GPCPD1
gene geneOn this page
Also known as KIAA1434GDE5GDPD6
Summary
GPCPD1 (glycerophosphocholine phosphodiesterase 1, HGNC:26957) is a protein-coding gene on chromosome 20p12.3, encoding Glycerophosphocholine phosphodiesterase GPCPD1 (Q9NPB8). May be involved in the negative regulation of skeletal muscle differentiation, independently of its glycerophosphocholine phosphodiesterase activity.
Predicted to enable glycerophosphocholine phosphodiesterase activity. Predicted to be involved in glycerophospholipid catabolic process. Predicted to act upstream of or within skeletal muscle tissue development. Predicted to be located in cytosol.
Source: NCBI Gene 56261 — RefSeq curated summary.
At a glance
- GWAS associations: 8
- Clinical variants (ClinVar): 82 total
- MANE Select transcript:
NM_019593
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:26957 |
| Approved symbol | GPCPD1 |
| Name | glycerophosphocholine phosphodiesterase 1 |
| Location | 20p12.3 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | KIAA1434, GDE5, GDPD6 |
| Ensembl gene | ENSG00000125772 |
| Ensembl biotype | protein_coding |
| OMIM | 614124 |
| Entrez | 56261 |
Gene structure
Transcript identifiers
Ensembl transcripts: 19 — 14 protein_coding, 2 retained_intron, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined
ENST00000379019, ENST00000418646, ENST00000462080, ENST00000473797, ENST00000481038, ENST00000481690, ENST00000633552, ENST00000718343, ENST00000873924, ENST00000873925, ENST00000873926, ENST00000873927, ENST00000922545, ENST00000922546, ENST00000959744, ENST00000959745, ENST00000959746, ENST00000959747, ENST00000959748
RefSeq mRNA: 1 — MANE Select: NM_019593
NM_019593
CCDS: CCDS13090
Canonical transcript exons
ENST00000379019 — 20 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001026553 | 5610842 | 5611006 |
| ENSE00001653615 | 5586194 | 5586269 |
| ENSE00003472832 | 5565017 | 5565078 |
| ENSE00003474022 | 5558684 | 5558819 |
| ENSE00003491073 | 5584281 | 5584322 |
| ENSE00003492572 | 5598725 | 5598821 |
| ENSE00003499249 | 5575413 | 5575545 |
| ENSE00003500174 | 5570147 | 5570239 |
| ENSE00003510368 | 5578380 | 5578611 |
| ENSE00003510615 | 5573915 | 5573969 |
| ENSE00003510709 | 5557945 | 5558105 |
| ENSE00003526831 | 5567483 | 5567560 |
| ENSE00003527439 | 5575816 | 5575978 |
| ENSE00003542687 | 5580008 | 5580131 |
| ENSE00003581846 | 5593327 | 5593411 |
| ENSE00003623456 | 5559940 | 5560076 |
| ENSE00003626525 | 5561465 | 5561530 |
| ENSE00003630006 | 5566733 | 5566772 |
| ENSE00003782897 | 5604364 | 5604440 |
| ENSE00004034829 | 5544439 | 5547850 |
Expression profiles
Bgee: expression breadth ubiquitous, 256 present calls, max score 97.53.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 49.9843 / max 1979.7405, expressed in 1812 samples.
FANTOM5 promoters (5 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 186315 | 43.2031 | 1806 |
| 186314 | 4.5322 | 1264 |
| 186313 | 1.5351 | 591 |
| 208980 | 0.3880 | 207 |
| 186307 | 0.3260 | 144 |
Top tissues by expression
256 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| palpebral conjunctiva | UBERON:0001812 | 97.53 | gold quality |
| monocyte | CL:0000576 | 97.00 | gold quality |
| bone marrow | UBERON:0002371 | 96.75 | gold quality |
| leukocyte | CL:0000738 | 96.61 | gold quality |
| bone marrow cell | CL:0002092 | 96.37 | gold quality |
| endothelial cell | CL:0000115 | 96.09 | gold quality |
| visceral pleura | UBERON:0002401 | 95.63 | gold quality |
| calcaneal tendon | UBERON:0003701 | 95.36 | gold quality |
| tibialis anterior | UBERON:0001385 | 95.32 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 94.91 | gold quality |
| trabecular bone tissue | UBERON:0002483 | 94.65 | gold quality |
| blood | UBERON:0000178 | 94.62 | gold quality |
| primary visual cortex | UBERON:0002436 | 94.48 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 94.12 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 94.00 | gold quality |
| sperm | CL:0000019 | 93.97 | gold quality |
| tonsil | UBERON:0002372 | 93.94 | gold quality |
| cartilage tissue | UBERON:0002418 | 93.73 | gold quality |
| cerebellar vermis | UBERON:0004720 | 93.67 | gold quality |
| occipital lobe | UBERON:0002021 | 93.57 | gold quality |
| tibia | UBERON:0000979 | 93.52 | gold quality |
| spleen | UBERON:0002106 | 93.44 | gold quality |
| pancreatic ductal cell | CL:0002079 | 93.13 | gold quality |
| saliva-secreting gland | UBERON:0001044 | 93.00 | gold quality |
| esophagus squamous epithelium | UBERON:0006920 | 93.00 | gold quality |
| minor salivary gland | UBERON:0001830 | 92.98 | gold quality |
| granulocyte | CL:0000094 | 92.95 | gold quality |
| lung | UBERON:0002048 | 92.95 | gold quality |
| parietal pleura | UBERON:0002400 | 92.88 | gold quality |
| adrenal tissue | UBERON:0018303 | 92.88 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 2.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-3929 | yes | 192.31 |
| E-ANND-3 | yes | 9.59 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
234 targeting GPCPD1, 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-190A-3P | 100.00 | 80.35 | 5520 |
| HSA-MIR-30A-5P | 100.00 | 76.31 | 3233 |
| HSA-MIR-30B-5P | 100.00 | 76.29 | 3248 |
| HSA-MIR-30C-5P | 100.00 | 76.29 | 3248 |
| HSA-MIR-30D-5P | 100.00 | 76.32 | 3233 |
| HSA-MIR-30E-5P | 100.00 | 76.32 | 3242 |
| HSA-MIR-196A-5P | 100.00 | 68.16 | 684 |
| HSA-MIR-196B-5P | 100.00 | 68.16 | 681 |
| HSA-MIR-29A-3P | 100.00 | 73.11 | 1835 |
| HSA-MIR-29B-3P | 100.00 | 73.18 | 1833 |
| HSA-MIR-29C-3P | 100.00 | 73.15 | 1833 |
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-3646 | 100.00 | 73.56 | 5283 |
| HSA-MIR-4262 | 100.00 | 73.26 | 3931 |
| 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-3120-5P | 100.00 | 65.56 | 965 |
| HSA-MIR-656-3P | 100.00 | 72.15 | 2788 |
| HSA-MIR-5011-5P | 100.00 | 83.46 | 5820 |
| HSA-MIR-1252-5P | 100.00 | 69.80 | 2774 |
| HSA-MIR-6748-5P | 100.00 | 65.81 | 1057 |
| HSA-MIR-4500 | 99.99 | 72.72 | 2367 |
| HSA-MIR-1184 | 99.99 | 68.19 | 1458 |
| HSA-MIR-186-5P | 99.99 | 70.83 | 3707 |
| HSA-MIR-4282 | 99.99 | 75.36 | 6408 |
