rs886041390
Variant summary
Our verdict is Pathogenic. Variant got 16 ACMG points: 16P and 0B. PM1PM2PM5PP3_ModeratePP5_Very_Strong
The NM_004960.4(FUS):c.1574C>T(p.Pro525Leu) 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 Pathogenic (★★). Another variant affecting the same amino acid position, but resulting in a different missense (i.e. P525A) has been classified as Uncertain significance.
Frequency
Genomes: not found (cov: 31)
Consequence
FUS
NM_004960.4 missense
NM_004960.4 missense
Scores
11
5
3
Clinical Significance
Conservation
PhyloP100: 6.47
Genes affected
FUS (HGNC:4010): (FUS RNA binding protein) This gene encodes a multifunctional protein component of the heterogeneous nuclear ribonucleoprotein (hnRNP) complex. The hnRNP complex is involved in pre-mRNA splicing and the export of fully processed mRNA to the cytoplasm. This protein belongs to the FET family of RNA-binding proteins which have been implicated in cellular processes that include regulation of gene expression, maintenance of genomic integrity and mRNA/microRNA processing. Alternative splicing results in multiple transcript variants. Defects in this gene result in amyotrophic lateral sclerosis type 6. [provided by RefSeq, Sep 2009]
Genome browser will be placed here
ACMG classification
Classification made for transcript
Verdict is Pathogenic. Variant got 16 ACMG points.
PM1
?
In a hotspot region, there are 6 aminoacids with missense pathogenic changes in the window of +-8 aminoacids around while only 0 benign, 6 uncertain in NM_004960.4
PM2
?
Very rare variant in population databases, with high coverage;
PM5
?
Other missense variant is known to change same aminoacid residue: Variant chr16-31191430-C-A is described in ClinVar as [Pathogenic]. Clinvar id is 2046744.Status of the report is criteria_provided_single_submitter, 1 stars.
PP3
?
MetaRNN computational evidence supports a deleterious effect, 0.915
PP5
?
Variant 16-31191431-C-T is Pathogenic according to our data. Variant chr16-31191431-C-T is described in ClinVar as [Pathogenic]. Clinvar id is 280110.Status of the report is criteria_provided_multiple_submitters_no_conflicts, 2 stars. Variant chr16-31191431-C-T is described in Lovd as [Pathogenic].
Transcripts
RefSeq
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | MANE | UniProt |
---|---|---|---|---|---|---|---|
FUS | NM_004960.4 | c.1574C>T | p.Pro525Leu | missense_variant | 15/15 | ENST00000254108.12 |
Ensembl
Gene | Transcript | HGVSc | HGVSp | Effect | #exon/exons | TSL | MANE | Appris | UniProt |
---|---|---|---|---|---|---|---|---|---|
FUS | ENST00000254108.12 | c.1574C>T | p.Pro525Leu | missense_variant | 15/15 | 1 | NM_004960.4 | P4 |
Frequencies
GnomAD3 genomes ? Cov.: 31
GnomAD3 genomes
?
Cov.:
31
GnomAD3 exomes AF: 0.00000398 AC: 1AN: 251428Hom.: 0 AF XY: 0.00 AC XY: 0AN XY: 135898
GnomAD3 exomes
AF:
AC:
1
AN:
251428
Hom.:
AF XY:
AC XY:
0
AN XY:
135898
Gnomad AFR exome
AF:
Gnomad AMR exome
AF:
Gnomad ASJ exome
AF:
Gnomad EAS exome
AF:
Gnomad SAS exome
AF:
Gnomad FIN exome
AF:
Gnomad NFE exome
AF:
Gnomad OTH exome
AF:
GnomAD4 exome Cov.: 36
GnomAD4 exome
Cov.:
36
GnomAD4 genome ? Cov.: 31
GnomAD4 genome
?
