CPNE7
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Summary
CPNE7 (copine 7, HGNC:2320) is a protein-coding gene on chromosome 16q24.3, encoding Copine-7 (Q9UBL6). Calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes. It is a selective cancer dependency (DepMap: 14.0% of cell lines).
This gene encodes a member of the copine family, which is composed of calcium-dependent membrane-binding proteins. The gene product contains two N-terminal C2 domains and one von Willebrand factor A domain. The encoded protein may be involved in membrane trafficking. Two alternatively spliced transcript variants encoding different isoforms have been found for this gene.
Source: NCBI Gene 27132 — RefSeq curated summary.
At a glance
- GWAS associations: 4
- Clinical variants (ClinVar): 184 total — 1 pathogenic
- Cancer dependency (DepMap): dependent in 14.0% of screened cell lines
- MANE Select transcript:
NM_153636
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:2320 |
| Approved symbol | CPNE7 |
| Name | copine 7 |
| Location | 16q24.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Ensembl gene | ENSG00000178773 |
| Ensembl biotype | protein_coding |
| OMIM | 605689 |
| Entrez | 27132 |
Gene structure
Transcript identifiers
Ensembl transcripts: 14 — 9 protein_coding, 2 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 1 retained_intron
ENST00000268720, ENST00000319518, ENST00000525982, ENST00000526232, ENST00000529800, ENST00000532500, ENST00000564421, ENST00000566398, ENST00000568977, ENST00000857691, ENST00000936168, ENST00000936169, ENST00000936170, ENST00000954262
RefSeq mRNA: 2 — MANE Select: NM_153636
NM_014427, NM_153636
CCDS: CCDS10980, CCDS10981
Canonical transcript exons
ENST00000319518 — 15 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001189454 | 89588675 | 89588808 |
| ENSE00001189469 | 89584774 | 89584857 |
| ENSE00001189473 | 89584028 | 89584102 |
| ENSE00001189483 | 89583697 | 89583771 |
| ENSE00001189505 | 89577539 | 89577721 |
| ENSE00001301526 | 89591127 | 89591260 |
| ENSE00001305527 | 89589897 | 89589951 |
| ENSE00001329934 | 89591007 | 89591058 |
| ENSE00001563411 | 89596484 | 89597246 |
| ENSE00001936455 | 89575758 | 89576071 |
| ENSE00003476931 | 89595367 | 89595603 |
| ENSE00003554295 | 89585464 | 89585553 |
| ENSE00003573796 | 89586670 | 89586756 |
| ENSE00003579453 | 89585687 | 89585785 |
| ENSE00003683666 | 89587043 | 89587102 |
Expression profiles
Bgee: expression breadth ubiquitous, 182 present calls, max score 93.84.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.2902 / max 151.4336, expressed in 1099 samples.
FANTOM5 promoters (5 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 155609 | 5.4936 | 989 |
| 155610 | 1.6280 | 661 |
| 155611 | 0.1045 | 41 |
| 155614 | 0.0326 | 18 |
| 155612 | 0.0316 | 8 |
Top tissues by expression
260 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| lateral nuclear group of thalamus | UBERON:0002736 | 93.84 | gold quality |
| triceps brachii | UBERON:0001509 | 93.22 | gold quality |
| gluteal muscle | UBERON:0002000 | 93.11 | gold quality |
| stromal cell of endometrium | CL:0002255 | 90.39 | gold quality |
| vena cava | UBERON:0004087 | 90.15 | silver quality |
| parotid gland | UBERON:0001831 | 89.86 | silver quality |
| pituitary gland | UBERON:0000007 | 89.42 | gold quality |
| type B pancreatic cell | CL:0000169 | 89.34 | gold quality |
| cingulate cortex | UBERON:0003027 | 89.15 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 89.14 | gold quality |
| olfactory bulb | UBERON:0002264 | 89.04 | gold quality |
| adenohypophysis | UBERON:0002196 | 88.68 | gold quality |
| right frontal lobe | UBERON:0002810 | 88.36 | gold quality |
| dorsal plus ventral thalamus | UBERON:0001897 | 87.56 | gold quality |
| skeletal muscle tissue of rectus abdominis | UBERON:0004511 | 86.89 | gold quality |
| hypothalamus | UBERON:0001898 | 86.43 | gold quality |
| dorsal motor nucleus of vagus nerve | UBERON:0002870 | 86.39 | silver quality |
| tongue squamous epithelium | UBERON:0006919 | 86.30 | silver quality |
| heart right ventricle | UBERON:0002080 | 86.29 | silver quality |
| nasal cavity epithelium | UBERON:0005384 | 86.02 | silver quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 85.70 | gold quality |
| cerebellar vermis | UBERON:0004720 | 85.68 | gold quality |
| vastus lateralis | UBERON:0001379 | 85.42 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 85.31 | gold quality |
| diaphragm | UBERON:0001103 | 85.27 | gold quality |
| buccal mucosa cell | CL:0002336 | 84.75 | silver quality |
| frontal cortex | UBERON:0001870 | 84.51 | gold quality |
| superficial temporal artery | UBERON:0001614 | 84.47 | gold quality |
| amygdala | UBERON:0001876 | 84.45 | gold quality |
| prefrontal cortex | UBERON:0000451 | 84.25 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-6678 | yes | 5.34 |
| E-ANND-3 | no | 1.68 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
23 targeting CPNE7, 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-3151-5P | 99.86 | 63.83 | 1069 |
| HSA-MIR-4447 | 99.85 | 67.81 | 2900 |
| HSA-MIR-92A-2-5P | 99.75 | 67.01 | 2164 |
| HSA-MIR-4472 | 99.56 | 66.08 | 1478 |
| HSA-MIR-4318 | 99.38 | 66.94 | 1505 |
| HSA-MIR-1273H-3P | 99.29 | 67.55 | 980 |
| HSA-MIR-361-3P | 99.19 | 66.45 | 1381 |
| HSA-MIR-491-5P | 99.13 | 65.98 | 1468 |
| HSA-MIR-485-5P | 99.10 | 64.78 | 1889 |
| HSA-MIR-6884-5P | 99.10 | 64.50 | 1987 |
| HSA-MIR-6846-5P | 98.81 | 65.86 | 1121 |
| HSA-MIR-6848-5P | 98.81 | 65.49 | 1126 |
| HSA-MIR-4755-3P | 98.77 | 65.59 | 1915 |
| HSA-MIR-6769B-5P | 98.73 | 64.91 | 1092 |
| HSA-MIR-3192-5P | 96.98 | 65.76 | 1926 |
| HSA-MIR-711 | 96.60 | 65.75 | 528 |
| HSA-MIR-4652-5P | 96.46 | 64.22 | 553 |
| HSA-MIR-6742-5P | 96.32 | 64.01 | 869 |
| HSA-MIR-1237-5P | 95.38 | 62.21 | 451 |
| HSA-MIR-4488 | 95.38 | 62.00 | 443 |
| HSA-MIR-4697-5P | 95.38 | 61.72 | 457 |
| HSA-MIR-6796-5P | 95.37 | 66.08 | 1120 |
| HSA-MIR-6879-3P | 93.93 | 64.00 | 759 |
Functional genomics
DepMap (CRISPR cell-line fitness): dependent in 14.0% of screened cell lines.
Literature-anchored findings (GeneRIF, showing 3)
- These results suggest Cpne7 is a diffusible signaling molecule that is secreted by preameloblasts, and regulates the differentiation of mesenchymal cells of dental or non-dental origin into odontoblasts. (PMID:25453951)
- The Role of CPNE7 (Copine-7) in Colorectal Cancer Prognosis and Metastasis. (PMID:38069026)
- Depletion of CPNE7 sensitizes colorectal cancer to 5-fluorouracil by downregulating ATG9B expression. (PMID:38526029)
Cross-species orthologs
7 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | cpne7 | ENSDARG00000102584 |
| mus_musculus | Cpne7 | ENSMUSG00000034796 |
| rattus_norvegicus | Cpne7 | ENSRNOG00000015397 |
| caenorhabditis_elegans | WBGENE00001577 | |
| caenorhabditis_elegans | WBGENE00006441 | |
| caenorhabditis_elegans | WBGENE00012128 | |
| caenorhabditis_elegans | WBGENE00015061 |
Paralogs (8): CPNE3 (ENSG00000085719), CPNE6 (ENSG00000100884), CPNE5 (ENSG00000124772), CPNE8 (ENSG00000139117), CPNE2 (ENSG00000140848), CPNE9 (ENSG00000144550), CPNE4 (ENSG00000196353), CPNE1 (ENSG00000214078)
Protein
Protein identifiers
Copine-7 — Q9UBL6 (reviewed: Q9UBL6)
Alternative names: Copine VII
All UniProt accessions (5): E9PJ31, Q9UBL6, H0YE30, H0YEH8, H3BP03
UniProt curated annotations — full annotation on UniProt →
Function. Calcium-dependent phospholipid-binding protein that may play a role in calcium-mediated intracellular processes.
Subcellular location. Cytoplasm. Nucleus. Cell membrane.
Tissue specificity. Expressed in the brain, testis, thymus and small intestine.
Domain organisation. The C2 domain 1 is not necessary for calcium-mediated translocation and association to the plasma membrane. The C2 domain 2 is necessary for calcium-mediated translocation and association to the plasma membrane.
Similarity. Belongs to the copine family.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q9UBL6-1 | 1 | yes |
| Q9UBL6-2 | 2 |
RefSeq proteins (2): NP_055242, NP_705900* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000008 | C2_dom | Domain |
| IPR002035 | VWF_A | Domain |
| IPR010734 | Copine_C | Domain |
| IPR035892 | C2_domain_sf | Homologous_superfamily |
| IPR036465 | vWFA_dom_sf | Homologous_superfamily |
| IPR037768 | C2B_Copine | Domain |
| IPR045052 | Copine | Family |
Pfam: PF00168, PF07002
UniProt features (17 total): binding site 8, sequence variant 4, domain 3, chain 1, splice variant 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9UBL6-F1 | 78.41 | 0.47 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Ligand- & substrate-binding residues (8): 309; 315; 245; 245; 251; 307; 307; 309
Function
Pathways and Gene Ontology
Reactome pathways
1 pathways
| ID | Pathway |
|---|---|
| R-HSA-1483206 | Glycerophospholipid biosynthesis |
MSigDB gene sets: 71 (showing top):
GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_RESPONSE_TO_METAL_ION, GOBP_PHOSPHOLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, MODULE_331, NIKOLSKY_BREAST_CANCER_16Q24_AMPLICON, GOBP_GLYCEROLIPID_BIOSYNTHETIC_PROCESS, GOBP_GLYCEROPHOSPHOLIPID_METABOLIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_LIPID_BIOSYNTHETIC_PROCESS, GOBP_CELLULAR_RESPONSE_TO_CALCIUM_ION, DOUGLAS_BMI1_TARGETS_UP, CTAWWWATA_RSRFC4_Q2
GO Biological Process (3): lipid metabolic process (GO:0006629), glycerophospholipid biosynthetic process (GO:0046474), cellular response to calcium ion (GO:0071277)
GO Molecular Function (4): phospholipid binding (GO:0005543), calcium-dependent phospholipid binding (GO:0005544), metal ion binding (GO:0046872), protein binding (GO:0005515)
GO Cellular Component (6): nucleus (GO:0005634), cytoplasm (GO:0005737), plasma membrane (GO:0005886), synapse (GO:0045202), extracellular exosome (GO:0070062), membrane (GO:0016020)
Reactome top-level categories
Rollup of top-1 pathways:
| Category | Pathways |
|---|---|
| Phospholipid metabolism | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 2 |
| primary metabolic process | 1 |
| glycerophospholipid metabolic process | 1 |
| phospholipid biosynthetic process | 1 |
| glycerolipid biosynthetic process | 1 |
| response to calcium ion | 1 |
| cellular response to metal ion | 1 |
| lipid binding | 1 |
| phospholipid binding | 1 |
| cation binding | 1 |
| binding | 1 |
| intracellular membrane-bounded organelle | 1 |
| intracellular anatomical structure | 1 |
| membrane | 1 |
| cell periphery | 1 |
| cell junction | 1 |
| extracellular vesicle | 1 |
Protein interactions and networks
STRING
640 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| CPNE7 | ZNF778 | Q96MU6 | 566 |
| CPNE7 | NUCLEOLIN | P19338 | 495 |
| CPNE7 | SPG7 | Q9UQ90 | 482 |
| CPNE7 | CDH15 | P55291 | 467 |
| CPNE7 | SRRM5 | B3KS81 | 453 |
| CPNE7 | SLC22A31 | A6NKX4 | 414 |
| CPNE7 | DBNDD1 | Q9H9R9 | 408 |
| CPNE7 | SPATA2L | Q8IUW3 | 406 |
| CPNE7 | OR1L3 | Q8NH93 | 400 |
| CPNE7 | ANKRD11 | Q6UB99 | 387 |
| CPNE7 | ZNF276 | Q8N554 | 384 |
| CPNE7 | OR1L1 | Q8NH94 | 376 |
| CPNE7 | DSPP | Q9NZW4 | 370 |
| CPNE7 | DPEP1 | P16444 | 355 |
| CPNE7 | STUM | Q69YW2 | 355 |
IntAct
39 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| CDCA4 | PPP2R1A | psi-mi:“MI:0914”(association) | 0.790 |
| DOCK8 | LRCH4 | psi-mi:“MI:0914”(association) | 0.620 |
| ADAMTSL4 | CPNE7 | psi-mi:“MI:0915”(physical association) | 0.560 |
| CPNE7 | ADAMTSL4 | psi-mi:“MI:0915”(physical association) | 0.560 |
| RNF19B | PIK3R2 | psi-mi:“MI:0914”(association) | 0.530 |
| WASF3 | CYFIP1 | psi-mi:“MI:0914”(association) | 0.530 |
| BRD1 | KAT7 | psi-mi:“MI:0914”(association) | 0.530 |
| GSTO1 | CPNE7 | psi-mi:“MI:0915”(physical association) | 0.400 |
| MS4A7 | CPNE7 | psi-mi:“MI:0915”(physical association) | 0.400 |
| MTRES1 | CPNE7 | psi-mi:“MI:0915”(physical association) | 0.400 |
| CPNE7 | CSNK2B | psi-mi:“MI:0915”(physical association) | 0.370 |
| CALCOCO2 | CPNE7 | psi-mi:“MI:0915”(physical association) | 0.370 |
| CAND1 | GTPBP10 | psi-mi:“MI:0914”(association) | 0.350 |
| COPS5 | FBLL1 | psi-mi:“MI:0914”(association) | 0.350 |
| CUL3 | PXDNL | psi-mi:“MI:0914”(association) | 0.350 |
| OTUB1 | STAMBP | psi-mi:“MI:0914”(association) | 0.350 |
| USP53 | ANXA2P2 | psi-mi:“MI:0914”(association) | 0.350 |
| CSAG2 | CAMK2D | psi-mi:“MI:0914”(association) | 0.350 |
| UVRAG | TUBAL3 | psi-mi:“MI:0914”(association) | 0.350 |
| GEMIN8 | GEMIN2 | psi-mi:“MI:0914”(association) | 0.350 |
| METTL2A | NDUFS6 | psi-mi:“MI:0914”(association) | 0.350 |
| CPNE4 | CPNE6 | psi-mi:“MI:0914”(association) | 0.350 |
| CPNE7 | UBTF | psi-mi:“MI:0914”(association) | 0.350 |
| CHMP4A | HSPA2 | psi-mi:“MI:0914”(association) | 0.350 |
| SURF6 | GTPBP10 | psi-mi:“MI:0914”(association) | 0.350 |
| FOXF2 | POTEF | psi-mi:“MI:0914”(association) | 0.350 |
| PLEKHG7 | MROH6 | psi-mi:“MI:0914”(association) | 0.350 |
| KLHL14 | ARHGAP32 | psi-mi:“MI:0914”(association) | 0.350 |
| OPALIN | FAM171A2 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (90): ADAMTSL4 (Two-hybrid), CPNE7 (Two-hybrid), CPNE7 (Affinity Capture-MS), CPNE7 (Affinity Capture-MS), BAHCC1 (Affinity Capture-MS), UBTF (Affinity Capture-MS), CPNE7 (Affinity Capture-MS), CPNE7 (Affinity Capture-MS), EBF3 (Affinity Capture-MS), CPNE7 (Affinity Capture-MS), RPS27A (Affinity Capture-MS), CPNE7 (Affinity Capture-MS), CPNE7 (Affinity Capture-MS), SETD2 (Affinity Capture-MS), CPNE7 (Affinity Capture-MS)
ESM2 similar proteins: A0A8I3NFE2, A0FGR8, A0FGR9, A2AP18, A4IJ05, O08625, O08874, O15357, O75038, P51432, P70218, P70268, Q01970, Q12851, Q3TZZ7, Q3U7R1, Q4VX76, Q5DTI8, Q5FWL4, Q5M7N9, Q5R8Q5, Q5RAG2, Q5RCK6, Q5RJH2, Q61161, Q62807, Q63433, Q6DN12, Q6XYQ8, Q7ZWU7, Q812E4, Q86SS6, Q8K394, Q8TDW5, Q920M7, Q925C0, Q92918, Q99JE6, Q99N48, Q9BSJ8
Diamond homologs: A8WMY4, D4A1R8, H1UBN0, H2KYS8, O75131, O95741, P59108, Q08DB4, Q0VE82, Q1RLL3, Q1ZXB3, Q2KHY1, Q54FY7, Q54P51, Q55GG1, Q5BJS7, Q5R4W6, Q5RAE1, Q5S1W2, Q5XQC7, Q7YXU4, Q86K21, Q86YQ8, Q8BLR2, Q8BT60, Q8C166, Q8IYJ1, Q8JZW4, Q941L3, Q96A23, Q96FN4, Q99829, Q9DC53, Q9HCH3, Q9UBL6, Q9XUB9, Q9Z140, A0JJX5, Q09219, Q12466
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
184 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 1 |
| Likely pathogenic | 0 |
| Uncertain significance | 155 |
| Likely benign | 7 |
| Benign | 1 |
Top pathogenic / likely-pathogenic (1)
| Variant ID | HGVS | Classification |
|---|---|---|
| 267483 | Single allele | Pathogenic |
SpliceAI
3394 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 16:89577680:G:GT | donor_gain | 1.0000 |
| 16:89584103:G:GG | donor_gain | 1.0000 |
| 16:89584103:G:T | donor_loss | 1.0000 |
| 16:89584769:CCCA:C | acceptor_loss | 1.0000 |
| 16:89584770:CCAG:C | acceptor_loss | 1.0000 |
| 16:89584773:GGAC:G | acceptor_gain | 1.0000 |
| 16:89584851:G:GT | donor_gain | 1.0000 |
| 16:89584854:GGAG:G | donor_gain | 1.0000 |
| 16:89584855:G:GT | donor_gain | 1.0000 |
| 16:89584855:GAG:G | donor_gain | 1.0000 |
| 16:89584856:AGGTG:A | donor_loss | 1.0000 |
| 16:89584857:GGTGA:G | donor_loss | 1.0000 |
| 16:89584858:G:GG | donor_gain | 1.0000 |
| 16:89585460:ACAGG:A | acceptor_loss | 1.0000 |
| 16:89585461:CAGGT:C | acceptor_loss | 1.0000 |
| 16:89585462:AGGT:A | acceptor_gain | 1.0000 |
| 16:89585463:GGTG:G | acceptor_gain | 1.0000 |
| 16:89585544:GCCTC:G | donor_gain | 1.0000 |
| 16:89585685:A:AG | acceptor_gain | 1.0000 |
| 16:89585686:G:GG | acceptor_gain | 1.0000 |
| 16:89585686:GT:G | acceptor_gain | 1.0000 |
| 16:89585783:CAG:C | donor_loss | 1.0000 |
| 16:89585784:AG:A | donor_loss | 1.0000 |
| 16:89585785:GGTG:G | donor_loss | 1.0000 |
| 16:89585786:G:A | donor_loss | 1.0000 |
| 16:89585787:T:A | donor_loss | 1.0000 |
| 16:89588798:GAC:G | donor_gain | 1.0000 |
| 16:89588807:AGGTG:A | donor_loss | 1.0000 |
| 16:89588809:G:GC | donor_loss | 1.0000 |
| 16:89588810:T:G | donor_loss | 1.0000 |
AlphaMissense
3656 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 16:89588684:G:C | D388H | 1.000 |
| 16:89588685:A:C | D388A | 1.000 |
| 16:89588685:A:T | D388V | 1.000 |
| 16:89588686:C:A | D388E | 1.000 |
| 16:89588686:C:G | D388E | 1.000 |
| 16:89588691:C:T | T390I | 1.000 |
| 16:89588701:T:A | N393K | 1.000 |
| 16:89588701:T:G | N393K | 1.000 |
| 16:89588759:T:C | Y413H | 1.000 |
| 16:89588760:A:G | Y413C | 1.000 |
| 16:89589922:T:C | F438L | 1.000 |
| 16:89589924:T:A | F438L | 1.000 |
| 16:89589924:T:G | F438L | 1.000 |
| 16:89595395:A:T | D519V | 1.000 |
| 16:89595396:C:A | D519E | 1.000 |
| 16:89595396:C:G | D519E | 1.000 |
| 16:89595397:G:C | G520R | 1.000 |
| 16:89595398:G:A | G520D | 1.000 |
| 16:89595398:G:T | G520V | 1.000 |
| 16:89595493:T:C | F552L | 1.000 |
| 16:89595494:T:C | F552S | 1.000 |
| 16:89595495:C:A | F552L | 1.000 |
| 16:89595495:C:G | F552L | 1.000 |
| 16:89595577:T:C | F580L | 1.000 |
| 16:89595579:C:A | F580L | 1.000 |
