CLEC17A

protein-coding

C-type lectin domain containing 17A, the group of C-type lectin domain containing

Gene summary

Enables D-mannose binding activity; fucose binding activity; and identical protein binding activity. Predicted to be involved in immune response. Located in cell surface. [provided by Alliance of Genome Resources, Jul 2025]

MANE transcript

NM_001204118.2

Inheritance

—

ClinVar variants

U:45B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.61

Max pathogenic AF

—

Genomic locus

chr19:14,583,084-14,612,035

External References & Databases

Ensembl (ENSG00000187912)

Transcript & Mutation Effects

hg38 • Region Span ~29.0 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 CLEC17A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 46

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001204118.2. 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			43 clinvar	6 clinvar		49
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			2 clinvar			2
Total	0	0	45	6	0	51

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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_001204118.2	RefSeq	NP_001191047.1	14	MANE Select
ENST00000417570.6	Ensembl	ENSP00000393719.2	14	MANE Select
NM_207390.4	RefSeq	NP_997273.3	13	Standard
ENST00000339847.9	Ensembl	ENSP00000341620.5	12	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Molecular Function

mannose binding
fucose binding
metal ion binding

Cellular Component

cell surface
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000417570
Coding exons: 14
Length: 28074
Individuals with no LoFs: 124080
Homozygous LoFs: 6
Heterozygous LoFs: 554
Defined: 124640
p: 0.00225

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.880	162	197	0.823	0.0000100	2457
Missense (PolyPhen)		35	56.281	0.62188		763
Synonymous	1.80	50	69.0	0.725	0.00000332	679
Loss of Function	1.79	15	24.6	0.611	0.00000131	286

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00014	0.00013	rare
Latino/Admixed American	0.015	0.014	notable
Ashkenazi Jewish	0.00011	0.000099	rare
East Asian	0.0022	0.0021	notable
Finnish	0.00070	0.00070	rare
European (Non-Finnish)	0.000062	0.000062	rare
South Asian	0.000066	0.000065	rare
Other	0.0010	0.00099	notable

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Cell surface receptor which may be involved in carbohydrate-mediated communication between cells in the germinal center. Binds glycans with terminal alpha-linked mannose or fucose residues. {ECO:0000269|PubMed:19419970}.;

Intolerance Scores

LoFtool: 0.695
RVIS EVS: 0.13
RVIS percentile EVS: 63

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.138

Gene Damage Prediction

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