CLEC12B

C-type lectin domain family 12 member B, the group of C-type lectin domain containing

Basic information

Region (hg38): 12:10010627-10018796

Links

ENSG00000256660 ∙ NCBI:387837 ∙ OMIM:617573 ∙ HGNC:31966 ∙ Uniprot:Q2HXU8 ∙ 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 CLEC12B gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the CLEC12B 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 CLEC12B

This is a list of pathogenic ClinVar variants found in the CLEC12B region.

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

Position	Type	Phenotype	Significance	ClinVar
12-10012857-T-C		not specified	Uncertain significance (Jan 10, 2022)
12-10012878-T-C		not specified	Uncertain significance (Nov 15, 2023)
12-10014529-A-G		not specified	Uncertain significance (Dec 19, 2022)
12-10014710-A-T		not specified	Uncertain significance (Dec 09, 2023)
12-10015261-G-T		not specified	Uncertain significance (Oct 04, 2022)
12-10015291-A-G		not specified	Uncertain significance (Mar 28, 2023)
12-10015353-G-A		not specified	Likely benign (Sep 07, 2022)
12-10015363-A-C		not specified	Uncertain significance (Jul 06, 2021)
12-10015696-T-C		not specified	Uncertain significance (Dec 05, 2022)
12-10018345-A-G		not specified	Uncertain significance (Feb 13, 2024)
12-10018362-G-C		not specified	Uncertain significance (Jun 09, 2022)
12-10018444-A-T		not specified	Uncertain significance (Sep 01, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
CLEC12B	protein_coding	protein_coding	ENST00000338896	6	7993

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00000990	0.803	125626	0	117	125743	0.000465

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0205	138	137	1.00	0.00000639	1831
Missense in Polyphen		31	32.053	0.96715		459
Synonymous	0.747	42	48.6	0.864	0.00000233	483
Loss of Function	1.28	10	15.4	0.648	7.41e-7	170

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00339	0.00335
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000544	0.0000544
Finnish	0.0000925	0.0000924
European (Non-Finnish)	0.000275	0.000273
Middle Eastern	0.0000544	0.0000544
South Asian	0.000752	0.000752
Other	0.000328	0.000326

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Cell surface receptor that protects target cells against natural killer cell-mediated lysis. Modulates signaling cascades and mediates tyrosine phosphorylation of target MAP kinases. {ECO:0000269|PubMed:17562706}.

Recessive Scores

• pRec: 0.128

Intolerance Scores

• loftool: 0.942
• rvis_EVS: 0.75
• rvis_percentile_EVS: 86.57

Haploinsufficiency Scores

• 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: 0.114

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Clec12b

Gene ontology

• Biological process: natural killer cell inhibitory signaling pathway;negative regulation of natural killer cell mediated cytotoxicity;negative regulation of signaling receptor activity
• Cellular component: external side of plasma membrane;integral component of membrane;protein-containing complex
• Molecular function: protein phosphatase binding;carbohydrate binding;receptor inhibitor activity