CLEC4D

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

Basic information

Region (hg38): 12:8509475-8522366

Previous symbols: [ "CLECSF8" ]

Links

ENSG00000166527 ∙ NCBI:338339 ∙ OMIM:609964 ∙ HGNC:14554 ∙ Uniprot:Q8WXI8 ∙ 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 CLEC4D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC4D 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			20	2	1	23
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	20	2	1

Variants in CLEC4D

This is a list of pathogenic ClinVar variants found in the CLEC4D region.

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

Position	Type	Phenotype	Significance	ClinVar
12-8515301-A-G		not specified	Benign (Mar 29, 2016)
12-8515317-C-A		not specified	Uncertain significance (Mar 30, 2022)
12-8518179-T-C		not specified	Uncertain significance (Mar 27, 2023)
12-8518212-A-G		not specified	Uncertain significance (Sep 22, 2023)
12-8518219-G-A			Likely benign (-)
12-8518239-G-T		not specified	Uncertain significance (Feb 27, 2023)
12-8518241-A-G		not specified	Uncertain significance (Oct 27, 2021)
12-8518260-T-C		not specified	Uncertain significance (Jul 25, 2023)
12-8519023-T-G		not specified	Uncertain significance (Jan 23, 2023)
12-8519069-C-A		not specified	Uncertain significance (May 24, 2023)
12-8519087-C-T		not specified	Uncertain significance (Jan 29, 2024)
12-8519106-G-C		not specified	Uncertain significance (Aug 02, 2021)
12-8519152-G-A		not specified	Uncertain significance (Oct 20, 2023)
12-8520253-C-T		not specified	Uncertain significance (Sep 22, 2023)
12-8520274-C-G		not specified	Uncertain significance (Jul 09, 2024)
12-8520299-A-G		not specified	Uncertain significance (Nov 17, 2023)
12-8520304-C-T		not specified	Uncertain significance (Oct 24, 2024)
12-8520320-C-T		not specified	Likely benign (Jan 27, 2022)
12-8521132-A-G		not specified	Uncertain significance (Oct 25, 2023)
12-8521133-T-A		not specified	Uncertain significance (Dec 09, 2023)
12-8521219-G-T		not specified	Uncertain significance (Nov 09, 2024)
12-8521225-T-C		not specified	Likely benign (Jun 27, 2022)
12-8521237-G-C		not specified	Uncertain significance (Jun 13, 2024)
12-8521239-A-G		not specified	Uncertain significance (Jun 21, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC4D	protein_coding	protein_coding	ENST00000299665	6	12892

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000245	0.307	125719	1	24	125744	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.116	120	116	1.03	0.00000594	1432
Missense in Polyphen		32	27.127	1.1796		385
Synonymous	0.0934	38	38.7	0.981	0.00000208	368
Loss of Function	0.252	9	9.85	0.913	4.86e-7	124

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000305	0.000304
Ashkenazi Jewish	0.0000993	0.0000992
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.0000529	0.0000527
Middle Eastern	0.0000545	0.0000544
South Asian	0.000394	0.000359
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: A calcium-dependent lectin involved in innate recognition of pathogen-associated molecular patterns (PAMPs). Interacts with signaling adapter Fc receptor gamma chain/FCER1G, likely via CLEC4E, to form a functional complex in myeloid cells (By similarity). Binding of mycobacterial trehalose 6,6'- dimycolate (TDM) to this receptor complex leads to phosphorylation of the immunoreceptor tyrosine-based activation motif (ITAM) of FCER1G, triggering activation of SYK, CARD9 and NF-kappa-B, consequently driving maturation of antigen-presenting cells and shaping antigen-specific priming of T-cells toward effector T- helper 1 and T-helper 17 cell subtypes (PubMed:23602766). Functions as an endocytic receptor. May be involved in antigen uptake at the site of infection, either for clearance of the antigen, or for processing and further presentation to T cells (PubMed:14971047). {ECO:0000250|UniProtKB:Q69FH1, ECO:0000269|PubMed:14971047, ECO:0000269|PubMed:23602766}.
• Pathway: C-type lectin receptor signaling pathway - Homo sapiens (human);Neutrophil degranulation;Dectin-2 family;C-type lectin receptors (CLRs);Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.0707

Intolerance Scores

• loftool: 0.858
• rvis_EVS: 0.35
• rvis_percentile_EVS: 74.37

Haploinsufficiency Scores

• pHI: 0.0475
• hipred: N
• hipred_score: 0.112
• ghis: 0.419

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.192

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec4d
• Phenotype: immune system phenotype; respiratory system phenotype; hematopoietic system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); endocrine/exocrine gland phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: stimulatory C-type lectin receptor signaling pathway;adaptive immune response;T cell differentiation involved in immune response;positive regulation of myeloid dendritic cell activation;Fc-gamma receptor signaling pathway;defense response to bacterium;neutrophil degranulation;innate immune response
• Cellular component: plasma membrane;integral component of membrane;specific granule membrane;tertiary granule membrane;ficolin-1-rich granule membrane
• Molecular function: protein binding;carbohydrate binding;immunoglobulin receptor binding;metal ion binding