CLEC10A

protein-coding

C-type lectin domain containing 10A, the group of C-type lectin domain containing|CD molecules

Gene summary

This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signalling, glycoprotein turnover, and roles in inflammation and immune response. The encoded type 2 transmembrane protein may function as a cell surface antigen. Two transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

Previous symbols:

CLECSF13
CLECSF14

MANE transcript

NM_001330070.2

Inheritance

—

ClinVar variants

U:27B:6

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.67

Max pathogenic AF

—

Genomic locus

chr17:7,074,537-7,080,307

External References & Databases

Ensembl (ENSG00000132514)

Transcript & Mutation Effects

hg38 • Region Span ~5.8 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 CLEC10A variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 34

not providedTotal: 2

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_001330070.2. 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			25 clinvar	5 clinvar	1 clinvar	31
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)			1 clinvar			1
Total	0	0	27	5	1	33

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 35 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_001330070.2	RefSeq	NP_001316999.1	8	MANE Select
ENST00000416562.7	Ensembl	ENSP00000414938.2	8	MANE Select
NM_006344.4	RefSeq	NP_006335.2	8	Standard
NM_182906.4	RefSeq	NP_878910.1	8	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Ebola Virus Pathway on Host
Ebola Virus Pathway on Host
Dectin-2 family
C-type lectin receptors (CLRs)
Innate Immune System

Biological Process

stimulatory C-type lectin receptor signaling pathway
adaptive immune response
endocytosis
innate immune response

Molecular Function

carbohydrate binding

Cellular Component

plasma membrane
integral component of membrane

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000254868
Coding exons: 8
Length: 5771
Individuals with no LoFs: 125666
Homozygous LoFs: 0
Heterozygous LoFs: 81
Defined: 125747
p: 0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	0.359	154	167	0.922	0.00000864	2068
Missense (PolyPhen)		40	41.806	0.95681		587
Synonymous	0.926	64	74.1	0.863	0.00000459	602
Loss of Function	1.18	10	14.9	0.670	7.24e-7	164

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.0011	0.0011	notable
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00043	0.00044	rare
Finnish	0.00019	0.00018	rare
European (Non-Finnish)	0.00016	0.00016	rare
South Asian	0.00039	0.00039	rare
Other	0.00033	0.00033	rare

dbNSFP Gene Annotations

Source: dbNSFP

Function: FUNCTION: Probable role in regulating adaptive and innate immune responses. Binds in a calcium-dependent manner to terminal galactose and N-acetylgalactosamine units, linked to serine or threonine. These sugar moieties are known as Tn-Ag and are expressed in a variety of carcinoma cells. {ECO:0000269|PubMed:8598452}.;

Recessive Scores

pRec: 0.110

Intolerance Scores

LoFtool: 0.959
RVIS EVS: 1.22
RVIS percentile EVS: 93.16

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0908

Gene Damage Prediction

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