HGNC Approved Gene Symbol: RFX5
Cytogenetic location: 1q21.3 Genomic coordinates (GRCh38) : 1:151,340,640-151,347,252 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 1q21.3 | ?MHC class II deficiency 5 | 620818 | Autosomal recessive | 3 |
| MHC class II deficiency 3 | 620816 | Autosomal recessive | 3 |
The RFX5 gene encodes a subunit of the nuclear protein complex RFX, which binds to the X box of MHC class II promoters (see RFX2; 142765). This gene was called RFX5 because it was the fifth member to be identified of the family of DNA-binding proteins sharing a novel and highly characteristic DNA-binding domain called the RFX motif (Steimle et al., 1995).
Major histocompatibility complex (MHC) class II molecules are heterodimeric transmembrane glycoproteins consisting of alpha and beta chains. In man, there are 3 MHC class II isotypes: HLA-DR, -DP, and -DQ. MHC class II molecules play a key role in the immune system. They present exogenous antigenic peptides to the receptor of CD4+ T-helper lymphocytes, thereby triggering the antigen-specific T-cell activation events required for the initiation and sustenance of immune responses (summary by Durand et al., 1997).
Emery et al. (1996) reviewed RFX1, RFX5, and other members of the RFX family of DNA-binding proteins.
Using an expression cloning approach, Steimle et al. (1995) cloned RFX5 as the gene mutated in MHC class II deficiency complementation group C (MHC2D3; 620816). The deduced 616-amino acid RFX5 protein has a calculated molecular mass of 65 kD. In vitro-translated RFX5 had an apparent molecular mass of 75 kD by SDS-PAGE. RFX5 is the most divergent member of the RFX family of DNA-binding proteins, and it contains a 75-amino acid sequence with strong homology to the RFX DNA-binding motif. RFX5 also has a proline-rich sequence downstream of the DNA-binding domain.
Villard et al. (1997) mapped the RFX5 gene to chromosome 1q21 by fluorescence in situ hybridization.
Using electrophoretic mobility shift assays, Steimle et al. (1995) showed that the DNA-binding domain of RFX5 bound specifically to the X-box motif of MHC class II promoters. Further analysis confirmed that RFX5 was a subunit of the nuclear RFX complex. Transfection of RFX5 into cells from a patient with MHC class II deficiency of complementation group C restored expression of endogenous MHC class II genes.
Scholl et al. (1997) demonstrated that RFX5 can activate transcription only in cooperation with CIITA (600005), which encodes a protein with a defined acidic transcriptional activation domain. RFX5 and CIITA associate to form a complex capable of activating transcription of class II MHC promoters. In this complex, promoter specificity is determined by the DNA binding domain of RFX5; the general transcription apparatus is recruited by the acidic activation domain of CIITA.
Nekrep et al. (2000) demonstrated a direct interaction between the C terminus of RFXAP (601861) and RFXANK (603200); mutant RFXAP or RFXANK proteins failed to bind. The authors found that RFX5 binds only to the RFXANK-RFXAP scaffold and not to either protein alone. However, neither the scaffold nor RFX5 alone can bind DNA. Nekrep et al. (2000) concluded that the binding of the RFXANK-RFXAP scaffold to RFX5 leads to a conformational change in the latter that exposes the DNA-binding domain of RFX5. The DNA-binding domain of RFX5 anchors the RFX complex to MHC class II X and S promoter boxes. Another part of the RFX5 protein interacts with MHC2TA.
Hosts and pathogens evolve various responses for controlling infection and evading destruction, respectively. Using column chromatography, Zhong et al. (2001) identified a factor in Chlamydia trachomatis, the causative organism of trachoma and chronic urogenital infection, that degrades the transcription factors RFX5 and USF1 (191523). The degradation of these host factors correlates with the suppression of MHC class I and class II antigen expression in infected cells, thereby suppressing the host immune response.
MHC Class II Deficiency 3
In cells derived from 2 sibs, identified as THF and EDF, with MHC class II deficiency-3 (MHC2D3; 620816), Villard et al. (1997) identified a homozygous splice site mutation in the RFX5 gene (601863.0001) that resulted in a small intragenic deletion, a frameshift, and premature termination. Both unaffected parents were heterozygous for the mutation.
In cells derived from a patient identified as Ro with MHC2D3, Steimle et al. (1995) demonstrated and Villard et al. (1997) confirmed a homozygous nonsense mutation in the RFX5 gene (601863.0002). Villard et al. (1997) demonstrated that the patient was homozygous for the mutated allele, whereas both parents were heterozygous.
In a patient (OSE) with MHC2D3, Peijnenburg et al. (1999) identified a homozygous splice site mutation in the RFX5 gene (601863.0004). Transfection of wildtype RFX5 cDNA into the patient's fibroblasts resulted in correction of the defect.
In 3 unrelated boys (P5, P6, and P7), each born of consanguineous Egyptian parents, with MHC2D3, El Hawary et al. (2019) identified homozygous mutations in the RFX5 gene (see, e.g., R239X; 601863.0006). The mutations were found by whole-exome sequencing and confirmed by Sanger sequencing. Familial segregation studies and functional studies of the variants were not performed.
In 2 unrelated patients (P18 and P17), each born of consanguineous Iranian parents, with MHC2D3, Mousavi Khorshidi et al. (2023) identified homozygous mutations in the RFX5 gene (c.1480dupC, 601863.0007 and D145H, 601863.0008), respectively. The mutations, which were found by whole-exome sequencing and confirmed by Sanger sequencing, were present in the heterozygous state in the unaffected parents. Functional studies of the variants were not performed. P17, with the D145H missense mutation, was alive at 12 years of age, without bone marrow transplant. P18, with the 1-bp duplication, died at 11 months of age.
In a 2.9-year-old boy (P4), born of consanguineous Turkish parents, with MHC2D3, Unsal et al. (2024) identified a homozygous frameshift mutation in the RFX5 gene (601863.0009). Two other patients (P1 and P8), also born of consanguineous Turkish parents, with a similar phenotype had a homozygous missense variant in the RFX5 gene (A206P) that was classified as a variant of uncertain significance according to ACMG criteria. The variants were found by whole-exome sequencing or Sanger sequencing; familial segregation studies and functional studies of the variants were not performed.
MHC Class II Deficiency 5
In cell lines (Ker) derived from a pair of Turkish twin brothers with MHC class II deficiency-5 (MHC2D5; 620818), originally reported by Wolf et al. (1995) and Douhan et al. (1996), Nekrep et al. (2002) identified a homozygous missense mutation in the RFX5 gene (R149Q; 601863.0005). The unaffected parents were heterozygous for the mutation. The mutation occurred in the DNA-binding domain of RFX5 (residues 92 to 168). Functional and structural modeling analyses indicated that the mutant protein was incapable of binding the X box of the HLA-DRA (142860) promoter; expression of wildtype RFX5 in the Ker cell lines rescued MHC class II expression.
In 2 sibs, identified as THF and EDF, with MHC class II deficiency-3 (MHC2D3; 620816), Villard et al. (1997) demonstrated a homozygous 10-nucleotide deletion involving nucleotides 259-268 in the RFX5 gene upstream of the DNA-binding domain region. The deletion led to a frameshift followed by an out-of-frame stop codon situated 66 nucleotides downstream. Only the deleted form of RFX5 mRNA was present in these sibs. Studies of genomic DNA demonstrated that the 10-nucleotide deletion resulted from a point mutation in a splice donor site. The primary mutation was a G-to-A transition at position +5 in the splice donor site situated 3-prime of exon 2. This resulted in the use of a cryptic splice donor site situated 10 nucleotides upstream in exon 2 and hence in the excision of the last 10 nucleotides of exon 2 from the mRNA. Both parents were heterozygous for the mutation.
In a patient identified as Ro, with MHC class II deficiency-3 (MHC2D3; 620816), Steimle et al. (1995) demonstrated and Villard et al. (1997) confirmed a homozygous c.1032C-T transition in the RFX5 gene, converting an arginine codon (CGA) to a premature stop codon (TGA). Villard et al. (1997) demonstrated that the patient was homozygous for the mutated allele, whereas both parents were heterozygous.
