HGNC Approved Gene Symbol: ZFX
Cytogenetic location: Xp22.11 Genomic coordinates (GRCh38) : X:24,148,982-24,216,255 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| Xp22.11 | Intellectual developmental disorder, X-linked syndromic 37 | 301118 | X-linked | 3 |
The ZFX gene encodes a transcription factor that has been linked to diverse processes such as development and oncogenesis (summary by Shepherdson et al., 2024).
Page et al. (1987) identified a Y-encoded zinc finger protein (ZFY; 490000). A similar DNA sequence, ZFX, was identified on the X chromosome.
Using PCR, Palmer et al. (1990) demonstrated close similarity of ZFY and ZFX. Both genes were expressed in a wide range of adult and fetal human tissues, and ZFX was expressed from the inactive X chromosome present in human-mouse hybrids. Schneider-Gadicke et al. (1989) also showed that ZFX escapes X inactivation in humans. Adler et al. (1991) showed that in the mouse, unlike the human, the Zfx gene is subject to X inactivation.
The human ZFX, human ZFY, and mouse Zfx genes have CpG islands near their 5-prime ends. These islands are typical in that they span about 1.5 kb, contain transcription initiation sites, and encompass some 5-prime untranslated exons and introns. However, comparative nucleotide sequencing of these human and mouse islands provided evidence of evolutionary conservation to a degree unprecedented among mammalian 5-prime CpG islands (Luoh et al., 1995). In one stretch of 165 nucleotides containing 19 CpGs, mouse Zfx and human ZFX are identical to each other and differ from human ZFY at only 9 nucleotides. In contrast, Luoh et al. (1995) found no evidence of homologous CpG islands in the mouse Zfy genes, whose transcription is more circumscribed than that of human ZFX, human ZFY, and mouse Zfx. Using the isoschizomers HpaII and MspI to examine a highly conserved segment of the ZFX CpG island, Luoh et al. (1995) detected methylation on inactive mouse X chromosomes but not on inactive human X chromosomes. These observations paralleled the previous findings that mouse Zfx undergoes X inactivation while human Zfx escapes it.
By analyzing data from chromatin immunoprecipitation-sequencing and -microarray analyses in mouse embryonic stem cells, Gokhman et al. (2013) found that Zfx repressed expression of linker histones.
The ZFX transcription factor contains an N-terminal transactivation domain followed by 13 zinc finger domains, of which the final 3 are necessary and sufficient for recruitment to target promoter regions (summary by Shepherdson et al., 2024).
In vitro fertilization (IVF), blastomere biopsy of the 6-8 cell embryo, and single cell DNA diagnosis allow couples at risk of transmitting a particular genetic disorder to start a pregnancy knowing their child will not be affected. Chong et al. (1993) developed a PCR strategy for sex determination at the single-cell level by simultaneous amplification and subsequent restriction fragment analysis of the homologous but nonallelic ZFX and ZFY genes. They showed that XY cells could be correctly genotyped as ZFX/ZFY and XX cells as ZFX only.
Muller and Schempp (1989) assigned the ZFX locus to Xp21.3 by in situ hybridization; the ZFY gene was assigned to Yp11.32. Page et al. (1990) concluded, from meiotic linkage analysis and physical mapping, that ZFX is distal to POLA (312040), near the boundary of bands Xp21.3 and Xp22.1.
Sinclair et al. (1988) showed that in marsupials sequences homologous to ZFY and ZFX map not to the X and Y but to autosomes. This implies that ZFY is not the primary sex-determining gene in marsupials. Either the genetic pathways of sex determination in marsupials and eutherians differ, or they are identical and ZFY is not the primary signal in human sex determination.
Scherer et al. (1989) described two 46,XY females with tandem duplications of an Xp segment resulting in a double dose of ZFX on the 1 active X chromosome. The duplicated segment in each case included the Xp22.2-p21.2 interval. The duplication was apparently responsible for sex inversion and favored the model of sex determination as an antagonistic interaction between ZFY and ZFX genes. Because of other abnormalities, 1 of the children died at age 2 years and the other was severely ill at age 7 months. In the second case internal genitalia was said to have been normal, but gonadotropin stimulation showed primary hypogonadism. Thus the cases do not help in resolution of the question of whether the XY female type of gonadal dysgenesis is due to mutation in the same locus.
In 18 individuals, including 14 males and 4 females, from 14 unrelated families with X-linked syndromic intellectual developmental disorder-37 (MRXS37; 301118), Shepherdson et al. (2024) identified heterozygous mutations in the ZFX gene (see, e.g., 314980.0001-314980.0005). The mutations, which were identified through exome sequencing, were not present in the gnomAD database. Four missense variants were identified in 11 individuals (including 3 individuals in family 6), and 7 frameshift mutations were identified in the 7 other patients. Ten patients had de novo mutations, whereas 8 inherited the mutation from a mildly affected or unaffected mother. Of note, 8 individuals carried variants affecting other genes that may have contributed to the phenotype. The missense ZFX mutations clustered in the penultimate and ultimate zinc finger domains, which are critical for DNA-binding activity. Expression of the missense variants in ZFX-null HEK293 cells showed that they had similar DNA binding patterns to wildtype, although some showed subtle alterations in DNA binding. RNA-seq analysis of cells carrying the missense variants showed evidence of transcriptional dysregulation, both decreased and increased, compared to controls, suggesting the potential for both loss- and gain-of-function mechanisms that could alter DNA binding specificity. The frameshift mutations were predicted to result in a loss of function either by triggering nonsense-mediated mRNA decay or by truncating the DNA-binding zinc finger domains. However, cellular studies of the frameshift mutations and studies of patient cells were not performed. Zebrafish with complete loss of zfx showed mild behavioral abnormalities in some assays, such as decreased anxiety behavior and poor habituation, compared to wildtype, although other behavioral assays were similar to wildtype (see ANIMAL MODEL). The authors suggested that truncating mutations resulting in a loss of zfx function may result in neurocognitive abnormalities.
Galan-Caridad et al. (2007) used conditional gene targeting to examine the role of Zfx in mouse embryonic and adult hematopoietic stem cells. Zfx was required for self-renewal of both stem cell types, but it was dispensable for growth and differentiation of their progeny. Galan-Caridad et al. (2007) concluded that ZFX is a shared transcriptional regulator of embryonic and adult stem cells, indicating a common molecular basis for stem cell self-renewal.
Shepherdson et al. (2024) found that CRISPR/Cas9-mediated knockdown of the zfx gene in zebrafish did not result in morphologic developmental abnormalities. Mutant zebrafish showed some behavioral abnormalities compared to wildtype, including decreased anxiety behavior in the novel tank diving and scototaxis assays. Mutant fish also did not habituate in the external tap assay compared to wildtype. Social interaction and mirror biting tests were similar in mutants and controls. These findings suggested to the authors that a loss of zfx function may result in subtle neurocognitive abnormalities.
In 3 unrelated patients (P3-P5), including 2 males and 1 female, with X-linked syndromic intellectual developmental disorder-37 (MRXS37; 301118), Shepherdson et al. (2024) identified a de novo hemizygous (in the males) or heterozygous (in the female) c.2312C-T transition (c.2312C-T, NM_003410.4) in the ZFX gene, resulting in a thr771-to-met (T771M) substitution at a conserved residue in the linker region between zinc fingers 12 and 13. The mutation, which was found by exome sequencing, was not present in the gnomAD database. Studies of patient cells were not performed. Expression of the mutant protein in ZFX-null HEK293 cells showed that it was expressed at normal levels and had similar DNA binding patterns as wildtype, but there were subtle effects on DNA binding, including globally decreased DNA binding and enhanced binding at a small set of promoters.
In 3 members (P6A, 6B, and 6C, including 2 males and 1 female) from a family (family 6) and in an unrelated male patient (P7) with X-linked syndromic intellectual developmental disorder-37 (MRXS37; 301118), Shepherdson et al. (2024) identified a heterozygous c.2321A-G transition (c.2321A-G, NM_003410.4) in the ZFX gene, resulting in a tyr774-to-cys (Y774C) substitution at a conserved residue in the linker region between zinc fingers 12 and 13. The mutation was maternally inherited in family 6, but occurred de novo in P7. The mutation was found by exome sequencing and was not present in the gnomAD database. Expression of the mutant protein in ZFX-null HEK293 cells showed that it had similar binding patterns as wildtype, but there were subtle effects on DNA binding (globally decreased DNA binding as well as enhanced binding at a small set of promoters). Several additional females from family 6 who were heterozygous for the mutation had hyperparathyroidism without additional features of the disorder.
In 2 unrelated patients, P8 (a male) and P9 (a biologic female who was a transgender male), with X-linked syndromic intellectual developmental disorder-37 (MRXS37; 301118), Shepherdson et al. (2024) identified a hemizygous (in P8) and de novo heterozygous (in P9) c.2357G-A transition (c.2357G-A, NM_003410.4) in the ZFX gene, resulting in an arg786-to-gln (R786Q) substitution at a conserved residue in zinc finger 13. The mutation, which was found by exome sequencing, was not present in the gnomAD database. P8 inherited the mutation from his mother; clinical details of the mother were not provided. Expression of the mutant protein in ZFX-null HEK293 cells showed that it had similar binding patterns as wildtype, but there were subtle effects on DNA binding (globally decreased DNA binding as well as enhanced binding at a small set of promoters). The authors noted that the R786Q mutation has been reported as a somatic variant in several neoplasms, including parathyroid adenomas, endometrioid carcinoma, and melanoma, among others.
In a 13-year-old boy (P11) with X-linked syndromic intellectual developmental disorder-37 (MRXS37; 301118), Shepherdson et al. (2024) identified a de novo hemizygous 1-bp insertion of a T nucleotide (g.24210271G-GT) in the ZFX gene, resulting in a frameshift and premature termination (Leu440PhefsTer21) in the first zinc finger domain. The authors referred to the mutation as c.1319dup (NM_003410.4). The mutation was found by exome sequencing and was not present in the gnomAD database. The authors stated that the mutation was predicted to escape nonsense-mediated mRNA decay and possibly produce a truncated protein, although studies of patient cells were not performed.
In a 16-year-old boy (P16) with X-linked syndromic intellectual developmental disorder-37 (MRXS37; 301118), Shepherdson et al. (2024) identified a de novo hemizygous 2-bp deletion (c.115_116delTG, NM_003410.4) in the ZFX gene, predicted to result in a frameshift and premature termination (Val39PhefsTer14) in the N-terminal domain. The mutation was found by exome sequencing and was not present in the gnomAD database. The mutation was predicted to trigger nonsense-mediated mRNA decay and result in a loss of function; however, studies of patient cells were not performed.
Adler, D. A., Bressler, S. L., Chapman, V. M., Page, D. C., Disteche, C. M. Inactivation of the Zfx gene on the mouse X chromosome. Proc. Nat. Acad. Sci. 88: 4592-4595, 1991. Note: Erratum: Proc. Nat. Acad. Sci. 88: 5937 only, 1991. [PubMed: 2052543] [Full Text: https://doi.org/10.1073/pnas.88.11.4592]
Chong, S. S., Kristjansson, K., Cota, J., Handyside, A. H., Hughes, M. R. Preimplantation prevention of X-linked disease: reliable and rapid sex determination of single human cells by restriction analysis of simultaneously amplified ZFX and ZFY sequences. Hum. Molec. Genet. 2: 1187-1191, 1993. [PubMed: 8401500] [Full Text: https://doi.org/10.1093/hmg/2.8.1187]
Galan-Caridad, J. M., Harel, S., Arenzana, T. L., Hou, Z. E., Doetsch, F. K., Mirny, L. A., Reizis, B. Zfx controls the self-renewal of embryonic and hematopoietic stem cells. Cell 129: 345-357, 2007. [PubMed: 17448993] [Full Text: https://doi.org/10.1016/j.cell.2007.03.014]
Gokhman, D., Livyatan, I., Sailaja, B. S., Melcer, S., Meshorer, E. Multilayered chromatin analysis reveals E2f, Smad and Zfx as transcriptional regulators of histones. Nature Struct. Molec. Biol. 20: 119-126, 2013. [PubMed: 23222641] [Full Text: https://doi.org/10.1038/nsmb.2448]
Luoh, S.-W., Jegalian, K., Lee, A., Chen, E. Y., Ridley, A., Page, D. C. CpG islands in human ZFX and ZFY and mouse Zfx genes: sequence similarities and methylation differences. Genomics 29: 353-363, 1995. [PubMed: 8666382] [Full Text: https://doi.org/10.1006/geno.1995.9994]
Muller, G., Schempp, W. Mapping the human ZFX locus to Xp21.3 by in situ hybridization. Hum. Genet. 82: 82-84, 1989. [PubMed: 2497060] [Full Text: https://doi.org/10.1007/BF00288279]
Page, D. C., Disteche, C. M., Simpson, E. M., de la Chapelle, A., Andersson, M., Alitalo, T., Brown, L. G., Green, P., Akots, G. Chromosomal localization of ZFX--a human gene that escapes X inactivation--and its murine homologs. Genomics 7: 37-46, 1990. [PubMed: 1970799] [Full Text: https://doi.org/10.1016/0888-7543(90)90516-w]
Page, D. C., Mosher, R., Simpson, E. M., Fisher, E. M. C., Mardon, G., Pollack, J., McGillivray, B., de la Chapelle, A., Brown, L. G. The sex-determining region of the human Y chromosome encodes a finger protein. Cell 51: 1091-1104, 1987. [PubMed: 3690661] [Full Text: https://doi.org/10.1016/0092-8674(87)90595-2]
Palmer, M. S., Berta, P., Sinclair, A. H., Pym, B., Goodfellow, P. N. Comparison of human ZFY and ZFX transcripts. Proc. Nat. Acad. Sci. 87: 1681-1685, 1990. [PubMed: 2308929] [Full Text: https://doi.org/10.1073/pnas.87.5.1681]
Scherer, G., Schempp, W., Baccichetti, C., Lenzini, E., Dagna Bricarelli, F., Carbone, L. D. L., Wolf, U. Duplication of an Xp segment that includes the ZFX locus causes sex inversion in man. Hum. Genet. 81: 291-294, 1989. [PubMed: 2921042] [Full Text: https://doi.org/10.1007/BF00279008]
Schneider-Gadicke, A., Beer-Romero, P., Brown, L. G., Nussbaum, R., Page, D. C. ZFX has a gene structure similar to ZFY, the putative human sex determinant, and escapes X inactivation. Cell 57: 1247-1258, 1989. [PubMed: 2500252] [Full Text: https://doi.org/10.1016/0092-8674(89)90061-5]
Shepherdson, J. L., Hutchison, K., Don, D. W., McGillivray, G., Choi, T.-I., Allan, C. A., Amor, D. J., Banka, S., Basel, D. G., Buch, L. D., Carere, D. A., Carroll, R., and 45 others. Variants in ZFX are associated with an X-linked neurodevelopmental disorder with recurrent facial gestalt. Am. J. Hum. Genet. 111: 487-508, 2024. [PubMed: 38325380] [Full Text: https://doi.org/10.1016/j.ajhg.2024.01.007]
Sinclair, A. H., Foster, J. W., Spencer, J. A., Page, D. C., Palmer, M., Goodfellow, P. N., Marshall Graves, J. A. Sequences homologous to ZFY, a candidate human sex-determining gene, are autosomal in marsupials. Nature 336: 780-783, 1988. [PubMed: 3144651] [Full Text: https://doi.org/10.1038/336780a0]