CLEC12B
protein-codingC-type lectin domain family 12 member B, the group of C-type lectin domain containing
Gene summary
Enables protein phosphatase binding activity and signaling receptor inhibitor activity. Involved in several processes, including melanocyte proliferation; natural killer cell inhibitory signaling pathway; and regulation of signal transduction. Located in external side of plasma membrane. Part of protein-containing complex. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~8.2 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to CLEC12B variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001129998.3. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 0 | |||||
| missense | 29 | 1 | 30 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 30 | 1 | 0 | 31 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001123470.1 | 6 | MANE Select | |
| Ensembl | ENSP00000344563.5 | 6 | MANE Select | |
| RefSeq | NP_001306170.1 | 4 | Standard | |
| RefSeq | NP_001306171.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- natural killer cell inhibitory signaling pathway
- negative regulation of natural killer cell mediated cytotoxicity
- negative regulation of signaling receptor activity
Molecular Function
- protein phosphatase binding
- carbohydrate binding
- receptor inhibitor activity
Cellular Component
- external side of plasma membrane
- integral component of membrane
- protein-containing complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000338896
- Coding exons
- 6
- Length
- 7993
- Individuals with no LoFs
- 125626
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 117
- Defined
- 125743
- p
- 0.000465
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.0205 | 138 | 137 | 1.00 | 0.00000639 | 1831 |
| Missense (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 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0032 | 0.0031 | notable |
| Latino/Admixed American | 0.00020 | 0.00020 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.000054 | 0.000054 | rare |
| Finnish | 0.000093 | 0.000092 | rare |
| European (Non-Finnish) | 0.00027 | 0.00027 | rare |
| South Asian | 0.00075 | 0.00075 | rare |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- 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
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | High |
| Cancer | Medium | Medium | Medium |