CHPF2
gene geneOn this page
Also known as KIAA1402ChSy-3CSGlcA-T
Summary
CHPF2 (chondroitin polymerizing factor 2, HGNC:29270) is a protein-coding gene on chromosome 7q36.1, encoding Chondroitin sulfate glucuronyltransferase (Q9P2E5). Transfers glucuronic acid (GlcUA) from UDP-GlcUA to N-acetylgalactosamine residues on the non-reducing end of the elongating chondroitin polymer.
Predicted to enable glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity. Located in membrane.
Source: NCBI Gene 54480 — RefSeq curated summary.
At a glance
- GWAS associations: 2
- Clinical variants (ClinVar): 157 total
- MANE Select transcript:
NM_019015
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:29270 |
| Approved symbol | CHPF2 |
| Name | chondroitin polymerizing factor 2 |
| Location | 7q36.1 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | KIAA1402, ChSy-3, CSGlcA-T |
| Ensembl gene | ENSG00000033100 |
| Ensembl biotype | protein_coding |
| OMIM | 608037 |
| Entrez | 54480 |
Gene structure
Transcript identifiers
Ensembl transcripts: 10 — 5 protein_coding, 3 nonsense_mediated_decay, 2 retained_intron
ENST00000035307, ENST00000465601, ENST00000482173, ENST00000495645, ENST00000685322, ENST00000689322, ENST00000690444, ENST00000690577, ENST00000691224, ENST00000692651
RefSeq mRNA: 5 — MANE Select: NM_019015
NM_001284295, NM_001389651, NM_001389652, NM_001389653, NM_019015
CCDS: CCDS34779, CCDS64803, CCDS94233, CCDS94234
Canonical transcript exons
ENST00000035307 — 4 exons
| Exon | Start | End |
|---|---|---|
| ENSE00000730163 | 151235048 | 151235612 |
| ENSE00000730164 | 151236408 | 151236590 |
| ENSE00001030935 | 151232483 | 151234274 |
| ENSE00001926893 | 151237374 | 151238822 |
Expression profiles
Bgee: expression breadth ubiquitous, 141 present calls, max score 95.95.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 44.0842 / max 328.3492, expressed in 1824 samples.
FANTOM5 promoters (2 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 82071 | 43.8279 | 1823 |
| 82072 | 0.2562 | 101 |
Top tissues by expression
144 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| stromal cell of endometrium | CL:0002255 | 95.95 | gold quality |
| pituitary gland | UBERON:0000007 | 94.10 | gold quality |
| adenohypophysis | UBERON:0002196 | 94.03 | gold quality |
| granulocyte | CL:0000094 | 93.15 | gold quality |
| left adrenal gland cortex | UBERON:0035825 | 92.07 | gold quality |
| thymus | UBERON:0002370 | 91.83 | silver quality |
| left adrenal gland | UBERON:0001234 | 91.80 | gold quality |
| right adrenal gland | UBERON:0001233 | 91.38 | gold quality |
| right adrenal gland cortex | UBERON:0035827 | 91.35 | gold quality |
| spleen | UBERON:0002106 | 91.30 | gold quality |
| blood | UBERON:0000178 | 91.25 | gold quality |
| thoracic aorta | UBERON:0001515 | 91.17 | gold quality |
| ascending aorta | UBERON:0001496 | 91.12 | gold quality |
| adrenal gland | UBERON:0002369 | 91.06 | gold quality |
| right coronary artery | UBERON:0001625 | 91.04 | gold quality |
| monocyte | CL:0000576 | 90.38 | gold quality |
| descending thoracic aorta | UBERON:0002345 | 90.28 | gold quality |
| leukocyte | CL:0000738 | 90.24 | gold quality |
| quadriceps femoris | UBERON:0001377 | 89.54 | gold quality |
| vermiform appendix | UBERON:0001154 | 89.31 | gold quality |
| body of stomach | UBERON:0001161 | 89.14 | gold quality |
| bone marrow cell | CL:0002092 | 89.13 | gold quality |
