CLEC2B

C-type lectin domain family 2 member B, the group of C-type lectin domain containing

Basic information

Region (hg38): 12:9852369-9869386

Previous symbols: [ "CLECSF2" ]

Links

ENSG00000110852 ∙ NCBI:9976 ∙ OMIM:603242 ∙ HGNC:2053 ∙ Uniprot:Q92478 ∙ 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 CLEC2B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC2B 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			11	1		12
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	11	1	0

Variants in CLEC2B

This is a list of pathogenic ClinVar variants found in the CLEC2B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-9853311-T-C		not specified	Uncertain significance (Nov 08, 2024)
12-9853316-C-T		not specified	Uncertain significance (Nov 08, 2024)
12-9853391-C-T		not specified	Likely benign (Feb 15, 2023)
12-9854422-A-T		not specified	Uncertain significance (May 04, 2023)
12-9854433-T-C		not specified	Uncertain significance (Aug 11, 2024)
12-9854450-T-C		not specified	Uncertain significance (Dec 17, 2024)
12-9854472-G-A		not specified	Uncertain significance (Mar 21, 2024)
12-9857480-T-G		not specified	Uncertain significance (Mar 23, 2023)
12-9857493-A-G		not specified	Uncertain significance (Jul 09, 2021)
12-9857553-T-A		not specified	Uncertain significance (Dec 02, 2022)
12-9857553-T-C		not specified	Uncertain significance (Jan 29, 2024)
12-9857579-G-T		not specified	Uncertain significance (Apr 11, 2023)
12-9857602-A-G		not specified	Uncertain significance (Dec 03, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC2B	protein_coding	protein_coding	ENST00000228438	4	17153

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0116	0.857	124139	0	6	124145	0.0000242

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.601	63	77.9	0.808	0.00000387	987
Missense in Polyphen		13	18.872	0.68884		240
Synonymous	1.72	14	24.9	0.562	0.00000133	251
Loss of Function	1.23	4	7.69	0.520	4.86e-7	82

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.0000464	0.0000464
European (Non-Finnish)	0.0000178	0.0000178
Middle Eastern	0.00	0.00
South Asian	0.0000662	0.0000662
Other	0.000166	0.000166

dbNSFP

Source: dbNSFP

• Pathway: Kaposi,s sarcoma-associated herpesvirus infection - Homo sapiens (human);Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

• pRec: 0.148

Intolerance Scores

• loftool: 0.753
• rvis_EVS: 0.17
• rvis_percentile_EVS: 65.33

Haploinsufficiency Scores

• pHI: 0.0631
• hipred: N
• hipred_score: 0.146
• ghis: 0.416

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.307

Gene Damage Prediction

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

Gene ontology

• Biological process: regulation of immune response
• Cellular component: plasma membrane;integral component of plasma membrane
• Molecular function: carbohydrate binding;identical protein binding