Alternative titles; symbols
HGNC Approved Gene Symbol: SLC19A1
Cytogenetic location: 21q22.3 Genomic coordinates (GRCh38): 21:45,502,517-45,563,025 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 21q22.3 | ?Megaloblastic anemia, folate-responsive | 601775 | Autosomal recessive | 3 |
| Immunodeficiency 114, folate-responsive | 620603 | Autosomal recessive | 3 |
The SLC19A1 gene encodes reduced folate carrier-1 (RFC1), a transmembrane protein that facilitates the cellular uptake of anionic folates and folate analogs such as methotrexate (summary by Svaton et al., 2020). SLC19A1 also facilitates transport of cyclic dinucleotides (CDNs) across the plasma membrane to stimulate intracellular signaling pathways (summary by Shiraishi et al., 2023).
Several groups independently cloned cDNAs encoding the 591-amino acid human folate transporter. Using a mouse reduced folate carrier (RFC) partial cDNA as a probe, Wong et al. (1995) cloned a human RFC cDNA from a library prepared from MTX transport-upregulated erythroleukemia cells. Using homologous murine cDNAs as probes, Williams and Flintoff (1995), Prasad et al. (1995), and Nguyen et al. (1997) independently isolated human folate transporter cDNAs from lymphoblast, placenta, and small intestine libraries, respectively.
Transport of folate compounds into mammalian cells can occur via receptor-mediated (see 136430) or carrier-mediated mechanisms. A functional coordination between these 2 mechanisms has been proposed to be the method of folate uptake in certain cell types. Prasad et al. (1995) reported that the human folate transporter, which they symbolized FOLT, had 65% amino acid sequence identity to mouse and hamster folate transporters. When transfected into COS-1 and HeLa cells, the human FOLT cDNA caused a significant increase in the uptake of 5-methyltetrahydrofolate. By Northern blot analysis, mRNA transcripts hybridizing to the human FOLT cDNA were detected in placenta and liver and also in several cell lines of human origin. The principal transcript was approximately 2.7 kb.
Williams and Flintoff (1995) and Wong et al. (1995) observed that human folate transport cDNAs expressed in MTX transport-deficient Chinese hamster ovary cells restored MTX transport and sensitivity.
Nguyen et al. (1997) injected human intestinal folate carrier-1 (IFC1) cRNA into Xenopus oocytes and observed increased uptake of methyltetrahydrofolic acid. Northern blot analysis revealed that the IFC1 gene was expressed as a 3.3-kb mRNA at a high level in placenta and at lower levels in a variety of other tissues, including the small intestine. In situ hybridization of thin sections of intestinal epithelia demonstrated IFC1 expression localized to the villus and crypt cells, particularly the upper half of the villi.
In luminal epithelial cells isolated from mouse small intestine, Chiao et al. (1997) found increased PH-dependent folate influx associated with RFC1 gene expression in the form of a 2.5-kb transcript and a 58-kD brush border membrane protein detected by folate-based affinity labeling and with antibodies against the transporter. The authors concluded that RFC1 mediates intestinal folate transport.
L1210/D3 mouse leukemia cells are resistant to 5,10-dideazatetrahydrofolate due to expansion of cellular folate pools which block polyglutamation of the drug. Tse et al. (1998) identified 2 point mutations in the RFC in these cells, resulting in the replacement of isoleucine-48 by phenylalanine (I48F) and of tryptophan-105 by glycine (W105G). Each mutation contributes to the resistance phenotype. Genomic DNA from resistant cells contained both the wildtype and mutant alleles, but wildtype message was not detected. Folic acid was a much better substrate, and 5-formyltetrahydrofolate was a poorer substrate, for transport in L1210/D3 cells relative to L1210 cells. Enhanced transport of folic acid was due to a marked, approximately 20-fold, decrease in the influx K(m). Influx of methotrexate and 5,10-dideazatetrahydrofolate were minimally altered. Tse et al. (1998) concluded that the I48F and W105G mutations in RFC caused resistance to 5,10-dideazatetrahydrofolate, that the region of the RFC protein near these 2 positions defines the substrate-binding site, that the wildtype allele was silenced during the multistep development of resistance, and that this mutant phenotype represents a genetically dominant trait.
Point mutations in the reduced folate carrier-1 gene and alterations resulting in the downregulation of its message are major factors in the resistance to antifolate chemotherapeutic agents. As a framework for understanding the significance of such changes in relation to gene expression and function, Williams and Flintoff (1998) described the organization of the RFC1 gene from human lymphoblasts. They found that the gene contains 5 exons (2 to 6) coding for protein. At least 4 5-prime exons, used in a mutually exclusive manner in the production of RFC1 message from lymphoblast cells, are spliced to exon 2, which contains the translational start site. Semiquantitative PCR indicated that exon 1 is preferentially used. The major transcriptional start site was mapped by RACE and RNase protection to a region 109 to 135 bp 5-prime to the start of exon 1.
Tolner et al. (1998) determined that the RFC1 gene spans 22.5 kb and is distributed in 8 exons, including 5 primary exons (exons 2 through 6) and 3 alternatives of exon 1. They identified 3 splice variants. By functional deletion analysis, they identified 2 TATA-less promoters that show substantial differences in the efficiency with which they drive transcription.
Yang-Feng et al. (1995) used the human folate transporter cDNA and a human genomic clone hybridizing to the cDNA to perform chromosomal mapping of the FOLT gene. Human/rodent somatic cell hybrid analysis using the cDNA as the probe demonstrated perfect segregation with chromosome 21. Isotopic in situ hybridization with the cDNA probe mapped the gene to 21q22.3. Fluorescence in situ hybridization using the genomic clone confirmed this chromosomal localization.
Folate-Responsive Megaloblastic Anemia
In a 17-year-old boy with folate-responsive megaloblastic anemia (MEGAF; 601775), Svaton et al. (2020) identified a homozygous 3-bp in-frame deletion in the SLC19A1 gene (600424.0001). The mutation, which was found by whole-exome sequencing, segregated with the disorder in the family. In vitro functional studies showed that the mutation caused decreased transport activity toward methotrexate compared to wildtype, suggesting that there was impaired folate transport into hematopoietic cells.
Folate-Responsive Immunodeficiency 114
In 2 male first cousins from a large consanguineous Turkish family with folate-responsive immunodeficiency-114 (IMD114; 620603), Gok et al. (2023) identified a homozygous missense mutation in the SLC19A1 gene (G348R; 600424.0002). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. Patient T cells showed proliferation defects in vitro when folic acid concentration was reduced. Patient cells were also resistant to apoptosis when exposed to methotrexate, suggesting impaired transporter function of the mutant SLC19A1 protein. In addition, patient CD4+ T cells showed reduced expression of several cytokine genes involved in antiviral immunity, including IFNA, IFNG, TNFA, and IL6, in reduced folic acid conditions compared to controls. Patient T cells had increased levels of GMCSF (CSF2; 138960) and IL10 (124092). The findings suggested that patients are vulnerable to infection when folate intake is insufficient, and that presence of the defective folate transporter becomes more apparent during infection when B and T cells undergo clonal expansion and their folate demands are high.
In 2 distantly related boys with IMD114, Shiraishi et al. (2023) identified a homozygous G348R mutation in the SLC19A1 gene. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was not present in the gnomAD database (v2.1.1). Although serum folate levels were normal, folate levels were reduced in patient red blood cells, indicating impaired cellular folate uptake. Additional in vitro functional studies showed that patient lymphocytes and cells transfected with the mutation had decreased phosphorylation of STING (612374) with reduced downstream activation of NFKB (see 164011) signaling and impaired induction of IFNB (147640) transcription compared to controls after stimulation with the cyclic dinucleotide cGAMP. Patient CD4+ T cells, which were decreased in number, showed defective proliferative responses to stimulation. These findings were consistent with reduced transporter activity for both cyclic dinucleotides and folate.
Functional Polymorphisms
Using data from a California population-based case-control interview study, Shaw et al. (2002) investigated whether spina bifida risk was influenced by an interaction between a polymorphism of infant RFC1 at nucleotide 80 (A80G) and maternal periconceptional use of vitamins containing folic acid. Although the study did not find an increased spina bifida risk for infants who were heterozygous or homozygous for RFC1 A80G, it did reveal modest evidence for a gene-nutrient interaction between infant homozygosity for the G80/G80 genotype and maternal periconceptional intake of vitamins containing folic acid on the risk of spina bifida.
In a 17-year-old boy with folate-responsive megaloblastic anemia (MEGAF; 601775), Svaton et al. (2020) identified a homozygous 3-bp in-frame deletion (c.634_636delTTC, NM_194255.3) in the SLC19A1 gene, resulting in the deletion of conserved residue phe121 (phe212del). The mutation, which was found by whole-exome sequencing, segregated with the disorder in the family. In vitro functional studies showed that the mutation caused decreased transport activity toward methotrexate compared to wildtype, suggesting impaired folate transport into cells. Svaton et al. (2020) observed the c.634_636delTTC variant in the gnomAD database with an allele frequency of 0.014% with no homozygotes, but noted that the Exome Variant Server NHLBI GO Exome Sequencing Project (ESP) reported 6 homozygotes for this mutation among 6,258 individuals without details on their phenotypes.
In 2 male first cousins from a large consanguineous Turkish family with folate-responsive immunodeficiency-114 (IMD114; 620603), Gok et al. (2023) identified a homozygous c.1042G-A transition in the SLC19A1 gene, resulting in a gly348-to-arg (G348R) substitution at a conserved residue in the ninth alpha helix in the transmembrane domain. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. Patient T cells showed normal SLC19A1 protein expression, correct shuttling to the plasma membrane, and increased gene expression during proliferation. However, patient T cells showed proliferation defects in vitro when folic acid concentration was reduced. Patient cells were also resistant to apoptosis when exposed to methotrexate, suggesting impaired transporter function of the mutant SLC19A1 protein. P2, who was diagnosed at 2 years of age, showed global developmental delay. Treatment with folinic acid supplementation resulted in improvement of the immunologic abnormalities and infections in both patients; P2 showed some neurologic progress after treatment. Of note, P1, who had features suggestive of hemophagocytic lymphohistiocytosis, carried a heterozygous mutation in the RAB27A gene (603868), and P2 carried a heterozygous mutation in the TNFRSF13B gene (C104R; 604907.0001), both of which are implicated in immunologic disorders.
In 2 distantly related Turkish boys with IMD14, Shiraishi et al. (2023) identified a homozygous c.1042G-A transition (c.1042G-A, NM_194255) in the SLC19A1 gene, resulting in a G348R substitution. The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family. It was not present in the gnomAD database (v2.1.1). Patient lymphocytes showed decreased expression of the mutant protein, suggesting decreased stability, but studies of transfected HeLa and HEK293 cells showed that the mutant protein did reach the plasma membrane. Although serum folate levels were normal, folate levels were reduced in patient red blood cells, indicating impaired cellular folate uptake. Additional in vitro functional studies showed that patient lymphocytes and cells transfected with the mutation had decreased phosphorylation of STING (612374) with reduced downstream activation of NFKB (see 164011) signaling and impaired induction of IFNB (147640) transcription compared to controls after stimulation with the cyclic dinucleotide cGAMP. Patient CD4+ T cells, which were decreased in number, showed defective proliferative responses to stimulation. These findings were consistent with reduced transporter activity for both cyclic dinucleotides and folate. The patients had recurrent infections from infancy and global neurodevelopmental delay. Folic acid supplementation was started in P1 at 5.5 years of age and in P2 at 3.5 years of age. Folic acid treatment improved the hematologic and immunologic features in both patients, but neurodevelopmental impairment persisted. P2 died of acute neurologic deterioration at 6.5 years of age.
Chiao, J. H., Roy, K., Tolner, B., Yang, C.-H., Sirotnak, F. M. RFC-1 gene expression regulates folate absorption in mouse small intestine. J. Biol. Chem. 272: 11165-11170, 1997. [PubMed: 9111015] [Full Text: https://doi.org/10.1074/jbc.272.17.11165]
Gok, V., Erdem, S., Haliloglu, Y., Bisgin, A., Belkaya, S., Basaran, K. E., Canatan, M. F., Ozcan, A., Yilmaz, E., Acipayam, C., Karakukcu, M., Canatan, H., Per, H., Patiroglu, T., Eken, A., Unal, E. Immunodeficiency associated with a novel functionally defective variant of SLC19A1 benefits from folinic acid treatment. Genes Immunity 24: 12-20, 2023. [PubMed: 36517554] [Full Text: https://doi.org/10.1038/s41435-022-00191-7]
Nguyen, T. T., Dyer, D. L., Dunning, D. D., Rubin, S. A., Grant, K. E., Said, H. M. Human intestinal folate transport: cloning, expression, and distribution of complementary RNA. Gastroenterology 112: 783-791, 1997. [PubMed: 9041240] [Full Text: https://doi.org/10.1053/gast.1997.v112.pm9041240]
Prasad, P. D., Ramamoorthy, S., Leibach, F. H., Ganapathy, V. Molecular cloning of the human placental folate transporter. Biochem. Biophys. Res. Commun. 206: 681-687, 1995. [PubMed: 7826387] [Full Text: https://doi.org/10.1006/bbrc.1995.1096]
Shaw, G. M., Lammer, E. J., Zhu, H., Baker, M. W., Neri, E., Finnell, R. H. Maternal periconceptional vitamin use, genetic variation of infant reduced folate carrier (A80G), and risk of spina bifida. Am. J. Med. Genet. 108: 1-6, 2002. Note: Erratum: Am. J. Med. Genet. 113: 392 only, 2002. [PubMed: 11857541] [Full Text: https://doi.org/10.1002/ajmg.10195]
Shiraishi, A., Uygun, V., Sharfe, N., Beldar, S., Sun, M. G. F., Dadi, H., Vong, L., Maxson, M., Karaca, N. E., Mevlitoglu, S., Grinstein, S., Artan, R., Merico, D., Roifman, C. M. Novel immunodeficiency caused by homozygous mutation in solute carrier family 19 member 1, which encodes the reduced folate carrier. Blood 141: 3226-3230, 2023. [PubMed: 36745868] [Full Text: https://doi.org/10.1182/blood.2022017968]
Svaton, M., Skvarova Kramarzova, K., Kanderova, V., Mancikova, A., Smisek, P., Jesina, P., Krijt, J., Stiburkova, B., Dobrovolny, R., Sokolova, J., Bakardjieva-Mihaylova, V., Vodickova, E., Rackova, M., Stuchly, J., Kalina, T., Stary, J., Trka, J., Fronkova, E., Kozich, V. A homozygous deletion in the SLC19A1 gene as a cause of folate-dependent recurrent megaloblastic anemia. Blood 135: 2427-2431, 2020. [PubMed: 32276275] [Full Text: https://doi.org/10.1182/blood.2019003178]
Tolner, B., Roy, K., Sirotnak, F. M. Structural analysis of the human RFC-1 gene encoding a folate transporter reveals multiple promoters and alternatively spliced transcripts with 5-prime end heterogeneity. Gene 211: 331-341, 1998. [PubMed: 9602167] [Full Text: https://doi.org/10.1016/s0378-1119(98)00123-1]
Tse, A., Brigle, K., Taylor, S. M., Moran, R. G. Mutations in the reduced folate carrier gene which confer dominant resistance to 5,10-dideazatetrahydrofolate. J. Biol. Chem. 273: 25953-25960, 1998. [PubMed: 9748272] [Full Text: https://doi.org/10.1074/jbc.273.40.25953]
Williams, F. M. R., Flintoff, W. F. Isolation of a human cDNA that complements a mutant hamster cell defective in methotrexate uptake. J. Biol. Chem. 270: 2987-2992, 1995. [PubMed: 7852378] [Full Text: https://doi.org/10.1074/jbc.270.7.2987]
Williams, F. M. R., Flintoff, W. F. Structural organization of the human reduced folate carrier gene: evidence for 5-prime heterogeneity in lymphoblast mRNA. Somat. Cell Molec. Genet. 24: 143-156, 1998. [PubMed: 10226652] [Full Text: https://doi.org/10.1023/b:scam.0000007117.50428.63]
Wong, S. C., Proefke, S. A., Bhushan, A., Matherly, L. H. Isolation of human cDNAs that restore methotrexate sensitivity and reduced folate carrier activity in methotrexate transport-defective Chinese hamster ovary cells. J. Biol. Chem. 270: 17468-17475, 1995. [PubMed: 7615551] [Full Text: https://doi.org/10.1074/jbc.270.29.17468]
Yang-Feng, T. L., Ma, Y.-Y., Liang, R., Prasad, P. D., Leibach, F. H., Ganapathy, V. Assignment of the human folate transporter gene to chromosome 21q22.3 by somatic cell hybrid analysis and in situ hybridization. Biochem. Biophys. Res. Commun. 210: 874-879, 1995. [PubMed: 7763259] [Full Text: https://doi.org/10.1006/bbrc.1995.1739]