LY86
protein-codinglymphocyte antigen 86, the group of MD-2 related lipid recognition domain containing
Gene summary
Acts upstream of or within positive regulation of lipopolysaccharide-mediated signaling pathway. Predicted to be located in extracellular region. [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 ~66.9 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 LY86 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_004271.4. 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 | 1 | 2 | |||
| missense | 24 | 1 | 25 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 27 | 0 | 2 | 29 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_004262.1 | 5 | MANE Select | |
| Ensembl | ENSP00000230568.3 | 5 | MANE Select | |
| Ensembl | ENSP00000369286.1 | 5 | Standard | |
| Ensembl | ENSP00000369286.1 | 5 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Toll-Like Receptors Cascades
- Innate Immune System
- Immune System
- Toll Like Receptor 4 (TLR4) Cascade
Biological Process
- apoptotic process
- inflammatory response
- humoral immune response
- cell population proliferation
- positive regulation of lipopolysaccharide-mediated signaling pathway
Molecular Function
- protein binding
Cellular Component
- extracellular space
- plasma membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000379953
- Coding exons
- 5
- Length
- 66876
- Individuals with no LoFs
- 125659
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 85
- Defined
- 125744
- p
- 0.000338
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.342 | 94 | 85.1 | 1.10 | 0.00000448 | 1042 |
| Missense (PolyPhen) | 36 | 31.518 | 1.1422 | 396 | ||
| Synonymous | -0.475 | 37 | 33.5 | 1.10 | 0.00000206 | 305 |
| Loss of Function | -0.00907 | 7 | 6.97 | 1.00 | 2.93e-7 | 95 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00028 | 0.00025 | rare |
| Latino/Admixed American | 0.0017 | 0.0017 | notable |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.00014 | 0.00012 | rare |
| South Asian | 0.000065 | 0.000065 | rare |
| Other | 0.00050 | 0.00049 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: May cooperate with CD180 and TLR4 to mediate the innate immune response to bacterial lipopolysaccharide (LPS) and cytokine production. Important for efficient CD180 cell surface expression (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.163
Intolerance Scores
- LoFtool
- 0.792
- RVIS EVS
- 0.37
- RVIS percentile EVS
- 75.12
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.853
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |