BBS9
protein-codingBardet-Biedl syndrome 9, the group of BBSome
Gene summary
This gene is downregulated by parathyroid hormone in osteoblastic cells, and therefore is thought to be involved in parathyroid hormone action in bones. The exact function of this gene has not yet been determined. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Jan 2017]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~767.6 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0014437
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0014437
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0700236
Submitter: ClinGen
The *BBS9* gene (also called *PTHB1*) was originally identified by differential display analysis as a gene down-regulated by parathyroid hormone (PTH) in an osteoblastic cell line. Multiple alternatively spliced isoforms of *PTHB1* are expressed in different tissues. Independent genetic studies, involving comparative mapping and gene expression analysis, led to the identification of *PTHB1* as a novel gene associated with Bardet-Biedl syndrome (Nishimura et al., 2005, PMID: 16380913). Bardet-Biedl syndrome 9 (MIM#: 615986) is typically an autosomal recessive disorder that exhibits variable expressivity and phenotypes including retinopathy, mental retardation, obesity, polydactyly, and renal abnormalities. The main alterations observed are nonsense variants along the gene (34%). Additionally, frameshift, splice site variants and large deletions, all leading to a truncated protein, summarize up to 80% of all known variants. Consequently, the main disease causing mechanism may be a loss of function of the BBS9 protein (PMID: 33771153, PMID: 34212515, PMID: 32165602, PMID: 26846096). The reported variant spectrum in *BBS9* includes 21 missense, 49 nonsense, 35 frameshift, 33 splice defects, and 4 exon deletions (PMID: 33771153). Altogether, variants in *BBS9* account for ∼6% of BBS cases. Because the published cases exhibit a recessive mode of inheritance and share overlapping retinal phenotypes consistent with a single spectrum of disease, this curation has lumped these cases into a single disease entity, BBS9-related ciliopathy. This curation has collected data from 3 consanguineous families and 1 isolated individual with 4 unique variants (PMID: 33771153, PMID: 34212515, PMID: 32165602, PMID: 26846096). Additional experimental evidence was found in studies of expression, biochemical function and animal model systems (PMID: 22479622, PMID: 16380913). Although the BBS9 protein has been shown to be a part of the Bardet-Biedl syndrome protein complex (BBSome) core, its precise physiological function has not been delineated, and the mechanism of disease pathogenesis caused by *BBS9* variants remains poorly understood. The BBSome is an octameric complex that transports membrane proteins into the primary cilium signaling organelle in eukaryotes and is implicated in human disease. The 99-kDa human BBS9 protein is one of the eight BBSome components. It is composed of four structured domains, including a β-stranded N-terminal domain (PMID: 26085087). Experimental studies in zebrafish have provided strong evidence in support of the role of BBS9 in cilia development as its morpholino-based knockdown results in a BBS-like syndromic phenotype in zebrafish. An orthologous human *BBS9* mRNA rescued the morphant phenotype, while a mutant mRNA failed to provide functional complementation, suggesting an evolutionary conservation of BBS9 function (PMID: 16380913, PMID: 22479622). In summary, *BBS9* is definitively associated with BBS9-related ciliopathy, in which one of the major features is retinal cone-rod dystrophy. This has been repeatedly demonstrated in both the research and clinical diagnostic settings, and has been upheld over time. This clinical validity classification was approved by the ClinGen Retina Gene Curation Expert Panel on August 3rd, 2023 (ClinGen Gene Clinical Validity Framework SOP verison 9).
Inheritance Pattern: AR
Disease ID:MONDO:0014437
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0014437
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:0014437
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0015229
Submitter: Orphanet
Clinical Genomic Database (CGD)
Manifestation: Cardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Endocrine; Musculoskeletal; Neurologic; Ophthalmologic; Renal
Intervention: Cardiovascular; Endocrine
Rationale: Individuals have been described with congenital heart anomalies, and awareness may enable early diagnosis and management; Medical management of obesity with melanocortin-4 receptor (MC4R) agonist (setmelanotide) may be beneficial
Comments: Variants may modify the severity of BBS and related disorders due to variants in other BBS-associated genes
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to BBS9 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_198428.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 4 | 296 | 1 | 301 | ||
| missense | 2 | 7 | 454 | 16 | 4 | 483 |
| nonsense | 22 | 37 | 3 | 62 | ||
| start loss | 0 | |||||
| frameshift | 26 | 33 | 4 | 63 | ||
| splice donor/acceptor (+/-2bp) | 5 | 38 | 11 | 54 | ||
| Total | 55 | 115 | 476 | 312 | 5 | 963 |
Highest pathogenic variant AF is 0.000088650064
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_940820.1 | 22 | MANE Select | |
| Ensembl | ENSP00000242067.6 | 22 | MANE Select | |
| RefSeq | NP_001028776.1 | 21 | Standard | |
| RefSeq | NP_001028777.1 | 21 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| bbs9 | Danio rerio | Structure: pronephric proximal convoluted tubule Quality: morphology abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- BBSome-mediated cargo-targeting to cilium
- Cargo trafficking to the periciliary membrane
- Cilium Assembly
- Organelle biogenesis and maintenance
Biological Process
- visual perception
- protein transport
- fat cell differentiation
- response to stimulus
- cilium assembly
Molecular Function
- molecular_function
- protein binding
Cellular Component
- pericentriolar material
- cytosol
- cilium
- membrane
- centriolar satellite
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000242067
- Coding exons
- 22
- Length
- 476825
- Individuals with no LoFs
- 125631
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 117
- Defined
- 125748
- p
- 0.000465
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.404 | 432 | 456 | 0.947 | 0.0000236 | 5777 |
| Missense (PolyPhen) | 128 | 149.38 | 0.85685 | 1892 | ||
| Synonymous | -0.473 | 175 | 167 | 1.05 | 0.00000909 | 1699 |
| Loss of Function | 2.51 | 35 | 55.1 | 0.635 | 0.00000326 | 599 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00043 | 0.00043 | rare |
| Latino/Admixed American | 0.00084 | 0.00084 | rare |
| Ashkenazi Jewish | 0.000099 | 0.000099 | rare |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.00054 | 0.00054 | rare |
| South Asian | 0.00034 | 0.00033 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: The BBSome complex is thought to function as a coat complex required for sorting of specific membrane proteins to the primary cilia. The BBSome complex is required for ciliogenesis but is dispensable for centriolar satellite function. This ciliogenic function is mediated in part by the Rab8 GDP/GTP exchange factor, which localizes to the basal body and contacts the BBSome. Rab8(GTP) enters the primary cilium and promotes extension of the ciliary membrane. Firstly the BBSome associates with the ciliary membrane and binds to RAB3IP/Rabin8, the guanosyl exchange factor (GEF) for Rab8 and then the Rab8-GTP localizes to the cilium and promotes docking and fusion of carrier vesicles to the base of the ciliary membrane. Required for proper BBSome complex assembly and its ciliary localization. {ECO:0000269|PubMed:17574030, ECO:0000269|PubMed:22072986}.;
- Disease
- DISEASE: Note=A chromosomal aberration involving PTHB1 has been found in Wilms tumor. Translocation t(1;7)(q42;p15) with OBSCN. {ECO:0000269|PubMed:12618763}.; DISEASE: Bardet-Biedl syndrome 9 (BBS9) [MIM:615986]: A syndrome characterized by usually severe pigmentary retinopathy, early- onset obesity, polydactyly, hypogenitalism, renal malformation and mental retardation. Secondary features include diabetes mellitus, hypertension and congenital heart disease. Bardet-Biedl syndrome inheritance is autosomal recessive, but three mutated alleles (two at one locus, and a third at a second locus) may be required for clinical manifestation of some forms of the disease. {ECO:0000269|PubMed:16380913, ECO:0000269|PubMed:26085087}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Recessive Scores
- pRec
- 0.201
Intolerance Scores
- LoFtool
- 0.157
- RVIS EVS
- 1.05
- RVIS percentile EVS
- 91.37
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.204
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |