ClinVar Miner

Submissions for variant NM_017780.4(CHD7):c.5459G>A (p.Arg1820Gln)

gnomAD frequency: 0.00001  dbSNP: rs372644599
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000472945 SCV000552228 uncertain significance CHARGE association 2022-08-09 criteria provided, single submitter clinical testing 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. Advanced modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) performed at Invitae indicates that this missense variant is expected to disrupt CHD7 protein function. ClinVar contains an entry for this variant (Variation ID: 411183). This missense change has been observed in individual(s) with CDH7-related conditions (PMID: 28191889, 31689711). This variant is present in population databases (rs372644599, gnomAD 0.007%). This sequence change replaces arginine, which is basic and polar, with glutamine, which is neutral and polar, at codon 1820 of the CHD7 protein (p.Arg1820Gln).
GeneDx RCV001584166 SCV001818410 uncertain significance not provided 2021-01-07 criteria provided, single submitter clinical testing Observed in a patient with idiopathic hypogonadotropic hypogonadism in published literature; patient was also heterozygous for variants in other genes (Zhao et al., 2019; Li et al., 2020); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; In-silico analysis is inconclusive as to whether the variant alters gene splicing. In the absence of RNA/functional studies, the actual effect of this sequence change is unknown.; This variant is associated with the following publications: (PMID: 31689711, 28191889, 30576231)
Ambry Genetics RCV002348330 SCV002649121 uncertain significance Inborn genetic diseases 2019-06-29 criteria provided, single submitter clinical testing The p.R1820Q variant (also known as c.5459G>A), located in coding exon 25 of the CHD7 gene, results from a G to A substitution at nucleotide position 5459. The arginine at codon 1820 is replaced by glutamine, 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 deleterious by in silico analysis. Since supporting evidence is limited at this time, the clinical significance of this alteration remains unclear.
Revvity Omics, Revvity RCV001584166 SCV003831948 uncertain significance not provided 2021-02-09 criteria provided, single submitter clinical testing

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