FCRL3 Fc receptor like 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: FCRL3provided by HGNC
Official Full Name: Fc receptor like 3provided by HGNC
Primary source: HGNC:HGNC:18506
See related: Ensembl:ENSG00000160856 MIM:606510; AllianceGenome:HGNC:18506
Gene type: protein coding
RefSeq status: REVIEWED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: MAIA; FCRH3; IFGP3; IRTA3; SPAP2; CD307c
Summary: This gene encodes a member of the immunoglobulin receptor superfamily and is one of several Fc receptor-like glycoproteins clustered on the long arm of chromosome 1. The encoded protein contains immunoreceptor-tyrosine activation motifs and immunoreceptor-tyrosine inhibitory motifs in its cytoplasmic domain and may play a role in regulation of the immune system. Mutations in this gene have been associated with rheumatoid arthritis, autoimmune thyroid disease, and systemic lupus erythematosus. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Feb 2016]
Expression: Biased expression in lymph node (RPKM 31.5), spleen (RPKM 20.4) and 2 other tissues See more
Orthologs: all
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Genomic context

Location:: 1q23.1

Exon count:: 17

Annotation release	Status	Assembly	Chr	Location
RS_2025_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (157676481..157700956, complement)
RS_2025_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (156813510..156838030, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (157646271..157670559, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Integrated analyses of single-cell transcriptome and Mendelian randomization reveal the protective role of FCRL3 in multiple sclerosis.
Title: Integrated analyses of single-cell transcriptome and Mendelian randomization reveal the protective role of FCRL3 in multiple sclerosis.
FCRL3 expression is upregulated and closely correlates with TIGIT expression in regulatory T cells of patients with systemic lupus erythematosus.
Title: FCRL3 expression is upregulated and closely correlates with TIGIT expression in regulatory T cells of patients with systemic lupus erythematosus.
No evidence for a direct extracellular interaction between human Fc receptor-like 3 (MAIA) and the sperm ligand IZUMO1.
Title: No evidence for a direct extracellular interaction between human Fc receptor-like 3 (MAIA) and the sperm ligand IZUMO1.
Single nucleotide polymorphisms of Interleukin - 4, Interleukin-18, FCRL3 and sPLA2IIa genes and their association in pathogenesis of endometriosis.
Title: Single nucleotide polymorphisms of Interleukin - 4, Interleukin-18, FCRL3 and sPLA2IIa genes and their association in pathogenesis of endometriosis.
FCRL3 promotes IL-10 expression in B cells through the SHP-1 and p38 MAPK signaling pathways.
Title: FCRL3 promotes IL-10 expression in B cells through the SHP-1 and p38 MAPK signaling pathways.
Expression profile of Fc receptor-like molecules in patients with IgA nephropathy.
Title: Expression profile of Fc receptor-like molecules in patients with IgA nephropathy.
Human Fc Receptor-like 3 Inhibits Regulatory T Cell Function and Binds Secretory IgA.
Title: Human Fc Receptor-like 3 Inhibits Regulatory T Cell Function and Binds Secretory IgA.
Three SNPs of FCRL3 and one SNP of MTMR3 are associated with immunoglobulin A nephropathy risk.
Title: Three SNPs of FCRL3 and one SNP of MTMR3 are associated with immunoglobulin A nephropathy risk.
The results indicate that FCRL3 gene polymorphisms are associated with the development and progression of IgA nephropathy (IgAN) in a Chinese Han population, and the rs11264794-A allele showed a protective role for IgAN due to reduced specific binding between miR-183-5p.1 and FCRL3 3'-untranslated region.
Title: Association of FCRL3 Gene Polymorphisms with IgA Nephropathy in a Chinese Han Population.
This study identified novel single nucleotide polymorphism in FCRL3 and FCRL5 significantly associated with the risk for asthma with comorbid allergic rhinitis in the Chinese population
Title: Genetic risk of FCRL3 and FCRL5 polymorphisms in children with asthma and allergic rhinitis in a Chinese Han population.

Submit: New GeneRIF Correction See all GeneRIFs (83)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

EBI GWAS Catalog

Description
A genome-wide association study identifies two new risk loci for Graves' disease. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetic risk and a primary role for cell-mediated immune mechanisms in multiple sclerosis. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genetics of rheumatoid arthritis contributes to biology and drug discovery. EBI GWAS Catalog EBI GWAS CatalogPubMed
Genome-wide association analysis of autoantibody positivity in type 1 diabetes cases. EBI GWAS Catalog EBI GWAS CatalogPubMed

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D1S3139 (e-PCR)
- UniSTS:12694

AL009767 (e-PCR)
- UniSTS:25081

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables kinase binding	IPI Inferred from Physical Interaction more info	PubMed
enables phosphatase binding	IEA Inferred from Electronic Annotation more info
enables phosphatase binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables transmembrane signaling receptor activity	IBA Inferred from Biological aspect of Ancestor more info

Process	Evidence Code	Pubs
involved_in cell surface receptor signaling pathway	IBA Inferred from Biological aspect of Ancestor more info
involved_in immune response	IBA Inferred from Biological aspect of Ancestor more info
involved_in negative regulation of B cell receptor signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in negative regulation of immunoglobulin production	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of B cell proliferation	IDA Inferred from Direct Assay more info	PubMed
involved_in positive regulation of MAPK cascade	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of B cell activation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of B cell differentiation	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of calcium ion import	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of toll-like receptor 9 signaling pathway	IDA Inferred from Direct Assay more info	PubMed
involved_in single fertilization	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in cell projection	IEA Inferred from Electronic Annotation more info
located_in cell surface	IDA Inferred from Direct Assay more info	PubMed
located_in cell surface	IEA Inferred from Electronic Annotation more info
is_active_in external side of plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in membrane	IEA Inferred from Electronic Annotation more info
located_in microvillus membrane	IEA Inferred from Electronic Annotation more info
located_in plasma membrane	IEA Inferred from Electronic Annotation more info

General protein information

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Preferred Names: Fc receptor-like protein 3

Names: Fc receptor homolog 3; IFGP family protein 3; SH2 domain-containing phosphatase anchor protein 2; fcR-like protein 3; hIFGP3; immune receptor translocation-associated protein 3; immunoglobulin superfamily receptor translocation associated protein 3

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

NG_023241.1 RefSeqGene

Range

5089..29377

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001320333.2 → NP_001307262.1 Fc receptor-like protein 3 isoform 3 precursor

Status: REVIEWED

Description

Transcript Variant: This variant (3) encodes the longer isoform (3).

Source sequence(s)

BC028933, BF514552, HY081176

Consensus CDS

CCDS81385.1

UniProtKB/TrEMBL

B3KUW8

Related

ENSP00000357169.5, ENST00000368186.9

Conserved Domains (4) summary

smart00410
Location:301 → 376

IG_like; Immunoglobulin like

pfam13895
Location:290 → 376

Ig_2; Immunoglobulin domain

pfam13927
Location:475 → 548

Ig_3; Immunoglobulin domain

cl11960
Location:23 → 97

Ig; Immunoglobulin domain
NM_052939.4 → NP_443171.2 Fc receptor-like protein 3 isoform 1 precursor

See identical proteins and their annotated locations for NP_443171.2

Status: REVIEWED

Source sequence(s)

AF459027, AL356276, CD690165

Consensus CDS

CCDS1167.1

UniProtKB/Swiss-Prot

A0N0M4, A8MTH7, D3DVD2, Q5VXZ8, Q8N6S2, Q96LA4, Q96P27, Q96P28, Q96P29, Q96P30, Q96P31

UniProtKB/TrEMBL

B3KUW8

Related

ENSP00000357167.3, ENST00000368184.8

Conserved Domains (4) summary

smart00410
Location:301 → 376

IG_like; Immunoglobulin like

pfam13895
Location:290 → 376

Ig_2; Immunoglobulin domain

pfam13927
Location:475 → 548

Ig_3; Immunoglobulin domain

cl11960
Location:23 → 97

Ig; Immunoglobulin domain

RNA

NR_135214.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (4) uses alternate splice sites in two internal exons, compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF416903, BF514552, HY081176

Related

ENST00000492769.5
NR_135215.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses an alternate splice site in an internal exon, compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF416901, BF514552, HY081176

Related

ENST00000480682.5
NR_135216.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (6) uses alternate splice sites in two internal exons, compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF416905, BF514552, HY081176

Related

ENST00000494724.5
NR_135217.2 RNA Sequence

Status: REVIEWED

Description

Transcript Variant: This variant (7) lacks an internal exon and uses an alternate splice site in an internal exon, compared to variant 3. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AF416902, BF514552, HY081176

Related

ENST00000477837.5

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2025_08

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

157676481..157700956 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_006711145.2 → XP_006711208.1 Fc receptor-like protein 3 isoform X1

See identical proteins and their annotated locations for XP_006711208.1

UniProtKB/Swiss-Prot

A0N0M4, A8MTH7, D3DVD2, Q5VXZ8, Q8N6S2, Q96LA4, Q96P27, Q96P28, Q96P29, Q96P30, Q96P31

UniProtKB/TrEMBL

B3KUW8

Related

ENSP00000540182.1, ENST00000870123.1

Conserved Domains (4) summary

smart00410
Location:301 → 376

IG_like; Immunoglobulin like

pfam13895
Location:290 → 376

Ig_2; Immunoglobulin domain

pfam13927
Location:475 → 548

Ig_3; Immunoglobulin domain

cl11960
Location:23 → 97

Ig; Immunoglobulin domain

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

156813510..156838030 complement

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054334160.1 → XP_054190135.1 Fc receptor-like protein 3 isoform X1

UniProtKB/TrEMBL

B3KUW8

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

NM_001024667.1: Suppressed sequence

Description

NM_001024667.1: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.