| 16:89595579:C:G | F580L | 1.000 |
| 16:89585491:T:A | W282R | 0.999 |
| 16:89585491:T:C | W282R | 0.999 |
| 16:89588682:T:A | I387N | 0.999 |
| 16:89588685:A:G | D388G | 0.999 |
dbSNP variants (sampled 300 via entrez): RS1000031435 (16:89575514 C>T), RS1000079252 (16:89594557 C>T), RS1000186637 (16:89579483 C>T), RS1000243934 (16:89597519 C>T), RS1000326963 (16:89579303 A>T), RS1000384012 (16:89597690 T>A), RS1000411641 (16:89574953 G>A), RS1000605299 (16:89591611 G>A), RS1000702090 (16:89584244 G>A), RS1000738376 (16:89591569 G>A,T), RS1000751449 (16:89594332 C>G), RS1000867284 (16:89575245 C>T), RS1000931027 (16:89588496 G>A,C), RS1001115867 (16:89584420 C>T), RS1001116209 (16:89586507 T>A,G)
Disease associations
OMIM: gene MIM:605689 | disease phenotypes:
GenCC curated gene-disease
Mondo (1): 16q24.3 microdeletion syndrome (MONDO:0016838)
Orphanet (1): 16q24.3 microdeletion syndrome (Orphanet:261250)
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
4 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST007335_29 | Age at first sexual intercourse | 7.000000e-10 |
| GCST008129_27 | Body mass index | 3.000000e-08 |
| GCST008803_14 | Smoking behaviour (cigarette pack-years) | 3.000000e-09 |
| GCST010703_280 | Brain morphology (MOSTest) | 2.000000e-15 |
EFO canonical traits (4, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0009749 | age at first sexual intercourse measurement |
| EFO:0004340 | body mass index |
| EFO:0009115 | tobacco smoke exposure measurement |
| EFO:0004346 | neuroimaging measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
26 total (human), top 26 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| bisphenol A | affects cotreatment, increases methylation, decreases expression | 2 |
| Smoke | increases expression | 2 |
| aristolochic acid I | increases expression | 1 |
| ethyl-p-hydroxybenzoate | decreases expression | 1 |
| o,p’-DDT | increases expression | 1 |
| aflatoxin B2 | increases methylation | 1 |
| perfluorooctane sulfonic acid | increases expression | 1 |
| jinfukang | increases expression | 1 |
| 3-hydroxy-4-prenyl-5-methoxystilbene-2-carboxylic acid | increases expression | 1 |
| (+)-JQ1 compound | decreases expression | 1 |
| Resveratrol | affects cotreatment, decreases expression | 1 |
| Fulvestrant | affects cotreatment, increases methylation | 1 |
| Arsenic | affects methylation | 1 |
| Benzo(a)pyrene | decreases methylation, increases methylation, affects methylation | 1 |
| Dexamethasone | increases expression | 1 |
| Diazinon | increases methylation | 1 |
| Drugs, Chinese Herbal | decreases expression | 1 |
| Estradiol | increases expression | 1 |
| Hydrogen Peroxide | increases expression | 1 |
| Lead | affects expression | 1 |
| Plant Extracts | affects cotreatment, decreases expression | 1 |
| Thiram | increases expression | 1 |
| Tobacco Smoke Pollution | decreases expression | 1 |
| Triclosan | increases expression | 1 |
| Cyclosporine | increases methylation | 1 |
| Okadaic Acid | 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): 16q24.3 microdeletion syndrome