| body of pancreas | UBERON:0001150 | 89.12 | gold quality |
| placenta | UBERON:0001987 | 89.01 | gold quality |
| bone marrow | UBERON:0002371 | 89.00 | gold quality |
| bone element | UBERON:0001474 | 88.99 | gold quality |
| adrenal tissue | UBERON:0018303 | 88.71 | gold quality |
| lymph node | UBERON:0000029 | 88.39 | gold quality |
| left coronary artery | UBERON:0001626 | 88.36 | gold quality |
| gall bladder | UBERON:0002110 | 88.36 | gold quality |
Single-cell (SCXA)
Detected in 2 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-ANND-3 | yes | 7.74 |
| E-MTAB-4850 | no | 183.53 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
14 targeting CHPF2, 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-1250-3P | 99.96 | 70.04 | 4038 |
| HSA-MIR-185-3P | 99.95 | 67.01 | 1743 |
| HSA-MIR-335-3P | 99.93 | 73.36 | 4958 |
| HSA-MIR-6783-3P | 99.89 | 67.92 | 2059 |
| HSA-MIR-548AG | 99.77 | 69.25 | 1492 |
| HSA-MIR-548AI | 99.69 | 69.24 | 1494 |
| HSA-MIR-548BA | 99.69 | 69.14 | 1514 |
| HSA-MIR-570-5P | 99.69 | 69.24 | 1494 |
| HSA-MIR-1827 | 99.63 | 68.57 | 3265 |
| HSA-MIR-3120-3P | 99.54 | 70.28 | 2669 |
| HSA-MIR-6852-5P | 99.17 | 66.69 | 2073 |
| HSA-MIR-3166 | 98.24 | 66.63 | 1223 |
| HSA-MIR-6730-5P | 98.03 | 68.12 | 1299 |
| HSA-MIR-6886-3P | 96.96 | 66.36 | 844 |
Literature-anchored findings (GeneRIF, showing 5)
- Results describe a novel human gene that possesses homology with chondroitin synthase. (PMID:12145278)
- chondroitin polymerization is achieved by multiple combinations of ChSy-1, ChSy-2, CSGlcA-T, and ChPF and each combination may play a unique role in the biosynthesis of CS; CSGlcA-T is identified as chondroitin synthase-3 (ChSy-3) (PMID:18316376)
- The present study focused on the expression of chondroitin-synthesizing enzymes in colorectal cancer. (PMID:21468578)
- MEK-mediated CHPF2 phosphorylation promotes colorectal cancer cell proliferation and metastasis by activating NF-kappaB signaling. (PMID:38253217)
- Exosomal lncRNA DUXAP8 affecting CHPF2 in the pathogenesis of intracranial aneurysms. (PMID:38341004)
Cross-species orthologs
5 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | chpf2 | ENSDARG00000059961 |
| mus_musculus | Chpf2 | ENSMUSG00000038181 |
| rattus_norvegicus | Chpf2 | ENSRNOG00000010466 |
| drosophila_melanogaster | Chpf | FBGN0263005 |
| caenorhabditis_elegans | WBGENE00003253 |
Paralogs (7): CHPF (ENSG00000123989), CHSY1 (ENSG00000131873), B4GALNT3 (ENSG00000139044), CSGALNACT1 (ENSG00000147408), CSGALNACT2 (ENSG00000169826), B4GALNT4 (ENSG00000182272), CHSY3 (ENSG00000198108)
Protein
Protein identifiers
Chondroitin sulfate glucuronyltransferase — Q9P2E5 (reviewed: Q9P2E5)
Alternative names: CSGlcA-T, Chondroitin glucuronyltransferase, Chondroitin polymerizing factor 2, Chondroitin synthase 3, N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase
All UniProt accessions (7): A0A8I5KRN5, A0A8I5KSK8, A0A8I5KUJ5, C9JZF7, Q9P2E5, G5E9W2, H7C5L5
UniProt curated annotations — full annotation on UniProt →
Function. Transfers glucuronic acid (GlcUA) from UDP-GlcUA to N-acetylgalactosamine residues on the non-reducing end of the elongating chondroitin polymer. Has no N-acetylgalactosaminyltransferase activity.
Subcellular location. Golgi apparatus. Golgi stack membrane.
Tissue specificity. Ubiquitous. Highly expressed in placenta, small intestine and pancreas.
Similarity. Belongs to the chondroitin N-acetylgalactosaminyltransferase family.
Isoforms (2)
| UniProt ID | Names | Canonical? |
|---|---|---|
| Q9P2E5-1 | 1 | yes |
| Q9P2E5-2 | 2 |
RefSeq proteins (5): NP_001271224, NP_001376580, NP_001376581, NP_001376582, NP_061888* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR008428 | Chond_GalNAc | Family |
| IPR051227 | CS_glycosyltransferase | Family |
Pfam: PF05679
Enzyme classification (BRENDA):
- EC 2.4.1.226 — N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase (BRENDA: 6 organisms, 31 substrates, 4 inhibitors, 6 Km, 0 kcat entries)
Substrate kinetics (BRENDA)
4 substrates with measured Km, best-characterized 4. Km ranges are aggregated across organisms/conditions.
| Substrate | Km (mM) | Measurements |
|---|---|---|
| UDP-GLUCURONIC ACID | 0.051–0.0824 | 2 |
| C11-OLIGOSACCHARIDE OF CHONDROITIN SULFATE A | 0.027 | 1 |
| CHONDROITIN SULFATE UNDECASACCHARIDE | 0.0653 | 1 |
| UDP-ALPHA-D-GLUCURONATE | 0.263 | 1 |
Catalyzed reactions (Rhea), 2 shown:
- 3-O-(beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl)-L-seryl-[protein] + UDP-alpha-D-glucuronate = 3-O-(beta-D-GlcA-(1->3)-beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl)-L-seryl-[protein] + UDP + H(+) (RHEA:23428)
- 3-O-{beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl}-L-seryl-[protein] + UDP-alpha-D-glucuronate = 3-O-{beta-D-GlcA-(1->3)-beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-GalNAc-(1->4)-beta-D-GlcA-(1->3)-beta-D-Gal-(1->3)-beta-D-Gal-(1->4)-beta-D-Xyl}-L-seryl-[protein] + UDP + H(+) (RHEA:54996)
UniProt features (10 total): topological domain 2, glycosylation site 2, splice variant 2, chain 1, transmembrane region 1, region of interest 1, compositionally biased region 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q9P2E5-F1 | 84.86 | 0.57 |
Functional residue map
Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.
Glycosylation sites (2): 121, 342
Function
Pathways and Gene Ontology
Reactome pathways
1 pathways
| ID | Pathway |
|---|---|
| R-HSA-2022870 | CS-GAG biosynthesis |
MSigDB gene sets: 102 (showing top):
BUYTAERT_PHOTODYNAMIC_THERAPY_STRESS_DN, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, GOBP_CHONDROITIN_SULFATE_PROTEOGLYCAN_BIOSYNTHETIC_PROCESS, GAZDA_DIAMOND_BLACKFAN_ANEMIA_PROGENITOR_DN, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, ROSS_AML_WITH_PML_RARA_FUSION, GOBP_CHONDROITIN_SULFATE_PROTEOGLYCAN_METABOLIC_PROCESS, MILI_PSEUDOPODIA_CHEMOTAXIS_DN, GOBP_PROTEIN_O_LINKED_GLYCOSYLATION, GOBP_GLYCOPROTEIN_METABOLIC_PROCESS, REACTOME_METABOLISM_OF_CARBOHYDRATES_AND_CARBOHYDRATE_DERIVATIVES, GOCC_GOLGI_STACK, GOCC_GOLGI_CISTERNA, GOCC_GOLGI_CISTERNA_MEMBRANE, GOCC_ORGANELLE_SUBCOMPARTMENT
GO Biological Process (1): chondroitin sulfate proteoglycan biosynthetic process (GO:0050650)
GO Molecular Function (7): glucuronosyl-N-acetylgalactosaminyl-proteoglycan 4-beta-N-acetylgalactosaminyltransferase activity (GO:0047238), N-acetylgalactosaminyl-proteoglycan 3-beta-glucuronosyltransferase activity (GO:0050510), UDP-glycosyltransferase activity (GO:0008194), acetylgalactosaminyltransferase activity (GO:0008376), transferase activity (GO:0016740), glycosyltransferase activity (GO:0016757), hexosyltransferase activity (GO:0016758)
GO Cellular Component (4): Golgi membrane (GO:0000139), Golgi apparatus (GO:0005794), membrane (GO:0016020), Golgi cisterna membrane (GO:0032580)
Reactome top-level categories
Rollup of top-1 pathways:
| Category | Pathways |
|---|---|
| Chondroitin sulfate/dermatan sulfate metabolism | 1 |
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| glycosyltransferase activity | 2 |
| proteoglycan biosynthetic process | 1 |
| chondroitin sulfate proteoglycan metabolic process | 1 |
