rs1555509693
Variant summary
Our verdict is Likely pathogenic. Variant got 6 ACMG points: 6P and 0B. PM1PM2PP3_Moderate
The NM_004960.4(FUS):c.1564A>G(p.Arg522Gly) variant causes a missense change involving the alteration of a non-conserved nucleotide. 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 Uncertain significance (★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. R522S) has been classified as Uncertain significance.
Frequency
Consequence
NM_004960.4 missense
Scores
Clinical Significance
Conservation
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ACMG classification
Verdict is Likely_pathogenic. Variant got 6 ACMG points.
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUS | NM_004960.4 | c.1564A>G | p.Arg522Gly | missense_variant | 15/15 | ENST00000254108.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUS | ENST00000254108.12 | c.1564A>G | p.Arg522Gly | missense_variant | 15/15 | 1 | NM_004960.4 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD4 exome Cov.: 36
GnomAD4 genome ? Cov.: 31
ClinVar
Submissions by phenotype
Amyotrophic lateral sclerosis type 6 Pathogenic:1
Pathogenic, no assertion criteria provided | clinical testing | Institute of Human Genetics, Cologne University | Apr 25, 2018 | - - |
Amyotrophic lateral sclerosis type 6;C3539195:Tremor, hereditary essential, 4 Uncertain:1
Uncertain significance, criteria provided, single submitter | clinical testing | Invitae | Dec 16, 2017 | This sequence change replaces arginine with glycine at codon 522 of the FUS protein (p.Arg522Gly). The arginine residue is highly conserved and there is a moderate physicochemical difference between arginine and glycine. This variant is not present in population databases (ExAC no frequency). This variant has been reported in a family with two individuals affected with amyotrophic lateral sclerosis (PMID: 19251627). Experimental studies have shown that this missense change results in moderate accumulation of the FUS protein in the cytoplasm and that this results in various downstream effects on transcription, protein translation, RNA splicing, and transport (PMID: 20606625, 24280224, 21949354, 24204307, 25289647). 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