LYPD3

gene
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Also known as C4.4A

Summary

LYPD3 (LY6/PLAUR domain containing 3, HGNC:24880) is a protein-coding gene on chromosome 19q13.31, encoding Ly6/PLAUR domain-containing protein 3 (O95274). Supports cell migration.

Predicted to enable laminin binding activity. Involved in negative regulation of smooth muscle cell apoptotic process. Located in extracellular space.

Source: NCBI Gene 27076 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 61 total
  • MANE Select transcript: NM_014400

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24880
Approved symbolLYPD3
NameLY6/PLAUR domain containing 3
Location19q13.31
Locus typegene with protein product
StatusApproved
AliasesC4.4A
Ensembl geneENSG00000124466
Ensembl biotypeprotein_coding
OMIM609484
Entrez27076

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 retained_intron, 1 protein_coding

ENST00000244333, ENST00000594326, ENST00000595970, ENST00000597741

RefSeq mRNA: 1 — MANE Select: NM_014400 NM_014400

CCDS: CCDS12620

Canonical transcript exons

ENST00000244333 — 5 exons

ExonStartEnd
ENSE000008474114346078743461847
ENSE000008474154346549343465608
ENSE000011616594346359943463769
ENSE000034721944346312643463287
ENSE000036721414346432543464456

Expression profiles

Bgee: expression breadth ubiquitous, 199 present calls, max score 99.70.

FANTOM5 (CAGE): breadth broad, TPM avg 5.4228 / max 285.8621, expressed in 346 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
1812704.1405266
1812720.6425219
1812710.4860205
1812730.084541
1812680.040920
1812690.02847

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
gingival epitheliumUBERON:000194999.70gold quality
lower esophagus mucosaUBERON:003583499.63gold quality
gingivaUBERON:000182899.61gold quality
cervix squamous epitheliumUBERON:000692299.45gold quality
pharyngeal mucosaUBERON:000035599.44gold quality
skin of abdomenUBERON:000141699.34gold quality
tongue squamous epitheliumUBERON:000691999.14gold quality
nippleUBERON:000203099.12gold quality
upper arm skinUBERON:000426399.09gold quality
squamous epitheliumUBERON:000691499.07gold quality
esophagus mucosaUBERON:000246999.01gold quality
mammalian vulvaUBERON:000099798.98gold quality
cervix epitheliumUBERON:000480198.98gold quality
penisUBERON:000098998.93gold quality
skin of legUBERON:000151198.85gold quality
zone of skinUBERON:000001498.82gold quality
upper leg skinUBERON:000426298.79gold quality
esophagus squamous epitheliumUBERON:000692098.67gold quality
body of tongueUBERON:001187698.42gold quality
oral cavityUBERON:000016798.39gold quality
epithelium of esophagusUBERON:000197698.09gold quality
skin of hipUBERON:000155496.51gold quality
tongueUBERON:000172395.67gold quality
vaginaUBERON:000099693.69gold quality
hair follicleUBERON:000207393.22gold quality
palpebral conjunctivaUBERON:000181292.14gold quality
amniotic fluidUBERON:000017391.52gold quality
superior surface of tongueUBERON:000737191.40gold quality
tonsilUBERON:000237288.77gold quality
mouth mucosaUBERON:000372988.21gold quality

Single-cell (SCXA)

Detected in 5 experiment(s), a significant marker in 5.

ExperimentMarker?Max mean expression
E-MTAB-8142yes3660.98
E-HCAD-1yes1511.57
E-CURD-114yes428.55
E-MTAB-6701yes47.72
E-ANND-3no0.00

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CEBPB, FOXC1, JUN, JUND, SP1, SP3

miRNA regulators (miRDB)

42 targeting LYPD3, 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-7110-3P100.0073.182486
HSA-LET-7A-3P100.0074.033932
HSA-LET-7B-3P100.0074.083913
HSA-LET-7F-1-3P100.0074.023928
HSA-MIR-98-3P100.0074.083907
HSA-MIR-27A-3P99.9872.132955
HSA-MIR-27B-3P99.9872.132955
HSA-MIR-998599.9872.112939
HSA-MIR-128-3P99.9571.172484
HSA-MIR-216A-3P99.9571.192505
HSA-MIR-651-3P99.9473.485177
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-3681-3P99.8870.462254
HSA-MIR-3617-5P99.7569.411968
HSA-MIR-64199.7569.351975
HSA-MIR-1255A99.7468.09744
HSA-MIR-1255B-5P99.7468.16741
HSA-MIR-6752-3P99.7266.711587
HSA-MIR-7-5P99.6770.531809
HSA-MIR-182799.6368.573265
HSA-MIR-6716-5P99.5668.621244
HSA-MIR-186-3P99.5166.241685
HSA-MIR-5584-5P99.4968.222814
HSA-MIR-125399.1267.081688
HSA-MIR-4738-3P98.9867.981846
HSA-MIR-6770-5P98.9766.761853
HSA-MIR-455-3P98.9467.68878
HSA-MIR-1304-5P98.9068.581054
HSA-MIR-2355-5P98.8365.511589
HSA-MIR-455-5P98.7467.31795

Literature-anchored findings (GeneRIF, showing 20)

  • hAG-2 and hAG-3, human homologues of genes involved in differentiation, are associated with oestrogen receptor-positive breast tumours and interact with metastasis gene C4.4a and dystroglycan (PMID:12592373)
  • High tumour cell C4.4A expression is associated with shorter survival for non-small cell lung cancer patients. (PMID:17706320)
  • Overexpression of C4.4A is associated with invasion and metastasis of esophageal squamous cell carcinoma (PMID:17849475)
  • we consider C4.4A as a candidate diagnostic marker in colorectal cancer, which possibly can be detected in body fluids (PMID:17912244)
  • cleavage of C4.4A by ADAM10 and ADAM17 contributes to tumor progression (PMID:18979631)
  • data indicate that expression of the C4.4A protein at the invasive front acts as a novel prognostic marker in colorectal cancer, possibly through invasion-related mechanisms (PMID:20825414)
  • findings suggest that a tight association between C4.4A and tumor budding may, in part, be due to C4.4A promoting epithelial-mesenchymal transition at the invasive front of colorectal cancer (PMID:22404718)
  • the first explanation for the C4.4A contribution to wound healing and metastasis. (PMID:22431918)
  • Tenascin-C expression was significantly associated with C4.4A expression in clinical esophageal squamous carcinoma samples suggesting that there may be a functional role for the C4.4A to induceTenascin-C in vivo. (PMID:23708783)
  • Highly expressed C4.4A protein in HER2-positive human breast cancers indicate a good prognosis. (PMID:23918676)
  • overexpression of C4.4A correlates with metastatic potential of gastric cancer and C4.4A could be a novel independent prognostic marker for predicting outcome. (PMID:24935570)
  • expression of the Ly6/uPAR-domain proteins C4.4A and Haldisin in non-invasive and invasive skin lesions (PMID:25414274)
  • LYPD3 has a role in the maintenance of colorectal cancer stem-like cells. (PMID:28238780)
  • Expression and crystallographic studies of the D1D2 domains of C4.4A have been reported. (PMID:28777093)
  • While in the healthy liver hepatocytes are C4.4A negative, data show that C4.4A is strongly expressed in hepatocellular carcinoma (HCC) with upregulation at the invasive front and in lung metastasis, indicating that C4.4A apparently contributes to HCC progression. (PMID:29048672)
  • Our results are consistent with previous data in mouse embryogenesis and wound healing. Based on these findings, we conclude that this human TES model provides an excellent surrogate for studies of C4.4A and Haldisin expressions in human stratified epithelia. (PMID:29075641)
  • Long non-coding RNA OGFRP1 contributed to progression of non-small cell lung cancer at least partly through upregulating LYPD3 expression by sponging miR-124-3p. (PMID:30274775)
  • The authors explored the related pathways through which LYPD3 affects the pathogenesis and prognosis of lung adenocarcinoma by gene set enrichment analysis, and found that LYPD3 might affect the clinical manifestations of lung adenocarcinoma by regulating the P53 signaling pathway. (PMID:32040344)
  • LY6/PLAUR domain containing 3 (LYPD3) maintains melanoma cell stemness and mediates an immunosuppressive microenvironment. (PMID:37924160)
  • m6A-dependent mature miR-151-5p accelerates the malignant process of HNSCC by targeting LYPD3. (PMID:39009906)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusLypd3ENSMUSG00000057454
rattus_norvegicusLypd3ENSRNOG00000019999

Paralogs (2): PLAUR (ENSG00000011422), LYPD5 (ENSG00000159871)

Protein

Protein identifiers

Ly6/PLAUR domain-containing protein 3O95274 (reviewed: O95274)

Alternative names: GPI-anchored metastasis-associated protein C4.4A homolog, Matrigel-induced gene C4 protein

All UniProt accessions (2): B2RBR3, O95274

UniProt curated annotations — full annotation on UniProt →

Function. Supports cell migration. May be involved in urothelial cell-matrix interactions. May be involved in tumor progression.

Subunit / interactions. Binds laminin-1 and laminin-5. Interacts with LGALS3. Interacts with AGR2 and AGR3.

Subcellular location. Cell membrane.

Tissue specificity. Expressed in placenta, skin and urothelium. Found in suprabasal keratinocytes of chronic wounds. Weak expression is found in esophagus and peripheral blood mononuclear cells. Found in the majority of primary and metastatic transitional cell carcinomas (TCCs) and as well in breast cancer tissues, but not in adjacent normal tissues. High expression is found in the tumor component of some noninvasive superficial lesions and in invasive and metastatic urothelial cancers.

Post-translational modifications. N-glycosylated and O-glycosylated.

Induction. Up-regulated in migrating keratinocytes during epithelization of incisional skin wounds.

RefSeq proteins (1): NP_055215* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR016054LY6_UPA_recep-likeDomain
IPR045860Snake_toxin-like_sfHomologous_superfamily

Pfam: PF00021

UniProt features (31 total): strand 13, glycosylation site 4, compositionally biased region 3, turn 2, helix 2, domain 2, signal peptide 1, chain 1, propeptide 1, region of interest 1, lipid moiety-binding region 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
6IOMX-RAY DIFFRACTION2.59
6IONX-RAY DIFFRACTION2.75

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O95274-F174.610.51

Antibody-complex structures (SAbDab): 16ION

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): 326

Glycosylation sites (4): 118, 163, 176, 183

Function

Pathways and Gene Ontology

Reactome pathways

3 pathways

IDPathway
R-HSA-163125Post-translational modification: synthesis of GPI-anchored proteins
R-HSA-392499Metabolism of proteins
R-HSA-597592Post-translational protein modification

MSigDB gene sets: 141 (showing top): JAEGER_METASTASIS_DN, ENK_UV_RESPONSE_KERATINOCYTE_UP, AREB6_01, NAGASHIMA_NRG1_SIGNALING_UP, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, AMIT_EGF_RESPONSE_480_MCF10A, GOBP_NEGATIVE_REGULATION_OF_MUSCLE_CELL_APOPTOTIC_PROCESS, MODULE_379, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN, MODULE_88, MODULE_242, GOBP_CELL_SUBSTRATE_ADHESION, CTTTGTA_MIR524

GO Biological Process (2): cell-matrix adhesion (GO:0007160), negative regulation of smooth muscle cell apoptotic process (GO:0034392)

GO Molecular Function (1): laminin binding (GO:0043236)

GO Cellular Component (5): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), plasma membrane (GO:0005886), side of membrane (GO:0098552), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Post-translational protein modification1
Metabolism of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
membrane2
cell-substrate adhesion1
negative regulation of muscle cell apoptotic process1
smooth muscle cell apoptotic process1
regulation of smooth muscle cell apoptotic process1
protein binding1
extracellular matrix binding1
cell periphery1
leaflet of membrane bilayer1

Protein interactions and networks

STRING

946 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
LYPD3AGR2O95994972
LYPD3AGR3Q8TD06893
LYPD3DAG1Q14118756
LYPD3PLAURQ03405685
LYPD3PLAUP00749550
LYPD3PINLYPA6NC86542
LYPD3LY6LH3BQJ8540
LYPD3CD59P13987536
LYPD3PHLDB3Q6NSJ2536
LYPD3TEX101Q9BY14521
LYPD3MMP14P50281516
LYPD3PATE3B3GLJ2507
LYPD3ESR1P03372501
LYPD3ZNF575Q86XF7468
LYPD3PATE2Q6UY27447

IntAct

23 interactions, top by confidence:

ABTypeScore
LYPD3SCAMP1psi-mi:“MI:0914”(association)0.640
Trim69psi-mi:“MI:0915”(physical association)0.400
LYPD3AURKApsi-mi:“MI:0915”(physical association)0.370
BAG4LYPD3psi-mi:“MI:0915”(physical association)0.370
BRMS1LYPD3psi-mi:“MI:0915”(physical association)0.370
LYPD3CASP8psi-mi:“MI:0915”(physical association)0.370
CHEK2LYPD3psi-mi:“MI:0915”(physical association)0.370
ERBB2LYPD3psi-mi:“MI:0915”(physical association)0.370
IGF1RLYPD3psi-mi:“MI:0915”(physical association)0.370
LSP1LYPD3psi-mi:“MI:0915”(physical association)0.370
PALB2LYPD3psi-mi:“MI:0915”(physical association)0.370
LYPD3PPM1Dpsi-mi:“MI:0915”(physical association)0.370
PTPRJLYPD3psi-mi:“MI:0915”(physical association)0.370
RB1CC1LYPD3psi-mi:“MI:0915”(physical association)0.370
SMAD4LYPD3psi-mi:“MI:0915”(physical association)0.370
LYPD3STK11psi-mi:“MI:0915”(physical association)0.370
LYPD3CLASP2psi-mi:“MI:0914”(association)0.350
TEX14DNAJB6psi-mi:“MI:0914”(association)0.350
LYPD3TNPO2psi-mi:“MI:0914”(association)0.350
LYPD3NEMP1psi-mi:“MI:0914”(association)0.350
INSRBLTP3Bpsi-mi:“MI:0914”(association)0.350
PCGF5LYPD3psi-mi:“MI:0914”(association)0.350

BioGRID (281): VDAC3 (Affinity Capture-MS), XPO7 (Affinity Capture-MS), TTI2 (Affinity Capture-MS), ATP2B4 (Affinity Capture-MS), BZW2 (Affinity Capture-MS), BZW1 (Affinity Capture-MS), SLC9A1 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS), TNPO2 (Affinity Capture-MS), SYMPK (Affinity Capture-MS), RBM26 (Affinity Capture-MS), PHTF2 (Affinity Capture-MS), TMEM214 (Affinity Capture-MS), GPAA1 (Affinity Capture-MS), TARBP1 (Affinity Capture-MS)

ESM2 similar proteins: A2VE33, A8HDK4, A8S6B0, C0STK8, C0STK9, I6PG79, O12962, O55006, O55162, O57690, O95274, P0DQP7, P0DQX3, P0DUK5, P0DUK6, P35459, P35460, P58019, P60591, P60592, P81827, P81828, P82143, P82144, P83121, Q05588, Q3UN54, Q66H42, Q6MG58, Q6UWN5, Q6UX82, Q78CF9, Q7LZI1, Q7LZI2, Q7TQN2, Q8BLC3, Q8N2G4, Q8VEN2, Q90358, Q91YK8

Diamond homologs: O55162, O95274, Q91YK8

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 24 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

GO biological processes:

GO termPartnersFoldFDR
protein autophosphorylation531.6×2e-04
negative regulation of cell population proliferation59.2×5e-03
negative regulation of apoptotic process57.5×1e-02

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance48
Likely benign2
Benign3

Top pathogenic / likely-pathogenic (0)

SpliceAI

621 predictions. Top by Δscore:

VariantEffectΔscore
19:43461844:TTAG:Tacceptor_gain1.0000
19:43461845:TAG:Tacceptor_gain1.0000
19:43461846:AG:Aacceptor_gain1.0000
19:43461848:C:CCacceptor_gain1.0000
19:43463121:CTCAC:Cdonor_loss1.0000
19:43463123:CACCT:Cdonor_loss1.0000
19:43463124:A:Tdonor_loss1.0000
19:43463124:ACCTG:Adonor_gain1.0000
19:43463125:C:CTdonor_loss1.0000
19:43463125:CCTG:Cdonor_gain1.0000
19:43463125:CCTGC:Cdonor_gain1.0000
19:43463128:G:Adonor_gain1.0000
19:43463283:ATTAC:Aacceptor_gain1.0000
19:43463284:TTAC:Tacceptor_gain1.0000
19:43463285:TAC:Tacceptor_gain1.0000
19:43463285:TACCT:Tacceptor_loss1.0000
19:43463286:AC:Aacceptor_gain1.0000
19:43463287:CC:Cacceptor_gain1.0000
19:43463288:C:CCacceptor_gain1.0000
19:43463291:C:CTacceptor_gain1.0000
19:43463292:G:Tacceptor_gain1.0000
19:43463301:C:CTacceptor_gain1.0000
19:43463301:C:Tacceptor_gain1.0000
19:43463302:G:Tacceptor_gain1.0000
19:43463595:GGAC:Gdonor_loss1.0000
19:43463596:GAC:Gdonor_loss1.0000
19:43463598:C:Adonor_loss1.0000
19:43463601:G:Adonor_gain1.0000
19:43463766:TGGA:Tacceptor_gain1.0000
19:43463770:C:CCacceptor_gain1.0000

AlphaMissense

2203 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:43461726:G:CN222K0.998
19:43461726:G:TN222K0.998
19:43463152:A:CF173C0.998
19:43463155:C:GC172S0.997
19:43463156:A:TC172S0.997
19:43463639:G:CN114K0.997
19:43463639:G:TN114K0.997
19:43464354:C:GC61S0.997
19:43464355:A:TC61S0.997
19:43461730:C:GC221S0.996
19:43461731:A:TC221S0.996
19:43461814:C:GC193S0.996
19:43461815:A:TC193S0.996
19:43463154:G:CC172W0.996
19:43463156:A:GC172R0.996
19:43463251:C:GC140S0.996
19:43463252:A:TC140S0.996
19:43463675:G:CF102L0.996
19:43463675:G:TF102L0.996
19:43463677:A:GF102L0.996
19:43461815:A:GC193R0.995
19:43461823:A:TV190D0.995
19:43463151:G:CF173L0.995
19:43463151:G:TF173L0.995
19:43463153:A:GF173L0.995
19:43463187:G:CC161W0.995
19:43463188:C:GC161S0.995
19:43463188:C:TC161Y0.995
19:43463189:A:TC161S0.995
19:43463252:A:GC140R0.995

dbSNP variants (sampled 300 via entrez): RS1000008650 (19:43462424 G>C), RS1000062519 (19:43462778 C>T), RS1000579335 (19:43467039 C>T), RS1001009941 (19:43461184 A>C,G), RS1001138918 (19:43465130 T>C), RS1001976838 (19:43465525 G>A), RS1003125420 (19:43462617 A>G), RS1003346279 (19:43465205 G>A), RS1003377302 (19:43465423 G>A,C), RS1003727613 (19:43460958 G>A), RS1004092301 (19:43464669 C>G), RS1004569940 (19:43465064 G>A,T), RS1005274412 (19:43463975 C>A,G,T), RS1005614800 (19:43464331 C>T), RS1005628974 (19:43460599 G>A)

Disease associations

OMIM: gene MIM:609484 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

1 associations (top):

StudyTraitp-value
GCST002652_14Cotinine glucuronidation4.000000e-08

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0006508cotinine glucuronidation measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, increases expression5
sodium arsenitedecreases expression, increases expression2
entinostatincreases expression, affects cotreatment2
Panobinostataffects cotreatment, increases expression2
Air Pollutantsdecreases expression, increases abundance, increases expression2
Smokedecreases expression, increases abundance, increases expression2
Tobacco Smoke Pollutionaffects expression, increases expression2
propionaldehydeincreases expression1
sodium arsenatedecreases expression, increases abundance1
pyrogallol 1,3-dimethyl etheraffects cotreatment, increases expression1
2-methyl-4-isothiazolin-3-oneincreases expression1
ethyl-p-hydroxybenzoateincreases expression1
beta-lapachoneincreases expression1
afimoxifenedecreases reaction, decreases expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
bleomycetinincreases expression1
cupric chloridedecreases expression1
benazol Paffects expression1
octa-2,4,6-trienoic aciddecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, increases expression1
erucylphospho-N,N,N-trimethylpropylammoniumincreases expression1
abrinedecreases expression1
dorsomorphinaffects cotreatment, increases expression1
LG 100815decreases expression1
Leflunomidedecreases expression1
Arsenicdecreases expression, increases abundance1
Atrazineincreases expression1
Benzo(a)pyrenedecreases methylation, affects methylation1
Calcitriolincreases expression1
Estradioldecreases expression1

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.