| protein O-linked glycosylation via xylose | 1 |
| acetylgalactosaminyltransferase activity | 1 |
| glucuronosyltransferase activity | 1 |
| UDP-glycosyltransferase activity | 1 |
| hexosyltransferase activity | 1 |
| catalytic activity | 1 |
| transferase activity | 1 |
| Golgi apparatus | 1 |
| bounding membrane of organelle | 1 |
| cytoplasm | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
| cellular anatomical structure | 1 |
| organelle membrane | 1 |
| Golgi cisterna | 1 |
Protein interactions and networks
STRING
804 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| CHPF2 | B4GALNT1 | Q00973 | 675 |
| CHPF2 | CHPF | Q8IZ52 | 675 |
| CHPF2 | B3GAT3 | O94766 | 638 |
| CHPF2 | CHST13 | Q8NET6 | 598 |
| CHPF2 | B4GALT7 | Q9UBV7 | 583 |
| CHPF2 | B3GALT6 | Q96L58 | 538 |
| CHPF2 | CHST12 | Q9NRB3 | 536 |
| CHPF2 | CHST15 | Q7LFX5 | 533 |
| CHPF2 | EXTL1 | Q92935 | 519 |
| CHPF2 | CHST14 | Q8NCH0 | 513 |
| CHPF2 | CHST3 | Q7LGC8 | 507 |
| CHPF2 | EXTL3 | O43909 | 497 |
| CHPF2 | XYLT1 | Q86Y38 | 490 |
| CHPF2 | DSE | Q9UL01 | 472 |
| CHPF2 | EXT1 | Q16394 | 455 |
IntAct
97 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| B3GNT3 | PGRMC1 | psi-mi:“MI:0914”(association) | 0.670 |
| SLC39A5 | FAM171A2 | psi-mi:“MI:0914”(association) | 0.640 |
| PLOD2 | psi-mi:“MI:0914”(association) | 0.530 | |
| C1orf54 | EXTL3 | psi-mi:“MI:0914”(association) | 0.530 |
| CREB3 | MYO9A | psi-mi:“MI:0914”(association) | 0.530 |
| CRP | QSOX1 | psi-mi:“MI:0914”(association) | 0.530 |
| CSGALNACT2 | TPST1 | psi-mi:“MI:0914”(association) | 0.530 |
| BGLF3.5 | SEC16A | psi-mi:“MI:0914”(association) | 0.350 |
| SCGB2A2 | GXYLT2 | psi-mi:“MI:0914”(association) | 0.350 |
| DPEP2 | KDELR3 | psi-mi:“MI:0914”(association) | 0.350 |
| MYO9A | psi-mi:“MI:0914”(association) | 0.350 | |
| PLOD2 | psi-mi:“MI:0914”(association) | 0.350 | |
| POMK | ESYT2 | psi-mi:“MI:0914”(association) | 0.350 |
| ATG16L1 | psi-mi:“MI:0914”(association) | 0.350 | |
| PI15 | GLS | psi-mi:“MI:0914”(association) | 0.350 |
| TMEM106A | QSOX1 | 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 |
| MPPE1 | FAM234B | psi-mi:“MI:0914”(association) | 0.350 |
| LLCFC1 | POTEF | psi-mi:“MI:0914”(association) | 0.350 |
| CCL3 | KRBA1 | psi-mi:“MI:0914”(association) | 0.350 |
| SCGB2A2 | RTL8C | psi-mi:“MI:0914”(association) | 0.350 |
| GPIHBP1 | SAC3D1 | psi-mi:“MI:0914”(association) | 0.350 |
| DPEP2 | GET1 | psi-mi:“MI:0914”(association) | 0.350 |
| C1orf54 | AGRN | psi-mi:“MI:0914”(association) | 0.350 |
| TMEM25 | NME4 | psi-mi:“MI:0914”(association) | 0.350 |
| TMEM106A | TMEM131L | psi-mi:“MI:0914”(association) | 0.350 |
| BTNL2 | TMEM131L | psi-mi:“MI:0914”(association) | 0.350 |
| SFTPC | TMEM131L | psi-mi:“MI:0914”(association) | 0.350 |
BioGRID (94): CHPF2 (Affinity Capture-MS), CHPF2 (Affinity Capture-MS), CHPF2 (Affinity Capture-MS), CHPF2 (Affinity Capture-MS), CHPF2 (Affinity Capture-MS), CHPF2 (Affinity Capture-MS), CHPF2 (Affinity Capture-RNA), CHPF2 (Affinity Capture-MS), CHPF2 (Affinity Capture-MS), CHPF2 (Proximity Label-MS), CHPF2 (Affinity Capture-MS), CHPF2 (Affinity Capture-MS), CHPF2 (Affinity Capture-MS), CHPF2 (Affinity Capture-MS), CHPF2 (Affinity Capture-MS)
ESM2 similar proteins: A0A1D5PJB7, A1A4Q9, A5YM72, A6NLP5, D3KCC4, I3L5V6, O43292, P10938, Q00973, Q05B52, Q09200, Q10468, Q14623, Q148G5, Q16586, Q2V8X7, Q3SZV0, Q561R2, Q5E9M9, Q5M868, Q5ZL13, Q66H45, Q69ZF3, Q6P3D0, Q6P7A1, Q6P9Z4, Q6SZW1, Q6TEC1, Q6ZPS2, Q7TMC8, Q864R5, Q86TX2, Q8IXI1, Q8N0W3, Q8N3Y3, Q8N6R0, Q8NF37, Q8NI29, Q8TCD5, Q8VBW8
Diamond homologs: Q6IQX7, Q8IZ52, Q9P2E5
SIGNOR signaling
0 interactions.
Enriched among interaction partners
Reactome pathways and GO biological processes over-represented among this gene’s 130 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.
Reactome pathways:
| Pathway | Partners | Fold | FDR |
|---|---|---|---|
| Metal ion SLC transporters | 5 | 34.1× | 3e-05 |
| R-HSA-425366 | 6 | 12.4× | 7e-04 |
| SLC transporter disorders | 5 | 11.6× | 5e-03 |
| Metabolism of carbohydrates and carbohydrate derivatives | 6 | 8.2× | 5e-03 |
| SLC-mediated transmembrane transport | 11 | 7.4× | 3e-05 |
| Transport of small molecules | 12 | 3.4× | 9e-03 |
GO biological processes:
| GO term | Partners | Fold | FDR |
|---|---|---|---|
| intracellular monoatomic cation homeostasis | 5 | 51.1× | 1e-05 |
| zinc ion transmembrane transport | 6 | 38.3× | 4e-06 |
| intracellular zinc ion homeostasis | 6 | 26.3× | 2e-05 |
Disease & clinical
Clinical variants and AI predictions
ClinVar
157 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 142 |
| Likely benign | 7 |
| Benign | 1 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
1721 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 7:151236406:A:AG | acceptor_gain | 1.0000 |
| 7:151236406:AG:A | acceptor_gain | 1.0000 |
| 7:151236406:AGG:A | acceptor_gain | 1.0000 |
| 7:151236407:G:GG | acceptor_gain | 1.0000 |
| 7:151236407:GG:G | acceptor_gain | 1.0000 |
| 7:151236407:GGG:G | acceptor_gain | 1.0000 |
| 7:151236589:AG:A | donor_loss | 1.0000 |
| 7:151236590:GG:G | donor_loss | 1.0000 |
| 7:151236591:GTGA:G | donor_loss | 1.0000 |
| 7:151236592:T:A | donor_loss | 1.0000 |
| 7:151239391:CATA:C | donor_loss | 1.0000 |
| 7:151239392:ATAC:A | donor_loss | 1.0000 |
| 7:151239393:TA:T | donor_loss | 1.0000 |
| 7:151239394:A:C | donor_loss | 1.0000 |
| 7:151239395:C:CA | donor_loss | 1.0000 |
| 7:151239395:CCTTG:C | donor_gain | 1.0000 |
| 7:151239494:TCAC:T | acceptor_gain | 1.0000 |
| 7:151239495:CAC:C | acceptor_gain | 1.0000 |
| 7:151239495:CACC:C | acceptor_gain | 1.0000 |
| 7:151239498:C:CC | acceptor_gain | 1.0000 |
| 7:151239569:T:A | donor_gain | 1.0000 |
| 7:151239573:T:A | donor_gain | 1.0000 |
| 7:151239601:ACTC:A | donor_gain | 1.0000 |
| 7:151239602:CTCC:C | donor_gain | 1.0000 |
| 7:151239604:C:CA | donor_gain | 1.0000 |
| 7:151239605:C:A | donor_gain | 1.0000 |
| 7:151239614:C:CA | donor_gain | 1.0000 |
| 7:151239742:TGGAT:T | acceptor_gain | 1.0000 |
| 7:151239743:GGAT:G | acceptor_gain | 1.0000 |
| 7:151239744:GAT:G | acceptor_gain | 1.0000 |
AlphaMissense
4901 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 7:151234079:G:A | G23E | 0.999 |
| 7:151234084:A:C | S25R | 0.999 |
| 7:151234086:C:A | S25R | 0.999 |
| 7:151234086:C:G | S25R | 0.999 |
| 7:151235451:T:A | C223S | 0.999 |
| 7:151235452:G:A | C223Y | 0.999 |
| 7:151235452:G:C | C223S | 0.999 |
| 7:151235453:T:G | C223W | 0.999 |
| 7:151235596:G:A | C271Y | 0.999 |
| 7:151234066:G:A | G19R | 0.998 |
| 7:151234066:G:C | G19R | 0.998 |
| 7:151234067:G:A | G19E | 0.998 |
| 7:151234078:G:A | G23R | 0.998 |
| 7:151234078:G:C | G23R | 0.998 |
| 7:151234081:T:C | C24R | 0.998 |
