CNIH3

gene
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Also known as FLJ38993CNIH-3

Summary

CNIH3 (cornichon family AMPA receptor auxiliary protein 3, HGNC:26802) is a protein-coding gene on chromosome 1q42.12, encoding Protein cornichon homolog 3 (Q8TBE1). Regulates the trafficking and gating properties of AMPA-selective glutamate receptors (AMPARs).

Predicted to enable channel regulator activity and signaling receptor binding activity. Involved in regulation of AMPA receptor activity. Predicted to be located in dendritic shaft and postsynaptic membrane. Predicted to be part of AMPA glutamate receptor complex. Predicted to be active in dendrite and glutamatergic synapse.

Source: NCBI Gene 149111 — RefSeq curated summary.

At a glance

  • GWAS associations: 9
  • Clinical variants (ClinVar): 34 total — 2 pathogenic
  • MANE Select transcript: NM_152495

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:26802
Approved symbolCNIH3
Namecornichon family AMPA receptor auxiliary protein 3
Location1q42.12
Locus typegene with protein product
StatusApproved
AliasesFLJ38993, CNIH-3
Ensembl geneENSG00000143786
Ensembl biotypeprotein_coding
Entrez149111

Gene structure

Transcript identifiers

Ensembl transcripts: 16 — 13 protein_coding_CDS_not_defined, 3 protein_coding

ENST00000272133, ENST00000470602, ENST00000470788, ENST00000471578, ENST00000478120, ENST00000479227, ENST00000481095, ENST00000483512, ENST00000489556, ENST00000492470, ENST00000496277, ENST00000496372, ENST00000498126, ENST00000498382, ENST00000860910, ENST00000933029

RefSeq mRNA: 5 — MANE Select: NM_152495 NM_001322302, NM_001322303, NM_001322304, NM_001322305, NM_152495

CCDS: CCDS1544

Canonical transcript exons

ENST00000272133 — 6 exons

ExonStartEnd
ENSE00001147221224739329224740554
ENSE00001215659224616317224617255
ENSE00003466788224734563224734706
ENSE00003483736224684796224684843
ENSE00003527670224730462224730574
ENSE00003685214224680958224681026

Expression profiles

Bgee: expression breadth ubiquitous, 204 present calls, max score 86.65.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 5.1978 / max 158.4408, expressed in 1428 samples.

FANTOM5 promoters (14 alternative TSS)

Promoter IDTPM avgSamples expressed
88061.4976519
88051.3510533
87931.0371630
87950.5274177
87920.3980193
88030.083330
88040.081725
87990.074423
88010.052320
88000.049718

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099186.65gold quality
cortical plateUBERON:000534386.56gold quality
endothelial cellCL:000011586.13gold quality
prefrontal cortexUBERON:000045185.47gold quality
stromal cell of endometriumCL:000225584.82gold quality
buccal mucosa cellCL:000233684.38gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047383.62gold quality
Brodmann (1909) area 9UBERON:001354083.47gold quality
right frontal lobeUBERON:000281083.37gold quality
dorsolateral prefrontal cortexUBERON:000983483.27gold quality
cingulate cortexUBERON:000302782.61gold quality
anterior cingulate cortexUBERON:000983582.38gold quality
frontal cortexUBERON:000187082.31gold quality
neocortexUBERON:000195082.11gold quality
amygdalaUBERON:000187681.86gold quality
nucleus accumbensUBERON:000188281.59gold quality
Ammon’s hornUBERON:000195481.52gold quality
cerebral cortexUBERON:000095681.50gold quality
body of pancreasUBERON:000115081.12gold quality
left ovaryUBERON:000211980.49gold quality
telencephalonUBERON:000189380.45gold quality
Brodmann (1909) area 23UBERON:001355480.42gold quality
caudate nucleusUBERON:000187379.68gold quality
forebrainUBERON:000189079.51gold quality
right ovaryUBERON:000211879.44gold quality
brainUBERON:000095578.45gold quality
pancreasUBERON:000126478.40gold quality
central nervous systemUBERON:000101778.31gold quality
calcaneal tendonUBERON:000370178.29gold quality
temporal lobeUBERON:000187178.23gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes5.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

46 targeting CNIH3, 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-6873-3P100.0071.422626
HSA-MIR-7110-3P100.0073.182486
HSA-MIR-103A-3P99.9869.141595
HSA-MIR-10799.9869.141595
HSA-MIR-211099.9666.681930
HSA-MIR-426799.9666.532368
HSA-MIR-101-3P99.9475.032230
HSA-MIR-806399.9169.763146
HSA-MIR-4731-5P99.8967.232537
HSA-MIR-6857-5P99.8765.32985
HSA-MIR-4799-5P99.8270.602663
HSA-MIR-2116-3P99.7464.32889
HSA-MIR-7161-5P99.6868.921592
HSA-MIR-450299.6566.991021
HSA-MIR-548U99.6567.781463
HSA-MIR-56799.6368.571219
HSA-MIR-613499.6365.681537
HSA-MIR-391199.3866.951087
HSA-MIR-190B-3P99.3368.291382
HSA-MIR-4667-3P99.2665.451608
HSA-MIR-593-3P99.2267.281327
HSA-MIR-122B-3P99.2168.901333
HSA-MIR-21-3P99.2168.951312
HSA-MIR-4795-5P99.1166.90876
HSA-MIR-62298.9966.481050
HSA-MIR-93698.8770.511124
HSA-MIR-7155-5P98.6566.141290
HSA-MIR-1301-3P98.6468.271071
HSA-MIR-504798.6468.621035
HSA-MIR-6811-3P98.6266.54944

Literature-anchored findings (GeneRIF, showing 2)

  • Significant upregulation of CNIH-3 mRNA expression was found in schizophrenia. (PMID:23103966)
  • Study’s convergent findings in humans and mice support CNIH3 involvement in the pathophysiology of opioid dependence, complementing prior studies implicating the alpha-amino-3-hydroxy-5-methyl-4-isoxazolepropionic acid (AMPA) glutamate system (PMID:26239289)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriocnih3ENSDARG00000014953
mus_musculusCnih3ENSMUSG00000026514
rattus_norvegicusCnih3ENSRNOG00000022724
drosophila_melanogastercniFBGN0000339
caenorhabditis_elegansWBGENE00011648

Paralogs (4): CNIH1 (ENSG00000100528), PPCS (ENSG00000127125), CNIH4 (ENSG00000143771), CNIH2 (ENSG00000174871)

Protein

Protein identifiers

Protein cornichon homolog 3Q8TBE1 (reviewed: Q8TBE1)

Alternative names: Cornichon family AMPA receptor auxiliary protein 3

All UniProt accessions (1): Q8TBE1

UniProt curated annotations — full annotation on UniProt →

Function. Regulates the trafficking and gating properties of AMPA-selective glutamate receptors (AMPARs). Promotes their targeting to the cell membrane and synapses and modulates their gating properties by regulating their rates of activation, deactivation and desensitization.

Subunit / interactions. Acts as an auxiliary subunit for AMPA-selective glutamate receptors (AMPARs). Found in a complex with GRIA1, GRIA2, GRIA3, GRIA4, CNIH2, CACNG2, CACNG3, CACNG4, CACNG5, CACNG7 and CACNG8.

Subcellular location. Postsynaptic cell membrane.

Tissue specificity. Expression is up-regulated in dorsolateral prefrontal cortex of patients with schizophrenia (postmortem brain study).

Similarity. Belongs to the cornichon family.

RefSeq proteins (5): NP_001309231, NP_001309232, NP_001309233, NP_001309234, NP_689708* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003377CornichonFamily
IPR033466Cornichon_conservedConserved_site

Pfam: PF03311

UniProt features (8 total): topological domain 4, transmembrane region 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q8TBE1-F185.150.48

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-204005COPII-mediated vesicle transport
R-HSA-5694530Cargo concentration in the ER

MSigDB gene sets: 163 (showing top): BERTUCCI_MEDULLARY_VS_DUCTAL_BREAST_CANCER_DN, GOBP_VESICLE_MEDIATED_TRANSPORT, REACTOME_MEMBRANE_TRAFFICKING, GOBP_PROTEIN_LOCALIZATION_TO_CELL_PERIPHERY, GOBP_CELL_CELL_SIGNALING, GOCC_COATED_VESICLE, TGACATY_UNKNOWN, GOBP_SYNAPTIC_SIGNALING, GOBP_PROTEIN_LOCALIZATION_TO_ORGANELLE, GOCC_NEURON_PROJECTION, GOBP_PROTEIN_LOCALIZATION_TO_SYNAPSE, AML1_01, GOBP_SYNAPTIC_TRANSMISSION_GLUTAMATERGIC, GOBP_REGULATION_OF_NEUROTRANSMITTER_RECEPTOR_ACTIVITY, GOMF_SIGNALING_RECEPTOR_BINDING

GO Biological Process (5): vesicle-mediated transport (GO:0016192), synaptic transmission, glutamatergic (GO:0035249), regulation of membrane potential (GO:0042391), neurotransmitter receptor localization to postsynaptic specialization membrane (GO:0099645), regulation of AMPA receptor activity (GO:2000311)

GO Molecular Function (3): signaling receptor binding (GO:0005102), channel regulator activity (GO:0016247), protein binding (GO:0005515)

GO Cellular Component (11): endoplasmic reticulum membrane (GO:0005789), ER to Golgi transport vesicle membrane (GO:0012507), dendrite (GO:0030425), AMPA glutamate receptor complex (GO:0032281), endoplasmic reticulum-Golgi intermediate compartment membrane (GO:0033116), dendritic shaft (GO:0043198), synapse (GO:0045202), postsynaptic membrane (GO:0045211), glutamatergic synapse (GO:0098978), plasma membrane (GO:0005886), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
ER to Golgi Anterograde Transport2

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure2
transport1
cellular process1
chemical synaptic transmission1
monoatomic ion transmembrane transport1
regulation of biological quality1
protein-containing complex localization1
receptor localization to synapse1
regulation of postsynaptic membrane neurotransmitter receptor levels1
protein localization to postsynaptic specialization membrane1
AMPA glutamate receptor activity1
regulation of transmembrane transporter activity1
regulation of neurotransmitter receptor activity1
protein binding1
channel activity1
transporter regulator activity1
binding1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
COPII-coated ER to Golgi transport vesicle1
transport vesicle membrane1
coated vesicle membrane1
neuron projection1
dendritic tree1
ionotropic glutamate receptor complex1
endoplasmic reticulum-Golgi intermediate compartment1
bounding membrane of organelle1
dendrite1
cell junction1
synaptic membrane1
postsynapse1
synapse1
membrane1
cell periphery1

Protein interactions and networks

STRING

956 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CNIH3NT5C1AQ9BXI3815
CNIH3KCNG2Q9UJ96748
CNIH3GRIA3P42263731
CNIH3GRIA2P42262690
CNIH3GSG1LQ6UXU4646
CNIH3GRIA1P42261598
CNIH3SYNDIG1Q9H7V2582
CNIH3GSG1L2A8MUP6564
CNIH3TGFAP01135560
CNIH3COL22A1Q8NFW1556
CNIH3ADAMTS14Q8WXS8552
CNIH3FAM53BQ14153550
CNIH3COL4A6Q14031546
CNIH3COL21A1Q96P44545
CNIH3GRIA4P48058542

IntAct

87 interactions, top by confidence:

ABTypeScore
CNIH3AQP6psi-mi:“MI:0915”(physical association)0.560
CNIH3CLDN20psi-mi:“MI:0915”(physical association)0.560
CNIH3TMEM80psi-mi:“MI:0915”(physical association)0.560
CNIH3ERGIC3psi-mi:“MI:0915”(physical association)0.560
CNIH3FAM210Bpsi-mi:“MI:0915”(physical association)0.560
CNIH3SMIM3psi-mi:“MI:0915”(physical association)0.560
CNIH3psi-mi:“MI:0915”(physical association)0.560
PLD3CNIH3psi-mi:“MI:0915”(physical association)0.560
TMPRSS2CNIH3psi-mi:“MI:0915”(physical association)0.560
CNIH3TMEM237psi-mi:“MI:0915”(physical association)0.560
BIKCNIH3psi-mi:“MI:0915”(physical association)0.560
CEACAM3CNIH3psi-mi:“MI:0915”(physical association)0.560
CNIH3SORT1psi-mi:“MI:0915”(physical association)0.560
AQP6CNIH3psi-mi:“MI:0915”(physical association)0.560
CNIH3TMEM14Bpsi-mi:“MI:0915”(physical association)0.560
LRRC25CNIH3psi-mi:“MI:0915”(physical association)0.560
CLDN20CNIH3psi-mi:“MI:0915”(physical association)0.560
STOMCNIH3psi-mi:“MI:0915”(physical association)0.560
ODF4CNIH3psi-mi:“MI:0915”(physical association)0.560
CNIH3GPX8psi-mi:“MI:0915”(physical association)0.560
NEMP1CNIH3psi-mi:“MI:0915”(physical association)0.560
TMEM52BCNIH3psi-mi:“MI:0915”(physical association)0.560
LEUTXCNIH3psi-mi:“MI:0915”(physical association)0.560
CD79ACNIH3psi-mi:“MI:0915”(physical association)0.560
CNIH3VSIRpsi-mi:“MI:0915”(physical association)0.560

BioGRID (29): CNIH3 (Two-hybrid), CNIH3 (Two-hybrid), CNIH3 (Two-hybrid), CNIH3 (Two-hybrid), CNIH3 (Two-hybrid), CNIH3 (Two-hybrid), CNIH3 (Two-hybrid), CNIH3 (Two-hybrid), CNIH3 (Two-hybrid), CNIH3 (Two-hybrid), CNIH3 (Two-hybrid), SLC16A2 (Two-hybrid), STOM (Two-hybrid), TMEM237 (Two-hybrid), SUSD3 (Two-hybrid)

ESM2 similar proteins: A4IFN5, A6NI61, A6QQ59, B0CM95, B2KI79, B2LYG4, B2RZC9, D0Q0Y7, O35089, P22234, P86229, Q15546, Q1RMP9, Q2TA01, Q3ZCD7, Q5BJU5, Q5QJU3, Q5R589, Q5RB59, Q5RDB5, Q5RL79, Q5U3C3, Q64232, Q6IQ69, Q6PHN7, Q6PI25, Q6ZWS4, Q719N3, Q865K8, Q86WK9, Q86YN1, Q8BWB6, Q8IY49, Q8IZV2, Q8N6L1, Q8N6M3, Q8NBT3, Q8NFT2, Q8R189, Q8TBE1

Diamond homologs: D0Q0Y7, O35089, O35372, O95406, P49858, P52159, Q0VFK3, Q22361, Q3T126, Q401C0, Q5BIN6, Q5BJU5, Q5BL21, Q5R9M4, Q5RDB5, Q68EY2, Q6P3N5, Q6PI25, Q6ZWS4, Q8TBE1, Q9CX13, Q9P003, P53173, O14038, P38312, Q0DET3, Q3EDD7, Q84W04, Q9P6K6, Q9C7D7, Q2QQ55, Q8GWT5, Q9SZ74

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic0
Uncertain significance24
Likely benign0
Benign2

Top pathogenic / likely-pathogenic (2)

Variant IDHGVSClassification
1703636GRCh37/hg19 1q42.11-42.12(chr1:224432682-225142704)Pathogenic
625540GRCh37/hg19 1q42.11-42.12(chr1:224340881-225147932)Pathogenic

SpliceAI

2129 predictions. Top by Δscore:

VariantEffectΔscore
1:224684781:T:Aacceptor_gain1.0000
1:224734705:TGGT:Tdonor_loss1.0000
1:224734706:GGTG:Gdonor_loss1.0000
1:224734707:G:GGdonor_gain1.0000
1:224734708:T:Adonor_loss1.0000
1:224734709:GAGTA:Gdonor_loss1.0000
1:224673859:A:Gacceptor_gain0.9900
1:224680957:GATA:Gacceptor_gain0.9900
1:224681024:GCG:Gdonor_gain0.9900
1:224681024:GCGGT:Gdonor_loss0.9900
1:224681025:CGGT:Cdonor_loss0.9900
1:224681026:GGTA:Gdonor_loss0.9900
1:224681027:G:GCdonor_loss0.9900
1:224681028:TAA:Tdonor_loss0.9900
1:224681029:A:AGdonor_loss0.9900
1:224684783:T:TAacceptor_gain0.9900
1:224684786:ATCCT:Aacceptor_gain0.9900
1:224684787:T:Gacceptor_gain0.9900
1:224730460:AGCT:Aacceptor_gain0.9900
1:224730461:GCTG:Gacceptor_gain0.9900
1:224734559:GCA:Gacceptor_loss0.9900
1:224734561:A:ACacceptor_loss0.9900
1:224734562:GGT:Gacceptor_gain0.9900
1:224734704:CTG:Cdonor_gain0.9900
1:224734705:TG:Tdonor_gain0.9900
1:224734706:GG:Gdonor_gain0.9900
1:224617256:G:GGdonor_gain0.9800
1:224632818:GTTC:Gdonor_gain0.9800
1:224680956:A:AGacceptor_gain0.9800
1:224680957:G:GGacceptor_gain0.9800

AlphaMissense

1061 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:224680977:T:CL34S0.999
1:224730545:T:AN94K0.999
1:224730545:T:GN94K0.999
1:224730550:C:GP96R0.999
1:224734665:G:CK138N0.999
1:224734665:G:TK138N0.999
1:224617199:T:CC9R0.998
1:224617200:G:AC9Y0.998
1:224617215:T:CL14P0.998
1:224617233:T:CL20P0.998
1:224730550:C:AP96H0.998
1:224734663:A:GK138E0.998
1:224617201:C:GC9W0.997
1:224730561:T:GY100D0.997
1:224734687:T:CF146L0.997
1:224734689:C:AF146L0.997
1:224734689:C:GF146L0.997
1:224734700:T:CL150P0.997
1:224617223:T:CC17R0.996
1:224730498:T:CC79R0.996
1:224730508:T:CF82S0.996
1:224730553:T:GL97R0.996
1:224734667:T:CL139P0.996
1:224734679:T:CL143P0.996
1:224734700:T:AL150H0.996
1:224617215:T:GL14R0.995
1:224617227:C:AA18D0.995
1:224684836:T:CL64P0.995
1:224730553:T:AL97Q0.995
1:224734693:T:GY148D0.995

dbSNP variants (sampled 300 via entrez): RS1000000663 (1:224529421 G>T), RS1000011439 (1:224493211 A>G), RS1000016082 (1:224648609 T>G), RS1000031254 (1:224628005 A>C), RS1000069345 (1:224578013 G>T), RS1000079348 (1:224674674 C>T), RS1000083767 (1:224668381 CAG>C), RS1000086597 (1:224637024 T>C), RS1000105762 (1:224446484 A>G), RS1000116201 (1:224692812 T>C), RS1000117547 (1:224465510 C>T), RS1000139495 (1:224661213 G>A), RS1000141838 (1:224535440 T>C), RS1000142582 (1:224554023 T>C), RS1000145491 (1:224635607 C>G,T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:612530

GenCC curated gene-disease

Mondo (1): chromosome 1q41-q42 deletion syndrome (MONDO:0012927)

Orphanet (2): Holoprosencephaly (Orphanet:2162), 1q41q42 microdeletion syndrome (Orphanet:250999)

HPO phenotypes

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

GWAS associations

9 associations (top):

StudyTraitp-value
GCST003614_1Opioid dependence4.000000e-09
GCST005275_21Cancer9.000000e-07
GCST010204_162Low density lipoprotein cholesterol levels1.000000e-09
GCST011780_14Neonatal white matter microstructure5.000000e-06
GCST90002390_339Mean corpuscular hemoglobin5.000000e-12
GCST90002398_511Neutrophil count8.000000e-25
GCST90002399_19Neutrophil percentage of white cells2.000000e-10
GCST90002407_202White blood cell count4.000000e-24
GCST90006991_8Gut microbiota relative abundance (Streptococcus)6.000000e-06

EFO canonical traits (6, from GWAS)

EFO IDTrait name
EFO:0004611low density lipoprotein cholesterol measurement
EFO:0005674white matter microstructure measurement
EFO:0004527mean corpuscular hemoglobin
EFO:0004833neutrophil count
EFO:0007990neutrophil percentage of leukocytes
EFO:0007874gut microbiome measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

PharmGKB clinical annotations

1 annotations.

VariantTypeLevelDrugsPhenotypes
rs10799590Toxicity3opioidsOpioid-Related Disorders

PharmGKB variants

1 variants.

VariantGenesLevelScore#Clin annotsDrugs
rs10799590CNIH331.751opioids

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Benzo(a)pyreneaffects methylation, decreases expression, increases methylation3
bisphenol Aincreases expression2
Estradioldecreases expression, affects cotreatment2
Progesteroneaffects cotreatment, decreases expression2
Cadmium Chloridedecreases expression, increases abundance, increases expression2
triphenyl phosphateaffects expression1
propionaldehydeincreases expression1
butyraldehydeincreases expression1
benzo(e)pyreneincreases methylation1
aflatoxin B2increases methylation1
S-(1,2-dichlorovinyl)cysteineaffects cotreatment, decreases expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608increases reaction, affects binding1
2,2’,4,4’,5-brominated diphenyl etherincreases expression1
ormosilaffects binding, increases expression1
licochalcone Bincreases expression1
(+)-JQ1 compounddecreases expression1
Resveratrolaffects cotreatment, decreases expression1
Temozolomidedecreases expression1
Acetaminophendecreases expression1
Amiodaroneincreases expression1
Cadmiumincreases abundance, increases expression1
Cisplatindecreases expression, increases expression1
Dexamethasonedecreases expression1
Leadaffects expression1
Lipopolysaccharidesaffects cotreatment, decreases expression1
Methapyrileneincreases methylation1
Phenobarbitalincreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Polyethylene Glycolsaffects binding, increases expression1

Clinical trials (associated diseases)

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