| HSA-MIR-181A-5P | 99.99 | 72.96 | 2995 |
| HSA-MIR-181B-5P | 99.99 | 72.97 | 2996 |
| HSA-MIR-181C-5P | 99.99 | 72.95 | 2996 |
Literature-anchored findings (GeneRIF, showing 8)
- common genetic variants in GPCPD1 are associated with scaling of visual cortical surface area in humans (PMID:22343285)
- We have identified EDI3, a key enzyme controlling GPC and choline metabolism; Because inhibition of it corrects the GPC/PC ratio and decreases the migration capacity of tumor cells, it represents a possible target for therapeutic intervention. (PMID:22570503)
- EDI3 links choline metabolism to integrin expression, cell adhesion and spreading (PMID:25482527)
- Circular RNA circSNX6 promotes sunitinib resistance in renal cell carcinoma through the miR-1184/GPCPD1/ lysophosphatidic acid axis. (PMID:34626691)
- Inhibiting the glycerophosphodiesterase EDI3 in ER-HER2+ breast cancer cells resistant to HER2-targeted therapy reduces viability and tumour growth. (PMID:36670508)
- Hypoxia-induced GPCPD1 depalmitoylation triggers mitophagy via regulating PRKN-mediated ubiquitination of VDAC1. (PMID:36803235)
- Gpcpd1-GPC metabolic pathway is dysfunctional in aging and its deficiency severely perturbs glucose metabolism. (PMID:38238601)
- EDI3 knockdown in ER-HER2+ breast cancer cells reduces tumor burden and improves survival in two mouse models of experimental metastasis. (PMID:38816770)
Cross-species orthologs
9 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | gpcpd1 | ENSDARG00000016011 |
| mus_musculus | Gpcpd1 | ENSMUSG00000027346 |
| rattus_norvegicus | Gpcpd1 | ENSRNOG00000053201 |
| drosophila_melanogaster | CG2818 | FBGN0031566 |
| drosophila_melanogaster | CG9394 | FBGN0034588 |
| drosophila_melanogaster | CG11619 | FBGN0036836 |
| drosophila_melanogaster | CG18135 | FBGN0036837 |
| drosophila_melanogaster | CG3942 | FBGN0038008 |
| caenorhabditis_elegans | WBGENE00011511 |
Protein
Protein identifiers
Glycerophosphocholine phosphodiesterase GPCPD1 — Q9NPB8 (reviewed: Q9NPB8)
Alternative names: Glycerophosphodiester phosphodiesterase 5
All UniProt accessions (4): Q9NPB8, A0A0J9YVP8, A0A0J9YY12, H0Y565
UniProt curated annotations — full annotation on UniProt →
Function. May be involved in the negative regulation of skeletal muscle differentiation, independently of its glycerophosphocholine phosphodiesterase activity.
Subcellular location. Cytoplasm. Cytosol.
Tissue specificity. Widely expressed, with highest expression in spinal chord.
Similarity. Belongs to the glycerophosphoryl diester phosphodiesterase family.
RefSeq proteins (1): NP_062539* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR002044 | CBM20 | Domain |
| IPR013783 | Ig-like_fold | Homologous_superfamily |
| IPR013784 | Carb-bd-like_fold | Homologous_superfamily |
| IPR017946 | PLC-like_Pdiesterase_TIM-brl | Homologous_superfamily |
| IPR030395 | GP_PDE_dom | Domain |
| IPR034839 | CBM20_GPCPD1 | Domain |
| IPR051578 | GDPD | Family |
| IPR057506 | C2_GPCPD1 | Domain |
Pfam: PF00686, PF03009, PF25329
Enzyme classification (BRENDA):
- EC 3.1.4.46 — glycerophosphodiester phosphodiesterase (BRENDA: 38 organisms, 62 substrates, 23 inhibitors, 29 Km, 19 kcat entries)
Substrate kinetics (BRENDA)
10 substrates with measured Km, best-characterized 10. Km ranges are aggregated across organisms/conditions.
| Substrate | Km (mM) | Measurements |
|---|---|---|
| BIS(P-NITROPHENYL) PHOSPHATE | 0.12–3.95 | 5 |
| GLYCEROPHOSPHOCHOLINE | 0.036–2 | 5 |
| P-NITROPHENYL PHOSPHATE | 0.12–49 | 5 |
| GLYCEROPHOSPHOETHANOLAMINE | 0.2–0.22 | 3 |
| GLYCEROPHOSPHOGLYCEROL | 0.2–0.62 | 3 |
| BIS(P-NITROPHENYL PHOSPHATE) | 3.5–7 | 2 |
| GLYCEROPHOSPHOINOSITOL | 0.39 | 2 |
| GLYCEROPHOSPHOSERINE | 0.66 | 2 |
| BIS(4-NITROPHENYL) PHOSPHATE | 3.56 | 1 |
| BIS(GLYCEROPHOSPHO)GLYCEROL | 0.6 | 1 |
Catalyzed reactions (Rhea), 1 shown:
- sn-glycerol 3-phosphocholine + H2O = sn-glycerol 3-phosphate + choline + H(+) (RHEA:16061)
UniProt features (19 total): strand 7, modified residue 3, domain 2, helix 2, binding site 2, chain 1, turn 1, sequence variant 1
Structure
Experimental structures (PDB)
1 structures.
| PDB | Method | Resolution (Å) |
|---|---|---|
| 2Z0B | X-RAY DIFFRACTION | 2 |
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9NPB8-F1 | 87.45 | 0.70 |
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 (2): 70; 88–89
Post-translational modifications (3): 175, 424, 608
Function
Pathways and Gene Ontology
Reactome pathways
2 pathways
| ID | Pathway |
|---|---|
| R-HSA-1483115 | Hydrolysis of LPC |
| R-HSA-1483152 | Hydrolysis of LPE |
MSigDB gene sets: 228 (showing top):
TGGTGCT_MIR29A_MIR29B_MIR29C, AAGCAAT_MIR137, GOBP_PHOSPHOLIPID_METABOLIC_PROCESS, ACTACCT_MIR196A_MIR196B, GOBP_MUSCLE_TISSUE_DEVELOPMENT, IVANOVA_HEMATOPOIESIS_MATURE_CELL, MORI_IMMATURE_B_LYMPHOCYTE_UP, GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_GLYCEROLIPID_METABOLIC_PROCESS, GERY_CEBP_TARGETS, UEDA_PERIFERAL_CLOCK, GOBP_MUSCLE_STRUCTURE_DEVELOPMENT, INGRAM_SHH_TARGETS_UP, GOBP_SKELETAL_MUSCLE_ORGAN_DEVELOPMENT, GOBP_ORGANOPHOSPHATE_CATABOLIC_PROCESS
GO Biological Process (3): skeletal muscle tissue development (GO:0007519), glycerophospholipid catabolic process (GO:0046475), lipid metabolic process (GO:0006629)
GO Molecular Function (6): glycerophosphocholine phosphodiesterase activity (GO:0047389), starch binding (GO:2001070), protein binding (GO:0005515), phosphoric diester hydrolase activity (GO:0008081), hydrolase activity (GO:0016787), carbohydrate binding (GO:0030246)
GO Cellular Component (2): cytosol (GO:0005829), cytoplasm (GO:0005737)
Reactome top-level categories
Rollup of top-1 pathways:
| Category | Pathways |
|---|---|
| Glycerophospholipid biosynthesis | 2 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| binding | 2 |
| cellular anatomical structure | 2 |
| striated muscle tissue development | 1 |
| skeletal muscle organ development | 1 |
| glycerophospholipid metabolic process | 1 |
| phospholipid catabolic process | 1 |
| glycerolipid catabolic process | 1 |
| primary metabolic process | 1 |
| phosphoric diester hydrolase activity | 1 |
| polysaccharide binding | 1 |
| phosphoric ester hydrolase activity | 1 |
| catalytic activity | 1 |
| cytoplasm | 1 |
| intracellular anatomical structure | 1 |
Protein interactions and networks
STRING
1269 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| GPCPD1 | GDPD5 | Q8WTR4 | 589 |
| GPCPD1 | CHPT1 | Q8WUD6 | 588 |
| GPCPD1 | CHKA | P35790 | 553 |
| GPCPD1 | GDE1 | Q9NZC3 | 536 |
| GPCPD1 | TATDN3 | Q17R31 | 530 |
| GPCPD1 | CEPT1 | Q9Y6K0 | 514 |
| GPCPD1 | OTOL1 | A6NHN0 | 472 |
| GPCPD1 | ANGEL2 | Q5VTE6 | 470 |
| GPCPD1 | PCYT1B | Q9Y5K3 | 464 |
| GPCPD1 | TDRP | Q86YL5 | 455 |
| GPCPD1 | BEND7 | Q8N7W2 | 453 |
| GPCPD1 | TMX4 | Q9H1E5 | 449 |
| GPCPD1 | SHLD1 | Q8IYI0 | 443 |
| GPCPD1 | LYPLA1 | O75608 | 434 |
| GPCPD1 | UTP20 | O75691 | 433 |
IntAct
7 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| SLC35D3 | GPCPD1 | psi-mi:“MI:0915”(physical association) | 0.670 |
| GPCPD1 | TK1 | psi-mi:“MI:0915”(physical association) | 0.370 |
| SLC35D3 | ATP6V0A1 | psi-mi:“MI:0914”(association) | 0.350 |
| PCBD1 | PTPDC1 | psi-mi:“MI:0914”(association) | 0.350 |
| ZNF418 | ZNF195 | psi-mi:“MI:0914”(association) | 0.350 |
| SLC35D3 | ERLIN2 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (14): GPCPD1 (Affinity Capture-MS), GPCPD1 (Affinity Capture-MS), GPCPD1 (Affinity Capture-MS), GPCPD1 (Affinity Capture-MS), GPCPD1 (Affinity Capture-MS), LYPLA1 (Affinity Capture-Western), GPCPD1 (Affinity Capture-Western), VDAC1 (Affinity Capture-MS), VDAC1 (Affinity Capture-Western), GPCPD1 (Affinity Capture-Western), GPCPD1 (Affinity Capture-MS), GPCPD1 (Affinity Capture-RNA), GPCPD1 (Proximity Label-MS), GPCPD1 (Two-hybrid)
ESM2 similar proteins: A0JN80, A2RV18, A2VE39, D2HRF1, D3ZG52, D3ZVK1, E1BMP7, G3GTP0, I0IUP3, O02697, P0DM58, P37202, P42338, P48736, P49717, P49917, Q08162, Q0P4R5, Q0V9Q6, Q0V9R3, Q0WPN0, Q17632, Q3EBC8, Q3V3E1, Q5F310, Q5R5N8, Q5R6L3, Q5R981, Q5U2P0, Q5U2Z5, Q5ZKG3, Q6GN11, Q6NQJ6, Q80VJ4, Q8BTF7, Q8BTI9, Q8C0L9, Q8C0S1, Q8CI75, Q8N1G2
Diamond homologs: A0A1D8PNZ7, A2X8A7, A2XNL6, A2Y8U6, P43585, P77736, Q02979, Q10003, Q10B79, Q21407, Q2V4F9, Q658H5, Q680A6, Q6EPQ3, Q74ZH9, Q80VJ4, Q8C0L9, Q8RB32, Q94A21, Q9NPB8, Q9SGA2, Q9ULT8, O14169, O90760, Q10728, Q1RJ28, Q5UQV3, Q9DBR7, Q9JL55, Q9JL56, Q9NZC3, O07592, Q9C104, P37965, Q3T0T0, Q86WC6, Q9D119, Q9FLM1
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
82 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 57 |
| Likely benign | 4 |
| Benign | 2 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
3629 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 20:5557966:A:C | donor_gain | 1.0000 |
| 20:5557969:C:CA | donor_gain | 1.0000 |
| 20:5557975:T:A | donor_gain | 1.0000 |
| 20:5557985:T:A | donor_gain | 1.0000 |
| 20:5558678:A:C | donor_gain | 1.0000 |
| 20:5558680:TTA:T | donor_loss | 1.0000 |
| 20:5558681:TA:T | donor_loss | 1.0000 |
| 20:5558682:A:AC | donor_gain | 1.0000 |
| 20:5558682:A:AT | donor_loss | 1.0000 |
| 20:5558682:AC:A | donor_gain | 1.0000 |
| 20:5558683:C:CG | donor_gain | 1.0000 |
| 20:5558683:CC:C | donor_gain | 1.0000 |
| 20:5558683:CCA:C | donor_gain | 1.0000 |
| 20:5558683:CCAG:C | donor_gain | 1.0000 |
| 20:5558683:CCAGT:C | donor_gain | 1.0000 |
| 20:5558815:GAACC:G | acceptor_gain | 1.0000 |
| 20:5558817:ACC:A | acceptor_gain | 1.0000 |
| 20:5558818:CC:C | acceptor_gain | 1.0000 |
| 20:5558818:CCC:C | acceptor_gain | 1.0000 |
| 20:5558819:CC:C | acceptor_gain | 1.0000 |
| 20:5558820:C:CA | acceptor_loss | 1.0000 |
| 20:5558820:C:CC | acceptor_gain | 1.0000 |
| 20:5558820:C:T | acceptor_gain | 1.0000 |
| 20:5558821:T:A | acceptor_loss | 1.0000 |
| 20:5559938:A:AC | donor_gain | 1.0000 |
| 20:5559939:C:CC | donor_gain | 1.0000 |
| 20:5559939:CATT:C | donor_gain | 1.0000 |
| 20:5560076:CCTAG:C | acceptor_gain | 1.0000 |
| 20:5561578:C:CT | acceptor_gain | 1.0000 |
| 20:5561579:A:T | acceptor_gain | 1.0000 |
AlphaMissense
4446 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 20:5558021:A:G | W585R | 0.999 |
| 20:5558021:A:T | W585R | 0.999 |
| 20:5558104:C:T | G557E | 0.999 |
| 20:5558105:C:A | G557W | 0.999 |
| 20:5558105:C:G | G557R | 0.999 |
| 20:5558105:C:T | G557R | 0.999 |
| 20:5558735:T:A | R539S | 0.999 |
| 20:5558735:T:G | R539S | 0.999 |
| 20:5558736:C:G | R539T | 0.999 |
| 20:5558807:C:A | K515N | 0.999 |
| 20:5558807:C:G | K515N | 0.999 |
| 20:5559945:G:C | C509W | 0.999 |
| 20:5559960:A:C | F504L | 0.999 |
| 20:5559960:A:T | F504L | 0.999 |
| 20:5559962:A:G | F504L | 0.999 |
| 20:5559981:C:A | R497S | 0.999 |
| 20:5559981:C:G | R497S | 0.999 |
| 20:5561483:T:A | K459N | 0.999 |
| 20:5561483:T:G | K459N | 0.999 |
| 20:5561484:T:A | K459I | 0.999 |
| 20:5567496:A:G | L405P | 0.999 |
| 20:5573925:G:T | A349D | 0.999 |
| 20:5573948:A:C | N341K | 0.999 |
| 20:5573948:A:T | N341K | 0.999 |
| 20:5575440:C:T | G325D | 0.999 |
| 20:5575443:C:G | R324P | 0.999 |
| 20:5575447:G:C | H323D | 0.999 |
| 20:5575449:C:T | G322D | 0.999 |
| 20:5580105:A:G | W126R | 0.999 |
| 20:5580105:A:T | W126R | 0.999 |
dbSNP variants (sampled 300 via entrez): RS1000046252 (20:5554494 C>T), RS1000111597 (20:5593406 A>T), RS1000208723 (20:5611785 C>G,T), RS1000268171 (20:5548016 A>T), RS1000269042 (20:5548780 G>A), RS1000324098 (20:5605576 C>T), RS1000378169 (20:5598540 A>C), RS1000395282 (20:5604968 CAA>C), RS1000472586 (20:5580827 C>T), RS1000473843 (20:5555368 G>A), RS1000556405 (20:5578894 T>A,C), RS1000630136 (20:5587874 C>T), RS1000662111 (20:5592546 C>T), RS1000675275 (20:5560684 C>T), RS1000818703 (20:5585206 G>A)
Disease associations
OMIM: gene MIM:614124 | 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):
| Study | Trait | p-value |
|---|---|---|
| GCST001411_1 | Occipital cortical area (total cortical area interaction) | 6.000000e-09 |
| GCST006473_2 | Diffusing capacity of the lung for carbon monoxide traits | 4.000000e-07 |
| GCST006616_4 | Uterine fibroid number (single vs multiple) | 1.000000e-06 |
| GCST009391_2087 | Metabolite levels | 2.000000e-06 |
| GCST010204_144 | Low density lipoprotein cholesterol levels | 1.000000e-11 |
| GCST010243_12 | Apolipoprotein B levels | 1.000000e-13 |
| GCST010245_100 | LDL cholesterol levels | 2.000000e-08 |
| GCST012232_37 | Lipoprotein (a) levels | 7.000000e-10 |
EFO canonical traits (8, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004771 | visual cortical surface area measurement |
| EFO:0008381 | total cortical area measurement |
| EFO:0009369 | diffusing capacity of the lung for carbon monoxide |
| EFO:0009410 | uterine fibroid measurement |
| EFO:0010373 | phosphatidylcholine 32:1 measurement |
| EFO:0004611 | low density lipoprotein cholesterol measurement |
| EFO:0004615 | apolipoprotein B measurement |
| EFO:0006925 | lipoprotein A measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
58 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| bisphenol A | affects cotreatment, decreases expression, affects expression, increases expression | 4 |
| sodium arsenite | decreases expression, affects cotreatment, increases abundance | 3 |
| Air Pollutants | affects expression, increases abundance, increases expression | 3 |
| Arsenic | affects methylation, affects cotreatment, decreases expression, increases abundance | 3 |
| Valproic Acid | affects expression, increases expression | 3 |
| Cyclosporine | increases expression | 3 |
| methylmercuric chloride | increases expression | 2 |
| Acetaminophen | affects expression, increases expression | 2 |
| Cadmium | increases abundance, increases expression, decreases expression | 2 |
| Folic Acid | decreases expression, affects cotreatment, increases expression | 2 |
| Nickel | increases expression | 2 |
| Ozone | affects expression, increases abundance | 2 |
| Phenylmercuric Acetate | affects cotreatment, decreases expression | 2 |
| GSK-J4 | increases expression | 1 |
| FR900359 | decreases phosphorylation | 1 |
| triphenyl phosphate | affects expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | increases expression | 1 |
| manganese chloride | decreases expression, increases abundance, affects cotreatment | 1 |
| resorcinol | decreases expression | 1 |
| di-n-butylphosphoric acid | affects expression | 1 |
| perfluoro-n-nonanoic acid | increases expression | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, decreases expression | 1 |
| clothianidin | increases expression | 1 |
| ICG 001 | increases expression | 1 |
| dorsomorphin | affects cotreatment, decreases expression | 1 |
| jinfukang | affects cotreatment, increases expression | 1 |
| prothioconazole | increases expression | 1 |
| NSC 689534 | affects binding, increases expression | 1 |
| 4-(4-((5-(4,5-dimethyl-2-nitrophenyl)-2-furanyl)methylene)-4,5-dihydro-3-methyl-5-oxo-1H-pyrazol-1-yl)benzoic acid | increases expression | 1 |
| Sunitinib | increases 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.