DPAGT1

gene
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Also known as GPTD11S366DGPTALG7CDG-Ij

Summary

DPAGT1 (dolichyl-phosphate N-acetylglucosaminephosphotransferase 1, HGNC:2995) is a protein-coding gene on chromosome 11q23.3, encoding UDP-N-acetylglucosamine–dolichyl-phosphate N-acetylglucosaminephosphotransferase (Q9H3H5). UDP-N-acetylglucosamine–dolichyl-phosphate N-acetylglucosaminephosphotransferase that operates in the biosynthetic pathway of dolichol-linked oligosaccharides, the glycan precursors employed in protein asparagine (N)-glycosylation. It is a common-essential gene (DepMap: required in 98.3% of cancer cell lines).

The protein encoded by this gene is an enzyme that catalyzes the first step in the dolichol-linked oligosaccharide pathway for glycoprotein biosynthesis. This enzyme belongs to the glycosyltransferase family 4. This protein is an integral membrane protein of the endoplasmic reticulum. The congenital disorder of glycosylation type Ij is caused by mutation in the gene encoding this enzyme.

Source: NCBI Gene 1798 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): DPAGT1-congenital disorder of glycosylation (Definitive, ClinGen) — +2 more curated relationships
  • GWAS associations: 4
  • Clinical variants (ClinVar): 344 total — 13 pathogenic, 20 likely-pathogenic
  • Phenotypes (HPO): 123
  • Druggable target: yes
  • Cancer dependency (DepMap): dependent in 98.3% of screened cell lines (common-essential)
  • Dosage sensitivity (ClinGen): haploinsufficiency autosomal recessive, triplosensitivity no evidence
  • MANE Select transcript: NM_001382

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2995
Approved symbolDPAGT1
Namedolichyl-phosphate N-acetylglucosaminephosphotransferase 1
Location11q23.3
Locus typegene with protein product
StatusApproved
AliasesGPT, D11S366, DGPT, ALG7, CDG-Ij
Ensembl geneENSG00000172269
Ensembl biotypeprotein_coding
OMIM191350
Entrez1798

Gene structure

Transcript identifiers

Ensembl transcripts: 52 — 23 retained_intron, 16 nonsense_mediated_decay, 13 protein_coding

ENST00000354202, ENST00000392834, ENST00000409993, ENST00000414373, ENST00000442480, ENST00000445653, ENST00000460183, ENST00000461999, ENST00000472016, ENST00000481084, ENST00000524658, ENST00000525456, ENST00000530052, ENST00000533687, ENST00000636404, ENST00000638850, ENST00000639704, ENST00000640102, ENST00000640747, ENST00000682191, ENST00000682192, ENST00000682232, ENST00000682326, ENST00000682404, ENST00000682517, ENST00000682652, ENST00000682665, ENST00000682691, ENST00000682791, ENST00000682811, ENST00000682883, ENST00000682946, ENST00000683143, ENST00000683373, ENST00000683558, ENST00000683567, ENST00000683955, ENST00000684142, ENST00000684252, ENST00000684255, ENST00000684315, ENST00000684345, ENST00000684499, ENST00000684682, ENST00000867497, ENST00000867498, ENST00000938549, ENST00000938550, ENST00000938551, ENST00000945326, ENST00000945327, ENST00000945328

RefSeq mRNA: 1 — MANE Select: NM_001382 NM_001382

CCDS: CCDS8411

Canonical transcript exons

ENST00000354202 — 9 exons

ExonStartEnd
ENSE00001260143119101018119101138
ENSE00001581587119096510119097063
ENSE00002155852119101495119101853
ENSE00003529452119097855119098043
ENSE00003552320119100262119100408
ENSE00003596267119097142119097297
ENSE00003620217119100630119100843
ENSE00003639998119098403119098487
ENSE00003682245119097464119097551

Expression profiles

Bgee: expression breadth ubiquitous, 271 present calls, max score 95.53.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 34.9320 / max 222.3272, expressed in 1808 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
12269324.49021798
1226949.04131760
1226910.7388436
1226920.2993119
1226900.200270
1226890.162258

