CD180
protein-codingCD180 molecule, the group of CD molecules
Gene summary
CD180 is a cell surface molecule consisting of extracellular leucine-rich repeats (LRR) and a short cytoplasmic tail. The extracellular LRR is associated with a molecule called MD-1 and form the cell surface receptor complex, RP105/MD-1. It belongs to the family of pathogen receptors, Toll-like receptors (TLR). RP105/MD1, by working in concert with TLR4, controls B cell recognition and signaling of lipopolysaccharide (LPS), a membrane constituent of Gram-negative bacteria. [provided by RefSeq, Jul 2008]
- LY64
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~17.2 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 CD180 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_005582.3. 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 | 1 | 3 | 3 | 7 | ||
| missense | 87 | 3 | 1 | 91 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 1 | 1 | ||||
| Total | 0 | 0 | 89 | 6 | 4 | 99 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_005573.2 | 3 | MANE Select | |
| Ensembl | ENSP00000256447.4 | 3 | MANE Select | |
| Ensembl | ENSP00000788359.1 | 2 | Standard | |
| RefSeq | XP_005248561.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Regulation of toll-like receptor signaling pathway
- Toll-Like Receptors Cascades
- Innate Immune System
- Immune System
- Toll Like Receptor 4 (TLR4) Cascade
Biological Process
- B cell proliferation involved in immune response
- inflammatory response
- positive regulation of lipopolysaccharide-mediated signaling pathway
- innate immune response
- cellular response to lipopolysaccharide
Molecular Function
- protein binding
Cellular Component
- extracellular space
- plasma membrane
- integral component of membrane
- extracellular matrix
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000256447
- Coding exons
- 3
- Length
- 14525
- Individuals with no LoFs
- 125341
- Homozygous LoFs
- 2
- Heterozygous LoFs
- 404
- Defined
- 125747
- p
- 0.00162
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.194 | 333 | 343 | 0.971 | 0.0000171 | 4416 |
| Missense (PolyPhen) | 87 | 92.806 | 0.93744 | 1329 | ||
| Synonymous | -0.303 | 143 | 138 | 1.03 | 0.00000740 | 1279 |
| Loss of Function | 1.59 | 9 | 15.8 | 0.569 | 6.70e-7 | 220 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00031 | 0.00031 | rare |
| Latino/Admixed American | 0.0016 | 0.0016 | notable |
| Ashkenazi Jewish | 0.0065 | 0.0065 | notable |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.0013 | 0.0013 | notable |
| European (Non-Finnish) | 0.0016 | 0.0016 | notable |
| South Asian | 0.0023 | 0.0022 | notable |
| Other | 0.00098 | 0.00098 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May cooperate with MD-1 and TLR4 to mediate the innate immune response to bacterial lipopolysaccharide (LPS) in B-cells. Leads to NF-kappa-B activation. Also involved in the life/death decision of B-cells (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.107
Intolerance Scores
- LoFtool
- 0.645
- RVIS EVS
- 0.07
- RVIS percentile EVS
- 59.11
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.769
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |