CD84

CD84 molecule, the group of CD molecules|Ig-like cell adhesion molecule family|Immunoglobulin like domain containing

Basic information

Region (hg38): 1:160541094-160579516

Links

ENSG00000066294 ∙ NCBI:8832 ∙ OMIM:604513 ∙ HGNC:1704 ∙ Uniprot:Q9UIB8 ∙ 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 CD84 gene.

• Inborn genetic diseases (14 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD84 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			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	14	0	0

Variants in CD84

This is a list of pathogenic ClinVar variants found in the CD84 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-160548308-C-T		not specified	Uncertain significance (Apr 19, 2023)
1-160549934-C-T		not specified	Uncertain significance (Jul 05, 2023)
1-160549952-T-C		not specified	Uncertain significance (Nov 14, 2023)
1-160551014-A-G		not specified	Uncertain significance (Jan 08, 2024)
1-160553423-T-C		not specified	Uncertain significance (Feb 12, 2024)
1-160553453-C-T		not specified	Uncertain significance (Jul 13, 2021)
1-160553480-G-A		not specified	Uncertain significance (Aug 17, 2021)
1-160553492-C-T		not specified	Uncertain significance (Jan 26, 2023)
1-160553910-G-A		not specified	Uncertain significance (Feb 06, 2023)
1-160553915-G-A		not specified	Uncertain significance (Apr 07, 2022)
1-160553985-G-C		not specified	Uncertain significance (Aug 09, 2021)
1-160554083-A-C		not specified	Uncertain significance (Nov 30, 2022)
1-160565461-T-A		not specified	Uncertain significance (Aug 02, 2023)
1-160565472-TA-T		Multisystem inflammatory syndrome in children	risk factor (Nov 14, 2021)
1-160565515-T-A		not specified	Uncertain significance (Dec 20, 2023)
1-160565523-G-A		not specified	Uncertain significance (Apr 08, 2022)
1-160565548-A-C		not specified	Uncertain significance (Feb 15, 2023)
1-160565577-G-A		not specified	Uncertain significance (Jul 13, 2021)
1-160565601-G-T		not specified	Uncertain significance (Dec 11, 2023)
1-160579424-T-A		not specified	Uncertain significance (Dec 28, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD84	protein_coding	protein_coding	ENST00000311224	8	38422

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
6.91e-9	0.262	125689	0	57	125746	0.000227

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.216	184	192	0.956	0.0000103	2243
Missense in Polyphen		40	47.599	0.84036		595
Synonymous	-0.271	75	72.1	1.04	0.00000394	679
Loss of Function	0.595	14	16.6	0.843	7.98e-7	202

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000181	0.000181
Ashkenazi Jewish	0.00	0.00
East Asian	0.000167	0.000163
Finnish	0.00	0.00
European (Non-Finnish)	0.000348	0.000325
Middle Eastern	0.000167	0.000163
South Asian	0.000399	0.000359
Other	0.000340	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Self-ligand receptor of the signaling lymphocytic activation molecule (SLAM) family. SLAM receptors triggered by homo- or heterotypic cell-cell interactions are modulating the activation and differentiation of a wide variety of immune cells and thus are involved in the regulation and interconnection of both innate and adaptive immune response. Activities are controlled by presence or absence of small cytoplasmic adapter proteins, SH2D1A/SAP and/or SH2D1B/EAT-2. Can mediate natural killer (NK) cell cytotoxicity dependent on SH2D1A and SH2D1B (By similarity). Increases proliferative responses of activated T- cells and SH2D1A/SAP does not seem be required for this process. Homophilic interactions enhance interferon gamma/IFNG secretion in lymphocytes and induce platelet stimulation via a SH2D1A-dependent pathway. May serve as a marker for hematopoietic progenitor cells (PubMed:11564780, PubMed:12115647. PubMed:12928397, PubMed:12962726, PubMed:16037392) Required for a prolonged T- cell:B-cell contact, optimal T follicular helper function, and germinal center formation. In germinal centers involved in maintaining B-cell tolerance and in preventing autoimmunity (By similarity). In mast cells negatively regulates high affinity immunoglobulin epsilon receptor signaling; independent of SH2D1A and SH2D1B but implicating FES and PTPN6/SHP-1 (PubMed:22068234). In macrophages enhances LPS-induced MAPK phosphorylation and NF- kappaB activation and modulates LPS-induced cytokine secretion; involving ITSM 2 (By similarity). Positively regulates macroautophagy in primary dendritic cells via stabilization of IRF8; inhibits TRIM21-mediated proteasomal degradation of IRF8 (PubMed:29434592). {ECO:0000250|UniProtKB:Q18PI6, ECO:0000269|PubMed:11564780, ECO:0000269|PubMed:12115647, ECO:0000269|PubMed:12928397, ECO:0000269|PubMed:12962726, ECO:0000269|PubMed:16037392, ECO:0000269|PubMed:22068234, ECO:0000269|PubMed:29434592, ECO:0000305}.
• Pathway: TYROBP Causal Network;TCR;Cell surface interactions at the vascular wall;Hemostasis (Consensus)

Recessive Scores

• pRec: 0.138

Intolerance Scores

• loftool: 0.925
• rvis_EVS: 0.04
• rvis_percentile_EVS: 57.15

Haploinsufficiency Scores

• pHI: 0.0662
• hipred: N
• hipred_score: 0.112
• ghis: 0.488

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0768

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Cd84
• Phenotype: immune system phenotype; hematopoietic system phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan); homeostasis/metabolism phenotype

Gene ontology

• Biological process: adaptive immune response;autophagy;defense response;homophilic cell adhesion via plasma membrane adhesion molecules;negative regulation of granulocyte macrophage colony-stimulating factor production;negative regulation of interleukin-18 production;negative regulation of mast cell activation;negative regulation of mast cell degranulation;innate immune response;leukocyte migration;regulation of store-operated calcium entry
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: protein binding;identical protein binding