LAT
Chr 16ARlinker for activation of T cells
Also known as: IMD52, LAT1, pp36
The protein encoded by this gene is phosphorylated by ZAP-70/Syk protein tyrosine kinases following activation of the T-cell antigen receptor (TCR) signal transduction pathway. This transmembrane protein localizes to lipid rafts and acts as a docking site for SH2 domain-containing proteins. Upon phosphorylation, this protein recruits multiple adaptor proteins and downstream signaling molecules into multimolecular signaling complexes located near the site of TCR engagement. Alternative splicing results in multiple transcript variants encoding different isoforms. [provided by RefSeq, Jul 2008]
Definitive — sufficient evidence for diagnostic panels
Population Genetics & Constraint
gnomAD v4 — loss-of-function & missense intolerance
Typical tolerance to LoF variation
Mild missense constraint
This gene — mechanism propensity
This gene has evidence for multiple mechanisms of pathogenicity (dominant-negative and gain-of-function). Both the Badonyi & Marsh prediction and the broader genomic evidence point to dominant-negative as the predominant mechanism. Different variants in this gene may act through different mechanisms — interpret in context of the specific variant.
Note: In-silico variant effect predictors (SIFT, PolyPhen, REVEL, CADD) may underestimate pathogenicity of missense variants in genes with GOF or DN mechanisms. Consider functional evidence and clinical context.
Predictions from Badonyi M, Marsh JA. PLoS ONE. 2024;19(8):e0307312.
ClinVar Variant Classifications
238 submitted variants in ClinVar
Classification Summary
Curated Variants Distribution
Classified variants from ClinVar · 5 ACMG categories
| Classification | LoF | Missense + Inframe | Non-coding | Synonymous | Total |
|---|---|---|---|---|---|
Pathogenic | 8 | 0 | 2 | 0 | 10 |
Likely Pathogenic | 1 | 0 | 0 | 0 | 1 |
VUS | 2 | 69 | 4 | 2 | 77 |
Likely Benign | 1 | 7 | 57 | 60 | 125 |
Benign | 0 | 3 | 10 | 1 | 14 |
Conflicting | — | 1 | |||
| Total | 12 | 79 | 73 | 63 | 228 |
LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly
View in ClinVar →112 pathogenic / likely-pathogenic (of 151) ClinVar copy-number / structural variants overlap LAT — these span large chromosomal regions, not the gene specifically, and are excluded from the counts above. Explore in CNV tools →
Protein Context — Lollipop Plot
LAT · protein map & ClinVar variants
Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.
External Resources
Links to major genomics databases and tools
Clinical Trials
Active and recruiting trials from ClinicalTrials.gov
Optimization of the Time and Dosage of Trametinib in BRAF Negative Juvenile Patients
RECRUITINGLanguage Development Deficits and Early Interactive Music Intervention
ACTIVE NOT RECRUITINGPrehabilitation in Older People Undergoing Total Hip Replacement
NOT YET RECRUITINGTraining Induced Muscle-Adipose EV Communication
NOT YET RECRUITINGTrial for Local Ablative Treatment (LAT) Optimization in Patients With Advanced Non-Small Cells Lung Cancer (NSCLC) Presenting an Anaplastic Lymphoma Kinase (ALK) Rearrangement Treated by Brigatinib
RECRUITINGFeasibility of ONCOhabitats for Surgical and Treatment Planning in IDH-Wildtype Glioblastoma (SINUE)
RECRUITINGNatural History of Autosomal Dominant Hearing Loss
RECRUITINGMapping Disease Pathways for Biliary Atresia
RECRUITINGExternal Resources
Links to major genomics databases and tools