ESAM

gene
On this page

Also known as W117m

Summary

ESAM (endothelial cell adhesion molecule, HGNC:17474) is a protein-coding gene on chromosome 11q24.2, encoding Endothelial cell-selective adhesion molecule (Q96AP7). Can mediate aggregation most likely through a homophilic molecular interaction.

Enables cell-cell adhesion mediator activity. Involved in several processes, including bicellular tight junction assembly; cell-cell adhesion; and regulation of actin filament polymerization. Located in cell-cell junction and plasma membrane. Part of protein-containing complex.

Source: NCBI Gene 90952 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): neurodevelopmental disorder with intracranial hemorrhage, seizures, and spasticity (Definitive, GenCC)
  • GWAS associations: 5
  • Clinical variants (ClinVar): 86 total — 1 pathogenic, 6 likely-pathogenic
  • Phenotypes (HPO): 93
  • MANE Select transcript: NM_138961

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:17474
Approved symbolESAM
Nameendothelial cell adhesion molecule
Location11q24.2
Locus typegene with protein product
StatusApproved
AliasesW117m
Ensembl geneENSG00000149564
Ensembl biotypeprotein_coding
OMIM614281
Entrez90952

Gene structure

Transcript identifiers

Ensembl transcripts: 12 — 9 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay

ENST00000278927, ENST00000417453, ENST00000435477, ENST00000444566, ENST00000464067, ENST00000485116, ENST00000906450, ENST00000906451, ENST00000906452, ENST00000906453, ENST00000942605, ENST00000942606

RefSeq mRNA: 1 — MANE Select: NM_138961 NM_138961

CCDS: CCDS8453

Canonical transcript exons

ENST00000278927 — 7 exons

ExonStartEnd
ENSE00000991328124756541124756742
ENSE00001014314124758349124758527
ENSE00001695509124762085124762290
ENSE00003494011124756207124756362
ENSE00003561465124753126124753961
ENSE00003568182124754641124754763
ENSE00003665246124754214124754340

Expression profiles

Bgee: expression breadth ubiquitous, 227 present calls, max score 98.57.

FANTOM5 (CAGE): breadth broad, TPM avg 10.7628 / max 505.7369, expressed in 787 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
12295910.4986732
1229600.264163

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right lungUBERON:000216798.57gold quality
right lobe of thyroid glandUBERON:000111998.47gold quality
left lobe of thyroid glandUBERON:000112098.40gold quality
upper lobe of left lungUBERON:000895298.35gold quality
right coronary arteryUBERON:000162598.31gold quality
popliteal arteryUBERON:000225098.12gold quality
tibial arteryUBERON:000761098.12gold quality
upper lobe of lungUBERON:000894898.05gold quality
thyroid glandUBERON:000204697.88gold quality
apex of heartUBERON:000209897.69gold quality
left coronary arteryUBERON:000162697.59gold quality
omental fat padUBERON:001041497.34gold quality
coronary arteryUBERON:000162197.27gold quality
peritoneumUBERON:000235897.27gold quality
aortaUBERON:000094796.74gold quality
adipose tissue of abdominal regionUBERON:000780896.72gold quality
subcutaneous adipose tissueUBERON:000219096.06gold quality
metanephros cortexUBERON:001053395.99gold quality
heart left ventricleUBERON:000208495.40gold quality
cardiac ventricleUBERON:000208295.11gold quality
ascending aortaUBERON:000149695.10gold quality
thoracic aortaUBERON:000151595.09gold quality
lungUBERON:000204894.82gold quality
tendon of biceps brachiiUBERON:000818894.69gold quality
left uterine tubeUBERON:000130394.56gold quality
heartUBERON:000094894.39gold quality
body of uterusUBERON:000985394.24gold quality
right atrium auricular regionUBERON:000663194.22gold quality
placentaUBERON:000198793.90gold quality
cardiac atriumUBERON:000208193.89gold quality

Single-cell (SCXA)

Detected in 29 experiment(s), a significant marker in 29.

ExperimentMarker?Max mean expression
E-MTAB-10662yes1501.59
E-MTAB-10137yes1127.78
E-MTAB-8142yes1005.99
E-MTAB-9906yes860.16
E-MTAB-8221yes822.81
E-MTAB-8271yes775.50
E-ANND-5yes524.26
E-CURD-7yes432.71
E-ENAD-21yes412.20
E-GEOD-83139yes309.56
E-MTAB-10287yes79.91
E-GEOD-134144yes53.45
E-HCAD-1yes48.23
E-HCAD-11yes48.18
E-HCAD-10yes46.36

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NFKB

miRNA regulators (miRDB)

41 targeting ESAM, 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-3924100.0072.092394
HSA-MIR-4476100.0068.182030
HSA-MIR-6876-5P100.0067.682126
HSA-MIR-188-3P100.0068.761240
HSA-MIR-12118100.0065.881270
HSA-MIR-6891-5P99.9866.531372
HSA-MIR-4650-5P99.9864.69999
HSA-MIR-3173-3P99.9866.491217
HSA-MIR-570-3P99.9672.414910
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-6756-5P99.8267.972466
HSA-MIR-430699.7270.503630
HSA-MIR-6766-5P99.6867.702325
HSA-MIR-444199.4966.563216
HSA-MIR-185-5P99.3568.602497
HSA-MIR-464499.3569.122514
HSA-MIR-429199.2068.882969
HSA-MIR-3152-3P99.1066.35678
HSA-MIR-427099.0266.261987
HSA-MIR-6737-3P98.9568.561577
HSA-MIR-7157-3P98.9568.701582
HSA-MIR-6889-3P98.8467.351198
HSA-MIR-5008-3P98.7367.501433
HSA-MIR-6529-3P98.6866.761020
HSA-MIR-4725-5P98.6765.42628
HSA-MIR-504-5P98.6765.40631
HSA-MIR-6754-5P98.6065.541627
HSA-MIR-4662A-5P98.4867.181007
HSA-MIR-6827-5P98.4664.881256
HSA-MIR-448398.0964.121642

Literature-anchored findings (GeneRIF, showing 7)

  • sESAM is a predictive biomarker and potential mediator of atherosclerosis. (PMID:19759376)
  • ESAM regulates tumor metastasis through endothelial cell migration and tube formation in metastatic nodules. (PMID:20153339)
  • sESAM is associated with albuminuria and reduced kidney function in patients with coronary artery disease in both cross-sectional and longitudinal analyses. (PMID:24177327)
  • Serum ESAM is higher in type 2 diabetes mellitus than in controls and parallels oxidative stress. (PMID:24456423)
  • sESAM levels associate with myocardial infarction, heart failure, and death after adjustment for demographic and clinical risk factors, but not after adjustment for kidney function. (PMID:26523992)
  • ESAM is a novel human hematopoietic stem cell marker associated with a subset of human leukemias (PMID:26774386)
  • Bi-allelic variants in the ESAM tight-junction gene cause a neurodevelopmental disorder associated with fetal intracranial hemorrhage. (PMID:36996813)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_rerioesambENSDARG00000076639
danio_rerioesamaENSDARG00000077039
danio_reriogpa33aENSDARG00000100223
mus_musculusEsamENSMUSG00000001946
rattus_norvegicusEsamENSRNOG00000033217

Paralogs (14): VSIG2 (ENSG00000019102), VSIG1 (ENSG00000101842), VSIR (ENSG00000107738), GPA33 (ENSG00000143167), IGSF11 (ENSG00000144847), CXADR (ENSG00000154639), JAM2 (ENSG00000154721), F11R (ENSG00000158769), MXRA8 (ENSG00000162576), JAM3 (ENSG00000166086), CLMP (ENSG00000166250), MUC15 (ENSG00000169550), VSTM2B (ENSG00000187135), VSIG8 (ENSG00000243284)

Protein

Protein identifiers

Endothelial cell-selective adhesion moleculeQ96AP7 (reviewed: Q96AP7)

All UniProt accessions (3): Q96AP7, C9JIE7, F8WDW9

UniProt curated annotations — full annotation on UniProt →

Function. Can mediate aggregation most likely through a homophilic molecular interaction.

Subunit / interactions. Interacts with MAGI1.

Subcellular location. Cell junction. Adherens junction. Tight junction. Cell membrane.

Tissue specificity. Highly expressed in endothelial cells.

Disease relevance. Neurodevelopmental disorder with intracranial hemorrhage, seizures, and spasticity (NEDIHSS) [MIM:620371] An autosomal recessive disease characterized by prenatal or neonatal onset of intracranial hemorrhage, ventriculomegaly and cerebral calcifications. Affected individuals have profound global developmental delay, intellectual disability, epilepsy, absent or severely delayed speech, and varying degrees of spasticity. Death in utero or in early childhood may occur. The disease is caused by variants affecting the gene represented in this entry.

Isoforms (2)

UniProt IDNamesCanonical?
Q96AP7-11yes
Q96AP7-22

RefSeq proteins (1): NP_620411* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR007110Ig-like_domDomain
IPR013106Ig_V-setDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily
IPR042757ESAMFamily

Pfam: PF07686, PF13927

UniProt features (27 total): modified residue 7, glycosylation site 4, splice variant 3, topological domain 2, sequence variant 2, domain 2, signal peptide 1, chain 1, disulfide bond 1, sequence conflict 1, transmembrane region 1, region of interest 1, compositionally biased region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96AP7-F178.130.53

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 (7): 332, 334, 336, 339, 344, 371, 301

Disulfide bonds (1): 174–224

Glycosylation sites (4): 108, 169, 213, 236

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-202733Cell surface interactions at the vascular wall

MSigDB gene sets: 421 (showing top): GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, BENPORATH_ES_WITH_H3K27ME3, GOBP_APICAL_JUNCTION_ASSEMBLY, TGACCTY_ERR1_Q2, MEF2_02, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GGGTGGRR_PAX4_03, CLASPER_LYMPHATIC_VESSELS_DURING_METASTASIS_UP, GOBP_REGULATION_OF_ACTIN_FILAMENT_BASED_PROCESS, GOBP_CELL_CELL_ADHESION, GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_SIZE, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_ACTIN_FILAMENT_ORGANIZATION, GOBP_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_ASSEMBLY, PU1_Q6

GO Biological Process (8): homophilic cell-cell adhesion (GO:0007156), intracellular protein localization (GO:0008104), regulation of actin filament polymerization (GO:0030833), regulation of actin cytoskeleton organization (GO:0032956), maintenance of blood-brain barrier (GO:0035633), bicellular tight junction assembly (GO:0070830), cell-cell adhesion (GO:0098609), cell adhesion (GO:0007155)

GO Molecular Function (2): cell-cell adhesion mediator activity (GO:0098632), protein binding (GO:0005515)

GO Cellular Component (7): plasma membrane (GO:0005886), cell-cell junction (GO:0005911), adherens junction (GO:0005912), bicellular tight junction (GO:0005923), protein-containing complex (GO:0032991), membrane (GO:0016020), anchoring junction (GO:0070161)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Hemostasis1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cell-cell adhesion2
macromolecule localization1
regulation of actin polymerization or depolymerization1
actin filament polymerization1
regulation of protein polymerization1
actin cytoskeleton organization1
regulation of actin filament-based process1
regulation of cytoskeleton organization1
tissue homeostasis1
apical junction assembly1
tight junction assembly1
cell adhesion1
cellular process1
cell adhesion mediator activity1
binding1
membrane1
cell periphery1
anchoring junction1
cell-cell junction1
apical junction complex1
tight junction1
cellular_component1
cellular anatomical structure1
cell junction1

Protein interactions and networks

STRING

1191 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
ESAMOCLNQ16625970
ESAMTJP1Q07157857
ESAMCDH5P33151811
ESAMCLDN5O00501754
ESAMATP1B1P05026746
ESAMSELEP16111734
ESAMVCAM1P19320734
ESAMSELPP16109712
ESAMVWFP04275654
ESAMPECAM1P16284639
ESAMIGSF5Q9NSI5604
ESAMKDRP35968598
ESAMCD34P28906590
ESAMMARVELD2Q8N4S9589
ESAMSELLP14151583

IntAct

11 interactions, top by confidence:

ABTypeScore
ESAMESAMpsi-mi:“MI:0915”(physical association)0.610
ESAMESAMpsi-mi:“MI:0407”(direct interaction)0.610
TTMPESAMpsi-mi:“MI:0915”(physical association)0.560
TMBIM6ESAMpsi-mi:“MI:0915”(physical association)0.560
ESAMTOP1psi-mi:“MI:0914”(association)0.350
ENGIGKV2-28psi-mi:“MI:0914”(association)0.350

BioGRID (11): MPHOSPH8 (Affinity Capture-MS), TOP1 (Affinity Capture-MS), MDC1 (Affinity Capture-MS), CENPF (Affinity Capture-MS), ESAM (Protein-RNA), ESAM (Two-hybrid), ESAM (Two-hybrid), ESAM (Affinity Capture-MS), ESAM (Affinity Capture-MS), ESAM (Protein-peptide), ESAM (Reconstituted Complex)

ESM2 similar proteins: A0A140LHF2, A6H8M9, A7LCJ3, A8E0Y8, D3YX43, D3YZF7, O14498, O15197, O70394, O70540, P01877, P0C0K6, P0C788, P0DP72, P35590, P40223, P43121, P50895, P70289, Q00657, Q06418, Q06805, Q15109, Q28173, Q5BK54, Q5NVQ6, Q5TJE4, Q61790, Q61826, Q62151, Q62230, Q63495, Q64612, Q6UVK1, Q6UWB1, Q7Z442, Q86VR7, Q8IZF5, Q8R2Y2, Q8VHY0

Diamond homologs: A0A0R4IGV4, A2AJ76, A2ASS6, A3KPA0, D3YXG0, G4SLH0, G5EBF1, O14511, O35569, O88792, P35969, P53767, P56974, P57087, Q00872, Q05793, Q14896, Q2WGK2, Q3UQ28, Q5VST9, Q62718, Q68FQ2, Q7TSU7, Q8NDA2, Q8WZ42, Q95KI3, Q96AP7, Q96RW7, Q99795, Q99PJ0, Q9BX67, Q9D8B7, Q9I7U4, Q9JHY1, Q9JI59, Q9PWR4, Q9VZZ4, Q9XT56, Q9Y624, B4LRN7

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic6
Uncertain significance59
Likely benign10
Benign1

Top pathogenic / likely-pathogenic (7)

Variant IDHGVSClassification
4086789NM_138961.3(ESAM):c.70+1G>TPathogenic
1810270NM_138961.3(ESAM):c.115del (p.Arg39fs)Likely pathogenic
1810271NM_138961.3(ESAM):c.287del (p.Pro96fs)Likely pathogenic
1810272NM_138961.3(ESAM):c.35T>A (p.Leu12Ter)Likely pathogenic
1810273NM_138961.3(ESAM):c.451+1G>ALikely pathogenic
3065558NM_138961.3(ESAM):c.949C>T (p.Arg317Ter)Likely pathogenic
4086169NM_138961.3(ESAM):c.608-1G>ALikely pathogenic

SpliceAI

1196 predictions. Top by Δscore:

VariantEffectΔscore
11:124754207:CACTT:Cdonor_loss1.0000
11:124754208:ACTTA:Adonor_loss1.0000
11:124754209:CTTAC:Cdonor_loss1.0000
11:124754210:TTA:Tdonor_loss1.0000
11:124754211:TACT:Tdonor_loss1.0000
11:124754212:A:ACdonor_gain1.0000
11:124754212:ACTTG:Adonor_loss1.0000
11:124754213:C:CAdonor_gain1.0000
11:124754213:CT:Cdonor_gain1.0000
11:124754213:CTT:Cdonor_gain1.0000
11:124754213:CTTG:Cdonor_gain1.0000
11:124754213:CTTGA:Cdonor_gain1.0000
11:124754337:GGCC:Gacceptor_gain1.0000
11:124754338:GCC:Gacceptor_gain1.0000
11:124754339:CC:Cacceptor_gain1.0000
11:124754339:CCC:Cacceptor_gain1.0000
11:124754340:CC:Cacceptor_gain1.0000
11:124754341:C:CAacceptor_loss1.0000
11:124754341:C:CCacceptor_gain1.0000
11:124754351:CGTCG:Cacceptor_gain1.0000
11:124754628:ACC:Adonor_gain1.0000
11:124754629:CCC:Cdonor_gain1.0000
11:124754761:CAT:Cacceptor_gain1.0000
11:124754762:AT:Aacceptor_gain1.0000
11:124754763:TCTGT:Tacceptor_loss1.0000
11:124754764:C:CCacceptor_gain1.0000
11:124754765:T:Aacceptor_loss1.0000
11:124756746:G:GCacceptor_gain1.0000
11:124753960:CC:Cacceptor_gain0.9900
11:124753961:CC:Cacceptor_gain0.9900

AlphaMissense

2470 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:124756253:C:AW187C0.999
11:124756253:C:GW187C0.999
11:124754700:C:GC224S0.995
11:124754701:A:TC224S0.995
11:124756255:A:GW187R0.993
11:124756255:A:TW187R0.993
11:124756622:A:CY124D0.993
11:124754700:C:TC224Y0.991
11:124758381:A:GW73R0.990
11:124758381:A:TW73R0.990
11:124754699:G:CC224W0.989
11:124754707:A:CY222D0.989
11:124756293:C:GC174S0.989
11:124756294:A:TC174S0.989
11:124754701:A:GC224R0.987
11:124754706:T:CY222C0.987
11:124756293:C:TC174Y0.984
11:124756294:A:GC174R0.984
11:124756341:C:GC158S0.982
11:124756342:A:TC158S0.982
11:124756292:G:CC174W0.981
11:124754667:C:GC235S0.980
11:124754668:A:TC235S0.980
11:124754700:C:AC224F0.980
11:124756341:C:TC158Y0.979
11:124756664:A:GS110P0.978
11:124758379:C:AW73C0.978
11:124758379:C:GW73C0.978
11:124754668:A:GC235R0.977
11:124756342:A:GC158R0.977

dbSNP variants (sampled 300 via entrez): RS1000088138 (11:124764272 G>A,C), RS1000496097 (11:124757502 G>A), RS1000650208 (11:124757228 C>T), RS1000783278 (11:124755928 G>A), RS1001000467 (11:124763278 A>C), RS1001170168 (11:124760416 C>A,G), RS1001230595 (11:124762686 G>A,T), RS1002166256 (11:124759347 G>A), RS1002187781 (11:124754406 C>T), RS1002538230 (11:124754885 C>T), RS1002654709 (11:124754535 C>T), RS1002778550 (11:124753122 C>T), RS1003156524 (11:124753442 A>C,G), RS1003172347 (11:124757843 G>A), RS1003540411 (11:124753352 G>C)

Disease associations

OMIM: gene MIM:614281 | disease phenotypes: MIM:620371

GenCC curated gene-disease

DiseaseClassificationInheritance
neurodevelopmental disorder with intracranial hemorrhage, seizures, and spasticityDefinitiveAutosomal recessive

Mondo (1): neurodevelopmental disorder with intracranial hemorrhage, seizures, and spasticity (MONDO:0957267)

Orphanet (0):

HPO phenotypes

93 total (30 of 93 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000028Cryptorchidism
HP:0000189Narrow palate
HP:0000218High palate
HP:0000232Everted lower lip vermilion
HP:0000238Hydrocephalus
HP:0000252Microcephaly
HP:0000293Full cheeks
HP:0000303Mandibular prognathia
HP:0000308Microretrognathia
HP:0000319Smooth philtrum
HP:0000325Triangular face
HP:0000337Broad forehead
HP:0000341Narrow forehead
HP:0000358Posteriorly rotated ears
HP:0000414Bulbous nose
HP:0000431Wide nasal bridge
HP:0000463Anteverted nares
HP:0000476Cystic hygroma
HP:0000506Telecanthus
HP:0000527Long eyelashes
HP:0000541Retinal detachment
HP:0000573Retinal hemorrhage
HP:0000582Upslanted palpebral fissure
HP:0000612Iris coloboma
HP:0000631Retinal arterial tortuosity
HP:0000639Nystagmus
HP:0000646Amblyopia
HP:0000664Synophrys
HP:0000750Delayed speech and language development

GWAS associations

5 associations (top):

StudyTraitp-value
GCST002539_10Schizophrenia3.000000e-12
GCST004521_214Autism spectrum disorder or schizophrenia5.000000e-13
GCST006585_44Blood protein levels3.000000e-12
GCST006585_807Blood protein levels5.000000e-22
GCST006803_11Schizophrenia2.000000e-15

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.

ChemicalActions (top 5)PubMed papers
Benzo(a)pyrenedecreases methylation, increases expression4
sodium arsenitedecreases expression, increases expression2
Tobacco Smoke Pollutionincreases expression2
Cyclosporineincreases expression2
aristolochic acid Iincreases expression1
methyleugenolincreases expression1
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
bisphenol Adecreases expression1
kojic acidincreases expression1
ethyl-p-hydroxybenzoateincreases expression1
trichostatin Aaffects expression1
tris(2-butoxyethyl) phosphateaffects expression1
tris(1,3-dichloro-2-propyl)phosphateincreases expression1
butyraldehydeincreases expression1
tetrabromobisphenol Adecreases expression1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression1
pentanalincreases expression1
CGP 52608increases reaction, affects binding1
2,2’,4,4’-tetrabromodiphenyl etherdecreases expression1
pentabrominated diphenyl ether 100decreases expression1
hexabrominated diphenyl ether 153decreases expression1
jinfukangaffects cotreatment, decreases expression1
Decitabineincreases expression1
Aldehydesincreases expression1
Cisplatinaffects cotreatment, decreases expression1
Doxorubicindecreases expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Quercetinincreases expression1
Smokedecreases expression1

Clinical trials (associated diseases)

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