BBS10

Bardet-Biedl syndrome 10, the group of Chaperonins

Basic information

Region (hg38): 12:76344474-76348415

Previous symbols: [ "C12orf58" ]

Links

ENSG00000179941 ∙ NCBI:79738 ∙ OMIM:610148 ∙ HGNC:26291 ∙ Uniprot:Q8TAM1 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• Bardet-Biedl syndrome 10 (Definitive), mode of inheritance: AR
• Bardet-Biedl syndrome 10 (Definitive), mode of inheritance: AR
• Bardet-Biedl syndrome 10 (Strong), mode of inheritance: AR
• Bardet-Biedl syndrome (Supportive), mode of inheritance: AR
• Bardet-Biedl syndrome 10 (Strong), mode of inheritance: AR
• ciliopathy (Definitive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Bardet-Biedl syndrome 10	AR	Cardiovascular; Endocrine	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	Cardiovascular; Craniofacial; Gastrointestinal; Genitourinary; Endocrine; Musculoskeletal; Neurologic; Ophthalmologic; Renal	16823392; 16582908; 20120035; 20301537; 20805367; 22410627; 25982971; 36356613
Variants may modify the severity of BBS and related disorders due to variants in other BBS-associated genes

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the BBS10 gene.

• Bardet-Biedl syndrome (88 variants)
• Bardet-Biedl syndrome 10 (27 variants)
• not provided (11 variants)
• BBS10-related disorder (6 variants)
• Bardet-Biedl syndrome 1 (3 variants)
• Inborn genetic diseases (2 variants)
• Retinal dystrophy (2 variants)
• Bardet-biedl syndrome 1/10, digenic (1 variants)
• Retinitis pigmentosa (1 variants)
• Bardet-biedl syndrome 6/10, digenic (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the BBS10 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			5	265	2	272
missense	5	17	257	5		284
nonsense	23	26	1			50
start loss			3			3
frameshift	62	79	1			142
inframe indel		1	6			7
splice donor/acceptor (+/-2bp)	1	2				3
splice region			2	6	2	10
non coding			27	11	9	47
Total	91	125	300	281	11

Highest pathogenic variant AF is 0.000592

Variants in BBS10

This is a list of pathogenic ClinVar variants found in the BBS10 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
12-76344488-A-G		Bardet-Biedl syndrome 10	Uncertain significance (Jan 13, 2018)
12-76344538-T-G		Bardet-Biedl syndrome 10	Uncertain significance (Jan 13, 2018)
12-76344563-T-C		Bardet-Biedl syndrome 10	Uncertain significance (Jan 12, 2018)
12-76344565-T-C		Bardet-Biedl syndrome 10	Benign (Jan 12, 2018)
12-76344568-CATAA-C		Bardet-Biedl syndrome	Uncertain significance (Jun 14, 2016)
12-76344609-A-T		Bardet-Biedl syndrome 10	Uncertain significance (Jan 12, 2018)
12-76344616-T-C		Bardet-Biedl syndrome 10	Uncertain significance (Jan 13, 2018)
12-76344623-G-GT		Bardet-Biedl syndrome	Uncertain significance (Jun 14, 2016)
12-76344649-T-C		Bardet-Biedl syndrome 10	Uncertain significance (Jan 12, 2018)
12-76344668-T-G		Bardet-Biedl syndrome 10	Uncertain significance (Jan 12, 2018)
12-76344673-T-C		Bardet-Biedl syndrome 10	Uncertain significance (Jan 13, 2018)
12-76344700-C-G		Bardet-Biedl syndrome 10	Uncertain significance (Jan 13, 2018)
12-76344762-G-A		Bardet-Biedl syndrome 10	Benign (Jan 12, 2018)
12-76344772-C-A		Bardet-Biedl syndrome 10	Uncertain significance (Jan 12, 2018)
12-76344858-A-G		Bardet-Biedl syndrome 10	Uncertain significance (Jan 12, 2018)
12-76344866-C-A		Bardet-Biedl syndrome 10	Uncertain significance (Jan 12, 2018)
12-76344883-T-C		Bardet-Biedl syndrome 10	Uncertain significance (Jan 13, 2018)
12-76344922-A-G		Bardet-Biedl syndrome 10	Uncertain significance (Jan 13, 2018)
12-76345008-A-G		Bardet-Biedl syndrome 10	Benign (Jan 12, 2018)
12-76345040-A-G		Bardet-Biedl syndrome 10	Uncertain significance (Jan 13, 2018)
12-76345044-C-G		Bardet-Biedl syndrome 10	Benign (Jan 12, 2018)
12-76345079-C-A		Bardet-Biedl syndrome 10	Uncertain significance (Jan 12, 2018)
12-76345166-CAT-C		Bardet-Biedl syndrome	Uncertain significance (Jun 14, 2016)
12-76345181-A-G		Bardet-Biedl syndrome 10	Benign (Jan 12, 2018)
12-76345284-G-A		Bardet-Biedl syndrome 10	Uncertain significance (Jan 13, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
BBS10	protein_coding	protein_coding	ENST00000393262	2	3969

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.75e-12	0.0584	125494	0	254	125748	0.00101

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.0950	372	377	0.986	0.0000174	4727
Missense in Polyphen		59	80.978	0.72859		1056
Synonymous	-0.167	140	138	1.02	0.00000669	1422
Loss of Function	0.314	19	20.5	0.925	9.01e-7	313

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00109	0.00109
Ashkenazi Jewish	0.00149	0.00149
East Asian	0.000871	0.000870
Finnish	0.0000959	0.0000924
European (Non-Finnish)	0.00148	0.00148
Middle Eastern	0.000871	0.000870
South Asian	0.000786	0.000784
Other	0.000987	0.000978

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probable molecular chaperone that assists the folding of proteins upon ATP hydrolysis (PubMed:20080638). Plays a role in the assembly of BBSome, a complex involved in ciliogenesis regulating transports vesicles to the cilia (PubMed:20080638). Involved in adipogenic differentiation (PubMed:19190184). {ECO:0000269|PubMed:19190184, ECO:0000269|PubMed:20080638}.
• Disease: DISEASE: Bardet-Biedl syndrome 10 (BBS10) [MIM:615987]: 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:16582908, ECO:0000269|PubMed:16823392, ECO:0000269|PubMed:20080638, ECO:0000269|PubMed:20120035, ECO:0000269|PubMed:21344540, ECO:0000269|PubMed:23219996, ECO:0000269|PubMed:28808579}. Note=The disease is caused by mutations affecting the gene represented in this entry.
• Pathway: BBSome-mediated cargo-targeting to cilium;Cargo trafficking to the periciliary membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

• pRec: 0.149

Intolerance Scores

• loftool: 0.249
• rvis_EVS: -0.35
• rvis_percentile_EVS: 29.43

Haploinsufficiency Scores

• pHI: 0.0985
• hipred: N
• hipred_score: 0.428
• ghis: 0.548

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.00418

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Bbs10
• Phenotype: renal/urinary system phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); vision/eye phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); homeostasis/metabolism phenotype; cellular phenotype; growth/size/body region phenotype

Zebrafish Information Network

• Gene name: bbs10
• Affected structure: pronephric proximal convoluted tubule
• Phenotype tag: abnormal
• Phenotype quality: morphology

Gene ontology

• Biological process: retina homeostasis;visual perception;regulation of protein complex assembly;photoreceptor cell maintenance;response to stimulus;chaperone-mediated protein complex assembly;non-motile cilium assembly
• Cellular component: cilium
• Molecular function: RNA polymerase II repressing transcription factor binding;protein binding;ATP binding