B4GALNT4
gene geneOn this page
Also known as FLJ25045NGalNAc-T1
Summary
B4GALNT4 (beta-1,4-N-acetyl-galactosaminyltransferase 4, HGNC:26315) is a protein-coding gene on chromosome 11p15.5, encoding N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase 1 (Q76KP1). Transfers N-acetylgalactosamine (GalNAc) from UDP-GalNAc to N-acetylglucosamine-beta-benzyl with a beta-1,4-linkage to form N,N’-diacetyllactosediamine, GalNAc-beta-1,4-GlcNAc structures in N-linked glycans and probably O-linked glycans.
Enables acetylgalactosaminyltransferase activity. Predicted to be located in Golgi cisterna membrane.
Source: NCBI Gene 338707 — RefSeq curated summary.
At a glance
- GWAS associations: 1
- Clinical variants (ClinVar): 239 total
- MANE Select transcript:
NM_178537
Identifiers
Gene identifiers
| Field | Value |
|---|---|
| HGNC ID | HGNC:26315 |
| Approved symbol | B4GALNT4 |
| Name | beta-1,4-N-acetyl-galactosaminyltransferase 4 |
| Location | 11p15.5 |
| Locus type | gene with protein product |
| Status | Approved |
| Aliases | FLJ25045, NGalNAc-T1 |
| Ensembl gene | ENSG00000182272 |
| Ensembl biotype | protein_coding |
| OMIM | 618560 |
| Entrez | 338707 |
Gene structure
Transcript identifiers
Ensembl transcripts: 9 — 5 protein_coding, 2 retained_intron, 2 nonsense_mediated_decay
ENST00000329962, ENST00000524443, ENST00000526584, ENST00000530717, ENST00000534778, ENST00000940110, ENST00000940111, ENST00000940112, ENST00000958308
RefSeq mRNA: 1 — MANE Select: NM_178537
NM_178537
CCDS: CCDS7694
Canonical transcript exons
ENST00000329962 — 20 exons
| Exon | Start | End |
|---|---|---|
| ENSE00001300327 | 380130 | 380202 |
| ENSE00001308961 | 379418 | 379701 |
| ENSE00001309479 | 379866 | 380019 |
| ENSE00001330059 | 376421 | 377327 |
| ENSE00001363959 | 373750 | 373828 |
| ENSE00001365167 | 369499 | 369954 |
| ENSE00001365279 | 373026 | 373116 |
| ENSE00001365695 | 375847 | 375956 |
| ENSE00001365894 | 376251 | 376351 |
| ENSE00001370533 | 375639 | 375773 |
| ENSE00001372415 | 373449 | 373516 |
| ENSE00001375220 | 372852 | 372947 |
| ENSE00001380062 | 372662 | 372754 |
| ENSE00001382984 | 376074 | 376174 |
| ENSE00001386501 | 373191 | 373291 |
| ENSE00002169286 | 381669 | 382117 |
| ENSE00003541639 | 372109 | 372212 |
| ENSE00003561511 | 375461 | 375527 |
| ENSE00003634938 | 380292 | 380445 |
| ENSE00003693205 | 380825 | 380951 |
Expression profiles
Bgee: expression breadth ubiquitous, 158 present calls, max score 98.47.
FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.7768 / max 178.9838, expressed in 1055 samples.
FANTOM5 promoters (2 alternative TSS)
| Promoter ID | TPM avg | Samples expressed |
|---|---|---|
| 112188 | 8.6796 | 1053 |
| 112187 | 0.0971 | 42 |
Top tissues by expression
245 total, by Bgee expression score (0-100, higher = more expressed):
| Tissue | Anatomy ID | Expression score | Quality |
|---|---|---|---|
| right hemisphere of cerebellum | UBERON:0014890 | 98.47 | gold quality |
| right frontal lobe | UBERON:0002810 | 98.04 | gold quality |
| cerebellar hemisphere | UBERON:0002245 | 98.01 | gold quality |
| cortical plate | UBERON:0005343 | 97.85 | gold quality |
| cerebellar cortex | UBERON:0002129 | 97.71 | gold quality |
| ganglionic eminence | UBERON:0004023 | 97.57 | gold quality |
| Brodmann (1909) area 9 | UBERON:0013540 | 97.45 | gold quality |
| anterior cingulate cortex | UBERON:0009835 | 96.92 | gold quality |
| ventricular zone | UBERON:0003053 | 96.12 | gold quality |
| C1 segment of cervical spinal cord | UBERON:0006469 | 95.30 | gold quality |
| male germ line stem cell (sensu Vertebrata) in testis | CL:0000089 ∩ UBERON:0000473 | 94.75 | silver quality |
| cerebellum | UBERON:0002037 | 94.54 | gold quality |
| amygdala | UBERON:0001876 | 93.99 | gold quality |
| hypothalamus | UBERON:0001898 | 93.98 | gold quality |
| sural nerve | UBERON:0015488 | 93.94 | gold quality |
| left ovary | UBERON:0002119 | 93.60 | gold quality |
| prefrontal cortex | UBERON:0000451 | 93.47 | gold quality |
| caudate nucleus | UBERON:0001873 | 92.90 | gold quality |
| nucleus accumbens | UBERON:0001882 | 92.89 | gold quality |
| putamen | UBERON:0001874 | 92.74 | gold quality |
| tibial nerve | UBERON:0001323 | 92.42 | gold quality |
| right ovary | UBERON:0002118 | 92.14 | gold quality |
| dorsolateral prefrontal cortex | UBERON:0009834 | 91.42 | gold quality |
| spinal cord | UBERON:0002240 | 90.34 | gold quality |
| adenohypophysis | UBERON:0002196 | 90.09 | gold quality |
| neocortex | UBERON:0001950 | 89.50 | gold quality |
| lower esophagus mucosa | UBERON:0035834 | 89.08 | gold quality |
| frontal cortex | UBERON:0001870 | 88.45 | gold quality |
| left uterine tube | UBERON:0001303 | 88.16 | gold quality |
| endocervix | UBERON:0000458 | 87.61 | gold quality |
Single-cell (SCXA)
Detected in 3 experiment(s), a significant marker in 1.
| Experiment | Marker? | Max mean expression |
|---|---|---|
| E-MTAB-9154 | yes | 478.27 |
| E-GEOD-36552 | no | 86.94 |
| E-ANND-3 | no | 3.37 |
Regulation
Is transcription factor: no
miRNA regulators (miRDB)
22 targeting B4GALNT4, 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-513A-5P | 100.00 | 69.77 | 2465 |
| HSA-MIR-4481 | 100.00 | 66.42 | 1669 |
| HSA-MIR-5696 | 99.98 | 72.36 | 4487 |
| 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-570-3P | 99.96 | 72.41 | 4910 |
| HSA-MIR-1468-3P | 99.96 | 72.74 | 3797 |
| HSA-MIR-545-3P | 99.95 | 70.74 | 2783 |
| HSA-MIR-205-3P | 99.92 | 69.92 | 3165 |
| HSA-MIR-579-3P | 99.86 | 71.66 | 3628 |
| HSA-MIR-664B-3P | 99.84 | 71.65 | 3590 |
| HSA-MIR-4766-5P | 99.75 | 69.23 | 2662 |
| HSA-MIR-3120-3P | 99.54 | 70.28 | 2669 |
| HSA-MIR-513A-3P | 99.39 | 70.63 | 3620 |
| HSA-MIR-513C-3P | 99.39 | 70.63 | 3620 |
| HSA-MIR-4427 | 99.34 | 70.33 | 1854 |
| HSA-MIR-3606-3P | 99.11 | 69.84 | 3254 |
| HSA-MIR-3144-5P | 97.64 | 65.45 | 646 |
| HSA-MIR-4640-5P | 97.42 | 66.33 | 1543 |
