Alternative titles; symbols
HGNC Approved Gene Symbol: FANCL
Cytogenetic location: 2p16.1 Genomic coordinates (GRCh38): 2:58,159,243-58,241,380 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 2p16.1 | Fanconi anemia, complementation group L | 614083 | Autosomal recessive | 3 |
By mass spectrometry, Meetei et al. (2003) identified a previously isolated 43-kD FA-associated polypeptide (Meetei et al., 2003) as PHD finger protein-9 (PHF9). The deduced 373-amino acid protein, which contains 3 potential WD40 repeats and a PHD-type zinc finger motif, shares 80% sequence identity with its mouse homolog.
Meetei et al. (2003) presented several pieces of evidence that suggested that PHF9 is a stable component of the FA core complex. They detected PHF9 in both the nuclear and cytoplasmic extracts of wildtype cells; however, in lysates from 2 FANCA (607139) cell lines, the level of PHF9 was markedly lower than wildtype in the nuclear extract but was normal in the cytoplasm, suggesting that the nuclear accumulation of PHF9 depends on FANCA. Meetei et al. (2003) found that PHF9 possessed E3 ubiquitin ligase activity in vitro and was essential for FANCD2 (227646) monoubiquitination in vivo. They concluded that PHF9 is crucial in the FA pathway as the catalytic subunit required for monoubiquitination of FANCD2.
Grompe (2003) pointed out that PHF9 was the first Fanconi anemia protein identified by a biochemical approach and the first Fanconi anemia protein with a defined enzymatic activity. In the Fanconi anemia core complex, which senses exogenous DNA damage associated with DNA replication, PHF9 had been designated FAAP43. Grompe (2003) stated that FAAP90, FAAP100, and FAAP250 probably represent additional Fanconi anemia proteins that hold promise of offering insight into the function of the pathway.
Using yeast 2-hybrid and coimmunoprecipitation assays, Tremblay et al. (2008) found that HES1 (139605), a NOTCH1 (190198) pathway component involved in hematopoietic stem cell (HSC) self-renewal, interacted directly with FANCA, FANCF (603467), FANCG (XRCC9; 602956), and FANCL, but not with other FA core complex components. Mutation analysis showed that interactions with individual FA core components required different domains within HES1. HES1 did not interact with FA core components if any of them contained an FA-related mutation, suggesting that a functional FA pathway is required for HES1 interaction. Depletion of HES1 from HeLa cells resulted in failure of normal interactions between individual FA core components, as well as altered protein levels and mislocalization of some FA core components. Depletion of HES1 also increased cell sensitivity to the DNA crosslinking agent mitomycin C (MMC) and reduced MMC-induced monoubiquitination of FANCD2 and localization of FANCD2 to MMC-induced foci. Tremblay et al. (2008) concluded that interaction with HES1 is required for normal FA core complex function in the DNA damage response. They proposed that the HSC defect in FA may result from the inability of HES1 to interact with the defective FA core complex.
Using yeast 2-hybrid analysis, Zhang et al. (2011) showed that mouse ubiquitin-conjugating enzyme-2W (UBE2W; 614277) interacted with Fancl. They confirmed the interaction by protein pull-down and coimmunoprecipitation analyses. Fancl showed a ubiquitous intracellular localization in the absence of Ube2w and a nuclear localization in the presence of Ube2w. Ube2w exhibited ubiquitin-conjugating activity and monoubiquitinated the PHD domain of Fancl in vitro.
Cryoelectron Microscopy
Shakeel et al. (2019) reconstituted an active, recombinant Fanconi anemia core complex, and used cryoelectron microscopy and mass spectrometry to determine its structure. The FA core complex comprises 2 central dimers of the FANCB (300515) and FA-associated protein of 100 kD (FAAP100; 611301) subunits, flanked by 2 copies of the RING finger subunit FANCL. These 2 heterotrimers act as a scaffold to assemble the remaining 5 subunits, resulting in an extended asymmetric structure. Destabilization of the scaffold would disrupt the entire complex, resulting in a nonfunctional FA pathway. Thus, the structure provides a mechanistic basis for the low numbers of patients with mutations in FANCB, FANCL, and FAAP100. Despite a lack of sequence homology, FANCB and FAAP100 adopt similar structures. The 2 FANCL subunits are in different conformations at opposite ends of the complex, suggesting that each FANCL has a distinct role. Shakeel et al. (2019) suggested that this structural and functional asymmetry of dimeric RING finger domains may be a general feature of E3 ligases.
Stumpf (2019) mapped the FANCL gene to chromosome 2p16.1 based on an alignment of the FANCL sequence (GenBank BC009042.1) with the genomic sequence (GRCh38). The mouse homolog maps to chromosome 11 (Agoulnik et al., 2002).
Meetei et al. (2003) detected little or no PHF9 protein in a cell line (EUFA868) derived from an individual with Fanconi anemia of an unassigned complementation group. PHF9 cDNA from this cell line was found to lack exon 11, which removed the conserved PHD finger and part of the third WD40 repeat (608111.0001). The complementation group was designated FANCL (614083).
In a male patient with FA of complementation group L, Ali et al. (2009) identified compound heterozygous mutations in the FANCL gene (608111.0002-608111.0003).
In 2 unrelated infants with lethal FANCL, Vetro et al. (2015) identified 2 different homozygous truncating mutations in the FANCL gene (608111.0004 and 608111.0005). The mutation in the first patient was found by whole-exome sequencing and segregated with the disorder in the family. The mutation in the second patient was found by targeted sequencing of known Fanconi anemia genes. Cell lines from both patients showed increased chromosomal breakage and increased sensitivity to MMC, which was rescued after transfection with wildtype FANCL. Both patients had a severe phenotype and multiple congenital anomalies reminiscent of VACTERL (192350) or VACTERL-H (276950).
Reviews
Levitus et al. (2004) tabulated 11 genetic subtypes of Fanconi anemia, giving the nature of the defects identified in each.
The mouse Fancl gene, previously named Pog (for proliferation of germ cells), underlies the germ cell-deficient (gcd) phenotype in mice. Gcd mice, like mice carrying Pog null alleles generated by targeted disruption, are less fertile and have defective proliferation of germ cells (Agoulnik et al., 2002), characteristics that are also found in FA knockout mice. Moreover, Koomen et al. (2002) found that bone marrow cells isolated from Pog knockout mice were hypersensitive to mitomycin C.
In a cell line (EUFA868) from an individual with Fanconi anemia of complementation group L (FANCL; 614083), Meetei et al. (2003) found little or no PHF9 protein. PHF9 cDNA from this cell line lacked exon 11, thus removing the conserved PHD finger and part of the third WD40 repeat. The genomic DNA from this individual showed a homo- or hemizygous insertion of 177 bp into a pyrimidine-rich sequence at the splice junction between intron 10 and exon 11. As pyrimidine-rich sequences serve as signals for intron-exon junctions, Meetei et al. (2003) concluded that this insertion disturbs splicing at this particular junction, resulting in the observed deletion.
In a male patient with Fanconi anemia of complementation group L (FANCL; 614083) who had a mild clinical phenotype, Ali et al. (2009) identified compound heterozygosity for 2 mutations in the FANCL gene. One allele carried an in-frame 3-bp deletion (1007_1009delTAT) in exon 12. The deletion was in the PHD/RING finger domain and resulted in the loss of ile366 and the conversion of cys337 to ser. The other allele carried a 4-bp duplication (1095_1098dupAATT) in exon 14 (608111.0003). The duplication was just outside the RING finger domain and resulted in a frameshift (Thr367AsnfsTer13). The mother was heterozygous for the deletion and the father was heterozygous for the duplication. Functional analyses indicated that the deletion was a null mutation and the duplication was a hypomorphic mutation.
For discussion of the 4-bp duplication in the FANCL gene (1095_1098dupAATT) that was found in compound heterozygous state in a patient with Fanconi anemia of complementation group L (FANCL; 614083) by Ali et al. (2009), see 608111.0002.
In an infant (case 1b), born of consanguineous Moroccan parents, with Fanconi anemia of complementation group L (FANCL; 614083), Vetro et al. (2015) identified a homozygous 1-bp deletion (c.268del, NM_018062.3) in exon 4 of the FANCL gene, resulting in a frameshift and premature termination (Leu90PhefsTer6). The mutation, which was found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in the family and was not found in the dbSNP (build 138), 1000 Genomes Project, or Exome Sequencing Project databases. Patient cells showed decreased mutant transcript, consistent with nonsense-mediated mRNA decay and a complete loss of function. Patient cell lines showed increased chromosomal breakage and increased sensitivity to MMC, which was rescued after after transfection with wildtype FANCL. The patient had a severe phenotype and multiple congenital anomalies reminiscent of VACTERL (192350); he died at 2 months of age.
In an infant (case 2), born of Dutch parents, with Fanconi anemia of complementation group L (FANCL; 614083), Vetro et al. (2015) identified a homozygous 1-bp deletion (c.430del, NM_018062.3) in exon 6 of the FANCL gene, resulting in a frameshift and premature termination (Ser144LeufsTer6). The mutation was found by targeted sequencing of known Fanconi anemia genes and confirmed by Sanger sequencing. DNA from the parents was unavailable for segregation analysis. Patient cell lines showed increased chromosomal breakage and increased sensitivity to MMC, which was rescued after after transfection with wildtype FANCL. The patient had a severe phenotype and multiple congenital anomalies reminiscent of VACTERL-H (276950); she died at 2 days of age.
Agoulnik, A. I., Lu, B., Zhu, Q., Truong, C., Ty, M. T., Arango, N., Chada, K. K., Bishop, C. E. A novel gene, Pog, is necessary for primordial germ cell proliferation in the mouse and underlies the germ cell deficient mutation, gcd. Hum. Molec. Genet. 11: 3047-3053, 2002. [PubMed: 12417526] [Full Text: https://doi.org/10.1093/hmg/11.24.3047]
Ali, A. M., Kirby, M., Jansen, M., Lach, F. P., Schulte, J., Singh, T. R., Batish, S. D., Auerbach, A. D., Williams, D. A., Meetei, A. R. Identification and characterization of mutations in FANCL gene: a second case of Fanconi anemia belonging to FA-L complementation group. Hum. Mutat. 30: E761-E770, 2009. Note: Electronic Article. [PubMed: 19405097] [Full Text: https://doi.org/10.1002/humu.21032]
Grompe, M. FANCL, as in ligase. Nature Genet. 35: 113-114, 2003.
Koomen, M., Cheng, N. C., van de Vrugt, H. J., Godthelp, B. C., van der Valk, M. A., Oostra, A. B., Zdzienicka, M. Z., Joenje, H., Arwert, F. Reduced fertility and hypersensitivity to mitomycin C characterize Fancg/Xrcc9 null mice. Hum. Molec. Genet. 11: 273-281, 2002. [PubMed: 11823446] [Full Text: https://doi.org/10.1093/hmg/11.3.273]
Levitus, M., Rooimans, M. A., Steltenpool, J., Cool, N. F. C., Oostra, A. B., Mathew, C. G., Hoatlin, M. E., Waisfisz, Q., Arwert, F., de Winter, J. P., Joenje, H. Heterogeneity in Fanconi anemia: evidence for 2 new genetic subtypes. Blood 103: 2498-2503, 2004. [PubMed: 14630800] [Full Text: https://doi.org/10.1182/blood-2003-08-2915]
Meetei, A. R., de Winter, J. P., Medhurst, A. L., Wallisch, M., Waisfisz, Q., van de Vrugt, H. J., Oostra, A. B., Yan, Z., Ling, C., Bishop, C. E., Hoatlin, M. E., Joenje, H., Wang, W. A novel ubiquitin ligase is deficient in Fanconi anemia. Nature Genet. 35: 165-170, 2003. [PubMed: 12973351] [Full Text: https://doi.org/10.1038/ng1241]
Meetei, A. R., Sechi, S., Wallisch, M., Yang, D., Young, M. K., Joenje, H., Hoatlin, M. E., Wang, W. A multiprotein nuclear complex connects Fanconi anemia and Bloom syndrome. Molec. Cell. Biol. 23: 3417-3426, 2003. [PubMed: 12724401] [Full Text: https://doi.org/10.1128/MCB.23.10.3417-3426.2003]
Shakeel, S., Rajendra, E., Alcon, P., O'Reilly, F., Chorev, D. S., Maslen, S., Degliesposti, G., Russo, C. J., He, S., Hill, C. H., Skehel, J. M., Scheres, S. H. W., Patel, K. J., Rappsilber, J., Robinson, C. V., Passmore, L. A. Structure of the Fanconi anaemia monoubiquitin ligase complex. Nature 575: 234-237, 2019. [PubMed: 31666700] [Full Text: https://doi.org/10.1038/s41586-019-1703-4]
Stumpf, A. M. Personal Communication. Baltimore, Md. 12/06/2019.
Tremblay, C. S., Huang, F. F., Habi, O., Huard, C. C., Godin, C., Levesque, G., Carreau, M. HES1 is a novel interactor of the Fanconi anemia core complex. Blood 112: 2062-2070, 2008. Note: Erratum: Blood 114: 3974 only, 2009. [PubMed: 18550849] [Full Text: https://doi.org/10.1182/blood-2008-04-152710]
Vetro, A., Iascone, M., Limongelli, I., Ameziane, N., Gana, S., Della Mina, E., Giussani, U., Ciccone, R., Forlino, A., Pezzoli, L., Rooimans, M. A., van Essen, A. J., Messa, J., Rizzuti, T., Bianchi, P., Dorsman, J., de Winter, J. P., Lalatta, F., Zuffardi, O. Loss-of-function FANCL mutations associate with severe Fanconi anemia overlapping the VACTERL association. Hum. Mutat. 36: 562-568, 2015. [PubMed: 25754594] [Full Text: https://doi.org/10.1002/humu.22784]
Zhang, Y., Zhou, X., Zhao, L., Li, C., Zhu, H., Xu, L., Shan, L., Liao, X., Guo, Z., Huang, P. UBE2W interacts with FANCL and regulates the monoubiquitination of Fanconi anemia protein FANCD2. Molec. Cells 31: 113-122, 2011. [PubMed: 21229326] [Full Text: https://doi.org/10.1007/s10059-011-0015-9]