Seroatlas · Human Serome Atlas

LIMS2

LIM and senescent cell antigen-like-containing domain protein 2

Also known as: LIMS2_HUMAN, PINCH-2, PINCH2

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

Protein identityUniProt · HPA

UniProt accession: Q7Z4I7
Gene: LIMS2
Ensembl: ENSG00000072163
Chromosome: 2
Canonical length: 341 aa
Protein class: Disease related genes, Human disease related genes, Predicted intracellular proteins
Subcellular location: Focal adhesion sites

OverviewNCBI Gene

This gene encodes a member of a small family of focal adhesion proteins which interacts with ILK (integrin-linked kinase), a protein which effects protein-protein interactions with the extraceullar matrix. The encoded protein has five LIM domains, each domain forming two zinc fingers, which permit interactions which regulate cell shape and migration. A pseudogene of this gene is located on chromosome 4. Multiple transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Nov 2011]

Canonical amino-acid sequenceUniProt

341 residues, UniProt reviewed canonical sequence.

>Q7Z4I7|LIMS2
     1  MTGSNMSDAL ANAVCQRCQA RFSPAERIVN SNGELYHEHC FVCAQCFRPF PEGLFYEFEG
    61  RKYCEHDFQM LFAPCCGSCG EFIIGRVIKA MNNNWHPGCF RCELCDVELA DLGFVKNAGR
   121  HLCRPCHNRE KAKGLGKYIC QRCHLVIDEQ PLMFRSDAYH PDHFNCTHCG KELTAEAREL
   181  KGELYCLPCH DKMGVPICGA CRRPIEGRVV NALGKQWHVE HFVCAKCEKP FLGHRHYEKK
   241  GLAYCETHYN QLFGDVCYNC SHVIEGDVVS ALNKAWCVSC FSCSTCNSKL TLKNKFVEFD
   301  MKPVCKRCYE KFPLELKKRL KKLSELTSRK AQPKATDLNS A

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against LIMS2 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): 0.38
Highest tissue expression: 474 nTPM

Expression across tissuesHPA

Tissue

colon: 474 nTPM
blood vessel: 273 nTPM
heart muscle: 253 nTPM
endometrium: 245 nTPM
urinary bladder: 216 nTPM
fallopian tube: 143 nTPM

Single-cell type

smooth muscle cells: 213 nCPM
vascular endothelial cells: 200 nCPM
vascular smooth muscle cells: 114 nCPM
cardiomyocytes: 106 nCPM
podocytes: 104 nCPM
granulosa cells: 104 nCPM

Immune cell

naive B-cell: 23 nTPM
memory B-cell: 15 nTPM
naive CD4 T-cell: 11 nTPM
T-reg: 8 nTPM
memory CD4 T-cell: 5.3 nTPM
naive CD8 T-cell: 4.4 nTPM

Brain region

thalamus: 32 nTPM
pons: 25 nTPM
amygdala: 25 nTPM
medulla oblongata: 24 nTPM
cerebral cortex: 22 nTPM
basal ganglia: 22 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about LIMS2.

Disease | AllUniProt

Conditions LIMS2 is implicated in, by any mechanism.

Muscular dystrophy, autosomal recessive, with cardiomyopathy and triangular tongue (MDRCMTT) MIM:616827

Disease | GeneticClinVar

3 pathogenic / likely-pathogenic of 398 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Autosomal recessive limb-girdle muscular dystrophy type 2W

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): 0.88
gnomAD pLI: 0
gnomAD missense Z: 0.37
DepMap mean gene effect: -0.1
DepMap dependency class: selective

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

metal ion binding

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of LIMS2 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 LIMS2 as an antibody target. Whether an autoantibody or antibody against LIMS2 could matter depends on whether native LIMS2 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

LIMS2 is annotated at the cell surface, where native LIMS2 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 LIMS2 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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