C3AR1

protein-coding

complement C3a receptor 1, the group of Complement system regulators and receptors|Complement component GPCRs

Gene summary

C3a is an anaphylatoxin released during activation of the complement system. The protein encoded by this gene is an orphan G protein-coupled receptor for C3a. Binding of C3a by the encoded receptor activates chemotaxis, granule enzyme release, superoxide anion production, and bacterial opsonization. [provided by RefSeq, May 2016]

MANE transcript

NM_004054.4

Inheritance

—

ClinVar variants

P:1U:72B:16

Top phenotype

C3AR1-related disorder

gnomAD constraint

pLI —, LoF o/e 1.01

Max pathogenic AF

—

Genomic locus

chr12:8,056,844-8,066,359

External References & Databases

Ensembl (ENSG00000171860)

Transcript & Mutation Effects

hg38 • Region Span ~9.5 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 C3AR1 variants in ClinVar

5 Conditions Cataloged

not specifiedTotal: 75

C3AR1-related disorderTotal: 10

not providedTotal: 8

Prostate cancerTotal: 1

Hemolytic uremic syndrome, atypical, susceptibility to, 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_004054.4. 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			1 clinvar	11 clinvar		12
missense			69 clinvar	4 clinvar	1 clinvar	74
nonsense						0
start loss						0
frameshift		1 clinvar	2 clinvar			3
splice donor/acceptor (+/-2bp)						0
Total	0	1	72	15	1	89

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 12 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_004054.4	RefSeq	NP_004045.1	1	MANE Select
ENST00000307637.5	Ensembl	ENSP00000302079.4	1	MANE Select
NM_001326475.2	RefSeq	NP_001313404.1	1	Standard
NM_001326477.2	RefSeq	NP_001313406.1	1	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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

Biological Process

complement receptor mediated signaling pathway
chemotaxis
inflammatory response
G protein-coupled receptor signaling pathway
phospholipase C-activating G protein-coupled receptor signaling pathway

Molecular Function

complement component C3a receptor activity
G protein-coupled receptor activity

Cellular Component

plasma membrane
integral component of plasma membrane
azurophil granule membrane
specific granule membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000307637
Coding exons: 1
Length: 8170
Individuals with no LoFs: 125628
Homozygous LoFs: 0
Heterozygous LoFs: 119
Defined: 125747
p: 0.000473

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.302	279	265	1.05	0.0000137	3159
Missense (PolyPhen)		91	84.495	1.077		1013
Synonymous	0.712	96	105	0.912	0.00000576	1002
Loss of Function	-0.0184	13	12.9	1.01	7.02e-7	137

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0.00040	0.00040	rare
East Asian	0.00016	0.00016	rare
Finnish	0.000046	0.000046	rare
European (Non-Finnish)	0.00072	0.00072	rare
South Asian	0.00039	0.00039	rare
Other	0.00049	0.00049	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Receptor for the chemotactic and inflammatory peptide anaphylatoxin C3a. This receptor stimulates chemotaxis, granule enzyme release and superoxide anion production.;

Recessive Scores

pRec: 0.0995

Intolerance Scores

LoFtool: 0.743
RVIS EVS: -0.29
RVIS percentile EVS: 33.34

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0116

Gene Damage Prediction

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