Human SBDS Protein
- Known as:
- Human SBDS Protein
- Catalog number:
- SBS-H5141
- Product Quantity:
- 1mg
- Category:
- -
- Supplier:
- acrobyosystems
- Gene target:
- Human SBDS Protein
Related genes to: Human SBDS Protein
- Gene:
- SBDS NIH gene
- Name:
- SBDS ribosome maturation factor
- Previous symbol:
- -
- Synonyms:
- CGI-97, FLJ10917, SDS, SWDS
- Chromosome:
- 7q11.21
- Locus Type:
- gene with protein product
- Date approved:
- 2003-07-02
- Date modifiied:
- 2019-04-23
- Gene:
- SBDSP1 NIH gene
- Name:
- SBDS pseudogene 1
- Previous symbol:
- SBDSP
- Synonyms:
- -
- Chromosome:
- 7q11.23
- Locus Type:
- pseudogene
- Date approved:
- 2003-07-02
- Date modifiied:
- 2019-01-22
Related products to: Human SBDS Protein
Related articles to: Human SBDS Protein
- This report describes two unrelated prenatal cases of Shwachman-Diamond syndrome (SDS) presenting primarily with severe skeletal anomalies. SDS is a rare autosomal recessive disorder characterized by a triad of bone marrow dysfunction, skeletal abnormalities, and exocrine pancreatic dysfunction. The most common postnatal features include faltering growth, short stature, and neutropenia resulting in recurrent infections. Prenatal presentations could be scarce as the most common features are typically not apparent before birth. Molecular diagnosis of SDS relies on the identification of biallelic loss-of-function pathogenic variants in the SBDS gene. However, molecular genetic analysis is hampered by the presence of a pseudogene (SBDSP1), which can lead to misalignment or gene conversion events. In both reported cases, initial genetic testing was inconclusive. Subsequently, through clinical phenotype reassessment and expanded molecular analysis, the diagnosis of SDS by germline pathogenic SBDS variants (c.258+2T>C p.(?) and c.184A>T p.Lys62Ter) was established. These cases underscore the diagnostic complexity of SDS in prenatal settings and the necessity of comprehensive molecular analysis when facing severe skeletal anomalies suggesting small thoracic skeletal dysplasia and are further supported by an added literature review that expands the prenatal phenotype. - Source: PubMed
Publication date: 2026/01/17
Vanden Eynde NathalieSlegers IleenVantroys EliseSymoens SofieDoné ElisaVorsselmans AnniekLeus AstridBrock StefanieKeymolen KathelijnHes Frederik JanDimitrov Boyanvan Berkel Kim - Long-read sequencing can characterize complex genome editing-induced DNA sequence changes such as large deletions, insertions, and inversions that are difficult to detect using short-read sequencing. However, PCR amplification and sequencing errors complicate accurate variant detection, and existing analysis tools are not optimized for gene editing specific allelic outcomes. Here we present CRISPRLungo, a computational pipeline specifically designed for long-read amplicon sequencing of gene edited samples. CRISPRLungo incorporates unique molecular identifier (UMI)-based error correction and statistical filtering to distinguish true editing events from background noise, enabling robust detection of small indels and structural variants. Through systematic benchmarking using simulated datasets, we demonstrate that CRISPRLungo outperforms existing approaches in both accuracy and read recovery. CRISPRLungo supports both Oxford Nanopore and PacBio platforms and identify previously undetected structural variant edits such as inversions in published CRISPR datasets. To demonstrate allele-specific edit quantification, we applied CRISPRLungo to analyze edited primary cells from a patient with harboring compound heterozygous mutations, accurately quantifying editing outcomes despite contaminating reads from the homologous pseudogene. To maximize accessibility, we developed a fully client-side web application requiring no installation, making advanced long-read analysis accessible to researchers regardless of computational expertise. CRISPRLungo is freely available at https://github.com/pinellolab/CRISPRLungo with a user-friendly web interface available at https://pinellolab.github.io/CRISPRLungo. - Source: PubMed
Publication date: 2025/10/21
Hwang Gue-HoVyshedskiy BenjaminBarry TimothyZeng JingManis John PShimamura AkikoBauer Daniel EPinello Luca - Shwachman-Diamond syndrome (SDS) is the second most common cause of exocrine pancreatic insufficiency, and 90% of patients carry mutations in the SBDS gene, the most common being the c.183_184delinsCT and c.258+2T>C variants. However, precise detection of these most contributory variants by conventional short-read next-generation sequencing data analysis is limited because of the SBDS/SBDSP1 highly homologous sequences. In this study, an efficient approach was established to infer the haplotype of SBDS based on the expectation-maximization algorithm. The workflow was retrospectively applied to detect the two most common SBDS variants in a Chinese SDS high-risk cohort, and a systematic comparison of variant detection results was performed between the workflow and conventional next-generation sequencing analysis based on Sanger sequencing validation. Among the Chinese SDS high-risk cohort (n = 47) and their available parents (n = 64), the established workflow improved the diagnostic rate for these two variants by 27.7% (95% CI, 15.6%-42.6%) compared with conventional analysis. For overall variant detection, the established workflow achieved 100% (95% CI, 92.5%-100%) concordance with Sanger sequencing, whereas conventional analysis showed only 65.8% accuracy; these results included 25.2% with missed variant calls, 7.2% with diagnosed but inaccurate variant calls, and 1.8% with false-positive calls. With its favorable result in both SDS patient diagnosis and carrier detection performance, the provided workflow showed its potential in clinical application for SDS molecular diagnosis. - Source: PubMed
Publication date: 2022/09/24
Peng XiaominDong XinranWang YaqiongWu BingbingWang HuijunLu WeiXiao FeifanYang LinLi GangZhou WenhaoLiu BoLu Yulan - Shwachman-Diamond syndrome (SDS) is a rare autosomal recessive ribosomopathy mainly characterized by exocrine pancreatic insufficiency, skeletal alterations, neutropenia, and a relevant risk of hematological transformation. At least 90% of SDS patients have pathogenic variants in the first gene associated with the disease with very low allelic heterogeneity; three variants, derived from events of genetic conversion between and its pseudogene, , provided the alleles observed in about 62% of SDS patients. We performed a reanalysis of the available WES files of a group of SDS patients with biallelic pathogenic variants, studying the results by next bioinformatic and protein structural analysis. Parallelly, careful clinical attention was given to the patient focused in this study. We found and confirmed in one SDS patient a germline heterozygous missense variant (c.100T>C; p.Phe34Leu) in the EIF6 gene. This variant, inherited from his mother, has a very low frequency, and it is predicted as pathogenic, according to several prediction tools. The protein structural analysis also envisages the variant could reduce the binding to the nascent 60S ribosomal. This study focused on the hypothesis that the germline variant mimics the effect of somatic deletions of chromosome 20, always including the locus of this gene, and similarly may rescue the ribosomal stress and ribosomal dysfunction due to mutations. It is likely that this rescue may contribute to the stable and not severe hematological status of the proband, but a definite answer on the role of this variant can be obtained only by adding a functional layer of evidence. In the future, these results are likely to be useful for selected cases in personalized medicine and therapy. - Source: PubMed
Publication date: 2022/08/12
Taha IbrahimForoni SelenaValli RobertoFrattini AnnalisaRoccia PamelaPorta GiovanniZecca MarcoBergami ElenaCipolli MarcoPasquali FrancescoDanesino CesareScotti ClaudiaMinelli Antonella - Shwachman-Diamond syndrome characterized by metaphyseal dysplasia, pancreatic insufficiency, and pancytopenia is caused by biallelic mutations in SBDS. Gene conversion between SBDS and its pseudogene SBDSP1 is the major cause. Here, we report two unrelated patients with Shwachman-Diamond syndrome who were shown to be compound heterozygotes for relatively frequent pathogenic alleles (the 258+2T>C allele and another allele composed of 183-184TA>CT and 201A>G) using an established polymerase chain reaction sequencing assay with SBDS-specific primers. Exome analysis of the patients showed discrepant results: 258+2T>C with variant allele frequency around 0.85, and no variants detected for the 183-184TA>CT allele. Parental exome analysis of the two families further supported this notion. Confronted with two patients with an unexpected segregation pattern, we performed a transcriptome analysis of peripheral blood-derived mRNA to demonstrate that the results were compatible with those obtained using SBDS-specific PCR primers. Both alleles could be accounted for by gene conversion events. The diagnostic discrepancy can be accounted for by a decreased efficiency in the computational mapping of the reads with 183-184TA>CT and 201A>G to the reference sequence of the SBDS locus during exome analysis. This report highlights the pitfall of exome analysis for genes with pseudogenes, such as SBDS and the alternative use of RNA-seq is recommended to circumvent this problem. - Source: PubMed
Publication date: 2020/05/15
Yamada MamikoUehara TomokoSuzuki HisatoTakenouchi ToshikiInui AyanoIkemiyagi MasakoKamimaki IsamuKosaki Kenjiro