Top tissues by expression

294 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
mucosa of transverse colonUBERON:000499195.53gold quality
body of pancreasUBERON:000115095.50gold quality
right adrenal glandUBERON:000123393.97gold quality
right adrenal gland cortexUBERON:003582793.80gold quality
stromal cell of endometriumCL:000225593.73gold quality
left adrenal glandUBERON:000123493.30gold quality
left adrenal gland cortexUBERON:003582593.22gold quality
right lobe of liverUBERON:000111492.71gold quality
pancreasUBERON:000126492.69gold quality
right uterine tubeUBERON:000130292.68gold quality
adrenal cortexUBERON:000123592.52gold quality
lower esophagus mucosaUBERON:003583492.17gold quality
rectumUBERON:000105292.15gold quality
body of stomachUBERON:000116192.02gold quality
adrenal glandUBERON:000236991.64gold quality
transverse colonUBERON:000115791.52gold quality
small intestine Peyer’s patchUBERON:000345491.49gold quality
endocervixUBERON:000045891.44gold quality
right lobe of thyroid glandUBERON:000111991.40gold quality
islet of LangerhansUBERON:000000691.33gold quality
esophagus mucosaUBERON:000246991.31gold quality
metanephros cortexUBERON:001053391.27gold quality
minor salivary glandUBERON:000183091.26gold quality
saliva-secreting glandUBERON:000104491.16gold quality
granulocyteCL:000009490.96gold quality
body of uterusUBERON:000985390.85gold quality
esophagusUBERON:000104390.79gold quality
adenohypophysisUBERON:000219690.72gold quality
omental fat padUBERON:001041490.53gold quality
peritoneumUBERON:000235890.52gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes11.59
E-MTAB-4850no462.62
E-MTAB-6379no461.11

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): NR3C1, STAT5A, STAT5B

miRNA regulators (miRDB)

33 targeting DPAGT1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4668-3P100.0068.742635
HSA-MIR-589-3P99.9169.622088
HSA-MIR-806399.9169.763146
HSA-MIR-76599.8468.242442
HSA-MIR-808099.8267.521342
HSA-MIR-11181-3P99.7566.382205
HSA-MIR-199A-3P99.7570.48929
HSA-MIR-199B-3P99.7570.48929
HSA-MIR-3129-5P99.7570.46914
HSA-MIR-430699.7270.503630
HSA-MIR-466399.6265.33957
HSA-MIR-516B-5P99.5666.331495
HSA-MIR-185-5P99.3568.602497
HSA-MIR-464499.3569.122514
HSA-MIR-2115-3P99.3169.682026
HSA-MIR-5584-3P99.2368.791351
HSA-MIR-807799.1766.67862
HSA-MIR-146A-3P99.1368.991881
HSA-MIR-7160-5P99.1167.172207
HSA-MIR-485-5P99.1064.781889
HSA-MIR-6884-5P99.1064.501987
HSA-MIR-570198.9769.541502
HSA-MIR-129498.9169.261030
HSA-MIR-998698.9169.281024
HSA-MIR-6818-3P98.5668.231307
HSA-MIR-376B-5P98.4666.40606
HSA-MIR-376C-5P98.4666.64589
HSA-MIR-4733-5P97.7567.44866
HSA-MIR-4714-5P97.0467.76955
HSA-MIR-34A-3P96.8067.70805

Functional genomics

ClinGen dosage: haploinsufficiency 30 (autosomal recessive), triplosensitivity 0 (no evidence). ClinGen Gene Dosage Map DepMap (CRISPR cell-line fitness): dependent in 98.3% of screened cell lines, common-essential.

Literature-anchored findings (GeneRIF, showing 20)

