Alternative titles; symbols
HGNC Approved Gene Symbol: SEPTIN9
Cytogenetic location: 17q25.3 Genomic coordinates (GRCh38): 17:77,281,499-77,500,596 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 17q25.3 | Amyotrophy, hereditary neuralgic | 162100 | Autosomal dominant | 3 |
The septin family of proteins, including SEPT9, are GTPases that interact with the cytoskeleton, including microtubules and actin, and function in cellular processes such as cytokinesis, motility, and cell polarity (summary by Collie et al., 2010).
Osaka et al. (1999) identified a gene fusion partner of the MLL (159555) gene in a 10-year-old female who developed therapy-related acute myeloid leukemia 17 months after treatment with DNA topoisomerase II inhibitors for Hodgkin disease (236000). Leukemia cells of this patient had a t(11;17)(q23;q25) translocation, which involved MLL. The partner gene was cloned from cDNA of the leukemia cells by use of a combination of adaptor reverse transcriptase-PCR, rapid amplification of 5-prime cDNA ends (RACE), and BLAST database analysis to identify ESTs. The full-length cDNA of 2.8 kb was found to be a member of the septin family, and Osaka et al. (1999) therefore designated the gene MSF for 'MLL septin-like fusion gene.' MSF encodes a putative protein of 568 amino acids with a predicted molecular mass of about 63 kD. Northern blot analysis revealed a major 4-kb transcript that was expressed ubiquitously, a 1.7-kb transcript that was found in most tissues, and a 3-kb transcript that was found only in hematopoietic tissues. MSF is highly homologous to CDCREL (602724), which is a partner gene of MLL in leukemias with a t(11;22)(q23;q11.2).
By screening size-fractionated human brain cDNA libraries for cDNAs encoding proteins larger than 50 kD, Nagase et al. (1999) identified an MSF cDNA, which they referred to as KIAA0991. The KIAA0991 cDNA encodes a predicted 422-amino acid protein that shares approximately 48% amino acid identity with the C. albicans CDC10 protein (603151).
Russell et al. (2000) isolated the same gene, which they designated ovarian/breast (Ov/Br) septin, as a candidate for the ovarian tumor suppressor gene that had been indirectly identified by up to 70% loss of heterozygosity (LOH) for a marker at chromosome 17q25 in a bank of malignant ovarian tumors (167000). Two splice variants were demonstrated within the 200-kb contig, which differed only at exon 1. The septins are a family of genes involved in cytokinesis and cell cycle control, whose known functions are consistent with the hypothesis that the human 17q25 septin gene is a candidate for the ovarian tumor suppressor gene.
By screening a breast cDNA library, followed by 5-prime RACE of a mammary gland cDNA library and EST database analysis, Kalikin et al. (2000) cloned 2 MSF splice variants that they designated MSFA and MSFB. MSFA, MSFB, the original MSF cDNA cloned by Osaka et al. (1999), and the KIAA0991 variant cloned by Nagase et al. (1999), which Kalikin et al. (2000) called MSFC, all differ at their 5-prime ends. The MSF cDNA cloned by Osaka et al. (1999) also differs from the other variants at its 3-prime end. The 4 MSF variants encode proteins of 586 (MSFA), 568 (MSF), and 422 (MSFB and MSFC) amino acids that differ only at their N termini; all 3 contain the conserved GTPase domain and a xylose isomerase-1 domain. Northern blot analysis detected variable and developmentally regulated expression of 4.0- and 3.0-kb transcripts in almost all adult and fetal tissues examined. Using variant-specific probes, Kalikin et al. (2000) detected a 4.0-kb MSFA transcript in all fetal and adult tissues examined and a 4.0-kb MSFB transcript in skeletal muscle only. No expression was detected using MSF- and MSFC-specific probes.
McIlhatton et al. (2001) showed that the SEPT9 gene has 18 distinct transcripts, based on multiple transcription start sites, that encode 15 polypeptides. Database analyses by McIlhatton et al. (2001) identified orthologous rodent cDNAs that corresponded to 5-prime splice variants of the Ov/Br septin gene, increasing the total number of such variants to 6. Investigation of isoforms by RT-PCR confirmed a complex transcriptional pattern, with several isoforms showing tissue-specific distribution.
McDade et al. (2007) described and characterized 6 SEPT9 variants that differ by transcriptional start site and 5-prime untranslated regions. The variants, designated v1a, v2a, v3a, v4a, and v4a*, all share exon 3 through to the stop codon in exon 12; the v5 polypeptide lacks exon 3 but shares exon 4 through the exon 12 stop codon. McDade et al. (2007) found that v4a and v4a* are translated with differing efficacy due to different 5-prime untranslated regions and an internal ribosomal entry site.
Sorensen et al. (2002) identified 4 mouse Sept9 variants that differ at their 5-prime ends; the 3-prime ends appear to be identical. Northern blot analysis detected several Sept9 transcripts, with variable expression in all tissues examined except skeletal muscle. In situ hybridization of mouse embryos detected strong expression in several areas, including neural crest cells, cephalic mesenchyme, and mesenchymal cells in the developing limb.
Kalikin et al. (2000) estimated that the SEPT9 gene spans 266 kb and contains at least 15 exons, including 4 alternative first exons.
McIlhatton et al. (2001) found that the SEPT9 gene has 17 exons distributed over 240 kb.
By analysis of a human-rodent hybrid panel, Nagase et al. (1999) mapped the SEPT9 gene to chromosome 17. Osaka et al. (1999) mapped the SEPT9 gene to chromosome 17q25.
Spiliotis et al. (2005) found that septins localized to the metaphase plate during mitosis. Septin depletion resulted in chromosome loss from the metaphase plate, lack of chromosome segregation and spindle elongation, and incomplete cytokinesis upon delayed mitotic exit. The authors showed that these defects correlated with the loss of the mitotic motor and the checkpoint regulator centromere-associated protein E (CENPE; 117143) from the kinetochores of congressing chromosomes. Spiliotis et al. (2005) suggested that mammalian septins may form a mitotic scaffold for CENP-E and other effectors to coordinate cytokinesis with chromosome congression and segregation.
Nagata et al. (2004) coprecipitated Sept11 (612887) with a septin complex that included Sept2 (601506), Sept7 (603151), Sept8 (608418), and Sept9b from a rat fibroblast cell line, and examined the interaction of Sept11 with Sept7 and Sept9b. They found that the C-terminal coiled-coil regions of Sept7 and Sept11 interact with each other, and that these coiled-coil regions interact with the N-terminal variable region of Sept9b. Sept7, Sept9b, and Sept11 formed thin filaments when expressed alone in COS-7 cells. Coexpression of Sept11 with Sept7 disrupted the filaments formed by each component alone, although Sept7 and Sept11 colocalized despite filament disruption. Conversely, coexpression of Sept11 and Sept9b increased filament bundling compared with filaments formed by each component alone. Nagata et al. (2004) concluded that the filaments formed by individual septins are affected by other septins in the filament complex.
Kuhlenbaumer et al. (2005) studied 10 previously reported multigeneration families with the classic phenotype of hereditary neuralgic amyotrophy (HNA; 162100) from different geographic regions, using short tandem repeat (STR) markers in informative recombinants of these families to further reduce the HNA locus to an interval of approximately 600 kb containing only 2 known genes, SEC14-like 1 (SEC14L1; 601504) and SEPT9. By sequencing the coding region of SEPT9, including its untranslated regions (UTRs), multiple splice variants, and alternative first exons, they identified 3 different mutations in 6 of the families (604061.0001-604061.0003).
