Alternative titles; symbols
HGNC Approved Gene Symbol: SPTBN4
Cytogenetic location: 19q13.2 Genomic coordinates (GRCh38) : 19:40,467,001-40,576,464 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 19q13.2 | Neurodevelopmental disorder with hypotonia, neuropathy, and deafness | 617519 | Autosomal recessive | 3 |
The SPTBN4 gene encodes a nonerythrocytic member of the beta-spectrin protein family that is expressed in the brain, peripheral nervous system, pancreas, and skeletal muscle. Spectrins are rod-shaped proteins that were originally identified as part of the lattice-like cytoskeleton under the erythrocyte membrane. Spectrins have also been found in the membranes of intracellular organelles, such as the Golgi, lysosomes, and secretory vesicles. The spectrin molecule is a tetramer consisting of 2 alpha (see, e.g., SPTA1, 182860) and 2 beta subunits, in which the N terminus of an alpha subunit is tightly connected with the C terminus of a beta subunit to form a heterodimer. Spectrin repeats contain approximately 106 amino acids. Alpha subunits have 20 spectrin repeats, while beta subunits have 17 (summary by Berghs et al., 2000).
By screening a size-fractionated adult brain cDNA library for cDNAs with the potential to encode large proteins, Nagase et al. (2000) isolated a partial cDNA encoding SPTBN4, which they called KIAA1642. RT-PCR analysis detected ubiquitous expression of SPTBN4, with relatively high levels in adult and fetal brain, low levels in lung, liver, pancreas, and spleen, and intermediate levels in the other tissues tested and in specific brain regions.
Using a yeast 2-hybrid screen of a brain cDNA library with the cytoplasmic domain of ICA512 (PTPRN; 601773) as bait, followed by probing a brain cDNA library, PCR, and genomic sequence analysis, Berghs et al. (2000) isolated cDNAs encoding SPTBN4 and several splice variants. Sequence analysis predicted that the full-length 2,559-amino acid SPTBN4 protein, designated sigma-1, contains 2 N-terminal calponin homology domains, which mediate interactions with actin; 16 complete spectrin repeats; 1 partial spectrin repeat; a unique proline-rich, basic domain containing 4 ERQES repeats; numerous SH3 binding sites; and a C-terminal pleckstrin homology domain. An insertion in exon 17 termed exon 17b yields a 1,302-residue splice variant, sigma-2, which terminates in spectrin repeat 9, and another variant, sigma-3, which begins at exon 17b to generate a 1,307-amino acid protein. Variant sigma-4 has an insertion in exon 30 termed exon 30b that introduces 42 amino acids and a stop codon, resulting in a 2,149-amino acid protein that lacks the ERQES and pleckstrin homology domains. Binding analysis indicated that the C terminus of SPTBN4 binds to PTPRN and only weakly to an active tyrosine phosphatase mutant of PTPRN and to PHOGRIN (601698). Northern blot analysis revealed expression of 9.0-, 5.1-, and 3.1-kb SPTBN4 transcripts that were predominantly expressed in brain. Western blot analysis showed expression of 250- and 160-kD proteins in rat brain and human pancreatic islets, as well as a 140-kD protein in rat brain only. Phosphatase treatment indicated that the 160-kD protein is phosphorylated, probably in the ERQES domain, which modifies its interaction with cytoskeletal and membrane proteins. Immunocytochemistry and confocal microscopy demonstrated coexpression of PTPRN and SPTBN4 in both insulin-secreting beta cells and glucagon-secreting alpha cells. In situ hybridization and immunocytochemistry suggested coexpression of SPTBN4 and ankyrin-G (ANK3; 600465) in rat brain. The protein localized to axon initial segments (AIS) and nodes of Ranvier in the central and peripheral nervous system of the rat. Berghs et al. (2000) postulated that SPTBN4 may be required for the anchoring of voltage-gated Na+ channels and cell adhesion molecules to the actin cytoskeleton and may play an important role in nerve conduction.
Tse et al. (2001) cloned SPTBN4, which they termed SPTBN3, as well as a splice variant, sigma-5, encoding a 678-amino acid protein. Whole-mount in situ hybridization analysis revealed Sptbn4 expression that was restricted to forebrain, hindbrain, and developing eye in postcoital day-9.5 mice. Western blot analysis with polyclonal antibodies detected expression of a predominant 72-kD protein, close to the expected size of the sigma-5 variant. Immunofluorescence microscopy demonstrated colocalization of SPTBN4 with PML (102578) and with SUMO1 (UBL1; 601912) in the cytoplasm and nucleus. The authors showed that both the N- and C-terminal helical coils of sigma-5 are needed to form nuclear dots and are associated with the nuclear matrix. Tse et al. (2001) proposed that a spectrin-based skeleton may be important for the structure of the nucleus.
In human muscle, Knierim et al. (2017) found expression of SPTBN4 at the sarcolemma and in the muscle capillaries.
By genomic sequence analysis, Berghs et al. (2000) determined that the SPTBN4 gene contains 36 exons. Tse et al. (2001) determined that the SPTBN4 gene spans over 145 kb.
By radiation hybrid analysis, Nagase et al. (2000) mapped the SPTBN4 gene to chromosome 19. Berghs et al. (2000) localized the gene to 19q13.13 by FISH. They identified a highly related gene that resides on chromosome 16. Tse et al. (2001) mapped the SPTBN4 gene to 19q13.13-q13.2 by radiation hybrid analysis.
Berghs et al. (2000) and Tse et al. (2001) mapped the mouse Sptnb4 gene to chromosome 7b2.
In a boy, born of consanguineous Kurdish parents, with neurodevelopmental disorder with hypotonia, neuropathy, and deafness (NEDHND; 617519), Knierim et al. (2017) identified a homozygous truncating mutation in the SPTBN4 gene (Q533X; 606214.0001). The mutation, which was found by a combination of autozygosity mapping and whole-exome sequencing, was confirmed by Sanger sequencing and segregated with the disorder in the family. Western blot analysis of patient fibroblasts showed absence of the SPTBN4 protein, and immunostaining of patient muscle sample showed absence of SPTBN4 at the sarcolemma. The phenotype was similar to that of the 'quivering' mouse, which results from a homozygous loss-of-function mutation in the Sptnb4 gene.
In 6 patients from 5 unrelated families with NEDHND, Wang et al. (2018) identified homozygous or compound heterozygous mutations in the SPTBN4 gene (see, e.g., 606214.0002-606214.0006). The mutations were found by exome sequencing; confirmed segregation of the mutations with the disorder was only possible in 1 family (family A). All patients except 1 (patient from family C) carried biallelic nonsense or frameshift mutations predicted to result in a complete loss of function. The patient from family C carried compound heterozygous missense mutations (R504Q, 606214.0004 and R2435C, 606214.0005). Five of the 7 variants were located N-terminal to SR10 and were predicted to affect only the longer sigma-1 splice variant; SR15 mediates the interaction with ankyrin-G (ANK3; 600465). The equivalent human variants in mouse Sptbn4 were expressed in cultured rat hippocampal neurons. Most of the truncating variants failed to localize to the AIS due to inability to interact with ANK3, whereas the 2 missense variants and 1 C-terminal frameshift mutation (c.7453delG; 606214.0006) were able to interact with ANK3 and localized properly to the AIS. The c.7453delG mutant was abnormally present in small intracellular puncta rather than normal diffuse distribution, suggesting that the mutation disrupted the PH domain and altered the distribution of SPTBN4 in membrane compartments. The mutant protein was also unable to bind phosphoinositides, further demonstrating an adverse effect on PH domain function. Examination of the nodes of Ranvier was possible for 2 patients. Sural nerve biopsy from the patient with a homozygous truncating mutation (W903X; 606214.0003) that only affected the sigma-1 variant showed significantly reduced neurofascin labeling at the nodes of Ranvier as well as decreased immunostaining for certain sodium and potassium channels and nearly undetectable nodal immunoreactivity for the shorter SPTBN4 isoform (sigma-6). The findings indicated that sigma-6 is not sufficient to rescue nodal abnormalities. Sural nerve biopsy from the patient with compound heterozygous missense mutations showed fairly normal structure at the nodes of Ranvier, with a small reduction in potassium channels. Wang et al. (2018) concluded that SPTBN4 mutations disrupt the cytoskeletal machinery that controls proper localization of ion channels and function of axonal domains mainly at the AIS and the nodes of Ranvier, resulting in severe neurologic dysfunction.
The autosomal recessive mouse mutation 'quivering' (qv), described by Yoon and Les (1957), produces progressive ataxia with hindlimb paralysis, deafness, and tremor. Ear twitch responses (Preyer reflex) to sound are absent in homozygous qv/qv mice, although cochlear morphology seems normal and cochlear potentials recorded at the round window are no different from those of control mice. However, responses from brainstem auditory nuclei show abnormal transmission of auditory inflammation, indicating that in contrast to the many mutations causing deafness originating in the cochlea, deafness in qv is central in origin (Deol et al., 1983; Bock et al., 1983). Parkinson et al. (2001) reported that qv mice carry loss-of-function mutations in the Sptnb4 gene that cause alterations in ion channel localization in myelinated nerves. They concluded that this finding provides a rationale for the auditory and motor neuropathies of these mice. Knierim et al. (2017) found absence of Sptbn4 immunostaining at the sarcolemma of muscle from the qv mouse, as well as complete absence of type 1 muscle fibers.
In a boy, born of consanguineous Kurdish parents, with neurodevelopmental disorder with hypotonia, neuropathy, and deafness (NEDHND; 617519), Knierim et al. (2017) identified a homozygous c.1597C-T transition (c.1597C-T, NM_020971.2) in the SPTBN4 gene, resulting in a gln533-to-ter (Q533X) substitution. The mutation, which was found by a combination of autozygosity mapping and whole-exome sequencing, was confirmed by Sanger sequencing and segregated with the disorder in the family. It was not found in the dbSNP, 1000 Genomes Project, Exome Variant Server, or ExAC databases, or in an in-house database of over 150 exomes. Western blot and PCR analysis of patient fibroblasts showed absence of the SPTBN4 protein and mRNA, consistent with nonsense-mediated mRNA decay. Immunostaining of patient muscle sample showed absence of SPTBN4 at the sarcolemma.
In 2 sibs (family A) with neurodevelopmental disorder with hypotonia, neuropathy, and deafness (NEDHND; 617519), Wang et al. (2018) identified a homozygous c.3820G-T transversion (c.3820G-T, NM_020971.2) in the SPTBN4 gene, resulting in a glu1274-to-ter (E1274X) substitution before SR10 and affecting only the sigma-1 isoform. The mutation, which was found by exome sequencing, segregated with the disorder in the family and was not found in the gnomAD database.
In a 5-year-old girl (family B) with neurodevelopmental disorder with hypotonia, neuropathy, and deafness (NEDHND; 617519), Wang et al. (2018) identified a homozygous c.2709G-A transition (c.2709G-A, NM_020971.2), resulting in a trp903-to-ter (W903X) substitution before SR10 and affecting only the sigma-1 isoform. Sural nerve biopsy from this patient showed significantly reduced neurofascin labeling at the nodes of Ranvier as well as decreased immunostaining for certain sodium and potassium channels and nearly undetectable levels of the shorter SPTBN4 isoform (sigma-6). The findings indicated that sigma-6 is not sufficient to rescue nodal abnormalities. The c.2709G-A variant was not found in the gnomAD database.
In a 3-year-old boy (family C) with neurodevelopmental disorder with hypotonia, neuropathy, and deafness (NEDHND; 617519), Wang et al. (2018) identified compound heterozygous missense mutations in the SPTBN4 gene: a c.1511G-A transition (c.1511G-A, NM_020971.2), resulting in an arg504-to-gln (R504Q) substitution at a conserved residue in the SR2 domain, and a c.7303C-T transition, resulting in an arg2435-to-cys (R2435C; 606214.0005) substitution at a conserved residue in the C-terminal PH domain. Expression of the equivalent mouse Sptbn4 in cultured rat hippocampal neurons showed that both variants retained the ability to interact with ANK3 and localized properly to the AIS, unlike most of the other SPTBN4 variants. The SR2 domain is reported to underlie alpha and beta subunit heterodimer interactions, but coexpression studies showed that the R504Q variant did not disrupt the interaction with alpha-2-spectrin (182810). Similarly, the R2435C variant showed diffuse intracellular distribution similar to the wildtype pattern when expressed in HEK293 cells and was able to bind normally to phosphoinositides, suggesting normal function of the PH domain. It was thus unclear how the R504Q and R2435C variants exerted pathogenicity in these studies, but the patient's phenotype was similar to that of patients with other SPTBN4 mutations. Sural nerve biopsy from this patient showed normal neurofascin immunostaining at the nodes of Ranvier as well as near normal labeling of certain sodium channels and only a slight decrease in potassium channels. The R504Q and R2435C variants were present in the gnomAD database at low allele frequencies, 6.887 x 10(-5) and 8.94 x 10(-5), respectively.
For discussion of the c.7303C-T transition (c.7303C-T, NM_020971.2) in the SPTBN4 gene, resulting in an arg2435-to-cys (R2435C) substitution, that was found in compound heterozygous state in a patient with neurodevelopmental disorder with hypotonia, neuropathy, and deafness (NEDHND; 617519) by Wang et al. (2018), see 606214.0004.
In a 5-year-old boy (family D) with neurodevelopmental disorder with hypotonia, neuropathy, and deafness (NEDHND; 617519), Wang et al. (2018) identified a homozygous 1-bp deletion (c.7453delG, NM_020971.2) in the SPTBN4 gene, resulting in a frameshift and premature termination (Ala2485LeufsTer31) within the PH domain. Expression of the mutation in HEK293 cells showed that the mutant protein was abnormally present in small intracellular puncta rather than normal diffuse distribution, suggesting that the mutation disrupted the PH domain and altered the distribution of SPTBN4 in membrane compartments. The mutant protein was also unable to bind phosphoinositides, further demonstrating an adverse effect on PH domain function. The c.7453delG variant was not present in the gnomAD database.
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