CBLN2

cerebellin 2 precursor, the group of C1q domain containing

Basic information

Region (hg38): 18:72536679-72638521

Links

ENSG00000141668 ∙ NCBI:147381 ∙ OMIM:600433 ∙ HGNC:1544 ∙ Uniprot:Q8IUK8 ∙ 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 CBLN2 gene.

• not provided (10 variants)
• Inborn genetic diseases (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBLN2 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					2	2
missense			3			3
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				1	7	8
Total	0	0	3	1	9

Variants in CBLN2

This is a list of pathogenic ClinVar variants found in the CBLN2 region.

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

Position	Type	Phenotype	Significance	ClinVar
18-72538166-G-A			Benign (Sep 06, 2018)
18-72538706-T-C		not specified	Uncertain significance (Dec 01, 2022)
18-72538723-A-G		not specified	Uncertain significance (Mar 07, 2024)
18-72541663-G-T			Benign (Sep 04, 2018)
18-72541942-C-T			Benign (Sep 06, 2018)
18-72541956-C-T		not specified	Uncertain significance (May 31, 2022)
18-72542051-G-A		not specified	Uncertain significance (Oct 29, 2021)
18-72542086-C-A			Benign (Sep 04, 2018)
18-72542245-T-C			Benign (May 10, 2021)
18-72542275-G-C			Benign (May 10, 2021)
18-72542403-C-T			Benign (Sep 06, 2018)
18-72542461-G-T			Likely benign (Jul 30, 2019)
18-72542514-C-A			Benign (Sep 06, 2018)
18-72542657-G-A			Benign (Sep 06, 2018)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CBLN2	protein_coding	protein_coding	ENST00000269503	3	101842

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.122	0.788	125741	0	2	125743	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.87	62	119	0.519	0.00000565	1422
Missense in Polyphen		8	45.294	0.17662		533
Synonymous	-0.779	63	55.6	1.13	0.00000289	482
Loss of Function	1.35	2	5.37	0.372	2.27e-7	71

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000307	0.0000307
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000462	0.0000462
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play role in synaptogenesis induction. {ECO:0000250}.

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.0867
• rvis_EVS: -0.1
• rvis_percentile_EVS: 46.2

Haploinsufficiency Scores

• pHI: 0.502
• hipred: Y
• hipred_score: 0.651
• ghis: 0.609

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.355

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cbln2

Gene ontology

• Biological process: positive regulation of synapse assembly;regulation of presynapse assembly
• Cellular component: extracellular space;glutamatergic synapse