PCDH18

gene
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Also known as KIAA1562PCDH68L

Summary

PCDH18 (protocadherin 18, HGNC:14268) is a protein-coding gene on chromosome 4q28.3, encoding Protocadherin-18 (Q9HCL0). Potential calcium-dependent cell-adhesion protein.

This gene belongs to the protocadherin gene family, a subfamily of the cadherin superfamily. This gene encodes a protein which contains 6 extracellular cadherin domains, a transmembrane domain and a cytoplasmic tail differing from those of the classical cadherins. Although its specific function is undetermined, the cadherin-related neuronal receptor is thought to play a role in the establishment and function of specific cell-cell connections in the brain.

Source: NCBI Gene 54510 — RefSeq curated summary.

At a glance

  • GWAS associations: 16
  • Clinical variants (ClinVar): 148 total
  • MANE Select transcript: NM_019035

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:14268
Approved symbolPCDH18
Nameprotocadherin 18
Location4q28.3
Locus typegene with protein product
StatusApproved
AliasesKIAA1562, PCDH68L
Ensembl geneENSG00000189184
Ensembl biotypeprotein_coding
OMIM608287
Entrez54510

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 6 protein_coding, 1 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000344876, ENST00000412923, ENST00000507846, ENST00000510305, ENST00000511115, ENST00000611581, ENST00000617302, ENST00000620262

RefSeq mRNA: 2 — MANE Select: NM_019035 NM_001300828, NM_019035

CCDS: CCDS34064, CCDS75193

Canonical transcript exons

ENST00000344876 — 4 exons

ExonStartEnd
ENSE00001365509137528732137528820
ENSE00001373644137518918137521696
ENSE00001376125137529602137532494
ENSE00001378073137528478137528641

Expression profiles

Bgee: expression breadth ubiquitous, 238 present calls, max score 97.69.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 30.7964 / max 1263.1084, expressed in 1041 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
5398329.47591037
539820.9690358
2033420.130745
539810.127353
539790.061921
539800.031613

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
stromal cell of endometriumCL:000225597.69gold quality
calcaneal tendonUBERON:000370195.86gold quality
parietal pleuraUBERON:000240095.72gold quality
mammary ductUBERON:000176595.17gold quality
ileal mucosaUBERON:000033195.11gold quality
epithelium of mammary glandUBERON:000324494.99gold quality
pigmented layer of retinaUBERON:000178294.87gold quality
tibiaUBERON:000097994.75gold quality
endometriumUBERON:000129594.31gold quality
thoracic mammary glandUBERON:000520093.27gold quality
mammary glandUBERON:000191193.14gold quality
placentaUBERON:000198793.08gold quality
skin of hipUBERON:000155493.05gold quality
visceral pleuraUBERON:000240192.90gold quality
cauda epididymisUBERON:000436092.06gold quality
colonic epitheliumUBERON:000039792.03gold quality
tibialis anteriorUBERON:000138591.51silver quality
endothelial cellCL:000011591.24gold quality
cardiac muscle of right atriumUBERON:000337990.21gold quality
urethraUBERON:000005790.18gold quality
layer of synovial tissueUBERON:000761690.10gold quality
tendonUBERON:000004389.84gold quality
gall bladderUBERON:000211089.76gold quality
uterusUBERON:000099589.65gold quality
seminal vesicleUBERON:000099889.39gold quality
synovial jointUBERON:000221789.04gold quality
smooth muscle tissueUBERON:000113588.51gold quality
adrenal tissueUBERON:001830388.09gold quality
left ventricle myocardiumUBERON:000656688.06gold quality
subcutaneous adipose tissueUBERON:000219087.81gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-HCAD-30yes99.18
E-HCAD-10yes57.81
E-ANND-3yes20.51
E-CURD-112yes9.07

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

125 targeting PCDH18, 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-3163100.0077.238605
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-5692A100.0074.406850
HSA-MIR-428299.9975.366408
HSA-MIR-4789-3P99.9970.752484
HSA-MIR-33A-5P99.9968.621055
HSA-MIR-33B-5P99.9968.581062
HSA-MIR-366299.9973.825684
HSA-MIR-548C-3P99.9974.017587
HSA-MIR-485-3P99.9870.681585
HSA-MIR-539-3P99.9870.741616
HSA-MIR-548P99.9872.253784
HSA-MIR-806899.9873.852376
HSA-MIR-1213699.9872.815713
HSA-MIR-477599.9875.006394
HSA-MIR-4789-5P99.9870.762721
HSA-MIR-3692-3P99.9870.272139
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-495-3P99.9672.814197
HSA-MIR-568899.9673.234504
HSA-MIR-493-5P99.9672.472382
HSA-MIR-365899.9673.874379
HSA-MIR-23A-3P99.9574.243163
HSA-MIR-23B-3P99.9574.243163
HSA-MIR-23C99.9573.923192
HSA-MIR-144-3P99.9473.982698
HSA-MIR-6845-3P99.9466.881439
HSA-MIR-9983-3P99.9471.483631
HSA-MIR-101-3P99.9475.032230

Literature-anchored findings (GeneRIF, showing 2)

  • A homozygous PCDH18 missense mutation (S1006L)from familial hemophagocytic lymphohistiocytosis type 2 patient destabilized the protein structure. (PMID:26739415)
  • Our results suggested that PCDH18 was a putative tumor suppressor with epigenetic silencing in colorectal cancer and a potential biomarker for colorectal cancer diagnosis. (PMID:28588296)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriopcdh18bENSDARG00000052494
danio_reriopcdh18aENSDARG00000089805
mus_musculusPcdh18ENSMUSG00000037892
rattus_norvegicusPcdh18ENSRNOG00000009949

Paralogs (61): PCDHB4 (ENSG00000081818), PCDHA6 (ENSG00000081842), PCDHGA2 (ENSG00000081853), PCDHB2 (ENSG00000112852), PCDHB3 (ENSG00000113205), PCDHB5 (ENSG00000113209), PCDHB6 (ENSG00000113211), PCDHB7 (ENSG00000113212), PCDHB15 (ENSG00000113248), PCDH12 (ENSG00000113555), PCDH17 (ENSG00000118946), PCDHB8 (ENSG00000120322), PCDHB10 (ENSG00000120324), PCDHB14 (ENSG00000120327), PCDHB12 (ENSG00000120328), PCDH8 (ENSG00000136099), PCDH10 (ENSG00000138650), PCDH15 (ENSG00000150275), PCDH19 (ENSG00000165194), CDH16 (ENSG00000166589), PCDHB1 (ENSG00000171815), PCDHB9 (ENSG00000177839), PCDHB13 (ENSG00000187372), CDHR4 (ENSG00000187492), PCDHB11 (ENSG00000197479), PCDHGA1 (ENSG00000204956), PCDHA9 (ENSG00000204961), PCDHA8 (ENSG00000204962), PCDHA7 (ENSG00000204963), PCDHA5 (ENSG00000204965), PCDHA4 (ENSG00000204967), PCDHA2 (ENSG00000204969), PCDHA1 (ENSG00000204970), PCDHA13 (ENSG00000239389), PCDHGC3 (ENSG00000240184), PCDHGC5 (ENSG00000240764), PCDHGC4 (ENSG00000242419), PCDHAC2 (ENSG00000243232), PCDHAC1 (ENSG00000248383), PCDHA11 (ENSG00000249158)

Protein

Protein identifiers

Protocadherin-18Q9HCL0 (reviewed: Q9HCL0)

All UniProt accessions (5): A0A087WTW3, B4DLR6, Q9HCL0, B4DQ29, D6RIG4

UniProt curated annotations — full annotation on UniProt →

Function. Potential calcium-dependent cell-adhesion protein.

Subunit / interactions. Interacts with DAB1.

Subcellular location. Cell membrane.

Tissue specificity. Expressed in all tissues, with highest expression in lung and ovary.

Isoforms (2)

UniProt IDNamesCanonical?
Q9HCL0-11yes
Q9HCL0-22

RefSeq proteins (2): NP_001287757, NP_061908* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR002126Cadherin-like_domDomain
IPR013164Cadherin_NDomain
IPR015919Cadherin-like_sfHomologous_superfamily
IPR020894Cadherin_CSConserved_site
IPR050174Protocadherin/Cadherin-CAFamily

Pfam: PF00028, PF08266

UniProt features (69 total): strand 30, helix 8, domain 6, glycosylation site 6, region of interest 5, turn 5, compositionally biased region 3, topological domain 2, signal peptide 1, chain 1, splice variant 1, transmembrane region 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
6VFRX-RAY DIFFRACTION2.79

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9HCL0-F168.890.39

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 (6): 103, 269, 420, 559, 583, 641

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 143 (showing top): FREAC2_01, BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, RORA1_01, ROVERSI_GLIOMA_COPY_NUMBER_UP, CHX10_01, AAAYRNCTG_UNKNOWN, CHANDRAN_METASTASIS_DN, CAGCTG_AP4_Q5, SHEPARD_BMYB_MORPHOLINO_DN, GOBP_CELL_CELL_ADHESION, BRN2_01, TGCTGAY_UNKNOWN, KINSEY_TARGETS_OF_EWSR1_FLII_FUSION_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_6HR_DN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_DN

GO Biological Process (3): cell adhesion (GO:0007155), homophilic cell-cell adhesion (GO:0007156), brain development (GO:0007420)

GO Molecular Function (3): calcium ion binding (GO:0005509), cell adhesion molecule binding (GO:0050839), 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:

CategoryTerms
cellular process1
cell-cell adhesion1
central nervous system development1
animal organ development1
head development1
metal ion binding1
protein binding1
binding1
membrane1
cell periphery1
cellular anatomical structure1

Protein interactions and networks

STRING

882 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PCDH18DIPK2AQ8NDZ4762
PCDH18LYSMD3Q7Z3D4458
PCDH18PKHD1P08F94437
PCDH18TM4SF1P30408424
PCDH18SIX1Q15475412
PCDH18KLK2P20151409
PCDH18NKX3-1Q99801401
PCDH18LPAR1P78351400
PCDH18LCKP06239399
PCDH18MDM4O15151396
PCDH18KLK3P07288389
PCDH18RNASELQ05823377
PCDH18TGFBR2P37173376
PCDH18SCN1AP35498373
PCDH18FGFR1P11362373

IntAct

26 interactions, top by confidence:

ABTypeScore
BRK1CYFIP1psi-mi:“MI:0914”(association)0.640
PCDH18UBQLN1psi-mi:“MI:0915”(physical association)0.560
PCDHGB1FAM171A2psi-mi:“MI:0914”(association)0.530
PCDH18HNRNPLpsi-mi:“MI:0915”(physical association)0.400
HAX1psi-mi:“MI:0914”(association)0.350
TEX101MAP4K4psi-mi:“MI:0914”(association)0.350
ATG5IGKV1-5psi-mi:“MI:0914”(association)0.350
CACNA1CIGLL5psi-mi:“MI:0914”(association)0.350
CACNA1CCACNB4psi-mi:“MI:0914”(association)0.350
CACNA1CSNRPGP15psi-mi:“MI:0914”(association)0.350
CACNA1CDISP2psi-mi:“MI:0914”(association)0.350
HCN1POTEFpsi-mi:“MI:0914”(association)0.350
SPSB4CCDC85Cpsi-mi:“MI:0914”(association)0.350
RYKTNFRSF10Bpsi-mi:“MI:0914”(association)0.350
CDH17TNFSF9psi-mi:“MI:0914”(association)0.350
PCDH10SHMT1psi-mi:“MI:0914”(association)0.350
PCDH20CAPN5psi-mi:“MI:0914”(association)0.350
UPK2IFT56psi-mi:“MI:0914”(association)0.350
PCDH18UBQLN1psi-mi:“MI:0915”(physical association)0.000
UBQLN1PCDH18psi-mi:“MI:0915”(physical association)0.000

BioGRID (27): PCDH18 (Affinity Capture-MS), PCDH18 (Proximity Label-MS), PCDH18 (Synthetic Lethality), PCDH18 (Affinity Capture-MS), PCDH18 (Two-hybrid), PCDH18 (Proximity Label-MS), PCDH18 (Affinity Capture-MS), PCDH18 (Affinity Capture-MS), PCDH18 (Affinity Capture-MS), PCDH18 (Affinity Capture-MS), PCDH18 (Affinity Capture-MS), PCDH18 (Affinity Capture-MS), PCDH18 (Affinity Capture-MS), PCDH18 (Proximity Label-MS), PCDH18 (Affinity Capture-MS)

