LMBR1L

gene
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Also known as LIMRFLJ10494KIAA1174

Summary

LMBR1L (limb development membrane protein 1 like, HGNC:18268) is a protein-coding gene on chromosome 12q13.12, encoding Protein LMBR1L (Q6UX01). Plays an essential role in lymphocyte development by negatively regulating the canonical Wnt signaling pathway.

Enables transmembrane signaling receptor activity. Involved in receptor-mediated endocytosis and signal transduction. Located in endoplasmic reticulum membrane and plasma membrane.

Source: NCBI Gene 55716 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 82 total — 2 likely-pathogenic
  • MANE Select transcript: NM_018113

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:18268
Approved symbolLMBR1L
Namelimb development membrane protein 1 like
Location12q13.12
Locus typegene with protein product
StatusApproved
AliasesLIMR, FLJ10494, KIAA1174
Ensembl geneENSG00000139636
Ensembl biotypeprotein_coding
OMIM610007
Entrez55716

Gene structure

Transcript identifiers

Ensembl transcripts: 42 — 20 protein_coding, 11 retained_intron, 7 nonsense_mediated_decay, 4 protein_coding_CDS_not_defined

ENST00000267102, ENST00000417750, ENST00000457164, ENST00000547382, ENST00000547670, ENST00000547675, ENST00000547698, ENST00000547813, ENST00000548983, ENST00000549296, ENST00000549429, ENST00000549587, ENST00000549730, ENST00000550137, ENST00000550815, ENST00000550867, ENST00000551115, ENST00000551143, ENST00000551169, ENST00000551272, ENST00000551535, ENST00000551782, ENST00000551854, ENST00000552141, ENST00000552153, ENST00000552449, ENST00000552577, ENST00000552879, ENST00000553040, ENST00000553204, ENST00000892061, ENST00000892062, ENST00000892063, ENST00000892064, ENST00000892065, ENST00000930615, ENST00000930616, ENST00000930617, ENST00000930618, ENST00000930619, ENST00000970441, ENST00000970442

RefSeq mRNA: 11 — MANE Select: NM_018113 NM_001300750, NM_001300751, NM_001352161, NM_001352162, NM_001352163, NM_001352164, NM_001352165, NM_001352166, NM_001352167, NM_001352168, NM_018113

CCDS: CCDS73466, CCDS8780

Canonical transcript exons

ENST00000267102 — 17 exons

ExonStartEnd
ENSE000019188344911048449110847
ENSE000034661324910212049102196
ENSE000034762864909713949097739
ENSE000034845184909794449098105
ENSE000035328764910288749102951
ENSE000035585214910696149107045
ENSE000035602994910592449105957
ENSE000035676554910309149103159
ENSE000035818494910246849102540
ENSE000035914894910038849100454
ENSE000036028944910474649104885
ENSE000036055204910055649100646
ENSE000036150104910368749103813
ENSE000036227904910147249101549
ENSE000036316124910125049101323
ENSE000036329894910444849104551
ENSE000036584204910229349102376

Expression profiles

Bgee: expression breadth ubiquitous, 282 present calls, max score 99.00.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 25.1012 / max 171.8694, expressed in 1811 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
13080313.16081788
1308047.85861697
1308054.08181395

Top tissues by expression

290 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
right testisUBERON:000453499.00gold quality
left testisUBERON:000453398.90gold quality
right uterine tubeUBERON:000130298.53gold quality
adenohypophysisUBERON:000219698.21gold quality
mucosa of stomachUBERON:000119998.17gold quality
left ovaryUBERON:000211998.17gold quality
tibial nerveUBERON:000132398.06gold quality
body of uterusUBERON:000985398.06gold quality
right hemisphere of cerebellumUBERON:001489097.96gold quality
right ovaryUBERON:000211897.88gold quality
cerebellar hemisphereUBERON:000224597.83gold quality
endocervixUBERON:000045897.77gold quality
cerebellar cortexUBERON:000212997.74gold quality
pituitary glandUBERON:000000797.49gold quality
ganglionic eminenceUBERON:000402397.47gold quality
muscle layer of sigmoid colonUBERON:003580597.44gold quality
esophagogastric junction muscularis propriaUBERON:003584197.38gold quality
ectocervixUBERON:001224997.27gold quality
lower esophagus muscularis layerUBERON:003583397.26gold quality
lower esophagusUBERON:001347397.25gold quality
right lungUBERON:000216797.23gold quality
descending thoracic aortaUBERON:000234597.23gold quality
left uterine tubeUBERON:000130397.14gold quality
right lobe of thyroid glandUBERON:000111997.13gold quality
left lobe of thyroid glandUBERON:000112097.09gold quality
small intestine Peyer’s patchUBERON:000345497.08gold quality
cortical plateUBERON:000534397.07gold quality
granulocyteCL:000009497.05gold quality
adrenal tissueUBERON:001830397.00gold quality
apex of heartUBERON:000209896.92gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

ExperimentMarker?Max mean expression
E-MTAB-9801yes5.77
E-ANND-3yes3.20
E-ENAD-17no301.84
E-GEOD-124858no22.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

32 targeting LMBR1L, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-30A-5P100.0076.313233
HSA-MIR-30B-5P100.0076.293248
HSA-MIR-30C-5P100.0076.293248
HSA-MIR-30D-5P100.0076.323233
HSA-MIR-30E-5P100.0076.323242
HSA-MIR-34A-5P99.9971.211784
HSA-MIR-449A99.9971.051776
HSA-MIR-32-5P99.9875.211964
HSA-MIR-92A-3P99.9875.211960
HSA-MIR-92B-3P99.9875.251955
HSA-MIR-25-3P99.9874.601817
HSA-MIR-363-3P99.9874.721821
HSA-MIR-367-3P99.9874.831819
HSA-MIR-807599.9767.20962
HSA-MIR-137-3P99.8774.742401
HSA-MIR-182799.6368.573265
HSA-MIR-24-3P99.5969.971934
HSA-MIR-431699.3765.751360
HSA-MIR-149-5P99.2567.161315
HSA-MIR-544B99.1867.411632
HSA-MIR-429299.1665.571767
HSA-MIR-6791-5P99.1665.921844
HSA-MIR-491-3P98.8868.861224
HSA-MIR-1910-3P98.4467.511695
HSA-MIR-4717-5P98.1967.97894
HSA-MIR-6511A-5P98.1367.471770
HSA-MIR-450B-3P97.5666.12512
HSA-MIR-96-3P97.4768.03839
HSA-MIR-4640-5P97.4266.331543
HSA-MIR-4726-5P97.2465.671299

Literature-anchored findings (GeneRIF, showing 6)

  • LIMR mediating internalization of lipocalin-1 (Lcn-1) in NT2 cells, leading to its degradation. (PMID:12591932)
  • Human LIMR, known to act as an endocytic receptor for lipocalin-1, also binds bovine BLG and mediates its cellular uptake. (PMID:17991420)
  • The receptor to which lipocalin binds is termed tear lipocalin-interacting membrane receptor and it appears to work by endocytosis. (PMID:21791187)
  • LIMR was shown to be highly specific for Lcn1, binding the lipocalin with low micromolar to high nanomolar affinity (PMID:23964685)
  • LMBR1L has an essential function during lymphopoiesis and lymphoid activation, acting as a negative regulator of the Wnt/beta-catenin pathway. (PMID:31073040)
  • LMBR1L regulates the proliferation and migration of endothelial cells through Norrin/beta-catenin signaling. (PMID:35146515)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriolmbr1lENSDARG00000004745
mus_musculusLmbr1lENSMUSG00000022999
rattus_norvegicusLmbr1lENSRNOG00000061607
drosophila_melanogasterliliFBGN0027539
caenorhabditis_elegansWBGENE00019877

Paralogs (1): LMBR1 (ENSG00000105983)

Protein

Protein identifiers

Protein LMBR1LQ6UX01 (reviewed: Q6UX01)

Alternative names: Limb region 1 protein homolog-like, Lipocalin-1-interacting membrane receptor

All UniProt accessions (15): A0A024R0Y9, A0A0S2Z6E3, E7ESX7, Q6UX01, F8VPB1, F8VVE2, F8VYZ9, F8VZU8, F8W054, F8W0N6, F8WE63, H0YHY8, H0YHZ2, H0YI83, H0YIX2

UniProt curated annotations — full annotation on UniProt →

Function. Plays an essential role in lymphocyte development by negatively regulating the canonical Wnt signaling pathway. In association with UBAC2 and E3 ubiquitin-protein ligase AMFR, promotes the ubiquitin-mediated degradation of CTNNB1 and Wnt receptors FZD6 and LRP6. LMBR1L stabilizes the beta-catenin destruction complex that is required for regulating CTNNB1 levels. Acts as a LCN1 receptor and can mediate its endocytosis.

Subunit / interactions. Dimer. Can also form higher oligomers. Interacts with LCN1; this interaction mediates the endocytosis of LCN1. Interacts with UBAC2, FAF2, VCP, AMFR, ZNRF3, CTNNB1, LRP6, GSK3A and GSK3B. Interacts with DVL2 and RNF43. Interaction with SCGB1A1 has been observed in PubMed:16423471, but not in PubMed:23964685. Interaction with LGB which mediates the endocytosis of LGB has been observed in PubMed:17991420, but not in PubMed:23964685.

Subcellular location. Cell membrane. Endoplasmic reticulum membrane.

Tissue specificity. Expressed in testis, pituitary gland, adrenal gland, trachea, placenta, thymus, cerebellum, stomach, mammary gland, spinal cord. A weaker expression is detected in colon, pancreas, and prostate.

Similarity. Belongs to the LIMR family.

Isoforms (5)

UniProt IDNamesCanonical?
Q6UX01-11yes
Q6UX01-22
Q6UX01-33
Q6UX01-44
Q6UX01-55

RefSeq proteins (11): NP_001287679, NP_001287680, NP_001339090, NP_001339091, NP_001339092, NP_001339093, NP_001339094, NP_001339095, NP_001339096, NP_001339097, NP_060583* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR006876LMBR1-like_membr_protFamily
IPR008075LIMRFamily

Pfam: PF04791

UniProt features (33 total): topological domain 10, transmembrane region 9, sequence conflict 6, splice variant 5, region of interest 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q6UX01-F180.660.32

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 146 (showing top): GOBP_HEMATOPOIETIC_PROGENITOR_CELL_DIFFERENTIATION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, GOBP_VESICLE_MEDIATED_TRANSPORT, GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, GOBP_HEMATOPOIETIC_STEM_CELL_DIFFERENTIATION, GOBP_LEUKOCYTE_PROLIFERATION, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, GOBP_CANONICAL_WNT_SIGNALING_PATHWAY, ROZANOV_MMP14_TARGETS_UP, BLALOCK_ALZHEIMERS_DISEASE_UP, MARTIN_VIRAL_GPCR_SIGNALING_DN, RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN, GOBP_LEUKOCYTE_APOPTOTIC_PROCESS, TGTTTAC_MIR30A5P_MIR30C_MIR30D_MIR30B_MIR30E5P, GOBP_STEM_CELL_DIFFERENTIATION

GO Biological Process (9): receptor-mediated endocytosis (GO:0006898), signal transduction (GO:0007165), Wnt signaling pathway (GO:0016055), T cell differentiation (GO:0030217), T cell proliferation (GO:0042098), hematopoietic stem cell differentiation (GO:0060218), T cell apoptotic process (GO:0070231), negative regulation of canonical Wnt signaling pathway (GO:0090090), endocytosis (GO:0006897)

GO Molecular Function (2): transmembrane signaling receptor activity (GO:0004888), protein binding (GO:0005515)

GO Cellular Component (5): endoplasmic reticulum membrane (GO:0005789), plasma membrane (GO:0005886), endoplasmic reticulum (GO:0005783), endomembrane system (GO:0012505), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
T cell activation2
cellular anatomical structure2
endocytosis1
cell communication1
cellular process1
signaling1
regulation of cellular process1
cellular response to stimulus1
cell surface receptor signaling pathway1
lymphocyte differentiation1
lymphocyte proliferation1
hematopoietic progenitor cell differentiation1
stem cell differentiation1
lymphocyte apoptotic process1
negative regulation of Wnt signaling pathway1
canonical Wnt signaling pathway1
regulation of canonical Wnt signaling pathway1
vesicle budding from membrane1
membrane invagination1
vesicle-mediated transport1
import into cell1
signaling receptor activity1
binding1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
membrane1
cell periphery1
cytoplasm1
endomembrane system1
intracellular membrane-bounded organelle1
vacuole1
plasma membrane1

Protein interactions and networks

STRING

2396 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LMBR1LLCN1P31025946
LMBR1LD6RE68D6RE68700
LMBR1LAHRRA9YTQ3674
LMBR1LFAM81AQ8TBF8503
LMBR1LDNAJC22Q8N4W6490
LMBR1LPTPN20Q4JDL3472
LMBR1LHTR5AP47898433
LMBR1LLMBRD1Q9NUN5421
LMBR1LFKBP10Q96AY3418
LMBR1LKCNK10P57789415
LMBR1LFBXL20Q96IG2406
LMBR1LTOR2AQ5JU69404
LMBR1LGRIN3AQ8TCU5403
LMBR1LGSTCDQ8NEC7402
LMBR1LKMT2EQ8IZD2401

IntAct

10 interactions, top by confidence:

ABTypeScore
CFTRLMBR1Lpsi-mi:“MI:0915”(physical association)0.370
ECE1LMBR1Lpsi-mi:“MI:0915”(physical association)0.370
CREB3LMBR1Lpsi-mi:“MI:0915”(physical association)0.370
CHRNA4TMEM223psi-mi:“MI:0914”(association)0.350
SLC19A2TMEM223psi-mi:“MI:0914”(association)0.350
TCTN2TMEM120Bpsi-mi:“MI:2364”(proximity)0.270
TCTN3TMEM120Bpsi-mi:“MI:2364”(proximity)0.270
EVC2PGRMC2psi-mi:“MI:2364”(proximity)0.270

BioGRID (955): LMBR1L (Proximity Label-MS), LMBR1L (Proximity Label-MS), LMBR1L (Proximity Label-MS), LMBR1L (Two-hybrid), LMBR1L (Affinity Capture-MS), MAGEA11 (Two-hybrid), LMBR1L (Affinity Capture-Western), LMBR1L (Affinity Capture-Western), LMBR1L (Affinity Capture-Western), LMBR1L (Affinity Capture-Western), LMBR1L (Affinity Capture-Western), LMBR1L (Affinity Capture-Western), LMBR1L (Affinity Capture-Western), SRPRB (Affinity Capture-MS), SRP68 (Affinity Capture-MS)

ESM2 similar proteins: A1A4P6, A1A5B4, A5PK40, A6NDV4, A6NFX1, A6NGC4, A6QL84, A6QLK4, B1AWJ5, B6ID01, E1BY51, P58749, Q2TA01, Q2YDG0, Q32PG7, Q3T9M1, Q4R7X9, Q5HZE5, Q5JZQ7, Q5R6H1, Q5RBY7, Q60HE8, Q6AY05, Q6AYM9, Q6PHN7, Q6TCG5, Q6UX01, Q6UXD7, Q7RTT9, Q7Z403, Q80ZE4, Q8CE47, Q8R139, Q8TBR7, Q96FZ5, Q96HE8, Q96S97, Q9BSA9, Q9BZW5, Q9CQC4

Diamond homologs: Q4R7X9, Q5RBY7, Q5U4X7, Q6UX01, Q7ZUA6, Q7ZX75, Q803C7, Q8WVP7, Q9D1E5, Q9JIT0, Q9VC35

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

82 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic2
Uncertain significance65
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
1285608NM_018113.4(LMBR1L):c.863G>A (p.Arg288Gln)Likely pathogenic
1285609NM_018113.4(LMBR1L):c.862C>T (p.Arg288Trp)Likely pathogenic

SpliceAI

2559 predictions. Top by Δscore:

VariantEffectΔscore
12:49097935:C:CAdonor_gain1.0000
12:49101529:C:CTacceptor_gain1.0000
12:49102192:CTTCT:Cacceptor_gain1.0000
12:49102195:CT:Cacceptor_gain1.0000
12:49102197:C:CCacceptor_gain1.0000
12:49102464:TTA:Tdonor_loss1.0000
12:49102465:TACTA:Tdonor_loss1.0000
12:49102466:A:ACdonor_gain1.0000
12:49102466:A:Cdonor_loss1.0000
12:49102467:C:CAdonor_gain1.0000
12:49102467:CT:Cdonor_gain1.0000
12:49102467:CTA:Cdonor_gain1.0000
12:49102467:CTACA:Cdonor_gain1.0000
12:49102536:AGCAG:Aacceptor_gain1.0000
12:49102537:GCAG:Gacceptor_gain1.0000
12:49102538:CAG:Cacceptor_gain1.0000
12:49102538:CAGC:Cacceptor_gain1.0000
12:49102539:AG:Aacceptor_gain1.0000
12:49102539:AGCT:Aacceptor_loss1.0000
12:49102540:GCTAG:Gacceptor_loss1.0000
12:49102541:C:CCacceptor_gain1.0000
12:49102541:C:Tacceptor_loss1.0000
12:49102548:C:CTacceptor_gain1.0000
12:49102549:A:Tacceptor_gain1.0000
12:49102948:CACA:Cacceptor_gain1.0000
12:49102950:CA:Cacceptor_gain1.0000
12:49102952:C:CCacceptor_gain1.0000
12:49103089:AC:Adonor_gain1.0000
12:49103090:CC:Cdonor_gain1.0000
12:49103157:AGTCT:Aacceptor_loss1.0000

AlphaMissense

3113 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
12:49102920:G:CF221L0.999
12:49102920:G:TF221L0.999
12:49102922:A:GF221L0.999
12:49102937:C:GG216R0.999
12:49100419:G:CS403R0.998
12:49100419:G:TS403R0.998
12:49100421:T:GS403R0.998
12:49100621:C:GG370R0.998
12:49102937:C:AG216C0.998
12:49103109:C:GG205R0.998
12:49103109:C:TG205R0.998
12:49104770:A:GW103R0.998
12:49104770:A:TW103R0.998
12:49098017:A:CF443L0.997
12:49098017:A:TF443L0.997
12:49098019:A:GF443L0.997
12:49100620:C:TG370D0.997
12:49102936:C:TG216D0.997
12:49104546:A:GW113R0.997
12:49104546:A:TW113R0.997
12:49102942:G:CP214R0.996
12:49102942:G:TP214Q0.996
12:49104497:G:CP129R0.996
12:49104768:C:AW103C0.996
12:49104768:C:GW103C0.996
12:49104813:G:CS88R0.996
12:49104813:G:TS88R0.996
12:49104815:T:GS88R0.996
12:49104829:G:CP83R0.996
12:49104873:G:CC68W0.996

dbSNP variants (sampled 300 via entrez): RS1000146181 (12:49098649 A>G), RS1000322578 (12:49111531 G>A), RS1000760827 (12:49097402 G>C), RS1000815726 (12:49109990 C>T), RS1000866048 (12:49099823 C>T), RS1000931238 (12:49110224 A>G,T), RS1001102807 (12:49103929 G>A), RS1001146620 (12:49100164 G>A,C), RS1001379480 (12:49112542 G>A), RS1001767551 (12:49106200 A>C,G), RS1002360574 (12:49107695 C>A), RS1002528613 (12:49100280 A>G), RS1002769063 (12:49100038 G>A), RS1002819262 (12:49112370 CCG>C), RS1003155772 (12:49103243 G>A,C)

Disease associations

OMIM: gene MIM:610007 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

3 associations (top):

StudyTraitp-value
GCST008103_109Bipolar disorder4.000000e-06
GCST010703_9Brain morphology (MOSTest)8.000000e-10
GCST010989_40Body size at age 109.000000e-19

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004346neuroimaging measurement
EFO:0009819comparative body size at age 10, self-reported

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

18 total (human), top 18 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Aaffects cotreatment, decreases methylation, increases expression, decreases expression3
bisphenol Faffects cotreatment, decreases expression1
triphenyl phosphateaffects expression1
pirinixic acidaffects binding, decreases expression, increases activity1
sodium arseniteincreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
abrineincreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Air Pollutantsaffects expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Dexamethasoneaffects cotreatment, decreases expression1
Indomethacindecreases expression, affects cotreatment1
Ozoneaffects expression, increases abundance1
Smokedecreases expression1
Tretinoinincreases expression1
Urethaneincreases expression1
1-Methyl-3-isobutylxanthineaffects cotreatment, decreases expression1

Cellosaurus cell lines

3 cell lines: 3 cancer cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_E2B6HAP1 LMBR1L (-) 1Cancer cell lineMale
CVCL_E2B7HAP1 LMBR1L (-) 2Cancer cell lineMale
CVCL_E2B8HAP1 LMBR1L (-) 3Cancer cell lineMale

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.