LRP11

Summary

LRP11 (LDL receptor related protein 11, HGNC:16936) is a protein-coding gene on chromosome 6q25.1, encoding Low-density lipoprotein receptor-related protein 11 (Q86VZ4).

Enables phosphoprotein binding activity. Predicted to be involved in several processes, including response to cold; response to heat; and response to water deprivation. Predicted to be located in plasma membrane.

Source: NCBI Gene 84918 — RefSeq curated summary.

At a glance

• GWAS associations: 7
• Clinical variants (ClinVar): 53 total
• MANE Select transcript: NM_032832

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:16936
Approved symbol	LRP11
Name	LDL receptor related protein 11
Location	6q25.1
Locus type	gene with protein product
Status	Approved
Aliases	bA350J20.3, MANSC3
Ensembl gene	ENSG00000120256
Ensembl biotype	protein_coding
Entrez	84918

Gene structure

Transcript identifiers

Ensembl transcripts: 7 — 6 protein_coding, 1 retained_intron

ENST00000239367, ENST00000367368, ENST00000463728, ENST00000862606, ENST00000862607, ENST00000942554, ENST00000942555

RefSeq mRNA: 2 — MANE Select: NM_032832 NM_001410946, NM_032832

CCDS: CCDS5220, CCDS94018

Canonical transcript exons

ENST00000239367 — 7 exons

Exon	Start	End
ENSE00000813634	149826264	149826359
ENSE00000896349	149836085	149836297
ENSE00000896350	149837338	149837463
ENSE00000896351	149842983	149843124
ENSE00000975765	149818757	149820703
ENSE00003685329	149853003	149853160
ENSE00003890665	149863408	149864359

Expression profiles

Bgee: expression breadth ubiquitous, 138 present calls, max score 96.12.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 17.7143 / max 136.2978, expressed in 1676 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
76148	13.7882	1632
76147	3.0853	1340
76145	0.3748	183
76149	0.1866	79
76150	0.1440	53
76146	0.1355	39

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
islet of Langerhans	UBERON:0000006	96.12	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	95.18	gold quality
stromal cell of endometrium	CL:0002255	93.73	gold quality
calcaneal tendon	UBERON:0003701	92.56	gold quality
superior frontal gyrus	UBERON:0002661	92.35	gold quality
Brodmann (1909) area 9	UBERON:0013540	92.32	gold quality
prefrontal cortex	UBERON:0000451	91.86	gold quality
smooth muscle tissue	UBERON:0001135	91.44	gold quality
primary visual cortex	UBERON:0002436	91.14	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	91.03	gold quality
corpus callosum	UBERON:0002336	90.54	gold quality
lower esophagus mucosa	UBERON:0035834	90.06	gold quality
frontal cortex	UBERON:0001870	90.04	gold quality
cerebral cortex	UBERON:0000956	89.89	gold quality
nucleus accumbens	UBERON:0001882	89.32	gold quality
gall bladder	UBERON:0002110	89.14	gold quality
anterior cingulate cortex	UBERON:0009835	89.01	gold quality
caudate nucleus	UBERON:0001873	88.75	gold quality
esophagus mucosa	UBERON:0002469	88.59	gold quality
hypothalamus	UBERON:0001898	88.49	gold quality
Ammon’s horn	UBERON:0001954	88.48	gold quality
brain	UBERON:0000955	88.12	gold quality
endometrium	UBERON:0001295	88.00	gold quality
right uterine tube	UBERON:0001302	87.78	gold quality
putamen	UBERON:0001874	87.77	gold quality
pancreas	UBERON:0001264	87.66	gold quality
temporal lobe	UBERON:0001871	87.26	gold quality
amygdala	UBERON:0001876	87.19	gold quality
minor salivary gland	UBERON:0001830	87.16	gold quality
fallopian tube	UBERON:0003889	87.11	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-GEOD-83139	yes	8.41
E-ANND-3	yes	4.99

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

98 targeting LRP11, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-340-5P	100.00	72.50	4437
HSA-MIR-4262	100.00	73.26	3931
HSA-MIR-568	99.98	69.86	2084
HSA-MIR-4482-3P	99.98	72.50	3147
HSA-MIR-607	99.97	73.62	5593
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-493-5P	99.96	72.47	2382
HSA-MIR-548AJ-3P	99.96	73.38	5345
HSA-MIR-548X-3P	99.96	73.38	5345
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-548J-3P	99.94	72.61	4881
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-548AE-3P	99.93	72.66	4867
HSA-MIR-548AH-3P	99.93	72.54	4872
HSA-MIR-548AM-3P	99.93	72.54	4872
HSA-MIR-548AQ-3P	99.93	72.66	4867
HSA-MIR-338-5P	99.92	72.34	2951
HSA-MIR-6508-5P	99.92	70.67	2465
HSA-MIR-3671	99.90	73.04	3897
HSA-MIR-3686	99.90	70.53	2432
HSA-MIR-95-5P	99.89	72.17	3973
HSA-MIR-548D-3P	99.87	70.67	4362
HSA-MIR-8067	99.86	69.59	2260
HSA-MIR-548BB-3P	99.86	70.58	4354

Cross-species orthologs

12 orthologs

Organism	Symbol	Gene ID
danio_rerio	spint1b	ENSDARG00000012467
danio_rerio	lrp11	ENSDARG00000034076
danio_rerio	wfikkn1	ENSDARG00000101364
danio_rerio	spint1a	ENSDARG00000102332
mus_musculus	Lrp11	ENSMUSG00000019796
rattus_norvegicus	Lrp11	ENSRNOG00000014303
drosophila_melanogaster	CG7565	FBGN0035833
caenorhabditis_elegans		WBGENE00008449
caenorhabditis_elegans		WBGENE00009386
caenorhabditis_elegans		WBGENE00010792
caenorhabditis_elegans		WBGENE00015355
caenorhabditis_elegans		WBGENE00021939

Paralogs (13): TFPI (ENSG00000003436), EPPIN (ENSG00000101448), TFPI2 (ENSG00000105825), AMBP (ENSG00000106927), WFIKKN1 (ENSG00000127578), KIAA0319 (ENSG00000137261), KIAA0319L (ENSG00000142687), SPINT4 (ENSG00000149651), WFDC8 (ENSG00000158901), SPINT1 (ENSG00000166145), SPINT2 (ENSG00000167642), WFIKKN2 (ENSG00000173714), WFDC6 (ENSG00000243543)

Protein

Protein identifiers

Low-density lipoprotein receptor-related protein 11 — Q86VZ4 (reviewed: Q86VZ4)

All UniProt accessions (2): Q86VZ4, Q5VYB9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Membrane.

Similarity. Belongs to the LDLR family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q86VZ4-1	1	yes
Q86VZ4-2	2

RefSeq proteins (2): NP_001397875, NP_116221* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR000601	PKD_dom	Domain
IPR002172	LDrepeatLR_classA_rpt	Repeat
IPR011106	MANSC_N	Domain
IPR013783	Ig-like_fold	Homologous_superfamily
IPR013980	MANSC_dom	Domain
IPR022409	PKD/Chitinase_dom	Domain
IPR023415	LDLR_class-A_CS	Conserved_site
IPR035986	PKD_dom_sf	Homologous_superfamily
IPR036055	LDL_receptor-like_sf	Homologous_superfamily

Pfam: PF00057, PF07502, PF22352

UniProt features (22 total): sequence variant 4, glycosylation site 3, disulfide bond 3, domain 3, splice variant 2, topological domain 2, signal peptide 1, chain 1, transmembrane region 1, region of interest 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86VZ4-F1	68.15	0.28

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 491

Disulfide bonds (3): 310–322, 317–335, 329–344

Glycosylation sites (3): 164, 291, 401

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 90 (showing top): GOBP_RESPONSE_TO_COLD, GOBP_RESPONSE_TO_ACID_CHEMICAL, GOBP_RESPONSE_TO_IMMOBILIZATION_STRESS, TTTGTAG_MIR520D, GOBP_MULTICELLULAR_ORGANISMAL_RESPONSE_TO_STRESS, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, chr6q25, MODULE_239, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_5, LIAO_METASTASIS, GOBP_RESPONSE_TO_ABIOTIC_STIMULUS, ACEVEDO_LIVER_CANCER_UP, GOBP_RESPONSE_TO_WATER

GO Biological Process (7): response to heat (GO:0009408), response to cold (GO:0009409), response to water deprivation (GO:0009414), response to mechanical stimulus (GO:0009612), multicellular organismal response to stress (GO:0033555), response to immobilization stress (GO:0035902), response to starvation (GO:0042594)

GO Molecular Function (2): phosphoprotein binding (GO:0051219), protein binding (GO:0005515)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
response to stress	6
response to temperature stimulus	2
response to water	1
response to external stimulus	1
response to abiotic stimulus	1
multicellular organismal process	1
response to nutrient levels	1
protein binding	1
binding	1
membrane	1
cell periphery	1
cellular anatomical structure	1

Protein interactions and networks

STRING

444 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LRP11	LRP3	O75074	546
LRP11	LRP4	O75096	505
LRP11	LRP12	Q9Y561	490
LRP11	SORL1	Q92673	479
LRP11	MAN2B2	Q9Y2E5	447
LRP11	LRP8	Q14114	446
LRP11	LRP10	Q7Z4F1	434
LRP11	DDX25	Q9UHL0	431
LRP11	ACOT13	Q9NPJ3	425
LRP11	MYADM	Q96S97	416
LRP11	LRP1B	Q9NZR2	412
LRP11	GSTM4	Q03013	398
LRP11	PCMT1	P22061	397
LRP11	PHYH	O14832	393
LRP11	FADS2	O95864	383

IntAct

57 interactions, top by confidence:

A	B	Type	Score
NIPAL1	ESYT2	psi-mi:“MI:0914”(association)	0.640
CD1B	TOR1B	psi-mi:“MI:0914”(association)	0.530
PLA2G10	CHEK1	psi-mi:“MI:0914”(association)	0.530
TAFA4	NRP1	psi-mi:“MI:0914”(association)	0.530
ANTXR1	POTEF	psi-mi:“MI:0914”(association)	0.530
LRRTM1	UPK3BL1	psi-mi:“MI:0914”(association)	0.530
SRPRB	CTDNEP1	psi-mi:“MI:0914”(association)	0.530
ARRB2		psi-mi:“MI:0914”(association)	0.350
LRRTM1	TMEM223	psi-mi:“MI:0914”(association)	0.350
TAFA3	FUOM	psi-mi:“MI:0914”(association)	0.350
CLEC12A	GOSR1	psi-mi:“MI:0914”(association)	0.350
SRPRB	GOSR1	psi-mi:“MI:0914”(association)	0.350
ST8SIA4	NRP1	psi-mi:“MI:0914”(association)	0.350
LYZL2	MANBA	psi-mi:“MI:0914”(association)	0.350
GINM1	TNFRSF10B	psi-mi:“MI:0914”(association)	0.350
IL27RA	NRP1	psi-mi:“MI:0914”(association)	0.350
PON2	ENTPD6	psi-mi:“MI:0914”(association)	0.350
P2RX2	C1QL1	psi-mi:“MI:0914”(association)	0.350
LYPD1	HSPA5	psi-mi:“MI:0914”(association)	0.350
	SHTN1	psi-mi:“MI:0914”(association)	0.350
PDGFRA	GXYLT2	psi-mi:“MI:0914”(association)	0.350
CLEC12B	GXYLT2	psi-mi:“MI:0914”(association)	0.350
GINM1	FAM234B	psi-mi:“MI:0914”(association)	0.350
IGHD	POTEF	psi-mi:“MI:0914”(association)	0.350
BRICD5	POTEF	psi-mi:“MI:0914”(association)	0.350

BioGRID (73): LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS), LRP11 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTW7, A0A1D5NSK0, A0A1L8HYT7, A0A286YEC0, D3ZT86, D3ZWJ9, D4A929, F8W3R9, G7PWZ3, I6M4H4, O08852, O43157, O43278, O75074, O88204, P17813, P49000, P59383, Q04912, Q17R55, Q499Z3, Q4R3B7, Q4TUC0, Q5ND34, Q62190, Q63961, Q6AXX1, Q76MJ5, Q7TN88, Q7TQH7, Q7Z442, Q7Z4F1, Q80W87, Q80YN4, Q866Y3, Q86VZ4, Q8BHW9, Q8BMN4, Q8BYI8, Q8BZT7

Diamond homologs: P0CI71, Q5RFR6, Q5SZV5, Q5VV43, Q86VZ4, Q8CB67, Q8IZA0, Q8K135, Q9X721, P06682, P79755

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	45
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1106 predictions. Top by Δscore:

Variant	Effect	Δscore
6:149836294:CCCA:C	acceptor_gain	1.0000
6:149836295:CCA:C	acceptor_gain	1.0000
6:149836295:CCAC:C	acceptor_gain	1.0000
6:149836296:CA:C	acceptor_gain	1.0000
6:149836296:CAC:C	acceptor_gain	1.0000
6:149836298:C:CC	acceptor_gain	1.0000
6:149836299:T:C	acceptor_loss	1.0000
6:149837336:A:AC	donor_gain	1.0000
6:149837337:C:CC	donor_gain	1.0000
6:149837337:CG:C	donor_gain	1.0000
6:149837337:CGATT:C	donor_gain	1.0000
6:149837460:CATC:C	acceptor_gain	1.0000
6:149842977:TCTCA:T	donor_loss	1.0000
6:149842978:CTCAC:C	donor_loss	1.0000
6:149842979:TCA:T	donor_loss	1.0000
6:149842980:CACCT:C	donor_loss	1.0000
6:149842981:ACC:A	donor_loss	1.0000
6:149842981:ACCT:A	donor_gain	1.0000
6:149842982:C:A	donor_loss	1.0000
6:149842982:CCTC:C	donor_gain	1.0000
6:149842984:T:TA	donor_gain	1.0000
6:149863406:AC:A	donor_gain	1.0000
6:149863407:CC:C	donor_gain	1.0000
6:149820721:A:C	acceptor_gain	0.9900
6:149826356:CTAT:C	acceptor_gain	0.9900
6:149836082:TA:T	donor_loss	0.9900
6:149836083:A:T	donor_loss	0.9900
6:149836084:C:CA	donor_loss	0.9900
6:149836293:GCCCA:G	acceptor_gain	0.9900
6:149836294:CCCAC:C	acceptor_gain	0.9900

AlphaMissense

3187 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:149853039:C:A	W245C	0.997
6:149853039:C:G	W245C	0.997
6:149853041:A:G	W245R	0.997
6:149853041:A:T	W245R	0.997
6:149853072:G:C	S234R	0.995
6:149853072:G:T	S234R	0.995
6:149853074:T:G	S234R	0.995
6:149843063:A:G	L278P	0.994
6:149863533:A:G	F163S	0.992
6:149863503:C:G	C173S	0.991
6:149863504:A:T	C173S	0.991
6:149863707:A:T	I105N	0.991
6:149863503:C:T	C173Y	0.990
6:149863533:A:C	F163C	0.990
6:149863496:G:C	F175L	0.989
6:149863496:G:T	F175L	0.989
6:149863497:A:C	F175C	0.989
6:149863498:A:G	F175L	0.989
6:149863526:G:C	C165W	0.989
6:149863593:G:T	A143D	0.989
6:149863707:A:G	I105T	0.989
6:149863527:C:T	C165Y	0.987
6:149863601:G:C	C140W	0.987
6:149863670:G:C	F117L	0.985
6:149863670:G:T	F117L	0.985
6:149863672:A:G	F117L	0.985
6:149853040:C:G	W245S	0.984
6:149863504:A:G	C173R	0.984
6:149863527:C:G	C165S	0.984
6:149863528:A:T	C165S	0.984

dbSNP variants (sampled 300 via entrez): RS1000023965 (6:149830258 G>A,C), RS1000045692 (6:149854765 C>T), RS1000059103 (6:149837813 T>C), RS1000084836 (6:149860879 G>A,T), RS1000191831 (6:149843231 C>T), RS1000193321 (6:149831265 C>T), RS1000251269 (6:149838946 A>G), RS1000286163 (6:149862231 A>T), RS1000415504 (6:149844822 T>C), RS1000620033 (6:149848909 A>T), RS1000659232 (6:149837521 G>A,C), RS1000735578 (6:149849246 T>C), RS1000901356 (6:149850135 G>A), RS1001004201 (6:149824758 G>C), RS1001050353 (6:149856698 T>C)

Disease associations

OMIM: gene `` | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

7 associations (top):

Study	Trait	p-value
GCST006088_23	Familial squamous cell lung carcinoma	4.000000e-06
GCST006585_1791	Blood protein levels	2.000000e-86
GCST006585_382	Blood protein levels	4.000000e-286
GCST006631_45	Nicotine dependence and major depression (severity of comorbidity)	7.000000e-06
GCST006976_29	Macular thickness	3.000000e-19
GCST010702_29	Subcortical volume (MOSTest)	7.000000e-11
GCST010703_317	Brain morphology (MOSTest)	7.000000e-22

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0006953	family history of lung cancer
EFO:0007006	depressive symptom measurement
EFO:0009262	nicotine dependence symptom count
EFO:0004346	neuroimaging measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

38 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases methylation	7
Benzo(a)pyrene	increases expression	4
sodium arsenite	decreases expression, increases abundance, increases expression	3
Tetrachlorodibenzodioxin	increases expression	3
Acetaminophen	increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
Aflatoxin B1	affects expression, increases methylation	2
methylmercuric chloride	increases expression	1
potassium perchlorate	increases expression	1
trichostatin A	increases expression	1
butyraldehyde	decreases expression	1
manganese chloride	increases abundance, increases expression	1
potassium chromate(VI)	affects cotreatment, decreases expression	1
epigallocatechin gallate	affects cotreatment, decreases expression	1
Am 580	decreases expression	1
perfluoro-n-nonanoic acid	affects expression	1
K 7174	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
abrine	decreases expression	1
2,2’,4,4’-tetrabromodiphenyl ether	decreases expression	1
dorsomorphin	affects cotreatment, increases expression	1
Rosiglitazone	decreases expression	1
Temozolomide	decreases expression	1
Leflunomide	increases expression	1
Air Pollutants	decreases expression, increases abundance	1
Arsenic	increases expression, increases abundance	1
Carbamazepine	affects expression	1
Cisplatin	increases expression	1
Doxorubicin	increases expression	1
Lead	affects expression	1

Clinical trials (associated diseases)

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