LAX1
protein-codinglymphocyte transmembrane adaptor 1
Gene summary
Enables SH2 domain binding activity and protein kinase binding activity. Involved in several processes, including B cell activation; negative regulation of MAPK cascade; and negative regulation of T cell activation. Located in Golgi apparatus; cytosol; and plasma membrane. [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 ~13.0 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 LAX1 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_017773.4. 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 | 3 | 2 | 5 | |||
| missense | 52 | 5 | 57 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 55 | 8 | 2 | 65 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_060243.2 | 5 | MANE Select | |
| Ensembl | ENSP00000406970.2 | 5 | MANE Select | |
| RefSeq | NP_001129662.1 | 5 | Standard | |
| RefSeq | NP_001269807.1 | 3 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- TCR
Biological Process
- inactivation of MAPK activity
- adaptive immune response
- immune response
- intracellular signal transduction
- B cell activation
Molecular Function
- protein binding
- protein kinase binding
- SH2 domain binding
Cellular Component
- Golgi apparatus
- cytosol
- plasma membrane
- membrane
- integral component of membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000442561
- Coding exons
- 5
- Length
- 11058
- Individuals with no LoFs
- 125705
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 40
- Defined
- 125745
- p
- 0.000159
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 0.432 | 202 | 220 | 0.918 | 0.0000114 | 2630 |
| Missense (PolyPhen) | 54 | 62.596 | 0.86267 | 804 | ||
| Synonymous | 0.0983 | 86 | 87.2 | 0.987 | 0.00000513 | 763 |
| Loss of Function | 1.17 | 7 | 11.2 | 0.623 | 8.35e-7 | 89 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00018 | 0.00018 | rare |
| Latino/Admixed American | 0.00014 | 0.00014 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00011 | 0.00011 | rare |
| Finnish | 0.00032 | 0.00032 | rare |
| European (Non-Finnish) | 0.00018 | 0.00018 | rare |
| South Asian | 0 | 0.0 | absent |
| Other | 0.00033 | 0.00033 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Negatively regulates TCR (T-cell antigen receptor)- mediated signaling in T-cells and BCR (B-cell antigen receptor)- mediated signaling in B-cells. {ECO:0000269|PubMed:12359715}.;
Recessive Scores
- pRec
- 0.282
Intolerance Scores
- LoFtool
- 0.127
- RVIS EVS
- 1.24
- RVIS percentile EVS
- 93.39
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.392
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |