rs139132326
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_002029.4(FPR1):c.409C>T(p.Arg137Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.000018 in 1,614,042 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R137H) has been classified as Uncertain significance.
Frequency
Consequence
NM_002029.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Uncertain_significance. Variant got 2 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FPR1 | NM_002029.4 | c.409C>T | p.Arg137Cys | missense_variant | 2/2 | ENST00000304748.5 | |
FPR1 | NM_001193306.2 | c.409C>T | p.Arg137Cys | missense_variant | 3/3 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FPR1 | ENST00000304748.5 | c.409C>T | p.Arg137Cys | missense_variant | 2/2 | 1 | NM_002029.4 | P1 | |
FPR1 | ENST00000594900.2 | c.409C>T | p.Arg137Cys | missense_variant | 3/3 | 4 | P1 | ||
FPR1 | ENST00000595042.5 | c.409C>T | p.Arg137Cys | missense_variant | 3/3 | 2 | P1 | ||
FPR1 | ENST00000600815.2 | c.409C>T | p.Arg137Cys | missense_variant | 2/2 | 3 | P1 |
Frequencies
GnomAD3 genomes ? AF: 0.0000263 AC: 4AN: 152150Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000199 AC: 5AN: 251234Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135784
GnomAD4 exome AF: 0.0000171 AC: 25AN: 1461892Hom.: 0 Cov.: 76 AF XY: 0.0000151 AC XY: 11AN XY: 727248
GnomAD4 genome ? AF: 0.0000263 AC: 4AN: 152150Hom.: 0 Cov.: 32 AF XY: 0.0000404 AC XY: 3AN XY: 74320
ClinVar
Submissions by phenotype
Gingival disorder Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Feb 03, 2023 | This sequence change replaces arginine, which is basic and polar, with cysteine, which is neutral and slightly polar, at codon 137 of the FPR1 protein (p.Arg137Cys). This variant is present in population databases (rs139132326, gnomAD 0.008%). This variant has not been reported in the literature in individuals affected with FPR1-related conditions. ClinVar contains an entry for this variant (Variation ID: 575041). Algorithms developed to predict the effect of missense changes on protein structure and function (SIFT, PolyPhen-2, Align-GVGD) all suggest that this variant is likely to be disruptive. 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. - |
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at