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.

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.

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			26			26
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding			2			2
Total	0	0	28	0	0

Variants in CLEC1B

This is a list of pathogenic ClinVar variants found in the CLEC1B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-9993168-A-T		not specified	Uncertain significance (Nov 17, 2022)
12-9993258-T-A		not specified	Uncertain significance (Feb 23, 2023)
12-9993267-C-G		not specified	Uncertain significance (Oct 27, 2023)
12-9995176-C-G		not specified	Uncertain significance (May 27, 2022)
12-9996882-A-C		not specified	Uncertain significance (Dec 02, 2022)
12-9996905-T-C		not specified	Uncertain significance (Dec 26, 2023)
12-9996925-T-C		not specified	Uncertain significance (Apr 27, 2022)
12-9996931-C-G		not specified	Uncertain significance (Sep 20, 2023)
12-9996943-T-A		not specified	Uncertain significance (Jan 03, 2024)
12-9996964-C-T		not specified	Uncertain significance (Mar 01, 2024)
12-9996998-C-A		not specified	Uncertain significance (Aug 28, 2023)
12-9997193-C-G		not specified	Likely benign (Mar 28, 2024)
12-9997202-A-T		not specified	Uncertain significance (Jun 09, 2022)
12-9997207-C-A		not specified	Uncertain significance (Jan 24, 2024)
12-9997207-C-T		not specified	Uncertain significance (Jun 17, 2024)
12-9997215-T-A		not specified	Uncertain significance (Sep 22, 2023)
12-9997220-G-C		not specified	Uncertain significance (Oct 25, 2023)
12-9997235-T-C		not specified	Uncertain significance (Dec 19, 2023)
12-9997238-G-C		not specified	Uncertain significance (Mar 07, 2023)
12-9997249-T-C		not specified	Uncertain significance (Dec 21, 2023)
12-9997256-G-T		not specified	Uncertain significance (Jul 13, 2022)
12-9997259-G-C		not specified	Uncertain significance (Mar 28, 2024)
12-9997262-A-G		not specified	Uncertain significance (Oct 12, 2022)
12-9998309-C-A		not specified	Uncertain significance (Jan 03, 2024)
12-9998317-C-A		not specified	Uncertain significance (Mar 01, 2023)

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