CLEC10A

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

Basic information

Region (hg38): 17:7074537-7080307

Previous symbols: [ "CLECSF13", "CLECSF14" ]

Links

ENSG00000132514 ∙ NCBI:10462 ∙ OMIM:605999 ∙ HGNC:16916 ∙ Uniprot:Q8IUN9 ∙ 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 CLEC10A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC10A 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			12	1	2	15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	12	1	2

Variants in CLEC10A

This is a list of pathogenic ClinVar variants found in the CLEC10A region.

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

Position	Type	Phenotype	Significance	ClinVar
17-7075139-C-G		not specified	Uncertain significance (May 23, 2024)
17-7075152-A-G		not specified	Uncertain significance (Jul 19, 2022)
17-7075164-C-T		not specified	Uncertain significance (Jul 14, 2023)
17-7075432-G-A		not specified	Uncertain significance (May 06, 2024)
17-7075747-T-C		not specified	Uncertain significance (Nov 12, 2021)
17-7075766-C-T		not specified	Uncertain significance (Jul 25, 2023)
17-7075798-G-C			Benign (Jun 21, 2018)
17-7075808-T-A		not specified	Uncertain significance (May 24, 2023)
17-7075850-C-T		not specified	Uncertain significance (Jan 19, 2022)
17-7076012-A-G			Benign (Jun 21, 2018)
17-7076098-G-A		not specified	Uncertain significance (Dec 21, 2022)
17-7076105-G-A		not specified	Uncertain significance (Jun 30, 2022)
17-7076132-G-A		not specified	Uncertain significance (Feb 22, 2023)
17-7076150-C-A		not specified	Uncertain significance (Dec 12, 2023)
17-7076919-C-T		not specified	Uncertain significance (Jun 17, 2024)
17-7076933-G-A		not specified	Uncertain significance (Mar 15, 2024)
17-7078083-C-T		not specified	Likely benign (May 03, 2023)
17-7078806-T-C		not specified	Uncertain significance (Jul 26, 2022)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC10A	protein_coding	protein_coding	ENST00000254868	8	5771

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000776	0.757	125666	0	81	125747	0.000322

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.359	154	167	0.922	0.00000864	2068
Missense in 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

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00107	0.00107
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.000185	0.000185
European (Non-Finnish)	0.000158	0.000158
Middle Eastern	0.000435	0.000435
South Asian	0.000392	0.000392
Other	0.000326	0.000326

dbNSFP

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}.
• Pathway: Ebola Virus Pathway on Host;Ebola Virus Pathway on Host;Dectin-2 family;C-type lectin receptors (CLRs);Innate Immune System;Immune System (Consensus)

Recessive Scores

• pRec: 0.110

Intolerance Scores

• loftool: 0.959
• rvis_EVS: 1.22
• rvis_percentile_EVS: 93.16

Haploinsufficiency Scores

• pHI: 0.0573
• 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: 0.0908

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Mgl2
• Phenotype: homeostasis/metabolism phenotype; immune system phenotype; hematopoietic system phenotype

Gene ontology

• Biological process: stimulatory C-type lectin receptor signaling pathway;adaptive immune response;endocytosis;innate immune response
• Cellular component: plasma membrane;integral component of membrane
• Molecular function: carbohydrate binding