CBLN4

cerebellin 4 precursor, the group of C1q domain containing

Basic information

Region (hg38): 20:55997357-56005519

Previous symbols: [ "CBLNL1" ]

Links

ENSG00000054803 ∙ NCBI:140689 ∙ OMIM:615029 ∙ HGNC:16231 ∙ Uniprot:Q9NTU7 ∙ 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 CBLN4 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBLN4 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			7			7
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	0

Variants in CBLN4

This is a list of pathogenic ClinVar variants found in the CBLN4 region.

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

Position	Type	Phenotype	Significance	ClinVar
20-55998690-C-T		not specified	Uncertain significance (Dec 14, 2023)
20-56000733-G-T		not specified	Uncertain significance (Jun 30, 2023)
20-56000823-A-G		not specified	Uncertain significance (Jan 17, 2024)
20-56003891-T-C		not specified	Uncertain significance (Jan 11, 2023)
20-56003903-G-C		not specified	Uncertain significance (Jan 02, 2024)
20-56003979-G-A		not specified	Uncertain significance (Nov 08, 2022)
20-56004146-G-A		not specified	Uncertain significance (Oct 24, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CBLN4	protein_coding	protein_coding	ENST00000064571	3	8033

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.167	0.778	125741	0	4	125745	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.96	61	122	0.500	0.00000725	1283
Missense in Polyphen		20	50.815	0.39359		509
Synonymous	0.396	56	59.9	0.935	0.00000407	436
Loss of Function	1.58	2	6.26	0.319	2.64e-7	77

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000331	0.0000331
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000912	0.00000879
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.000164	0.000163

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in synaptic functions in the CNS. May play a role in CBLN3 export from the endoplasmic reticulum and secretion (By similarity). {ECO:0000250}.

Recessive Scores

• pRec: 0.120

Intolerance Scores

• loftool: 0.132
• rvis_EVS: -0.01
• rvis_percentile_EVS: 52.85

Haploinsufficiency Scores

• pHI: 0.339
• hipred: Y
• hipred_score: 0.752
• ghis: 0.612

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cbln4
• Phenotype: normal phenotype

Gene ontology

• Biological process: protein secretion
• Cellular component: extracellular space;cell junction;synapse