CLEC2D

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

Basic information

Region (hg38): 12:9664969-9699553

Links

ENSG00000069493

∙ NCBI:29121 ∙ OMIM:605659 ∙ HGNC:14351 ∙ Uniprot:Q9UHP7 ∙ 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 CLEC2D gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC2D 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			2 clinvar			2
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	2	0	0

Variants in CLEC2D

This is a list of pathogenic ClinVar variants found in the CLEC2D region.

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

Position	Phenotype	Significance	ClinVar
12-9669775-C-T	not specified	Uncertain significance (Jun 02, 2023)	2520801
12-9688007-C-A	not specified	Uncertain significance (Mar 29, 2024)	3267682
12-9693093-G-A	not specified	Uncertain significance (Aug 14, 2023)	2588766

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC2D	protein_coding	protein_coding	ENST00000261340	6	30849

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.230	0.763	125025	0	2	125027	0.00000800

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.514	85	99.4	0.855	0.00000449	1280
Missense in Polyphen		14	21.66	0.64636		315
Synonymous	-1.03	39	31.6	1.23	0.00000136	333
Loss of Function	2.34	3	11.6	0.259	4.91e-7	140

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000565	0.0000546
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.0000565	0.0000546
South Asian	0.0000333	0.0000330
Other	0.00	0.00

dbNSFP

Source: dbNSFP

Function: FUNCTION: Receptor for KLRB1 that protects target cells against natural killer cell-mediated lysis (PubMed:20843815, PubMed:16339513). Inhibits osteoclast formation (PubMed:14753741, PubMed:15123656). Inhibits bone resorption (PubMed:14753741). Modulates the release of interferon-gamma (PubMed:15104121). Binds high molecular weight sulfated glycosaminoglycans (PubMed:15123656). {ECO:0000269|PubMed:14753741, ECO:0000269|PubMed:15104121, ECO:0000269|PubMed:15123656, ECO:0000269|PubMed:16339513, ECO:0000269|PubMed:20843815}.;
Pathway: Immune System;Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell;Adaptive Immune System (Consensus)

Recessive Scores

pRec: 0.0869

Intolerance Scores

loftool: 0.391
rvis_EVS: 0.86
rvis_percentile_EVS: 88.62

Haploinsufficiency Scores

pHI: 0.0884
hipred: N
hipred_score: 0.252
ghis: 0.420

Essentials

essential_gene_CRISPR: N
essential_gene_CRISPR2: N
essential_gene_gene_trap: N
gene_indispensability_pred: N
gene_indispensability_score: 0.222

Gene Damage Prediction

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

Gene ontology

Biological process: cell surface receptor signaling pathway;regulation of immune response
Cellular component: endoplasmic reticulum;plasma membrane;integral component of plasma membrane;cell surface;membrane
Molecular function: transmembrane signaling receptor activity;carbohydrate binding