B9D2

B9 domain containing 2, the group of MKS complex|B9 domain containing

Basic information

Region (hg38): 19:41354417-41364165

Links

ENSG00000123810

∙ NCBI:80776 ∙ OMIM:611951 ∙ HGNC:28636 ∙ Uniprot:Q9BPU9 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

Meckel syndrome (Supportive), mode of inheritance: AR
Meckel syndrome, type 10 (Strong), mode of inheritance: AR
ciliopathy (Moderate), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Meckel syndrome 10	AR	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Gastrointestinal; Musculoskeletal; Neurologic; Renal	21763481

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the B9D2 gene.

Joubert_syndrome (39 variants)
Meckel-Gruber_syndrome (36 variants)
not_specified (31 variants)
not_provided (17 variants)
Meckel_syndrome,_type_10 (8 variants)
Joubert_syndrome_and_related_disorders (5 variants)
B9D2-related_disorder (4 variants)
Joubert_syndrome_34 (3 variants)
Ciliopathy (2 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the B9D2 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000030578.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous				20 clinvar		20
missense	2 clinvar	4 clinvar	38 clinvar	2 clinvar		46
nonsense		1 clinvar				1
start loss						0
frameshift		3 clinvar	1 clinvar			4
splice donor/acceptor (+/-2bp)						0
Total	2	8	39	22	0

Highest pathogenic variant AF is 0.0000130109

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
B9D2	protein_coding	protein_coding	ENST00000243578	3	9753

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000526	0.456	125708	0	23	125731	0.0000915

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.130	124	120	1.03	0.00000853	1123
Missense in Polyphen		35	39.925	0.87663		344
Synonymous	0.170	50	51.6	0.970	0.00000384	363
Loss of Function	0.380	7	8.17	0.857	4.37e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000213	0.000213
Ashkenazi Jewish	0.000426	0.000397
East Asian	0.00	0.00
Finnish	0.0000988	0.0000924
European (Non-Finnish)	0.0000805	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000980	0.0000980
Other	0.000163	0.000163

dbNSFP

Source: dbNSFP

Function: FUNCTION: Component of the tectonic-like complex, a complex localized at the transition zone of primary cilia and acting as a barrier that prevents diffusion of transmembrane proteins between the cilia and plasma membranes. {ECO:0000269|PubMed:21763481}.;
Disease: DISEASE: Meckel syndrome 10 (MKS10) [MIM:614175]: A disorder characterized by a combination of renal cysts and variably associated features including developmental anomalies of the central nervous system (typically encephalocele), hepatic ductal dysplasia and cysts, and polydactyly. {ECO:0000269|PubMed:21763481}. Note=The disease is caused by mutations affecting the gene represented in this entry.; DISEASE: Joubert syndrome 34 (JBTS34) [MIM:614175]: A form of Joubert syndrome, a disorder presenting with cerebellar ataxia, oculomotor apraxia, hypotonia, neonatal breathing abnormalities and psychomotor delay. Neuroradiologically, it is characterized by cerebellar vermian hypoplasia/aplasia, thickened and reoriented superior cerebellar peduncles, and an abnormally large interpeduncular fossa, giving the appearance of a molar tooth on transaxial slices (molar tooth sign). Additional variable features include retinal dystrophy, renal disease, liver fibrosis, and polydactyly. JBTS34 inheritance is autosomal recessive. {ECO:0000269|PubMed:26092869}. Note=The disease is caused by mutations affecting the gene represented in this entry.;
Pathway: Signal Transduction;Amplification of signal from unattached kinetochores via a MAD2 inhibitory signal;Amplification of signal from the kinetochores;Mitotic Spindle Checkpoint;Cell Cycle Checkpoints;RHO GTPases Activate Formins;RHO GTPase Effectors;Signaling by Rho GTPases;Mitotic Prometaphase;Separation of Sister Chromatids;Mitotic Anaphase;Mitotic Metaphase and Anaphase;M Phase;Cell Cycle;Resolution of Sister Chromatid Cohesion;Cell Cycle, Mitotic;Anchoring of the basal body to the plasma membrane;Cilium Assembly;Organelle biogenesis and maintenance (Consensus)

Recessive Scores

pRec: 0.133

Intolerance Scores

loftool: 0.574
rvis_EVS: -0.12
rvis_percentile_EVS: 44.89

Haploinsufficiency Scores

pHI: 0.142
hipred: N
hipred_score: 0.344
ghis: 0.566

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.481

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: B9d2
Phenotype: growth/size/body region phenotype; endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype; cellular phenotype; muscle phenotype; craniofacial phenotype; vision/eye phenotype; cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system 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); reproductive system phenotype; neoplasm; embryo phenotype; respiratory system phenotype; liver/biliary system phenotype; immune system phenotype; skeleton phenotype; renal/urinary system phenotype; digestive/alimentary 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); limbs/digits/tail phenotype;

Zebrafish Information Network

Gene name: b9d2
Affected structure: photoreceptor cell
Phenotype tag: abnormal
Phenotype quality: morphology

Gene ontology

Biological process: cilium assembly;ciliary basal body-plasma membrane docking
Cellular component: nucleus;centrosome;cytosol;membrane;MKS complex;ciliary basal body
Molecular function: protein binding;gamma-tubulin binding