Alternative titles; symbols
HGNC Approved Gene Symbol: FXR1
Cytogenetic location: 3q26.33 Genomic coordinates (GRCh38) : 3:180,912,670-180,982,753 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 3q26.33 | ?Congenital myopathy 9A with respiratory insufficiency and bone fractures | 618822 | Autosomal recessive | 3 |
| Congenital myopathy 9B, proximal, with minicore lesions | 618823 | Autosomal recessive | 3 |
The FXR1 gene encodes an RNA-binding protein involved in posttranscriptional mRNA regulation. FXR1 belongs to a family of homologous genes, including FMR1 (309550) on chromosome Xq27.3 and FXR2 (605339) on chromosome 17p13. FXR1 is expressed in a wide variety of tissues and is subject to extensive alternative splicing, sometimes with tissue-specific expression (summary by Estan et al., 2019).
Siomi et al. (1995) cloned a cDNA related to FMR1 from a Xenopus laevis ovary library. This cDNA was then used to screen a HeLa cell library. They identified a cDNA that encodes a predicted protein of 621 amino acids. The gene, designated FXR1 (FMR1 cross-reacting relative) by them, shows 86% amino acid sequence identity to the KH RNA binding domains of FMR1 and 70% identity over the amino-terminal domain. However, the carboxyl domains are entirely unrelated. RT-PCR analysis showed that many cell types express FXR1 mRNA.
Coy et al. (1995) cloned a short variant of FXR1 that encodes a 539-amino acid protein that shares 99% sequence identity with the short variant of mouse Fxr1. Northern blot analysis revealed expression of 2.4- and 2.2-kb transcripts in all adult and fetal human tissues tested, with strongest expression in skeletal muscle. The 2.2-kb transcript, which represents the short FXR1 variant, was more abundant in all tissues except brain and skeletal muscle, where the larger transcript was slightly more abundant. A 6-kb transcript was also found in skeletal muscle. In situ hybridization of mouse embryos and adult tissues detected near ubiquitous expression of Fxr1 mRNA. During embryonic development, expression was prominent in skeletal muscle, gonads, and in distinct regions of the central nervous system. In all tissues, expression was restricted to proliferating cells. Within gonads, Fmr1 was highly expressed in proliferating spermatogonia, while Fxr1 was highly expressed in postmeiotic spermatids.
By Western blot analysis, Khandjian et al. (1998) observed 2 major protein isoforms of FXR1 at 70 and 78 kD, which they designated p70 and p78, expressed in several mammalian cell lines and in the majority of mouse tissues examined. By immunohistochemical analysis, they found coexpression of Fmr1 and the p70 and p78 isoforms of Fxr1 within the cytoplasm of mouse brain neurons. In contrast, skeletal muscle expressed no Fmr1, while a larger Fxr1 isoform, designated p81-84, was localized in structures within the contractile bands.
Kirkpatrick et al. (2001) identified several motifs that are shared between FXR1, FXR2, and FMR1, including a nuclear localization signal, a nuclear export signal, a KH domain, and an arginine/glycine-rich (RGG) box. In addition, FXR1 and FXR2 contain 2 unique nucleolar targeting sequences (NoSs).
Davidovic et al. (2008) identified FXR1P splice variants in human myoblasts and myotubes. Six different isoforms were detected, and expression was developmentally regulated. Immature myoblasts showed expression of all isoforms, but predominantly short and medium isoforms, whereas differentiated myotubes showed expression of longer isoforms containing exon 15. The splicing pattern was similar to that found in mice.
Estan et al. (2019) stated that 7 different FXR1 mRNA isoforms (a to g) have been identified, some of which are tissue-specific. Whereas most tissues express FXR1 variants ranging from 70 to 80 kD, cardiac and skeletal muscle generate only 2 isoforms of 82 and 84 kD, which contain an additional 81-nucleotide exon (exon 15) exclusive to these variants. During muscle differentiation, myoblasts synthesize all FXR1 isoforms, while myotubes express only the 82- and 84-kD variants.
Kirkpatrick et al. (2001) determined that the FXR1 gene contains 17 exons and spans up to 70 kb.
Siomi et al. (1995) mapped the FXR1 gene to chromosome 12 using a somatic cell hybrid mapping panel and to 12q13 by fluorescence in situ hybridization. However, Coy et al. (1995) determined that this localization represents an intronless pseudogene. Using FISH, they mapped the functional FXR1 gene to chromosome 3q28. By BAC analysis, Kirkpatrick et al. (2001) mapped the FXR1 gene to chromosome 3q27. They mapped mouse Fxr1 to the proximal region of chromosome 3.
Siomi et al. (1995) showed in vitro that FXR1 protein has RNA binding properties similar to FMR1 and that both are present in the cytoplasm. Cells from patients with fragile X syndrome that lack FMR1 expression make normal levels of FXR1 transcript. This argues that the autosomal gene cannot complement FMR1 and that the 2 proteins have different functions.
Tamanini et al. (1999) found that FMR1 and FXR1 proteins shuttle between cytoplasm and nucleoplasm, while FXR2 protein shuttles between cytoplasm and nucleolus. Tamanini et al. (2000) showed that FXR1 and FXR2 proteins contain in their C-terminal parts a stretch of basic amino acids 'RPQRRNRSRRRRFR' that resembles the NoS of the viral protein Rev. This particular sequence is present within exon 15 of the FXR1 gene, which undergoes alternative splicing. Cells which were transfected with constructs of FXR1 protein and FXR2 protein isoforms with the potential NoS and also treated with the nuclear export inhibitor leptomycin B showed a nucleolar localization; expressed constructs lacking the NoS showed signal in the nucleoplasm outside the nucleoli. The authors hypothesized that the intranuclear distribution of FXR1 protein and FXR2 protein isoforms is likely to be mediated by a similar NoS localized in their C-terminal regions. This domain is absent in some FXR1 protein isoforms as well as in all FMR1 protein isoforms, suggesting functional differences for this family of proteins, possibly related to RNA metabolism in different tissues.
FXR1 is widely expressed in mammals and its expression pattern is complex, since several mRNA variants and protein isoforms are detected. In mouse, Huot et al. (2001) observed that the highest level of FXR1 is found in the adult testis. This tissue is an exception, since all known FXR1 protein isoforms, some of which have been considered tissue-specific, are detected in it. In young animals, changes in mRNA-spliced variants and their corresponding protein isoforms occur during spermatogenesis. Using biochemical, immunohistochemical, and electron microscopic techniques, the authors showed that FXR1 protein is associated with microtubule elements. Since the cytoskeletal framework is implicated in cellular plasticity as well as in mRNA transport, the authors proposed possible functions of the FXR proteins in these processes.
Siomi et al. (1996) noted that both FXR1 and FXR2 interact strongly with FMR1 and with each other. Using cell fractionation and sedimentation techniques, they found that FMR1, FRX1, and FXR2 associate with ribosomes, predominantly with the 60S large ribosomal subunit. FXR1 and FXR2 associated with 60S ribosomal subunits even in cells lacking FMR1 and in cells derived from a fragile X syndrome patient, indicating that FMR1 is not required for this association. Siomi et al. (1996) determined that the domain of FMR1 necessary for RNA binding is not necessary for FMR1 interaction with either FXR1 or FXR2.
Bolivar et al. (1998) identified FXR1 as an autoimmune antigen in a patient suffering from scleroderma, although it did not appear to be the major autoantigen. Immunolocalization studies with Jurkat cells undergoing induced apoptosis revealed redistribution of endogenous FXR1 from the cytoplasm to specific foci that resembled the bleb-like structures observed during apoptotic cell death.
Darnell et al. (2009) demonstrated that FXR1P and FXR2P (605339) KH2 domains bound kissing complex RNA ligands with the same affinity as the FMRP KH2 domain, although other KH domains did not. RNA ligand recognition by this family was highly conserved, as the KH2 domain of the single Drosophila ortholog of FMRP also bound kissing complex RNA. Kissing complex RNA was able to displace FXR1P and FXR2P from polyribosomes as it did for FMRP, and this displacement was FMRP-independent. Darnell et al. (2009) suggested that all 3 family members may recognize the same binding site on RNA mediating their polyribosome association, and that they may be functionally redundant with regard to this aspect of translational control. In contrast, FMRP was unique in its ability to recognize G-quadruplexes, suggesting the FMRP RGG domain may play a nonredundant role in the pathophysiology of fragile X syndrome.
Congenital Myopathy 9A with Respiratory Insufficiency and Bone Fractures
In a male infant and his affected fetus sib, conceived of consanguineous Egyptian parents (family 1), with congenital myopathy-9A with respiratory insufficiency and bone fractures (CMYO9A; 618822), Estan et al. (2019) identified a homozygous 4-bp deletion (c.1764_1767delACAG; 600819.0001) at the 3-prime end of exon 15 of the FXR1 gene, predicted to result in a frameshift and premature termination (Arg588SerfsTer37). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. Primary myoblasts derived from 1 of the patients with the delACAG mutation showed the presence of truncated 82- and 84-kD proteins, consistent with escape from nonsense-mediated mRNA decay (NMD). These abnormal proteins were localized in ring-shaped cytoplasmic granules that contained mRNA. Skeletal muscle from mutant mice carrying the homologous 4-bp deletion showed similar abnormalities (see ANIMAL MODEL).
Congenital Myopathy 9B, Proximal, with Minicore Lesions
In 3 adult sibs, born of unrelated parents (family 2), with congenital proximal myopathy-9B with minicore lesions (CMYO9B; 618823), Estan et al. (2019) identified a homozygous 1-bp deletion (c.1707delA; 600819.0002) at the 5-prime end of exon 15 of the FXR1 gene, predicted to result in a frameshift and premature termination (Lys569AsnfsTer57). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was found in heterozygous state in the unaffected mother; array CGH of the paternal allele indicated that the deceased father may have carried the mutation. The mutation was predicted to result in NMD (see ANIMAL MODEL).
In 3 patients from 2 unrelated families (A and B) with CMYO9B, Mroczek et al. (2022) identified a homozygous frameshift mutation in the FXR1 gene (c.1707dupA; 600819.0003). Two sibs, born of consanguineous Turkish parents (family C), with CMYO9B carried a homozygous frameshift mutation in the FXR1 gene (c.1699dupG; 600819.0004). Both mutations occurred at the 5-prime end of exon 15 of the FXR1 muscle isoform. The mutations were found by exome sequencing and segregated with the disorder in families B and C. Functional studies of the variants were not performed.
Mientjes et al. (2004) generated an Fxr1 knockout mouse model. Homozygous Fxr1 knockout neonates died shortly after birth. Histochemical analyses of both skeletal and cardiac muscle showed a disruption of cellular architecture and structure in embryonic day 19 (E19) Fxr1 neonates compared with wildtype littermates. In wildtype E19 skeletal and cardiac muscles, Fxr1 was localized to the costameric regions within the muscles. In E19 Fxr1 knockout littermates, in addition to the absence of Fxr1, costameric proteins vinculin (VCL; 193065), dystrophin (DMD; 300377), and alpha-actinin (ACTN1; 102575) were delocalized. A second mouse model (Fxr1 + neo), which expressed strongly reduced levels of Fxr1 relative to wildtype littermates, did not display the neonatal lethal phenotype seen in the Fxr1 knockouts, but did display a strongly reduced limb musculature and had a reduced life span of approximately 18 weeks. The authors proposed a role for Fxr1 in muscle mRNA transport/translation control, similar to that seen for Fmrp in neuronal cells.
Estan et al. (2019) found that inactivation of all isoforms of Fxr1 specifically in skeletal muscle myoblasts in mice resulted in neonatal lethality. Generation of the 4-bp deletion (ACAGdel) in exon 15 of the Fxr1 gene, similar to the mutation found in a family (family 1) with MYORIBF, caused a myopathic phenotype in mice, with decreased body weight, muscle mass, muscle strength, and bone mineral density compared to controls. Skeletal muscle from mutant mice showed reduced fiber size, increased central nuclei, predominance of type 1 fibers, and cores devoid of NADH-TR enzymatic activity. Transmission electron microscopy showed disintegration of Z-bands and sarcomere structure, or disorganized Z-lines and Z-line streaming with abnormal mitochondrial accumulation. Mutant mice with a different mutation, a 1-bp duplication (dupA), showed similar but much less severe abnormalities compared to those with the ACAGdel mutation. RT-PCR analysis showed that the ACAGdel mutation escaped NMD and resulted in Fxr1 expression at 74.7% of control levels, whereas the dupA mutation was subjected to NMD with decreased Fxr1 expression at about 30% of control levels. The mutant truncated protein resulting from the ACAGdel mutation was detected in cytoplasmic granules that contained mRNA, but were not stress granules, suggesting altered mRNA trafficking; this was confirmed by the finding of differentially expressed genes. Fxr1 protein expression was essentially absent in dupA myotubes, there were no abnormal ring-shaped granules, and cores were only sporadically observed. These findings indicated that skeletal muscle-specific FXR1 82- and 84-kD proteins are required for maintaining alignment and organization of Z-lines, and that dysregulated translation of specific mRNAs involved in Z-line organization may underlie the myopathic phenotype. The results also indicated that the severity of the disorder depends on the location of the FXR1 mutation, which leads to different pathogenetic mechanisms.
In a male infant, born of consanguineous Egyptian parents (family 1), with congenital myopathy-9A with respiratory insufficiency and bone fractures (CMYO9A; 618822), Estan et al. (2019) identified a homozygous 4-bp deletion (c.1764_1767delACAG) at the 3-prime end of exon 15 of the FXR1 gene, predicted to result in a frameshift and premature termination (Arg588SerfsTer37). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was not found in the 1000 Genomes Project, Exome Variant Server, ExAC, or gnomAD databases. An affected fetus from the same family was also homozygous for the mutation. The mutation was predicted to affect only the muscle-specific isoforms, the 82- and 84-kD proteins, and to escape nonsense-mediated mRNA decay with production of a truncated protein.
In 3 adult sibs, born of unrelated parents (family 2), with congenital myopathy-9B (CMYO9B; 618823), Estan et al. (2019) identified a homozygous 1-bp deletion (c.1707delA) at the 5-prime end of exon 15 of the FXR1 gene, predicted to result in a frameshift and premature termination (Lys569AsnfsTer57). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, was found in heterozygous state in the unaffected mother; array CGH of the paternal allele indicated that the deceased father may have carried the mutation. The mutation was predicted to result in nonsense-mediated mRNA decay.
In 3 patients from 2 unrelated families (families A and B) with congenital myopathy-9B (CMYO9B; 618823), Mroczek et al. (2022) identified a homozygous 1-bp duplication (c.1707dupA) in exon 15 of the FXR1 gene, predicted to result in a frameshift and premature termination (Pro570ThrfsTer7). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in family B; parental DNA was not available for family A. Functional studies of the variant were not performed. The patients, who were 45, 58, and 53 years of age, had onset of symptoms in early childhood, and remained ambulatory with difficulties as adults. The patient from family B had respiratory dysfunction.
In 2 sibs, born of consanguineous Turkish parents (family C), with congenital myopathy-9B (CMYO9B; 618823), Mroczek et al. (2022) identified a homozygous 1-bp duplication (c.1699dupG) in exon 15 of the FXR1 gene, predicted to result in a frameshift and premature termination (Glu567GlyfsTer10). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. Functional studies of the variant were not performed. The patients presented in early infancy with hypotonia and proximal muscle weakness. One sib had a progressive course with scoliosis and respiratory involvement, resulting in death at age 17 years. Her 2.5-year-old younger brother was unable to walk and showed axial hypotonia.
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