AMER3

gene
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Also known as FLJ38377

Summary

AMER3 (APC membrane recruitment protein 3, HGNC:26771) is a protein-coding gene on chromosome 2q21.1, encoding APC membrane recruitment protein 3 (Q8N944). Regulator of the canonical Wnt signaling pathway.

Predicted to enable beta-catenin binding activity and phosphatidylinositol-4,5-bisphosphate binding activity. Predicted to be involved in regulation of canonical Wnt signaling pathway. Predicted to be active in plasma membrane.

Source: NCBI Gene 205147 — RefSeq curated summary.

At a glance

  • GWAS associations: 1
  • Clinical variants (ClinVar): 205 total — 1 pathogenic, 8 likely-pathogenic
  • Phenotypes (HPO): 1
  • MANE Select transcript: NM_152698

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26771
Approved symbolAMER3
NameAPC membrane recruitment protein 3
Location2q21.1
Locus typegene with protein product
StatusApproved
AliasesFLJ38377
Ensembl geneENSG00000178171
Ensembl biotypeprotein_coding
Entrez205147

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 3 protein_coding

ENST00000321420, ENST00000431758, ENST00000458606

RefSeq mRNA: 4 — MANE Select: NM_152698 NM_001105193, NM_001105194, NM_001105195, NM_152698

CCDS: CCDS2164

Canonical transcript exons

ENST00000321420 — 2 exons

ExonStartEnd
ENSE00001281884130755540130755674
ENSE00001281894130762054130768134

Expression profiles

Bgee: expression breadth broad, 66 present calls, max score 80.67.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.8423 / max 94.7987, expressed in 145 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
225170.4475113
225220.159280
225210.097459
225200.050824
225190.050331
225180.037015

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534380.67gold quality
cerebellar cortexUBERON:000212979.80gold quality
cerebellar hemisphereUBERON:000224579.71gold quality
middle temporal gyrusUBERON:000277179.57gold quality
right hemisphere of cerebellumUBERON:001489079.45gold quality
cerebellumUBERON:000203779.41gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047377.58gold quality
endothelial cellCL:000011577.38silver quality
buccal mucosa cellCL:000233676.64gold quality
Brodmann (1909) area 23UBERON:001355474.87gold quality
prefrontal cortexUBERON:000045174.30gold quality
primary visual cortexUBERON:000243673.58gold quality
islet of LangerhansUBERON:000000673.18gold quality
Brodmann (1909) area 9UBERON:001354073.12gold quality
frontal cortexUBERON:000187072.97gold quality
right frontal lobeUBERON:000281072.79gold quality
tendon of biceps brachiiUBERON:000818872.75gold quality
neocortexUBERON:000195072.12gold quality
dorsolateral prefrontal cortexUBERON:000983472.12gold quality
superior frontal gyrusUBERON:000266171.05gold quality
left ventricle myocardiumUBERON:000656671.04gold quality
cardiac muscle of right atriumUBERON:000337970.79gold quality
cerebral cortexUBERON:000095670.34gold quality
occipital lobeUBERON:000202169.85gold quality
entorhinal cortexUBERON:000272869.31gold quality
anterior cingulate cortexUBERON:000983569.18gold quality
myocardiumUBERON:000234969.17gold quality
ganglionic eminenceUBERON:000402369.08gold quality
brainUBERON:000095568.52gold quality
postcentral gyrusUBERON:000258167.90gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-MTAB-7303no528.91
E-ANND-3no2.11

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

125 targeting AMER3, 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-3613-3P100.0076.367965
HSA-MIR-6867-5P100.0082.213464
HSA-MIR-4692100.0067.322066
HSA-MIR-4283100.0066.422097
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-3646100.0073.565283
HSA-MIR-451499.9967.101870
HSA-MIR-450099.9972.722367
HSA-MIR-371B-5P99.9975.344759
HSA-MIR-453199.9969.703181
HSA-MIR-373-5P99.9875.364753
HSA-MIR-616-5P99.9875.584775
HSA-LET-7A-5P99.9872.291790
HSA-LET-7B-5P99.9872.311790
HSA-LET-7C-5P99.9872.291790
HSA-LET-7E-5P99.9872.291790
HSA-LET-7F-5P99.9872.561784
HSA-LET-7G-5P99.9872.371784
HSA-LET-7I-5P99.9872.371788
HSA-MIR-98-5P99.9872.331787
HSA-MIR-7152-3P99.9767.47849
HSA-MIR-590-3P99.9674.346478
HSA-LET-7D-5P99.9671.761632
HSA-MIR-445899.9671.641650
HSA-MIR-448799.9664.581252
HSA-MIR-6783-3P99.8967.922059
HSA-MIR-1343-3P99.8966.781815
HSA-MIR-7162-3P99.8968.161682
HSA-MIR-6780A-5P99.8866.692776
HSA-MIR-7845-5P99.8864.88771

Literature-anchored findings (GeneRIF, showing 1)

  • Data suggest Amer3 activates Wnt signaling, in contrast to Amer1/Amer2 which inhibit Wnt, suggesting non-redundant role of Amer proteins in regulation of Wnt pathway. Knockdown of Amer3 reduces Wnt target gene expression in colorectal cancer cells. (PMID:24251807)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioamer3ENSDARG00000095819
mus_musculusAmer3ENSMUSG00000045174
rattus_norvegicusAmer3ENSRNOG00000023603

Paralogs (2): AMER2 (ENSG00000165566), AMER1 (ENSG00000184675)

Protein

Protein identifiers

APC membrane recruitment protein 3Q8N944 (reviewed: Q8N944)

Alternative names: Protein FAM123C

All UniProt accessions (3): Q8N944, C9J4B8, C9JS07

UniProt curated annotations — full annotation on UniProt →

Function. Regulator of the canonical Wnt signaling pathway. Acts by specifically binding phosphatidylinositol 4,5-bisphosphate (PtdIns(4,5)P2), translocating to the cell membrane.

Subcellular location. Cell membrane.

Similarity. Belongs to the Amer family.

RefSeq proteins (4): NP_001098663, NP_001098664, NP_001098665, NP_689911* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR019003AMERFamily

Pfam: PF09422

UniProt features (16 total): region of interest 8, compositionally biased region 6, chain 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8N944-F145.300.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 50 (showing top): GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY, GOBP_CANONICAL_WNT_SIGNALING_PATHWAY, NRSF_01, GOCC_NUCLEAR_BODY, GOMF_BETA_CATENIN_BINDING, GOMF_PHOSPHATIDYLINOSITOL_4_5_BISPHOSPHATE_BINDING, GOMF_PHOSPHATIDYLINOSITOL_PHOSPHATE_BINDING, GOMF_PHOSPHATIDYLINOSITOL_BINDING, GOMF_PHOSPHATIDYLINOSITOL_BISPHOSPHATE_BINDING, GOMF_LIPID_BINDING, GOMF_PHOSPHOLIPID_BINDING, MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3, MIKKELSEN_NPC_HCP_WITH_H3K4ME3_AND_H3K27ME3, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, MARTENS_TRETINOIN_RESPONSE_UP

GO Biological Process (2): Wnt signaling pathway (GO:0016055), regulation of canonical Wnt signaling pathway (GO:0060828)

GO Molecular Function (4): phosphatidylinositol-4,5-bisphosphate binding (GO:0005546), beta-catenin binding (GO:0008013), protein binding (GO:0005515), lipid binding (GO:0008289)

GO Cellular Component (2): plasma membrane (GO:0005886), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding2
cell surface receptor signaling pathway1
regulation of Wnt signaling pathway1
canonical Wnt signaling pathway1
phosphatidylinositol phosphate binding1
phosphatidylinositol bisphosphate binding1
protein binding1
membrane1
cell periphery1
cellular anatomical structure1

Protein interactions and networks

STRING

762 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
AMER3ZNF518BQ9C0D4585
AMER3AMER2Q8N7J2533
AMER3SVOPQ8N4V2512
AMER3ARHGEF4Q9NR80488
AMER3GPR148Q8TDV2475
AMER3REPS2Q8NFH8473
AMER3KLF14Q8TD94473
AMER3PLEKHB2Q96CS7455
AMER3GNPNAT1Q96EK6448
AMER3FAM168BA1KXE4430
AMER3SP6Q3SY56430
AMER3ARHGEF9O43307420
AMER3CTXN2P0C2S0417
AMER3FHL2Q14192412
AMER3TMEM179Q6ZVK1411

IntAct

15 interactions, top by confidence:

ABTypeScore
AMER3APCpsi-mi:“MI:0914”(association)0.630
APCAMER3psi-mi:“MI:0915”(physical association)0.630
AMER3APCpsi-mi:“MI:0915”(physical association)0.630
AMER3APCpsi-mi:“MI:0403”(colocalization)0.630
AMER1AMER3psi-mi:“MI:0915”(physical association)0.540
AMER1AMER3psi-mi:“MI:0403”(colocalization)0.540
AMER3AMER1psi-mi:“MI:0915”(physical association)0.540
AMER3AXIN2psi-mi:“MI:0915”(physical association)0.500
Axin2AMER3psi-mi:“MI:0915”(physical association)0.400
AMER3Axin2psi-mi:“MI:0915”(physical association)0.400

BioGRID (1): AMER3 (Affinity Capture-MS)

ESM2 similar proteins: A0A096LP49, A0A8V8TNH8, A0A8V8TPE2, A2VE02, A5D7I0, A6NDY2, A6NGG8, A6NIJ5, A6NNJ1, A8MXJ8, A8MYA2, B1ASB6, B2RW88, D6RGX4, O60269, P0C7V4, P0C7W8, P0C7W9, P0C7X0, P0DV75, P0DV76, Q2KIS6, Q2NL68, Q3SY00, Q4R736, Q4V8B5, Q5RCQ2, Q5SZB4, Q5VZ46, Q5XIK6, Q658T7, Q66JV7, Q6NS69, Q6PAC4, Q6ZMY3, Q76N32, Q7TSA6, Q7Z591, Q80VW7, Q80X53

Diamond homologs: A4IGN8, E1C2Q8, F1QGH6, F1RDM5, Q6INC4, Q6NS69, Q8CCJ4, Q8N7J2, Q8N944, Q5JTC6, Q7TS75

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic8
Uncertain significance171
Likely benign21
Benign1

Top pathogenic / likely-pathogenic (9)

Variant IDHGVSClassification
625693GRCh37/hg19 2q21.1(chr2:131487820-132166509)Pathogenic
152346GRCh38/hg38 2q21.1(chr2:130720173-131278036)x1Likely pathogenic
441546GRCh37/hg19 2q21.1(chr2:131477947-131950529)x1Likely pathogenic
442575GRCh37/hg19 2q21.1(chr2:131477947-131975365)x1Likely pathogenic
442906GRCh37/hg19 2q21.1(chr2:131477947-131956516)x1Likely pathogenic
443891GRCh37/hg19 2q21.1(chr2:131477947-131933576)x1Likely pathogenic
545243NC_000002.12:g.(?130725519)(131168548_?)delLikely pathogenic
625692GRCh37/hg19 2q21.1(chr2:131486951-131933628)Likely pathogenic
916554NM_152698.3(AMER3):c.2236C>T (p.Arg746Ter)Likely pathogenic

SpliceAI

241 predictions. Top by Δscore:

VariantEffectΔscore
2:130762052:A:AGacceptor_gain1.0000
2:130762053:G:GGacceptor_gain1.0000
2:130755675:G:GGdonor_gain0.9900
2:130759522:G:Tdonor_gain0.9900
2:130762053:GC:Gacceptor_gain0.9900
2:130762053:GCA:Gacceptor_gain0.9900
2:130755673:CA:Cdonor_gain0.9800
2:130762048:CCACA:Cacceptor_loss0.9800
2:130762049:CACAG:Cacceptor_loss0.9800
2:130762050:ACAGC:Aacceptor_loss0.9800
2:130762052:AG:Aacceptor_loss0.9800
2:130762053:G:Aacceptor_loss0.9800
2:130762053:GCAGC:Gacceptor_gain0.9800
2:130755671:CACA:Cdonor_gain0.9700
2:130755672:ACA:Adonor_gain0.9700
2:130755673:CAGT:Cdonor_loss0.9700
2:130755674:AG:Adonor_loss0.9700
2:130755675:GT:Gdonor_loss0.9700
2:130755676:TG:Tdonor_loss0.9700
2:130755677:GAG:Gdonor_loss0.9700
2:130755678:AGTA:Adonor_loss0.9700
2:130759568:G:GTdonor_gain0.9700
2:130755670:ACACA:Adonor_gain0.9600
2:130756379:GCG:Gdonor_gain0.9500
2:130762050:A:AGacceptor_gain0.9500
2:130762051:C:Gacceptor_gain0.9500
2:130762056:G:GAacceptor_gain0.9500
2:130755691:C:Tdonor_gain0.9400
2:130762055:A:AGacceptor_gain0.9400
2:130762054:CAG:Cacceptor_loss0.9300

AlphaMissense

5560 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:130763219:A:CS383R0.994
2:130763221:T:AS383R0.994
2:130763221:T:GS383R0.994
2:130762802:T:CF244L0.992
2:130762804:C:AF244L0.992
2:130762804:C:GF244L0.992
2:130763591:G:CG507R0.990
2:130762097:T:CF9L0.988
2:130762099:C:AF9L0.988
2:130762099:C:GF9L0.988
2:130762832:T:CF254L0.988
2:130762834:C:AF254L0.988
2:130762834:C:GF254L0.988
2:130763534:T:AW488R0.988
2:130763534:T:CW488R0.988
2:130763536:G:CW488C0.987
2:130763536:G:TW488C0.987
2:130762484:T:CF138L0.986
2:130762486:T:AF138L0.986
2:130762486:T:GF138L0.986
2:130762524:T:CI151T0.986
2:130762799:A:CS243R0.986
2:130762801:C:AS243R0.986
2:130762801:C:GS243R0.986
2:130763577:T:CL502P0.986
2:130763553:T:CL494P0.985
2:130763568:A:TD499V0.985
2:130763598:T:AV509D0.984
2:130763545:G:CK491N0.983
2:130763545:G:TK491N0.983

dbSNP variants (sampled 300 via entrez): RS1000059749 (2:130760972 C>G), RS1000126975 (2:130765853 T>G), RS1000127328 (2:130753614 C>T), RS1000128977 (2:130759842 G>A), RS1000148985 (2:130762890 C>G), RS1000215190 (2:130756045 C>A), RS1000259494 (2:130757155 A>G), RS1000310657 (2:130765624 G>A,T), RS1000569146 (2:130755900 C>T), RS1000596414 (2:130767735 G>A,T), RS1000607451 (2:130762357 C>A,T), RS1000698447 (2:130757370 G>T), RS1000837785 (2:130756160 G>A,C), RS1000954658 (2:130756907 A>G,T), RS1001402011 (2:130761656 G>A)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:181500, MIM:189960

GenCC curated gene-disease

Mondo (3): schizophrenia (MONDO:0005090), neurodevelopmental disorder (MONDO:0700092), esophageal atresia/tracheoesophageal fistula (MONDO:0008586)

Orphanet (2): Esophageal atresia (Orphanet:1199), NON RARE IN EUROPE: Schizophrenia (Orphanet:3140)

HPO phenotypes

1 total (1 of 1 shown, HPO-id order):

HPOTerm
HP:0100753Schizophrenia

GWAS associations

1 associations (top):

StudyTraitp-value
GCST012046_2Fasting insulin1.000000e-07

MeSH disease descriptors (2)

DescriptorNameTree numbers
D065886Neurodevelopmental DisordersF03.625
C531835Esophageal atresia with or without tracheoesophageal fistula (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

12 total (human), top 12 by PubMed support.

ChemicalActions (top 5)PubMed papers
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
Resveratrolaffects cotreatment, decreases expression1
Arsenicaffects methylation1
Benzo(a)pyreneaffects methylation, increases methylation1
Cadmiumdecreases expression, increases abundance1
Copperdecreases expression, affects cotreatment1
Methapyrileneincreases methylation1
Rotenonedecreases expression1
Aflatoxin M1decreases expression1
Cadmium Chloridedecreases expression, increases abundance1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

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

TrialPhaseStatusTitle
NCT00000374PHASE4COMPLETEDTreatment for First-Episode Schizophrenia
NCT00001656PHASE4COMPLETEDComparison of Clozapine vs Olanzapine in Childhood-Onset Psychotic Disorders
NCT00007774PHASE4COMPLETEDTo Determine if Olanzapine is More Cost Effective Than Haloperidol for the Treatment of Schizophrenia
NCT00014001PHASE4COMPLETEDCATIE- Schizophrenia Trial
NCT00018668PHASE4COMPLETEDAntipsychotic Response in Schizophrenia
NCT00034801PHASE4COMPLETEDOlanzapine Versus Active Comparator in the Treatment of Depression in Patients With Schizophrenia
NCT00034905PHASE4COMPLETEDA Comparison of Seroquel vs. Risperidone in Schizophrenia
NCT00036088PHASE4COMPLETEDOlanzapine Versus An Active Comparator in the Treatment of Schizophrenia
NCT00044187PHASE4COMPLETEDThe Assessment of a Weight-Gain Agent for the Treatment of Olanzapine-Associated Anti-Obesity Agent in Patients With Schizophrenia, Schizophreniform Disorder, Schizoaffective Disorder, and Bipolar I Disorder
NCT00044655PHASE4COMPLETEDSwitching Medication to Treat Schizophrenia
NCT00048828PHASE4COMPLETEDTreating Drug-Resistant Childhood Schizophrenia
NCT00053703PHASE4COMPLETEDTreatment of Early Onset Schizophrenia Spectrum Disorders (TEOSS)
NCT00056498PHASE4COMPLETEDRisperidone Treatment in Schizophrenia Patients Who Are Currently Taking Clozapine
NCT00061802PHASE4COMPLETEDEfficacy and Safety of Two Atypical Antipsychotics vs. Placebo in Patients With an Acute Exacerbation of Either Schizophrenia or Schizoaffective Disorder
NCT00080327PHASE4COMPLETEDStudy of Three Doses of Aripiprazole in Patients With Acute Schizophrenia
NCT00088049PHASE4COMPLETEDStudy of Olanzapine vs. Aripiprazole in the Treatment of Schizophrenia
NCT00090012PHASE4COMPLETEDComparison of Continuing Olanzapine to Switching to Quetiapine in Overweight or Obese Patients With Schizophrenia and Schizoaffective Disorder
NCT00100776PHASE4COMPLETEDEfficacy of High Dose Olanzapine for the Treatment of Schizophrenia and Schizoaffective Disorder
NCT00103571PHASE4COMPLETEDOlanzapine Versus Aripiprazole in the Treatment of Acutely Ill Patients With Schizophrenia
NCT00108368PHASE4COMPLETEDThe Effects of Risperidone and Olanzapine on Thinking
NCT00114595PHASE4COMPLETEDEthyl-Eicosapentaenoic Acid and Tardive Dyskinesia
NCT00130923PHASE4COMPLETEDRisperidone Long-acting Versus Oral Risperidone in Patients With Schizophrenia and Alcohol Use Disorder
NCT00137020PHASE4COMPLETEDClinical Effect Of Cross Titration Of Antipsychotics With Ziprasidone In Schizophrenia Or Schizoaffective Disorder
NCT00140166PHASE4COMPLETEDTreatment of Acute Schizophrenia With Vitamin Therapy
NCT00145847PHASE4COMPLETEDNaltrexone Treatment of Alcohol Abuse in Schizophrenia
NCT00148564PHASE4COMPLETEDEnergy Homeostasis Under Treatment With Atypical Antipsychotics
NCT00156715PHASE4COMPLETEDEfficacy of Quetiapine in the Treatment of Patients With Schizophrenia and a Comorbid Substance Use Disorder
NCT00158223PHASE4COMPLETEDEffectiveness of Pimozide in Augmenting the Effects of Clozapine in the Treatment of Schizophrenia
NCT00159081PHASE4COMPLETEDOne Year Drug Treatment in First-Episode Schizophrenia
NCT00159120PHASE4COMPLETEDMaintenance Treatment vs. Stepwise Drug Discontinuation in First-Episode Schizophrenia
NCT00159133PHASE4COMPLETEDProdrome-Based Early Intervention With Antipsychotics vs. Benzodiazepines in First-Episode Schizophrenia
NCT00159757PHASE4TERMINATED12 Week Open, Non-Comparative Switch Study Of Oral Ziprazidone In Previously Treated Schizophrenic Patients
NCT00167817PHASE4COMPLETEDEffect of Switch to Aripiprazole on Health and Smoking Parameters in Patients With Schizophrenia: A Pilot Study
NCT00169026PHASE4TERMINATEDAlcoholism and Schizophrenia: Effects of Clozapine
NCT00169039PHASE4TERMINATEDClozapine Versus Chlorpromazine for Treatment-Unresponsive Schizophrenia
NCT00169065PHASE4COMPLETEDEffectiveness of Clozapine Versus Olanzapine for Treatment-resistant Schizophrenia
NCT00169091PHASE4TERMINATEDClozapine Versus Haloperidol for Treating the First Episode of Schizophrenia
NCT00176423PHASE4COMPLETEDEfficacy Study of Galantamine for Cognitive Impairments in Schizophrenia
NCT00176436PHASE4COMPLETEDAtomoxetine for Treatment of Weight Gain in Olanzapine or Clozapine Patients
NCT00177008PHASE4COMPLETEDAripiprazole for the Treatment of Schizophrenia With Co-Morbid Social Anxiety