FXR1
FMR1 autosomal homolog 1
Basic information
Region (hg38): 3:180868141-180982753
Links
Phenotypes
GenCC
Source:
- myopathy, congenital proximal, with minicore lesions (Limited), mode of inheritance: AR
- myopathy, congenital, with respiratory insufficiency and bone fractures (Strong), mode of inheritance: AR
- congenital myopathy (Strong), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Congenital myopathy 9A; Congenital myopathy 9B, proximal, with minicore lesions | AR | General | 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 | Musculoskeletal; Neurologic; Pulmonary | 30770808; 35393337 |
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (42 variants)
- not_provided (10 variants)
- Myopathy,_congenital_proximal,_with_minicore_lesions (4 variants)
- Myopathy,_congenital,_with_respiratory_insufficiency_and_bone_fractures (3 variants)
- Congenital_myopathy (2 variants)
- Neonatal_respiratory_distress (1 variants)
- Delayed_gross_motor_development (1 variants)
- Multiminicore_myopathy (1 variants)
- Scoliosis (1 variants)
- Intellectual_disability (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the FXR1 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000005087.4. Only rare variants are included in the table.
In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.
Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 8 | |||||
| missense | 46 | 48 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 1 | 46 | 6 | 3 |
Highest pathogenic variant AF is 0.000109033
Loading clinvar variants...
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| FXR1 | protein_coding | protein_coding | ENST00000357559 | 17 | 114613 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 1.00 | 0.00000327 | 125654 | 0 | 3 | 125657 | 0.0000119 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 3.20 | 182 | 351 | 0.519 | 0.0000194 | 4068 |
| Missense in 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 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000183 | 0.0000176 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.000164 | 0.000163 |
dbNSFP
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}.;
- Pathway
- RNA transport - Homo sapiens (human);Disease;Signaling by BRAF and RAF fusions;Oncogenic MAPK signaling;Diseases of signal transduction
(Consensus)
Recessive Scores
- pRec
- 0.194
Intolerance Scores
- loftool
- 0.425
- rvis_EVS
- -0.65
- rvis_percentile_EVS
- 16.36
Haploinsufficiency Scores
- pHI
- 0.833
- hipred
- Y
- hipred_score
- 0.777
- ghis
- 0.619
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.763
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Fxr1
- Phenotype
- hematopoietic system phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); reproductive system phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); respiratory system phenotype; immune system phenotype; muscle phenotype; endocrine/exocrine gland phenotype; growth/size/body region phenotype;
Zebrafish Information Network
- Gene name
- fxr1
- Affected structure
- skeletal muscle myoblast
- Phenotype tag
- abnormal
- Phenotype quality
- circular
Gene ontology
- Biological process
- apoptotic process;muscle organ development;negative regulation of translation;cell differentiation;regulation of mRNA stability;positive regulation of translation;positive regulation of gene silencing by miRNA
- Cellular component
- nucleus;nucleolus;cytoplasm;cytosol;polysome;postsynaptic density;membrane;axon;ribonucleoprotein granule;cytoplasmic ribonucleoprotein granule;neuronal cell body;costamere;dendritic spine;perinuclear region of cytoplasm;glutamatergic synapse
- Molecular function
- RNA binding;mRNA binding;mRNA 3'-UTR binding;protein binding;RNA strand annealing activity;protein homodimerization activity;translation regulator activity;protein heterodimerization activity