Alternative titles; symbols
HGNC Approved Gene Symbol: RFC1
SNOMEDCT: 1236804009;
Cytogenetic location: 4p14 Genomic coordinates (GRCh38): 4:39,287,456-39,366,362 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 4p14 | Cerebellar ataxia, neuropathy, and vestibular areflexia syndrome | 614575 | Autosomal recessive | 3 |
The RFC1 gene encodes the large subunit of replication factor C, a 5-subunit DNA polymerase accessory protein required for the coordinated synthesis of both DNA strands during replication or after DNA damage (summary by Cortese et al., 2019). It is a DNA-dependent ATPase that binds in a structure-specific manner to the 3-prime end of a primer hybridized to a template DNA, an activity thought intrinsic to the 140-kD component of this multisubunit complex (Bunz et al., 1993).
Bunz et al. (1993) isolated and analyzed cDNAs encoding the 140-kD subunit. An open reading frame of 3.4 kb was predicted to encode a 1,148-amino acid protein with a predicted molecular mass of 130 kD. A putative ATP-binding motif was observed that is similar to a motif in several of the smaller subunits of RFC and in functionally homologous replication factors of bacterial and viral origin. The predicted protein showed similarities to other DNA-binding proteins.
Luckow et al. (1994) isolated a full-length mouse cDNA encoding a protein that binds in a sequence-unspecific manner to DNA, is localized exclusively in the nucleus, and represents, they concluded, the 140-kD subunit of mouse replication factor C. They found that it showed 83% identity to the human protein.
Human replication factor C (RFC), also called activator-1, is a multimeric primer-recognition protein consisting of 5 distinct subunits of 145, 40, 38, 37, and 36.5 kD. Human RFC was purified from extracts of HeLa cells as a host factor essential for the in vitro replication of simian virus 40 (SV40) DNA (Okumura et al., 1995). RFC, in the presence of ATP, assembles proliferating-cell nuclear antigen (PCNA; 176740) and DNA polymerase-delta (174761) or polymerase-epsilon (174762) on primed DNA templates. The complex of primed DNA-RFC-PCNA-DNA polymerase, when supplemented with dNTPs, results in the efficient elongation of DNA in the presence of human single-stranded DNA binding protein. Studies with the complete 5-subunit holoenzyme indicated that the large subunit binds to DNA and the 40-kD subunit binds ATP. The other subunits may play discrete roles in the elongation process catalyzed by polymerase. The subunit genes are numbered in sequence of decreasing molecular weight: RFC1, RFC2 (600404), RFC3 (600405), RFC4 (102577), and RFC5 (600407).
Using interaction cloning, Uchiumi et al. (1996) found that the large subunit of RFC interacts with the DNA sequence repeats of telomeres. They found that RFC recognizes the 5-prime-phosphate termini of double-stranded telomeric repeats. The authors suggested that RFC may be involved in telomere stability or turnover.
Wang et al. (2000) used immunoprecipitation and mass spectrometry analyses to identify BRCA1 (113705)-associated proteins. They found that BRCA1 is part of a large multisubunit protein complex of tumor suppressors, DNA damage sensors, and signal transducers. They named this complex BASC, for 'BRCA1-associated genome surveillance complex.' Among the DNA repair proteins identified in the complex were ATM (607585), BLM (604610), MSH2 (609309), MSH6 (600678), MLH1 (120436), the RAD50 (604040)-MRE11 (600814)-NBS1 (602667) complex, and the RFC1-RFC2 (600404)-RFC4 (102577) complex. Wang et al. (2000) suggested that BASC may serve as a sensor of abnormal DNA structures and/or as a regulator of the postreplication repair process.
The RB1 protein (614041) promotes cell survival after DNA damage. Pennaneach et al. (2001) showed that the LxCxE-binding site in RB1 mediates both cell survival and cell cycle arrest after DNA damage. RFC complex plays an important role in DNA replication. Pennaneach et al. (2001) described a function of RFC1 in promoting cell survival after DNA damage. RFC1 contains an LxCxE motif, and mutation of this motif abolished the protective effect of RFC1. The inability of wildtype RFC1 to promote cell survival in RB1 null cells was rescued by RB1 but not by RB1 mutants defective in binding LxCxE proteins. RFC thus enhances cell survival after DNA damage in an RB1-dependent manner.
