CLEC4C

C-type lectin domain family 4 member C, the group of CD molecules|C-type lectin domain containing

Basic information

Region (hg38): 12:7729383-7751605

Previous symbols: [ "CLECSF11", "CLECSF7" ]

Links

ENSG00000198178 ∙ NCBI:170482 ∙ OMIM:606677 ∙ HGNC:13258 ∙ Uniprot:Q8WTT0 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• amyotrophic lateral sclerosis (Limited), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the CLEC4C gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC4C 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			12	1	2	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	2

Variants in CLEC4C

This is a list of pathogenic ClinVar variants found in the CLEC4C region.

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

Position	Type	Phenotype	Significance	ClinVar
12-7729633-T-C		not specified	Uncertain significance (May 15, 2023)
12-7729681-C-T		not specified	Uncertain significance (Dec 28, 2022)
12-7729682-G-A		not specified	Uncertain significance (Jan 12, 2024)
12-7730810-T-C		not specified	Uncertain significance (Oct 30, 2023)
12-7730845-C-T		not specified	Uncertain significance (Apr 09, 2024)
12-7730863-A-G		not specified	Uncertain significance (Apr 04, 2024)
12-7737444-G-T			Benign (Dec 31, 2019)
12-7741427-T-C		not specified	Uncertain significance (Dec 02, 2021)
12-7741463-G-A		not specified	Likely benign (Jun 30, 2022)
12-7741484-A-C			Benign (Jul 23, 2018)
12-7741487-T-G		not specified	Uncertain significance (Mar 07, 2023)
12-7741515-C-A		not specified	Uncertain significance (Feb 05, 2024)
12-7746364-G-T		not specified	Uncertain significance (Jan 31, 2024)
12-7746376-C-T		not specified	Uncertain significance (Dec 21, 2023)
12-7746415-G-A		not specified	Uncertain significance (Dec 18, 2023)
12-7746420-T-C		not specified	Uncertain significance (Sep 29, 2023)
12-7747345-C-T		not specified	Uncertain significance (Mar 20, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC4C	protein_coding	protein_coding	ENST00000542353	6	22191

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
5.77e-7	0.444	125709	0	39	125748	0.000155

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.696	96	117	0.819	0.00000598	1416
Missense in Polyphen		30	32.073	0.93536		419
Synonymous	-0.476	41	37.3	1.10	0.00000182	361
Loss of Function	0.702	11	13.8	0.796	8.73e-7	128

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00140	0.00140
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.0000793	0.0000791
Middle Eastern	0.00	0.00
South Asian	0.0000653	0.0000653
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Lectin-type cell surface receptor which may play a role in antigen capturing by dendritic cells (PubMed:11748283, PubMed:21880719, PubMed:25995448). Specifically recognizes non- sialylated galactose-terminated biantennary glycans containing the trisaccharide epitope Gal(beta1-3/4)GlcNAc(beta1-2)Man (PubMed:21880719, PubMed:25995448). Binds to serum IgG (PubMed:25995448). Efficiently targets ligand into antigen- processing and peptide-loading compartments for presentation to T- cells (PubMed:11748283). May mediate potent inhibition of induction of IFN-alpha/beta expression in plasmacytoid dendritic cells (PubMed:11748283, PubMed:21880719). May act as a signaling receptor that activates protein-tyrosine kinases and mobilizes intracellular calcium (PubMed:11748283). {ECO:0000269|PubMed:11748283, ECO:0000269|PubMed:21880719, ECO:0000269|PubMed:25995448}.
• Pathway: Neutrophil degranulation;Dectin-2 family;C-type lectin receptors (CLRs);Innate Immune System;Immune System (Consensus)

Intolerance Scores

• loftool: 0.889
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.48

Haploinsufficiency Scores

• pHI: 0.0636
• hipred: N
• hipred_score: 0.316

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.622

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec4b1

Gene ontology

• Biological process: stimulatory C-type lectin receptor signaling pathway;adaptive immune response;neutrophil degranulation;innate immune response
• Cellular component: plasma membrane;integral component of membrane;secretory granule membrane;tertiary granule membrane;ficolin-1-rich granule membrane
• Molecular function: carbohydrate binding;metal ion binding