The arginine 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.
Ambry Genetics RCV002378996 SCV002700912 likely benign Hereditary cancer-predisposing syndrome 2022-04-19 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.
PreventionGenetics, part of Exact Sciences RCV003417821 SCV004118334 uncertain significance ALK-related condition 2023-06-02 criteria provided, single submitter clinical testing The ALK c.1376A>G variant is predicted to result in the amino acid substitution p.Gln459Arg. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.0071% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-29551254-T-C) and interpreted as uncertain in ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/239795/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.

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