Alternative titles; symbols
HGNC Approved Gene Symbol: SPTBN1
Cytogenetic location: 2p16.2 Genomic coordinates (GRCh38): 2:54,456,327-54,671,446 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 2p16.2 | Developmental delay, impaired speech, and behavioral abnormalities | 619475 | Autosomal dominant | 3 |
The SPTBN1 gene encodes neuronal beta-II spectrin, which is the most abundant beta-spectrin in the brain. It forms tetramers with alpha-II spectrin (SPTAN1; 182810) that intercalate F-actin rings to build a submembranous periodic skeleton (summary by Cousin et al., 2021).
Spectrin is a tetrameric cytoskeletal protein essential for determination of cell shape, resilience of membranes to mechanical stress, positioning of transmembrane proteins, and organization of organelles and molecular traffic. Alpha- and beta-spectrin subunits form antiparallel dimers that self associate to give the spectrin tetramer. Beta subunits, such as SPTBN1, contain most of the spectrin binding activity (Hayes et al., 2000).
Immunochemical studies demonstrate the existence of beta-spectrin-like polypeptides in nonerythroid tissues. Watkins et al. (1988) obtained a genomic clone for nonerythroid beta-spectrin by screening a DNA library with a synthetic oligonucleotide probe corresponding to human erythroid beta-spectrin (182870) cDNA. The genomic clone showed 76% homology to the erythroid beta-spectrin cDNA when translated to amino acid sequence.
By screening a human brainstem expression library with bovine alpha-spectrin, followed by screening a human hippocampus cDNA library, Hu et al. (1992) cloned SPTBN1, which they designated 'general form of beta-spectrin,' or beta-G spectrin, to distinguish it from erythrocyte beta-spectrin, or beta-R spectrin (SPTB). The deduced 2,364-amino acid SPTBN1 protein has a calculated molecular mass of 274.5 kD. Like SPTB, SPTBN1 has a putative N-terminal actin-binding domain, a central tandem series of 17 repeats of a 106-amino acid motif, and a C-terminal domain. Northern blot analysis of several rat tissues detected highest expression in lung, followed by kidney, brain, thymus, heart, and liver. Western blot analysis of cytosolic and membrane fractions of rat tissues revealed Sptbn1 proteins of 275 to 285 kD that were enriched in membrane fractions of brain, kidney, and lung.
Chang et al. (1993) found that the genomic DNA for human brain beta-fodrin contained regions that cross-hybridized with an erythroid beta-spectrin cDNA probe and that the DNA sequence of these regions showed a high degree of identity and a similar exon/intron organization.
Mishra et al. (1999) cloned 3 isoforms of mouse beta-spectrin, which they called Elf for 'embryonic liver beta-fodrin.' The longest isoform, Elf3, comprises 2,154 residues and is characterized by an actin-binding domain, a long repeat domain, and a short regulatory domain remarkable for the absence of a PH domain. Northern blot analysis demonstrated an abundant 9.0-kb Elf3 transcript in brain, liver, and heart tissues. Immunohistochemical studies demonstrated Elf labeling of the basolateral or sinusoidal membrane surface, as well as a granular cytoplasmic pattern in hepatocytes. Mishra et al. (1999) demonstrated that Elf3 plays a vital role in hepatocyte differentiation and intrahepatic bile duct formation.
By database analysis and PCR of a skeletal muscle cDNA library, Hayes et al. (2000) cloned 2 partial SPTBN1 3-prime splice variants, which they designated sigma-1 and sigma-2. The sigma-1 variant is identical to the 3-prime sequence of the SPTBN1 cDNA cloned by Hu et al. (1992). The sigma-2 variant encodes a protein with a shorter C terminus that lacks the pleckstrin homology domain of the longer isoform and has 28 unique C-terminal residues. Antibodies raised to the short C terminus detected 240-kD proteins in rat cardiac and skeletal muscle and in rat nervous tissue; in cerebellum and forebrain, additional 270-kD proteins were detected. In rat heart and skeletal muscle, both long and short C-terminal forms localized in the region of the Z line. The central region of the sarcomere, coincident with the M line, was selectively labeled with antibodies to the short C-terminal isoform. In cerebellum, parallel fibers showed the long form, but not the short form. In cultured cerebellar granule neurons, the long form was dominant in neurites, while the short form was more abundant in cell bodies. The long form was also readily detected in postsynaptic density preparations of fractionated rat brain, but the short form was only weakly represented.
By database analysis and PCR of a brain cDNA library, Chen et al. (2001) cloned a full-length cDNA encoding the short SPTBN1 isoform. The deduced 2,155-amino acid protein has a calculated molecular mass of 251 kD. In addition to the variation found by Hayes et al. (2000) in the C-terminal domain, Chen et al. (2001) found that the first 36 N-terminal amino acids differ from those in the long isoform, and the actin-binding domain is 13 amino acids shorter. Northern blot analysis of several human tissues detected a 7.5-kb transcript expressed abundantly in brain, kidney, and lung, and more weakly in liver. A 9.5-kb transcript was also detected in lung. Western blot analysis detected the short SPTBN1 isoform at an apparent molecular mass of 225 kD in brain, lung, kidney, and liver. The longer isoform was found at an apparent molecular mass of 240 kD in the same tissues.
Hayes et al. (2000) found that the C terminus of the long SPTBN1 isoform bound fodaxin partially purified from rat brain, but the short isoform did not.
Chen et al. (2001) determined that the SPTBN1 gene spans more than 180 kb and contains a total of 38 exons. Alternative splicing results in transcripts with unique 5-prime and 3-prime ends. The first exon and part of the second exon in each transcript is noncoding.
Watkins et al. (1988) used a genomic clone to map the nonerythroid beta-spectrin gene to human chromosome 2 by study of DNA from somatic cell hybrids.
By hybridization to DNA of a panel of somatic hybrid cell lines, Chang et al. (1993) mapped the SPTBN1 gene to chromosome 2 and localized the gene to 2p21 by isotopic in situ hybridization.
Stumpf (2021) mapped the SPTBN1 gene to chromosome 2p16.2 based on an alignment of the SPTBN1 sequence (GenBank BC137282) with the genomic sequence (GRCh38).
In 29 patients from 28 unrelated families with developmental delay, impaired speech, and behavioral abnormalities (DDISBA; 619475), Cousin et al. (2021) identified heterozygous mutations in the SPTBN1 gene (see, e.g., 182790.0001-182790.0005). The mutations were found by whole-genome or whole-exome sequencing and confirmed by Sanger sequencing; almost all were absent from the gnomAD database. The mutations occurred de novo in all patients except for 1 family in which 2 affected sibs inherited a variant from their unaffected mother who was mosaic. One patient (P10) had 2 de novo SPTBN1 variants in the cis configuration. The mutations occurred at conserved residues throughout the gene: although about half clustered in the CH2 region in the N-terminal domain, whereas the others occurred in spectrin repeat domains. There were 22 missense, 3 nonsense, and 3 splice site mutations. In vitro functional expression studies in HEK293 cells transfected with a subset of the variants demonstrated variable effects. Most resulted in normal protein expression, although some reduced protein levels. The nonsense mutations yielded protein fragments of the expected size, suggesting that the truncated proteins are structurally stable. Several mutant proteins formed cytosolic aggregates, and some caused abnormal membrane protrusions, suggesting an impact on cytoskeletal structures. Further studies showed that some mutations disrupted normal protein-protein interactions and binding to F-actin and ankyrin-B (ANK2; 106410). Studies of cortical neurons derived from Sptbn1-null mice showed impaired organization of the axon initial segment (AIS) with reduced axonal growth, dendritic abnormalities, and aberrant lysosome dynamics. These defects could not be fully rescued by expression of some of the mutations found in patients, suggesting pathogenicity. Heterozygous knockdown of the Sptbn1 gene in mice caused thinning of the corpus callosum consistent with neuronal miswiring or abnormal connectivity. Heterozygous mutant mice demonstrated dysmorphic facial features, hyperactivity, impaired motor abilities, and social deficits, similar to the human phenotype. The authors concluded that some of the mutations resulted in haploinsufficiency, whereas others had a dominant-negative or gain-of-function effect, the latter possibly due to cytosolic aggregates or abnormal membrane morphology.
Disruption of ELF leads to the disruption of TGF-beta (190180) signaling by Smad proteins in mice. Elf -/- mice exhibit a phenotype similar to Smad2/Smad3 double heterozygous mice, with midgestational death due to gastrointestinal, liver, neural, and heart defects. Tang et al. (2003) showed that TGF-beta triggers phosphorylation and association of Elf with Smad3 and Smad4, followed by nuclear translocation. Elf deficiency results in mislocalization of Smad3 and Smad4 and loss of TGF-beta-dependent transcriptional response, which could be rescued by overexpression of the carboxy-terminal region of Elf. Tang et al. (2003) concluded that their study revealed an unexpected molecular link between a major dynamic scaffolding protein and a key signaling pathway.
Lorenzo et al. (2019) found that mice with neural progenitor-specific knockout of beta-II spectrin were born at expected mendelian ratios, but they were smaller than controls, had motor coordination deficits and multiple seizures, and exhibited early postnatal lethality. Histologic characterization revealed that loss of beta-II spectrin in central nervous system resulted in major loss of long-range axonal connectivity and larger caliber axons, as well as axonal degeneration. Beta-II spectrin-deficient neurons exhibited reduced axon growth, loss of actin-spectrin-based periodic membrane skeleton, and impaired bidirectional axonal transport of synaptic cargo. Beta-II spectrin associated with the dynein/dynactin motor complex and several kinesins, implicating spectrin in coupling of motors and synaptic cargo. Beta-II spectrin required phosphoinositide lipid binding to promote axonal transport and restore axon growth. Knockout of Ankb, a beta-II spectrin partner, primarily impaired retrograde organelle transport, while double knockout of beta-II spectrin and Ankb nearly eliminated transport. The authors concluded that beta-II spectrin promoted both axon growth and axon stability through establishing the actin-spectrin-based membrane-associated periodic skeleton and enabling axonal transport of synaptic cargo.
Cousin et al. (2021) found that heterozygous knockdown of the Sptbn1 gene in mice caused thinning of the corpus callosum consistent with neuronal miswiring or abnormal connectivity. Heterozygous mutant mice demonstrated dysmorphic facial features, hyperactivity, impaired motor abilities, and social deficits, recapitulating some of the features observed in human patients with heterozygous SPTBN1 mutations.
In a male patient (P3) with developmental delay, impaired speech, and behavioral abnormalities (DDISBA; 619475), Cousin et al. (2021) identified a de novo heterozygous c.549C-A transversion (c.549C-A, NM_003128.2) in the SPTBN1 gene, resulting in a cys183-to-ter (C183X) substitution in the CH2 domain. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in the gnomAD database. In vitro studies in HEK293 cells transfected with the mutation showed that the mutant protein was truncated and formed cytosolic aggregates. The mutation caused defects in cytoskeletal organization and dynamics in cultured murine cortical neurons.
In a 6-year-old boy (P5) with developmental delay, impaired speech, and behavioral abnormalities (DDISBA; 619475), Cousin et al. (2021) identified a de novo heterozygous c.614G-A transition (c.614G-A, NM_003128.2) in the SPTBN1 gene, resulting in a gly205-to-asp (G205D) substitution at a conserved residue in the CH2 domain. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in the gnomAD database. In vitro studies in HEK293 cells transfected with the mutant protein showed reduced protein levels; the mutant protein formed cytosolic aggregates.
In a 7.8-year-old girl (P8) with developmental delay, impaired speech, and behavioral abnormalities (DDISBA; 619475), Cousin et al. (2021) identified a de novo heterozygous c.749T-G transversion (c.749T-G, NM_003128.2) in the SPTBN1 gene, resulting in a leu250-to-arg (L250R) substitution at a conserved residue in the CH2 domain. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in the gnomAD database. In vitro studies in HEK293 cells transfected with the mutant protein showed that it formed cytosolic aggregates.
In a 7-year-old boy (P19) with developmental delay, impaired speech, and behavioral abnormalities (DDISBA; 619475), Cousin et al. (2021) identified a de novo heterozygous c.2674G-T transversion (c.2674G-T, NM_003128.2) in the SPTBN1 gene, resulting in a glu892-to-ter (E892X) substitution in the SR6 domain. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in the gnomAD database. In vitro studies in transfected HEK293 cells detected a truncated protein.
In a 4-year-old girl (P28) with developmental delay, impaired speech, and behavioral abnormalities (DDISBA; 619475), Cousin et al. (2021) identified a de novo heterozygous c.5656G-C transversion (c.5656G-C, NM_003128.2) in the SPTBN1 gene, resulting in a glu1886-to-gln (E1886Q) substitution at a highly conserved residue in the SR15 domain. The mutation, which was found by exome sequencing and confirmed by Sanger sequencing, was not present in the gnomAD database. In vitro functional expression studies in HEK293 cells transfected with the mutant protein showed that it caused abnormal membrane protrusions, suggesting defects in the cytoskeleton.
Chang, J. G., Scarpa, A., Eddy, R. L., Byers, M. G., Harris, A. S., Morrow, J. S., Watkins, P., Shows, T. B., Forget, B. G. Cloning of a portion of the chromosomal gene and cDNA for human beta-fodrin, the nonerythroid form of beta-spectrin. Genomics 17: 287-293, 1993. [PubMed: 8406479] [Full Text: https://doi.org/10.1006/geno.1993.1323]
Chen, Y., Yu, P., Lu, D., Tagle, D. A., Cai, T. A novel isoform of beta-spectrin II localizes to cerebellar-Purkinje-cell bodies and interacts with neurofibromatosis type 2 gene product schwannomin. J. Molec. Neurosci. 17: 59-70, 2001. [PubMed: 11665863] [Full Text: https://doi.org/10.1385/JMN:17:1:59]
Cousin, M. A., Creighton, B. A., Breau, K. A., Spillmann, R. C., Torti, E., Dontu, S., Tripathi, S., Ajit, D., Edwards, R. J., Afriyie, S., Bay, J. C., Harper, K. M., and 64 others. Pathogenic SPTBN1 variants cause an autosomal dominant neurodevelopmental syndrome. Nature Genet. 53: 1006-1021, 2021. [PubMed: 34211179] [Full Text: https://doi.org/10.1038/s41588-021-00886-z]
Hayes, N. V. L., Scott, C., Heerkens, E., Ohanian, V., Maggs, A. M., Pinder, J. C., Kordeli, E., Baines, A. J. Identification of a novel C-terminal variant of beta-II spectrin: two isoforms of beta-II spectrin have distinct intracellular locations and activities. J. Cell Sci. 113: 2023-2034, 2000. [PubMed: 10806113] [Full Text: https://doi.org/10.1242/jcs.113.11.2023]
Hu, R.-J., Watanabe, M., Bennett, V. Characterization of human brain cDNA encoding the general isoform of beta-spectrin. J. Biol. Chem. 267: 18715-18722, 1992. [PubMed: 1527002]
Lorenzo, D. N., Badea, A., Zhou, R., Mohler, P. J., Zhuang, X., Bennett, V. Beta-II-spectrin promotes mouse brain connectivity through stabilizing axonal plasma membranes and enabling axonal organelle transport. Proc. Nat. Acad. Sci. 116: 15686-15695, 2019. [PubMed: 31209033] [Full Text: https://doi.org/10.1073/pnas.1820649116]
Mishra, L., Cai, T., Yu, P., Monga, S. P., Mishra, B. Elf3 encodes a novel 200-kD beta-spectrin: role in liver development. Oncogene 18: 353-364, 1999. [PubMed: 9927192] [Full Text: https://doi.org/10.1038/sj.onc.1202313]
Stumpf, A. M. Personal Communication. Baltimore, Md. 08/12/2021.
Tang, Y., Katuri, V., Dillner, A., Mishra, B., Deng, C.-X., Mishra, L. Disruption of transforming growth factor-beta signaling in ELF beta-spectrin-deficient mice. Science 299: 574-577, 2003. [PubMed: 12543979] [Full Text: https://doi.org/10.1126/science.1075994]
Watkins, P. C., Eddy, R., Forget, B. G., Chang, J. G., Rochelle, R., Shows, T. B. Assignment of a non-erythroid spectrin gene to human chromosome 2. (Abstract) Am. J. Hum. Genet. 43: A161, 1988.