ClinVar Miner

Submissions for variant NM_001042492.3(NF1):c.2764G>A (p.Gly922Ser)

dbSNP: rs1135402831
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Total submissions: 4
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Submitter RCV SCV Clinical significance Condition Last evaluated Review status Method Comment
Women's Health and Genetics/Laboratory Corporation of America, LabCorp RCV000497105 SCV001478609 likely pathogenic Neurofibromatosis, type 1 2021-01-28 criteria provided, single submitter clinical testing Variant summary: NF1 c.2764G>A (p.Gly922Ser) results in a non-conservative amino acid change in the encoded protein sequence. Three of five in-silico tools predict a damaging effect of the variant on protein function. Several computational tools predict a significant impact on normal splicing: Four predict the variant strengthens a cryptic exonic 5' splice donor site. At least one publication reports experimental evidence that this variant affects mRNA splicing (Ars_2003). The variant was absent in 251090 control chromosomes. c.2764G>A has been reported in the literature in at-least two individuals affected with some but not all diagnostic features of Neurofibromatosis Type 1 as well as in at-least one individual with a suspected diagnosis of Neurofibromatosis type 1 and also subsequently cited by others (example, Ars_2003, Pros_2008, Anastaski_2017, Bonatti_2017, Yoshida_2018). These data indicate that the variant may be associated with disease. One clinical diagnostic laboratory has submitted clinical-significance assessments for this variant to ClinVar after 2014 without evidence for independent evalution and classified the variant as uncertain significance. Based on the evidence outlined above, the variant was classified as likely pathogenic.
Labcorp Genetics (formerly Invitae), Labcorp RCV000497105 SCV001586754 pathogenic Neurofibromatosis, type 1 2020-08-04 criteria provided, single submitter clinical testing Experimental studies have shown that this variant disrupts mRNA splicing (PMID: 10607834). For these reasons, this variant has been classified as Pathogenic. 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 NF1 protein function. This variant has been observed in individual(s) with neurofibromatosis type 1 (PMID: 10607834, 28961165). ClinVar contains an entry for this variant (Variation ID: 431608). This variant is not present in population databases (ExAC no frequency). This sequence change replaces glycine with serine at codon 922 of the NF1 protein (p.Gly922Ser). The glycine residue is moderately conserved and there is a small physicochemical difference between glycine and serine.
Genome-Nilou Lab RCV000497105 SCV002561801 likely pathogenic Neurofibromatosis, type 1 2022-03-15 criteria provided, single submitter clinical testing
Medical Genetics, University of Parma RCV000497105 SCV000588747 uncertain significance Neurofibromatosis, type 1 2017-02-02 no assertion criteria provided clinical testing

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