GeneBe

CBLN1

cerebellin 1 precursor, the group of C1q domain containing

Basic information

Region (hg38): 16:49277917-49281838

Links

ENSG00000102924 ∙ NCBI:869 ∙ OMIM:600432 ∙ HGNC:1543 ∙ Uniprot:P23435 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CBLN1 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBLN1 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
0
missense
10
clinvar
 10
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 10 0 0

Variants in CBLN1

This is a list of pathogenic ClinVar variants found in the CBLN1 region.

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

Position Type Phenotype Significance ClinVar
16-49279493-C-A not specified Uncertain significance (Dec 06, 2024)3485675
16-49279574-C-A not specified Uncertain significance (Jun 19, 2024)3263646
16-49279591-A-G not specified Uncertain significance (Nov 21, 2024)3485674
16-49280925-G-C not specified Uncertain significance (Dec 01, 2022)2330681
16-49280952-C-G not specified Uncertain significance (Apr 26, 2024)3263647
16-49280988-G-A not specified Uncertain significance (Nov 03, 2023)3138014
16-49281012-A-T not specified Uncertain significance (Mar 25, 2024)3263648
16-49281208-G-C not specified Uncertain significance (Nov 17, 2022)2303474
16-49281221-A-C not specified Uncertain significance (Apr 12, 2023)2536507
16-49281408-G-A not specified Uncertain significance (Nov 30, 2022)2230328

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CBLN1protein_codingprotein_codingENST00000219197 33915
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.1760.773125742031257450.0000119
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense1.68601100.5470.000004921249
Missense in Polyphen1444.9330.31157495
Synonymous0.9013946.80.8320.00000216399
Loss of Function1.6226.420.3122.80e-769

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.000.00
Ashkenazi Jewish0.000.00
East Asian0.00005440.0000544
Finnish0.000.00
European (Non-Finnish)0.00001760.0000176
Middle Eastern0.00005440.0000544
South Asian0.000.00
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Required for synapse integrity and synaptic plasticity. During cerebellar synapse formation, essential for the matching and maintenance of pre- and post-synaptic elements at parallel fiber-Purkinje cell synapses, the establishment of the proper pattern of climbing fiber-Purkinje cell innervation, and induction of long-term depression at parallel fiber-Purkinje cell synapses. Plays a role as a synaptic organizer that acts bidirectionally on both pre- and post-synaptic components. On the one hand induces accumulation of synaptic vesicles in the pre-synaptic part by binding with NRXN1 and in other hand induces clustering of GRID2 and its associated proteins at the post-synaptic site through association of GRID2. NRXN1-CBLN1-GRID2 complex directly induces parallel fiber protrusions that encapsulate spines of Purkinje cells leading to accumulation of GRID2 and synaptic vesicles. Required for CBLN3 export from the endoplasmic reticulum and secretion (By similarity). NRXN1-CBLN1-GRID2 complex mediates the D-Serine-dependent long term depression signals and AMPA receptor endocytosis (PubMed:27418511). {ECO:0000250|UniProtKB:Q9R171, ECO:0000269|PubMed:27418511}.;

Recessive Scores

pRec
0.147

Intolerance Scores

loftool
0.113
rvis_EVS
0.01
rvis_percentile_EVS
54.63

Haploinsufficiency Scores

pHI
0.847
hipred
Y
hipred_score
0.669
ghis
0.628

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.354

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cbln1
Phenotype
normal phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); 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);

Gene ontology

Biological process
heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules;chemical synaptic transmission;nervous system development;protein secretion;cerebellar granule cell differentiation;positive regulation of synapse assembly;negative regulation of excitatory postsynaptic potential;regulation of postsynaptic density assembly;positive regulation of long-term synaptic depression;regulation of presynapse assembly
Cellular component
cell junction;synaptic cleft;postsynaptic membrane;parallel fiber to Purkinje cell synapse;glutamatergic synapse
Molecular function
protein binding;protein homodimerization activity