ClinVar Miner

Submissions for variant NM_020778.5(ALPK3):c.3104G>A (p.Cys1035Tyr)

gnomAD frequency: 0.00003  dbSNP: rs758388457
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Total submissions: 3
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Labcorp Genetics (formerly Invitae), Labcorp RCV001960074 SCV002214735 uncertain significance not provided 2024-06-30 criteria provided, single submitter clinical testing This sequence change replaces cysteine, which is neutral and slightly polar, with tyrosine, which is neutral and polar, at codon 1237 of the ALPK3 protein (p.Cys1237Tyr). This variant is present in population databases (rs758388457, gnomAD 0.002%). This variant has not been reported in the literature in individuals affected with ALPK3-related conditions. ClinVar contains an entry for this variant (Variation ID: 1433321). 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 RCV002344078 SCV002623093 uncertain significance Cardiovascular phenotype 2024-01-22 criteria provided, single submitter clinical testing The p.C1237Y variant (also known as c.3710G>A), located in coding exon 6 of the ALPK3 gene, results from a G to A substitution at nucleotide position 3710. The cysteine at codon 1237 is replaced by tyrosine, an amino acid with highly dissimilar properties. This amino acid position is conserved. 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.
ARUP Laboratories, Molecular Genetics and Genomics, ARUP Laboratories RCV005232726 SCV005877893 uncertain significance Cardiomyopathy, familial hypertrophic 27 2024-03-21 criteria provided, single submitter clinical testing The ALPK3 c.3104G>A; p.Cys1035Tyr variant (rs758388457), to our knowledge, is not reported in the medical literature but is reported in ClinVar (Variation ID: 1433321). This variant is found in the non-Finnish European population with an allele frequency of 0.002% (2/111,184 alleles) in the Genome Aggregation Database (v2.1.1). Computational analyses predict that this variant is neutral (REVEL: 0.11). However, due to limited information, the clinical significance of this variant is uncertain at this time.

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