LAYN

Summary

LAYN (layilin, HGNC:29471) is a protein-coding gene on chromosome 11q23.1, encoding Layilin (Q6UX15). Receptor for hyaluronate.

Enables hyaluronic acid binding activity. Located in focal adhesion.

Source: NCBI Gene 143903 — RefSeq curated summary.

At a glance

• GWAS associations: 10
• Clinical variants (ClinVar): 78 total
• MANE Select transcript: NM_178834

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29471
Approved symbol	LAYN
Name	layilin
Location	11q23.1
Locus type	gene with protein product
Status	Approved
Aliases	FLJ30977, FLJ31092
Ensembl gene	ENSG00000204381
Ensembl biotype	protein_coding
OMIM	618843
Entrez	143903

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 12 protein_coding, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000375614, ENST00000375615, ENST00000436913, ENST00000525126, ENST00000525866, ENST00000528102, ENST00000528924, ENST00000530962, ENST00000533265, ENST00000533999, ENST00000851628, ENST00000851629, ENST00000851630, ENST00000935731

RefSeq mRNA: 4 — MANE Select: NM_178834 NM_001258390, NM_001258391, NM_001318799, NM_178834

CCDS: CCDS31676, CCDS58178, CCDS58179

Canonical transcript exons

ENST00000375614 — 7 exons

Exon	Start	End
ENSE00003503128	111554561	111554593
ENSE00003504896	111560095	111561745
ENSE00003537210	111549618	111549775
ENSE00003560918	111540720	111540928
ENSE00003573304	111543923	111544220
ENSE00003679299	111555207	111555290
ENSE00003789150	111557541	111557643

Expression profiles

Bgee: expression breadth ubiquitous, 225 present calls, max score 96.36.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 18.5099 / max 288.0773, expressed in 1310 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter ID	TPM avg	Samples expressed
116627	17.9865	1307
116628	0.2612	158
116629	0.2236	110
116626	0.0386	10

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
decidua	UBERON:0002450	96.36	gold quality
stromal cell of endometrium	CL:0002255	93.81	gold quality
amniotic fluid	UBERON:0000173	93.38	gold quality
ascending aorta	UBERON:0001496	90.67	gold quality
thoracic aorta	UBERON:0001515	90.58	gold quality
epithelial cell of pancreas	CL:0000083	90.39	gold quality
descending thoracic aorta	UBERON:0002345	90.32	gold quality
muscle layer of sigmoid colon	UBERON:0035805	88.54	gold quality
smooth muscle tissue	UBERON:0001135	88.24	gold quality
urethra	UBERON:0000057	88.16	gold quality
left ovary	UBERON:0002119	87.97	gold quality
aorta	UBERON:0000947	87.54	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	87.45	gold quality
gall bladder	UBERON:0002110	87.23	gold quality
right ovary	UBERON:0002118	86.59	gold quality
left lobe of thyroid gland	UBERON:0001120	86.26	gold quality
thyroid gland	UBERON:0002046	86.16	gold quality
calcaneal tendon	UBERON:0003701	86.07	gold quality
corpus callosum	UBERON:0002336	85.99	gold quality
body of uterus	UBERON:0009853	85.81	gold quality
left uterine tube	UBERON:0001303	85.70	gold quality
right lobe of thyroid gland	UBERON:0001119	85.36	gold quality
tibial artery	UBERON:0007610	85.30	gold quality
popliteal artery	UBERON:0002250	85.29	gold quality
ovary	UBERON:0000992	85.25	gold quality
germinal epithelium of ovary	UBERON:0001304	85.25	gold quality
visceral pleura	UBERON:0002401	84.82	gold quality
myometrium	UBERON:0001296	84.57	gold quality
mucosa of stomach	UBERON:0001199	84.49	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	84.06	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-MTAB-11121	yes	486.14
E-HCAD-1	yes	17.40
E-CURD-88	yes	16.30
E-ANND-3	yes	5.73

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

62 targeting LAYN, 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-3120-5P	100.00	65.56	965
HSA-MIR-4283	100.00	66.42	2097
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-223-3P	99.99	70.14	1140
HSA-MIR-6888-3P	99.97	65.95	1170
HSA-MIR-3065-5P	99.97	71.56	3281
HSA-MIR-507	99.97	70.11	1915
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-557	99.96	70.01	1640
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-651-3P	99.94	73.48	5177
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-627-3P	99.90	71.42	3316
HSA-MIR-153-5P	99.89	73.86	6317
HSA-MIR-3617-5P	99.75	69.41	1968
HSA-MIR-641	99.75	69.35	1975
HSA-MIR-6885-3P	99.75	70.36	3187
HSA-MIR-3680-3P	99.75	72.51	3095
HSA-MIR-1303	99.65	69.77	1662
HSA-MIR-4663	99.62	65.33	957
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-510-3P	99.54	70.06	2965
HSA-MIR-3915	99.45	68.49	1905
HSA-MIR-19A-5P	99.36	66.93	1675
HSA-MIR-4999-5P	99.35	69.15	926
HSA-MIR-1244	99.33	68.38	832
HSA-MIR-133A-5P	99.28	69.13	941
HSA-MIR-4505	99.27	67.81	2678

Literature-anchored findings (GeneRIF, showing 10)

• Hyaluronan and layilin mediate loss of airway epithelial barrier function induced by cigarette smoke by decreasing E-cadherin. (PMID:23048036)
• results indicate that LAYN would be involved in the enhancement of inflammation and degradation of cartilage in joint diseases such as RA and OA (PMID:25150153)
• Renal biopsy samples from patients with glomerulonephritis showed high expression of LAYN in tubular epithelial cells. (PMID:26410531)
• increased LAYN expression correlates with poor prognosis and increased immune infiltration levels in CD8+ T cells, CD4+ T cells, macrophages, neutrophils and DCs of multiple cancers, especially in colon and gastric cancers. (PMID:30761122)
• Layilin augments integrin activation to promote antitumor immunity. (PMID:32539073)
• Layilin promotes mitochondrial fission by cyclin-dependent kinase 1 and dynamin-related protein 1 activation in HEK293T cells. (PMID:33676182)
• ncRNA-Regulated LAYN Serves as a Prognostic Biomarker and Correlates with Immune Cell Infiltration in Hepatocellular Carcinoma: A Bioinformatics Analysis. (PMID:36398067)
• Comprehensive landscape of the miRNA-regulated prognostic marker LAYN with immune infiltration and stemness in pan-cancer. (PMID:37335337)
• Elevated Layilin-Positive Monocyte Levels in the Peripheral Blood of Patients with Systemic Lupus Erythematosus Reflect Their Autoimmune Status. (PMID:37642473)
• Role of layilin in regulating mitochondria-mediated apoptosis: a study on B cell lymphoma (BCL)-2 family proteins. (PMID:39455917)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	layna	ENSDARG00000035169
danio_rerio	laynb	ENSDARG00000056835
mus_musculus	Layn	ENSMUSG00000060594
rattus_norvegicus	Layn	ENSRNOG00000011228

Paralogs (1): CHODL (ENSG00000154645)

Protein

Protein identifiers

Layilin — Q6UX15 (reviewed: Q6UX15)

All UniProt accessions (7): A0A0D9SFG0, E9PK64, E9PMI0, E9PQU7, E9PQY8, E9PR90, Q6UX15

UniProt curated annotations — full annotation on UniProt →

Function. Receptor for hyaluronate.

Subunit / interactions. Interacts with NF2, RDX and TLN1.

Subcellular location. Membrane.

Domain organisation. The C-terminal domain interacts with the N-terminal domain of RDX.

Isoforms (3)

UniProt ID	Names	Canonical?
Q6UX15-1	1	yes
Q6UX15-2	2
Q6UX15-3	3

RefSeq proteins (4): NP_001245319, NP_001245320, NP_001305728, NP_849156* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR001304	C-type_lectin-like	Domain
IPR016186	C-type_lectin-like/link_sf	Homologous_superfamily
IPR016187	CTDL_fold	Homologous_superfamily
IPR051505	C-type_lectin_domain	Family

Pfam: PF00059

UniProt features (27 total): repeat 5, region of interest 5, splice variant 3, modified residue 2, disulfide bond 2, topological domain 2, sequence conflict 2, signal peptide 1, chain 1, glycosylation site 1, sequence variant 1, transmembrane region 1, domain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6UX15-F1	69.27	0.34

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 (2): 286, 299

Disulfide bonds (2): 71–184, 150–176

Glycosylation sites (1): 117

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 85 (showing top): BENPORATH_ES_WITH_H3K27ME3, GOCC_CELL_SURFACE, GOCC_RUFFLE, CAGCTG_AP4_Q5, ATF1_Q6, GOMF_GLYCOSAMINOGLYCAN_BINDING, RYTTCCTG_ETS2_B, NERF_Q2, GOCC_ANCHORING_JUNCTION, MGGAAGTG_GABP_B, GOCC_CELL_LEADING_EDGE, GOMF_HYALURONIC_ACID_BINDING, HAMAI_APOPTOSIS_VIA_TRAIL_UP, DODD_NASOPHARYNGEAL_CARCINOMA_DN, CHEN_METABOLIC_SYNDROM_NETWORK

GO Biological Process (0):

GO Molecular Function (3): hyaluronic acid binding (GO:0005540), carbohydrate binding (GO:0030246), protein binding (GO:0005515)

GO Cellular Component (4): ruffle (GO:0001726), focal adhesion (GO:0005925), cell surface (GO:0009986), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	2
cellular anatomical structure	2
carboxylic acid binding	1
cell leading edge	1
plasma membrane bounded cell projection	1
cell-substrate junction	1

Protein interactions and networks

STRING

596 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
LAYN	TLN1	Q9Y490	947
LAYN	TLN2	Q9Y4G6	940
LAYN	NF2	P35240	828
LAYN	RDX	P35241	758
LAYN	LYVE1	Q9Y5Y7	546
LAYN	MAGEH1	Q9H213	515
LAYN	MSN	P26038	510
LAYN	HMMR	O75330	507
LAYN	EZR	P15311	481
LAYN	TIGIT	Q495A1	479
LAYN	HAVCR2	Q8TDQ0	475
LAYN	LAG3	P18627	471
LAYN	GZMK	P49863	448
LAYN	CTLA4	P16410	448
LAYN	CCR8	P51685	446

IntAct

5 interactions, top by confidence:

A	B	Type	Score
KCNE3	RIOK3	psi-mi:“MI:0914”(association)	0.530
LPAR1	TMEM223	psi-mi:“MI:0914”(association)	0.530
	SNAP23	psi-mi:“MI:0914”(association)	0.350
P		psi-mi:“MI:0914”(association)	0.350

BioGRID (30): LAYN (Reconstituted Complex), LAYN (Two-hybrid), LAYN (Two-hybrid), LAYN (Two-hybrid), DEFB121 (Two-hybrid), PPAPDC2 (Two-hybrid), LAYN (Affinity Capture-RNA), LAYN (Two-hybrid), NACA (Proximity Label-MS), TXNL1 (Proximity Label-MS), POLR1A (Proximity Label-MS), NACAP1 (Proximity Label-MS), BTF3 (Proximity Label-MS), HSPA8 (Proximity Label-MS), HSPA6 (Proximity Label-MS)

ESM2 similar proteins: A0JNA2, A2RRU4, A4FUY1, A5D7V5, A8MVS5, D4A6L0, E1BBQ2, O19131, O54693, O75144, P09564, P15151, P19438, P29590, P31994, P32506, P32507, P50555, P97260, Q14CZ8, Q28110, Q3TEW6, Q53EL9, Q5BJT4, Q5DRQ8, Q5T848, Q61190, Q640R3, Q6AYP5, Q6AYT8, Q6BAA4, Q6GQT6, Q6P6J9, Q6UX15, Q70EL4, Q75VT8, Q7TSK2, Q7Z692, Q8C419, Q8N126

Diamond homologs: A0ZT93, A5PMY6, A6QP79, B0VXV0, B0VXV1, D3ZWT9, O14594, P02707, P06734, P07307, P07897, P07898, P08290, P08661, P0DQV8, P10716, P13608, P13611, P16112, P20693, P22897, P24721, P41317, P48304, P49300, P49874, P50403, P55066, P55067, P55068, P70194, P81018, P81282, P82596, Q28062, Q28343, Q28670, Q29011, Q2LK54, Q2LK95

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	66
Likely benign	2
Benign	4

Top pathogenic / likely-pathogenic (0)

SpliceAI

992 predictions. Top by Δscore:

Variant	Effect	Δscore
11:111540926:GTG:G	donor_gain	1.0000
11:111542801:G:GT	donor_gain	1.0000
11:111554554:A:AG	acceptor_gain	1.0000
11:111554559:A:AG	acceptor_gain	1.0000
11:111554560:G:GG	acceptor_gain	1.0000
11:111554591:AAGGT:A	donor_loss	1.0000
11:111554592:AGG:A	donor_loss	1.0000
11:111554593:GGT:G	donor_loss	1.0000
11:111554594:GTA:G	donor_loss	1.0000
11:111554595:T:A	donor_loss	1.0000
11:111555282:A:T	donor_gain	1.0000
11:111557538:CAGAA:C	acceptor_loss	1.0000
11:111557539:A:AG	acceptor_gain	1.0000
11:111557540:G:GG	acceptor_gain	1.0000
11:111557540:GAA:G	acceptor_gain	1.0000
11:111560093:A:AG	acceptor_gain	1.0000
11:111560094:G:GG	acceptor_gain	1.0000
11:111560094:GA:G	acceptor_gain	1.0000
11:111560094:GAA:G	acceptor_gain	1.0000
11:111540924:GAGTG:G	donor_gain	0.9900
11:111540929:G:GA	donor_loss	0.9900
11:111540929:G:GG	donor_gain	0.9900
11:111540930:TGAG:T	donor_loss	0.9900
11:111540931:GAGT:G	donor_loss	0.9900
11:111542797:TTAGG:T	donor_gain	0.9900
11:111549234:A:G	donor_gain	0.9900
11:111549744:G:GT	donor_gain	0.9900
11:111554543:T:TA	acceptor_gain	0.9900
11:111554555:C:G	acceptor_gain	0.9900
11:111554556:TACAG:T	acceptor_gain	0.9900

AlphaMissense

2465 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:111549624:G:C	W138C	0.999
11:111549624:G:T	W138C	0.999
11:111549721:T:A	W171R	0.999
11:111549721:T:C	W171R	0.999
11:111549723:G:C	W171C	0.999
11:111549723:G:T	W171C	0.999
11:111544128:G:C	W105C	0.997
11:111544128:G:T	W105C	0.997
11:111544194:G:C	W127C	0.997
11:111544194:G:T	W127C	0.997
11:111549622:T:A	W138R	0.997
11:111549622:T:C	W138R	0.997
11:111549658:T:C	C150R	0.997
11:111549658:T:A	C150S	0.996
11:111549659:G:C	C150S	0.996
11:111549722:G:C	W171S	0.996
11:111549659:G:A	C150Y	0.995
11:111544126:T:A	W105R	0.994
11:111544126:T:C	W105R	0.994
11:111549660:C:G	C150W	0.994
11:111549736:T:A	C176S	0.994
11:111549737:G:C	C176S	0.994
11:111549760:T:A	C184S	0.994
11:111549761:G:C	C184S	0.994
11:111544192:T:A	W127R	0.993
11:111544192:T:C	W127R	0.993
11:111549726:T:A	N172K	0.993
11:111549726:T:G	N172K	0.993
11:111549659:G:T	C150F	0.992
11:111544026:C:G	C71W	0.991

dbSNP variants (sampled 300 via entrez): RS1000114802 (11:111551774 G>A,C,T), RS1000154255 (11:111543899 T>C), RS1000166849 (11:111551470 G>A,T), RS1000230443 (11:111550471 C>T), RS1000341042 (11:111545083 C>T), RS1000342014 (11:111557761 T>C), RS1000457093 (11:111538422 C>A), RS1000615343 (11:111543031 G>A), RS1000678311 (11:111556504 G>A), RS1001081371 (11:111543380 G>C), RS1001254155 (11:111538290 G>A), RS1001383934 (11:111550386 C>T), RS1001457908 (11:111558547 A>C), RS1001510336 (11:111558218 TTA>T), RS1001564440 (11:111557685 T>C)

Disease associations

OMIM: gene MIM:618843 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

10 associations (top):

Study	Trait	p-value
GCST001762_38	Obesity-related traits	4.000000e-06
GCST005038_73	Allergic disease (asthma, hay fever or eczema)	7.000000e-15
GCST007563_14	Allergic disease (asthma, hay fever or eczema)	1.000000e-10
GCST007564_5	Asthma or allergic disease (pleiotropy)	6.000000e-11
GCST007798_134	Asthma	2.000000e-09
GCST007799_31	Asthma (adult onset)	6.000000e-09
GCST008103_146	Bipolar disorder	3.000000e-06
GCST010135_36	Oily fish consumption	9.000000e-09
GCST010140_26	Pork consumption	9.000000e-09
GCST010142_27	Fish- and plant-related diet	3.000000e-09

EFO canonical traits (3, from GWAS)

EFO ID	Trait name
EFO:0004626	IGFBP-3 measurement
EFO:1002011	adult onset asthma
EFO:0008111	diet measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	increases expression, affects expression, decreases methylation, affects cotreatment	8
trichostatin A	affects cotreatment, increases expression	3
mercuric bromide	increases expression, affects cotreatment	2
entinostat	increases expression, affects cotreatment	2
Panobinostat	affects cotreatment, increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
p-Chloromercuribenzoic Acid	affects cotreatment, increases expression	2
GSK-J4	increases expression	1
methylmercuric chloride	increases expression	1
propionaldehyde	increases expression	1
arsenite	increases methylation	1
sodium arsenite	affects cotreatment, increases abundance, increases expression	1
butyraldehyde	increases expression	1
manganese chloride	affects cotreatment, increases abundance, increases expression	1
pentanal	increases expression	1
perfluorooctane sulfonic acid	decreases expression	1
CGP 52608	increases reaction, affects binding	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	affects cotreatment, increases expression	1
incobotulinumtoxinA	increases expression	1
Temozolomide	increases expression	1
Vorinostat	increases expression	1
Aldehydes	increases expression	1
Arsenic	increases abundance, increases expression, affects cotreatment	1
Calcitriol	decreases expression	1
Lead	decreases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Silicon Dioxide	increases expression	1
Silver	increases expression	1
Tetrachlorodibenzodioxin	affects expression	1

Clinical trials (associated diseases)

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