HGNC Approved Gene Symbol: RFX3
Cytogenetic location: 9p24.2 Genomic coordinates (GRCh38) : 9:3,218,297-3,526,001 (from NCBI)
The RFX3 gene encodes a transcription factor with a highly conserved DNA-binding domain. It is expressed in several tissues, including the developing and adult brain (summary by Harris et al., 2021).
Reith et al. (1994) commented that the RFX family members, particularly RFX3 and RFX1 (600006), constitute the nuclear complexes referred to previously as enhancer factor C (EF-C), EP, and methylation-dependent DNA-binding protein (MDBP), or rpL30-alpha.
Reith et al. (1994) identified and cloned 3 members of the RFX gene family from both human and mouse using lambda gt11 cDNA libraries. The RFX3 gene encodes a deduced 707-amino acid polypeptide. Homology between the 3 RFX proteins is restricted largely to 5 conserved regions, including the 2 domains required for DNA binding and dimerization. RFX1, RFX2 (142765), and RFX3 all have similar DNA-binding specificities. The RFX monomers can heterodimerize both in vivo and in vitro but all 3 are capable of binding DNA as monomers. Reith et al. (1994) showed that the RFX3 transcript is expressed in many mouse tissues, with highest expression in the brain, intestine, and testis but low expression in the seminal vesicle.
Using immunostaining analysis, Baas et al. (2006) showed that Rfx3 was expressed in the subcommissural organ (SCO), choroid plexuses (CPs), and ventricular ependymocytes during mouse brain development. Expression in ventricular ependymal cells increased progressively during development.
Harris et al. (2021) noted that RFX3 is highly expressed in maturing excitatory neurons in the cerebral cortex during human brain development. RFX3 shows highest expression in glutamatergic layer 2/3 neurons, followed by astrocytes.
Emery et al. (1996) reviewed the evolution and function of members of the RFX family of DNA binding proteins.
Hartz (2015) mapped the RFX3 gene to chromosome 9p24.2 based on an alignment of the RFX3 sequence (GenBank BC022191) with the genomic sequence (GRCh38).
Using functional genomic analysis, Elkon et al. (2015) identified RFX transcription factors as essential and evolutionarily conserved regulators of mouse hair cell-specific transcriptomes. Several RFXs, including Rfx1 and Rfx3, were expressed in developing mouse hair cells.
Associations Pending Confirmation
Harris et al. (2021) identified 15 probands with an autosomal dominant neurodevelopmental disorder with behavioral abnormalities associated with heterozygous variants in the RFX3 gene identified by exome sequencing through the GeneMatcher Program (see, e.g., 601337.0001). All variants occurred de novo, except for 1 family (family 8) in which an affected parent transmitted the variant to 3 affected children (601337.0002). Of the 15 variants identified, there were 2 frameshifts, 2 splice site variants, 8 missense variants affecting conserved residues in functional domains, 1 in-frame deletion, 1 two-exon deletion, and 1 gene deletion. None were present in the gnomAD database. Functional studies of the variants were not performed, but a few caused decreased protein expression when expressed in HeLa cells. The authors postulated haploinsufficiency with a loss-of-function effect. The patients, who ranged from 4 to 33 years of age, showed neurodevelopmental delays, with global developmental delay in young children (78%), variably impaired intellectual development (borderline to moderate), speech and language delay in most, and behavioral abnormalities, including autism spectrum disorder (ASD, 72%) and ADHD (56%). Most showed additional behavioral disorders marked by easy excitability/overstimulation, hypersensitivity to sensory stimuli, and emotional dysregulation and/or aggression. In some cases, behavioral problems and/or cognitive decline occurred around puberty/adolescence. Three patients were described as having manic and/or psychotic symptoms, including 2 with hallucinations. Other features included seizures (3 patients, 17%), hypotonia (in about half), sleep difficulties (44%), and nonspecific dysmorphic features (in 61%), such as broad nasal bridge, high-arched palate, macro- or microcephaly, and hand and foot abnormalities (tapered fingers, widely spaced toes). However, no consistent recognizable features were shared by all individuals. Brain imaging, performed in 8 patients, was normal in 4 and showed variable abnormalities in 4.
Bonnafe et al. (2004) found that Rfx3 -/- mice had a high rate of embryonic lethality. Mice that survived exhibited growth retardation that increased with age. Loss of Rfx3 resulted in a severe perturbation of mechanisms controlling left-right (LR) asymmetry determination during embryonic development, leading to situs inversus in approximately 6% of newborns. Rfx3 was expressed in ciliated cells of embryonic node and regulated ciliary growth, and Rfx3 -/- embryos showed severe defects in nodal cilia. The authors found that Rfx3 controlled expression of D2lic (DYNC2LI1; 617083), a gene implicated in intraflagellar transport.
Elkon et al. (2015) found that conditional knockout mice lacking Rfx1 or Rfx3 in inner ear hair cells had normal hearing, but that mice lacking both Rfx1 and Rfx3 had rapidly progressive hearing loss. Loss of both Rfx1 and Rfx3 did not affect early development and maturation of hair cells, but it led to programmed cell death in outer hair cells. The authors concluded that RFX1 and RFX3 have critical roles in regulating survival of postnatal terminally differentiating outer hair cells.
Baas et al. (2006) found that Rfx3 -/- mice that survived past birth had congenital hydrocephalus accompanied by a general deterioration in health characterized by prostration and weight loss, which eventually led to killing of the mice. Ventricular ependymal cells did not have clear ciliary defects in Rfx3 -/- mice, but CP cells showed a global cell polarity defect, and specialized ependymal cells of the SCO were either absent or inappropriately differentiated. Absence of Rfx3 also led to deregulation of expression SCO-spondin (SSPO; 617356), an early and specific marker protein for secretory ependymal cells of the SCO.
Magnani et al. (2015) noted that deletion of Rfx3 in mice causes defects in right-left symmetry, malformation of the corpus callosum, and hydrocephalus. They found that Rfx3 -/- mice also showed malformation of the thalamocortical tract. Only a small proportion of thalamocortical axons reached the dorsal telencephalon, and most either failed to leave the diencephalon or migrated toward the amygdala. These defects correlated with abnormal patterning of the prethalamus. Some corticothalamic axons also migrated toward the amygdala. In addition, the pial surface of rostroventral telencephalon showed neural heterotopias that contained a mixture of cells originating from the lateral ganglionic eminence and medial ganglionic eminence. These defects were accompanied by abnormal patterning of attractive and repulsive guidance molecules.
Laclef et al. (2015) found that overexpression of the short repressor isoform of Gli3 (165240), Gli3r, rescued corpus callosum malformation, guidepost organization, and midline patterning in Rfx3 -/- embryos. However, expression of Gli3r did not rescue the ventral telencephalic phenotype in Rfx3 -/- mutants.
This variant is classified as a variant of unknown significance because its contribution to an autosomal dominant intellectual developmental disorder with behavioral abnormalities has not been confirmed.
In a 20-year-old male patient (RFX3-1) with an intellectual developmental disorder with behavioral abnormalities, Harris et al. (2021) identified a de novo heterozygous 3-bp in-frame deletion (c.584_586delGAA, NM_134428.2) in the RFX3 gene, resulting in the deletion of conserved residue glu195 (glu195del) within the DNA binding domain. The variant, which was found by exome sequencing, was not present in either parent or in the dbSNP or gnomAD databases. Expression of the variant in HeLa cells resulted in decreased RFX3 protein expression, suggesting that it causes protein instability. The findings suggested haploinsufficiency with a loss-of-function effect. The patient showed development delay in early childhood, with delayed language and motor skills. He was subsequently diagnosed with intellectual disability, autism spectrum disorder (ASD), and ADHD. Additional features included aggressive behaviors beginning around adolescence, mood lability, impulsivity, and hypersensitivity to noise. Growth parameters, including head circumference, were normal. He also had mild hypotonia, joint laxity, and mild dysmorphic features, including high-arched palate and downturned corners of the mouth. Neuroimaging was not performed.
This variant is classified as a variant of unknown significance because its contribution to an autosomal dominant intellectual developmental disorder with behavioral abnormalities has not been confirmed.
In a 33-year-old woman and her 3 children (family 8) with an intellectual developmental disorder with behavioral abnormalities, Harris et al. (2021) identified a heterozygous 2-bp deletion (c.1486_1487, NM_134428.2) in the RFX3 gene, predicted to result in a frameshift and premature termination (Leu496AlafsTer7). The variant, which was found by exome sequencing, was not present in the gnomAD database. Functional studies of the variant and studies of patient cells were not performed, but it was predicted to result in haploinsufficiency with a loss-of-function effect. The patients had global developmental delay with variably impaired intellectual development and language delay. Two had features of autism spectrum disorder, 1 showed aggression, and 1 had ADHD. One of the affected children had challenging behaviors and was not talking at 6 years of age.
Baas, D., Meiniel, A., Benadiba, C., Bonnafe, E., Meiniel, O., Reith, W., Durand, B. A deficiency in RFX3 causes hydrocephalus associated with abnormal differentiation of ependymal cells. Europ. J. Neurosci. 24: 1020-1030, 2006. [PubMed: 16930429] [Full Text: https://doi.org/10.1111/j.1460-9568.2006.05002.x]
Bonnafe, E., Touka, M., AitLounis, A., Baas, D., Barras, E., Ucla, C., Moreau, A., Flamant, F., Dubruille, R., Couble, P., Collignon, J., Durand, B., Reith, W. The transcription factor RFX3 directs nodal cilium development and left-right asymmetry specification. Molec. Cell. Biol. 24: 4417-4427, 2004. [PubMed: 15121860] [Full Text: https://doi.org/10.1128/MCB.24.10.4417-4427.2004]
Elkon, R., Milon, B., Morrison, L., Shah, M., Vijayakumar, S., Racherla, M., Leitch, C. C., Silipino, L., Hadi, S., Weiss-Gayet, M., Barras, E., Schmid, C. D., and 12 others. RFX transcription factors are essential for hearing in mice. Nature Commun. 6: 8549, 2015. Note: Electronic Article. [PubMed: 26469318] [Full Text: https://doi.org/10.1038/ncomms9549]
Emery, P., Durand, B., Mach, B., Reith, W. RFX proteins, a novel family of DNA binding proteins conserved in the eukaryotic kingdom. Nucleic Acids Res. 24: 803-807, 1996. [PubMed: 8600444] [Full Text: https://doi.org/10.1093/nar/24.5.803]
Harris, H. K., Nakayama, T., Lai, J., Zhao, B., Argyrou, N., Gubbels, C. S., Soucy, A., Genetti, C. A., Suslovitch, V., Rodan, L. H., Tiller, G. E., Lesca, G., and 69 others. Disruption of RFX family transcription factors causes autism, attention-deficit/hyperactivity disorder, intellectual disability, and dysregulated behavior. Genet. Med. 23: 1028-1040, 2021. [PubMed: 33658631] [Full Text: https://doi.org/10.1038/s41436-021-01114-z]
Hartz, P. A. Personal Communication. Baltimore, Md. 7/17/2015.
Laclef, C., Anselme, I., Besse, L., Catala, M., Palmyre, A., Baas, D., Paschaki, M., Pedraza, M., Metin, C., Durand, B., Schneider-Maunoury, S. The role of primary cilia in corpus callosum formation is mediated by production of the Gli3 repressor. Hum. Molec. Genet. 24: 4997-5014, 2015. [PubMed: 26071364] [Full Text: https://doi.org/10.1093/hmg/ddv221]
Magnani, D., Morle, L., Hasenpusch-Theil, K., Paschaki, M., Jacoby, M., Schurmans, S., Durand, B., Theil, T. The ciliogenic transcription factor Rfx3 is required for the formation of the thalamocortical tract by regulating the patterning of prethalamus and ventral telencephalon. Hum. Molec. Genet. 24: 2578-2593, 2015. [PubMed: 25631876] [Full Text: https://doi.org/10.1093/hmg/ddv021]
Reith, W., Ucla, C., Barras, E., Gaud, A., Durand, B., Herrero-Sanchez, C., Kobr, M., Mach, B. RFX1, a transactivator of hepatitis B virus enhancer I, belongs to a novel family of homodimeric and heterodimeric DNA-binding proteins. Molec. Cell. Biol. 14: 1230-1244, 1994. [PubMed: 8289803] [Full Text: https://doi.org/10.1128/mcb.14.2.1230-1244.1994]