CD83

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

Basic information

Region (hg38): 6:14117255-14136918

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.

• Inborn genetic diseases (7 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.

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			7		1	8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	7	0	1

Variants in CD83

This is a list of pathogenic ClinVar variants found in the CD83 region.

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

Position	Type	Phenotype	Significance	ClinVar
6-14117816-C-T		not specified	Uncertain significance (Nov 10, 2021)
6-14117976-G-A		not specified	Uncertain significance (Nov 08, 2022)
6-14118000-G-A		not specified	Uncertain significance (Nov 17, 2023)
6-14118037-A-G		not specified	Uncertain significance (May 17, 2023)
6-14131562-G-T		not specified	Uncertain significance (Jan 22, 2024)
6-14131602-A-T		not specified	Uncertain significance (Jan 17, 2024)
6-14131650-G-A		not specified	Likely benign (Oct 30, 2023)
6-14131658-A-G		not specified	Uncertain significance (Nov 18, 2023)
6-14131700-C-T		not specified	Uncertain significance (Jan 26, 2022)
6-14131725-G-A		not specified	Uncertain significance (Jan 22, 2024)
6-14131730-G-T		not specified	Uncertain significance (Mar 01, 2024)
6-14135118-G-A		not specified	Uncertain significance (Aug 12, 2021)
6-14135147-A-G		not specified	Uncertain significance (Apr 05, 2023)
6-14135163-G-A			Benign (Dec 31, 2019)
6-14135213-C-T		not specified	Uncertain significance (Jul 21, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CD83	protein_coding	protein_coding	ENST00000379153	5	19278

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00521	0.900	125730	0	18	125748	0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.316	101	110	0.915	0.00000555	1303
Missense in Polyphen		27	33.289	0.81108		444
Synonymous	-0.910	54	46.1	1.17	0.00000245	412
Loss of Function	1.43	5	9.82	0.509	5.01e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000125	0.000120
Ashkenazi Jewish	0.00	0.00
East Asian	0.000217	0.000217
Finnish	0.00	0.00
European (Non-Finnish)	0.0000708	0.0000615
Middle Eastern	0.000217	0.000217
South Asian	0.000133	0.000131
Other	0.00	0.00

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

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

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