FXR1
protein-codingFMR1 autosomal homolog 1
Gene summary
The protein encoded by this gene is an RNA binding protein that interacts with the functionally-similar proteins FMR1 and FXR2. These proteins shuttle between the nucleus and cytoplasm and associate with polyribosomes, predominantly with the 60S ribosomal subunit. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~114.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0032937
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0032937
Submitter: Ambry Genetics
Inheritance Pattern: AR
Disease ID:MONDO:0019952
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0032936
Submitter: Labcorp Genetics (formerly Invitae)
Clinical Genomic Database (CGD)
Manifestation: Musculoskeletal; Neurologic; Pulmonary
Intervention: General
Rationale: Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to FXR1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005087.4. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 6 | 3 | 10 | ||
| missense | 1 | 52 | 1 | 54 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 5 | 5 | ||||
| Total | 0 | 1 | 58 | 7 | 3 | 69 |
Highest pathogenic variant AF is 0.0001090328
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005078.2 | 17 | MANE Select | |
| Ensembl | ENSP00000350170.3 | 17 | MANE Select | |
| RefSeq | NP_001013456.1 | 16 | Standard | |
| RefSeq | NP_001013457.1 | 14 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| fxr1 | Danio rerio | Structure: skeletal muscle myoblast Quality: circular abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- RNA transport - Homo sapiens (human)
- Disease
- Signaling by BRAF and RAF fusions
- Oncogenic MAPK signaling
- Diseases of signal transduction
Biological Process
- apoptotic process
- muscle organ development
- negative regulation of translation
- cell differentiation
- regulation of mRNA stability
Molecular Function
- RNA binding
- mRNA binding
- mRNA 3'-UTR binding
- protein binding
- RNA strand annealing activity
Cellular Component
- nucleus
- nucleolus
- cytoplasm
- cytosol
- polysome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000357559
- Coding exons
- 17
- Length
- 114613
- Individuals with no LoFs
- 125654
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 3
- Defined
- 125657
- p
- 0.0000119
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 3.20 | 182 | 351 | 0.519 | 0.0000194 | 4068 |
| Missense (PolyPhen) | 56 | 152.31 | 0.36768 | 1715 | ||
| Synonymous | 0.913 | 101 | 113 | 0.891 | 0.00000587 | 1170 |
| Loss of Function | 5.69 | 1 | 39.7 | 0.0252 | 0.00000252 | 429 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0 | 0.0 | absent |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.000018 | 0.000018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: RNA-binding protein required for embryonic and postnatal development of muscle tissue. May regulate intracellular transport and local translation of certain mRNAs (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.194
Intolerance Scores
- LoFtool
- 0.425
- RVIS EVS
- -0.65
- RVIS percentile EVS
- 16.36
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.763
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |