CD83

protein-coding

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

Gene summary

The protein encoded by this gene is a single-pass type I membrane protein and member of the immunoglobulin superfamily of receptors. The encoded protein may be involved in the regulation of antigen presentation. A soluble form of this protein can bind to dendritic cells and inhibit their maturation. Three transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

MANE transcript

NM_004233.4

Inheritance

—

ClinVar variants

U:33B:2

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.51

Max pathogenic AF

—

Genomic locus

chr6:14,117,256-14,140,682

External References & Databases

Ensembl (ENSG00000112149)

Transcript & Mutation Effects

hg38 • Region Span ~23.4 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to CD83 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 31

not providedTotal: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004233.4. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			32 clinvar	1 clinvar	1 clinvar	34
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	33	1	1	35

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004233.4	RefSeq	NP_004224.1	5	MANE Select
ENST00000379153.4	Ensembl	ENSP00000368450.3	5	MANE Select
NM_001040280.3	RefSeq	NP_001035370.1	5	Standard
NM_001251901.1	RefSeq	NP_001238830.1	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Macrophage markers
Macrophage markers
T-Cell antigen Receptor (TCR) Signaling Pathway

Biological Process

defense response
humoral immune response
signal transduction
response to organic cyclic compound
negative regulation of interleukin-4 production

Molecular Function

protein binding

Cellular Component

plasma membrane
integral component of plasma membrane
external side of plasma membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000379153
Coding exons: 5
Length: 19278
Individuals with no LoFs: 125730
Homozygous LoFs: 0
Heterozygous LoFs: 18
Defined: 125748
p: 0.0000716

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.316	101	110	0.915	0.00000555	1303
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.000067	0.000062	rare
Latino/Admixed American	0.000058	0.000058	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00022	0.00022	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.000071	0.000062	rare
South Asian	0.00013	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May play a significant role in antigen presentation or the cellular interactions that follow lymphocyte activation.;

Recessive Scores

pRec: 0.406

Intolerance Scores

LoFtool: 0.622
RVIS EVS: 0.44
RVIS percentile EVS: 77.57

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.247

Gene Damage Prediction

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