BBS4
protein-codingBardet-Biedl syndrome 4, the group of BBSome|Tetratricopeptide repeat domain containing
Gene summary
This gene is a member of the Bardet-Biedl syndrome (BBS) gene family. Bardet-Biedl syndrome is an autosomal recessive disorder characterized by severe pigmentary retinopathy, obesity, polydactyly, renal malformation and cognitive disability. The proteins encoded by BBS gene family members are structurally diverse. The similar phenotypes exhibited by mutations in BBS gene family members are likely due to the protein's shared roles in cilia formation and function. Many BBS proteins localize to the basal bodies, ciliary axonemes, and pericentriolar regions of cells. BBS proteins may also be involved in intracellular trafficking via microtubule-related transport. The protein encoded by this gene has sequence similarity to O-linked N-acetylglucosamine (O-GlcNAc) transferases in plants and archaebacteria and in human forms a multi-protein "BBSome" complex with seven other BBS proteins. Alternate splicing results in multiple transcript variants. [provided by RefSeq, Mar 2016]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~55.8 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
Inheritance Pattern: AR
Disease ID:MONDO:0015229
Submitter: Orphanet
Inheritance Pattern: AR
Disease ID:MONDO:0014433
Submitter: Labcorp Genetics (formerly Invitae)
Inheritance Pattern: AR
Disease ID:MONDO:0014433
Submitter: PanelApp Australia
Inheritance Pattern: AR
Disease ID:MONDO:0014433
Submitter: G2P
Inheritance Pattern: AR
Disease ID:MONDO:0014433
Submitter: Genomics England PanelApp
Inheritance Pattern: AR
Disease ID:MONDO:0014433
Submitter: Natera
Inheritance Pattern: AR
Disease ID:MONDO:1040044
Submitter: ClinGen
The *BBS4* gene was first reported in relation to autosomal recessive Bardet-Biedl syndrome (BBS) in five consanguineous families in 2001 (PMID: 11381270) after the authors mapped the locus to a region of chromosome 15 (PMIDs: 7711739, 8588586). Initial reports and subsequent publications describe Bardet-Biedl syndrome 4 (MIM# 615982) as characterized by retinal degeneration (typically described as rod-cone dystrophy) plus a range of extraocular features, most commonly obesity, intellectual disability, developmental delay, polydactyly, and/or male hypogonadism. Other reported features of BBS4-related cases include additional ocular findings (myopia, strabismus), hearing anomalies, additional skeletal differences (syndactyly, brachydactyly, clinodactyly, club foot), dental anomalies, atypical behavior, poor coordination, kidney disease, abnormal renal morphology, liver abnormalities, cardiac anomalies, cryptorchidism, gastrointestinal concerns, hypertension, metabolic dysfunction, anosmia, and sleep apnea. Most affected individuals are reported to meet clinical criteria for BBS as described by Beales et al., 1999 (PMID: 10874630). Both intra- and inter-familial variability is observed. To our knowledge, there have not been any reports of non-syndromic retinal degeneration due to *BBS4* as has been described with other BBS genes, most notably *BBS1* (PMID: 23143442). However, there is one report of a consanguineous family with three affected siblings reported to have Leber congenital amaurosis (with classic signs of extinguished electroretinogram, infantile nystagmus, and pigmentary retinopathy) with only mild extraocular features reported (delayed walking, delayed speech, mild facial dysmorphism, and enophthalmos) (PMID: 22219648). Per the Retina GCEP, to remain consistent with the disease entities of other *BBS* genes and to reflect the phenotypic variability observed, cases caused by inherited biallelic *BBS4* variants have been referred to as BBS4-related ciliopathy. Thirteen variants (missense, splice site, nonsense, deletion, insertion) that have been reported in fourteen probands in eight publications (PMIDs: 11381270, 12016587, 20177705, 22219648, 24849935, 26518167, 27894351, 31196119) are included in this curation. Most reported individuals have a homozygous *BBS4* variant as the likely disease-causing variant, and consanguinity is commonly reported in these affected individuals. Of note, while oligogenic inheritance has been suggested for BBS, including BBS4-related BBS (PMID: 12016587), probands with other disease-causing *BBS* variants or biallelic variants (regardless of classification) in other BBS genes were excluded from the curation. More evidence is available in the literature, but the maximum score for genetic evidence (12 points) has been reached. The mechanism of pathogenicity is known to be loss of function. This gene-disease relationship is also supported by animal and cell culture models, expression studies, and *in vitro* functional assays (PMIDs: 11381270, 15107855, 15173597, 15322545, 16794820, 17574030, 22219648, 23716571, 24500759, 30665891, 32759308). *BBS4* is ubiquitously expressed, and studies show expression