JAML
protein-codingjunction adhesion molecule like, the group of V-set domain containing|Ig-like cell adhesion molecule family
Gene summary
Enables integrin binding activity and protein homodimerization activity. Involved in heterophilic cell-cell adhesion and myeloid leukocyte migration. Located in bicellular tight junction and plasma membrane. [provided by Alliance of Genome Resources, Jun 2026]
- AMICA1
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~31.4 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 JAML variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_001098526.2. 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 | 8 | 8 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 2 | 2 | ||||
| Total | 0 | 0 | 10 | 0 | 0 | 10 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_001091996.1 | 9 | MANE Select | |
| Ensembl | ENSP00000348635.5 | 9 | MANE Select | |
| RefSeq | NP_001273499.1 | 8 | Standard | |
| RefSeq | NP_001273500.1 | 8 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Immune System
- Immunoregulatory interactions between a Lymphoid and a non-Lymphoid cell
- Adaptive Immune System
- Cell surface interactions at the vascular wall
- Hemostasis
Biological Process
- heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules
- neutrophil chemotaxis
- monocyte extravasation
- gamma-delta T cell activation
- regulation of immune response
Molecular Function
- integrin binding
- protein homodimerization activity
- cell adhesion molecule binding
Cellular Component
- plasma membrane
- bicellular tight junction
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000356289
- Coding exons
- 9
- Length
- 31355
- Individuals with no LoFs
- 125455
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 293
- Defined
- 125748
- p
- 0.00117
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.340 | 211 | 225 | 0.936 | 0.0000124 | 2566 |
| Missense (PolyPhen) | 49 | 58.414 | 0.83883 | 704 | ||
| Synonymous | 0.214 | 83 | 85.5 | 0.971 | 0.00000473 | 782 |
| Loss of Function | 2.12 | 8 | 17.6 | 0.454 | 8.08e-7 | 228 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00043 | 0.00043 | rare |
| Latino/Admixed American | 0.0022 | 0.0022 | notable |
| Ashkenazi Jewish | 0.00030 | 0.00030 | rare |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0.0017 | 0.0017 | notable |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.0018 | 0.0018 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Transmembrane protein of the plasma membrane of leukocytes that control their migration and activation through interaction with CXADR, a plasma membrane receptor found on adjacent epithelial and endothelial cells. The interaction between both receptors mediates the activation of gamma-delta T-cells, a subpopulation of T-cells residing in epithelia and involved in tissue homeostasis and repair. Upon epithelial CXADR-binding, JAML induces downstream cell signaling events in gamma-delta T-cells through PI3-kinase and MAP kinases. It results in proliferation and production of cytokines and growth factors by T-cells that in turn stimulate epithelial tissues repair. It also controls the transmigration of leukocytes within epithelial and endothelial tissues through adhesive interactions with epithelial and endothelial CXADR. {ECO:0000269|PubMed:12869515, ECO:0000269|PubMed:15800062, ECO:0000269|PubMed:18948633, ECO:0000269|PubMed:19064666}.;
Recessive Scores
- pRec
- 0.120
Intolerance Scores
- RVIS EVS
- 0.6
- RVIS percentile EVS
- 82.74
Essentials
- Essential (gene trap)
- N