PXYLP1
gene geneOn this page
Also known as FLJ23751
Summary
PXYLP1 (2-phosphoxylose phosphatase 1, HGNC:26303) is a protein-coding gene on chromosome 3q23, encoding 2-phosphoxylose phosphatase 1 (Q8TE99). Responsible for the 2-O-dephosphorylation of xylose in the glycosaminoglycan-protein linkage region of proteoglycans thereby regulating the amount of mature glycosaminoglycan (GAG) chains.
Enables phosphatase activity. Involved in chondroitin sulfate proteoglycan biosynthetic process and positive regulation of heparan sulfate proteoglycan biosynthetic process. Located in Golgi apparatus.
Source: NCBI Gene 92370 — RefSeq curated summary.
At a glance
- GWAS associations: 12
- Clinical variants (ClinVar): 77 total
- MANE Select transcript:
NM_001037172
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:26303 |
| Approved symbol | PXYLP1 |
| Name | 2-phosphoxylose phosphatase 1 |
| Location | 3q23 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ23751 |
| Ensembl gene | ENSG00000155893 |
| Ensembl biotype | protein_coding |
| OMIM | 619732 |
| Entrez | 92370 |
Gene structure
Transcript identifiers
Ensembl transcripts: 31 — 22 protein_coding, 5 nonsense_mediated_decay, 2 protein_coding_CDS_not_defined, 2 retained_intron
ENST00000286353, ENST00000393010, ENST00000502783, ENST00000504264, ENST00000505013, ENST00000505502, ENST00000508812, ENST00000511968, ENST00000512457, ENST00000513007, ENST00000513528, ENST00000514263, ENST00000514680, ENST00000514880, ENST00000636601, ENST00000637579, ENST00000637751, ENST00000879101, ENST00000879102, ENST00000879103, ENST00000879104, ENST00000925230, ENST00000925231, ENST00000925232, ENST00000971913, ENST00000971914, ENST00000971915, ENST00000971916, ENST00000971917, ENST00000971918, ENST00000971919
RefSeq mRNA: 3 — MANE Select: NM_001037172
NM_001037172, NM_001282728, NM_152282
CCDS: CCDS3116, CCDS63797
Canonical transcript exons
ENST00000286353 — 6 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001023284 | 141279378 | 141279504 |
| ENSE00002025423 | 141292268 | 141294924 |
| ENSE00002048205 | 141231825 | 141231911 |
| ENSE00003468577 | 141287314 | 141287453 |
| ENSE00003480344 | 141260123 | 141260254 |
| ENSE00003648560 | 141278342 | 141278500 |
Expression profiles
Bgee: expression breadth ubiquitous, 251 present calls, max score 99.36.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.0475 / max 104.4298, expressed in 1586 samples.
FANTOM5 promoters (9 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 38874 | 7.5754 | 1570 |
| 38872 | 0.1689 | 76 |
| 38871 | 0.0944 | 37 |
| 38880 | 0.0750 | 29 |
| 38873 | 0.0676 | 24 |
| 38876 | 0.0201 | 3 |
| 38879 | 0.0178 | 4 |
| 38875 | 0.0162 | 4 |
| 38870 | 0.0122 | 2 |
Top tissues by expression
261 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| corpus epididymis | UBERON:0004359 | 99.36 | gold quality |
| secondary oocyte | CL:0000655 | 98.67 | gold quality |
| tibia | UBERON:0000979 | 98.55 | gold quality |
| thymus | UBERON:0002370 | 98.34 | gold quality |
| oocyte | CL:0000023 | 97.69 | gold quality |
| cauda epididymis | UBERON:0004360 | 97.32 | gold quality |
| seminal vesicle | UBERON:0000998 | 96.98 | gold quality |
| cartilage tissue | UBERON:0002418 | 94.30 | gold quality |
| caput epididymis | UBERON:0004358 | 93.99 | gold quality |
| tendon of biceps brachii | UBERON:0008188 | 93.74 | gold quality |
| cortical plate | UBERON:0005343 | 93.55 | gold quality |
| left testis | UBERON:0004533 | 93.44 | gold quality |
| Brodmann (1909) area 23 | UBERON:0013554 | 93.38 | gold quality |
| endothelial cell | CL:0000115 | 93.30 | gold quality |
| right testis | UBERON:0004534 | 93.09 | gold quality |
| ileal mucosa | UBERON:0000331 | 92.57 | gold quality |
| testis | UBERON:0000473 | 91.84 | gold quality |
| calcaneal tendon | UBERON:0003701 | 91.47 | gold quality |
| middle temporal gyrus | UBERON:0002771 | 90.59 | gold quality |
| tendon | UBERON:0000043 | 90.50 | gold quality |
| epithelial cell of pancreas | CL:0000083 | 89.73 | gold quality |
| ventricular zone | UBERON:0003053 | 89.41 | gold quality |
| layer of synovial tissue | UBERON:0007616 | 89.32 | gold quality |
| embryo | UBERON:0000922 | 89.14 | gold quality |
| ganglionic eminence | UBERON:0004023 | 89.14 | gold quality |
| primary visual cortex | UBERON:0002436 | 88.86 | gold quality |
| germinal epithelium of ovary | UBERON:0001304 | 88.78 | gold quality |
| decidua | UBERON:0002450 | 88.55 | gold quality |
| pigmented layer of retina | UBERON:0001782 | 88.20 | gold quality |
| retina | UBERON:0000966 | 88.18 | gold quality |
Single-cell (SCXA)
Detected in 1 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 5.37 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
111 targeting PXYLP1, 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-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-4747-5P | 100.00 | 67.90 | 2681 |
| HSA-MIR-5196-5P | 100.00 | 67.98 | 2761 |
| HSA-MIR-4481 | 100.00 | 66.42 | 1669 |
| HSA-MIR-3163 | 100.00 | 77.23 | 8605 |
| HSA-MIR-340-5P | 100.00 | 72.50 | 4437 |
| HSA-MIR-188-3P | 100.00 | 68.76 | 1240 |
| HSA-MIR-4282 | 99.99 | 75.36 | 6408 |
| HSA-MIR-548C-3P | 99.99 | 74.01 | 7587 |
| HSA-MIR-4745-5P | 99.98 | 65.95 | 1028 |
| HSA-MIR-551B-5P | 99.96 | 71.28 | 3493 |
| HSA-MIR-545-3P | 99.95 | 70.74 | 2783 |
| HSA-MIR-767-5P | 99.95 | 70.85 | 993 |
| HSA-MIR-454-3P | 99.91 | 74.01 | 1925 |
| HSA-MIR-106A-5P | 99.90 | 73.94 | 2683 |
| HSA-MIR-301A-3P | 99.90 | 73.15 | 1839 |
| HSA-MIR-130A-3P | 99.90 | 73.31 | 1861 |
| HSA-MIR-130B-3P | 99.90 | 73.27 | 1850 |
| HSA-MIR-301B-3P | 99.90 | 73.19 | 1836 |
| HSA-MIR-3666 | 99.90 | 73.24 | 1833 |
| HSA-MIR-4295 | 99.90 | 73.11 | 1838 |
| HSA-MIR-5682 | 99.89 | 72.56 | 1005 |
| HSA-MIR-17-5P | 99.89 | 73.83 | 2665 |
| HSA-MIR-106B-5P | 99.88 | 74.72 | 2795 |
| HSA-MIR-20A-5P | 99.88 | 74.76 | 2769 |
| HSA-MIR-20B-5P | 99.88 | 74.01 | 2621 |
| HSA-MIR-93-5P | 99.88 | 73.98 | 2606 |
| HSA-MIR-5582-3P | 99.86 | 72.48 | 4221 |
Literature-anchored findings (GeneRIF, showing 1)
- this study describes the cloning of a human cDNA encoding a novel protein designated 2-phosphoxylose phosphatase capable of dephosphorylating this Xyl residue. (PMID:24425863)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | pxylp1 | ENSDARG00000040644 |
| mus_musculus | Pxylp1 | ENSMUSG00000043587 |
| rattus_norvegicus | Pxylp1 | ENSRNOG00000012480 |
| drosophila_melanogaster | CG15385 | FBGN0031397 |
| caenorhabditis_elegans | WBGENE00014076 |
Paralogs (5): ACP3 (ENSG00000014257), ACP2 (ENSG00000134575), ACP4 (ENSG00000142513), FRA10AC1 (ENSG00000148690), ACP6 (ENSG00000162836)
Protein
Protein identifiers
2-phosphoxylose phosphatase 1 — Q8TE99 (reviewed: Q8TE99)
Alternative names: Acid phosphatase-like protein 2, Xylosyl phosphatase, epididymis luminal protein 124
All UniProt accessions (10): Q8TE99, A0A1B0GUH7, A0A1B0GWB5, B7Z3R9, B7Z4T2, D6R928, D6RDP0, D6RE60, D6RGE3, E9PDB7
UniProt curated annotations — full annotation on UniProt →
Function. Responsible for the 2-O-dephosphorylation of xylose in the glycosaminoglycan-protein linkage region of proteoglycans thereby regulating the amount of mature glycosaminoglycan (GAG) chains. Sulfated glycosaminoglycans (GAGs), including heparan sulfate and chondroitin sulfate, are synthesized on the so-called common GAG-protein linkage region (GlcUAbeta1-3Galbeta1-3Galbeta1-4Xylbeta1-O-Ser) of core proteins, which is formed by the stepwise addition of monosaccharide residues by the respective specific glycosyltransferases. Xylose 2-O-dephosphorylation during completion of linkage region formation is a prerequisite for the initiation and efficient elongation of the repeating disaccharide region of GAG chains.
Subunit / interactions. Interacts with B3GAT3; the interaction increases the 2-phosphoxylose phosphatase activity of PXYLP1 during completion of linkage region formation in a B3GAT3-mediated manner.
Subcellular location. Golgi apparatus membrane.
Tissue specificity. Widely expressed. Strongly expressed in spleen, fetal liver, moderately in placenta, pancreas, kidney, thymus and colon.
Similarity. Belongs to the histidine acid phosphatase family.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q8TE99-1 | 1 | yes |
| Q8TE99-2 | 2 |
RefSeq proteins (3): NP_001032249, NP_001269657, NP_689495 (=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR000560 | His_Pase_clade-2 | Family |
| IPR029033 | His_PPase_superfam | Homologous_superfamily |
| IPR050645 | Histidine_acid_phosphatase | Family |
Pfam: PF00328
Catalyzed reactions (Rhea), 1 shown:
- 3-O-[beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-2-O-P-Xyl]-L-seryl-[protein] + H2O = 3-O-(beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl)-L-seryl-[protein] + phosphate (RHEA:56512)
UniProt features (9 total): topological domain 2, active site 2, glycosylation site 2, chain 1, transmembrane region 1, splice variant 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q8TE99-F1 | 89.61 | 0.80 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Catalytic / active sites (2): 97 (nucleophile); 379 (proton donor)
Glycosylation sites (2): 305, 354
Function
Pathways and Gene Ontology
Reactome pathways
1 pathways
| ID | Pathway |
|---|---|
| R-HSA-1971475 | Glycosaminoglycan-protein linkage region biosynthesis |
MSigDB gene sets: 198 (showing top):
GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_UP, GSE37336_LY6C_POS_VS_NEG_NAIVE_CD4_TCELL_UP, TAL1ALPHAE47_01, LHX3_01, BOYLAN_MULTIPLE_MYELOMA_D_DN, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_AMINOGLYCAN_BIOSYNTHETIC_PROCESS, GOBP_CHONDROITIN_SULFATE_PROTEOGLYCAN_BIOSYNTHETIC_PROCESS, GOBP_REGULATION_OF_GLYCOPROTEIN_METABOLIC_PROCESS, GOBP_HEPARAN_SULFATE_PROTEOGLYCAN_METABOLIC_PROCESS, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, BILD_E2F3_ONCOGENIC_SIGNATURE, GOBP_AMINOGLYCAN_METABOLIC_PROCESS, PYEON_CANCER_HEAD_AND_NECK_VS_CERVICAL_UP, GOBP_POSITIVE_REGULATION_OF_GLYCOPROTEIN_METABOLIC_PROCESS
GO Biological Process (4): glycosaminoglycan biosynthetic process (GO:0006024), positive regulation of heparan sulfate proteoglycan biosynthetic process (GO:0010909), chondroitin sulfate proteoglycan biosynthetic process (GO:0050650), positive regulation of proteoglycan biosynthetic process (GO:1902730)
GO Molecular Function (3): phosphatase activity (GO:0016791), protein binding (GO:0005515), hydrolase activity (GO:0016787)
GO Cellular Component (3): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), membrane (GO:0016020)
Reactome top-level categories
Rollup of top-1 pathways:
| Category | Pathways |
|---|---|
| Glycosaminoglycan metabolism | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| proteoglycan biosynthetic process | 2 |
| aminoglycan biosynthetic process | 1 |
| glycosaminoglycan metabolic process | 1 |
| regulation of heparan sulfate proteoglycan biosynthetic process | 1 |
| heparan sulfate proteoglycan biosynthetic process | 1 |
| positive regulation of proteoglycan biosynthetic process | 1 |
| positive regulation of protein O-linked glycosylation | 1 |
| chondroitin sulfate proteoglycan metabolic process | 1 |
| protein O-linked glycosylation via xylose | 1 |
| positive regulation of glycoprotein biosynthetic process | 1 |
| phosphoric ester hydrolase activity | 1 |
| binding | 1 |
| catalytic activity | 1 |
| Golgi apparatus | 1 |
| bounding membrane of organelle | 1 |
| cytoplasm | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
740 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| PXYLP1 | GALP | Q9UBC7 | 936 |
| PXYLP1 | ARAF | P07557 | 932 |
| PXYLP1 | B3GAT3 | O94766 | 743 |
| PXYLP1 | FAM20B | O75063 | 669 |
| PXYLP1 | ALG11 | Q2TAA5 | 584 |
| PXYLP1 | EXTL2 | Q9UBQ6 | 578 |
| PXYLP1 | B3GALT6 | Q96L58 | 516 |
| PXYLP1 | B4GALT7 | Q9UBV7 | 497 |
| PXYLP1 | EXT2 | Q93063 | 483 |
| PXYLP1 | XYLT1 | Q86Y38 | 464 |
| PXYLP1 | XYLT2 | Q9H1B5 | 440 |
| PXYLP1 | MEOX2 | P50222 | 433 |
| PXYLP1 | EXTL3 | O43909 | 431 |
| PXYLP1 | TMEM196 | Q5HYL7 | 421 |
| PXYLP1 | XYLB | O75191 | 413 |
IntAct
27 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| PXYLP1 | ADCY9 | psi-mi:“MI:0914”(association) | 0.500 |
| PXYLP1 | ADCY9 | psi-mi:“MI:0915”(physical association) | 0.500 |
| HTR3B | TMEM223 | psi-mi:“MI:0914”(association) | 0.350 |
| LDLRAD1 | GXYLT2 | psi-mi:“MI:0914”(association) | 0.350 |
| PDGFRA | GXYLT2 | psi-mi:“MI:0914”(association) | 0.350 |
| CLEC12B | GXYLT2 | psi-mi:“MI:0914”(association) | 0.350 |
| CHRNB2 | TMEM131L | psi-mi:“MI:0914”(association) | 0.350 |
| CCL3 | KRBA1 | psi-mi:“MI:0914”(association) | 0.350 |
| KLRC4 | RAP1BL | psi-mi:“MI:0914”(association) | 0.350 |
| KLRC1 | METTL15 | psi-mi:“MI:0914”(association) | 0.350 |
| SCGB2A2 | RTL8C | psi-mi:“MI:0914”(association) | 0.350 |
| C1orf54 | AGRN | psi-mi:“MI:0914”(association) | 0.350 |
| HFE | PODXL | psi-mi:“MI:0914”(association) | 0.350 |
| CHRNE | PODXL | psi-mi:“MI:0914”(association) | 0.350 |
| KLRC2 | CLGN | psi-mi:“MI:0914”(association) | 0.350 |
| LY86 | PLXNB2 | psi-mi:“MI:0914”(association) | 0.350 |
| PTCH1 | PLXNB2 | psi-mi:“MI:0914”(association) | 0.350 |
| INS | LAMA5 | psi-mi:“MI:0914”(association) | 0.350 |
| GALNT10 | PLXNA2 | psi-mi:“MI:0914”(association) | 0.350 |
| PXYLP1 | GNPTAB | psi-mi:“MI:0914”(association) | 0.350 |
| FURIN | RHOBTB3 | psi-mi:“MI:0914”(association) | 0.350 |
| ADCY9 | COX7A2L | psi-mi:“MI:0914”(association) | 0.350 |
| FURIN | ESYT2 | psi-mi:“MI:0914”(association) | 0.350 |
| SLC39A12 | ESYT2 | psi-mi:“MI:0914”(association) | 0.350 |
| SLC39A7 | ESYT2 | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (39): PXYLP1 (Affinity Capture-MS), PXYLP1 (Affinity Capture-MS), PXYLP1 (Affinity Capture-MS), ADCY9 (Affinity Capture-MS), FURIN (Affinity Capture-MS), GNPTAB (Affinity Capture-MS), PXYLP1 (Affinity Capture-MS), PXYLP1 (Affinity Capture-MS), PXYLP1 (Affinity Capture-MS), PXYLP1 (Two-hybrid), PXYLP1 (Affinity Capture-MS), PXYLP1 (Affinity Capture-MS), PXYLP1 (Affinity Capture-MS), PXYLP1 (Affinity Capture-MS), PXYLP1 (Affinity Capture-MS)
ESM2 similar proteins: A8E7N9, E9Q6D8, F4J2C8, O43173, O75072, P13671, P54631, P61131, P61134, P61135, P61644, P85857, Q02745, Q0IHQ9, Q11206, Q19187, Q23534, Q4G148, Q5FVM7, Q5MD89, Q5RCM7, Q5SP46, Q5ZKI6, Q60HG0, Q619N4, Q64689, Q66H78, Q68G12, Q6DE37, Q6DH46, Q6GX83, Q6KB55, Q70D51, Q80TN4, Q811M5, Q8BHA9, Q8R507, Q8RXE1, Q8TE99, Q91Y74
Diamond homologs: A6H757, Q09448, Q09451, Q09549, Q0IHQ9, Q19076, Q54P71, Q54P72, Q5R8C0, Q66H78, Q8BHA9, Q8TE99, Q9NPH0, Q6DH46, A6H730, P15309, Q54PR9, Q8CE08
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
77 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 66 |
| Likely benign | 3 |
| Benign | 0 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
1521 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 3:141231907:GGGCG:G | donor_gain | 1.0000 |
| 3:141231908:GGCGG:G | donor_gain | 1.0000 |
| 3:141260117:TCACA:T | acceptor_loss | 1.0000 |
| 3:141260118:CACA:C | acceptor_loss | 1.0000 |
| 3:141260119:ACAGG:A | acceptor_loss | 1.0000 |
| 3:141260120:CAG:C | acceptor_loss | 1.0000 |
| 3:141260121:AGGAC:A | acceptor_loss | 1.0000 |
| 3:141260122:GGAC:G | acceptor_gain | 1.0000 |
| 3:141260250:GTTCT:G | donor_gain | 1.0000 |
| 3:141260255:G:GG | donor_gain | 1.0000 |
| 3:141278340:A:AG | acceptor_gain | 1.0000 |
| 3:141278341:G:GA | acceptor_gain | 1.0000 |
| 3:141278341:GTC:G | acceptor_gain | 1.0000 |
| 3:141278341:GTCC:G | acceptor_gain | 1.0000 |
| 3:141231908:GGCG:G | donor_gain | 0.9900 |
| 3:141231909:GCG:G | donor_gain | 0.9900 |
| 3:141231909:GCGG:G | donor_gain | 0.9900 |
| 3:141231910:CGGTG:C | donor_loss | 0.9900 |
| 3:141231911:GGTG:G | donor_loss | 0.9900 |
| 3:141231912:G:C | donor_loss | 0.9900 |
| 3:141231912:G:GG | donor_gain | 0.9900 |
| 3:141231913:T:G | donor_loss | 0.9900 |
| 3:141231914:G:GG | donor_loss | 0.9900 |
| 3:141260121:A:AG | acceptor_gain | 0.9900 |
| 3:141260121:AG:A | acceptor_gain | 0.9900 |
| 3:141260122:G:GA | acceptor_gain | 0.9900 |
| 3:141260122:GG:G | acceptor_gain | 0.9900 |
| 3:141260122:GGA:G | acceptor_gain | 0.9900 |
| 3:141260122:GGACA:G | acceptor_gain | 0.9900 |
| 3:141260251:TTCT:T | donor_gain | 0.9900 |
AlphaMissense
3180 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 3:141279438:G:T | R100M | 1.000 |
| 3:141287426:T:A | C160S | 0.999 |
| 3:141287427:G:C | C160S | 0.999 |
| 3:141292399:A:C | S213R | 0.999 |
| 3:141292401:T:A | S213R | 0.999 |
| 3:141292401:T:G | S213R | 0.999 |
| 3:141292670:G:A | C303Y | 0.999 |
| 3:141278465:G:A | C68Y | 0.998 |
| 3:141279432:G:T | G98V | 0.998 |
| 3:141279438:G:C | R100T | 0.998 |
| 3:141279439:G:C | R100S | 0.998 |
| 3:141279439:G:T | R100S | 0.998 |
| 3:141279485:T:A | C116S | 0.998 |
| 3:141279485:T:C | C116R | 0.998 |
| 3:141279486:G:A | C116Y | 0.998 |
| 3:141279486:G:C | C116S | 0.998 |
| 3:141287426:T:C | C160R | 0.998 |
| 3:141287427:G:A | C160Y | 0.998 |
| 3:141292501:T:C | C247R | 0.998 |
| 3:141292820:T:C | L353P | 0.998 |
| 3:141292898:A:C | D379A | 0.998 |
| 3:141292898:A:T | D379V | 0.998 |
| 3:141293021:G:C | R420P | 0.998 |
| 3:141293065:T:A | C435S | 0.998 |
| 3:141293066:G:C | C435S | 0.998 |
| 3:141293101:T:A | C447S | 0.998 |
| 3:141293102:G:C | C447S | 0.998 |
| 3:141278464:T:A | C68S | 0.997 |
| 3:141278465:G:C | C68S | 0.997 |
| 3:141279425:C:A | R96S | 0.997 |
dbSNP variants (sampled 300 via entrez): RS1000045846 (3:141288831 G>A), RS1000125232 (3:141240547 G>A), RS1000146448 (3:141271310 C>T), RS1000147214 (3:141276643 C>T), RS1000308327 (3:141265841 C>G), RS1000334426 (3:141259931 T>G), RS1000335897 (3:141241788 G>A), RS1000341660 (3:141258373 A>C), RS1000367070 (3:141259624 T>C), RS1000492664 (3:141240750 G>A), RS1000502000 (3:141254593 C>G,T), RS1000551925 (3:141283725 G>A), RS1000564175 (3:141235730 T>C), RS1000579601 (3:141236117 C>G), RS1000616426 (3:141265648 C>T)
Disease associations
OMIM: gene MIM:619732 | disease phenotypes:
GenCC curated gene-disease
Mondo (0):
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
12 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST000477_10 | Cognitive performance | 8.000000e-06 |
| GCST000522_8 | Height | 8.000000e-08 |
| GCST004620_136 | Sum basophil neutrophil counts | 2.000000e-11 |
| GCST004626_30 | Myeloid white cell count | 1.000000e-11 |
| GCST004629_55 | Neutrophil count | 4.000000e-11 |
| GCST008152_24 | Weight | 6.000000e-08 |
| GCST008156_35 | Hip circumference adjusted for BMI | 6.000000e-07 |
| GCST008161_16 | Waist circumference adjusted for body mass index | 5.000000e-06 |
| GCST008163_510 | Height | 5.000000e-15 |
| GCST008163_546 | Height | 5.000000e-10 |
| GCST009391_432 | Metabolite levels | 9.000000e-06 |
| GCST90002407_411 | White blood cell count | 9.000000e-19 |
EFO canonical traits (7, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0003926 | neuropsychological test |
| EFO:0004833 | neutrophil count |
| EFO:0005090 | basophil count |
| EFO:0004338 | body weight |
| EFO:0008039 | BMI-adjusted hip circumference |
| EFO:0007789 | BMI-adjusted waist circumference |
| EFO:0010384 | phosphatidylcholine 38:2 measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
50 total (human), top 30 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Valproic Acid | increases expression, increases methylation, affects expression | 6 |
| trichostatin A | affects cotreatment, decreases expression, increases expression | 3 |
| Cyclosporine | decreases expression | 3 |
| sodium arsenite | decreases expression, increases abundance | 2 |
| Benzo(a)pyrene | decreases expression, increases methylation, affects methylation | 2 |
| Phenylmercuric Acetate | affects cotreatment, decreases expression | 2 |
| Tetrachlorodibenzodioxin | decreases expression | 2 |
| Cadmium Chloride | decreases expression, increases abundance, increases expression | 2 |
| aristolochic acid I | decreases expression | 1 |
| bisphenol F | affects cotreatment, increases expression | 1 |
| methylmercuric chloride | decreases expression | 1 |
| triphenyl phosphate | affects expression | 1 |
| pirinixic acid | affects binding, increases activity, increases expression | 1 |
| bisphenol A | affects cotreatment, increases expression | 1 |
| sulforaphane | decreases expression | 1 |
| cupric chloride | decreases expression | 1 |
| nickel sulfate | decreases expression | 1 |
| coumarin | decreases phosphorylation | 1 |
| S-(1,2-dichlorovinyl)cysteine | increases expression, affects response to substance | 1 |
| 4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide | affects cotreatment, decreases expression | 1 |
| abrine | decreases expression | 1 |
| dorsomorphin | affects cotreatment, decreases expression | 1 |
| Sunitinib | decreases expression | 1 |
| Acetaminophen | increases expression | 1 |
| Arsenic | decreases expression, increases abundance | 1 |
| Azathioprine | decreases expression | 1 |
| Cadmium | increases abundance, increases expression | 1 |
| Carbamazepine | affects expression | 1 |
| Dexamethasone | affects cotreatment, increases expression | 1 |
| Diazinon | increases methylation | 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.