  • REVIEW: Structure, expression, and regulation (PMID:19519349)
  • Studies show for the first time that DPAGT1 is an upstream regulator of E-cadherin N-glycosylation status and adherens junction composition and suggest that dysregulation of DPAGT1 causes disturbances in intercellular adhesion in oral cancer. (PMID:19549906)
  • up-regulation of DPAGT1 transcripts by Wnt3a led to altered N-glycosylation of E-cadherin. (PMID:20693288)
  • Mutations in DPAGT1 gene is associated with Congenital disorder of glycosylation type Ij. (PMID:22304930)
  • Overexpression of DPAGT1 in human oral squamous cell carcinoma specimens is linked to aberrant activation of canonical Wnt signaling. (PMID:22341307)
  • We identify DPAGT1 as a gene in which mutations cause a congenital myasthenic syndrome. (PMID:22742743)
  • Studies show that cells coordinate DPAGT1 expression and protein N-glycosylation with canonical Wnt signaling and E-cadherin adhesion via positive and negative feedback mechanisms. (PMID:23178939)
  • Results indicate that the clinical spectrum of dolichyl-phosphate alpha-N-acetylglucosaminyltransferase (DPAGT1)-congenital disorders of glycosylation (CDG) is much broader than appreciated so far. (PMID:23249953)
  • suggest that the primary pathogenic mechanism of DPAGT1-associated CMS is reduced levels of AChRs at the endplate region. This finding demonstrates that impairment of the N-linked glycosylation pathway can lead to the development of CMS (PMID:23278575)
  • Patients with DPAGT1 CMS share similar clinical features with patients who have CMS caused by mutations in GFPT1, another recently identified CMS subtype. (PMID:23447650)
  • prominent limb-girdle weakness and minimal craniobulbar symptoms who harbour a novel mutation in DPAGT1 (PMID:23591138)
  • Data suggest that in oral squamous cell carcinoma (OSCC), dysregulation of canonical Wnt signaling and DPAGT1-dependent N-glycosylation induces CTHRC1, thereby driving OSCC cell migration and tumor spread. (PMID:23703614)
  • Data suggest that N-acetylglucosaminyl 1-phosphate transferase is a breast cancer therapeutic target. (PMID:25408354)
  • present work improves our knowledge of DPAGT1-CDG and provides bases for developing tailored splicing and folding therapies (PMID:28662078)
  • we studied serum asialotransferrin (2009), which revealed a type 1 pattern compatible with type 1 glycosylation. Diagnosis of DPAGT1-CDG was confirmed by massive sequencing, which identified 2 mutations: c.329T>C (p.Phe110Ser, which had not previously been described), and c.902G>A (p.Arg301His) in the DPAGT1 gene. (PMID:28712839)
  • Congenital glycosylation disorder: a novel presentation of coexisting anterior and posterior segment pathology and its implications in pediatric cataract management. (PMID:31153949)
  • LncRNA LINC00467 acted as an oncogene in esophageal squamous cell carcinoma by accelerating cell proliferation and preventing cell apoptosis via the miR-485-5p/DPAGT1 axis. (PMID:32720371)
  • NFAT5 promotes oral squamous cell carcinoma progression in a hyperosmotic environment. (PMID:32901097)
  • Novel DPAGT1 Gene Mutation in Two Twins with Congenital Myasthenic Syndrome and a Review of the Literature. (PMID:37005892)
  • DPAGT1-CDG: Recurrent fetal death. (PMID:37421173)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriodpagt1ENSDARG00000061061
mus_musculusDpagt1ENSMUSG00000032123
rattus_norvegicusDpagt1ENSRNOG00000009799
drosophila_melanogasterAlg7FBGN0032477
caenorhabditis_elegansWBGENE00013362

Protein

Protein identifiers

UDP-N-acetylglucosamine–dolichyl-phosphate N-acetylglucosaminephosphotransferaseQ9H3H5 (reviewed: Q9H3H5)

Alternative names: GlcNAc-1-P transferase, N-acetylglucosamine-1-phosphate transferase

All UniProt accessions (16): A0A1B0GV58, A0A1W2PPC6, A0A1W2PQD1, A0A1W2PQH0, A0A1W2PRR6, A0A804HHX1, A0A804HI18, A0A804HIP7, A0A804HJ11, A0A804HJ22, Q9H3H5, A0A804HKZ3, A0A804HL46, F8W681, F8WE55, H7C2L6

UniProt curated annotations — full annotation on UniProt →

Function. UDP-N-acetylglucosamine–dolichyl-phosphate N-acetylglucosaminephosphotransferase that operates in the biosynthetic pathway of dolichol-linked oligosaccharides, the glycan precursors employed in protein asparagine (N)-glycosylation. The assembly of dolichol-linked oligosaccharides begins on the cytosolic side of the endoplasmic reticulum membrane and finishes in its lumen. The sequential addition of sugars to dolichol pyrophosphate produces dolichol-linked oligosaccharides containing fourteen sugars, including two GlcNAcs, nine mannoses and three glucoses. Once assembled, the oligosaccharide is transferred from the lipid to nascent proteins by oligosaccharyltransferases. Catalyzes the initial step of dolichol-linked oligosaccharide biosynthesis, transferring GlcNAc-1-P from cytosolic UDP-GlcNAc onto the carrier lipid dolichyl phosphate (P-dolichol), yielding GlcNAc-P-P-dolichol embedded in the cytoplasmic leaflet of the endoplasmic reticulum membrane.