Dilley et al. (2016) defined break-induced telomere synthesis and showed that it utilizes a specialized replisome, which underlies alternate lengthening of telomeres (ALT) maintenance. DNA double-strand breaks enact nascent telomere synthesis by long-tract unidirectional replication. PCNA loading by RFC acts as the initial sensor of telomere damage to establish predominance of DNA polymerase delta through its POLD3 (611415) subunit. Break-induced telomere synthesis requires the RFC-PCNA-Pol-delta axis, but is independent of other canonical replisome components, ATM and ATR (601215), or the homologous recombination protein RAD51 (179617).
Cannavo et al. (2020) showed that human MutS-gamma, a complex of MSH4 (602105) and MSH5 (603382) that supports crossing over, bound branched recombination intermediates and associated with MutL-gamma, a complex of MLH1 and MLH3 (604395), stabilizing the ensemble at joint molecule structures and adjacent double-stranded DNA. MutS-gamma directly stimulated DNA cleavage by the MutL-gamma endonuclease. MutL-gamma activity was further stimulated by exonuclease-1 (EXO1; 606063), but only when MutS-gamma was present. RFC and PCNA were additional components of the nuclease ensemble, thereby triggering crossing over. S. cerevisiae strains in which MutL-gamma could not interact with Pcna presented defects in forming crossovers. The MutL-gamma-MutS-gamma-EXO1-RFC-PCNA nuclease ensemble preferentially cleaved DNA with Holliday junctions, but it showed no canonical resolvase activity. Instead, the data suggested that the nuclease ensemble processed meiotic recombination intermediates by nicking double-stranded DNA adjacent to the junction points. The authors proposed that, since DNA nicking by MutL-gamma depends on its cofactors, the asymmetric distribution of MutS-gamma and RFC-PCNA on meiotic recombination intermediates may drive biased DNA cleavage. They suggested that this mode of MutL-gamma nuclease activation may explain crossover-specific processing of Holliday junctions or their precursors in meiotic chromosomes.
Independently, Kulkarni et al. (2020) showed that PCNA was important for crossover-biased resolution. In vitro assays with human enzymes showed that PCNA and RFC were sufficient to activate the MutL-gamma endonuclease. MutL-gamma was further stimulated by the codependent activity of the pro-crossover factors EXO1 and MutS-gamma, the latter of which binds Holliday junctions. The authors found that MutL-gamma also bound various branched DNAs, including Holliday junctions, but it did not show canonical resolvase activity, suggesting that the endonuclease incises adjacent to junction branch points to achieve resolution. In vivo, Rfc facilitated MutL-gamma-dependent crossing over in budding yeast. Moreover, Pcna localized to prospective crossover sites along synapsed chromosomes. Kulkarni et al. (2020) concluded that their data highlight similarities between crossover resolution and the initiation steps of DNA mismatch repair and evoke a novel model for crossover-specific resolution of double Holliday junctions during meiosis.
Crystal Structure
Bowman et al. (2004) reported the crystal structure of the 5-protein clamp loader complex (replication factor-C, RFC) of the yeast S. cerevisiae, bound to the sliding clamp (proliferating cell nuclear antigen, or PCNA). Tight interfacial coordination of the ATP analog ATP-gamma-S by RFC resulted in a spiral arrangement of the ATPase domains of the clamp loader above the PCNA ring. Placement of a model for primed DNA within the central hole of PCNA revealed a striking correspondence between the RFC spiral and the grooves of the DNA double helix. Bowman et al. (2004) concluded that this model, in which the clamp loader complex locks into primed DNA in a screwcap-like arrangement, provides a simple explanation for the process by which the engagement of primer-template junctions by the RFC:PCNA complex results in ATP hydrolysis and release of the sliding clamp on DNA.
Luckow et al. (1994) assigned RFC1, the gene for the largest subunit of replication factor C, to 4p14-p13 by fluorescence in situ hybridization. They mapped the homolog in the mouse to chromosome 5. Lossie et al. (1995) likewise mapped this gene, which they symbolized Recc1, to human chromosome 4 by human/rodent somatic cell hybrid analysis and to mouse chromosome 5 by haplotype analysis of an interspecific backcross.
