GPR183

G protein-coupled receptor 183, the group of G protein-coupled receptors, Class A orphans

Basic information

Region (hg38): 13:99294539-99307399

Previous symbols: [ "EBI2" ]

Links

ENSG00000169508 ∙ NCBI:1880 ∙ OMIM:605741 ∙ HGNC:3128 ∙ Uniprot:P32249 ∙ 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 GPR183 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the GPR183 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			23	1		24
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	23	1	0

Variants in GPR183

This is a list of pathogenic ClinVar variants found in the GPR183 region.

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

Position	Type	Phenotype	Significance	ClinVar
13-99295073-G-A		not specified	Likely benign (Oct 03, 2022)
13-99295088-A-G		not specified	Uncertain significance (Jun 25, 2024)
13-99295095-T-C		not specified	Uncertain significance (Mar 01, 2025)
13-99295101-T-C		not specified	Uncertain significance (Mar 08, 2024)
13-99295115-C-T		not specified	Uncertain significance (Jul 19, 2023)
13-99295173-G-A		not specified	Uncertain significance (Aug 07, 2024)
13-99295180-C-G		not specified	Uncertain significance (Nov 20, 2024)
13-99295202-T-C		not specified	Uncertain significance (Aug 01, 2024)
13-99295217-A-G		not specified	Uncertain significance (Jun 29, 2023)
13-99295233-G-A		not specified	Uncertain significance (Feb 15, 2025)
13-99295329-G-A		not specified	Uncertain significance (Dec 29, 2024)
13-99295345-A-T		not specified	Uncertain significance (Dec 27, 2023)
13-99295395-C-T		not specified	Uncertain significance (Aug 16, 2021)
13-99295580-T-A		not specified	Uncertain significance (Mar 08, 2024)
13-99295656-G-A		not specified	Uncertain significance (Mar 19, 2024)
13-99295733-C-T		not specified	Uncertain significance (Jul 25, 2023)
13-99295823-G-A		not specified	Uncertain significance (Oct 20, 2024)
13-99295851-T-A		not specified	Uncertain significance (Jan 03, 2024)
13-99295877-T-A		not specified	Uncertain significance (Jan 23, 2024)
13-99295944-G-A		not specified	Uncertain significance (Jan 17, 2024)
13-99296007-C-T		not specified	Uncertain significance (Oct 30, 2023)
13-99296025-C-T		not specified	Uncertain significance (Jan 18, 2023)
13-99296045-A-G		not specified	Uncertain significance (Dec 13, 2022)
13-99296048-A-G		not specified	Uncertain significance (Jul 10, 2024)
13-99296060-G-A		not specified	Uncertain significance (Feb 22, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
GPR183	protein_coding	protein_coding	ENST00000376414	1	12876

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0173	0.899	125729	0	5	125734	0.0000199

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	1.27	153	204	0.749	0.0000107	2404
Missense in Polyphen		32	80.983	0.39514		975
Synonymous	-1.23	87	73.5	1.18	0.00000413	704
Loss of Function	1.46	4	8.62	0.464	4.59e-7	115

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000868	0.0000868
Ashkenazi Jewish	0.0000999	0.0000992
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
South Asian	0.0000330	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: G-protein coupled receptor expressed in lymphocytes that acts as a chemotactic receptor for B-cells, T-cells, splenic dendritic cells, monocytes/macrophages and astrocytes (By similarity). Receptor for oxysterol 7-alpha,25- dihydroxycholesterol (7-alpha,25-OHC) and other related oxysterols (PubMed:21796212, PubMed:22875855, PubMed:22930711). Mediates cell positioning and movement of a number of cells by binding the 7- alpha,25-OHC ligand that forms a chemotactic gradient (By similarity). Binding of 7-alpha,25-OHC mediates the correct localization of B-cells during humoral immune responses (By similarity). Guides B-cell movement along the B-cell zone-T-cell zone boundary and later to interfollicular and outer follicular regions (By similarity). Its specific expression during B-cell maturation helps position B-cells appropriately for mounting T- dependent antibody responses (By similarity). Collaborates with CXCR5 to mediate B-cell migration; probably by forming a heterodimer with CXCR5 that affects the interaction between of CXCL13 and CXCR5 (PubMed:22913878). Also acts as a chemotactic receptor for some T-cells upon binding to 7-alpha,25-OHC ligand (By similarity). Promotes follicular helper T (Tfh) cells differentiation by positioning activated T-cells at the follicle- T-zone interface, promoting contact of newly activated CD4 T-cells with activated dendritic cells and exposing them to Tfh-cell- promoting inducible costimulator (ICOS) ligand (By similarity). Expression in splenic dendritic cells is required for their homeostasis, localization and ability to induce B- and T-cell responses: GPR183 acts as a chemotactic receptor in dendritic cells that mediates the accumulation of CD4(+) dendritic cells in bridging channels (By similarity). Regulates migration of astrocytes and is involved in communication between astrocytes and macrophages (PubMed:25297897). Promotes osteoclast precursor migration to bone surfaces (By similarity). Signals constitutively through G(i)-alpha, but not G(s)-alpha or G(q)-alpha (PubMed:21673108, PubMed:25297897). Signals constitutively also via MAPK1/3 (ERK1/2) (By similarity). {ECO:0000250|UniProtKB:Q3U6B2, ECO:0000269|PubMed:16540462, ECO:0000269|PubMed:21673108, ECO:0000269|PubMed:21796212, ECO:0000269|PubMed:22875855, ECO:0000269|PubMed:22913878, ECO:0000269|PubMed:22930711, ECO:0000269|PubMed:25297897}.
• Pathway: GPCRs, Other;Signaling by GPCR;Signal Transduction;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;G alpha (i) signalling events;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.115

Intolerance Scores

• loftool: 0.332
• rvis_EVS: 0.06
• rvis_percentile_EVS: 58.53

Haploinsufficiency Scores

• pHI: 0.121
• hipred: N
• hipred_score: 0.398
• ghis: 0.534

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.558

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Gpr183
• Phenotype: immune system phenotype; hematopoietic system phenotype; homeostasis/metabolism phenotype

Zebrafish Information Network

• Gene name: gpr183a
• Affected structure: ventral wall of dorsal aorta
• Phenotype tag: abnormal
• Phenotype quality: decreased amount

Gene ontology

• Biological process: adaptive immune response;mature B cell differentiation involved in immune response;dendritic cell chemotaxis;immune response;humoral immune response;G protein-coupled receptor signaling pathway;T cell chemotaxis;osteoclast differentiation;leukocyte chemotaxis;positive regulation of B cell proliferation;dendritic cell homeostasis;T follicular helper cell differentiation;positive regulation of ERK1 and ERK2 cascade;regulation of astrocyte chemotaxis
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: G protein-coupled receptor activity;oxysterol binding