BBS9

protein-coding

Bardet-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

NM_198428.3

Inheritance

AR

ClinVar variants

P:170U:476B:317

Top phenotype

Bardet-Biedl syndrome 9

gnomAD constraint

pLI —, LoF o/e 0.63

Max pathogenic AF

—

Genomic locus

chr7:33,109,557-33,877,180

External References & Databases

Transcript & Mutation Effects

hg38 • Region Span ~767.6 kb
Loading mutation effect viewer...

GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

Bardet-Biedl syndrome 9DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014437

Submitter: G2P

Bardet-Biedl syndrome 9STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014437

Submitter: Labcorp Genetics (formerly Invitae)

BBS9-related ciliopathyDEFINITIVE

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).

Bardet-Biedl syndrome 9STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014437

Submitter: Genomics England PanelApp

Bardet-Biedl syndrome 9DEFINITIVE

Inheritance Pattern: AR

Disease ID:MONDO:0014437

Submitter: Natera

Bardet-Biedl syndrome 9STRONG

Inheritance Pattern: AR

Disease ID:MONDO:0014437

Submitter: PanelApp Australia

Bardet-Biedl syndromeSUPPORTIVE

Inheritance Pattern: AR

Disease ID:MONDO:0015229

Submitter: Orphanet

Clinical Genomic Database (CGD)

Bardet-Biedl syndrome 9AR

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: 16380913; 20301537; 36356613Source: CGD (NHGRI)

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to BBS9 variants in ClinVar

18 Conditions Cataloged
Bardet-Biedl syndromeTotal: 904
BBS9-related disorderTotal: 432
Bardet-Biedl syndrome 9Total: 345
not providedTotal: 176
Inborn genetic diseasesTotal: 113
not specifiedTotal: 110
Retinal dystrophyTotal: 10
Bardet-Biedl syndrome 1Total: 9

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.

EffectPLPVUSLBBSum
synonymous
4
clinvar
296
clinvar
1
clinvar
301
missense
2
clinvar
7
clinvar
454
clinvar
16
clinvar
4
clinvar
483
nonsense
22
clinvar
37
clinvar
3
clinvar
62
start loss
0
frameshift
26
clinvar
33
clinvar
4
clinvar
63
splice donor/acceptor (+/-2bp)
5
clinvar
38
clinvar
11
clinvar
54
Total551154763125963

Highest pathogenic variant AF is 0.000088650064

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 71 transcripts
Transcript IDSourceProtein IDCoding ExonsMANE Status
NM_198428.3RefSeqNP_940820.122MANE Select
ENST00000242067.11EnsemblENSP00000242067.622MANE Select
NM_001033604.2RefSeqNP_001028776.121Standard
NM_001033605.2RefSeqNP_001028777.121Standard

Model Organisms & Knockout Phenotypes

Observed phenotypic effects in mouse and zebrafish models

Gene / ModelOrganismObserved Phenotype
bbs9Danio 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: gnomAD

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-ScoreObservedExpectedObserved/ExpectedMutation RateTotal Possible
Missense0.4044324560.9470.00002365777
Missense (PolyPhen)128149.380.856851892
Synonymous-0.4731751671.050.000009091699
Loss of Function2.513555.10.6350.00000326599

Population LoF Frequency

PopulationCAFp-valueStatus
African0.000430.00043rare
Latino/Admixed American0.000840.00084rare
Ashkenazi Jewish0.0000990.000099rare
East Asian0.000220.00022rare
Finnish0.000140.00014rare
European (Non-Finnish)0.000540.00054rare
South Asian0.000340.00033rare
Other0.000330.00033rare

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. 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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium
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