CLEC12A
protein-codingC-type lectin domain family 12 member A, the group of CD molecules|C-type lectin domain containing
Gene summary
This gene encodes a member of the C-type lectin/C-type lectin-like domain (CTL/CTLD) superfamily. Members of this family share a common protein fold and have diverse functions, such as cell adhesion, cell-cell signaling, glycoprotein turnover, and roles in inflammation and immune response. The protein encoded by this gene is a negative regulator of granulocyte and monocyte function. Several alternatively spliced transcript variants of this gene have been described, but the full-length nature of some of these variants has not been determined. This gene is closely linked to other CTL/CTLD superfamily members in the natural killer gene complex region on chromosome 12p13. [provided by RefSeq, May 2011]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~44.4 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 CLEC12A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_138337.6. 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 | 33 | 6 | 39 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 34 | 6 | 0 | 40 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_612210.4 | 6 | MANE Select | |
| Ensembl | ENSP00000302804.4 | 6 | MANE Select | |
| RefSeq | NP_001193939.1 | 7 | Standard | |
| RefSeq | NP_001287659.1 | 6 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Neutrophil degranulation
- Innate Immune System
- Immune System
Biological Process
- neutrophil degranulation
Molecular Function
- carbohydrate binding
Cellular Component
- plasma membrane
- integral component of membrane
- specific granule membrane
- tertiary granule membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000355690
- Coding exons
- 7
- Length
- 44379
- Individuals with no LoFs
- 125218
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 382
- Defined
- 125601
- p
- 0.00153
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.217 | 141 | 134 | 1.05 | 0.00000617 | 1827 |
| Missense (PolyPhen) | 36 | 38.791 | 0.92806 | 575 | ||
| Synonymous | -0.234 | 46 | 44.0 | 1.04 | 0.00000197 | 465 |
| Loss of Function | 0.441 | 11 | 12.7 | 0.866 | 5.35e-7 | 168 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00019 | 0.00018 | rare |
| Latino/Admixed American | 0.0013 | 0.0013 | notable |
| Ashkenazi Jewish | 0.0027 | 0.0027 | notable |
| East Asian | 0.00060 | 0.00060 | rare |
| Finnish | 0.00014 | 0.00014 | rare |
| European (Non-Finnish) | 0.0022 | 0.0022 | notable |
| South Asian | 0.0013 | 0.0013 | notable |
| Other | 0.0018 | 0.0018 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Cell surface receptor that modulates signaling cascades and mediates tyrosine phosphorylation of target MAP kinases. {ECO:0000269|PubMed:14739280, ECO:0000269|PubMed:16239426}.;
Recessive Scores
- pRec
- 0.128
Intolerance Scores
- LoFtool
- 0.819
- RVIS EVS
- 0.19
- RVIS percentile EVS
- 67.03
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.0925
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |