CBLN3

cerebellin 3 precursor, the group of C1q domain containing

Basic information

Region (hg38): 14:24426545-24430954

Links

ENSG00000139899 ∙ NCBI:643866 ∙ OMIM:612978 ∙ HGNC:20146 ∙ Uniprot:Q6UW01 ∙ 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 CBLN3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CBLN3 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			22			22
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	22	0	0

Variants in CBLN3

This is a list of pathogenic ClinVar variants found in the CBLN3 region.

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

Position	Type	Phenotype	Significance	ClinVar
14-24427794-G-C		not specified	Uncertain significance (Jan 16, 2024)
14-24427853-C-T		not specified	Uncertain significance (Nov 16, 2021)
14-24427925-G-C		not specified	Uncertain significance (Sep 14, 2021)
14-24427935-G-A		not specified	Uncertain significance (Oct 18, 2021)
14-24428342-C-T		not specified	Uncertain significance (Jul 06, 2021)
14-24428345-G-A		not specified	Uncertain significance (Nov 07, 2022)
14-24428350-G-A		not specified	Uncertain significance (Dec 21, 2022)
14-24428350-G-C		not specified	Uncertain significance (May 24, 2023)
14-24428357-C-T		not specified	Uncertain significance (May 18, 2023)
14-24428375-G-A		not specified	Uncertain significance (Aug 08, 2023)
14-24428387-C-T		not specified	Uncertain significance (Jun 17, 2024)
14-24428390-C-T		not specified	Uncertain significance (Aug 28, 2024)
14-24428392-T-G		not specified	Uncertain significance (Jan 19, 2022)
14-24428393-C-T		not specified	Uncertain significance (Oct 30, 2024)
14-24428760-C-T		not specified	Uncertain significance (Jul 30, 2023)
14-24428786-T-C		not specified	Uncertain significance (Dec 08, 2023)
14-24428795-T-C		not specified	Uncertain significance (Oct 26, 2022)
14-24428879-G-A		not specified	Uncertain significance (Aug 14, 2023)
14-24428920-G-C		not specified	Uncertain significance (Oct 04, 2024)
14-24428924-T-G		not specified	Uncertain significance (Oct 26, 2022)
14-24428945-T-G		not specified	Uncertain significance (May 18, 2023)
14-24428967-C-T		not specified	Uncertain significance (Aug 02, 2022)
14-24428972-C-A		not specified	Uncertain significance (Apr 28, 2023)
14-24429036-G-A		not specified	Uncertain significance (May 17, 2023)
14-24429038-G-A		not specified	Uncertain significance (Dec 26, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CBLN3	protein_coding	protein_coding	ENST00000267406	3	4423

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.000662	0.756	125713	0	25	125738	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.213	122	129	0.947	0.00000807	1271
Missense in Polyphen		53	60.886	0.87047		601
Synonymous	-2.71	82	56.2	1.46	0.00000344	485
Loss of Function	0.973	6	9.18	0.653	7.31e-7	69

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000149	0.000149
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.000139	0.000139
European (Non-Finnish)	0.000125	0.000123
Middle Eastern	0.0000544	0.0000544
South Asian	0.0000983	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May be involved in synaptic functions in the CNS. {ECO:0000250}.

Recessive Scores

• pRec: 0.121

Intolerance Scores

• loftool: 0.596
• rvis_EVS: -0.23
• rvis_percentile_EVS: 36.86

Haploinsufficiency Scores

• pHI: 0.115
• hipred: N
• hipred_score: 0.248
• ghis: 0.628

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.849

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cbln3
• Phenotype: homeostasis/metabolism 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); 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

• Cellular component: extracellular space;endoplasmic reticulum;Golgi apparatus;cell junction;synapse