ClinVar Miner

Submissions for variant NM_130468.4(CHST14):c.143C>T (p.Ala48Val)

gnomAD frequency: 0.00002  dbSNP: rs780919131
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Eurofins Ntd Llc (ga) RCV000724922 SCV000332429 uncertain significance not provided 2015-06-30 criteria provided, single submitter clinical testing
GeneDx RCV000724922 SCV000582121 uncertain significance not provided 2017-05-11 criteria provided, single submitter clinical testing The A48V variant of uncertain significance in the CHST14 gene has not been published as pathogenic or been reported as benign to our knowledge. This variant is not observed at a significant frequency in large population cohorts (Lek et al., 2016; 1000 Genomes Consortium et al., 2015; Exome Variant Server). However, the A48V variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. Furthermore, this substitution occurs at a position that is not conserved across species, and in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function.
Invitae RCV001859550 SCV002162168 uncertain significance Ehlers-Danlos syndrome, musculocontractural type 2022-03-25 criteria provided, single submitter clinical testing This sequence change replaces alanine, which is neutral and non-polar, with valine, which is neutral and non-polar, at codon 48 of the CHST14 protein (p.Ala48Val). The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This variant has not been reported in the literature in individuals affected with CHST14-related conditions. ClinVar contains an entry for this variant (Variation ID: 281584). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be tolerated. 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 RCV002392794 SCV002702892 uncertain significance Cardiovascular phenotype 2022-12-14 criteria provided, single submitter clinical testing The p.A48V variant (also known as c.143C>T), located in coding exon 1 of the CHST14 gene, results from a C to T substitution at nucleotide position 143. The alanine at codon 48 is replaced by valine, an amino acid with similar properties. This amino acid position is not well 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.

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