CLEC11A
protein-codingC-type lectin domain containing 11A, the group of C-type lectin domain containing
Gene summary
This gene encodes a member of the C-type lectin superfamily. The encoded protein is a secreted sulfated glycoprotein and functions as a growth factor for primitive hematopoietic progenitor cells. An alternative splice variant has been described but its biological nature has not been determined. [provided by RefSeq, Jul 2008]
- SCGF
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~2.3 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 CLEC11A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002975.3. 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 | 59 | 59 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 1 | 1 | ||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 60 | 1 | 0 | 61 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002966.1 | 4 | MANE Select | |
| Ensembl | ENSP00000250340.3 | 4 | MANE Select | |
| Ensembl | ENSP00000471075.1 | 4 | Standard | |
| Ensembl | ENSP00000471075.1 | 4 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- ossification
- positive regulation of cell population proliferation
- regulation of signaling receptor activity
Molecular Function
- growth factor activity
- carbohydrate binding
Cellular Component
- extracellular region
- extracellular space
- cytoplasm
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000250340
- Coding exons
- 4
- Length
- 2389
- Individuals with no LoFs
- 125076
- Homozygous LoFs
- 4
- Heterozygous LoFs
- 658
- Defined
- 125738
- p
- 0.00264
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.407 | 188 | 173 | 1.09 | 0.00000805 | 2012 |
| Missense (PolyPhen) | 60 | 60.311 | 0.99484 | 697 | ||
| Synonymous | 0.447 | 72 | 77.0 | 0.935 | 0.00000371 | 669 |
| Loss of Function | 1.29 | 7 | 11.8 | 0.594 | 5.17e-7 | 130 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.013 | 0.012 | notable |
| Latino/Admixed American | 0.0032 | 0.0031 | notable |
| Ashkenazi Jewish | 0.0072 | 0.0069 | notable |
| East Asian | 0.00033 | 0.00033 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0025 | 0.0022 | notable |
| South Asian | 0.00013 | 0.00013 | rare |
| Other | 0.0045 | 0.0039 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Promotes osteogenesis by stimulating the differentiation of mesenchymal progenitors into mature osteoblasts (PubMed:27976999). Important for repair and maintenance of adult bone (By similarity). {ECO:0000250|UniProtKB:O88200, ECO:0000269|PubMed:27976999}.;
Recessive Scores
- pRec
- 0.173
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.283
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |