ClinVar Miner

Submissions for variant NM_004304.5(ALK):c.4200A>C (p.Glu1400Asp)

gnomAD frequency: 0.00018  dbSNP: rs143647372
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000471219 SCV000541823 uncertain significance Neuroblastoma, susceptibility to, 3 2024-01-28 criteria provided, single submitter clinical testing This sequence change replaces glutamic acid, which is acidic and polar, with aspartic acid, which is acidic and polar, at codon 1400 of the ALK protein (p.Glu1400Asp). This variant is present in population databases (rs143647372, gnomAD 0.03%). 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: 404316). An algorithm developed to predict the effect of missense changes on protein structure and function (PolyPhen-2) suggests that this variant is likely to be disruptive. 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 RCV001022040 SCV001183728 uncertain significance Hereditary cancer-predisposing syndrome 2018-09-14 criteria provided, single submitter clinical testing The p.E1400D variant (also known as c.4200A>C), located in coding exon 29 of the ALK gene, results from an A to C substitution at nucleotide position 4200. The glutamic acid at codon 1400 is replaced by aspartic acid, an amino acid with highly similar properties. This amino acid position is highly conserved in available vertebrate species. In addition, this alteration is predicted to be tolerated by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Illumina Laboratory Services, Illumina RCV000471219 SCV001296882 uncertain significance Neuroblastoma, susceptibility to, 3 2018-01-12 criteria provided, single submitter clinical testing This variant was observed in the ICSL laboratory as part of a predisposition screen in an ostensibly healthy population. It had not been previously curated by ICSL or reported in the Human Gene Mutation Database (HGMD: prior to June 1st, 2018), and was therefore a candidate for classification through an automated scoring system. Utilizing variant allele frequency, disease prevalence and penetrance estimates, and inheritance mode, an automated score was calculated to assess if this variant is too frequent to cause the disease. Based on the score, this variant could not be ruled out of causing disease and therefore its association with disease required further investigation. A literature search was performed for the gene, cDNA change, and amino acid change (if applicable). No publications were found based on this search. This variant was therefore classified as a variant of unknown significance for this disease.
Sema4, Sema4 RCV001022040 SCV002528501 likely benign Hereditary cancer-predisposing syndrome 2021-03-31 criteria provided, single submitter curation
Preventiongenetics, part of Exact Sciences RCV003392267 SCV004120183 uncertain significance ALK-related condition 2023-02-07 criteria provided, single submitter clinical testing The ALK c.4200A>C variant is predicted to result in the amino acid substitution p.Glu1400Asp. To our knowledge, this variant has not been reported in the literature. This variant is reported in 0.028% of alleles in individuals of European (Non-Finnish) descent in gnomAD (http://gnomad.broadinstitute.org/variant/2-29416753-T-G). In ClinVar, this variant has conflicting interpretations of likely benign and uncertain significance (https://www.ncbi.nlm.nih.gov/clinvar/variation/404316/). At this time, the clinical significance of this variant is uncertain due to the absence of conclusive functional and genetic evidence.
Baylor Genetics RCV000471219 SCV004195496 uncertain significance Neuroblastoma, susceptibility to, 3 2023-10-23 criteria provided, single submitter clinical testing

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