ClinVar Miner

Submissions for variant NM_005249.5(FOXG1):c.506G>C (p.Gly169Ala)

gnomAD frequency: 0.00003  dbSNP: rs796052480
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Total submissions: 2
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
GeneDx RCV000187482 SCV000241076 uncertain significance not provided 2015-11-20 criteria provided, single submitter clinical testing p.Gly169Ala (GGC>GCC): c.506 G>C in exon 1 of the FOXG1 gene (NM_005249.3). A variant of unknown significance has been identified in the FOXG1 gene. The G169A variant has not been published as a mutation, nor has it been reported as a benign polymorphism to our knowledge. It was not observed in approximately 6,500 individuals of European and African American ancestry in the NHLBI Exome Sequencing Project, indicating it is not a common benign variant in these populations. The G169A variant is a conservative amino acid substitution, which is not likely to impact secondary protein structure as these residues share similar properties. Additionally, G169A alters a position that is not well conserved through evolution, and it does not occur within the forkhead binding domain where all previously reported missense mutations in FOXG1 have been identified. However, in silico analysis is inconsistent in its predictions as to whether or not the variant is damaging to the protein structure/function. Therefore, based on the currently available information, it is unclear whether this variant is a pathogenic mutation or a rare benign variant. The variant is found in EPILEPSY panel(s).
Labcorp Genetics (formerly Invitae), Labcorp RCV001857612 SCV002189996 uncertain significance Rett syndrome, congenital variant 2022-12-02 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 not expected to disrupt FOXG1 protein function. ClinVar contains an entry for this variant (Variation ID: 205506). This variant has not been reported in the literature in individuals affected with FOXG1-related conditions. 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 sequence change replaces glycine, which is neutral and non-polar, with alanine, which is neutral and non-polar, at codon 169 of the FOXG1 protein (p.Gly169Ala).

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