Cov.:
31
ClinVar
Significance: Pathogenic
Submissions summary: Pathogenic:6
Revision: criteria provided, multiple submitters, no conflicts
LINK: link
Submissions by phenotype
not provided Pathogenic:3
Pathogenic, criteria provided, single submitter | clinical testing | CeGaT Center for Human Genetics Tuebingen | Jan 01, 2024 | FUS: PM1, PM2, PM5, PM6, PS3:Moderate, PS4:Moderate - |
Pathogenic, criteria provided, single submitter | clinical testing | GeneDx | Mar 26, 2019 | Published in vitro functional studies demonstrate mislocalization of the FUS protein product in the cytoplasm instead of the nucleus (Dormann et al., 2010; Coady et al., 2015); Not observed at a significant frequency in large population cohorts (Lek et al., 2016); In silico analysis, which includes protein predictors and evolutionary conservation, supports a deleterious effect; This variant is associated with the following publications: (PMID: 24899262, 19450904, 20668261, 21280085, 25173930, 21604077, 20606625, 21949354, 24280224, 25625564, 22778397, 20579074, 22980027, 21907581, 26251528, 25792726, 20668259, 27123482, 25912081, 26298469, 23881933, 21881207, 23056579, 30808650, 19251627, 30684766, 30455313, 31682085, 31630970, 32579787, 32307925, 33580145, 32479602) - |
Pathogenic, criteria provided, single submitter | clinical testing | Athena Diagnostics | May 28, 2014 | - - |
FUS-related disorder Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | PreventionGenetics, part of Exact Sciences | Feb 20, 2023 | The FUS c.1574C>T variant is predicted to result in the amino acid substitution p.Pro525Leu. This variant has been repeatedly reported to be causative for amyotrophic lateral sclerosis (e.g., Kwiatkowski et al. 2009. PubMed ID: 19251627; Mackenzie et al. 2011. PubMed ID: 21604077). Of note, the Pro525 residue is located in the final 13 amino acid residues of the FUS protein, a region highly conserved among species. A significant number of FUS causative variants that have been reported in patients with ALS are located in the final 13 amino acids, between amino acid 514 and 526 (Kwiatkowski et al. 2009. PubMed ID: 19251627; Lagier-Tourenne and Cleveland. 2009. PubMed ID: 19303844). This variant has been interpreted as pathogenic by multiple submitters to ClinVar (https://www.ncbi.nlm.nih.gov/clinvar/variation/280110). Taken together, this variant is interpreted as pathogenic. - |
Juvenile amyotrophic lateral sclerosis Pathogenic:1
Pathogenic, criteria provided, single submitter | research | Suna and Inan Kirac Foundation Neurodegeneration Research Laboratory, Koc University | Mar 31, 2020 | - - |
Amyotrophic lateral sclerosis type 6;C3539195:Tremor, hereditary essential, 4 Pathogenic:1
Pathogenic, criteria provided, single submitter | clinical testing | Invitae | Dec 03, 2022 | Algorithms developed to predict the effect of missense changes on protein structure and function are either unavailable or do not agree on the potential impact of this missense change (SIFT: "Tolerated"; PolyPhen-2: "Probably Damaging"; Align-GVGD: "Class C0"). ClinVar contains an entry for this variant (Variation ID: 280110). This missense change has been observed in individual(s) with juvenile ALS and amyotrophic lateral sclerosis (ALS) (PMID: 19251627, 20579074, 21604077, 21907581, 22980027, 27123482). In at least one individual the variant was observed to be de novo. The frequency data for this variant in the population databases is considered unreliable, as metrics indicate poor data quality at this position in the gnomAD database. This sequence change replaces proline, which is neutral and non-polar, with leucine, which is neutral and non-polar, at codon 525 of the FUS protein (p.Pro525Leu). For these reasons, this variant has been classified as Pathogenic. Experimental studies have shown that this missense change affects FUS function (PMID: 20606625, 21280085, 24899262, 25173930, 25625564, 26251528). - |
Computational scores
Source:
Name
Calibrated prediction
Score
Prediction
AlphaMissense
Pathogenic
BayesDel_addAF
Pathogenic
D
BayesDel_noAF
Pathogenic
Cadd
Pathogenic
Dann
Uncertain
DEOGEN2
Pathogenic
D;.;T
Eigen
Benign
Eigen_PC
Benign
FATHMM_MKL
Pathogenic
D
LIST_S2
Uncertain
D;D;D
M_CAP
Pathogenic
D
MetaRNN
Pathogenic
D;D;D
MetaSVM
Uncertain
D
MutationAssessor
Uncertain
M;.;.
MutationTaster
Benign
D;D;D
PrimateAI
Uncertain
T
PROVEAN
Pathogenic
D;D;D
REVEL
Pathogenic
Sift
Pathogenic
D;D;D
Sift4G
Pathogenic
D;D;D
Polyphen
B;P;.
Vest4
MutPred
Loss of glycosylation at P525 (P = 0.0444);.;.;
MVP
MPC
ClinPred
D
GERP RS
RBP_binding_hub_radar
RBP_regulation_power_radar
Varity_R
gMVP
Splicing
Name
Calibrated prediction
Score
Prediction
SpliceAI score (max)
Details are displayed if max score is > 0.2
Find out detailed SpliceAI scores and Pangolin per-transcript scores at