Alternative titles; symbols
HGNC Approved Gene Symbol: SBDS
Cytogenetic location: 7q11.21 Genomic coordinates (GRCh38) : 7:66,987,680-66,995,586 (from NCBI)
| Location | Phenotype |
Phenotype MIM number |
Inheritance |
Phenotype mapping key |
|---|---|---|---|---|
| 7q11.21 | {Aplastic anemia, susceptibility to} | 609135 | 3 | |
| Shwachman-Diamond syndrome 1 | 260400 | Autosomal recessive | 3 |
Boocock et al. (2003) screened 18 positional candidate genes in the critical region on chromosome 7q11 identified by linkage analysis for Shwachman-Diamond syndrome (SDS1; 260400), an autosomal recessive disorder with clinical features that include pancreatic exocrine insufficiency, hematologic dysfunction, and skeletal abnormalities. They discovered mutations associated with Shwachman-Diamond syndrome in an uncharacterized gene represented by the 1.6-kb cDNA clone FLJ10917 (GenBank AK001779). They designated the gene SBDS for 'Shwachman-Bodian-Diamond syndrome.' SBDS is a member of a highly conserved protein family, with orthologs in species ranging from archaea to vertebrates and plants. Indirect lines of evidence suggested that the orthologs may function in RNA metabolism. The predicted protein is 28.8 kD with a pI of 8.9.
Boocock et al. (2003) determined that the SBDS gene contains of 5 exons spanning 7.9 kb.
By genomic sequence analysis, Boocock et al. (2003) mapped the SBDS gene to chromosome 7q11. SBDS and an adjacent gene reside in a block of 305 kb that is locally duplicated. The paralogous duplicon is located 5.8 Mb distally and contains an unprocessed pseudogene copy of SBDS designated SBDSP. The pseudogene transcript is 97% identical to SBDS and contains deletions and nucleotide changes that disrupt coding potential.
Austin et al. (2005) found that SBDS protein was present in both the nucleus and the cytoplasm of normal control fibroblasts, but was particularly concentrated within the nucleolus. SBDS localization was cell cycle-dependent, with nucleolar localization during G1 and G2 and diffuse nuclear localization during S phase. The intranucleolar localization of SBDS provided further supportive evidence for its postulated role in the processing of ribosomal RNA (rRNA).
Ganapathi et al. (2007) presented in vitro evidence indicating that the SBDS gene is involved with ribosomal RNA. Nucleolar localization of SBDS was dependent on active ribosomal RNA transcription. Lymphoblast cell lines derived from SDS patients showed hypersensitivity to actinomycin D, which inhibits RNA polymerase I, indicating an underlying impairment of ribosome biogenesis. SBDS migrated with the 60S ribosomal precursor protein, and associated with the 28S subunit (see 180450) and nucleophosmin (see 164040). SBDS knockdown markedly decreased production of newly synthesized rRNA, although an imbalance of ribosomal subunits could not be detected.
Menne et al. (2007) identified the function of the yeast SBDS ortholog Sdo1, showing that it is critical for the release and recycling of the nucleolar shuttling factor Tif6 from pre-60S ribosomes, a key step in 60S maturation and translational activation of ribosomes. Using genome-wide synthetic genetic array mapping, they identified multiple TIF6 gain-of-function alleles that suppressed the pre-60S nuclear export defects and cytoplasmic mislocalization of Tif6 observed in sdo1-delta cells. Sdo1 appears to function within a pathway containing elongation factor-like 1, and together they control translational activation of ribosomes. The data of Menne et al. (2007) linked defective 60S ribosomal subunit maturation to an inherited bone marrow failure syndrome associated with leukemia predisposition.
Austin et al. (2008) found that SBDS colocalized with mitotic spindles and bound to purified microtubules, thus preventing genomic instability, in wildtype human bone marrow stromal cells, lymphoblasts, and skin fibroblasts. Primary bone marrow stromal cells and lymphoblasts from SDS patients exhibited an increased incidence of abnormal mitoses. Depletion of the SBDS gene using siRNA in normal skin fibroblasts resulted in increased mitotic abnormalities and aneuploidy that accumulated over time. Treatment of primary cells from SDS patients with nocodazole, a microtubule destabilizing agent, led to increased mitotic arrest and apoptosis compared to treated wildtype cells. In addition, SDS patient cells were resistant to taxol, a microtubule stabilizing agent. These findings suggested that spindle instability in SDS contributes to bone marrow failure and leukemogenesis.
