ClinVar Miner

Submissions for variant NM_005249.5(FOXG1):c.460del (p.Glu154fs)

dbSNP: rs398124204
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Total submissions: 5
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
HudsonAlpha Institute for Biotechnology, HudsonAlpha Institute for Biotechnology RCV000209851 SCV000265612 pathogenic Rett syndrome, congenital variant 2016-02-11 criteria provided, single submitter research
GeneDx RCV000414502 SCV000490904 pathogenic not provided 2024-07-03 criteria provided, single submitter clinical testing Frameshift variant predicted to result in abnormal protein length as the last 336 amino acids are replaced with 37 different amino acids, and other similar variants have been reported in HGMD; Not observed at significant frequency in large population cohorts (gnomAD); This variant is associated with the following publications: (PMID: 26344814, 24836831, 19806373, 37308910, 33149276, 31440721, 28661489)
Labcorp Genetics (formerly Invitae), Labcorp RCV000209851 SCV000952234 pathogenic Rett syndrome, congenital variant 2022-04-28 criteria provided, single submitter clinical testing This sequence change creates a premature translational stop signal (p.Glu154Argfs*38) in the FOXG1 gene. While this is not anticipated to result in nonsense mediated decay, it is expected to disrupt the last 336 amino acid(s) of the FOXG1 protein. 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 FOXG1-related conditions. ClinVar contains an entry for this variant (Variation ID: 372563). This variant disrupts a region of the FOXG1 protein in which other variant(s) (p.Gly169Alafs*23) have been determined to be pathogenic (PMID: 24836831, 25356899). This suggests that this is a clinically significant region of the protein, and that variants that disrupt it are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic.
Institute of Medical Genetics and Applied Genomics, University Hospital Tübingen RCV000414502 SCV001762142 pathogenic not provided 2021-06-17 criteria provided, single submitter clinical testing
Institute of Human Genetics, University of Leipzig Medical Center RCV000209851 SCV002026229 pathogenic Rett syndrome, congenital variant 2018-01-20 criteria provided, single submitter clinical testing

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