FCRL6

protein-coding

Fc receptor like 6, the group of Immunoglobulin like domain containing|Fc receptors

Gene summary

Enables MHC class II protein binding activity and protein phosphatase binding activity. Predicted to be involved in cell surface receptor signaling pathway and immune response. Located in external side of plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001004310.3

Inheritance

—

ClinVar variants

U:80B:12

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 1.34

Max pathogenic AF

—

Genomic locus

chr1:159,800,511-159,816,257

External References & Databases

Ensembl (ENSG00000181036)

Transcript & Mutation Effects

hg38 • Region Span ~15.7 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 FCRL6 variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 80

not providedTotal: 6

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001004310.3. 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			2 clinvar	1 clinvar	2 clinvar	5
missense			74 clinvar	7 clinvar	2 clinvar	83
nonsense						0
start loss						0
frameshift			2 clinvar			2
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	80	8	4	92

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 18 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001004310.3	RefSeq	NP_001004310.2	10	MANE Select
ENST00000368106.4	Ensembl	ENSP00000357086.3	10	MANE Select
NM_001284217.2	RefSeq	NP_001271146.1	11	Standard
NM_001426231.1	RefSeq	NP_001413160.1	11	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

protein binding
phosphatase binding
protein phosphatase binding
MHC class II protein binding

Cellular Component

plasma membrane
external side of plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000368106
Coding exons: 10
Length: 15741
Individuals with no LoFs: 125702
Homozygous LoFs: 0
Heterozygous LoFs: 45
Defined: 125747
p: 0.000179

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-1.55	299	232	1.29	0.0000112	2784
Missense (PolyPhen)		64	52.893	1.21		723
Synonymous	-2.44	124	94.0	1.32	0.00000500	892
Loss of Function	-1.49	30	22.4	1.34	0.00000104	245

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.00012	0.00012	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00072	0.00071	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00018	0.00018	rare
South Asian	0.00010	0.000098	rare
Other	0.00066	0.00065	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Acts as a MHC class II receptor (PubMed:20519654). When stimulated on its own, does not play a role in cytokine production or the release of cytotoxic granules by NK cells and cytotoxic CD8(+) T cells (PubMed:17213291, PubMed:18991291). Does not act as an Fc receptor (PubMed:18991291). {ECO:0000269|PubMed:17213291, ECO:0000269|PubMed:18991291, ECO:0000269|PubMed:20519654}.;

Recessive Scores

pRec: 0.0735

Intolerance Scores

LoFtool: 0.957
RVIS EVS: 0.27
RVIS percentile EVS: 70.69

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0508

Gene Damage Prediction

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