Vitiello et al. (2010) demonstrated that CLN3 (607042) interacts with SBDS. The protein-protein interaction was conserved between Btn1 and Sdo1, the respective S. cerevisiae orthologs of CLN3 and SBDS. It had been shown that deletion of Btn1 resulted in alterations in vacuolar pH and vacuolar (H+)-ATPase (V-ATPase)-dependent H+ transport and ATP hydrolysis. Vitiello et al. (2010) found that an Sdo1 deletion strain had decreased vacuolar pH and V-ATPase-dependent H+ transport and ATP hydrolysis; the alterations resulted from decreased V-ATPase subunit expression. Overexpression of Btn1 or the presence of ionophore carbonyl cyanide chlorophenil hydrazone (CCCP) caused decreased growth in yeast lacking Sdo1. In normal cells, overexpression of Btn1 mirrored the effect of CCCP, with both resulting in increased vacuolar pH due to alterations in the coupling of V-ATPase-dependent H+ transport and ATP hydrolysis. Vitiello et al. (2010) proposed that Sdo1 and SBDS work to regulate Btn1 and CLN3, respectively.
Raaijmakers et al. (2010) demonstrated that deletion of Dicer1 (606241) specifically in mouse osteoprogenitors, but not in mature osteoblasts, disrupts the integrity of hematopoiesis. Myelodysplasia resulted and acute myelogenous leukemia emerged that had acquired several genetic abnormalities while having intact Dicer1. Examining gene expression altered in osteoprogenitors as a result of Dicer1 deletion showed reduced expression of Sbds, the gene mutated in Shwachman-Bodian-Diamond syndrome, a human bone marrow failure and leukemia predisposition condition. Deletion of Sbds in mouse osteoprogenitors induced bone marrow dysfunction with myelodysplasia. Therefore, Raaijmakers et al. (2010) concluded that perturbation of specific mesenchymal subsets of stromal cells can disorder differentiation, proliferation, and apoptosis of heterologous cells, and disrupt tissue homeostasis. Furthermore, Raaijmakers et al. (2010) concluded that primary stromal dysfunction can result in secondary neoplastic disease, supporting the concept of niche-induced oncogenesis.
Using affinity capture and mass spectrometry, Ball et al. (2009) developed an SBDS interactome and reported SBDS binding partners with diverse molecular functions, notably components of the large ribosomal subunit and proteins involved in DNA metabolism. Reciprocal coimmunoprecipitation confirmed the interaction of SBDS with the large ribosomal subunit protein RPL4 (180479) and with DNA-PK (PRKDC; 600899) and RPA70 (RPA1; 179835), 2 proteins with critical roles in DNA repair. SBDS-depleted HEK293 cells were hypersensitive to multiple types of DNA damage as well as chemically induced endoplasmic reticulum stress, suggesting a role for SBDS in response to cellular stress. SBDS-dependent hypersensitivity of HEK293 cells to UV irradiation could be distinguished from a role of SBDS in translation.
Finch et al. (2011) showed that GTP and recombinant human SBDS and elongation factor-like-1 (EFL1, or EFTUD1) cooperated to trigger release of human EIF6 (602912) from pre60S ribosomes isolated from Sbds-deficient mouse livers. EFL1 and SBDS independently and noncooperatively bound to the 60S subunit in vitro. The 60S subunit activated the GTPase activity of EFL1, but SBDS was required to stimulate EIF6 release. Two SBDS mutants with different SDS-associated missense mutations varied in their ability to enhance 60S-dependent GTPase activity of EFL1, but neither triggered EIF6 release. Finch et al. (2011) concluded that SBDS and EFL1 catalyze translational activation and proposed that SDS is a ribosomopathy caused by uncoupling GTP hydrolysis from EIF6 release.
Garcia-Marquez et al. (2015) determined that the affinity of EFL1 for GTP was 10-fold lower than that calculated for GDP. Association of EFL1 with SBDS did not alter the affinity of EFL1 for GTP, but significantly reduced its dissociation constant for GDP. Thus, SBDS acted as a guanine nucleotide exchange factor (GEF) for EFL1, promoting activation of EFL1 by release of GDP. Garcia-Marquez et al. (2015) concluded that SBDS couples the energy liberated from the hydrolysis of GTP by EFL1 for release of EIF6 from the surface of the 60S ribosomal subunit. They further found that SBDS mutations found in patients with Shwachman-Diamond syndrome disrupted the interaction of SBDS with EFL1 and prevented SBDS regulation of the affinity of EFL1 toward guanine nucleotides.
Independently, Savchenko et al. (2005) and Shammas et al. (2005) determined the crystal structure of the Archaeglobus fulgidus ortholog of SBDS. They found that A. fulgidus Sbds assumes a highly conserved 3-domain structure consisting of an N-terminal domain with a novel 3-dimensional fold structure, a central domain containing a winged helix-turn-helix motif, and a C-terminal domain that shares structural homology with RNA-binding proteins.