| 7:151234090:A:C | S27R | 0.998 |
| 7:151234092:C:A | S27R | 0.998 |
| 7:151234092:C:G | S27R | 0.998 |
| 7:151235331:G:C | D183H | 0.998 |
| 7:151235406:G:C | G208R | 0.998 |
| 7:151235451:T:C | C223R | 0.998 |
| 7:151235595:T:A | C271S | 0.998 |
| 7:151235595:T:C | C271R | 0.998 |
| 7:151235596:G:C | C271S | 0.998 |
| 7:151235597:T:G | C271W | 0.998 |
| 7:151238181:T:C | C607R | 0.998 |
| 7:151238182:G:A | C607Y | 0.998 |
| 7:151238183:T:G | C607W | 0.998 |
| 7:151238397:T:G | Y679D | 0.998 |
| 7:151234274:G:T | R88M | 0.997 |
dbSNP variants (sampled 300 via entrez): RS1000065234 (7:151235909 G>A,C), RS1000870549 (7:151236756 A>G), RS1001138882 (7:151234454 A>G,T), RS1001575878 (7:151238408 C>T), RS1001618165 (7:151233226 G>A), RS1001686787 (7:151232949 C>T), RS1001785167 (7:151234565 C>G,T), RS1002177323 (7:151237541 C>G,T), RS1002468555 (7:151233033 T>G), RS1002654153 (7:151237354 G>A), RS1003248598 (7:151236013 G>A), RS1003574065 (7:151233500 C>G,T), RS1004450141 (7:151236719 C>G), RS1004655575 (7:151234757 C>T), RS1004741382 (7:151233346 C>T)
Disease associations
OMIM: gene MIM:608037 | disease phenotypes: MIM:261740
GenCC curated gene-disease
Mondo (1): lethal congenital glycogen storage disease of heart (MONDO:0009867)
Orphanet (1): Fatal congenital hypertrophic cardiomyopathy due to glycogen storage disease (Orphanet:439854)
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
2 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST003476_9 | Eyebrow thickness | 7.000000e-06 |
| GCST004483_3 | Multiple myeloma | 1.000000e-08 |
MeSH disease descriptors (1)
| Descriptor | Name | Tree numbers |
|---|---|---|
| C564888 | Glycogen Storage Disease of Heart, Lethal Congenital (supp.) |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
23 total (human), top 23 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| sodium arsenite | increases expression | 2 |
| Tobacco Smoke Pollution | increases expression | 2 |
| Valproic Acid | increases expression, increases methylation | 2 |
| aristolochic acid I | decreases expression | 1 |
| GSK-J4 | decreases expression | 1 |
| FR900359 | decreases phosphorylation | 1 |
| triphenyl phosphate | affects expression | 1 |
| tris(1,3-dichloro-2-propyl)phosphate | decreases expression | 1 |
| cobaltous chloride | increases expression | 1 |
| cupric chloride | increases expression | 1 |
| beta-methylcholine | affects expression | 1 |
| Temozolomide | decreases expression | 1 |
| Air Pollutants | affects expression, increases abundance | 1 |
| Atrazine | increases expression | 1 |
| Benzo(a)pyrene | increases methylation | 1 |
| Cadmium | increases expression | 1 |
| Doxorubicin | increases expression | 1 |
| Estradiol | increases expression, affects cotreatment | 1 |
| Ozone | affects expression, increases abundance | 1 |
| Smoke | decreases expression | 1 |
| Cyclosporine | increases expression | 1 |
| Okadaic Acid | increases expression | 1 |
| Acrylamide | 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): lethal congenital glycogen storage disease of heart, plasma cell myeloma