GeneBe

CD83

CD83 molecule, the group of V-set domain containing|CD molecules

Basic information

Region (hg38): 6:14117256-14140682

Links

ENSG00000112149 ∙ NCBI:9308 ∙ OMIM:604534 ∙ HGNC:1703 ∙ Uniprot:Q01151 ∙ 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 CD83 gene.

  • not_specified (26 variants)
  • not_provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CD83 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000004233.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
0
missense
25
clinvar
1
clinvar
1
clinvar
 27
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 25 1 1
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
CD83protein_codingprotein_codingENST00000379153 519278
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
0.005210.9001257300181257480.0000716
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.3161011100.9150.000005551303
Missense in Polyphen2733.2890.81108444
Synonymous-0.9105446.11.170.00000245412
Loss of Function1.4359.820.5095.01e-7115

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.0001250.000120
Ashkenazi Jewish0.000.00
East Asian0.0002170.000217
Finnish0.000.00
European (Non-Finnish)0.00007080.0000615
Middle Eastern0.0002170.000217
South Asian0.0001330.000131
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: May play a significant role in antigen presentation or the cellular interactions that follow lymphocyte activation.;
Pathway
Macrophage markers;Macrophage markers;T-Cell antigen Receptor (TCR) Signaling Pathway (Consensus)

Recessive Scores

pRec
0.406

Intolerance Scores

loftool
0.622
rvis_EVS
0.44
rvis_percentile_EVS
77.57

Haploinsufficiency Scores

pHI
0.272
hipred
N
hipred_score
0.215
ghis
0.483

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.247

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Mouse Genome Informatics

Gene name
Cd83
Phenotype
normal phenotype; reproductive system 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); hematopoietic system phenotype; immune system phenotype; endocrine/exocrine gland phenotype;

Gene ontology

Biological process
defense response;humoral immune response;signal transduction;response to organic cyclic compound;negative regulation of interleukin-4 production;positive regulation of interleukin-10 production;positive regulation of interleukin-2 production;positive regulation of CD4-positive, alpha-beta T cell differentiation
Cellular component
plasma membrane;integral component of plasma membrane;external side of plasma membrane
Molecular function
protein binding