C5AR1

complement C5a receptor 1, the group of Complement component GPCRs|Complement system regulators and receptors|CD molecules

Basic information

Region (hg38): 19:47290022-47322066

Previous symbols: [ "C5R1" ]

Links

ENSG00000197405 ∙ NCBI:728 ∙ OMIM:113995 ∙ HGNC:1338 ∙ Uniprot:P21730 ∙ 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 C5AR1 gene.

• Inborn genetic diseases (11 variants)
• not provided (6 variants)
• C5AR1-related condition (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the C5AR1 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				2	1	3
missense			13			13
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					3	3
Total	0	0	13	2	4

Variants in C5AR1

This is a list of pathogenic ClinVar variants found in the C5AR1 region.

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

Position	Type	Phenotype	Significance	ClinVar
19-47319781-G-G			Benign (Dec 31, 2019)
19-47319863-C-A		not specified	Uncertain significance (Dec 22, 2023)
19-47319877-C-T		C5AR1-related disorder	Uncertain significance (May 08, 2023)
19-47319907-T-C		not specified	Uncertain significance (Sep 28, 2022)
19-47319932-T-C		not specified	Uncertain significance (Aug 17, 2022)
19-47320012-G-A		not specified	Uncertain significance (Apr 22, 2022)
19-47320066-G-A		not specified	Likely benign (Aug 10, 2021)
19-47320072-C-T		not specified	Uncertain significance (Dec 26, 2023)
19-47320093-G-A		C5AR1-related disorder • not specified	Uncertain significance (May 08, 2023)
19-47320227-T-T			Benign (Dec 31, 2019)
19-47320267-G-T		not specified	Uncertain significance (Nov 09, 2022)
19-47320268-C-A		not specified	Uncertain significance (Jan 04, 2022)
19-47320286-C-A		C5AR1-related disorder	Uncertain significance (Mar 27, 2023)
19-47320309-C-T		C5AR1-related disorder	Uncertain significance (Dec 29, 2023)
19-47320314-G-A			Likely benign (Dec 31, 2019)
19-47320330-A-C		not specified	Uncertain significance (Jan 10, 2022)
19-47320333-G-T		not specified	Uncertain significance (Dec 07, 2023)
19-47320392-C-G			Benign (Jun 12, 2018)
19-47320434-G-A		C5AR1-related disorder	Likely benign (Sep 19, 2023)
19-47320459-C-T		not specified	Uncertain significance (Feb 28, 2024)
19-47320556-T-G		not specified	Uncertain significance (Apr 25, 2022)
19-47320589-C-T		not specified	Uncertain significance (Dec 21, 2023)
19-47320590-G-A		C5AR1-related disorder	Likely benign (Sep 04, 2023)
19-47320614-G-G			Benign (Dec 31, 2019)
19-47320623-C-G		not specified	Uncertain significance (Jun 06, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
C5AR1	protein_coding	protein_coding	ENST00000355085	2	32044

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.402	0.480	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.158	211	218	0.970	0.0000150	2235
Missense in Polyphen		81	86.897	0.93213		921
Synonymous	-0.670	109	100	1.08	0.00000693	792
Loss of Function	0.964	0	1.08	0.00	4.60e-8	12

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
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	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Receptor for the chemotactic and inflammatory peptide anaphylatoxin C5a (PubMed:1847994, PubMed:8182049, PubMed:7622471, PubMed:9553099, PubMed:10636859, PubMed:15153520, PubMed:29300009). The ligand interacts with at least two sites on the receptor: a high-affinity site on the extracellular N- terminus, and a second site in the transmembrane region which activates downstream signaling events (PubMed:8182049, PubMed:7622471, PubMed:9553099). Receptor activation stimulates chemotaxis, granule enzyme release, intracellular calcium release and superoxide anion production (PubMed:10636859, PubMed:15153520). {ECO:0000269|PubMed:10636859, ECO:0000269|PubMed:15153520, ECO:0000269|PubMed:1847994, ECO:0000269|PubMed:29300009, ECO:0000269|PubMed:7622471, ECO:0000269|PubMed:8182049, ECO:0000269|PubMed:9553099}.
• Pathway: Complement and coagulation cascades - Homo sapiens (human);Staphylococcus aureus infection - Homo sapiens (human);Neuroactive ligand-receptor interaction - Homo sapiens (human);Peptide GPCRs;Human Complement System;Dengue-2 Interactions with Complement and Coagulation Cascades;Oxidative Damage;Complement and Coagulation Cascades;Signaling by GPCR;Neutrophil degranulation;Signal Transduction;Innate Immune System;Immune System;Peptide ligand-binding receptors;Class A/1 (Rhodopsin-like receptors);GPCR ligand binding;Regulation of Complement cascade;G alpha (i) signalling events;Complement cascade;GPCR downstream signalling (Consensus)

Recessive Scores

• pRec: 0.466

Intolerance Scores

• loftool: 0.650
• rvis_EVS: -0.6
• rvis_percentile_EVS: 18.14

Haploinsufficiency Scores

• pHI: 0.136
• hipred: N
• hipred_score: 0.213
• ghis: 0.542

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.715

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: C5ar1
• Phenotype: homeostasis/metabolism phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); hematopoietic system phenotype; skeleton phenotype; immune system phenotype

Gene ontology

• Biological process: activation of MAPK activity;complement receptor mediated signaling pathway;apoptotic process;chemotaxis;inflammatory response;immune response;cellular defense response;signal transduction;G protein-coupled receptor signaling pathway;phospholipase C-activating G protein-coupled receptor signaling pathway;activation of phospholipase C activity;positive regulation of cytosolic calcium ion concentration;sensory perception of chemical stimulus;positive regulation of vascular endothelial growth factor production;positive regulation of macrophage chemotaxis;cell proliferation in hindbrain;regulation of complement activation;neutrophil chemotaxis;animal organ regeneration;response to peptidoglycan;response to lipopolysaccharide;complement component C5a signaling pathway;mRNA transcription by RNA polymerase II;neutrophil degranulation;negative regulation of neuron apoptotic process;positive regulation of angiogenesis;positive regulation of epithelial cell proliferation;defense response to Gram-positive bacterium;positive regulation of ERK1 and ERK2 cascade;positive regulation of neutrophil chemotaxis
• Cellular component: plasma membrane;integral component of plasma membrane;cell surface;basolateral plasma membrane;secretory granule membrane;apical part of cell
• Molecular function: complement component C5a binding;complement component C5a receptor activity;G protein-coupled receptor activity