CNIH4

gene
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Also known as HSPC163

Summary

CNIH4 (cornichon family member 4, HGNC:25013) is a protein-coding gene on chromosome 1q42.11, encoding Protein cornichon homolog 4 (Q9P003). Involved in G protein-coupled receptors (GPCRs) trafficking from the endoplasmic reticulum to the cell surface; it promotes the exit of GPCRs from the early secretory pathway, likely through interaction with the COPII machinery. It is a selective cancer dependency (DepMap: 47.6% of cell lines).

Enables CCR5 chemokine receptor binding activity. Involved in endoplasmic reticulum to Golgi vesicle-mediated transport. Located in endoplasmic reticulum and endoplasmic reticulum-Golgi intermediate compartment.

Source: NCBI Gene 29097 — RefSeq curated summary.

At a glance

  • GWAS associations: 8
  • Clinical variants (ClinVar): 31 total — 1 pathogenic
  • Cancer dependency (DepMap): dependent in 47.6% of screened cell lines
  • MANE Select transcript: NM_014184

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:25013
Approved symbolCNIH4
Namecornichon family member 4
Location1q42.11
Locus typegene with protein product
StatusApproved
AliasesHSPC163
Ensembl geneENSG00000143771
Ensembl biotypeprotein_coding
OMIM617483
Entrez29097

Gene structure

Transcript identifiers

Ensembl transcripts: 14 — 10 protein_coding, 4 protein_coding_CDS_not_defined

ENST00000366856, ENST00000366857, ENST00000366858, ENST00000366860, ENST00000465271, ENST00000468318, ENST00000469200, ENST00000477413, ENST00000895496, ENST00000895497, ENST00000933590, ENST00000933591, ENST00000933592, ENST00000933593

RefSeq mRNA: 5 — MANE Select: NM_014184 NM_001277197, NM_001277198, NM_001277199, NM_001277200, NM_014184

CCDS: CCDS1543, CCDS60429, CCDS60430

Canonical transcript exons

ENST00000465271 — 5 exons

ExonStartEnd
ENSE00000961880224360495224360563
ENSE00001949026224356879224356993
ENSE00001955275224375795224379452
ENSE00003478805224365879224365991
ENSE00003505731224371283224371423

Expression profiles

Bgee: expression breadth ubiquitous, 288 present calls, max score 97.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 39.2584 / max 362.7416, expressed in 1822 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
879134.41671820
87904.84171651

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
jejunal mucosaUBERON:000039997.55gold quality
mammalian vulvaUBERON:000099797.41gold quality
pericardiumUBERON:000240797.36gold quality
heart right ventricleUBERON:000208096.95gold quality
penisUBERON:000098996.87gold quality
oral cavityUBERON:000016796.72gold quality
cartilage tissueUBERON:000241896.67gold quality
pharyngeal mucosaUBERON:000035596.55gold quality
adult organismUBERON:000702396.51gold quality
biceps brachiiUBERON:000150796.49gold quality
esophagus squamous epitheliumUBERON:000692096.49gold quality
gingivaUBERON:000182896.48gold quality
tendon of biceps brachiiUBERON:000818896.41gold quality
upper leg skinUBERON:000426296.33gold quality
pigmented layer of retinaUBERON:000178296.21gold quality
gingival epitheliumUBERON:000194996.17gold quality
jejunumUBERON:000211596.17gold quality
skeletal muscle tissue of biceps brachiiUBERON:000450296.16gold quality
trabecular bone tissueUBERON:000248396.12gold quality
body of tongueUBERON:001187696.08gold quality
squamous epitheliumUBERON:000691495.74gold quality
lower lobe of lungUBERON:000894995.65gold quality
monocyteCL:000057695.61gold quality
deciduaUBERON:000245095.61gold quality
epithelium of esophagusUBERON:000197695.47gold quality
mononuclear cellCL:000084295.44gold quality
stromal cell of endometriumCL:000225595.43gold quality
parietal pleuraUBERON:000240095.38gold quality
colonic mucosaUBERON:000031795.31gold quality
leukocyteCL:000073895.23gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes19.85
E-MTAB-6379no502.93

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): E2F1

miRNA regulators (miRDB)

54 targeting CNIH4, 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-5011-5P100.0083.465820
HSA-MIR-1277-5P100.0073.955056
HSA-MIR-190A-3P100.0080.355520
HSA-MIR-3646100.0073.565283
HSA-MIR-548P99.9872.253784
HSA-MIR-19A-3P99.9875.332762
HSA-MIR-19B-3P99.9875.442754
HSA-MIR-146A-5P99.9668.93988
HSA-MIR-146B-5P99.9669.13977
HSA-MIR-545-3P99.9570.742783
HSA-MIR-7153-5P99.9468.891006
HSA-MIR-6842-5P99.8067.541587
HSA-MIR-7110-5P99.8067.841712
HSA-MIR-4659A-3P99.8072.624248
HSA-MIR-4659B-3P99.8072.624248
HSA-MIR-148A-3P99.7473.771700
HSA-MIR-148B-3P99.7473.751700
HSA-MIR-152-3P99.7473.751703
HSA-MIR-518A-5P99.7069.012209
HSA-MIR-52799.7069.012209
HSA-MIR-580-3P99.6769.231841
HSA-MIR-447099.6669.351767
HSA-MIR-5003-5P99.6169.131624
HSA-MIR-6752-5P99.5967.321243
HSA-MIR-6513-3P99.5969.771102
HSA-MIR-182-3P99.5767.57825
HSA-MIR-6751-5P99.5664.991145
HSA-MIR-3120-3P99.5470.282669
HSA-MIR-312899.5067.851258
HSA-MIR-444199.4966.563216

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 47.6% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 4)

  • hsa_circ_0000190 (gene symbol is CNIH4) may be a novel non-invasive biomarker for the diagnosis of gastric cancer (PMID:28130019)
  • Screening and identification of CNIH4 gene associated with cell proliferation in gastric cancer based on a large-scale CRISPR-Cas9 screening database DepMap. (PMID:36220450)
  • Potential roles of Cornichon Family AMPA Receptor Auxiliary Protein 4 (CNIH4) in head and neck squamous cell carcinoma. (PMID:36404537)
  • Comprehensive analysis of clinical prognosis and biological significance of CNIH4 in cervical cancer. (PMID:38087815)

Cross-species orthologs

4 orthologs

OrganismSymbolGene ID
danio_reriocnih4ENSDARG00000087759
mus_musculusCnih4ENSMUSG00000062169
rattus_norvegicusCnih4ENSRNOG00000003717
drosophila_melanogastercnirFBGN0243513

Paralogs (4): CNIH1 (ENSG00000100528), PPCS (ENSG00000127125), CNIH3 (ENSG00000143786), CNIH2 (ENSG00000174871)

Protein

Protein identifiers

Protein cornichon homolog 4Q9P003 (reviewed: Q9P003)

Alternative names: Cornichon family AMPA receptor auxiliary protein 4

All UniProt accessions (3): Q9P003, A6NJ96, A6NLH6

UniProt curated annotations — full annotation on UniProt →

Function. Involved in G protein-coupled receptors (GPCRs) trafficking from the endoplasmic reticulum to the cell surface; it promotes the exit of GPCRs from the early secretory pathway, likely through interaction with the COPII machinery.

Subunit / interactions. Interacts with Sec23/24 complex components SEC24B and SEC24D. Interacts with CCR5. Interacts with ADRB2 in the early secretory pathway.

Subcellular location. Membrane. Endoplasmic reticulum. Endoplasmic reticulum-Golgi intermediate compartment.

Similarity. Belongs to the cornichon family.

Isoforms (2)

UniProt IDNamesCanonical?
Q9P003-11yes
Q9P003-22

RefSeq proteins (5): NP_001264126, NP_001264127, NP_001264128, NP_001264129, NP_054903* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR003377CornichonFamily

Pfam: PF03311

UniProt features (6 total): transmembrane region 3, chain 1, splice variant 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9P003-F193.030.84

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 169 (showing top): GOBP_VESICLE_MEDIATED_TRANSPORT, PATIL_LIVER_CANCER, ONKEN_UVEAL_MELANOMA_UP, GOBP_ENDOPLASMIC_RETICULUM_TO_GOLGI_VESICLE_MEDIATED_TRANSPORT, GOCC_COATED_VESICLE, CASORELLI_APL_SECONDARY_VS_DE_NOVO_UP, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GOMF_G_PROTEIN_COUPLED_RECEPTOR_BINDING, DOUGLAS_BMI1_TARGETS_UP, GOMF_SIGNALING_RECEPTOR_BINDING, ACEVEDO_LIVER_CANCER_UP, LAIHO_COLORECTAL_CANCER_SERRATED_UP, TGGAAA_NFAT_Q4_01, GOCC_NUCLEAR_OUTER_MEMBRANE_ENDOPLASMIC_RETICULUM_MEMBRANE_NETWORK, GOCC_ENDOPLASMIC_RETICULUM_GOLGI_INTERMEDIATE_COMPARTMENT

GO Biological Process (3): endoplasmic reticulum to Golgi vesicle-mediated transport (GO:0006888), protein transport (GO:0015031), vesicle-mediated transport (GO:0016192)

GO Molecular Function (3): signaling receptor binding (GO:0005102), CCR5 chemokine receptor binding (GO:0031730), protein binding (GO:0005515)

GO Cellular Component (5): endoplasmic reticulum (GO:0005783), endoplasmic reticulum membrane (GO:0005789), endoplasmic reticulum-Golgi intermediate compartment (GO:0005793), COPII-coated ER to Golgi transport vesicle (GO:0030134), membrane (GO:0016020)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm3
transport2
intracellular membrane-bounded organelle2
intercellular transport1
intracellular transport1
Golgi vesicle transport1
intracellular protein localization1
establishment of protein localization1
cellular process1
protein binding1
CCR chemokine receptor binding1
binding1
endomembrane system1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
coated vesicle1
cellular anatomical structure1

Protein interactions and networks

STRING

910 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CNIH4CACNG8Q8WXS5908
CNIH4GRIA1P42261865
CNIH4NT5C1AQ9BXI3832
CNIH4GRIA3P42263815
CNIH4SHISA9B4DS77813
CNIH4GRIA2P42262781
CNIH4GSG1LQ6UXU4723
CNIH4CACNG2Q9Y698722
CNIH4GRIA4P48058643
CNIH4SYNDIG1Q9H7V2624
CNIH4DLG4P78352616
CNIH4SEC24DO94855589
CNIH4TGFAP01135561
CNIH4NETO2Q8NC67505
CNIH4GSG1L2A8MUP6499

IntAct

57 interactions, top by confidence:

ABTypeScore
CFTRESYT2psi-mi:“MI:0914”(association)0.710
TSNARE1CNIH4psi-mi:“MI:0915”(physical association)0.560
TMEM14BCNIH4psi-mi:“MI:0915”(physical association)0.560
GPR25CNIH4psi-mi:“MI:0915”(physical association)0.560
TNFSF8LGALS8psi-mi:“MI:0914”(association)0.530
TACR3C6orf47psi-mi:“MI:0914”(association)0.530
WLSCNIH4psi-mi:“MI:0915”(physical association)0.490
WLSCNIH4psi-mi:“MI:0915”(physical association)0.370
KSR1DDX39Apsi-mi:“MI:0914”(association)0.350
KSR1FBLL1psi-mi:“MI:0914”(association)0.350
DND1RPSA2psi-mi:“MI:0914”(association)0.350
CCDC47ESYT2psi-mi:“MI:0914”(association)0.350
LPAR2EI24psi-mi:“MI:0914”(association)0.350
CMKLR1BTAF1psi-mi:“MI:0914”(association)0.350
SERINC2PGRMC2psi-mi:“MI:0914”(association)0.350
MFSD10NDUFS8psi-mi:“MI:0914”(association)0.350
MFSD5ILVBLpsi-mi:“MI:0914”(association)0.350
MFSD8STXBP3psi-mi:“MI:0914”(association)0.350
MFSD9PGRMC1psi-mi:“MI:0914”(association)0.350
SLC19A2TMEM223psi-mi:“MI:0914”(association)0.350
SLC1A4MGST3psi-mi:“MI:0914”(association)0.350
SLC22A9ESYT2psi-mi:“MI:0914”(association)0.350
SLC35A4PGRMC1psi-mi:“MI:0914”(association)0.350
SLC37A1ESYT2psi-mi:“MI:0914”(association)0.350
SLC39A4ESYT2psi-mi:“MI:0914”(association)0.350
SLC44A2CLGNpsi-mi:“MI:0914”(association)0.350
SLC51ATNPO2psi-mi:“MI:0914”(association)0.350
SLC5A3PGRMC1psi-mi:“MI:0914”(association)0.350
SLC5A4CLGNpsi-mi:“MI:0914”(association)0.350

BioGRID (79): CNIH4 (Affinity Capture-MS), CNIH4 (Affinity Capture-RNA), CNIH4 (Proximity Label-MS), CNIH4 (Proximity Label-MS), CNIH4 (PCA), CNIH4 (Affinity Capture-MS), CNIH4 (Affinity Capture-MS), CNIH4 (Affinity Capture-MS), CNIH4 (Affinity Capture-MS), CNIH4 (Affinity Capture-MS), CNIH4 (Affinity Capture-MS), CNIH4 (Proximity Label-MS), CNIH4 (Affinity Capture-MS), CNIH4 (Proximity Label-MS), CNIH4 (Two-hybrid)

ESM2 similar proteins: A0A8I3PI99, A0M8U1, A7Y521, B5DEN9, C5HGF3, O88544, O94973, P13666, P17427, P18484, P38024, Q00765, Q0VCK5, Q0X0A5, Q13098, Q1RLU8, Q28635, Q2PG42, Q3KNM2, Q3SZA0, Q3T0N3, Q3T126, Q3T178, Q3ZC24, Q4R5E6, Q5F418, Q5I0H4, Q5M7T4, Q5R648, Q5R9B0, Q5R9M4, Q5RE33, Q5ZJ41, Q5ZJD7, Q6DGW9, Q6GM44, Q6NRT5, Q7TQ48, Q8C407, Q8R1Z9

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

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 66 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Amino acid transport across the plasma membrane641.9×1e-06
R-HSA-425366625.3×9e-06
SLC-mediated transmembrane transport912.4×4e-06
Transport of small molecules95.3×2e-03

GO biological processes:

GO termPartnersFoldFDR
amino acid transport737.0×3e-07
transport across blood-brain barrier618.2×2e-04
sodium ion transmembrane transport517.2×1e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance16
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
979935GRCh37/hg19 1q42.11-42.12(chr1:224442473-224794913)x1Pathogenic

SpliceAI

959 predictions. Top by Δscore:

VariantEffectΔscore
1:224365877:A:AGacceptor_gain1.0000
1:224365877:AGT:Aacceptor_gain1.0000
1:224365877:AGTG:Aacceptor_gain1.0000
1:224365877:AGTGG:Aacceptor_gain1.0000
1:224365878:G:GAacceptor_gain1.0000
1:224365878:GT:Gacceptor_gain1.0000
1:224365878:GTG:Gacceptor_gain1.0000
1:224365878:GTGG:Gacceptor_gain1.0000
1:224365878:GTGGG:Gacceptor_gain1.0000
1:224365989:TCGGT:Tdonor_loss1.0000
1:224365990:CGG:Cdonor_loss1.0000
1:224365991:GGT:Gdonor_loss1.0000
1:224365992:G:Adonor_loss1.0000
1:224365992:G:GGdonor_gain1.0000
1:224365993:TGA:Tdonor_loss1.0000
1:224365994:G:GTdonor_loss1.0000
1:224371277:TATCA:Tacceptor_loss1.0000
1:224371278:ATCAG:Aacceptor_loss1.0000
1:224371279:TCA:Tacceptor_loss1.0000
1:224371281:A:AGacceptor_gain1.0000
1:224371281:AGATA:Aacceptor_loss1.0000
1:224371282:G:GGacceptor_gain1.0000
1:224371282:GATAC:Gacceptor_gain1.0000
1:224371421:TAG:Tdonor_gain1.0000
1:224371424:GT:Gdonor_loss1.0000
1:224371425:T:Gdonor_loss1.0000
1:224375869:T:Gdonor_gain1.0000
1:224357450:GGA:Gdonor_gain0.9900
1:224357451:GA:Gdonor_gain0.9900
1:224365874:TGCA:Tacceptor_loss0.9900

AlphaMissense

920 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:224360514:T:CL30S0.999
1:224371333:T:AI101K0.999
1:224360523:A:TD33V0.998
1:224360545:T:GC40W0.998
1:224360548:C:GC41W0.998
1:224360556:T:CL44S0.998
1:224371321:A:GD97G0.998
1:224371333:T:CI101T0.998
1:224371333:T:GI101R0.998
1:224371386:G:CG119R0.998
1:224371417:T:CL129P0.998
1:224360507:T:CS28P0.997
1:224360510:G:CD29H0.997
1:224360511:A:CD29A0.997
1:224360511:A:GD29G0.997
1:224360511:A:TD29V0.997
1:224360522:G:CD33H0.997
1:224360523:A:CD33A0.997
1:224360533:T:AN36K0.997
1:224360533:T:GN36K0.997
1:224360543:T:CC40R0.997
1:224360544:G:AC40Y0.997
1:224360547:G:AC41Y0.997
1:224371324:C:AP98Q0.997
1:224371351:T:CL107P0.997
1:224371387:G:AG119D0.997
1:224371404:T:CF125L0.997
1:224371406:C:AF125L0.997
1:224371406:C:GF125L0.997
1:224371407:T:CF126L0.997

dbSNP variants (sampled 300 via entrez): RS1000050423 (1:224376610 A>G), RS1000061791 (1:224363349 T>C), RS1000092634 (1:224359297 CAAG>C), RS1000425144 (1:224359657 A>G), RS1000453330 (1:224378246 A>C,G), RS1000480488 (1:224367103 T>G), RS1000693742 (1:224373439 G>A), RS1000728900 (1:224373679 T>C), RS1000735489 (1:224360794 G>A), RS1000807880 (1:224378461 G>C,T), RS1000902398 (1:224356151 C>T), RS1001102924 (1:224371825 C>T), RS1001237458 (1:224360128 G>C,T), RS1001239200 (1:224367146 T>A), RS1001322763 (1:224366704 A>G)

Disease associations

OMIM: gene MIM:617483 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

8 associations (top):

StudyTraitp-value
GCST000856_1Major depressive disorder4.000000e-06
GCST010241_437Apolipoprotein A1 levels1.000000e-11
GCST010242_381HDL cholesterol levels4.000000e-10
GCST011743_68HDL cholesterol levels in HIV infection8.000000e-06
GCST90002385_109High light scatter reticulocyte count2.000000e-09
GCST90002386_229High light scatter reticulocyte percentage of red cells5.000000e-12
GCST90002405_102Reticulocyte count1.000000e-10
GCST90002406_123Reticulocyte fraction of red cells1.000000e-14

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0004614apolipoprotein A 1 measurement
EFO:0004612high density lipoprotein cholesterol measurement
EFO:0007986reticulocyte count

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
Tretinoindecreases expression, increases expression2
Valproic Acidincreases expression2
dicrotophosdecreases expression1
bisphenol Aincreases expression1
salinomycindecreases expression1
trichostatin Adecreases expression1
beta-lapachonedecreases expression, increases expression1
arseniteaffects binding, increases reaction1
sodium arsenitedecreases expression1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
4-phenylbutyric aciddecreases expression1
CGP 52608affects binding, increases reaction1
chloropicrinaffects expression1
Sunitinibincreases expression1
Vorinostatincreases expression1
Acetaminophenincreases expression1
Air Pollutantsdecreases expression, increases abundance1
Benzo(a)pyreneaffects methylation1
Cisplatinincreases expression1
Ethyl Methanesulfonateincreases expression1
Formaldehydeincreases expression1
Ivermectindecreases expression1
Methyl Methanesulfonateincreases expression1
Seleniumdecreases expression1
Smokedecreases expression, increases abundance1
Thiramdecreases expression1
Tobacco Smoke Pollutionincreases expression1
Cyclosporineincreases expression1
Copper Sulfatedecreases expression1

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_B2ULAbcam HEK293T CNIH4 KOTransformed cell lineFemale

Clinical trials (associated diseases)

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

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.