In a patient identified as SJO, with MHC class II deficiency-3 (MHC2D3; 620816), Villard et al. (1997) identified compound heterozygous mutations in the RFX5 gene. One allele had a G-to-A transition at position -1 resulting in the use of a cryptic splice acceptor site situated 5 nucleotides downstream in exon 5 and deletion of the first 5 nucleotides (386-390) of exon 5 from the mRNA. The precise mutation affecting the second RFX5 allele in SJO had not been defined; however, no intact mRNA derived from that allele was detectable in SJO (Steimle et al., 1995).
In a patient of Turkish origin (OSE) with MHC class II deficiency-3 (MHC2D3; 620816), Peijnenburg et al. (1999) identified a homozygous G-to-A transition in a splice acceptor site in the RFX5 gene. The splicing defect resulted in a 4-bp deletion (c.312_315CAAGdel), a frameshift, and premature termination. Transfection of wildtype RFX5 cDNA into the patient's fibroblasts resulted in correction of the defect. As a result, the mutated RFX5 mRNA encoded a truncated protein of 82 amino acids which lacked the DNA binding domain (DBD). Both parents were heterozygous for the mutation.
In cell lines (Ker) derived from a pair of Turkish twin brothers with MHC class II deficiency-5 (MHC2D5; 620818) originally reported by Wolf et al. (1995), Nekrep et al. (2002) identified a G-to-A transition at nucleotide 446 of the RFX5 gene, resulting in an arg149-to-gln (R149Q) mutation in the DNA-binding domain. In vitro functional expression studies showed that the mutant protein was unable to bind to the promoter of HLA-DRA (142860). In contrast to patients with other RFX5 mutations, the twin boys had a relatively mild phenotype.
In a male infant (P7), born of consanguineous Egyptian parents, with MHC class II deficiency-3 (MHC2D3; 620816), El Hawary et al. (2019) identified a homozygous c.715C-T transition in exon 9 of the RFX5 gene, predicted to result in an arg239-to-ter (R239X) substitution. The mutation was found by whole-exome sequencing and confirmed by Sanger sequencing; familial segregation studies and functional studies of the variant were not performed. Hamosh (2024) noted that the R239X variant was present in 5 of 1,613,894 alleles in the gnomAD database (v4.1.0, frequency of 3.1 x 10(-6)), never in homozygosity.
In a male infant (P18), born of consanguineous Iranian parents, with MHC class II deficiency-3 (MHC2D3; 620816), Mousavi Khorshidi et al. (2023) identified a homozygous 1-bp duplication (c.1480dupC) in exon 10 of the RFX5 gene, predicted to result in several amino acid changes at residue gln494 in the C terminus, which would likely modify the protein structure. The mutation was found by whole-exome sequencing and confirmed by Sanger sequencing. The unaffected parents were heterozygous for the mutation. Functional studies of the variant were not performed. He died at 11 months of age.
In a 12-year-old boy (P17), born of consanguineous Iranian parents, with MHC class II deficiency-3 (MHC2D3; 620816), Mousavi Khorshidi et al. (2023) identified a homozygous c.433G-C transversion in exon 6 of the RFX5 gene, resulting in an asp145-to-his (D145H) substitution in the DNA-binding domain. The mutation was found by whole-exome sequencing and confirmed by Sanger sequencing. The unaffected parents were heterozygous for the mutation. Functional studies of the variant were not performed. The patient was alive at 12 years of age, without bone marrow transplantation. Hamosh (2024) noted that the D145H variant was present in 69 of 1,614,086 alleles in the gnomAD database (v4.1.0, frequency of 4.3 x 10(-5)), never in homozygosity.
In a 2.9-year-old boy (P4), born of consanguineous Turkish parents, with MHC class II deficiency-3 (MHC2D3; 620816), Unsal et al. (2024) identified a homozygous 2-bp deletion (c.1239_1240delGA) in exon 11 of the RFX5 gene, predicted to result in a frameshift and premature termination (Asn414fsTer8). The mutation was found by whole-exome sequencing; familial segregation studies and functional studies of the variant was not performed.
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