FCRL5

protein-coding

Fc receptor like 5, the group of Fc receptors|Immunoglobulin like domain containing|CD molecules

Gene summary

This gene encodes a member of the immunoglobulin receptor superfamily and the Fc-receptor like family. This gene and several other Fc receptor-like gene members are clustered on the long arm of chromosome 1. The encoded protein is a single-pass type I membrane protein and contains 8 immunoglobulin-like C2-type domains. This gene is implicated in B cell development and lymphomagenesis. Alternatively spliced transcript variants encoding different isoforms have been identified. [provided by RefSeq, Sep 2010]

MANE transcript

NM_031281.3

Inheritance

—

ClinVar variants

U:133B:27

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.78

Max pathogenic AF

—

Genomic locus

chr1:157,513,377-157,552,515

External References & Databases

Ensembl (ENSG00000143297)

Transcript & Mutation Effects

hg38 • Region Span ~39.1 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 FCRL5 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 141

not providedTotal: 9

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_031281.3. 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			4 clinvar	3 clinvar	3 clinvar	10
missense			127 clinvar	18 clinvar	3 clinvar	148
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	133	21	6	160

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 16 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_031281.3	RefSeq	NP_112571.2	17	MANE Select
ENST00000361835.8	Ensembl	ENSP00000354691.3	17	MANE Select
NM_001195388.2	RefSeq	NP_001182317.1	17	Standard
ENST00000368189.3	Ensembl	ENSP00000357172.3	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Cellular Component

plasma membrane
cell surface
integral component of membrane
receptor complex

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000361835
Coding exons: 17
Length: 39144
Individuals with no LoFs: 125553
Homozygous LoFs: 0
Heterozygous LoFs: 195
Defined: 125748
p: 0.000776

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.611	486	525	0.925	0.0000281	6224
Missense (PolyPhen)		125	157.27	0.79479		2121
Synonymous	-0.0146	216	216	1.00	0.0000117	2068
Loss of Function	1.24	30	38.3	0.784	0.00000163	490

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00012	0.00012	rare
Latino/Admixed American	0.00020	0.00020	rare
Ashkenazi Jewish	0.0012	0.0011	notable
East Asian	0.00038	0.00038	rare
Finnish	0.0029	0.0029	notable
European (Non-Finnish)	0.00076	0.00076	rare
South Asian	0.00024	0.00023	rare
Other	0.0022	0.0021	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: May be involved in B-cell development and differentiation in peripheral lymphoid organs and may be useful markers of B-cell stages. May have an immunoregulatory role in marginal zone B-cells. {ECO:0000269|PubMed:11453668}.;
Disease: DISEASE: Note=A chromosomal aberration involving FCRL5 has been found in cell lines with 1q21 abnormalities derived from Burkitt lymphoma. Duplication dup(1)(q21q32). {ECO:0000269|PubMed:11290337}.;

Intolerance Scores

LoFtool: 0.911
RVIS EVS: 2.27
RVIS percentile EVS: 98.25

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.115

Gene Damage Prediction

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