| HSA-MIR-4726-5P | 97.24 | 65.67 | 1299 |
| HSA-MIR-1298-5P | 95.96 | 64.81 | 573 |
Literature-anchored findings (GeneRIF, showing 6)
- molecular cloning and characterization; specificity toward oligosaccharide acceptor substrates was quite similar to beta4GalNAc-T3 in vitro but the tissue distributions of the two enzymes were quite different (PMID:15044014)
- betaGT3 and betaGT4, that are able to transfer GalNAc to GlcNAc in beta1,4-linkage display the necessary glycoprotein specificity in vivo. (PMID:18048353)
- Molecular basis for protein-specific transfer of N-acetylgalactosamine to N-linked glycans by the glycosyltransferases beta1,4-N-acetylgalactosaminyl transferase 3 (beta4GalNAc-T3) and beta4GalNAc-T4. (PMID:22722937)
- Peptide-specific transfer of N-acetylgalactosamine to O-linked glycans by the glycosyltransferases beta1,4-N-acetylgalactosaminyl transferase 3 (beta4GalNAc-T3) and beta4GalNAc-T4. (PMID:22722940)
- These results indicate that the expression of the LacdiNAc group is quite important for the suppression of malignancies of the MDA-MB-231 cells. (PMID:25858323)
- Expression and Malignant Potential of B4GALNT4 in Esophageal Squamous Cell Carcinoma. (PMID:32253672)
Cross-species orthologs
4 orthologs
| Organism | Symbol | Gene ID |
|---|---|---|
| danio_rerio | b4galnt4a | ENSDARG00000046150 |
| danio_rerio | b4galnt4b | ENSDARG00000076701 |
| mus_musculus | B4galnt4 | ENSMUSG00000055629 |
| rattus_norvegicus | B4galnt4 | ENSRNOG00000053075 |
Paralogs (7): CHPF2 (ENSG00000033100), CHPF (ENSG00000123989), CHSY1 (ENSG00000131873), B4GALNT3 (ENSG00000139044), CSGALNACT1 (ENSG00000147408), CSGALNACT2 (ENSG00000169826), CHSY3 (ENSG00000198108)
Protein
Protein identifiers
N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase 1 — Q76KP1 (reviewed: Q76KP1)
Alternative names: Beta-1,4-N-acetylgalactosaminyltransferase IV
All UniProt accessions (3): Q76KP1, H0YCU7, H0YDW6
UniProt curated annotations — full annotation on UniProt →
Function. Transfers N-acetylgalactosamine (GalNAc) from UDP-GalNAc to N-acetylglucosamine-beta-benzyl with a beta-1,4-linkage to form N,N’-diacetyllactosediamine, GalNAc-beta-1,4-GlcNAc structures in N-linked glycans and probably O-linked glycans.
Subcellular location. Golgi apparatus. Golgi stack membrane.
Tissue specificity. Highly expressed in ovary, adult and fetal brain. Also expressed in fetal kidney and lung.
Similarity. Belongs to the chondroitin N-acetylgalactosaminyltransferase family.
RefSeq proteins (1): NP_848632* (*=MANE)
Domains & families (InterPro)
| ID | Name | Type |
|---|---|---|
| IPR008428 | Chond_GalNAc | Family |
| IPR011658 | PA14_dom | Domain |
| IPR029044 | Nucleotide-diphossugar_trans | Homologous_superfamily |
| IPR037524 | PA14/GLEYA | Domain |
| IPR051227 | CS_glycosyltransferase | Family |
Pfam: PF05679
Enzyme classification (BRENDA):
- EC 2.4.1.244 — N-acetyl-beta-glucosaminyl-glycoprotein 4-beta-N-acetylgalactosaminyltransferase (BRENDA: 3 organisms, 33 substrates, 1 inhibitors, 0 Km, 0 kcat entries)
- EC 2.4.1.92 — (N-acetylneuraminyl)-galactosylglucosylceramide N-acetylgalactosaminyltransferase (BRENDA: 8 organisms, 60 substrates, 14 inhibitors, 20 Km, 0 kcat entries)
Substrate kinetics (BRENDA)
11 substrates with measured Km, best-characterized 11. Km ranges are aggregated across organisms/conditions.
| Substrate | Km (mM) | Measurements |
|---|---|---|
| UDP-N-ACETYL-D-GALACTOSAMINE | 0.007–0.082 | 6 |
| GM3 | 0.0166–0.19 | 3 |
| UDP-GALNAC | 0.097–0.19 | 2 |
| GANGLIOSIDE GD3 | 0.152 | 1 |
| GANGLIOSIDE GM3 | 0.385 | 1 |
| GD3(N-ACETYLNEURAMINIC ACID) | 0.35 | 1 |
| GD3(N-GLYCOLYLNEURAMINIC ACID)-GANGLIOSIDE | 0.027 | 1 |
| GM3(N-ACETYLNEURAMINIC ACID) | 2.1 | 1 |
| GM3(N-GLYCOLYLNEURAMINIC ACID) | 0.16 | 1 |
| P-NITROPHENYL-GLCNAC | 0.38 | 1 |
| UDP-N-ACETYLGALACTOSAMINE | 1.64 | 1 |
Catalyzed reactions (Rhea), 1 shown:
- an N-acetyl-beta-D-glucosaminyl derivative + UDP-N-acetyl-alpha-D-galactosamine = an N-acetyl-beta-D-galactosaminyl-(1->4)-N-acetyl-beta-D-glucosaminyl derivative + UDP + H(+) (RHEA:20493)
UniProt features (20 total): compositionally biased region 6, region of interest 5, topological domain 2, sequence variant 2, chain 1, glycosylation site 1, sequence conflict 1, transmembrane region 1, domain 1
Structure
Experimental structures (PDB)
0 structures.
Predicted structure (AlphaFold)
| Model | pLDDT | Fraction very-high |
|---|---|---|
| AF-Q76KP1-F1 | 70.89 | 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.
Glycosylation sites (1): 105
Function
Pathways and Gene Ontology
Reactome pathways
0 pathways
MSigDB gene sets: 84 (showing top):
GAUSSMANN_MLL_AF4_FUSION_TARGETS_A_DN, GOCC_GOLGI_STACK, GOCC_GOLGI_CISTERNA, GOCC_GOLGI_CISTERNA_MEMBRANE, GOCC_ORGANELLE_SUBCOMPARTMENT, GOMF_ACETYLGALACTOSAMINYLTRANSFERASE_ACTIVITY, GOMF_HEXOSYLTRANSFERASE_ACTIVITY, GOMF_GLYCOSYLTRANSFERASE_ACTIVITY, GOMF_UDP_GLYCOSYLTRANSFERASE_ACTIVITY, LI_INDUCED_T_TO_NATURAL_KILLER_UP, MARTENS_TRETINOIN_RESPONSE_UP, CHYLA_CBFA2T3_TARGETS_UP, WANG_MLL_TARGETS, KRIEG_HYPOXIA_NOT_VIA_KDM3A, GSE13522_WT_VS_IFNAR_KO_SKIN_DN
GO Biological Process (0):
GO Molecular Function (3): acetylgalactosaminyltransferase activity (GO:0008376), N-acetyl-beta-glucosaminyl-derivative 4-beta-N-acetylgalactosaminyltransferase activity (GO:0033842), transferase activity (GO:0016740)
GO Cellular Component (3): Golgi cisterna membrane (GO:0032580), Golgi apparatus (GO:0005794), membrane (GO:0016020)
GO top-level categories
Rollup of top GO terms by namespace:
| Category | Terms |
|---|---|
| UDP-glycosyltransferase activity | 1 |
| hexosyltransferase activity | 1 |
| acetylgalactosaminyltransferase activity | 1 |
| catalytic activity | 1 |
| organelle membrane | 1 |
| Golgi cisterna | 1 |
| cytoplasm | 1 |
| endomembrane system | 1 |
| intracellular membrane-bounded organelle | 1 |
| cellular anatomical structure | 1 |
Protein interactions and networks
STRING
600 interactions, top by confidence (×1000):
| Protein A | Protein B | Partner UniProt | Score |
|---|---|---|---|
| B4GALNT4 | PGGHG | Q32M88 | 705 |
| B4GALNT4 | TTF2 | Q9UNY4 | 389 |
| B4GALNT4 | TMEM178B | H3BS89 | 384 |
| B4GALNT4 | TMEM254 | Q8TBM7 | 377 |
| B4GALNT4 | ZNF614 | Q8N883 | 357 |
| B4GALNT4 | IFITM3 | Q01628 | 348 |
| B4GALNT4 | IFITM2 | Q01629 | 348 |
| B4GALNT4 | ST6GAL2 | Q96JF0 | 326 |
| B4GALNT4 | B4GALNT1 | Q00973 | 324 |
| B4GALNT4 | PATE2 | Q6UY27 | 323 |
| B4GALNT4 | CCDC9 | Q9Y3X0 | 322 |
| B4GALNT4 | ST3GAL5 | Q9UNP4 | 320 |
| B4GALNT4 | B3GALT4 | O96024 | 319 |
| B4GALNT4 | GALNT18 | Q6P9A2 | 318 |
| B4GALNT4 | YPEL4 | Q96NS1 | 312 |
IntAct
11 interactions, top by confidence:
| A | B | Type | Score |
|---|---|---|---|
| ANTXR1 | POTEF | psi-mi:“MI:0914”(association) | 0.530 |
| HTRA1 | B4GALNT4 | psi-mi:“MI:0915”(physical association) | 0.370 |
| INSL5 | LAMA5 | psi-mi:“MI:0914”(association) | 0.350 |
| LYZL2 | MANBA | psi-mi:“MI:0914”(association) | 0.350 |
| PILRA | PODXL | psi-mi:“MI:0914”(association) | 0.350 |
| CSN1S1 | HSPA5 | psi-mi:“MI:0914”(association) | 0.350 |
| CLEC12B | GXYLT2 | psi-mi:“MI:0914”(association) | 0.350 |
| C1orf54 | AGRN | psi-mi:“MI:0914”(association) | 0.350 |
| PILRA | NID2 | psi-mi:“MI:0914”(association) | 0.350 |
| DISC1 | B4GALNT4 | psi-mi:“MI:0915”(physical association) | 0.000 |
BioGRID (10): B4GALNT4 (Affinity Capture-MS), B4GALNT4 (Affinity Capture-MS), B4GALNT4 (Affinity Capture-MS), B4GALNT4 (Affinity Capture-MS), B4GALNT4 (Affinity Capture-MS), B4GALNT4 (Affinity Capture-MS), B4GALNT4 (Affinity Capture-MS), B4GALNT4 (Affinity Capture-MS), B4GALNT4 (Affinity Capture-MS), B4GALNT4 (Affinity Capture-RNA)
ESM2 similar proteins: A0JPN4, A1YF56, A2A288, A2A9T0, A2AEV7, A6QQJ8, A7MCY6, A8MVW0, D3ZG83, D3ZZN9, O09039, O15037, O75427, O94983, O95382, O95947, P0C5W1, P98077, Q02779, Q16584, Q2M3V2, Q53LP3, Q5D1E7, Q5D1E8, Q66HA1, Q66K74, Q66L42, Q6DG50, Q6ZUM4, Q6ZW31, Q76KP1, Q7T0L4, Q7TSG2, Q80XI6, Q80Y50, Q8BIY3, Q8BLS7, Q8K120, Q8K1S6, Q8R5G7
Diamond homologs: Q6L8S8, Q6L9W6, Q766D5, Q76KP1, Q0VC84, Q5DTK1, Q6ZQ11, Q70JA7, Q7Z1Z1, Q86X52, Q8BJQ9, Q8C1F4, Q8N6G5, Q8TDX6, Q9JJ05, Q9JJ06, Q9NS00
SIGNOR signaling
0 interactions.
Disease & clinical
Clinical variants and AI predictions
ClinVar
239 variants total. Per-class counts are floors (≥ shown; pagination cap):
| Classification | Count (floor) |
|---|---|
| Pathogenic | 0 |
| Likely pathogenic | 0 |
| Uncertain significance | 195 |
| Likely benign | 13 |
| Benign | 4 |
Top pathogenic / likely-pathogenic (0)
SpliceAI
3093 predictions. Top by Δscore:
| Variant | Effect | Δscore |
|---|---|---|
| 11:369950:GCGAG:G | donor_gain | 1.0000 |
| 11:369952:GAG:G | donor_gain | 1.0000 |
| 11:369954:GGTA:G | donor_loss | 1.0000 |
| 11:369955:G:C | donor_loss | 1.0000 |
| 11:369955:G:GG | donor_gain | 1.0000 |
| 11:369956:T:A | donor_loss | 1.0000 |
| 11:372656:CTGCA:C | acceptor_gain | 1.0000 |
| 11:372657:T:TA | acceptor_gain | 1.0000 |
| 11:372657:TGCA:T | acceptor_gain | 1.0000 |
| 11:372658:GCAGC:G | acceptor_gain | 1.0000 |
| 11:372659:CAGCC:C | acceptor_gain | 1.0000 |
| 11:372660:A:AG | acceptor_gain | 1.0000 |
| 11:372660:AGCC:A | acceptor_gain | 1.0000 |
| 11:372660:AGCCC:A | acceptor_gain | 1.0000 |
| 11:372661:G:A | acceptor_gain | 1.0000 |
| 11:372661:G:GT | acceptor_gain | 1.0000 |
| 11:372661:GC:G | acceptor_gain | 1.0000 |
| 11:372661:GCC:G | acceptor_gain | 1.0000 |
| 11:372661:GCCC:G | acceptor_gain | 1.0000 |
| 11:372661:GCCCG:G | acceptor_gain | 1.0000 |
| 11:372751:GGAG:G | donor_gain | 1.0000 |
| 11:372752:G:GT | donor_gain | 1.0000 |
| 11:372752:GAGG:G | donor_loss | 1.0000 |
| 11:372755:G:GA | donor_loss | 1.0000 |
| 11:372756:T:G | donor_loss | 1.0000 |
| 11:373025:GACGC:G | acceptor_gain | 1.0000 |
| 11:373113:G:T | donor_gain | 1.0000 |
| 11:373820:G:GT | donor_gain | 1.0000 |
| 11:373825:GGGC:G | donor_gain | 1.0000 |
| 11:373826:GGCG:G | donor_gain | 1.0000 |
AlphaMissense
6705 scored. Top likely-pathogenic:
| Variant | Protein change | am_pathogenicity |
|---|---|---|
| 11:373463:G:C | W217C | 0.999 |
| 11:373463:G:T | W217C | 0.999 |
| 11:376140:T:A | C388S | 0.999 |
| 11:376140:T:C | C388R | 0.999 |
| 11:376141:G:C | C388S | 0.999 |
| 11:376142:C:G | C388W | 0.999 |
| 11:377169:G:C | W682C | 0.999 |
| 11:377169:G:T | W682C | 0.999 |
| 11:377236:T:C | C705R | 0.999 |
| 11:377238:C:G | C705W | 0.999 |
| 11:377248:G:T | G709W | 0.999 |
| 11:377253:C:A | N710K | 0.999 |
| 11:377253:C:G | N710K | 0.999 |
| 11:380845:T:C | F964L | 0.999 |
| 11:380847:T:A | F964L | 0.999 |
| 11:380847:T:G | F964L | 0.999 |
| 11:380908:T:C | F985L | 0.999 |
| 11:380909:T:C | F985S | 0.999 |
| 11:380909:T:G | F985C | 0.999 |
| 11:380910:C:A | F985L | 0.999 |
| 11:380910:C:G | F985L | 0.999 |
| 11:380920:T:A | W989R | 0.999 |
| 11:380920:T:C | W989R | 0.999 |
| 11:380922:G:C | W989C | 0.999 |
| 11:380922:G:T | W989C | 0.999 |
| 11:380933:A:T | D993V | 0.999 |
| 11:380935:T:A | W994R | 0.999 |
| 11:380935:T:C | W994R | 0.999 |
| 11:380937:G:C | W994C | 0.999 |
| 11:380937:G:T | W994C | 0.999 |
dbSNP variants (sampled 300 via entrez): RS1000273459 (11:376375 C>T), RS1000429010 (11:380122 C>G,T), RS1000436225 (11:371929 G>A,C,T), RS1000819402 (11:381836 C>G), RS1000891739 (11:372214 T>A), RS1001273630 (11:371586 C>T), RS1001483034 (11:379193 GC>G), RS1001513325 (11:369755 G>A,C,T), RS1001593078 (11:374496 CAG>C), RS1001755377 (11:369978 G>A,C,T), RS1001984944 (11:381283 A>G), RS1002371336 (11:378365 C>T), RS1002516120 (11:368381 G>A), RS1003139767 (11:374433 T>A), RS1003401989 (11:375264 C>T)
Disease associations
OMIM: gene MIM:618560 | disease phenotypes:
GenCC curated gene-disease
Mondo (1): developmental and epileptic encephalopathy (MONDO:0100620)
Orphanet (0):
HPO phenotypes
0 total (0 of 0 shown, HPO-id order):
GWAS associations
1 associations (top):
| Study | Trait | p-value |
|---|---|---|
| GCST010244_208 | Triglyceride levels | 1.000000e-08 |
EFO canonical traits (1, from GWAS)
| EFO ID | Trait name |
|---|---|
| EFO:0004530 | triglyceride measurement |
Drugs & pharmacology
Drug and pharmacology data
Is drug target: no
PharmGKB: 1 entry (VIP=true, CPIC=false)
CTD chemical–gene interactions
28 total (human), top 28 by PubMed support.
| Chemical | Actions (top 5) | PubMed papers |
|---|---|---|
| Air Pollutants | decreases expression, increases expression, affects methylation, increases abundance | 3 |
| Valproic Acid | increases methylation | 3 |
| Particulate Matter | increases expression, decreases expression, increases abundance | 2 |
| dicrotophos | decreases expression | 1 |
| bisphenol A | decreases methylation | 1 |
| kojic acid | decreases expression | 1 |
| sodium arsenite | decreases expression | 1 |
| benzo(e)pyrene | increases methylation | 1 |
| maleic acid | decreases expression | 1 |
| CGP 52608 | affects binding, increases reaction | 1 |
| 2-palmitoylglycerol | increases expression | 1 |
| abrine | decreases expression | 1 |
| Resveratrol | affects cotreatment, decreases expression | 1 |
| Sunitinib | decreases expression | 1 |
| Arbutin | decreases expression | 1 |
| Arsenic | affects methylation | 1 |
| Benzo(a)pyrene | affects methylation, increases methylation | 1 |
| Cadmium | increases expression | 1 |
| Cisplatin | decreases expression | 1 |
| Methapyrilene | increases methylation | 1 |
| Ozone | increases abundance, affects methylation | 1 |
| Plant Extracts | affects cotreatment, decreases expression | 1 |
| Smoke | decreases expression | 1 |
| Tobacco Smoke Pollution | decreases expression | 1 |
| Triclosan | increases expression | 1 |
| Urethane | decreases expression | 1 |
| Cadmium Chloride | increases expression | 1 |
| Okadaic Acid | increases expression | 1 |
Cellosaurus cell lines
2 cell lines: 2 cancer cell line
First 10 cell lines (id-ordered, not curated):
| Cellosaurus | Name | Category | Sex |
|---|---|---|---|
| CVCL_SE52 | HAP1 B4GALNT4 (-) 1 | Cancer cell line | Male |
| CVCL_SE53 | HAP1 B4GALNT4 (-) 2 | Cancer cell line | Male |
Clinical trials (associated diseases)
22 trials via MONDO — disease-level, not drug-specific.
| Trial | Phase | Status | Title |
|---|---|---|---|
| NCT03347526 | PHASE3 | SUSPENDED | A Novel Approach to Infantile Spasms |
| NCT03421496 | PHASE3 | TERMINATED | A Study to Assess Cannabidiol Oral Solution With Vigabatrin as Initial Therapy in Participants With Infantile Spasms |
| NCT06719141 | PHASE3 | RECRUITING | A Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathies (DEE) |
| NCT06908226 | PHASE3 | ENROLLING_BY_INVITATION | A Study to Investigate LP352 in Children and Adults With Developmental and Epileptic Encephalopathy (DEE) |
| NCT04289467 | PHASE2 | RECRUITING | Treatment of Refractory Infantile Spasms With Fenfluramine |
| NCT05626634 | PHASE2 | COMPLETED | Open-label, Long-term Safety Study of LP352 in Subjects With Developmental and Epileptic Encephalopathy |
| NCT04727970 | PHASE1 | COMPLETED | Tricaprilin Infantile Spasms Pilot Study |
| NCT06700811 | PHASE1 | RECRUITING | Ketogenic Diet for Prevention of Epileptic Spasms in Infantile Onset Genetic Epilepsies |
| NCT03876444 | PHASE2/PHASE3 | UNKNOWN | Intravenous Methylprednisolone Versus Oral Prednisolone for Infantile Spasms |
| NCT05279118 | PHASE2/PHASE3 | ACTIVE_NOT_RECRUITING | Ketogenic Diet vs ACTH for the Treatment of Children With West Syndrome |
| NCT05364021 | PHASE1/PHASE2 | COMPLETED | Study to Investigate LP352 in Subjects With Developmental and Epileptic Encephalopathies |
| NCT06983158 | PHASE1/PHASE2 | SUSPENDED | A Clinical Trial of CAP-002 Gene Therapy in Pediatric Patients With Syntaxin-Binding Protein 1 (STXBP1) Encephalopathy |
| NCT04937062 | EARLY_PHASE1 | ACTIVE_NOT_RECRUITING | Phenylbutyrate for Monogenetic Developmental and Epileptic Encephalopathy |
| NCT04302116 | Not specified | RECRUITING | Vigabatrin With High Dose Prednisolone Combination Therapy vs Vigabatrin Alone for Infantile Spasm |
| NCT05538936 | Not specified | COMPLETED | The Effect of Spa and Massage on Babies on Colic Symptoms |
| NCT06149663 | Not specified | AVAILABLE | Intermediate-Size Expanded Access Protocol (EAP) for LP352 |
| NCT06266234 | Not specified | RECRUITING | Characterization by Automated System on Infantile Spasmes |
| NCT06380192 | Not specified | RECRUITING | Developmental and Epileptic Encephalopathy of Genetic Etiology: Natural History Through Reuse of Clinical Data |
| NCT07396883 | Not specified | NOT_YET_RECRUITING | Developmental and Epileptic Encephalopathies Diagnosed Via Long-read Genome Sequencing |
| NCT07413211 | Not specified | RECRUITING | Genetic Developmental and Epileptic Encephalopathy Natural History Study for Clinical Trial Readiness |
| NCT07531511 | Not specified | NOT_YET_RECRUITING | SLC6A1-NDD Prospective Longitudinal Natural History Study |
| NCT07585643 | Not specified | NOT_YET_RECRUITING | IBIS - Investigating Reliability of BIS and SEDLINE Monitoring in Children With Developmental and Epileptic Encephalopathies (DEE). |
Related Atlas pages
- Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): developmental and epileptic encephalopathy