3-180968173-C-T
Variant summary
Our verdict is Uncertain significance. Variant got 2 ACMG points: 2P and 0B. PM2
The NM_005087.4(FXR1):c.1321C>T(p.Arg441Cys) variant causes a missense change involving the alteration of a non-conserved nucleotide. The variant allele was found at a frequency of 0.0000236 in 1,613,558 control chromosomes in the GnomAD database, with no homozygous occurrence. Variant has been reported in ClinVar as Uncertain significance (★).
Frequency
Consequence
NM_005087.4 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 rank | MANE | Protein | UniProt |
---|---|---|---|---|---|---|---|---|
FXR1 | NM_005087.4 | c.1321C>T | p.Arg441Cys | missense_variant | Exon 14 of 17 | ENST00000357559.9 | NP_005078.2 | |
FXR1 | NM_001013438.3 | c.1321C>T | p.Arg441Cys | missense_variant | Exon 14 of 16 | NP_001013456.1 | ||
FXR1 | NM_001013439.3 | c.1066C>T | p.Arg356Cys | missense_variant | Exon 15 of 18 | NP_001013457.1 | ||
FXR1 | NM_001363882.1 | c.1066C>T | p.Arg356Cys | missense_variant | Exon 15 of 17 | NP_001350811.1 |
Ensembl
Frequencies
GnomAD3 genomes AF: 0.0000263 AC: 4AN: 152130Hom.: 0 Cov.: 32
GnomAD3 exomes AF: 0.0000159 AC: 4AN: 251260Hom.: 0 AF XY: 0.0000147 AC XY: 2AN XY: 135794
GnomAD4 exome AF: 0.0000233 AC: 34AN: 1461428Hom.: 0 Cov.: 30 AF XY: 0.0000261 AC XY: 19AN XY: 727050
GnomAD4 genome AF: 0.0000263 AC: 4AN: 152130Hom.: 0 Cov.: 32 AF XY: 0.00 AC XY: 0AN XY: 74314
ClinVar
Submissions by phenotype
not specified Uncertain:1
The c.1321C>T (p.R441C) alteration is located in exon 14 (coding exon 14) of the FXR1 gene. This alteration results from a C to T substitution at nucleotide position 1321, causing the arginine (R) at amino acid position 441 to be replaced by a cysteine (C). Based on insufficient or conflicting evidence, the clinical significance of this alteration remains unclear. -
Computational scores
Source:
Splicing
Find out detailed SpliceAI scores and Pangolin per-transcript scores at