FCRL1
protein-codingFc receptor like 1, the group of CD molecules|Immunoglobulin like domain containing|Fc receptors
Gene 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 three extracellular C2-like immunoglobulin domains, a transmembrane domain and a cytoplasmic domain with two immunoreceptor-tyrosine activation motifs. This protein may play a role in the regulation of cancer cell growth. Alternative splicing results in multiple transcript variants. [provided by RefSeq, Apr 2009]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~27.9 kbGenCC 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 FCRL1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_052938.5. 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 | 2 | 3 | |||
| missense | 48 | 3 | 51 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 49 | 5 | 0 | 54 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_443170.1 | 11 | MANE Select | |
| Ensembl | ENSP00000357158.3 | 11 | MANE Select | |
| RefSeq | NP_001152869.1 | 10 | Standard | |
| RefSeq | NP_001152870.1 | 11 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- B cell activation
Molecular Function
- coreceptor activity
Cellular Component
- plasma membrane
- cell surface
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000368176
- Coding exons
- 11
- Length
- 25703
- Individuals with no LoFs
- 125628
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 111
- Defined
- 125739
- p
- 0.000441
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.0643 | 234 | 237 | 0.988 | 0.0000123 | 2755 |
| Missense (PolyPhen) | 47 | 59.224 | 0.79359 | 794 | ||
| Synonymous | -1.17 | 110 | 95.5 | 1.15 | 0.00000521 | 867 |
| Loss of Function | 1.87 | 12 | 21.3 | 0.563 | 9.06e-7 | 264 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00012 | 0.00012 | rare |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.0010 | 0.0010 | notable |
| European (Non-Finnish) | 0.00066 | 0.00065 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00098 | 0.00098 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May function as an activating coreceptor in B-cells. May function in B-cells activation and differentiation. {ECO:0000269|PubMed:15479727}.;
Recessive Scores
- pRec
- 0.0890
Intolerance Scores
- LoFtool
- 0.740
- RVIS EVS
- 0.64
- RVIS percentile EVS
- 84.1
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- S
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0785
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |