LYPD3
gene geneOn this page
Also known as C4.4A
Summary
LYPD3 (LY6/PLAUR domain containing 3, HGNC:24880) is a protein-coding gene on chromosome 19q13.31, encoding Ly6/PLAUR domain-containing protein 3 (O95274). Supports cell migration.
Predicted to enable laminin binding activity. Involved in negative regulation of smooth muscle cell apoptotic process. Located in extracellular space.
Source: NCBI Gene 27076 — RefSeq curated summary.
At a glance
- GWAS associations: 1
- Clinical variants (ClinVar): 61 total
- MANE Select transcript:
NM_014400
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:24880 |
| Approved symbol | LYPD3 |
| Name | LY6/PLAUR domain containing 3 |
| Location | 19q13.31 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | C4.4A |
| Ensembl gene | ENSG00000124466 |
| Ensembl biotype | protein_coding |
| OMIM | 609484 |
| Entrez | 27076 |
Gene structure
Transcript identifiers
Ensembl transcripts: 4 — 3 retained_intron, 1 protein_coding
ENST00000244333, ENST00000594326, ENST00000595970, ENST00000597741
RefSeq mRNA: 1 — MANE Select: NM_014400
NM_014400
CCDS: CCDS12620
Canonical transcript exons
ENST00000244333 — 5 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000847411 | 43460787 | 43461847 |
| ENSE00000847415 | 43465493 | 43465608 |
| ENSE00001161659 | 43463599 | 43463769 |
| ENSE00003472194 | 43463126 | 43463287 |
| ENSE00003672141 | 43464325 | 43464456 |
Expression profiles
Bgee: expression breadth ubiquitous, 199 present calls, max score 99.70.
FANTOM5 (CAGE): breadth broad, TPM avg 5.4228 / max 285.8621, expressed in 346 samples.
FANTOM5 promoters (6 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 181270 | 4.1405 | 266 |
| 181272 | 0.6425 | 219 |
| 181271 | 0.4860 | 205 |
| 181273 | 0.0845 | 41 |
| 181268 | 0.0409 | 20 |
| 181269 | 0.0284 | 7 |
Top tissues by expression
291 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| gingival epithelium | UBERON:0001949 | 99.70 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 99.63 | gold quality |
| gingiva | UBERON:0001828 | 99.61 | gold quality |
| cervix squamous epithelium | UBERON:0006922 | 99.45 | gold quality |
| pharyngeal mucosa | UBERON:0000355 | 99.44 | gold quality |
| skin of abdomen | UBERON:0001416 | 99.34 | gold quality |
| tongue squamous epithelium | UBERON:0006919 | 99.14 | gold quality |
| nipple | UBERON:0002030 | 99.12 | gold quality |
| upper arm skin | UBERON:0004263 | 99.09 | gold quality |
| squamous epithelium | UBERON:0006914 | 99.07 | gold quality |
| esophagus mucosa | UBERON:0002469 | 99.01 | gold quality |
| mammalian vulva | UBERON:0000997 | 98.98 | gold quality |
| cervix epithelium | UBERON:0004801 | 98.98 | gold quality |
| penis | UBERON:0000989 | 98.93 | gold quality |
| skin of leg | UBERON:0001511 | 98.85 | gold quality |
| zone of skin | UBERON:0000014 | 98.82 | gold quality |
| upper leg skin | UBERON:0004262 | 98.79 | gold quality |
| esophagus squamous epithelium | UBERON:0006920 | 98.67 | gold quality |
| body of tongue | UBERON:0011876 | 98.42 | gold quality |
| oral cavity | UBERON:0000167 | 98.39 | gold quality |
| epithelium of esophagus | UBERON:0001976 | 98.09 | gold quality |
| skin of hip | UBERON:0001554 | 96.51 | gold quality |
| tongue | UBERON:0001723 | 95.67 | gold quality |
| vagina | UBERON:0000996 | 93.69 | gold quality |
| hair follicle | UBERON:0002073 | 93.22 | gold quality |
| palpebral conjunctiva | UBERON:0001812 | 92.14 | gold quality |
| amniotic fluid | UBERON:0000173 | 91.52 | gold quality |
| superior surface of tongue | UBERON:0007371 | 91.40 | gold quality |
| tonsil | UBERON:0002372 | 88.77 | gold quality |
| mouth mucosa | UBERON:0003729 | 88.21 | gold quality |
Single-cell (SCXA)
Detected in 5 experiment(s), a significant marker in 5.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-8142 | yes | 3660.98 |
| E-HCAD-1 | yes | 1511.57 |
| E-CURD-114 | yes | 428.55 |
| E-MTAB-6701 | yes | 47.72 |
| E-ANND-3 | no | 0.00 |
Regulation
Is transcription factor: no
Upstream regulators (CollecTRI, top): CEBPB, FOXC1, JUN, JUND, SP1, SP3
miRNA regulators (miRDB)
42 targeting LYPD3, 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-7110-3P | 100.00 | 73.18 | 2486 |
| HSA-LET-7A-3P | 100.00 | 74.03 | 3932 |
| HSA-LET-7B-3P | 100.00 | 74.08 | 3913 |
| HSA-LET-7F-1-3P | 100.00 | 74.02 | 3928 |
| HSA-MIR-98-3P | 100.00 | 74.08 | 3907 |
| HSA-MIR-27A-3P | 99.98 | 72.13 | 2955 |
| HSA-MIR-27B-3P | 99.98 | 72.13 | 2955 |
| HSA-MIR-9985 | 99.98 | 72.11 | 2939 |
| HSA-MIR-128-3P | 99.95 | 71.17 | 2484 |
| HSA-MIR-216A-3P | 99.95 | 71.19 | 2505 |
| HSA-MIR-651-3P | 99.94 | 73.48 | 5177 |
| HSA-MIR-4731-5P | 99.89 | 67.23 | 2537 |
| HSA-MIR-3681-3P | 99.88 | 70.46 | 2254 |
| HSA-MIR-3617-5P | 99.75 | 69.41 | 1968 |
| HSA-MIR-641 | 99.75 | 69.35 | 1975 |
| HSA-MIR-1255A | 99.74 | 68.09 | 744 |
| HSA-MIR-1255B-5P | 99.74 | 68.16 | 741 |
| HSA-MIR-6752-3P | 99.72 | 66.71 | 1587 |
| HSA-MIR-7-5P | 99.67 | 70.53 | 1809 |
| HSA-MIR-1827 | 99.63 | 68.57 | 3265 |
| HSA-MIR-6716-5P | 99.56 | 68.62 | 1244 |
| HSA-MIR-186-3P | 99.51 | 66.24 | 1685 |
| HSA-MIR-5584-5P | 99.49 | 68.22 | 2814 |
| HSA-MIR-1253 | 99.12 | 67.08 | 1688 |
| HSA-MIR-4738-3P | 98.98 | 67.98 | 1846 |
| HSA-MIR-6770-5P | 98.97 | 66.76 | 1853 |
| HSA-MIR-455-3P | 98.94 | 67.68 | 878 |
| HSA-MIR-1304-5P | 98.90 | 68.58 | 1054 |
| HSA-MIR-2355-5P | 98.83 | 65.51 | 1589 |
| HSA-MIR-455-5P | 98.74 | 67.31 | 795 |
Literature-anchored findings (GeneRIF, showing 20)
- hAG-2 and hAG-3, human homologues of genes involved in differentiation, are associated with oestrogen receptor-positive breast tumours and interact with metastasis gene C4.4a and dystroglycan (PMID:12592373)
- High tumour cell C4.4A expression is associated with shorter survival for non-small cell lung cancer patients. (PMID:17706320)
- Overexpression of C4.4A is associated with invasion and metastasis of esophageal squamous cell carcinoma (PMID:17849475)
- we consider C4.4A as a candidate diagnostic marker in colorectal cancer, which possibly can be detected in body fluids (PMID:17912244)
- cleavage of C4.4A by ADAM10 and ADAM17 contributes to tumor progression (PMID:18979631)
- data indicate that expression of the C4.4A protein at the invasive front acts as a novel prognostic marker in colorectal cancer, possibly through invasion-related mechanisms (PMID:20825414)
- findings suggest that a tight association between C4.4A and tumor budding may, in part, be due to C4.4A promoting epithelial-mesenchymal transition at the invasive front of colorectal cancer (PMID:22404718)
- the first explanation for the C4.4A contribution to wound healing and metastasis. (PMID:22431918)
- Tenascin-C expression was significantly associated with C4.4A expression in clinical esophageal squamous carcinoma samples suggesting that there may be a functional role for the C4.4A to induceTenascin-C in vivo. (PMID:23708783)
- Highly expressed C4.4A protein in HER2-positive human breast cancers indicate a good prognosis. (PMID:23918676)
- overexpression of C4.4A correlates with metastatic potential of gastric cancer and C4.4A could be a novel independent prognostic marker for predicting outcome. (PMID:24935570)
- expression of the Ly6/uPAR-domain proteins C4.4A and Haldisin in non-invasive and invasive skin lesions (PMID:25414274)
- LYPD3 has a role in the maintenance of colorectal cancer stem-like cells. (PMID:28238780)
- Expression and crystallographic studies of the D1D2 domains of C4.4A have been reported. (PMID:28777093)
- While in the healthy liver hepatocytes are C4.4A negative, data show that C4.4A is strongly expressed in hepatocellular carcinoma (HCC) with upregulation at the invasive front and in lung metastasis, indicating that C4.4A apparently contributes to HCC progression. (PMID:29048672)
- Our results are consistent with previous data in mouse embryogenesis and wound healing. Based on these findings, we conclude that this human TES model provides an excellent surrogate for studies of C4.4A and Haldisin expressions in human stratified epithelia. (PMID:29075641)
- Long non-coding RNA OGFRP1 contributed to progression of non-small cell lung cancer at least partly through upregulating LYPD3 expression by sponging miR-124-3p. (PMID:30274775)
- The authors explored the related pathways through which LYPD3 affects the pathogenesis and prognosis of lung adenocarcinoma by gene set enrichment analysis, and found that LYPD3 might affect the clinical manifestations of lung adenocarcinoma by regulating the P53 signaling pathway. (PMID:32040344)
- LY6/PLAUR domain containing 3 (LYPD3) maintains melanoma cell stemness and mediates an immunosuppressive microenvironment. (PMID:37924160)
- m6A-dependent mature miR-151-5p accelerates the malignant process of HNSCC by targeting LYPD3. (PMID:39009906)
Cross-species orthologs
2 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| mus_musculus | Lypd3 | ENSMUSG00000057454 |
| rattus_norvegicus | Lypd3 | ENSRNOG00000019999 |
Paralogs (2): PLAUR (ENSG00000011422), LYPD5 (ENSG00000159871)
Protein
Protein identifiers
Ly6/PLAUR domain-containing protein 3 — O95274 (reviewed: O95274)
Alternative names: GPI-anchored metastasis-associated protein C4.4A homolog, Matrigel-induced gene C4 protein
All UniProt accessions (2): B2RBR3, O95274
UniProt curated annotations — full annotation on UniProt →
Function. Supports cell migration. May be involved in urothelial cell-matrix interactions. May be involved in tumor progression.
Subunit / interactions. Binds laminin-1 and laminin-5. Interacts with LGALS3. Interacts with AGR2 and AGR3.
Subcellular location. Cell membrane.
Tissue specificity. Expressed in placenta, skin and urothelium. Found in suprabasal keratinocytes of chronic wounds. Weak expression is found in esophagus and peripheral blood mononuclear cells. Found in the majority of primary and metastatic transitional cell carcinomas (TCCs) and as well in breast cancer tissues, but not in adjacent normal tissues. High expression is found in the tumor component of some noninvasive superficial lesions and in invasive and metastatic urothelial cancers.
Post-translational modifications. N-glycosylated and O-glycosylated.
Induction. Up-regulated in migrating keratinocytes during epithelization of incisional skin wounds.
RefSeq proteins (1): NP_055215* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR016054 | LY6_UPA_recep-like | Domain |
| IPR045860 | Snake_toxin-like_sf | Homologous_superfamily |
Pfam: PF00021
UniProt features (31 total): strand 13, glycosylation site 4, compositionally biased region 3, turn 2, helix 2, domain 2, signal peptide 1, chain 1, propeptide 1, region of interest 1, lipid moiety-binding region 1
Structure
Experimental structures (PDB)
2 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 6IOM | X-RAY DIFFRACTION | 2.59 |
| 6ION | X-RAY DIFFRACTION | 2.75 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-O95274-F1 | 74.61 | 0.51 |
Antibody-complex structures (SAbDab): 1 — 6ION
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Post-translational modifications (1): 326
Glycosylation sites (4): 118, 163, 176, 183
Function
Pathways and Gene Ontology
Reactome pathways
3 pathways
| ID | Pathway |
|---|---|
| R-HSA-163125 | Post-translational modification: synthesis of GPI-anchored proteins |
| R-HSA-392499 | Metabolism of proteins |
| R-HSA-597592 | Post-translational protein modification |
MSigDB gene sets: 141 (showing top):
JAEGER_METASTASIS_DN, ENK_UV_RESPONSE_KERATINOCYTE_UP, AREB6_01, NAGASHIMA_NRG1_SIGNALING_UP, MONNIER_POSTRADIATION_TUMOR_ESCAPE_UP, AMIT_EGF_RESPONSE_480_MCF10A, GOBP_NEGATIVE_REGULATION_OF_MUSCLE_CELL_APOPTOTIC_PROCESS, MODULE_379, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, SHETH_LIVER_CANCER_VS_TXNIP_LOSS_PAM1, RUTELLA_RESPONSE_TO_HGF_VS_CSF2RB_AND_IL4_DN, MODULE_88, MODULE_242, GOBP_CELL_SUBSTRATE_ADHESION, CTTTGTA_MIR524
GO Biological Process (2): cell-matrix adhesion (GO:0007160), negative regulation of smooth muscle cell apoptotic process (GO:0034392)
GO Molecular Function (1): laminin binding (GO:0043236)
GO Cellular Component (5): extracellular region (GO:0005576), obsolete extracellular space (GO:0005615), plasma membrane (GO:0005886), side of membrane (GO:0098552), membrane (GO:0016020)
Reactome top-level categories
Rollup of top-2 pathways:
| Category | Pathways |
|---|---|
| Post-translational protein modification | 1 |
| Metabolism of proteins | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| cellular anatomical structure | 3 |
| membrane | 2 |
| cell-substrate adhesion | 1 |
| negative regulation of muscle cell apoptotic process | 1 |
| smooth muscle cell apoptotic process | 1 |
| regulation of smooth muscle cell apoptotic process | 1 |
| protein binding | 1 |
| extracellular matrix binding | 1 |
| cell periphery | 1 |
| leaflet of membrane bilayer | 1 |
Protein interactions and networks
STRING
946 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| LYPD3 | AGR2 | O95994 | 972 |
| LYPD3 | AGR3 | Q8TD06 | 893 |
| LYPD3 | DAG1 | Q14118 | 756 |
| LYPD3 | PLAUR | Q03405 | 685 |
| LYPD3 | PLAU | P00749 | 550 |
| LYPD3 | PINLYP | A6NC86 | 542 |
| LYPD3 | LY6L | H3BQJ8 | 540 |
| LYPD3 | CD59 | P13987 | 536 |
| LYPD3 | PHLDB3 | Q6NSJ2 | 536 |
| LYPD3 | TEX101 | Q9BY14 | 521 |
| LYPD3 | MMP14 | P50281 | 516 |
| LYPD3 | PATE3 | B3GLJ2 | 507 |
| LYPD3 | ESR1 | P03372 | 501 |
| LYPD3 | ZNF575 | Q86XF7 | 468 |
| LYPD3 | PATE2 | Q6UY27 | 447 |
IntAct
23 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| LYPD3 | SCAMP1 | psi-mi:“MI:0914”(association) | 0.640 |
| Trim69 | psi-mi:“MI:0915”(physical association) | 0.400 | |
| LYPD3 | AURKA | psi-mi:“MI:0915”(physical association) | 0.370 |
| BAG4 | LYPD3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| BRMS1 | LYPD3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| LYPD3 | CASP8 | psi-mi:“MI:0915”(physical association) | 0.370 |
| CHEK2 | LYPD3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| ERBB2 | LYPD3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| IGF1R | LYPD3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| LSP1 | LYPD3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| PALB2 | LYPD3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| LYPD3 | PPM1D | psi-mi:“MI:0915”(physical association) | 0.370 |
| PTPRJ | LYPD3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| RB1CC1 | LYPD3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| SMAD4 | LYPD3 | psi-mi:“MI:0915”(physical association) | 0.370 |
| LYPD3 | STK11 | psi-mi:“MI:0915”(physical association) | 0.370 |
| LYPD3 | CLASP2 | psi-mi:“MI:0914”(association) | 0.350 |
| TEX14 | DNAJB6 | psi-mi:“MI:0914”(association) | 0.350 |
| LYPD3 | TNPO2 | psi-mi:“MI:0914”(association) | 0.350 |
| LYPD3 | NEMP1 | psi-mi:“MI:0914”(association) | 0.350 |
| INSR | BLTP3B | psi-mi:“MI:0914”(association) | 0.350 |
| PCGF5 | LYPD3 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (281): VDAC3 (Affinity Capture-MS), XPO7 (Affinity Capture-MS), TTI2 (Affinity Capture-MS), ATP2B4 (Affinity Capture-MS), BZW2 (Affinity Capture-MS), BZW1 (Affinity Capture-MS), SLC9A1 (Affinity Capture-MS), FLVCR1 (Affinity Capture-MS), TNPO2 (Affinity Capture-MS), SYMPK (Affinity Capture-MS), RBM26 (Affinity Capture-MS), PHTF2 (Affinity Capture-MS), TMEM214 (Affinity Capture-MS), GPAA1 (Affinity Capture-MS), TARBP1 (Affinity Capture-MS)
ESM2 similar proteins: A2VE33, A8HDK4, A8S6B0, C0STK8, C0STK9, I6PG79, O12962, O55006, O55162, O57690, O95274, P0DQP7, P0DQX3, P0DUK5, P0DUK6, P35459, P35460, P58019, P60591, P60592, P81827, P81828, P82143, P82144, P83121, Q05588, Q3UN54, Q66H42, Q6MG58, Q6UWN5, Q6UX82, Q78CF9, Q7LZI1, Q7LZI2, Q7TQN2, Q8BLC3, Q8N2G4, Q8VEN2, Q90358, Q91YK8
Diamond homologs: O55162, O95274, Q91YK8
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 24 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.
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| protein autophosphorylation | 5 | 31.6× | 2e-04 |
| negative regulation of cell population proliferation | 5 | 9.2× | 5e-03 |
| negative regulation of apoptotic process | 5 | 7.5× | 1e-02 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
61 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 48 |
| Likely benign | 2 |
| Benign | 3 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
621 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 19:43461844:TTAG:T | acceptor_gain | 1.0000 |
| 19:43461845:TAG:T | acceptor_gain | 1.0000 |
| 19:43461846:AG:A | acceptor_gain | 1.0000 |
| 19:43461848:C:CC | acceptor_gain | 1.0000 |
| 19:43463121:CTCAC:C | donor_loss | 1.0000 |
| 19:43463123:CACCT:C | donor_loss | 1.0000 |
| 19:43463124:A:T | donor_loss | 1.0000 |
| 19:43463124:ACCTG:A | donor_gain | 1.0000 |
| 19:43463125:C:CT | donor_loss | 1.0000 |
| 19:43463125:CCTG:C | donor_gain | 1.0000 |
| 19:43463125:CCTGC:C | donor_gain | 1.0000 |
| 19:43463128:G:A | donor_gain | 1.0000 |
| 19:43463283:ATTAC:A | acceptor_gain | 1.0000 |
| 19:43463284:TTAC:T | acceptor_gain | 1.0000 |
| 19:43463285:TAC:T | acceptor_gain | 1.0000 |
| 19:43463285:TACCT:T | acceptor_loss | 1.0000 |
| 19:43463286:AC:A | acceptor_gain | 1.0000 |
| 19:43463287:CC:C | acceptor_gain | 1.0000 |
| 19:43463288:C:CC | acceptor_gain | 1.0000 |
| 19:43463291:C:CT | acceptor_gain | 1.0000 |
| 19:43463292:G:T | acceptor_gain | 1.0000 |
| 19:43463301:C:CT | acceptor_gain | 1.0000 |
| 19:43463301:C:T | acceptor_gain | 1.0000 |
| 19:43463302:G:T | acceptor_gain | 1.0000 |
| 19:43463595:GGAC:G | donor_loss | 1.0000 |
| 19:43463596:GAC:G | donor_loss | 1.0000 |
| 19:43463598:C:A | donor_loss | 1.0000 |
| 19:43463601:G:A | donor_gain | 1.0000 |
| 19:43463766:TGGA:T | acceptor_gain | 1.0000 |
| 19:43463770:C:CC | acceptor_gain | 1.0000 |
AlphaMissense
2203 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 19:43461726:G:C | N222K | 0.998 |
| 19:43461726:G:T | N222K | 0.998 |
| 19:43463152:A:C | F173C | 0.998 |
| 19:43463155:C:G | C172S | 0.997 |
| 19:43463156:A:T | C172S | 0.997 |
| 19:43463639:G:C | N114K | 0.997 |
| 19:43463639:G:T | N114K | 0.997 |
| 19:43464354:C:G | C61S | 0.997 |
| 19:43464355:A:T | C61S | 0.997 |
| 19:43461730:C:G | C221S | 0.996 |
| 19:43461731:A:T | C221S | 0.996 |
| 19:43461814:C:G | C193S | 0.996 |
| 19:43461815:A:T | C193S | 0.996 |
| 19:43463154:G:C | C172W | 0.996 |
| 19:43463156:A:G | C172R | 0.996 |
| 19:43463251:C:G | C140S | 0.996 |
| 19:43463252:A:T | C140S | 0.996 |
| 19:43463675:G:C | F102L | 0.996 |
| 19:43463675:G:T | F102L | 0.996 |
| 19:43463677:A:G | F102L | 0.996 |
| 19:43461815:A:G | C193R | 0.995 |
| 19:43461823:A:T | V190D | 0.995 |
| 19:43463151:G:C | F173L | 0.995 |
| 19:43463151:G:T | F173L | 0.995 |
| 19:43463153:A:G | F173L | 0.995 |
| 19:43463187:G:C | C161W | 0.995 |
| 19:43463188:C:G | C161S | 0.995 |
| 19:43463188:C:T | C161Y | 0.995 |
| 19:43463189:A:T | C161S | 0.995 |
| 19:43463252:A:G | C140R | 0.995 |
dbSNP variants (sampled 300 via entrez): RS1000008650 (19:43462424 G>C), RS1000062519 (19:43462778 C>T), RS1000579335 (19:43467039 C>T), RS1001009941 (19:43461184 A>C,G), RS1001138918 (19:43465130 T>C), RS1001976838 (19:43465525 G>A), RS1003125420 (19:43462617 A>G), RS1003346279 (19:43465205 G>A), RS1003377302 (19:43465423 G>A,C), RS1003727613 (19:43460958 G>A), RS1004092301 (19:43464669 C>G), RS1004569940 (19:43465064 G>A,T), RS1005274412 (19:43463975 C>A,G,T), RS1005614800 (19:43464331 C>T), RS1005628974 (19:43460599 G>A)
Disease associations
OMIM: gene MIM:609484 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
1 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST002652_14 | Cotinine glucuronidation | 4.000000e-08 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0006508 | cotinine glucuronidation measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
41 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | affects cotreatment, increases expression | 5 |
| sodium arsenite | decreases expression, increases expression | 2 |
| entinostat | increases expression, affects cotreatment | 2 |
| Panobinostat | affects cotreatment, increases expression | 2 |
| Air Pollutants | decreases expression, increases abundance, increases expression | 2 |
| Smoke | decreases expression, increases abundance, increases expression | 2 |
| Tobacco Smoke Pollution | affects expression, increases expression | 2 |
| propionaldehyde | increases expression | 1 |
| sodium arsenate | decreases expression, increases abundance | 1 |
| pyrogallol 1,3-dimethyl ether | affects cotreatment, increases expression | 1 |
| 2-methyl-4-isothiazolin-3-one | increases expression | 1 |
| ethyl-p-hydroxybenzoate | increases expression | 1 |
| beta-lapachone | increases expression | 1 |
| afimoxifene | decreases reaction, decreases expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | increases expression | 1 |
| bleomycetin | increases expression | 1 |
| cupric chloride | decreases expression | 1 |
| benazol P | affects expression | 1 |
| octa-2,4,6-trienoic acid | decreases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, increases expression | 1 |
| erucylphospho-N,N,N-trimethylpropylammonium | increases expression | 1 |
| abrine | decreases expression | 1 |
| dorsomorphin | affects cotreatment, increases expression | 1 |
| LG 100815 | decreases expression | 1 |
| Leflunomide | decreases expression | 1 |
| Arsenic | decreases expression, increases abundance | 1 |
| Atrazine | increases expression | 1 |
| Benzo(a)pyrene | decreases methylation, affects methylation | 1 |
| Calcitriol | increases expression | 1 |
| Estradiol | decreases expression | 1 |
Clinical trials (associated diseases)
0 trials via MONDO — disease-level, not drug-specific.
Related Atlas pages
No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.