LTK
protein-codingleukocyte receptor tyrosine kinase, the group of Receptor tyrosine kinases
Gene summary
The protein encoded by this gene is a member of the ros/insulin receptor family of tyrosine kinases. Tyrosine-specific phosphorylation of proteins is a key to the control of diverse pathways leading to cell growth and differentiation. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2008]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~10.3 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 LTK variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002344.6. 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 | 151 | 4 | 1 | 156 | ||
| nonsense | 1 | 1 | 2 | |||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 155 | 6 | 2 | 163 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002335.2 | 20 | MANE Select | |
| Ensembl | ENSP00000263800.6 | 20 | MANE Select | |
| RefSeq | NP_001129157.1 | 18 | Standard | |
| RefSeq | NP_996844.1 | 19 | Standard |
Model Organisms & Knockout Phenotypes
Observed phenotypic effects in mouse and zebrafish models
| Gene / Model | Organism | Observed Phenotype |
|---|---|---|
| ltk | Danio rerio | Structure: iridophore Quality: decreased amount abnormal |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- IL-7 signaling
- JAK STAT pathway and regulation
- EPO signaling
- VEGF
Biological Process
- protein phosphorylation
- signal transduction
- transmembrane receptor protein tyrosine kinase signaling pathway
- cell population proliferation
- positive regulation of cardiac muscle cell apoptotic process
Molecular Function
- protein kinase activity
- protein tyrosine kinase activity
- transmembrane receptor protein tyrosine kinase activity
- protein binding
- ATP binding
Cellular Component
- plasma membrane
- integral component of plasma membrane
- membrane
- receptor complex
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000263800
- Coding exons
- 20
- Length
- 10250
- Individuals with no LoFs
- 124542
- Homozygous LoFs
- 3
- Heterozygous LoFs
- 1203
- Defined
- 125748
- p
- 0.00481
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.490 | 492 | 462 | 1.06 | 0.0000248 | 5421 |
| Missense (PolyPhen) | 201 | 191.11 | 1.0518 | 2333 | ||
| Synonymous | -0.439 | 204 | 196 | 1.04 | 0.0000107 | 1858 |
| Loss of Function | 0.380 | 40 | 42.7 | 0.937 | 0.00000217 | 468 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0016 | 0.0015 | notable |
| Latino/Admixed American | 0.0037 | 0.0037 | notable |
| Ashkenazi Jewish | 0.00010 | 0.000099 | rare |
| East Asian | 0.0014 | 0.0014 | notable |
| Finnish | 0.0069 | 0.0069 | notable |
| European (Non-Finnish) | 0.0071 | 0.0070 | notable |
| South Asian | 0.0017 | 0.0017 | notable |
| Other | 0.0051 | 0.0049 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Receptor with a tyrosine-protein kinase activity. The exact function of this protein is not known. Studies with chimeric proteins (replacing its extracellular region with that of several known growth factor receptors, such as EGFR and CSFIR) demonstrate its ability to promote growth and specifically neurite outgrowth, and cell survival. Signaling appears to involve the PI3 kinase pathway. Involved in regulation of the secretory pathway involving endoplasmic reticulum (ER) export sites (ERESs) and ER to Golgi transport. {ECO:0000269|PubMed:20548102}.;
Intolerance Scores
- LoFtool
- 0.0997
- RVIS EVS
- -0.77
- RVIS percentile EVS
- 13.16
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.779
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |