LUZP2

Summary

LUZP2 (leucine zipper protein 2, HGNC:23206) is a protein-coding gene on chromosome 11p14.3, encoding Leucine zipper protein 2 (Q86TE4).

This gene encodes a leucine zipper protein. This protein is deleted in some patients with Wilms tumor-Aniridia-Genitourinary anomalies-mental Retardation (WAGR) syndrome. Alternate splicing results in multiple transcript variants.

Source: NCBI Gene 338645 — RefSeq curated summary.

At a glance

• GWAS associations: 29
• Clinical variants (ClinVar): 58 total
• MANE Select transcript: NM_001009909

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:23206
Approved symbol	LUZP2
Name	leucine zipper protein 2
Location	11p14.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000187398
Ensembl biotype	protein_coding
OMIM	608178
Entrez	338645

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 4 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000336930, ENST00000405855, ENST00000449567, ENST00000528970, ENST00000529015, ENST00000531187, ENST00000533227, ENST00000620308

RefSeq mRNA: 3 — MANE Select: NM_001009909 NM_001009909, NM_001252008, NM_001252010

CCDS: CCDS31446, CCDS58128

Canonical transcript exons

ENST00000336930 — 12 exons

Exon	Start	End
ENSE00001353824	25077329	25077406
ENSE00001353828	25050038	25050130
ENSE00001353835	24983126	24983293
ENSE00001353842	24976591	24976665
ENSE00001353849	24914476	24914538
ENSE00001353857	24905991	24906053
ENSE00001621017	25078554	25082638
ENSE00002148388	24497053	24497305
ENSE00003533866	24732118	24732188
ENSE00003568822	24763246	24763308
ENSE00003577624	24738221	24738302
ENSE00003582092	24729169	24729286

Expression profiles

Bgee: expression breadth ubiquitous, 153 present calls, max score 86.21.

FANTOM5 (CAGE): breadth broad, TPM avg 3.6863 / max 198.8063, expressed in 405 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter ID	TPM avg	Samples expressed
113507	1.5624	269
113504	0.5430	207
113509	0.5039	149
113508	0.3642	113
113505	0.2810	131
113506	0.2477	104
113510	0.1412	75
113503	0.0429	12

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adrenal tissue	UBERON:0018303	86.21	gold quality
hypothalamus	UBERON:0001898	82.45	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	81.60	gold quality
amygdala	UBERON:0001876	81.53	gold quality
spinal cord	UBERON:0002240	79.81	gold quality
right adrenal gland cortex	UBERON:0035827	77.81	gold quality
substantia nigra	UBERON:0002038	76.83	gold quality
cingulate cortex	UBERON:0003027	76.74	gold quality
anterior cingulate cortex	UBERON:0009835	76.47	gold quality
left adrenal gland	UBERON:0001234	76.21	gold quality
left adrenal gland cortex	UBERON:0035825	75.89	gold quality
corpus callosum	UBERON:0002336	75.88	gold quality
adrenal gland	UBERON:0002369	75.68	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.57	gold quality
midbrain	UBERON:0001891	75.54	gold quality
adrenal cortex	UBERON:0001235	75.45	gold quality
cortical plate	UBERON:0005343	75.35	gold quality
nucleus accumbens	UBERON:0001882	74.94	gold quality
prefrontal cortex	UBERON:0000451	74.66	gold quality
temporal lobe	UBERON:0001871	74.04	gold quality
right adrenal gland	UBERON:0001233	73.62	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	72.22	gold quality
Ammon’s horn	UBERON:0001954	72.13	gold quality
caudate nucleus	UBERON:0001873	71.82	gold quality
telencephalon	UBERON:0001893	70.96	gold quality
neocortex	UBERON:0001950	70.80	gold quality
Brodmann (1909) area 9	UBERON:0013540	70.66	gold quality
putamen	UBERON:0001874	70.30	gold quality
medial globus pallidus	UBERON:0002477	70.29	gold quality
cerebral cortex	UBERON:0000956	70.13	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-35	yes	91.32
E-HCAD-25	yes	30.09
E-GEOD-84465	yes	26.80
E-ANND-3	yes	6.29

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

124 targeting LUZP2, 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-340-5P	100.00	72.50	4437
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-3163	100.00	77.23	8605
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-3662	99.99	73.82	5684
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-548P	99.98	72.25	3784
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-3605-5P	99.96	67.12	932
HSA-MIR-3912-5P	99.95	66.11	925
HSA-MIR-144-3P	99.94	73.98	2698
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-515-5P	99.92	69.82	2343
HSA-MIR-519E-5P	99.92	69.62	2358
HSA-MIR-1305	99.91	71.43	3443
HSA-MIR-10527-5P	99.91	72.28	3754
HSA-MIR-589-3P	99.91	69.62	2088
HSA-MIR-5680	99.91	69.83	3421
HSA-MIR-374A-5P	99.90	71.34	2923
HSA-MIR-374B-5P	99.90	69.98	2734
HSA-MIR-6780A-5P	99.88	66.69	2776

Literature-anchored findings (GeneRIF, showing 1)

• Downregulation of LUZP2 Is Correlated with Poor Prognosis of Low-Grade Glioma. (PMID:32695826)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	luzp2	ENSDARG00000068247
mus_musculus	Luzp2	ENSMUSG00000063297
rattus_norvegicus	Luzp2	ENSRNOG00000021507

Protein

Protein identifiers

Leucine zipper protein 2 — Q86TE4 (reviewed: Q86TE4)

All UniProt accessions (2): E9PP05, Q86TE4

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Secreted.

Isoforms (4)

UniProt ID	Names	Canonical?
Q86TE4-1	1	yes
Q86TE4-2	2
Q86TE4-3	3
Q86TE4-4	4

RefSeq proteins (3): NP_001009909, NP_001238937, NP_001238939 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR026718	Luzp2	Family

UniProt features (18 total): splice variant 5, glycosylation site 3, region of interest 3, compositionally biased region 3, signal peptide 1, chain 1, sequence variant 1, coiled-coil region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q86TE4-F1	73.61	0.53

Functional residue map

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

Glycosylation sites (3): 264, 302, 133

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 66 (showing top): ACTTTAT_MIR1425P, chr11p14, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, PDGF_ERK_DN.V1_UP, NME2_TARGET_GENES, MIR12136, MIR340_5P, MIR186_5P, MIR4719, MIR137_3P, MIR944, MIR576_5P, MIR5700, MIR221_3P, GSE10325_MYELOID_VS_LUPUS_MYELOID_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (1): extracellular region (GO:0005576)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	1

Protein interactions and networks

STRING

564 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LUZP2	GAS2	O43903	910
LUZP2	CLHC1	Q8NHS4	489
LUZP2	ZDHHC19	Q8WVZ1	430
LUZP2	CREB3	O43889	416
LUZP2	FAM81A	Q8TBF8	415
LUZP2	ANKRD55	Q3KP44	409
LUZP2	FBXW10B	O95170	388
LUZP2	SLC35G2	Q8TBE7	385
LUZP2	AKAP8	O43823	374
LUZP2	MTARC1	Q5VT66	374
LUZP2	TMEM72	A0PK05	367
LUZP2	GPR171	O14626	353
LUZP2	SBK2	P0C263	353
LUZP2	LHFPL3	Q86UP9	351
LUZP2	MS4A10	Q96PG2	350

IntAct

4 interactions, top by confidence:

A	B	Type	Score
CBX5	KPNA3	psi-mi:“MI:0914”(association)	0.530
ESR1		psi-mi:“MI:0914”(association)	0.350
TNIK	LUZP2	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (2): LUZP2 (Affinity Capture-RNA), LUZP2 (Synthetic Lethality)

ESM2 similar proteins: A2AM05, A2BDC9, A2VD12, A2VE10, A5D8S1, B1AJZ9, O00461, O75071, P04233, P04441, P07106, P10247, P24054, P70663, Q08D19, Q14515, Q32N32, Q4KLH6, Q4V9H3, Q5BJK8, Q5PQS2, Q5R5X4, Q5R6R3, Q5R8Y4, Q5R9L2, Q5T8D3, Q5TB80, Q5ZHQ6, Q5ZKQ5, Q5ZM60, Q640L3, Q6P2L7, Q6P4E1, Q6Y685, Q6ZQ06, Q70YC5, Q86TE4, Q8BG89, Q8BMK4, Q8BVV7

Diamond homologs: A5D8S1, Q5R8Y4, Q86TE4, Q8BGY3

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	47
Likely benign	3
Benign	1

Top pathogenic / likely-pathogenic (0)

SpliceAI

4572 predictions. Top by Δscore:

Variant	Effect	Δscore
11:24497306:G:C	donor_loss	1.0000
11:24497307:T:G	donor_loss	1.0000
11:24525492:T:G	donor_gain	1.0000
11:24729163:TGTTA:T	acceptor_loss	1.0000
11:24729164:GTTAG:G	acceptor_loss	1.0000
11:24729165:TTAG:T	acceptor_loss	1.0000
11:24729166:TA:T	acceptor_loss	1.0000
11:24729167:A:AG	acceptor_gain	1.0000
11:24729167:AGA:A	acceptor_loss	1.0000
11:24729168:G:GA	acceptor_gain	1.0000
11:24729168:GA:G	acceptor_gain	1.0000
11:24729168:GACA:G	acceptor_gain	1.0000
11:24729284:CAGGT:C	donor_loss	1.0000
11:24729285:AGG:A	donor_loss	1.0000
11:24729286:GGTGA:G	donor_loss	1.0000
11:24729287:GT:G	donor_loss	1.0000
11:24729288:T:A	donor_loss	1.0000
11:24732116:A:AG	acceptor_gain	1.0000
11:24732117:G:GG	acceptor_gain	1.0000
11:24732117:GT:G	acceptor_gain	1.0000
11:24732117:GTC:G	acceptor_gain	1.0000
11:24738211:A:AG	acceptor_gain	1.0000
11:24738212:C:G	acceptor_gain	1.0000
11:24738214:A:AG	acceptor_gain	1.0000
11:24738215:A:G	acceptor_gain	1.0000
11:24738217:ATAG:A	acceptor_loss	1.0000
11:24738218:T:G	acceptor_gain	1.0000
11:24738219:A:AG	acceptor_gain	1.0000
11:24738219:A:T	acceptor_loss	1.0000
11:24738220:G:A	acceptor_loss	1.0000

AlphaMissense

2275 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:24763298:T:C	L129P	0.998
11:24976601:T:C	L178P	0.998
11:24914498:T:C	L161P	0.997
11:24906013:T:C	L140P	0.996
11:24914476:T:C	S154P	0.993
11:24976610:T:C	L181P	0.993
11:24983165:T:C	C213R	0.993
11:24763292:G:C	R127P	0.992
11:24906005:A:C	K137N	0.992
11:24906005:A:T	K137N	0.992
11:24914507:T:C	L164P	0.992
11:24976643:T:C	L192P	0.991
11:24906004:A:T	K137I	0.990
11:24983167:C:G	C213W	0.990
11:24729240:T:C	L45P	0.989
11:24914491:G:C	A159P	0.989
11:24976630:G:C	A188P	0.989
11:24738262:T:C	L98P	0.988
11:24763301:A:C	Q130P	0.987
11:24729198:T:C	L31P	0.986
11:24906001:T:C	L136S	0.986
11:24976591:G:C	A175P	0.986
11:24729219:G:C	R38P	0.985
11:24738250:T:C	L94P	0.985
11:24983141:G:C	A205P	0.985
11:24763256:T:C	L115S	0.984
11:24976622:T:C	L185S	0.984
11:24738238:T:C	L90P	0.983
11:24738282:G:C	A105P	0.983
11:24738297:G:C	A110P	0.983

dbSNP variants (sampled 300 via entrez): RS1000001959 (11:24828268 G>A), RS1000002689 (11:25064954 T>A), RS1000003041 (11:24772743 T>C), RS1000004476 (11:24550900 G>A), RS1000012608 (11:24789610 C>A,T), RS1000014893 (11:24940941 T>G), RS1000016241 (11:24919722 A>C,T), RS1000025445 (11:24976566 A>G), RS1000027749 (11:24954685 A>G), RS1000028012 (11:24512376 T>C), RS1000030422 (11:25015056 G>A), RS1000046742 (11:24555713 T>C), RS1000047814 (11:24995920 A>C,G), RS1000053405 (11:24733537 C>T), RS1000053773 (11:24848049 A>C)

Disease associations

OMIM: gene MIM:608178 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

29 associations (top):

Study	Trait	p-value
GCST000301_6	Iron status biomarkers	2.000000e-06
GCST000756_9	Magnesium levels	3.000000e-07
GCST001428_10	Intelligence	8.000000e-08
GCST001524_27	Visceral adipose tissue/subcutaneous adipose tissue ratio	7.000000e-06
GCST001658_11	Alzheimer’s disease (late onset)	8.000000e-07
GCST002539_5	Schizophrenia	3.000000e-09
GCST002755_2	Depressive symptoms (SSRI exposure interaction)	2.000000e-07
GCST003992_38	Photic sneeze reflex	1.000000e-18
GCST004059_1	Exhaled nitric oxide levels	2.000000e-06
GCST004060_4	Exhaled nitric oxide output	2.000000e-07
GCST004403_5	Bone fracture in osteoporosis	5.000000e-06
GCST004946_113	Schizophrenia	5.000000e-09
GCST005713_1	Plasma neurofilament light levels	1.000000e-06
GCST006428_9	Suicide attempts	3.000000e-06
GCST006803_70	Schizophrenia	1.000000e-09
GCST007201_117	Schizophrenia	2.000000e-08
GCST007201_319	Schizophrenia	2.000000e-08
GCST008154_32	Trunk fat mass	7.000000e-06
GCST008155_26	Waist-hip ratio	2.000000e-06
GCST008159_83	Waist-to-hip ratio adjusted for BMI	6.000000e-07
GCST008395_7	End-stage kidney disease	6.000000e-07
GCST009213_12	Superior temporal gyrus volume	4.000000e-06
GCST009302_15	Antipsychotic drug-induced weight gain in schizophrenia	5.000000e-06
GCST009302_7	Antipsychotic drug-induced weight gain in schizophrenia	6.000000e-06
GCST009524_33	Household income (MTAG)	5.000000e-10
GCST009849_9	Hallux valgus	5.000000e-06
GCST012490_116	Femur bone mineral density x serum urate levels interaction	1.000000e-08
GCST012490_498	Femur bone mineral density x serum urate levels interaction	2.000000e-08
GCST90002409_39	Childhood body mass index	1.000000e-06

EFO canonical traits (16, from GWAS)

EFO ID	Trait name
EFO:0004461	iron biomarker measurement
EFO:0004845	magnesium measurement
EFO:0004337	intelligence
EFO:0004767	visceral:subcutaneous adipose tissue ratio
EFO:0007006	depressive symptom measurement
EFO:0007010	drug use measurement
EFO:0007011	SSRI use measurement
EFO:0007887	autosomal dominant compelling helio-ophthalmic outburst syndrome
EFO:0005536	nitric oxide exhalation measurement
EFO:0004321	attempted suicide
EFO:0004343	waist-hip ratio
EFO:0007788	BMI-adjusted waist-hip ratio
EFO:0004567	antipsychotic drug related weight gain
EFO:0009695	household income
EFO:0004531	urate measurement
EFO:0004340	body mass index

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	affects splicing, decreases expression	2
Aflatoxin B1	decreases methylation, increases expression	2
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment	1
clothianidin	increases expression	1
Benzo(a)pyrene	affects methylation	1
Calcitriol	decreases expression, affects cotreatment	1
Daunorubicin	affects response to substance	1
Diethylhexyl Phthalate	decreases expression	1
Lipopolysaccharides	affects response to substance, increases expression, affects cotreatment	1
Testosterone	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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