CNIH3
geneOn this page
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
| Field | Value |
|---|---|
| HGNC ID | HGNC:26802 |
| Approved symbol | CNIH3 |
| Name | cornichon family AMPA receptor auxiliary protein 3 |
| Location | 1q42.12 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ38993, CNIH-3 |
| Ensembl gene | ENSG00000143786 |
| Ensembl biotype | protein_coding |
| Entrez | 149111 |
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
| Exon | Start | End |
|---|---|---|
| ENSE00001147221 | 224739329 | 224740554 |
| ENSE00001215659 | 224616317 | 224617255 |
| ENSE00003466788 | 224734563 | 224734706 |
| ENSE00003483736 | 224684796 | 224684843 |
| ENSE00003527670 | 224730462 | 224730574 |
| ENSE00003685214 | 224680958 | 224681026 |
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 ID | TPM avg | Samples expressed |
|---|---|---|
| 8806 | 1.4976 | 519 |
| 8805 | 1.3510 | 533 |
| 8793 | 1.0371 | 630 |
| 8795 | 0.5274 | 177 |
| 8792 | 0.3980 | 193 |
| 8803 | 0.0833 | 30 |
| 8804 | 0.0817 | 25 |
| 8799 | 0.0744 | 23 |
| 8801 | 0.0523 | 20 |
| 8800 | 0.0497 | 18 |
Top tissues by expression
279 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| primordial germ cell in gonad | CL:0000670 ∩ UBERON:0000991 | 86.65 | gold quality |
| cortical plate | UBERON:0005343 | 86.56 | gold quality |
| endothelial cell | CL:0000115 | 86.13 | gold quality |
| prefrontal cortex | UBERON:0000451 | 85.47 | gold quality |
| stromal cell of endometrium | CL:0002255 | 84.82 | gold quality |
| buccal mucosa cell | CL:0002336 | 84.38 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 83.62 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 83.47 | gold quality |
| right frontal lobe | UBERON:0002810 | 83.37 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 83.27 | gold quality |
| cingulate cortex | UBERON:0003027 | 82.61 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 82.38 | gold quality |
| frontal cortex | UBERON:0001870 | 82.31 | gold quality |
| neocortex | UBERON:0001950 | 82.11 | gold quality |
| amygdala | UBERON:0001876 | 81.86 | gold quality |
| nucleus accumbens | UBERON:0001882 | 81.59 | gold quality |
| Ammon’s horn | UBERON:0001954 | 81.52 | gold quality |
| cerebral cortex | UBERON:0000956 | 81.50 | gold quality |
| body of pancreas | UBERON:0001150 | 81.12 | gold quality |
| left ovary | UBERON:0002119 | 80.49 | gold quality |
| telencephalon | UBERON:0001893 | 80.45 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 80.42 | gold quality |
| caudate nucleus | UBERON:0001873 | 79.68 | gold quality |
| forebrain | UBERON:0001890 | 79.51 | gold quality |
| right ovary | UBERON:0002118 | 79.44 | gold quality |
| brain | UBERON:0000955 | 78.45 | gold quality |
| pancreas | UBERON:0001264 | 78.40 | gold quality |
| central nervous system | UBERON:0001017 | 78.31 | gold quality |
| calcaneal tendon | UBERON:0003701 | 78.29 | gold quality |
| temporal lobe | UBERON:0001871 | 78.23 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 5.60 |
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):
| miRNA | Max score | Avg score | miRNA target_count |
|---|---|---|---|
| HSA-MIR-6873-3P | 100.00 | 71.42 | 2626 |
| HSA-MIR-7110-3P | 100.00 | 73.18 | 2486 |
| HSA-MIR-103A-3P | 99.98 | 69.14 | 1595 |
| HSA-MIR-107 | 99.98 | 69.14 | 1595 |
| HSA-MIR-2110 | 99.96 | 66.68 | 1930 |
| HSA-MIR-4267 | 99.96 | 66.53 | 2368 |
| HSA-MIR-101-3P | 99.94 | 75.03 | 2230 |
| HSA-MIR-8063 | 99.91 | 69.76 | 3146 |
| HSA-MIR-4731-5P | 99.89 | 67.23 | 2537 |
| HSA-MIR-6857-5P | 99.87 | 65.32 | 985 |
| HSA-MIR-4799-5P | 99.82 | 70.60 | 2663 |
| HSA-MIR-2116-3P | 99.74 | 64.32 | 889 |
| HSA-MIR-7161-5P | 99.68 | 68.92 | 1592 |
| HSA-MIR-4502 | 99.65 | 66.99 | 1021 |
| HSA-MIR-548U | 99.65 | 67.78 | 1463 |
| HSA-MIR-567 | 99.63 | 68.57 | 1219 |
| HSA-MIR-6134 | 99.63 | 65.68 | 1537 |
| HSA-MIR-3911 | 99.38 | 66.95 | 1087 |
| HSA-MIR-190B-3P | 99.33 | 68.29 | 1382 |
| HSA-MIR-4667-3P | 99.26 | 65.45 | 1608 |
| HSA-MIR-593-3P | 99.22 | 67.28 | 1327 |
| HSA-MIR-122B-3P | 99.21 | 68.90 | 1333 |
| HSA-MIR-21-3P | 99.21 | 68.95 | 1312 |
| HSA-MIR-4795-5P | 99.11 | 66.90 | 876 |
| HSA-MIR-622 | 98.99 | 66.48 | 1050 |
| HSA-MIR-936 | 98.87 | 70.51 | 1124 |
| HSA-MIR-7155-5P | 98.65 | 66.14 | 1290 |
| HSA-MIR-1301-3P | 98.64 | 68.27 | 1071 |
| HSA-MIR-5047 | 98.64 | 68.62 | 1035 |
| HSA-MIR-6811-3P | 98.62 | 66.54 | 944 |
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
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | cnih3 | ENSDARG00000014953 |
| mus_musculus | Cnih3 | ENSMUSG00000026514 |
| rattus_norvegicus | Cnih3 | ENSRNOG00000022724 |
| drosophila_melanogaster | cni | FBGN0000339 |
| caenorhabditis_elegans | WBGENE00011648 |
Paralogs (4): CNIH1 (ENSG00000100528), PPCS (ENSG00000127125), CNIH4 (ENSG00000143771), CNIH2 (ENSG00000174871)
Protein
Protein identifiers
Protein cornichon homolog 3 — Q8TBE1 (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)
| ID | Name | Type |
|---|---|---|
| IPR003377 | Cornichon | Family |
| IPR033466 | Cornichon_conserved | Conserved_site |
Pfam: PF03311
UniProt features (8 total): topological domain 4, transmembrane region 3, chain 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q8TBE1-F1 | 85.15 | 0.48 |
Function
Pathways and Gene Ontology
Reactome pathways
2 pathways
| ID | Pathway |
|---|---|
| R-HSA-204005 | COPII-mediated vesicle transport |
| R-HSA-5694530 | Cargo 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:
| Category | Pathways |
|---|---|
| ER to Golgi Anterograde Transport | 2 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 2 |
| transport | 1 |
| cellular process | 1 |
| chemical synaptic transmission | 1 |
| monoatomic ion transmembrane transport | 1 |
| regulation of biological quality | 1 |
| protein-containing complex localization | 1 |
| receptor localization to synapse | 1 |
| regulation of postsynaptic membrane neurotransmitter receptor levels | 1 |
| protein localization to postsynaptic specialization membrane | 1 |
| AMPA glutamate receptor activity | 1 |
| regulation of transmembrane transporter activity | 1 |
| regulation of neurotransmitter receptor activity | 1 |
| protein binding | 1 |
| channel activity | 1 |
| transporter regulator activity | 1 |
| binding | 1 |
| organelle membrane | 1 |
| nuclear outer membrane-endoplasmic reticulum membrane network | 1 |
| endoplasmic reticulum subcompartment | 1 |
| COPII-coated ER to Golgi transport vesicle | 1 |
| transport vesicle membrane | 1 |
| coated vesicle membrane | 1 |
| neuron projection | 1 |
| dendritic tree | 1 |
| ionotropic glutamate receptor complex | 1 |
| endoplasmic reticulum-Golgi intermediate compartment | 1 |
| bounding membrane of organelle | 1 |
| dendrite | 1 |
| cell junction | 1 |
| synaptic membrane | 1 |
| postsynapse | 1 |
| synapse | 1 |
| membrane | 1 |
| cell periphery | 1 |
Protein interactions and networks
STRING
956 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| CNIH3 | NT5C1A | Q9BXI3 | 815 |
| CNIH3 | KCNG2 | Q9UJ96 | 748 |
| CNIH3 | GRIA3 | P42263 | 731 |
| CNIH3 | GRIA2 | P42262 | 690 |
| CNIH3 | GSG1L | Q6UXU4 | 646 |
| CNIH3 | GRIA1 | P42261 | 598 |
| CNIH3 | SYNDIG1 | Q9H7V2 | 582 |
| CNIH3 | GSG1L2 | A8MUP6 | 564 |
| CNIH3 | TGFA | P01135 | 560 |
| CNIH3 | COL22A1 | Q8NFW1 | 556 |
| CNIH3 | ADAMTS14 | Q8WXS8 | 552 |
| CNIH3 | FAM53B | Q14153 | 550 |
| CNIH3 | COL4A6 | Q14031 | 546 |
| CNIH3 | COL21A1 | Q96P44 | 545 |
| CNIH3 | GRIA4 | P48058 | 542 |
IntAct
87 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| CNIH3 | AQP6 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CNIH3 | CLDN20 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CNIH3 | TMEM80 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CNIH3 | ERGIC3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CNIH3 | FAM210B | psi-mi:“MI:0915”(physical association) | 0.560 |
| CNIH3 | SMIM3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 | |
| PLD3 | CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| TMPRSS2 | CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CNIH3 | TMEM237 | psi-mi:“MI:0915”(physical association) | 0.560 |
| BIK | CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CEACAM3 | CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CNIH3 | SORT1 | psi-mi:“MI:0915”(physical association) | 0.560 |
| AQP6 | CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CNIH3 | TMEM14B | psi-mi:“MI:0915”(physical association) | 0.560 |
| LRRC25 | CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CLDN20 | CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| STOM | CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| ODF4 | CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CNIH3 | GPX8 | psi-mi:“MI:0915”(physical association) | 0.560 |
| NEMP1 | CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| TMEM52B | CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| LEUTX | CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CD79A | CNIH3 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CNIH3 | VSIR | psi-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):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 2 |
| Likely pathogenic | 0 |
| Uncertain significance | 24 |
| Likely benign | 0 |
| Benign | 2 |
Top pathogenic / likely-pathogenic (2)
| Variant ID | HGVS | Classification |
|---|---|---|
| 1703636 | GRCh37/hg19 1q42.11-42.12(chr1:224432682-225142704) | Pathogenic |
| 625540 | GRCh37/hg19 1q42.11-42.12(chr1:224340881-225147932) | Pathogenic |
SpliceAI
2129 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 1:224684781:T:A | acceptor_gain | 1.0000 |
| 1:224734705:TGGT:T | donor_loss | 1.0000 |
| 1:224734706:GGTG:G | donor_loss | 1.0000 |
| 1:224734707:G:GG | donor_gain | 1.0000 |
| 1:224734708:T:A | donor_loss | 1.0000 |
| 1:224734709:GAGTA:G | donor_loss | 1.0000 |
| 1:224673859:A:G | acceptor_gain | 0.9900 |
| 1:224680957:GATA:G | acceptor_gain | 0.9900 |
| 1:224681024:GCG:G | donor_gain | 0.9900 |
| 1:224681024:GCGGT:G | donor_loss | 0.9900 |
| 1:224681025:CGGT:C | donor_loss | 0.9900 |
| 1:224681026:GGTA:G | donor_loss | 0.9900 |
| 1:224681027:G:GC | donor_loss | 0.9900 |
| 1:224681028:TAA:T | donor_loss | 0.9900 |
| 1:224681029:A:AG | donor_loss | 0.9900 |
| 1:224684783:T:TA | acceptor_gain | 0.9900 |
| 1:224684786:ATCCT:A | acceptor_gain | 0.9900 |
| 1:224684787:T:G | acceptor_gain | 0.9900 |
| 1:224730460:AGCT:A | acceptor_gain | 0.9900 |
| 1:224730461:GCTG:G | acceptor_gain | 0.9900 |
| 1:224734559:GCA:G | acceptor_loss | 0.9900 |
| 1:224734561:A:AC | acceptor_loss | 0.9900 |
| 1:224734562:GGT:G | acceptor_gain | 0.9900 |
| 1:224734704:CTG:C | donor_gain | 0.9900 |
| 1:224734705:TG:T | donor_gain | 0.9900 |
| 1:224734706:GG:G | donor_gain | 0.9900 |
| 1:224617256:G:GG | donor_gain | 0.9800 |
| 1:224632818:GTTC:G | donor_gain | 0.9800 |
| 1:224680956:A:AG | acceptor_gain | 0.9800 |
| 1:224680957:G:GG | acceptor_gain | 0.9800 |
AlphaMissense
1061 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 1:224680977:T:C | L34S | 0.999 |
| 1:224730545:T:A | N94K | 0.999 |
| 1:224730545:T:G | N94K | 0.999 |
| 1:224730550:C:G | P96R | 0.999 |
| 1:224734665:G:C | K138N | 0.999 |
| 1:224734665:G:T | K138N | 0.999 |
| 1:224617199:T:C | C9R | 0.998 |
| 1:224617200:G:A | C9Y | 0.998 |
| 1:224617215:T:C | L14P | 0.998 |
| 1:224617233:T:C | L20P | 0.998 |
| 1:224730550:C:A | P96H | 0.998 |
| 1:224734663:A:G | K138E | 0.998 |
| 1:224617201:C:G | C9W | 0.997 |
| 1:224730561:T:G | Y100D | 0.997 |
| 1:224734687:T:C | F146L | 0.997 |
| 1:224734689:C:A | F146L | 0.997 |
| 1:224734689:C:G | F146L | 0.997 |
| 1:224734700:T:C | L150P | 0.997 |
| 1:224617223:T:C | C17R | 0.996 |
| 1:224730498:T:C | C79R | 0.996 |
| 1:224730508:T:C | F82S | 0.996 |
| 1:224730553:T:G | L97R | 0.996 |
| 1:224734667:T:C | L139P | 0.996 |
| 1:224734679:T:C | L143P | 0.996 |
| 1:224734700:T:A | L150H | 0.996 |
| 1:224617215:T:G | L14R | 0.995 |
| 1:224617227:C:A | A18D | 0.995 |
| 1:224684836:T:C | L64P | 0.995 |
| 1:224730553:T:A | L97Q | 0.995 |
| 1:224734693:T:G | Y148D | 0.995 |
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):
| Study | Trait | p-value |
|---|---|---|
| GCST003614_1 | Opioid dependence | 4.000000e-09 |
| GCST005275_21 | Cancer | 9.000000e-07 |
| GCST010204_162 | Low density lipoprotein cholesterol levels | 1.000000e-09 |
| GCST011780_14 | Neonatal white matter microstructure | 5.000000e-06 |
| GCST90002390_339 | Mean corpuscular hemoglobin | 5.000000e-12 |
| GCST90002398_511 | Neutrophil count | 8.000000e-25 |
| GCST90002399_19 | Neutrophil percentage of white cells | 2.000000e-10 |
| GCST90002407_202 | White blood cell count | 4.000000e-24 |
| GCST90006991_8 | Gut microbiota relative abundance (Streptococcus) | 6.000000e-06 |
EFO canonical traits (6, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004611 | low density lipoprotein cholesterol measurement |
| EFO:0005674 | white matter microstructure measurement |
| EFO:0004527 | mean corpuscular hemoglobin |
| EFO:0004833 | neutrophil count |
| EFO:0007990 | neutrophil percentage of leukocytes |
| EFO:0007874 | gut microbiome measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
PharmGKB clinical annotations
1 annotations.
| Variant | Type | Level | Drugs | Phenotypes |
|---|---|---|---|---|
| rs10799590 | Toxicity | 3 | opioids | Opioid-Related Disorders |
PharmGKB variants
1 variants.
| Variant | Genes | Level | Score | #Clin annots | Drugs |
|---|---|---|---|---|---|
| rs10799590 | CNIH3 | 3 | 1.75 | 1 | opioids |
CTD chemical–gene interactions
38 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Benzo(a)pyrene | affects methylation, decreases expression, increases methylation | 3 |
| bisphenol A | increases expression | 2 |
| Estradiol | decreases expression, affects cotreatment | 2 |
| Progesterone | affects cotreatment, decreases expression | 2 |
| Cadmium Chloride | decreases expression, increases abundance, increases expression | 2 |
| triphenyl phosphate | affects expression | 1 |
| propionaldehyde | increases expression | 1 |
| butyraldehyde | increases expression | 1 |
| benzo(e)pyrene | increases methylation | 1 |
| aflatoxin B2 | increases methylation | 1 |
| S-(1,2-dichlorovinyl)cysteine | affects cotreatment, decreases expression | 1 |
| perfluorooctane sulfonic acid | increases expression | 1 |
| CGP 52608 | increases reaction, affects binding | 1 |
| 2,2’,4,4’,5-brominated diphenyl ether | increases expression | 1 |
| ormosil | affects binding, increases expression | 1 |
| licochalcone B | increases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| Resveratrol | affects cotreatment, decreases expression | 1 |
| Temozolomide | decreases expression | 1 |
| Acetaminophen | decreases expression | 1 |
| Amiodarone | increases expression | 1 |
| Cadmium | increases abundance, increases expression | 1 |
| Cisplatin | decreases expression, increases expression | 1 |
| Dexamethasone | decreases expression | 1 |
| Lead | affects expression | 1 |
| Lipopolysaccharides | affects cotreatment, decreases expression | 1 |
| Methapyrilene | increases methylation | 1 |
| Phenobarbital | increases expression | 1 |
| Plant Extracts | affects cotreatment, decreases expression | 1 |
| Polyethylene Glycols | affects binding, increases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): cancer, chromosome 1q41-q42 deletion syndrome, opiate dependence