BBS4

protein-coding

Bardet-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

NM_033028.5

Inheritance

AR

ClinVar variants

P:167U:325B:203

Top phenotype

Bardet-Biedl syndrome 4

gnomAD constraint

pLI —, LoF o/e 0.86

Max pathogenic AF

—

Genomic locus

chr15:72,686,186-72,742,006

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~55.8 kb
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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Bardet-Biedl syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0015229

Submitter: Orphanet

Bardet-Biedl syndrome 4STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014433

Submitter: Labcorp Genetics (formerly Invitae)

Bardet-Biedl syndrome 4STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014433

Submitter: PanelApp Australia

Bardet-Biedl syndrome 4DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014433

Submitter: G2P

Bardet-Biedl syndrome 4STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014433

Submitter: Genomics England PanelApp

Bardet-Biedl syndrome 4DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014433

Submitter: Natera

BBS4-related ciliopathyDEFINITIVE

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)

Bardet-Biedl syndrome 4AR

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

Refs: 7711739; 11381270; 12016587; 15654695; 20301537; 22219648; 36356613Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BBS4 variants in ClinVar

9 Conditions Cataloged
Bardet-Biedl syndromeTotal: 643
BBS4-related disorderTotal: 308
Bardet-Biedl syndrome 4Total: 241
not providedTotal: 115
not specifiedTotal: 87
Inborn genetic diseasesTotal: 71
Retinal dystrophyTotal: 5
Retinitis pigmentosaTotal: 4

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.

EffectPLPVUSLBBSum
synonymous
9
clinvar
184
clinvar
2
clinvar
195
missense
3
clinvar
8
clinvar
301
clinvar
10
clinvar
5
clinvar
327
nonsense
15
clinvar
25
clinvar
2
clinvar
42
start loss
2
clinvar
2
frameshift
21
clinvar
42
clinvar
8
clinvar
1
clinvar
72
splice donor/acceptor (+/-2bp)
10
clinvar
41
clinvar
5
clinvar
1
clinvar
57
Total491183251958695

Highest pathogenic variant AF is 0.009850169

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 53 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_033028.5RefSeqNP_149017.216MANE Select
ENST00000268057.9EnsemblENSP00000268057.416MANE Select
NM_001252678.2RefSeqNP_001239607.19Standard
NM_001320665.2RefSeqNP_001307594.115Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
bbs4Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense-0.9563012581.170.00001283375
Missense (PolyPhen)7776.6611.00441009
Synonymous-1.2511296.41.160.00000511954
Loss of Function0.7352731.40.8580.00000146398

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000250.00025rare
Latino/Admixed American0.000320.00032rare
Ashkenazi Jewish0.000200.00020rare
East Asian0.000160.00016rare
Finnish0.0000460.000046rare
European (Non-Finnish)0.000310.00031rare
South Asian0.000290.00029rare
Other0.000820.00081rare

dbNSFP Gene Annotations

Source: dbNSFP

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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