McDade et al. (2007) demonstrated that SEPT9 v4*a variant has a longer 5-prime untranslated region (UTR) than v4a but that both variants have a common initiating codon in exon 3. A putative internal ribosome entry site was identified in the common region of the v4 and v4* 5'-UTRs and translation was modulated by an upstream open reading frame in the unique region of the v4 5'-UTR. A 262C-T mutation (604061.0001) in exon 3 was found to lie in a predicted stem-loop structure of the v4 5-prime UTR and was found to result in greater translation of v4 under hypoxic conditions. McDade et al. (2007) concluded that the disease-associated mutation leads to deregulation of SEPT9 v4 translation under stress conditions, which may change the ratio of SEPT9 isoforms and lead to altered function. These physiologic findings correlated to the known episodic nature of the disorder.
In 8 of 42 unrelated pedigrees with HNA, Hannibal et al. (2009) identified mutations in the SEPT9 gene. One of the mutations (R88W; 604061.0001) was consistent with a founder effect.
Landsverk et al. (2009) identified an intragenic 38-kb tandem duplication in the SEPT9 gene (604061.0004) that was linked to HNA in 12 North American families that shared a common founder haplotype. The duplication was identical in all pedigrees and included the 645-bp exon in which 2 previous HNA mutations had been found.
Collie et al. (2010) identified heterozygous tandem duplications affecting the SEPT9 gene in affected individuals from 6 unrelated families with HNA. All of the duplications were of different sizes with unique breakpoints and ranged in size from 30 to 330 kb. The smallest common region shared by all duplications encompassed the proline-rich 645-bp exon in which HNA-linked mutations had previously been identified, suggesting that this region is involved in the pathogenesis of the disorder. Five of the duplications generated larger protein products compared to the wildtype protein. The largest 330-kb duplication spanned the entire SEPT9 gene and included a portion of the adjacent gene SEC14L1 (601504); this duplication did not generate aberrant transcripts or proteins, suggesting that increased dosage of SEPT9 alone may be responsible for the disorder. There was no single mechanism responsible for the generation of these duplications. The HNA phenotype was the same as that observed for other mutations in the SEPT9 gene.
Sudo et al. (2007) detected Sept9 expression in rat astrocytes and Schwann cells as well as murine mammary gland cells. In murine mesenchymal and epithelial mammary gland cells, mutant R88W (604061.0001) and S93F (604061.0002) proteins showed similar localization as wildtype protein; however, mutant Sept9 proteins showed altered interaction with Sept4 (603696) and Sept11 (612887) compared to wildtype protein. In mesenchymal cells, mutant Sept9 localized with Sept4 in thin, straight filaments along stress fibers, and in epithelial cells, mutant Sept9 was enriched at cell-cell contact sites with Sept11. Further studies showed that mutant Sept9 did not respond to Rho (180380)/rhotekin (602288) signaling. Sudo et al. (2007) concluded that pathogenic mutations in SEPT9 alter its mode of interaction with partner molecules within cells.
In 4 families of different geographic origins, Kuhlenbaumer et al. (2005) found that hereditary neuralgic amyotrophy (HNA; 162100) was associated with a heterozygous 262C-T transition in exon 2 of the SEPT9 gene, resulting in an arg88-to-trp (R88W) amino acid change. The 4 families did not share a common disease-associated haplotype, suggestive of a mutation hotspot rather than a founder mutation. Genomic variation occurred at a potential hypermutable CG dinucleotide. One of the 4 families was North American of European descent, 2 were Spanish, and 1 was Finnish. Dysmorphic features were present in affected members of each of the 4 families.
Laccone et al. (2008) identified heterozygosity for the R88W mutation in 4 affected members of a 3-generation family with HNA. Two sibs had dysmorphic features as children, including hypotelorism, upslanting palpebral fissures, deep-set eyes, blepharophimosis, and epicanthal folds. Developmental milestones were normal. On history, the father and paternal grandmother reported painful episodes of brachial muscle weakness with residual wasting and paralysis, consistent with HNA. Photographs of the father and grandmother as children showed similar dysmorphic features as in the 2 sibs. Both sibs also developed brachial neuritis.
Hannibal et al. (2009) identified the R88W mutation in affected members of 7 of 42 unrelated pedigrees with HNA. Haplotype analysis indicated a founder effect.
In a North American family of European descent, Kuhlenbaumer et al. (2005) found that individuals with hereditary neuralgic amyotrophy (HNA; 162100) carried a transition mutation, 278C-T, in the SEPT9 gene, resulting in a ser93-to-phe (S93F) amino acid substitution. The affected individuals showed dysmorphic features.
Hannibal et al. (2009) identified the S93F mutation in affected members of a French kindred with HNA.
In a family of Turkish origin, Kuhlenbaumer et al. (2005) found that individuals with hereditary neuralgic amyotrophy (HNA; 162100) had a sequence variation, -131G-C, in the 5-prime UTR of the SEPT9 alpha transcript. Dysmorphic features were absent in this family.
Landsverk et al. (2009) identified an intragenic 38-kb tandem duplication in the SEPT9 gene that was linked to hereditary neuralgic amyotrophy (HNA; 162100) in 12 North American families that shared a common founder haplotype. The duplication was identical in all pedigrees and included the 645-bp exon in which 2 previous HNA mutations had been found, as well as the first 2 exons of SEPT9 variants 2 and 6. The SEPT9 variants that spanned this duplication contained 2 in-frame repeats of the 645-bp exon, and immunoblotting demonstrated larger molecular mass SEPT9 protein isoforms. The 645-bp exon encodes most of the N-terminal proline-rich region of SEPT9, suggesting that this region may play a role in HNA pathogenesis.
Collie, A. M. B., Landsverk, M. L., Ruzzo, E., Mefford, H. C., Buysse, K., Adkins, J. R., Knutzen, D. M., Barnett, K., Brown, R. H., Jr., Parry, G. J., Yum, S. W., Simpson, D. A., Olney, R. K., Chinnery, P. F., Eichler, E. E., Chance, P. F., Hannibal, M. C. Non-recurrent SEPT9 duplications cause hereditary neuralgic amyotrophy. J. Med. Genet. 47: 601-607, 2010. [PubMed: 19939853] [Full Text: https://doi.org/10.1136/jmg.2009.072348]
Hannibal, M. C., Ruzzo, E. K., Miller, L. R., Betz, B., Buchan, J. G., Knutzen, D. M., Barnett, K., Landsverk, M. L., Brice, A., LeGuern, E., Bedford, H. M., Worrall, B. B., Lovitt, S., Appel, S. H., Andermann, E., Bird, T. D., Chance, P. F. SEPT9 gene sequencing analysis reveals recurrent mutations in hereditary neuralgic amyotrophy. Neurology 72: 1755-1759, 2009. [PubMed: 19451530] [Full Text: https://doi.org/10.1212/WNL.0b013e3181a609e3]
Kalikin, L. M., Sims, H. L., Petty, E. M. Genomic and expression analyses of alternatively spliced transcripts of the MLL septin-like fusion gene (MSF) that map to a 17q25 region of loss in breast and ovarian tumors. Genomics 63: 165-172, 2000. [PubMed: 10673329] [Full Text: https://doi.org/10.1006/geno.1999.6077]
Kuhlenbaumer, G., Hannibal, M. C., Nelis, E., Schirmacher, A., Verpoorten, N., Meuleman, J., Watts, G. D. J., De Vriendt, E., Young, P., Stogbauer, F., Halfter, H., Irobi, J., and 15 others. Mutations in SEPT9 cause hereditary neuralgic amyotrophy. Nature Genet. 37: 1044-1046, 2005. [PubMed: 16186812] [Full Text: https://doi.org/10.1038/ng1649]
Laccone, F., Hannibal, M. C., Neeson, J., Grisold, W., Chance, P. F., Rehder, H. Dysmorphic syndrome of hereditary neuralgic amyotrophy associated with a SEPT9 gene mutation--a family study. Clin. Genet. 74: 279-283, 2008. [PubMed: 18492087] [Full Text: https://doi.org/10.1111/j.1399-0004.2008.01022.x]
Landsverk, M. L., Ruzzo, E. K., Mefford, H. C., Buysse, K., Buchan, J. G., Eichler, E. E., Petty, E. M., Peterson, E. A., Knutzen, D. M., Barnett, K., Farlow, M. R., Caress, J., Parry, G. J., Quan, D., Gardner, K. L., Hong, M., Simmons, Z., Bird, T. D., Chance, P. F., Hannibal, M. C. Duplication within the SEPT9 gene associated with a founder effect in North American families with hereditary neuralgic amyotrophy. Hum. Molec. Genet. 18: 1200-1208, 2009. [PubMed: 19139049] [Full Text: https://doi.org/10.1093/hmg/ddp014]
McDade, S. S., Hall, P. A., Russell, S. E. H. Translational control of SEPT9 isoforms is perturbed in disease. Hum. Molec. Genet. 16: 742-752, 2007. [PubMed: 17468182] [Full Text: https://doi.org/10.1093/hmg/ddm003]
McIlhatton, M. A., Burrows, J. F., Donaghy, P. G., Chanduloy, S., Johnston, P. G., Russell, S. E. H. Genomic organization, complex splicing pattern and expression of a human septin gene on chromosome 17q25.3. Oncogene 20: 5930-5939, 2001. [PubMed: 11593400] [Full Text: https://doi.org/10.1038/sj.onc.1204752]
Nagase, T., Ishikawa, K., Suyama, M., Kikuno, R., Hirosawa, M., Miyajima, N., Tanaka, A., Kotani, H., Nomura, N., Ohara, O. Prediction of the coding sequences of unidentified human genes. XIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro. DNA Res. 6: 63-70, 1999. [PubMed: 10231032] [Full Text: https://doi.org/10.1093/dnares/6.1.63]
Nagata, K., Asano, T., Nozawa, Y., Inagaki, M. Biochemical and cell biological analyses of a mammalian septin complex, Sept7/9b/11. J. Biol. Chem. 279: 55895-55904, 2004. [PubMed: 15485874] [Full Text: https://doi.org/10.1074/jbc.M406153200]
Osaka, M., Rowley, J. D., Zeleznik-Le, N. J. MSF (MLL septin-like fusion), a fusion partner gene of MLL, in a therapy-related acute myeloid leukemia with a t(11;17)(q23;q25). Proc. Nat. Acad. Sci. 96: 6428-6433, 1999. [PubMed: 10339604] [Full Text: https://doi.org/10.1073/pnas.96.11.6428]
Russell, S. E. H., McIlhatton, M. A., Burrows, J. F., Donaghy, P. G., Chanduloy, S., Petty, E. M., Kalikin, L. M., Church, S. W., McIlroy, S., Harkin, D. P., Keilty, G. W., Cranston, A. N., Weissenbach, J., Hickey, I., Johnston, P. G. Isolation and mapping of a human septin gene to a region on chromosome 17q, commonly deleted in sporadic epithelial ovarian tumors. Cancer Res. 60: 4729-4734, 2000. [PubMed: 10987277]
Sorensen, A. B., Warming, S., Fuchtbauer, E.-M., Pedersen, F. S. Alternative splicing, expression, and gene structure of the septin-like putative proto-oncogene Sint1. Gene 285: 79-89, 2002. [PubMed: 12039034] [Full Text: https://doi.org/10.1016/s0378-1119(02)00406-7]
Spiliotis, E. T., Kinoshita, M., Nelson, W. J. A mitotic septin scaffold required for mammalian chromosome congression and segregation. Science 307: 1781-1785, 2005. [PubMed: 15774761] [Full Text: https://doi.org/10.1126/science.1106823]
Sudo, K., Ito, H., Iwamoto, I., Morishita, R., Asano, T., Nagata, K. SEPT9 sequence alternations (sic) causing hereditary neuralgic amyotrophy are associated with altered interactions with SEPT4/SEPT11 and resistance to Rho/Rhotekin-signaling. Hum. Mutat. 28: 1005-1013, 2007. [PubMed: 17546647] [Full Text: https://doi.org/10.1002/humu.20554]