GeneBe

FCRL3

Fc receptor like 3, the group of Fc receptors|Immunoglobulin like domain containing|CD molecules

Basic information

Region (hg38): 1:157674321-157700769

Links

ENSG00000160856 ∙ NCBI:115352 ∙ OMIM:606510 ∙ HGNC:18506 ∙ Uniprot:Q96P31 ∙ 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 FCRL3 gene.

  • not_specified (108 variants)
  • not_provided (5 variants)
  • EBV-positive_nodal_T-_and_NK-cell_lymphoma (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the FCRL3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_000052939.4. Only rare variants are included in the table.

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.

EffectPLPVUSLBBSum
synonymous
1
clinvar
 1
missense
97
clinvar
14
clinvar
2
clinvar
 113
nonsense
0
start loss
0
frameshift
0
splice donor/acceptor (+/-2bp)
0
Total 0 0 97 14 3
Loading clinvar variants...

GnomAD

Source: gnomAD

GeneTypeBio TypeTranscript Coding Exons Length
FCRL3protein_codingprotein_codingENST00000368184 1426537
pLI Probability
LOF Intolerant 		pRec Probability
LOF Recessive 		Individuals with
no LOFs 		Individuals with
Homozygous LOFs 		Individuals with
Heterozygous LOFs 		Defined p
5.97e-210.0030912561201361257480.000541
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense-1.174533881.170.00001974729
Missense in Polyphen131110.381.18681476
Synonymous-1.141801611.110.000009081503
Loss of Function0.2553233.60.9530.00000172392

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.001770.00176
Ashkenazi Jewish0.0009930.000993
East Asian0.0002180.000217
Finnish0.000.00
European (Non-Finnish)0.0001240.000123
Middle Eastern0.0002180.000217
South Asian0.002410.00232
Other0.000.00

dbNSFP

Source: dbNSFP

Function
FUNCTION: Promotes TLR9-induced B-cell proliferation, activation and survival but inhibits antibody production and suppresses plasma cell differentiation. Enhances activation of NF-kappa-B and MAPK signaling pathways in TLR9 stimulated B-cells (PubMed:23857366). Has inhibitory potentional on B-cell receptor (BCR)-mediated signaling, possibly through association with SH2 domain-containing phosphatases. Inhibits cell tyrosine phosphorylation, calcium mobilization and activation-induced cell death induced through BCR signaling (PubMed:19843936). Regulatory T-cells expressing FCRL3 exhibit a memory phenotype, are relatively nonresponsive to antigenic stimulation in presence of IL2 and have reduced capacity to suppress the proliferation of effector T-cells (PubMed:20190142, PubMed:19494275). {ECO:0000269|PubMed:19494275, ECO:0000269|PubMed:19843936, ECO:0000269|PubMed:20190142, ECO:0000269|PubMed:23857366}.;
Disease
DISEASE: Rheumatoid arthritis (RA) [MIM:180300]: An inflammatory disease with autoimmune features and a complex genetic component. It primarily affects the joints and is characterized by inflammatory changes in the synovial membranes and articular structures, widespread fibrinoid degeneration of the collagen fibers in mesenchymal tissues, and by atrophy and rarefaction of bony structures. {ECO:0000269|PubMed:15838509, ECO:0000269|PubMed:16176992, ECO:0000269|PubMed:16476711, ECO:0000269|PubMed:16859508, ECO:0000269|PubMed:17133579, ECO:0000269|PubMed:17179172, ECO:0000269|PubMed:17763442, ECO:0000269|PubMed:22392608, ECO:0000269|PubMed:26746625}. Note=Disease susceptibility is associated with variations affecting the gene represented in this entry.; DISEASE: Note=Genetic variation in FCRL3 may influence susceptibility to autoimmune disorders, including Graves disease or multiple sclerosis. Graves disease is an autoimmune disorder associated with overactivity of the thyroid gland and hyperthyroidism. Multiple sclerosis is an autoimmune/inflammatory neurodegenerative disease which mainly affects young adults and is characterized by destruction of myelin in the central nervous system. {ECO:0000269|PubMed:15838509, ECO:0000269|PubMed:16384851, ECO:0000269|PubMed:17952073, ECO:0000269|PubMed:25862376, ECO:0000269|PubMed:26629249}.;
Pathway
TCR (Consensus)

Intolerance Scores

loftool
0.949
rvis_EVS
1.25
rvis_percentile_EVS
93.48

Haploinsufficiency Scores

pHI
0.110
hipred
N
hipred_score
0.112
ghis
0.440

Essentials

essential_gene_CRISPR
N
essential_gene_CRISPR2
N
essential_gene_gene_trap
N
gene_indispensability_pred
N
gene_indispensability_score
0.199

Gene Damage Prediction

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

Gene ontology

Biological process
negative regulation of immunoglobulin production;positive regulation of B cell proliferation;regulation of toll-like receptor 9 signaling pathway;positive regulation of MAPK cascade;regulation of B cell differentiation;negative regulation of B cell receptor signaling pathway;regulation of B cell activation;regulation of calcium ion import;positive regulation of protein serine/threonine phosphatase activity
Cellular component
plasma membrane;cell surface;integral component of membrane
Molecular function
kinase binding;phosphatase binding;protein phosphatase binding;protein tyrosine kinase binding