in disease-associated tissues including retina, kidney, and adipose tissue, with the highest expression in kidney (PMID: 11381270). This gene-disease association is also supported by biochemical evidence that *BBS4* encodes a component of the BBSome, a protein complex that functions in ciliogenesis (PMID: 32759308). BBS4 localizes to the primary cilia, and BBS4 immunoprecipitation results in co-purification of BBS1 and 6 other proteins encoded by genes implicated in Bardet-Biedl syndrome (BBS1, BBS2, BBS5, BBS7, BBS8, and BBS9) (PMIDs: 17574030, 32759308). Bbs4-deficient renal cells and retinal pigment epithelial cells show abnormal ciliogenesis (PMID: 23716571, 32759308). In addition, *BBS4* silenced preadipocytes have increased fat accumulation and increased triglycerides (PMID: 24500759). *Bbs4* knockdown in zebrafish results in shortened body axis, broadened somites, kinked notochord, and mislocalization of rhodopsin in the retina. The abnormal phenotypes in morphant zebrafish are rescued by wild-type *BBS4* mRNA (PMID: 22219648). Phenotypes observed in *Bbs4* null mice reflect both retinal and syndromic features from the human disease. Retinal degeneration, obesity, metabolic disturbances, liver dysfunction, decreased olfactory responses, and atypical behaviors have been observed in *Bbs4* null mice in addition to ciliary defects (PMIDs: 15173597, 15322545, 16794820). In summary, *BBS4* is definitively associated with BBS4-related ciliopathy. This has been repeatedly demonstrated in both research and diagnostic settings, and has been upheld over time without the emergence of contradictory evidence. This classification was approved by the ClinGen Retina Gene Curation Expert Panel on December 7th, 2023 (SOP Version 10).
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 BBS4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_033028.5. 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 | 9 | 184 | 2 | 195 | ||
| missense | 3 | 8 | 301 | 10 | 5 | 327 |
| nonsense | 15 | 25 | 2 | 42 | ||
| start loss | 2 | 2 | ||||
| frameshift | 21 | 42 | 8 | 1 | 72 | |
| splice donor/acceptor (+/-2bp) | 10 | 41 | 5 | 1 | 57 | |
| Total | 49 | 118 | 325 | 195 | 8 | 695 |
Highest pathogenic variant AF is 0.009850169
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_149017.2 | 16 | MANE Select | |
| Ensembl | ENSP00000268057.4 | 16 | MANE Select | |
| RefSeq | NP_001239607.1 | 9 | Standard | |
| RefSeq | NP_001307594.1 | 15 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| bbs4 | Danio rerio | Structure: pancreatic B cell Quality: increased area abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Prader-Willi and Angelman Syndrome
- BBSome-mediated cargo-targeting to cilium
- Cargo trafficking to the periciliary membrane
- Cilium Assembly
- Organelle biogenesis and maintenance
Biological Process
- microtubule cytoskeleton organization
- mitotic cytokinesis
- neuron migration
- neural tube closure
- retina homeostasis
Molecular Function
- RNA polymerase II repressing transcription factor binding
- microtubule motor activity
- protein binding
- dynactin binding
- alpha-tubulin binding
Cellular Component
- pericentriolar material
- photoreceptor outer segment
- photoreceptor inner segment
- nucleus
- centrosome
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000268057
- Coding exons
- 16
- Length
- 52291
- Individuals with no LoFs
- 125678
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 70
- Defined
- 125748
- p
- 0.000278
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.956 | 301 | 258 | 1.17 | 0.0000128 | 3375 |
| Missense (PolyPhen) | 77 | 76.661 | 1.0044 | 1009 | ||
| Synonymous | -1.25 | 112 | 96.4 | 1.16 | 0.00000511 | 954 |
| Loss of Function | 0.735 | 27 | 31.4 | 0.858 | 0.00000146 | 398 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00025 | 0.00025 | rare |
| Latino/Admixed American | 0.00032 | 0.00032 | rare |
| Ashkenazi Jewish | 0.00020 | 0.00020 | rare |
| East Asian | 0.00016 | 0.00016 | rare |
| Finnish | 0.000046 | 0.000046 | rare |
| European (Non-Finnish) | 0.00031 | 0.00031 | rare |
| South Asian | 0.00029 | 0.00029 | rare |
| Other | 0.00082 | 0.00081 | 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. The BBSome complex, together with the LTZL1, controls SMO ciliary trafficking and contributes to the sonic hedgehog (SHH) pathway regulation. Required for proper BBSome complex assembly and its ciliary localization. Required for microtubule anchoring at the centrosome but not for microtubule nucleation. May be required for the dynein-mediated transport of pericentriolar proteins to the centrosome. {ECO:0000269|PubMed:15107855, ECO:0000269|PubMed:17574030, ECO:0000269|PubMed:22072986}.;
Recessive Scores
- pRec
- 0.328
Intolerance Scores
- LoFtool
- 0.571
- RVIS EVS
- 0.11
- RVIS percentile EVS
- 62.1
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.921
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |