Seroatlas · Human Serome Atlas

LCK

Tyrosine-protein kinase Lck

Also known as: LCK_HUMAN

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: P06239
Gene: LCK
Ensembl: ENSG00000182866
Chromosome: 1
Canonical length: 509 aa
Protein class: Cancer-related genes, Disease related genes, Enzymes, FDA approved drug targets, Human disease related genes, Predicted intracellular proteins
Subcellular location: Golgi apparatus

OverviewNCBI Gene

This gene is a member of the Src family of protein tyrosine kinases (PTKs). The encoded protein is a key signaling molecule in the selection and maturation of developing T-cells. It contains N-terminal sites for myristylation and palmitylation, a PTK domain, and SH2 and SH3 domains which are involved in mediating protein-protein interactions with phosphotyrosine-containing and proline-rich motifs, respectively. The protein localizes to the plasma membrane and pericentrosomal vesicles, and binds to cell surface receptors, including CD4 and CD8, and other signaling molecules. Multiple alternatively spliced variants encoding different isoforms have been described. [provided by RefSeq, Aug 2016]

Canonical amino-acid sequenceUniProt

509 residues, UniProt reviewed canonical sequence.

>P06239|LCK
     1  MGCGCSSHPE DDWMENIDVC ENCHYPIVPL DGKGTLLIRN GSEVRDPLVT YEGSNPPASP
    61  LQDNLVIALH SYEPSHDGDL GFEKGEQLRI LEQSGEWWKA QSLTTGQEGF IPFNFVAKAN
   121  SLEPEPWFFK NLSRKDAERQ LLAPGNTHGS FLIRESESTA GSFSLSVRDF DQNQGEVVKH
   181  YKIRNLDNGG FYISPRITFP GLHELVRHYT NASDGLCTRL SRPCQTQKPQ KPWWEDEWEV
   241  PRETLKLVER LGAGQFGEVW MGYYNGHTKV AVKSLKQGSM SPDAFLAEAN LMKQLQHQRL
   301  VRLYAVVTQE PIYIITEYME NGSLVDFLKT PSGIKLTINK LLDMAAQIAE GMAFIEERNY
   361  IHRDLRAANI LVSDTLSCKI ADFGLARLIE DNEYTAREGA KFPIKWTAPE AINYGTFTIK
   421  SDVWSFGILL TEIVTHGRIP YPGMTNPEVI QNLERGYRMV RPDNCPEELY QLMRLCWKER
   481  PEDRPTFDYL RSVLEDFFTA TEGQYQPQP

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against LCK can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.

Antibody reachability: Cell surface
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.31
Highest tissue expression: 326 nTPM

Expression across tissuesHPA

Tissue

thymus: 326 nTPM
lymph node: 93 nTPM
tonsil: 70 nTPM
appendix: 42 nTPM
spleen: 34 nTPM
small intestine: 19 nTPM

Single-cell type

t-cells: 256 nCPM
nk-cells: 172 nCPM
innate lymphoid cells: 54 nCPM
thymocytes: 53 nCPM
b-cells: 24 nCPM
epididymal principal cells: 20 nCPM

Immune cell

total PBMC: 1,794 nTPM
T-reg: 1,617 nTPM
naive CD4 T-cell: 1,226 nTPM
memory CD8 T-cell: 1,163 nTPM
naive CD8 T-cell: 1,132 nTPM
memory CD4 T-cell: 1,091 nTPM

Brain region

medulla oblongata: 1 nTPM
choroid plexus: 0.9 nTPM
white matter: 0.8 nTPM
spinal cord: 0.7 nTPM
basal ganglia: 0.6 nTPM
pons: 0.6 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about LCK.

Disease | AllUniProt

Conditions LCK is implicated in, by any mechanism.

Immunodeficiency 22 (IMD22) MIM:615758

Disease | GeneticClinVar

18 pathogenic / likely-pathogenic of 328 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Severe combined immunodeficiency due to LCK deficiency
Severe combined immunodeficiency disease

Disease | ImmuneIEDB

Conditions an epitope on LCK was assayed in.

cancer B and T cell
castration-resistant prostate carcinoma B and T cell
prostate cancer B and T cell
Her2-receptor negative breast cancer B and T cell
esophageal cancer B and T cell
colorectal cancer B and T cell
prostate adenocarcinoma B and T cell
Her2-receptor positive breast cancer B and T cell
triple-receptor negative breast cancer B and T cell
biliary tract cancer B and T cell
carcinoma B and T cell
cervical cancer B and T cell
pancreatic carcinoma B cell
lung small cell carcinoma B cell
adult hepatocellular carcinoma B cell
hematologic cancer B cell
hepatocellular carcinoma B cell
osteosarcoma B and T cell
lung cancer B and T cell
prostatic urethral cancer B and T cell

Genetic constraint and essentialitygnomAD · DepMap

Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.

gnomAD LOEUF (loss-of-function intolerance): 0.21
gnomAD pLI: 1
gnomAD missense Z: 3.48
DepMap mean gene effect: -0.06
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of LCK in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads LCK as an antibody target. Whether an autoantibody or antibody against LCK could matter depends on whether native LCK is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

LCK is annotated at the cell surface, where native LCK is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label LCK as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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