ESM2 similar proteins: A7MB46, F8W3X3, O14917, O35902, O54800, O97799, P05622, P16234, P20786, P26618, P26619, P32926, P35546, P55286, P55289, P79749, P97291, Q05030, Q08DJ5, Q13634, Q14126, Q28889, Q5RJH3, Q68SP4, Q6KEQ9, Q6W3B0, Q6WXV7, Q6WYY1, Q6X862, Q71M42, Q7TMD7, Q7TSF0, Q7YRU7, Q80TF3, Q86SJ6, Q8AXC6, Q8AXC7, Q8BIZ0, Q8N6Y1, Q8TAB3

Diamond homologs: A7MB46, D3ZE55, F8W3X3, O14917, O55134, O60330, O88689, O95206, Q5DRA2, Q5DRA3, Q5DRA4, Q5DRA5, Q5DRA6, Q5DRA7, Q5DRA8, Q5DRA9, Q5DRB0, Q5DRB1, Q5DRB2, Q5DRB3, Q5DRB4, Q5DRB5, Q5DRB6, Q5DRB7, Q5DRB8, Q5DRB9, Q5DRC0, Q5DRC1, Q5DRC2, Q5DRC6, Q5DRD3, Q5DRD6, Q5DRE0, Q5DRE1, Q5DRE3, Q5DRE4, Q5DRE5, Q5DRE6, Q5DRE7, Q5DRE8

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance137
Likely benign3
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

614 predictions. Top by Δscore:

VariantEffectΔscore
4:137528473:CTTA:Cdonor_loss1.0000
4:137528474:TTA:Tdonor_loss1.0000
4:137528475:TA:Tdonor_loss1.0000
4:137528476:A:ACdonor_gain1.0000
4:137528476:A:Cdonor_loss1.0000
4:137528477:C:CAdonor_loss1.0000
4:137528477:C:CCdonor_gain1.0000
4:137528477:CCTG:Cdonor_gain1.0000
4:137528637:CATAT:Cacceptor_gain1.0000
4:137528638:ATAT:Aacceptor_gain1.0000
4:137528639:TAT:Tacceptor_gain1.0000
4:137528639:TATC:Tacceptor_loss1.0000
4:137528640:AT:Aacceptor_gain1.0000
4:137528641:TCTGG:Tacceptor_loss1.0000
4:137528642:C:CCacceptor_gain1.0000
4:137528642:C:CGacceptor_loss1.0000
4:137528643:T:Aacceptor_loss1.0000
4:137528650:A:ACacceptor_gain1.0000
4:137528650:A:Cacceptor_gain1.0000
4:137528656:C:CTacceptor_gain1.0000
4:137528726:TCATA:Tdonor_loss1.0000
4:137528727:CATA:Cdonor_loss1.0000
4:137528728:ATAC:Adonor_loss1.0000
4:137528729:TACC:Tdonor_loss1.0000
4:137528731:C:CGdonor_loss1.0000
4:137528818:CTG:Cacceptor_gain1.0000
4:137529598:TTAC:Tdonor_loss1.0000
4:137529599:TA:Tdonor_loss1.0000
4:137529600:ACCTC:Adonor_loss1.0000
4:137528640:ATCT:Aacceptor_gain0.9900

AlphaMissense

7537 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
4:137531358:G:TP244H1.000
4:137531367:T:AD241V1.000
4:137531367:T:GD241A1.000
4:137531436:G:TA218D1.000
4:137531472:C:GR206P1.000
4:137531694:T:GD132A1.000
4:137521054:A:GL1128P0.999
4:137521644:G:CC931W0.999
4:137521645:C:GC931S0.999
4:137521646:A:GC931R0.999
4:137521646:A:TC931S0.999
4:137521672:C:GC922S0.999
4:137521673:A:GC922R0.999
4:137521673:A:TC922S0.999
4:137530731:A:TV453D0.999
4:137530951:C:GA380P0.999
4:137531269:C:GD274H0.999
4:137531274:T:CD272G0.999
4:137531274:T:GD272A0.999
4:137531275:C:GD272H0.999
4:137531280:G:TA270D0.999
4:137531366:G:CD241E0.999
4:137531366:G:TD241E0.999
4:137531367:T:CD241G0.999
4:137531368:C:GD241H0.999
4:137531369:A:CN240K0.999
4:137531369:A:TN240K0.999
4:137531370:T:AN240I0.999
4:137531375:G:CD238E0.999
4:137531375:G:TD238E0.999

dbSNP variants (sampled 300 via entrez): RS1000030683 (4:137519356 T>A), RS1000046391 (4:137522412 G>A), RS1000078640 (4:137523951 A>C), RS1000271264 (4:137528740 C>A,T), RS10004843 (4:137523207 C>G,T), RS10006580 (4:137528658 C>A,G,T), RS1000845548 (4:137528969 C>A,T), RS10010962 (4:137524975 C>A,G), RS1001106512 (4:137522506 C>A), RS1001361633 (4:137528697 T>C), RS1001706073 (4:137532246 T>C), RS1001726808 (4:137533749 C>T), RS10018837 (4:137528529 A>G), RS1001961231 (4:137527274 T>C), RS1002000071 (4:137533595 T>C)

Disease associations

OMIM: gene MIM:608287 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

16 associations (top):

StudyTraitp-value
GCST001531_7Temperament2.000000e-06
GCST001762_942Obesity-related traits8.000000e-07
GCST001854_2Retinopathy in non-diabetics5.000000e-06
GCST002034_3Adverse response to radiation therapy1.000000e-06
GCST002826_11Urate levels (BMI interaction)9.000000e-07
GCST002938_36Copper levels7.000000e-06
GCST004703_4Obsessive-compulsive disorder or autism spectrum disorder4.000000e-06
GCST004735_31Epstein-Barr virus copy number in lymphoblastoid cell lines1.000000e-06
GCST004824_8P wave terminal force3.000000e-09
GCST007927_17Medication use (beta blocking agents)1.000000e-09
GCST007930_49Medication use (agents acting on the renin-angiotensin system)4.000000e-09
GCST009363_49Triglyceride levels x short total sleep time interaction (2df test)1.000000e-09
GCST010002_15Refractive error5.000000e-11
GCST010774_20Essential hypertension (time to event)4.000000e-08
GCST010988_78Adult body size3.000000e-17
GCST010989_245Body size at age 106.000000e-10

EFO canonical traits (10, from GWAS)

EFO IDTrait name
EFO:0004825temperament and character inventory
EFO:0003939energy intake
EFO:0004340body mass index
EFO:0004531urate measurement
EFO:0008379P wave terminal force measurement
EFO:0009929Beta blocking agent use measurement
EFO:0009931Agents acting on the renin-angiotensin system use measurement
EFO:0004530triglyceride measurement
EFO:0004918age at diagnosis
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

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

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression5
trichostatin Aaffects cotreatment, decreases expression3
sodium arseniteincreases abundance, decreases expression3
Air Pollutantsincreases expression, decreases expression, affects cotreatment, increases abundance3
Estradiolaffects cotreatment, decreases expression3
Particulate Matterdecreases expression, increases abundance3
bisphenol Adecreases methylation, increases expression2
S-(1,2-dichlorovinyl)cysteineaffects response to substance, increases expression, decreases expression2
mercuric bromidedecreases expression, affects cotreatment2
Phenylmercuric Acetateaffects cotreatment, decreases expression2
Aflatoxin B1decreases expression, decreases methylation2
p-Chloromercuribenzoic Aciddecreases expression, affects cotreatment2
bisphenol Faffects cotreatment, increases methylation1
methylmercuric chloridedecreases expression1
alpha-pineneaffects cotreatment, increases expression, increases abundance1
2-methyl-4-isothiazolin-3-oneincreases expression1
potassium chromate(VI)affects cotreatment, decreases expression1
methacrylaldehydeincreases expression, increases abundance, affects cotreatment1
diallyl trisulfidedecreases expression1
beta-methylcholineaffects expression1
epigallocatechin gallateincreases expression, affects cotreatment, decreases expression1
perfluorooctane sulfonic aciddecreases expression1
pentabromodiphenyl etherdecreases expression1
CGP 52608affects binding, increases reaction1
entinostatdecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
abrinedecreases expression1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
dorsomorphinaffects cotreatment, decreases expression1
incobotulinumtoxinAincreases expression1

Clinical trials (associated diseases)

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