CLEC4F

protein-coding

C-type lectin domain family 4 member F, the group of C-type lectin domain containing

Gene summary

Predicted to enable galactose binding activity; glycolipid binding activity; and pattern recognition receptor activity. Predicted to be involved in immune response. Predicted to act upstream of or within NK T cell activation. Predicted to be located in plasma membrane. Predicted to be active in external side of plasma membrane. [provided by Alliance of Genome Resources, Jul 2025]

Previous symbols:

CLECSF13

MANE transcript

NM_173535.3

Inheritance

—

ClinVar variants

U:81B:16

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.92

Max pathogenic AF

—

Genomic locus

chr2:70,808,643-70,820,599

External References & Databases

Ensembl (ENSG00000152672)

Transcript & Mutation Effects

hg38 • Region Span ~12.0 kb

Loading mutation effect viewer...

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 CLEC4F variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 90

not providedTotal: 4

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_173535.3. 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						0
missense			80 clinvar	14 clinvar	2 clinvar	96
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	81	14	2	97

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_173535.3	RefSeq	NP_775806.2	7	MANE Select
ENST00000272367.7	Ensembl	ENSP00000272367.2	7	MANE Select
NM_001258027.2	RefSeq	NP_001244956.1	7	Standard
NM_001321308.2	RefSeq	NP_001308237.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Biological Process

endocytosis

Molecular Function

carbohydrate binding

Cellular Component

integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000272367
Coding exons: 7
Length: 11958
Individuals with no LoFs: 125693
Homozygous LoFs: 1
Heterozygous LoFs: 54
Defined: 125748
p: 0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.257	319	306	1.04	0.0000150	3902
Missense (PolyPhen)		42	50.833	0.82624		780
Synonymous	0.139	118	120	0.984	0.00000661	1092
Loss of Function	0.386	22	24.0	0.915	0.00000121	283

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00062	0.00062	rare
Latino/Admixed American	0.00017	0.00017	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00060	0.00060	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.00013	0.00012	rare
South Asian	0.00050	0.00046	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Receptor with an affinity for galactose and fucose. Could be involved in endocytosis (By similarity). {ECO:0000250}.;

Recessive Scores

pRec: 0.0855

Intolerance Scores

LoFtool: 0.919
RVIS EVS: 3.14
RVIS percentile EVS: 99.29

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0443

Gene Damage Prediction

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