Alternative titles; symbols
HGNC Approved Gene Symbol: NCKAP1L
Cytogenetic location: 12q13.13-q13.2 Genomic coordinates (GRCh38): 12:54,497,752-54,548,243 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 12q13.13-q13.2 | Immunodeficiency 72 with autoinflammation | 618982 | Autosomal recessive | 3 |
The NCKAP1L gene encodes HEM1, a protein subunit of the membrane-associated scaffold that supports the WAVE regulatory complex (WRC). This complex controls the dynamics of ARP2/3 (604221)-mediated filamentous F-actin nucleation and polymerization. The NCKAP1L protein also likely plays a role in other signaling pathways, including mTORC2 (601231) (summary by Cook et al., 2020).
Hromas et al. (1991) obtained cDNAs 3.8 kb in length containing a long open reading frame and showing hybridization exclusively to transcripts from hematopoietic cells. The protein, which they called HEM1, contains 8 potential membrane domains and 2 possible cAMP/cGMP phosphorylation sites.
By hybridization to flow-sorted chromosomes, Hromas et al. (1991) mapped the HEM1 gene to chromosome 12. Using in situ hybridization, they localized it to chromosome 12q13.1, a region of occasional translocations in hematopoietic neoplasia and the site of a rare folic acid fragile site.
In 5 patients from 4 unrelated families with immunodeficiency-72 with autoinflammation and lymphoproliferation (IMD72; 618982), Cook et al. (2020) identified homozygous or compound heterozygous missense mutations in the NCKAP1L gene (141180.0001-141180.0004). The mutations, which were found by exome sequencing, segregated with the disorder in the families. In vitro functional expression studies showed that the mutations either destabilized the WAVE actin regulatory complex (WRC) or disrupted binding to the ARF1 (103180) regulator, consistent with a loss of function. Detailed studies on patient T cells and NCKAP1L-null HEK293 cells showed complex effects. There was hypersecretion of perforin (170280), granzymes (see 140050), and granule contents in response to IL2 (147680), suggesting loss of a restrictive function. These and other abnormalities were associated with defects in cortical F-actin polymerization. Patient cells showed aberrant membrane spikes and puncta, defective cell spreading, formation of abnormal lamellipodia, defective membrane ruffling, loss of lamellipodial extensions, and reduced migratory velocity. Similar migration defects were observed in neutrophils and NK cells. The F-actin abnormalities also corresponded to defects in formation of the immunologic synapse. In addition, NCKAP1L-deficient T cells showed defective TCR-induced phosphorylation of AKT (164730), which is part of the mTORC2 (601231) signaling complex involved in T-cell proliferation, differentiation, and survival. The findings demonstrated that loss-of-function mutations in the NCKAP1L gene disrupt WRC-mediated actin polymerization and abrogate mTORC2 activation of AKT. Cook et al. (2020) concluded that the abnormalities affect actin polymerization and other signaling in multiple hematopoietic lineages, resulting in dysregulation of the immune system with immunodeficiency as well as autoimmunity, cytokine overproduction, and lymphoproliferative disease.
In 2 sisters, born of consanguineous parents, with IMD72, Salzer et al. (2020) identified a homozygous missense mutation in the NCKAP1L gene (R129W; 141180.0005). The mutation, which was found by exome sequencing, segregated with the disorder in the family. Patient peripheral white blood cells showed decreased NCKAP1L protein expression compared to controls. Detailed in vitro functional expression studies in patient cells and cells transfected with the mutation showed that it caused destabilization of the WRC complex, reduction in F-actin levels, and failure to assemble lamellipodia. Patient B and T lymphocytes showed altered levels of cell subtypes, defective antigen-induced proliferation in T cells, and dysregulation of B-cell development.
In 2 unrelated patients, each born of consanguineous parents, with IMD72, Castro et al. (2020) identified homozygous mutations in the NCKAP1L gene (141180.0006 and 141180.0007). The mutations, which were found by whole-exome sequencing and confirmed by Sanger sequencing, segregated with the disorder in both families. Neither variant was present in the gnomAD database. Patient CD4+ T cells showed reduced early activation, but T cells showed a normal proliferative response in vitro. T-cell and NK cell cytotoxicity was normal. Patient T cells showed abnormal actin polymerization, abnormal immune synapse morphology, and defective leading edge formation and migration. Transcriptome and proteome analysis of patient immune cells showed an immune activation signature, with increased IFN signaling and T-cell exhaustion, consistent with an inflammatory response. The patients showed hyperinflammation with the development of hemophagocytic lymphohistiocytosis (HLH).
Using chemical mutagenesis and positional cloning, Park et al. (2008) obtained mice with a mutation in exon 13 of the Hem1 gene, resulting in a gln445-to-ter substitution. Mice lacking Hem1 had defective F-actin (see 102610) polymerization and actin capping in lymphocytes and neutrophils due to loss of the Rac (see 602048)-controlled actin regulatory WAVE (WASF1; 605035) protein complex. T-cell development was disrupted at the Cd4 (186940)/Cd8 (see 186910) double-negative to Cd4/Cd8 double-positive stage, and T-cell activation and adhesion were impaired. Hem1-deficient neutrophils failed to migrate in response to chemotactic signals and were deficient in phagocytosing bacteria. Other Rac-dependent functions, such as Th1 differentiation and Nfkb (see 164011)-dependent proinflammatory cytokine transcription, were unimpaired, whereas production of Th17 cells (see 603149) was enhanced. Park et al. (2008) concluded that HEM1 is essential for hematopoietic cell development, function, and homeostasis by controlling a pathway leading to cytoskeletal reorganization.
Salzer et al. (2020) found that Hem1 -/- mice had aberrant B-cell development and multifaceted autoimmunity, replicating human IMD72 with autoimmunity. Single-cell RNA sequencing confirmed dysregulated B-cell development in Hem1 -/- mice.
Castro et al. (2020) found that morpholino knockdown of the nckap1l gene in zebrafish affected hematopoiesis, with mutant animals showing a decrease in red cells and neutrophils, as well as defective recruitment of neutrophils to a site of tail injury. Expression of the wildtype gene was able to rescue the defects.
In an 11-year-old girl (family 1), born of Canadian First Nation parents, with immunodeficiency-72 with autoinflammation and lymphoproliferation (IMD72; 618982), Cook et al. (2020) identified a homozygous c.1076C-T transition (c.1076C-T, NM_005337.4) in the NCKAP1L gene, resulting in a pro359-to-leu (P359L) substitution. Two Mexican sibs from another family (family 2) with IMD72 were compound heterozygous for P359L and a c.1555G-C transversion, resulting in a val519-to-leu (V519L; 141180.0002) substitution. The mutations, which were found by whole-exome sequencing and occurred at conserved residues, segregated with the disorder in the families. Neither mutation was present in homozygous state in the gnomAD database. Patient T cells showed decreased levels of NCKAP1L, CYFIP1 (606323), and WAVE2 (WASF2; 605875), suggesting destabilization of the WRC actin regulatory complex.
For discussion of the c.1555G-C transversion (c.1555G-C, NM_005337.4) in the NCKAP1L gene, resulting in a val519-to-leu (V519L) substitution, that was found in compound heterozygous state in 2 sibs with immunodeficiency-72 with autoinflammation and lymphoproliferation (IMD72; 618982) by Cook et al. (2020), see 141180.0001.
In an 11.5-year-old boy, born of consanguineous Arab parents (family 3), with immunodeficiency-72 with autoinflammation and lymphoproliferation (IMD72; 618982), Cook et al. (2020) identified a homozygous c.1111A-G transition (c.1111A-G, NM_005337.4) in the NCKAP1L gene, resulting in a met371-to-val (M371V) substitution at a highly conserved residue. The mutation, which was found by whole-exome sequencing, segregated with the disorder in the family. It was not present in homozygous state in the gnomAD database. Patient T cells showed normal levels of NCKAP1L, CYFIP1 (606323), and WAVE2 (605875), suggesting a different mechanism than destabilization of the WRC actin regulatory complex. Immunoprecipitation studies showed that the M371V variant maintained association with WRC proteins. However, in vitro studies of a similar M373V variant in the related HEM2 gene showed that it interacted poorly with ARF1 (103180) and could not promote F-actin polymerization upon stimulation. The authors concluded that M371V in the NCKAP1L gene disrupted ARF1-mediated activation.
In a 2.5-year-old girl, born of unrelated North African parents (family 4), with immunodeficiency-72 with autoinflammation and lymphoproliferation (IMD72; 618982), Cook et al. (2020) identified a homozygous c.773G-T transversion (c.773G-T, NM_005337.4) in the NCKAP1L gene, resulting in an arg258-to-leu (R258L) substitution at a highly conserved residue. The mutation, which was found by whole-exome sequencing, segregated with the disorder in the family. The variant was not present in homozygous state in the gnomAD database. Patient T cells showed decreased levels of NCKAP1L, CYFIP1 (606323), and WAVE2 (605875), suggesting destabilization of the WRC actin regulatory complex.
In 2 sisters, born of consanguineous parents, with immunodeficiency-72 with autoinflammation and lymphoproliferation (IMD72; 618982), Salzer et al. (2020) identified a homozygous c.385C-T transition in the NCKAP1L gene, resulting in an arg129-to-trp (R129W) substitution. The mutation, which was found by exome sequencing, segregated with the disorder in the family and was not present in the ExAC or gnomAD databases (January 1, 2020). Patient peripheral white blood cells showed decreased NCKAP1L protein expression compared to controls. In vitro functional expression studies in a murine melanoma cell line showed that the R129W mutant protein had reduced coprecipitation with its WRC-interacting subunits compared to controls. R129W failed to restore proper lamellipodia formation in Hem1-null cells. Cells expressing the mutation also displayed reduced F-actin upon stimulation; patient T cells had reduced cell spreading area compared to controls. Detailed studies of patient B and T lymphocytes showed altered levels of cell subtypes, defective antigen-induced proliferation in T cells, and dysregulation of B-cell development.
In a 15-month-old girl (P1), born of consanguineous Iranian parents, with immunodeficiency-72 with autoinflammation and lymphoproliferation (IMD72; 618982), Castro et al. (2020) identified a homozygous c.421G-T transversion (c.421G-T, NM_005337) in the NCKAP1L gene, resulting in a val141-to-phe (V141F) 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. The patient showed hyperinflammation with the development of hemophagocytic lymphohistiocytosis (HLH).
In an 11-year-old boy (P2), born of consanguineous Saudi Arabian parents, with immunodeficiency-72 with autoinflammation and lymphoproliferation (IMD72; 618982), Castro et al. (2020) identified a homozygous G-to-A transition (c.2862+1G-A, NM_005337) in intron 26 of the NCKAP1L gene, resulting in a splicing abnormality. 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. Patient T cells showed abnormal actin polymerization, abnormal immune synapse morphology, and defective leading edge formation and migration. The patient had recurrent infections and showed hyperinflammation with the development of hemophagocytic lymphohistiocytosis (HLH).
Castro, C. N., Rosenzwajg, M., Carapito, R., Shahrooei, M., Konantz, M., Khan, A., Miao, Z., Gross, M., Tranchant, T., Radosavljevic, M., Paul, N., Stemmelen, T., and 20 others. NCKAP1L defects lead to a novel syndrome combining immunodeficiency, lymphoproliferation, and hyperinflammation. J. Exp. Med. 217: e20192275, 2020. [PubMed: 32766723] [Full Text: https://doi.org/10.1084/jem.20192275]
Cook, S. A., Comrie, W. A., Poli, M. C., Similuk, M., Oler, A. J., Faruqi, A. J., Kuhns,, D. B., Yang, S., Vargas-Hernandez, A., Carisey, A. F., Fournier, B., Anderson, D. E., and 27 others. HEM1 deficiency disrupts mTORC2 and F-actin control in inherited immunodysregulatory disease. Science 369: 202-207, 2020. [PubMed: 32647003] [Full Text: https://doi.org/10.1126/science.aay5663]
Hromas, R., Collins, S., Raskind, W., Deaven, L., Kaushansky, K. Hem-1, a potential membrane protein, with expression restricted to blood cells. Biochim. Biophys. Acta 1090: 241-244, 1991. [PubMed: 1932118] [Full Text: https://doi.org/10.1016/0167-4781(91)90109-y]
Park, H., Staehling-Hampton, K., Appleby, M. W., Brunkow, M. E., Habib, T., Zhang, Y., Ramsdell, F., Liggitt, H. D., Freie, B., Tsang, M., Carlson, G., Friend, S., Frevert, C., Iritani, B. M. A point mutation in the murine Hem1 gene reveals an essential role for hematopoietic protein 1 in lymphopoiesis and innate immunity. J. Exp. Med. 205: 2899-2913, 2008. [PubMed: 19015308] [Full Text: https://doi.org/10.1084/jem.20080340]
Salzer, E., Zoghi, S., Kiss, M. G., Kage, F., Rashkova, C., Stahnke, S., Haimel, M., Platzer, R., Caldera, M., Ardy, R. C., Hoeger, B., Block, J., and 17 others. The cytoskeletal regulator HEM1 governs B cell development and prevents autoimmunity. Sci. Immun. 5: eabc3979, 2020. [PubMed: 32646852] [Full Text: https://doi.org/10.1126/sciimmunol.abc3979]