ClinVar Miner

Submissions for variant NM_024996.7(GFM1):c.788A>G (p.Gln263Arg)

gnomAD frequency: 0.00158  dbSNP: rs115984741
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Total submissions: 6
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Invitae RCV000886511 SCV001030021 benign not provided 2024-01-31 criteria provided, single submitter clinical testing
GeneDx RCV000886511 SCV001783687 likely benign not provided 2020-02-26 criteria provided, single submitter clinical testing
CeGaT Center for Human Genetics Tuebingen RCV000886511 SCV002821227 likely benign not provided 2022-10-01 criteria provided, single submitter clinical testing GFM1: BP4
PreventionGenetics, part of Exact Sciences RCV003968054 SCV004776520 likely benign GFM1-related disorder 2022-12-22 criteria provided, single submitter clinical testing This variant is classified as likely benign based on ACMG/AMP sequence variant interpretation guidelines (Richards et al. 2015 PMID: 25741868, with internal and published modifications).
Natera, Inc. RCV001272460 SCV001454457 likely benign Hepatoencephalopathy due to combined oxidative phosphorylation defect type 1 2019-11-11 no assertion criteria provided clinical testing
Department of Pathology and Laboratory Medicine, Sinai Health System RCV000886511 SCV001548780 uncertain significance not provided no assertion criteria provided clinical testing The GFM1 p.Gln263Arg variant was not identified in the literature nor was it identified in ClinVar or Cosmic. The variant was identified in dbSNP (ID: rs115984741) and LOVD 3.0 databases. The variant was identified in control databases in 147 of 282872 chromosomes (1 homozygous) at a frequency of 0.00052 increasing the likelihood this could be a low frequency benign variant (Genome Aggregation Database Feb 27, 2017). The variant was observed in the following populations: African in 136 of 24964 chromosomes (freq: 0.005448), Latino in 11 of 35440 chromosomes (freq: 0.00031), while the variant was not observed in the Ashkenazi Jewish, East Asian, European (Finnish), European (non-Finnish), Other, and South Asian populations. The variant is located within the protein synthesis factor, GTP-binding translation elongation factor EFG/EF2 functional domain(s) increasing the likelihood that it may have clinical significance. The p.Gln263 residue is conserved in mammals but not in more distantly related organisms. Computational analyses (PolyPhen-2, SIFT, AlignGVGD, BLOSUM, MutationTaster) do not suggest a high likelihood of impact to the protein; this information is not predictive enough to rule out pathogenicity. The variant occurs outside of the splicing consensus sequence and 1 of 4 in silico or computational prediction software programs (NNSPLICE) predicts a greater than 10% difference in splicing (decreased 5' splicing activity near the variant location); this is not very predictive of pathogenicity. In summary, based on the above information the clinical significance of this variant cannot be determined with certainty at this time. This variant is classified as a variant of uncertain significance.

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