CLEC1B

C-type lectin domain family 1 member B, the group of C-type lectin domain containing

Basic information

Region (hg38): 12:9985642-10013424

Links

ENSG00000165682

∙ NCBI:51266 ∙ OMIM:606783 ∙ HGNC:24356 ∙ Uniprot:Q9P126 ∙ 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 CLEC1B gene.

not_specified (50 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC1B gene is commonly pathogenic or not. These statistics are base on transcript: NM_000016509.4. Only rare variants are included in the table.

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.

Effect	PathogenicP	Likely pathogenicLP	VUSVUS	Likely benignLB	BenignB	Sum
synonymous						0
missense			45 clinvar	5 clinvar		50
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	45	5	0

Loading clinvar variants...

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC1B	protein_coding	protein_coding	ENST00000298527	6	27783

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
4.94e-8	0.229	124958	0	33	124991	0.000132

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.725	154	131	1.18	0.00000730	1504
Missense in Polyphen		28	39.802	0.70348		453
Synonymous	-2.56	67	45.1	1.49	0.00000233	403
Loss of Function	0.358	12	13.4	0.894	5.71e-7	157

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000526	0.000526
Ashkenazi Jewish	0.00	0.00
East Asian	0.000277	0.000275
Finnish	0.0000466	0.0000463
European (Non-Finnish)	0.000106	0.000106
Middle Eastern	0.000277	0.000275
South Asian	0.0000980	0.0000980
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: C-type lectin-like receptor that functions as a platelet receptor for the lymphatic endothelial marker, PDPN (PubMed:18215137). After ligand activation, signals via sequential activation of SRC and SYK tyrosine kinases leading to activation of PLCG2 (PubMed:18955485). {ECO:0000269|PubMed:18215137, ECO:0000269|PubMed:18955485}.; FUNCTION: (Microbial infection) Acts as an attachment factor for Human immunodeficiency virus type 1 (HIV-1) and facilitates its capture by platelets (PubMed:16940507). {ECO:0000305|PubMed:16940507}.;
Pathway: C-type lectin receptor signaling pathway - Homo sapiens (human);GPVI-mediated activation cascade;Platelet activation, signaling and aggregation;Hemostasis (Consensus)

Recessive Scores

pRec: 0.0990

Intolerance Scores

loftool: 0.763
rvis_EVS: 0.68
rvis_percentile_EVS: 85.04

Haploinsufficiency Scores

pHI: 0.0980
hipred: N
hipred_score: 0.112
ghis: 0.405

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.179

Gene Damage Prediction

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

Mouse Genome Informatics

Gene name: Clec1b
Phenotype: immune system phenotype; digestive/alimentary phenotype; nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); cardiovascular system phenotype (the observable morphological and physiological characteristics of the mammalian heart, blood vessels, or circulatory system that are manifested through development and lifespan); hematopoietic system phenotype; reproductive system phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); respiratory system phenotype; homeostasis/metabolism phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan);

Gene ontology

Biological process: defense response;cell surface receptor signaling pathway;signal transduction by protein phosphorylation;platelet activation;platelet formation
Cellular component: plasma membrane;integral component of plasma membrane
Molecular function: transmembrane signaling receptor activity;protein binding;carbohydrate binding