NM_001042492.3:c.5488C>G
Variant summary
Our verdict is Pathogenic. Variant got 19 ACMG points: 19P and 0B. PM1PM2PM5PP2PP3_StrongPP5_Very_Strong
The NM_001042492.3(NF1):c.5488C>G(p.Arg1830Gly) variant causes a missense change. The variant was absent in control chromosomes in GnomAD project. In-silico tool predicts a pathogenic outcome for this variant. Variant has been reported in ClinVar as Likely pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R1830C) has been classified as Pathogenic.
Frequency
Consequence
NM_001042492.3 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Pathogenic. Variant got 19 ACMG points.
Transcripts
RefSeq
Ensembl
Frequencies
GnomAD3 genomes Cov.: 31
GnomAD4 exome Cov.: 32
GnomAD4 genome Cov.: 31
ClinVar
Submissions by phenotype
Neurofibromatosis, type 1 Pathogenic:3Other:1
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This sequence change replaces arginine, which is basic and polar, with glycine, which is neutral and non-polar, at codon 1809 of the NF1 protein (p.Arg1809Gly). This variant is not present in population databases (gnomAD no frequency). This missense change has been observed in individual(s) with neurofibromatosis type 1 (PMID: 24451118, 26178382). It has also been observed to segregate with disease in related individuals. ClinVar contains an entry for this variant (Variation ID: 208857). Invitae Evidence Modeling of protein sequence and biophysical properties (such as structural, functional, and spatial information, amino acid conservation, physicochemical variation, residue mobility, and thermodynamic stability) indicates that this missense variant is expected to disrupt NF1 protein function with a positive predictive value of 95%. This variant disrupts the p.Arg1809 amino acid residue in NF1. Other variant(s) that disrupt this residue have been determined to be pathogenic (PMID: 12807981, 19120036, 24357598, 24789688, 26178382). This suggests that this residue is clinically significant, and that variants that disrupt this residue are likely to be disease-causing. For these reasons, this variant has been classified as Pathogenic. -
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not provided Pathogenic:2
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Not observed at significant frequency in large population cohorts (gnomAD); In silico analysis supports that this missense variant has a deleterious effect on protein structure/function; Individuals with p.Arg1809 missense variants largely have not been reported to have cutaneous or plexiform neurofibromas or optic gliomas, and some individuals are reported to have clinical features of Noonan syndrome (Rojnueangnit et al., 2015; Pinna et al., 2015; Santoro et al., 2015; Friedman, 2019); This variant is associated with the following publications: (PMID: 31979111, 23656349, 25541118, 26178382) -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at