AMIGO3

gene
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Summary

AMIGO3 (adhesion molecule with Ig like domain 3, HGNC:24075) is a protein-coding gene on chromosome 3p21.31, encoding Amphoterin-induced protein 3 (Q86WK7). May mediate heterophilic cell-cell interaction.

Predicted to be involved in brain development; heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules; and positive regulation of synapse assembly. Predicted to be active in membrane.

Source: NCBI Gene 386724 — RefSeq curated summary.

At a glance

  • GWAS associations: 12
  • Clinical variants (ClinVar): 99 total — 3 pathogenic
  • MANE Select transcript: NM_198722

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24075
Approved symbolAMIGO3
Nameadhesion molecule with Ig like domain 3
Location3p21.31
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000176020
Ensembl biotypeprotein_coding
OMIM615691
Entrez386724

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000320431

RefSeq mRNA: 1 — MANE Select: NM_198722 NM_198722

CCDS: CCDS33759

Canonical transcript exons

ENST00000320431 — 1 exons

ExonStartEnd
ENSE000012412764971682949719684

Expression profiles

Bgee: expression breadth ubiquitous, 129 present calls, max score 81.25.

FANTOM5 (CAGE): breadth broad, TPM avg 1.6192 / max 81.5612, expressed in 603 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter IDTPM avgSamples expressed
422701.6192603

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099181.25silver quality
hindlimb stylopod muscleUBERON:000425269.71gold quality
stromal cell of endometriumCL:000225567.92gold quality
adenohypophysisUBERON:000219667.28gold quality
pituitary glandUBERON:000000767.16gold quality
skeletal muscle tissueUBERON:000113466.25gold quality
granulocyteCL:000009466.08gold quality
skin of abdomenUBERON:000141665.22gold quality
skin of legUBERON:000151165.17gold quality
zone of skinUBERON:000001464.86gold quality
right lobe of liverUBERON:000111464.77gold quality
lower esophagus mucosaUBERON:003583464.22gold quality
mucosa of stomachUBERON:000119963.10gold quality
right hemisphere of cerebellumUBERON:001489062.72gold quality
sural nerveUBERON:001548862.48silver quality
left adrenal glandUBERON:000123462.13gold quality
cerebellar hemisphereUBERON:000224562.13gold quality
cerebellumUBERON:000203762.05gold quality
cerebellar cortexUBERON:000212961.92gold quality
right adrenal gland cortexUBERON:003582761.78gold quality
ventricular zoneUBERON:000305361.57gold quality
bloodUBERON:000017861.49gold quality
mucosa of transverse colonUBERON:000499161.48gold quality
right adrenal glandUBERON:000123360.99gold quality
muscle of legUBERON:000138360.91gold quality
left uterine tubeUBERON:000130360.76gold quality
left adrenal gland cortexUBERON:003582560.57gold quality
muscle tissueUBERON:000238560.39gold quality
gastrocnemiusUBERON:000138859.53gold quality
esophagus mucosaUBERON:000246959.50gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no0.45

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

26 targeting AMIGO3, 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-589-3P99.9169.622088
HSA-MIR-444799.8567.812900
HSA-MIR-3059-5P99.7069.932491
HSA-MIR-4743-3P99.6268.122095
HSA-MIR-1260A99.6166.671098
HSA-MIR-1260B99.6166.671098
HSA-MIR-6836-5P99.6065.621538
HSA-MIR-613299.6065.831554
HSA-MIR-608199.4866.071446
HSA-MIR-6722-3P99.4567.621919
HSA-MIR-3191-5P99.2466.521722
HSA-MIR-6852-5P99.1766.692073
HSA-MIR-6510-5P99.1466.591081
HSA-MIR-66199.0965.942062
HSA-MIR-6756-3P98.9466.791104
HSA-MIR-3127-3P98.9467.341055
HSA-MIR-6846-5P98.8165.861121
HSA-MIR-518C-5P98.5369.201640
HSA-MIR-4708-5P97.7767.82831
HSA-MIR-4761-3P96.2766.26524
HSA-MIR-316596.1866.22473
HSA-MIR-452295.7666.23742
HSA-MIR-4520-5P93.5465.23140
HSA-MIR-4649-5P93.0263.85141
HSA-MIR-6729-5P93.0262.76138
HSA-MIR-3944-3P91.0162.2744

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioamigo3ENSDARG00000074469
mus_musculusAmigo3ENSMUSG00000032593
rattus_norvegicusAmigo3ENSRNOG00000064183

Paralogs (2): AMIGO2 (ENSG00000139211), AMIGO1 (ENSG00000181754)

Protein

Protein identifiers

Amphoterin-induced protein 3Q86WK7 (reviewed: Q86WK7)

Alternative names: AMIGO-3, Alivin-3

All UniProt accessions (1): Q86WK7

UniProt curated annotations — full annotation on UniProt →

Function. May mediate heterophilic cell-cell interaction. May contribute to signal transduction through its intracellular domain.

Subunit / interactions. Binds AMIGO1 or AMIGO2.

Subcellular location. Membrane.

Similarity. Belongs to the immunoglobulin superfamily. AMIGO family.

RefSeq proteins (1): NP_942015* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001611Leu-rich_rptRepeat
IPR003591Leu-rich_rpt_typical-subtypRepeat
IPR003598Ig_sub2Domain
IPR003599Ig_subDomain
IPR007110Ig-like_domDomain
IPR013783Ig-like_foldHomologous_superfamily
IPR031283AMIGOFamily
IPR032675LRR_dom_sfHomologous_superfamily
IPR036179Ig-like_dom_sfHomologous_superfamily

Pfam: PF00560, PF13855

UniProt features (26 total): repeat 6, glycosylation site 5, disulfide bond 5, domain 3, topological domain 2, signal peptide 1, chain 1, region of interest 1, compositionally biased region 1, transmembrane region 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q86WK7-F173.900.37

Functional residue map

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

Disulfide bonds (5): 34–40, 38–47, 223–251, 225–273, 300–352

Glycosylation sites (5): 107, 272, 301, 362, 368

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 50 (showing top): GOBP_HETEROPHILIC_CELL_CELL_ADHESION, GOBP_SYNAPSE_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_SYNAPSE_ASSEMBLY, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_CELL_JUNCTION_ASSEMBLY, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_POSITIVE_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_NEGATIVE_REGULATION_OF_CELLULAR_COMPONENT_ORGANIZATION, GOBP_CELL_CELL_ADHESION, GOBP_POSITIVE_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_CELL_JUNCTION_ORGANIZATION, GOBP_REGULATION_OF_SYNAPSE_ASSEMBLY, GOBP_POSITIVE_REGULATION_OF_CELL_JUNCTION_ASSEMBLY

GO Biological Process (6): heterophilic cell-cell adhesion (GO:0007157), brain development (GO:0007420), negative regulation of neuron projection development (GO:0010977), positive regulation of synapse assembly (GO:0051965), cell adhesion (GO:0007155), nervous system development (GO:0007399)

GO Molecular Function (2): protein-containing complex binding (GO:0044877), protein binding (GO:0005515)

GO Cellular Component (1): membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
cell-cell adhesion1
central nervous system development1
animal organ development1
head development1
regulation of neuron projection development1
neuron projection development1
negative regulation of cell projection organization1
synapse assembly1
positive regulation of nervous system development1
regulation of synapse assembly1
positive regulation of cell junction assembly1
cellular process1
system development1
cellular anatomical structure1

Protein interactions and networks

STRING

732 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
AMIGO3TMEM131Q92545535
AMIGO3LINGO1Q96FE5490
AMIGO3NGFRP08138476
AMIGO3ZDHHC14Q8IZN3472
AMIGO3OMGP23515418
AMIGO3CYTH2Q99418396
AMIGO3RTN4Q9NQC3395
AMIGO3BRSK2Q8IWQ3388
AMIGO3GPR137Q96N19371
AMIGO3SH3BP2P78314360
AMIGO3CLHC1Q8NHS4333
AMIGO3CDHR4A6H8M9327
AMIGO3TNFRSF19Q9NS68321
AMIGO3TRAPPC3LQ5T215309
AMIGO3MAGP20916306

IntAct

11 interactions, top by confidence:

ABTypeScore
GTPBP8HSPD1psi-mi:“MI:0914”(association)0.530
AMIGO3CANXpsi-mi:“MI:0914”(association)0.530
FBXO2TMEM131Lpsi-mi:“MI:0914”(association)0.530
PTPRKMANBApsi-mi:“MI:0914”(association)0.350
CLEC12BGXYLT2psi-mi:“MI:0914”(association)0.350
C1orf54AGRNpsi-mi:“MI:0914”(association)0.350
AMIGO3CLGNpsi-mi:“MI:0914”(association)0.350
GALNT10PLXNA2psi-mi:“MI:0914”(association)0.350

BioGRID (35): AMIGO3 (Affinity Capture-MS), AMIGO3 (Affinity Capture-MS), C9orf91 (Affinity Capture-MS), GOLPH3 (Affinity Capture-MS), AMIGO3 (Affinity Capture-MS), C1QL4 (Affinity Capture-MS), FBXO2 (Affinity Capture-MS), SEL1L (Affinity Capture-MS), UFSP2 (Affinity Capture-MS), CANX (Affinity Capture-MS), SLC22A18 (Affinity Capture-MS), OMA1 (Affinity Capture-MS), ZDHHC17 (Affinity Capture-MS), AMIGO3 (Affinity Capture-Western), AMIGO3 (Affinity Capture-Western)

ESM2 similar proteins: A3KNN3, A4IFA6, A6H789, A6H793, A6NDA9, A8WHP9, E7FE13, O08644, O08742, O08770, O14498, O15197, P0C0K6, P0C0K7, P14616, P14617, P21709, P54760, P54761, P59034, P59035, Q149C3, Q3ZBI5, Q5BK65, Q5JZY3, Q5NVQ6, Q5R7M3, Q60750, Q62178, Q64716, Q6GU68, Q6P7C4, Q6PFC5, Q6UY18, Q80ZD5, Q86SJ2, Q86WK7, Q86YC3, Q8BGX3, Q8BMT4

Diamond homologs: A6H789, D3ZTV3, G5EFX6, O02678, O15335, O43155, O46377, O46378, O46379, O46390, O46403, O46542, O55226, O70210, O75093, O75094, O88279, O88280, O94813, P07585, P0DM44, P21793, P21809, P21810, P28653, P28654, P28675, P47853, Q01129, Q27972, Q28888, Q29393, Q3ZBN5, Q5R1V9, Q5RI43, Q7TQ62, Q80TR4, Q86WK7, Q8BLU0, Q8VCH9

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic3
Likely pathogenic0
Uncertain significance90
Likely benign5
Benign1

Top pathogenic / likely-pathogenic (3)

Variant IDHGVSClassification
1068732NC_000003.11:g.(?48507870)(50340407_?)delPathogenic
1456135NC_000003.11:g.(?49547968)(50685477_?)delPathogenic
980510GRCh37/hg19 3p21.31-21.2(chr3:48807193-51363558)x1Pathogenic

SpliceAI

424 predictions. Top by Δscore:

VariantEffectΔscore
3:49718384:T:TAacceptor_gain0.9800
3:49719266:TCG:Tdonor_gain0.9800
3:49718378:T:TAacceptor_gain0.9700
3:49718563:GTTGC:Gdonor_gain0.9600
3:49718780:T:TAdonor_gain0.9600
3:49718781:G:GAdonor_gain0.9600
3:49719285:C:Tdonor_gain0.9500
3:49719621:TTCCC:Tdonor_gain0.9400
3:49717343:G:GTdonor_gain0.9300
3:49718156:C:Gdonor_gain0.9300
3:49718153:GTGC:Gdonor_gain0.9200
3:49718154:TGCT:Tdonor_gain0.9200
3:49718155:GCTG:Gdonor_gain0.9200
3:49718538:C:Tdonor_gain0.9200
3:49718390:AGGCG:Aacceptor_gain0.9100
3:49718391:GGCGG:Gacceptor_gain0.9100
3:49719083:T:TAdonor_gain0.9100
3:49718568:A:AGdonor_gain0.8900
3:49718569:G:GGdonor_gain0.8900
3:49718674:G:GTdonor_gain0.8900
3:49719187:GTC:Gdonor_gain0.8900
3:49719188:TCT:Tdonor_gain0.8900
3:49718385:G:Aacceptor_gain0.8700
3:49718782:G:GGdonor_gain0.8700
3:49718379:G:Aacceptor_gain0.8500
3:49718386:GTGCA:Gacceptor_loss0.8500
3:49718387:TGCA:Tacceptor_loss0.8500
3:49718388:GCA:Gacceptor_loss0.8500
3:49718389:CAGGC:Cacceptor_loss0.8500
3:49718390:A:Tacceptor_loss0.8500

AlphaMissense

3238 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
3:49718533:C:AW311C0.993
3:49718533:C:GW311C0.993
3:49718098:A:CF456L0.990
3:49718098:A:TF456L0.990
3:49718100:A:GF456L0.990
3:49718456:A:GL337S0.990
3:49718417:A:CF350C0.989
3:49718535:A:GW311R0.988
3:49718535:A:TW311R0.988
3:49718417:A:GF350S0.983
3:49718410:G:CC352W0.982
3:49718295:A:GC391R0.977
3:49718412:A:GC352R0.977
3:49718411:C:GC352S0.976
3:49718412:A:TC352S0.976
3:49718286:C:GG394R0.975
3:49718099:A:CF456C0.974
3:49718766:A:GW234R0.974
3:49718766:A:TW234R0.974
3:49718416:G:CF350L0.972
3:49718416:G:TF350L0.972
3:49718418:A:GF350L0.972
3:49718411:C:TC352Y0.970
3:49718567:C:TC300Y0.966
3:49718764:C:AW234C0.966
3:49718764:C:GW234C0.966
3:49718809:G:CN219K0.965
3:49718809:G:TN219K0.965
3:49718285:C:TG394D0.963
3:49718567:C:GC300S0.963

dbSNP variants (sampled 300 via entrez): RS1000783242 (3:49720182 G>A,C), RS1000848134 (3:49721336 C>T), RS1001399602 (3:49721226 T>G), RS1002239690 (3:49719828 A>G), RS1002489068 (3:49716617 T>G), RS1003244818 (3:49718796 C>A), RS1003912296 (3:49716746 G>A,C), RS1003983678 (3:49716946 AC>A,ACC), RS1005096711 (3:49720342 G>A,T), RS1008348412 (3:49721374 A>G), RS1008613216 (3:49720158 A>C,G), RS1009054923 (3:49719666 C>G,T), RS1009101756 (3:49719866 C>G,T), RS1009222175 (3:49716640 G>A), RS1009607759 (3:49720374 T>G)

Disease associations

OMIM: gene MIM:615691 | disease phenotypes: MIM:192315, MIM:225750, MIM:610448

GenCC curated gene-disease

Mondo (4): retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (MONDO:0008641), Aicardi-Goutieres syndrome 1 (MONDO:0009165), chilblain lupus 1 (MONDO:0012500), developmental and epileptic encephalopathy (MONDO:0100620)

Orphanet (5): Retinal vasculopathy with cerebral leukoencephalopathy and systemic manifestations (Orphanet:247691), Cerebroretinal vasculopathy (Orphanet:3421), Aicardi-Goutières syndrome (Orphanet:51), HERNS syndrome (Orphanet:63261), Hereditary vascular retinopathy (Orphanet:71291)

HPO phenotypes

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

GWAS associations

12 associations (top):

StudyTraitp-value
GCST000964_6Ulcerative colitis2.000000e-17
GCST006920_7Regular attendance at a gym or sports club6.000000e-10
GCST006922_9Regular attendance at a religious group3.000000e-08
GCST007044_11Extremely high intelligence4.000000e-08
GCST007559_24Sleep duration (short sleep)3.000000e-08
GCST008357_20Mood instability4.000000e-11
GCST008512_6Multisite chronic pain8.000000e-10
GCST010698_80Subcortical volume (min-P)3.000000e-24
GCST010699_110Brain morphology (min-P)4.000000e-08
GCST010701_52Cortical surface area (MOSTest)1.000000e-16
GCST010702_36Subcortical volume (MOSTest)1.000000e-10
GCST010703_262Brain morphology (MOSTest)2.000000e-13

EFO canonical traits (5, from GWAS)

EFO IDTrait name
EFO:0009592social interaction measurement
EFO:0004337intelligence
EFO:0008475mood instability measurement
EFO:0010100multisite chronic pain
EFO:0004346neuroimaging measurement

MeSH disease descriptors (1)

DescriptorNameTree numbers
C566007Vasculopathy, Retinal, With Cerebral Leukodystrophy (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

22 total (human), top 22 by PubMed support.

ChemicalActions (top 5)PubMed papers
bisphenol Faffects cotreatment, increases expression1
bisphenol Aaffects cotreatment, increases expression1
CGP 52608affects binding, increases reaction1
2-palmitoylglycerolincreases expression1
jinfukangdecreases expression, affects cotreatment1
(+)-JQ1 compoundincreases expression1
2,6-dichloro-(1,4)benzoquinoneincreases expression1
2,3,5-trichloro-6-phenyl-(1,4)benzoquinonedecreases expression1
Acetaminophenincreases expression1
Benzo(a)pyreneaffects methylation, increases methylation1
Cisplatinaffects cotreatment, decreases expression1
Dexamethasoneaffects cotreatment, increases expression1
Indomethacinaffects cotreatment, increases expression1
Rotenonedecreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutionincreases expression1
Urethaneincreases expression1
Valproic Acidincreases methylation1
1-Methyl-3-isobutylxanthineaffects cotreatment, increases expression1
Okadaic Acidincreases expression1
Acrylamideincreases expression1
S-Nitrosoglutathioneaffects expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT03347526PHASE3SUSPENDEDA Novel Approach to Infantile Spasms
NCT03421496PHASE3TERMINATEDA Study to Assess Cannabidiol Oral Solution With Vigabatrin as Initial Therapy in Participants With Infantile Spasms
NCT06719141PHASE3RECRUITINGA Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathies (DEE)
NCT06908226PHASE3ENROLLING_BY_INVITATIONA Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathy (DEE)
NCT04289467PHASE2RECRUITINGTreatment of Refractory Infantile Spasms With Fenfluramine
NCT05626634PHASE2COMPLETEDOpen-label, Long-term Safety Study of LP352 in Subjects With Developmental and Epileptic Encephalopathy
NCT02723448PHASE1COMPLETEDAclarubicin for the Treatment of Retinal Vasculopathy With Cerebral Leukodystrophy
NCT04727970PHASE1COMPLETEDTricaprilin Infantile Spasms Pilot Study
NCT06700811PHASE1RECRUITINGKetogenic Diet for Prevention of Epileptic Spasms in Infantile Onset Genetic Epilepsies
NCT03876444PHASE2/PHASE3UNKNOWNIntravenous Methylprednisolone Versus Oral Prednisolone for Infantile Spasms
NCT05279118PHASE2/PHASE3ACTIVE_NOT_RECRUITINGKetogenic Diet vs ACTH for the Treatment of Children With West Syndrome
NCT05364021PHASE1/PHASE2COMPLETEDStudy to Investigate LP352 in Subjects With Developmental and Epileptic Encephalopathies
NCT06983158PHASE1/PHASE2SUSPENDEDA Clinical Trial of CAP-002 Gene Therapy in Pediatric Patients With Syntaxin-Binding Protein 1 (STXBP1) Encephalopathy
NCT04937062EARLY_PHASE1ACTIVE_NOT_RECRUITINGPhenylbutyrate for Monogenetic Developmental and Epileptic Encephalopathy
NCT04302116Not specifiedRECRUITINGVigabatrin With High Dose Prednisolone Combination Therapy vs Vigabatrin Alone for Infantile Spasm
NCT05538936Not specifiedCOMPLETEDThe Effect of Spa and Massage on Babies on Colic Symptoms
NCT06149663Not specifiedAVAILABLEIntermediate-Size Expanded Access Protocol (EAP) for LP352
NCT06266234Not specifiedRECRUITINGCharacterization by Automated System on Infantile Spasmes
NCT06380192Not specifiedRECRUITINGDevelopmental and Epileptic Encephalopathy of Genetic Etiology: Natural History Through Reuse of Clinical Data
NCT07396883Not specifiedNOT_YET_RECRUITINGDevelopmental and Epileptic Encephalopathies Diagnosed Via Long-read Genome Sequencing
NCT07413211Not specifiedRECRUITINGGenetic Developmental and Epileptic Encephalopathy Natural History Study for Clinical Trial Readiness
NCT07531511Not specifiedNOT_YET_RECRUITINGSLC6A1-NDD Prospective Longitudinal Natural History Study
NCT07585643Not specifiedNOT_YET_RECRUITINGIBIS - Investigating Reliability of BIS and SEDLINE Monitoring in Children With Developmental and Epileptic Encephalopathies (DEE).