Seroatlas · Human Serome Atlas

LMX1B

LIM homeobox transcription factor 1-beta

Also known as: LMX1B_HUMAN, NPS1

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

Protein identityUniProt · HPA

UniProt accession: O60663
Gene: LMX1B
Ensembl: ENSG00000136944
Chromosome: 9
Canonical length: 402 aa
Protein class: Disease related genes, Human disease related genes, Predicted intracellular proteins, Transcription factors
Subcellular location: Nucleoplasm

OverviewNCBI Gene

This gene encodes a member of LIM-homeodomain family of proteins containing two N-terminal zinc-binding LIM domains, 1 homeodomain, and a C-terminal glutamine-rich domain. It functions as a transcription factor, and is essential for the normal development of dorsal limb structures, the glomerular basement membrane, the anterior segment of the eye, and dopaminergic and serotonergic neurons. Mutations in this gene are associated with nail-patella syndrome. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Mar 2010]

Canonical amino-acid sequenceUniProt

402 residues, UniProt reviewed canonical sequence.

>O60663|LMX1B
     1  MDIATGPESL ERCFPRGQTD CAKMLDGIKM EEHALRPGPA TLGVLLGSDC PHPAVCEGCQ
    61  RPISDRFLMR VNESSWHEEC LQCAACQQAL TTSCYFRDRK LYCKQDYQQL FAAKCSGCME
   121  KIAPTEFVMR ALECVYHLGC FCCCVCERQL RKGDEFVLKE GQLLCKGDYE KEKDLLSSVS
   181  PDESDSVKSE DEDGDMKPAK GQGSQSKGSG DDGKDPRRPK RPRTILTTQQ RRAFKASFEV
   241  SSKPCRKVRE TLAAETGLSV RVVQVWFQNQ RAKMKKLARR HQQQQEQQNS QRLGQEVLSS
   301  RMEGMMASYT PLAPPQQQIV AMEQSPYGSS DPFQQGLTPP QMPGDHMNPY GNDSIFHDID
   361  SDTSLTSLSD CFLGSSDVGS LQARVGNPID RLYSMQSSYF AS

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against LMX1B 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: Intracellular
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.5
Highest tissue expression: 18 nTPM

Expression across tissuesHPA

Tissue

salivary gland: 18 nTPM
breast: 3.8 nTPM
kidney: 3.1 nTPM
midbrain: 3.1 nTPM
skin: 1.7 nTPM
heart muscle: 1.5 nTPM

Single-cell type

podocytes: 269 nCPM
lacrimal acinar cells: 78 nCPM
salivary acinar cells: 58 nCPM
breast myoepithelial cells: 29 nCPM
breast hormone-responsive cells: 24 nCPM
breast secretory cells: 19 nCPM

Immune cell

basophil: 0.1 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM
MAIT T-cell: 0 nTPM

Brain region

midbrain: 20 nTPM
spinal cord: 14 nTPM
cerebral cortex: 12 nTPM
medulla oblongata: 8.3 nTPM
pons: 7.5 nTPM
thalamus: 5.9 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about LMX1B.

Disease | AllUniProt

Conditions LMX1B is implicated in, by any mechanism.

Nail-patella syndrome (NPS) MIM:161200
Focal segmental glomerulosclerosis 10 (FSGS10) MIM:256020

Disease | GeneticClinVar

150 pathogenic / likely-pathogenic of 701 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Nail-patella syndrome
Nail-patella-like renal disease
LMX1B-related disorder
Inborn genetic diseases
Autosomal recessive Alport syndrome

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): 0.42
gnomAD pLI: 0.75
gnomAD missense Z: 2.02
DepMap mean gene effect: -0.03
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 LMX1B 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 LMX1B as an antibody target. Whether an autoantibody or antibody against LMX1B could matter depends on whether native LMX1B is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

LMX1B is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.

Annotation status

The present source text does not explicitly label LMX1B as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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