CLEC4F

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

Basic information

Region (hg38): 2:70808643-70820599

Previous symbols: [ "CLECSF13" ]

Links

ENSG00000152672 ∙ NCBI:165530 ∙ OMIM:620105 ∙ HGNC:25357 ∙ Uniprot:Q8N1N0 ∙ 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 CLEC4F gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC4F gene is commonly pathogenic or not.

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			38	6	4	48
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	38	6	4

Variants in CLEC4F

This is a list of pathogenic ClinVar variants found in the CLEC4F region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-70809332-G-A		not specified	Uncertain significance (Jun 07, 2023)
2-70809341-A-G		not specified	Uncertain significance (Dec 21, 2023)
2-70809349-C-A		not specified	Uncertain significance (Jul 17, 2023)
2-70809351-T-C		not specified	Uncertain significance (Nov 08, 2022)
2-70809362-C-T		not specified	Uncertain significance (Feb 04, 2025)
2-70809369-C-T		not specified	Uncertain significance (Jul 02, 2024)
2-70809745-T-C		not specified	Likely benign (Feb 25, 2025)
2-70809799-C-T			Benign (Mar 27, 2018)
2-70809801-C-G		not specified	Uncertain significance (Nov 09, 2023)
2-70809821-A-G		not specified	Uncertain significance (May 27, 2022)
2-70809836-T-C		not specified	Likely benign (Jun 24, 2022)
2-70809839-T-C		not specified	Uncertain significance (Dec 16, 2021)
2-70812476-G-T		not specified	Uncertain significance (Mar 02, 2023)
2-70812523-T-C		not specified	Uncertain significance (Sep 27, 2021)
2-70812571-C-T		not specified	Uncertain significance (Nov 05, 2021)
2-70816033-C-G		not specified	Uncertain significance (Jul 14, 2024)
2-70816050-C-A		not specified	Uncertain significance (Sep 13, 2023)
2-70816060-C-T		not specified	Uncertain significance (May 31, 2022)
2-70816176-G-C		not specified	Uncertain significance (Jan 24, 2023)
2-70816194-C-T		not specified	Likely benign (Dec 26, 2023)
2-70816233-A-G		not specified	Uncertain significance (Mar 18, 2024)
2-70816275-A-G			Benign (Mar 27, 2018)
2-70816285-T-C		not specified	Uncertain significance (Jan 08, 2024)
2-70816288-C-G		not specified	Uncertain significance (May 01, 2024)
2-70816417-C-T		not specified	Uncertain significance (Feb 24, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC4F	protein_coding	protein_coding	ENST00000272367	7	11958

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
3.07e-14	0.0389	125693	1	54	125748	0.000219

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.257	319	306	1.04	0.0000150	3902
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000790	0.000789
Ashkenazi Jewish	0.00	0.00
East Asian	0.000598	0.000598
Finnish	0.00	0.00
European (Non-Finnish)	0.000127	0.000123
Middle Eastern	0.000598	0.000598
South Asian	0.000496	0.000457
Other	0.00	0.00

dbNSFP

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

Haploinsufficiency Scores

• pHI: 0.0534
• hipred: N
• hipred_score: 0.112

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0443

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec4f
• Phenotype: immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: endocytosis
• Cellular component: integral component of membrane
• Molecular function: carbohydrate binding