In 25 affected individuals from 11 unrelated families with cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS; 614575), Cortese et al. (2019) identified a homozygous expanded 5-bp intronic repeat, (AAGGG)n, in the RFC1 gene. The variant, which was found by a combination of linkage analysis and whole-genome and whole-exome sequencing, was confirmed by Sanger sequencing. Screening of an additional cohort of 150 patients with sporadic late-onset ataxia identified the homozygous (AAGGG)n expansion in 33 cases (22%). Haplotype analysis showed that all affected individuals from the 11 families and 32 of the sporadic cases shared the same haplotype. The reference allele, a simple tandem pentanucleotide AAAAG repeat of 11 (AAAAG)11, was replaced by a variable number of expanded pentanucleotide AAGGG repeated units. The expansion size varied across different families, ranging from about 400 to 2,000 repeats, but the majority of cases had about 1,000 repeats. Repeat size was relatively stable in sibs, and there was no association between age at onset and repeat size. There were no instances of vertical transmission; all families studied consisted of affected sibs or first cousins in the same generation. Patient cells showed normal expression levels of RFC1 mRNA and protein, and postmortem brain tissue from 1 CANVAS patient had normal levels of RFC1 and FXN (606829) compared to controls. However, patient cells showed some evidence of altered pre-mRNA processing with an increase in the retention of intron 2 compared to controls. Patient fibroblasts did not show increased susceptibility to DNA damage. Cortese et al. (2019) noted that their studies did not show evidence of a loss-of-function effect.
Beecroft et al. (2020) identified a biallelic (AAAGG)10-25(AAGGG)n intronic repeat expansion of the RFC1 gene (102579.0002) in 13 patients with CANVAS: 2 from a Cook Island Maori family, 6 from a New Zealand Maori family, and 5 from unrelated New Zealand Maori families. Two of the affected individuals also had an additional repeat sequence, (AAAGG)4-6, at the distal end of the repeat sequence. A common haplotype was identified in these patients, suggesting a founder effect, with the most recent common ancestor estimated to date to 1369-1499 CE. There were no apparent phenotypic differences between this patient cohort and patients with the (AAGGG)n repeat expansion (102579.0001).
In 2 patients with CANVAS, Benkirane et al. (2022) identified compound heterozygous mutations in the RFC1 gene, an AAGGG repeat expansion on one allele in both patients and a nonsense mutation (R388X; 102579.0003) in patient 1 and a frameshift mutation (c.575delA; 102579.0004) in patient 2 on the other allele. In both patients, RFC1 expression was reduced from the allele with the truncating mutation. Benkirane et al. (2022) concluded that CANVAS likely results from a loss of function of RFC1. Clinical features in these 2 patients did not differ from what had been reported in patients with homozygosity for repeat expansion mutations in RFC1.
Weber et al. (2023) identified compound heterozygous mutations in the RFC1 gene in 2 unrelated patients with CANVAS; both patients had an AAGGG repeat expansion on one allele with a different mutation on the other allele, c.2535+2T-C (102579.0005) or c.2690+1G-A (102579.0006). Both patients had an earlier onset of disease than that reported for classical CANVAS.
In 25 affected individuals from 11 unrelated families with cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS; 614575), Cortese et al. (2019) identified a homozygous expanded 5-bp intronic repeat, (AAGGG)n, in the RFC1 gene. The variant, which was found by a combination of linkage analysis and whole-genome and whole-exome sequencing, was confirmed by Sanger sequencing. Screening of an additional cohort of 150 patients with sporadic late-onset ataxia identified the homozygous (AAGGG)n expansion in 33 patients (22%). The reference allele, a simple tandem pentanucleotide AAAAG repeat of 11 (AAAAG)11, was replaced by a variable number of expanded pentanucleotide AAGGG repeated units. The expansion size varied across different families, ranging from about 400 to 2,000 repeats, but the majority of cases had about 1,000 repeats. Repeat size was relatively stable in sibs, and there was no association between age at onset and repeat size. There were no instances of vertical transmission; all families studied consisted of affected sibs or first cousins in the same generation. The expansion resides at the 3-prime end of a deep intronic AluSx3 element and increases the size of the poly(A) tail. Haplotype analysis showed that all affected individuals from the 11 families and 32 of the sporadic cases shared the same haplotype, which had had a carrier frequency of 18% in the 1000 Genomes Project database. Biallelic AAGGG repeat expansions were not found in 304 controls, although 0.7% carried an AAGGG expansion in heterozygous state. The region where the expansions occurred was highly polymorphic and often showed interruptions and nucleotide changes in the expanded sequence. Patient cells showed normal expression levels of RFC1 mRNA and protein, and postmortem brain tissue from 1 CANVAS patient had normal levels of RFC1 and FXN (606829) compared to controls. However, patient cells showed some evidence of altered pre-mRNA processing with an increase in the retention of intron 2 compared to controls. Patient fibroblasts did not show increased susceptibility to DNA damage. Cortese et al. (2019) noted that their studies did not show evidence of a loss-of-function effect.
In 2 patients with CANVAS, Benkirane et al. (2022) identified compound heterozygosity for mutations in the RFC1 gene. Both patients had the AAGGG repeat expansion on one allele; patient 1 also carried a c.1162C-T transition, resulting in an arg388-to-ter (R388X; 102579.0003) substitution, and patient 2 carried a 1-bp deletion (c.575delA; 102579.0004), resulting in a frameshift and premature termination (Asn192IlefsTer7). The mutations were identified by whole-exome sequencing and repeat primer PCR. In patient 1, the repeat expansion was inherited from the mother, and although the father was not available for testing, SNP analysis determined that the R388X mutation presumably occurred de novo on the paternal allele. In patient 2, the repeat expansion was inherited from the father, and the c.575delA mutation was inherited from the mother. RFC1 expression analysis in patient blood demonstrated that both the R388X and c.575delA mutations resulted in decreased gene expression.
In 2 patients with CANVAS, Weber et al. (2023) identified compound heterozygosity for mutations in the RFC1 gene. Both patients carried the AAGGG repeat expansion on one allele. Case 1 also carried a c.2535+2T-C transition (102579.0005) at the splice acceptor site of exon 19, predicted to cause a splicing abnormality. Case 2 carried a c.2690+1G-A transition (102579.0006) at the splice acceptor site of exon 20, predicted to cause a splicing abnormality. The mutations were identified by whole-exome sequencing, repeat primer PCR, or RFC1 gene screening.
In 2 patients from a Cook Island Maori family, 6 patients from a New Zealand Maori family, and 5 unrelated New Zealand Maori patients with cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS; 614575), Beecroft et al. (2020) identified a biallelic (AAAGG)10-25(AAGGG)n intronic repeat expansion of the RFC1 gene. Two of the affected individuals also had an additional repeat, (AAAGG)4-6, at the distal end of the repeat sequence. The mutations were identified by whole-genome sequencing, whole-exome sequencing, or direct gene analysis. The repeat expansions were characterized by repeat-primed PCR. One unaffected individual from each family was found to be a carrier for the repeat expansion. A common haplotype was identified in these patients, suggesting a founder effect with the most recent common ancestor estimated to date to 1369-1499 CE.
For discussion of the c.1162C-T transition (c.1162C-T, NM_002913.5) in the RFC1 gene, resulting in an arg388-to-ter (R388X) substitution, that was identified in compound heterozygous state in a patient (patient 1) with cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS; 614575) by Benkirane et al. (2022), see 102579.0001.
For discussion of the 1-bp deletion (c.575delA, NM_002913.5) in the RFC1 gene, resulting in a frameshift and premature termination (Asn192IlefsTer7), that was identified in compound heterozygous state in a patient (patient 2) with cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS; 614575) by Benkirane et al. (2022), see 102579.0001.
For discussion of the c.2535+2T-C transition (c.2535+2T-C, NM_002913.5) in the RFC1 gene, predicted to cause a splicing abnormality, that was identified in compound heterozygous state in a patient (case 1) with cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS; 614575) by Weber et al. (2023), see 102579.0001.
For discussion of the c.2690+1G-A transition (c.2690+1G-A, NM_002913.5) in the RFC1 gene, predicted to cause a splicing abnormality, that was identified in compound heterozygous state in a patient (case 2) with cerebellar ataxia, neuropathy, and vestibular areflexia syndrome (CANVAS; 614575) by Weber et al. (2023), see 102579.0001.
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