Shwachman-Diamond Syndrome 1
Boocock et al. (2003) reported mutations in the SBDS gene in affected individuals from 158 families with Shwachman-Diamond syndrome (SDS1; 260400). Gene conversion mutations accounted for 74.4% of alleles associated with Shwachman-Diamond syndrome (235 of 316). Observations indicated that gene conversion due to recombination between SBDS and its pseudogene had occurred. Conversion mutations were found in 89% of individuals with Shwachman-Diamond syndrome (141 of 158). Boocock et al. (2003) suggested that the conversion events are confined to a short segment spanning approximately 240 bp in exon 2. In 79 of 141 families with Shwachman-Diamond syndrome with conversion mutations, Boocock et al. (2003) found that affected individuals were compound heterozygous for 2 mutations in exon 2 of the SBDS gene: 183-184TA-CT (607444.0001) and 258+2T-C (IVS2DS+2T-C; 607444.0002).
In a study of Japanese patients with SDS, Nakashima et al. (2004) likewise found mutations in the SBDS gene caused by gene conversion. The sites of the gene conversion events varied, extending from intron 1 to exon 3.
Abnormalities in chromosome 7 have been reported in association with Shwachman-Diamond syndrome, especially an isochromosome i(7)(q10). In a 25-year-old patient with SDS who suffered from mild aplastic anemia but showed no signs of either myelodysplasia or leukemic transformation, Mellink et al. (2004) identified an isochromosome i(7)(q10) in the bone marrow and also identified 2 different mutations in the SBDS gene: the 183-184TA-CT mutation was present in 1 allele and the splice site mutation 258+2T-C was present in the other. The 2 mutations were the most commonly found in the study of Boocock et al. (2003). Mellink et al. (2004) concluded that the isochromosome 7q phenomenon may have a very indirect association with the pathogenesis of malignant transformation in SDS patients. It may be the first presentation of chromosome instability that could eventually result in more significant additional chromosomal aberrations involved in the clinical manifestation of acute myeloid leukemia and myelodysplasia syndrome.
Austin et al. (2005) characterized the SBDS protein expression and intracellular localization in 7 patients with Shwachman-Diamond syndrome and healthy controls. As predicted by gene mutation, 4 patients with SDS exhibited no detectable full-length SBDS protein. One patient, who was homozygous for the IVS2DS+2T-C mutation (607444.0002), expressed scant levels of SBDS protein. A second patient, harboring a missense mutation, expressed low levels of SBDS protein. A third patient, who carried no detectable gene mutations, expressed wildtype levels of SBDS protein, adding further support to the growing body of evidence for additional genes that might contribute to the pathogenesis of the disease phenotype.
By Sanger sequencing in 2 patients with SDS, Yamada et al. (2020) identified compound heterozygous mutations in the SBDS gene: c.258+2T-C on one allele and c.183-184TA-CT and c.201A-G on the other allele. However, the c.183-184TA-CT and c.201A-G variants were not identified by whole-exome sequencing in either patient. Yamada et al. (2020) concluded that these variants were missed by whole-exome analysis due to mismapping of reads resulting from the inability to discriminate between SBDS and the SBDSP1 pseudogene. All 3 variants were identified with transcriptome analysis via RNAseq in blood samples from both patients, leading Yamada et al. (2020) to conclude that RNA-seq is an effective assay for the diagnosis of SDS.
Aplastic Anemia, Susceptibility to
Calado et al. (2007) identified heterozygosity for the IVS2DS+2T-C mutation (607444.0002) in the SBDS gene in 4 of 91 unrelated patients with aplastic anemia (609135). These patients were younger on average (5 to 19 years) compared to other patients with aplastic anemia. Two mothers tested were carriers of the mutation; these 2 and another mother who was not tested had histories of subclinical mild anemia. Heterozygous mutation carriers had partial loss of SBDS protein expression, indicating haploinsufficiency. Although telomere shortening was observed in patients' granulocytes, lymphocytes had normal telomere length. None of the patients with aplastic anemia had pancreatic exocrine failure or skeletal anomalies as seen in SDS. One of the 4 probands was also heterozygous for a presumed pathogenic variant in the TERT gene (187270). The outcome of these patients was poor, with 2 deaths. Calado et al. (2007) concluded that SBDS deficiency predisposes to marrow failure by causing telomere shortening, thus indicating a role for SBDS in the maintenance of telomere length.
Kuijpers et al. (2005) sequenced the SBDS gene in 20 unrelated patients with clinical SDS and identified mutations in 15 (75%), with identical compound heterozygosity in 11 patients (see 607444.0001 and 607444.0002). The authors examined hematologic parameters over 5 years of follow-up and observed persistent neutropenia in 43% in the absence of apoptosis and unrelated to chemotaxis defects or infection rate. Irrespective of the absolute neutrophil count in vivo, abnormal granulocyte-monocyte colony formation was observed in all patients with SDS tested (14 of 14), whereas erythroid and myeloid colony formation was less often affected (9 of 14). Cytogenetic aberrations occurred in 5 of 19 patients in the absence of myelodysplasia. Kuijpers et al. (2005) concluded that in patients with genetically proven SDS, a genotype/phenotype relationship does not exist in clinical and hematologic terms.
Zhang et al. (2006) reported that loss of the Sbds gene resulted in early lethality in mice prior to embryonic day 6.5. Heterozygous mutant mice had a normal phenotype and were indistinguishable from wildtype littermates.
Finch et al. (2011) also found that Sbds deletion in mice was embryonic lethal. Sbds -/- mice showed prominent histologic abnormalities in liver, with disordered architecture between the portal triads and central veins, degenerative hepatocyte appearance, and scattered subcapsular areas of hepatocyte necrosis with an associated acute inflammatory reaction. Sbds-deleted liver extracts showed accumulation of free cytoplasmic 40S and 60S subunits and 43S initiation complexes that were stalled at the AUG start codon awaiting binding of 60S subunits, suggesting a ribosomal subunit-joining defect.
In 79 of 141 families with Shwachman-Diamond syndrome (SDS1; 260400) with conversion mutations, Boocock et al. (2003) found that affected individuals were compound heterozygous for 2 mutations in exon 2 of the SBDS gene: 183-184TA-CT and 258+2T-C (IVS2DS+2T-C; 607444.0002). The dinucleotide alteration 183-184TA-CT introduced an in-frame stop codon (lys62 to ter; K62X). The 258+2T-C mutation was predicted to disrupt the donor splice site of intron 2; it resulted in an 8-bp deletion consistent with use of an upstream cryptic splice donor site at position 251-252. The 258+2T-C and the resultant 8-bp deletion caused premature termination of the encoded protein by frameshift. In 44 families there was compound heterozygosity of 258+2T-C with another allele. In 7 families there was homozygosity for 258+2T-C. No incidence of homozygosity for 183-184TA-CT was observed. In 8 alleles of the SBDS gene found by Boocock et al. (2003) in patients with SDS, both the 183-184TA-CT and the 258+2T-C change were on the same allele.
In 11 patients with SDS, Kuijpers et al. (2005) identified compound heterozygosity for the K62X and 258+2T-C mutations in the SBDS gene.
By Sanger sequencing in 2 patients with SDS, Yamada et al. (2020) identified compound heterozygous mutations in the SBDS gene: c.183-184TA-CT and c.201A-G on one allele and c.258+2T-C the other allele. However, the c.183-184TA-CT and c.201A-G variants were not identified by whole-exome sequencing in either patient. Yamada et al. (2020) concluded that these variants were missed by whole-exome analysis due to mismapping of reads resulting from the inability to discriminate between SBDS and the SBDSP1 pseudogene. All 3 variants were identified with transcriptome analysis via RNAseq in blood samples from both patients, leading Yamada et al. (2020) to conclude that RNA-seq is an effective assay for the diagnosis of SDS.
Shwachman-Diamond Syndrome 1
For discussion of the splice site mutation in the SBDS gene (IVS2DS+2T-C) that was found in compound heterozygous state in patients with Shwachman-Diamond syndrome (SDS1; 260400) by Boocock et al. (2003) and Kuijpers et al. (2005), see 607444.0001. Boocock et al. (2003) referred to this mutation as 258+2T-C.
Nakashima et al. (2004) identified this mutation in affected members of 4 Japanese families with SDS, making it the most prevalent mutation. Recurrent gene conversion was considered the most likely explanation for the recurrence, rather than founder effect.
Aplastic Anemia, Susceptibility to
Calado et al. (2007) identified heterozygosity for the IVS2DS+2T-C mutation in 4 of 91 unrelated patients with aplastic anemia (609135). These patients were younger on average (5 to 19 years) compared to other patients with aplastic anemia. Two mothers tested were carriers of the mutation; these 2 and another mother who was not tested had histories of subclinical mild anemia. Heterozygous mutation carriers had partial loss of SBDS protein expression, indicating haploinsufficiency. Although telomere shortening was observed in patients' granulocytes, lymphocytes had normal telomere length. None of the patients with aplastic anemia had pancreatic exocrine failure or skeletal anomalies as seen in SDS. One of the 4 probands was also heterozygous for a presumed pathogenic variant in the TERT gene (187270).
In 1 allele from individuals with Shwachman-Diamond syndrome (SDS1; 260400), Boocock et al. (2003) found a 24C-A transversion in the SBDS gene, predicted to result in an asn8-to-lys (N8K) amino acid change. The mutation on the other allele was not identified.
In affected members of 4 Japanese families with Shwachman-Diamond syndrome (SDS1; 260400), Nakashima et al. (2004) found compound heterozygosity for 2 recurrent mutations in the SBDS gene: IVS2DS+2T-C (607444.0002) and a 1-bp insertion (96insA) in exon 1.
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