Subunit / interactions. Homodimer.

Subcellular location. Endoplasmic reticulum membrane.

Disease relevance. Congenital disorder of glycosylation 1J (CDG1J) [MIM:608093] A form of congenital disorder of glycosylation, a multisystem disorder caused by a defect in glycoprotein biosynthesis and characterized by under-glycosylated serum glycoproteins. Congenital disorders of glycosylation result in a wide variety of clinical features, such as defects in the nervous system development, psychomotor retardation, dysmorphic features, hypotonia, coagulation disorders, and immunodeficiency. The broad spectrum of features reflects the critical role of N-glycoproteins during embryonic development, differentiation, and maintenance of cell functions. The disease is caused by variants affecting the gene represented in this entry. Myasthenic syndrome, congenital, 13 (CMS13) [MIM:614750] A form of congenital myasthenic syndrome, a group of disorders characterized by failure of neuromuscular transmission, including pre-synaptic, synaptic, and post-synaptic disorders that are not of autoimmune origin. Clinical features are easy fatigability and muscle weakness. CMS13 is characterized by muscle weakness mostly affecting proximal limb muscles, minimal involvement of facial, ocular and bulbar muscles, and tubular aggregates present on muscle biopsy. Symptoms include difficulty walking and frequent falls. Younger patients show hypotonia and poor head control. Neurophysiological features indicate a disorder of neuromuscular transmission on electromyography. The disease is caused by variants affecting the gene represented in this entry.

Activity regulation. Inhibited by natural nucleoside antibiotic tunicamycin, which acts as a structural analog and competitor of UDP-GlcNAc. Activated by mannosylphosphoryldolichol and phospholipids such as phosphatidylglycerol and phosphatidylcholine.

Pathway. Protein modification; protein glycosylation.

Similarity. Belongs to the glycosyltransferase 4 family.

Isoforms (3)

UniProt IDNamesCanonical?
Q9H3H5-11yes
Q9H3H5-22
Q9H3H5-33

RefSeq proteins (1): NP_001373* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000715Glycosyl_transferase_4Family
IPR033895GPTFamily
IPR048439DPAGT1_insDomain

Pfam: PF00953, PF21383

Enzyme classification (BRENDA):

  • EC 2.7.8.15 — UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase (BRENDA: 15 organisms, 17 substrates, 34 inhibitors, 14 Km, 0 kcat entries)

Substrate kinetics (BRENDA)

2 substrates with measured Km, best-characterized 2. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
DOLICHYL PHOSPHATE0.0007–0.187
UDP-GLCNAC0.0001–0.0156

Catalyzed reactions (Rhea), 1 shown:

  • a di-trans,poly-cis-dolichyl phosphate + UDP-N-acetyl-alpha-D-glucosamine = an N-acetyl-alpha-D-glucosaminyl-diphospho-di-trans,poly-cis-dolichol + UMP (RHEA:13289)

UniProt features (95 total): mutagenesis site 18, helix 16, binding site 13, topological domain 11, transmembrane region 10, sequence variant 9, strand 9, turn 3, splice variant 2, sequence conflict 2, chain 1, glycosylation site 1

Structure

Experimental structures (PDB)

8 structures.

PDBMethodResolution (Å)
6JQ3X-RAY DIFFRACTION2.5
9ZNNELECTRON MICROSCOPY2.9
6BW6X-RAY DIFFRACTION2.95
6BW5X-RAY DIFFRACTION3.1
6FWZX-RAY DIFFRACTION3.1
5LEVX-RAY DIFFRACTION3.2
5O5EX-RAY DIFFRACTION3.4
6FM9X-RAY DIFFRACTION3.6

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H3H5-F194.500.88

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 (13): 44–46; 46; 56; 119; 125; 178–186; 185; 185; 191; 252; 252; 301–303

Glycosylation sites (1): 146

Mutagenesis-validated functional residues (18):

PositionPhenotype
30mildly reduced udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
69no significant effect on udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
103impairs protein stability.
114no significant effect on udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
115strongly reduced udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
115mildly reduced udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
116strongly reduced udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
122strongly reduced udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
125loss of udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
168strongly reduced udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
182loss of udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
185loss of udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
252reduces binding to inhibitor. nearly abolishes udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotran
264no significant effect on udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
301loss of udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
302loss of udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
303reduced udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.
385no significant effect on udp-n-acetylglucosamine-dolichyl-phosphate n-acetylglucosaminephosphotransferase activity.

Function

Pathways and Gene Ontology

Reactome pathways

2 pathways

IDPathway
R-HSA-446193Biosynthesis of the N-glycan precursor (dolichol lipid-linked oligosaccharide, LLO) and transfer to a nascent protein
R-HSA-4549356Defective DPAGT1 causes CDG-1j, CMSTA2

MSigDB gene sets: 581 (showing top): GOBP_PROTEIN_N_LINKED_GLYCOSYLATION, GOBP_ALPHA_AMINO_ACID_METABOLIC_PROCESS, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, KEGG_N_GLYCAN_BIOSYNTHESIS, MODULE_503, GOBP_CARBOHYDRATE_DERIVATIVE_METABOLIC_PROCESS, RUTELLA_RESPONSE_TO_CSF2RB_AND_IL4_UP, HOSHIDA_LIVER_CANCER_SUBCLASS_S3, GOBP_CARBOHYDRATE_DERIVATIVE_BIOSYNTHETIC_PROCESS, GOBP_ORGANIC_ACID_CATABOLIC_PROCESS, HSIAO_LIVER_SPECIFIC_GENES, MOOTHA_GLUCONEOGENESIS, GOBP_ORGANIC_ACID_METABOLIC_PROCESS, GOBP_SMALL_MOLECULE_CATABOLIC_PROCESS

GO Biological Process (3): protein N-linked glycosylation (GO:0006487), dolichol-linked oligosaccharide biosynthetic process (GO:0006488), obsolete protein glycosylation (GO:0006486)

GO Molecular Function (8): UDP-N-acetylglucosamine-dolichyl-phosphate N-acetylglucosaminephosphotransferase activity (GO:0003975), UDP-N-acetylglucosamine-lysosomal-enzyme N-acetylglucosaminephosphotransferase activity (GO:0003976), glycosyltransferase activity (GO:0016757), identical protein binding (GO:0042802), metal ion binding (GO:0046872), protein binding (GO:0005515), transferase activity (GO:0016740), phosphotransferase activity, for other substituted phosphate groups (GO:0016780)

GO Cellular Component (6): endoplasmic reticulum membrane (GO:0005789), Golgi apparatus (GO:0005794), membrane (GO:0016020), intracellular membrane-bounded organelle (GO:0043231), endoplasmic reticulum (GO:0005783), endomembrane system (GO:0012505)

Reactome top-level categories

Rollup of top-2 pathways:

CategoryPathways
Asparagine N-linked glycosylation1
Diseases associated with N-glycosylation of proteins1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
phosphotransferase activity, for other substituted phosphate groups2
cytoplasm2
endomembrane system2
intracellular membrane-bounded organelle2
cellular anatomical structure2
glycoprotein biosynthetic process1
protein N-linked glycosylation1
carbohydrate derivative biosynthetic process1
transferase activity1
protein binding1
cation binding1
binding1
catalytic activity1
transferase activity, transferring phosphorus-containing groups1
organelle membrane1
nuclear outer membrane-endoplasmic reticulum membrane network1
endoplasmic reticulum subcompartment1
intracellular anatomical structure1
membrane-bounded organelle1
intracellular organelle1
vacuole1
plasma membrane1

Protein interactions and networks

STRING

1892 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DPAGT1ALG13Q9NP73995
DPAGT1ALG14Q96F25994
DPAGT1PMM2O15305891
DPAGT1ALG1Q9BT22799
DPAGT1ALG6Q9Y672793
DPAGT1GFPT1Q06210773
DPAGT1ALG11Q2TAA5760
DPAGT1ALG8Q9BVK2759
DPAGT1ALG12Q9BV10744
DPAGT1ALG3Q92685743
DPAGT1DPM1O60762729
DPAGT1ALG5Q9Y673719
DPAGT1GMPPBQ9Y5P6714
DPAGT1REPS1Q96D71692
DPAGT1DOLKQ9UPQ8689

IntAct

13 interactions, top by confidence:

ABTypeScore
HTTDPAGT1psi-mi:“MI:0915”(physical association)0.560
DPAGT1DPAGT1psi-mi:“MI:0407”(direct interaction)0.440
MFSD3DPAGT1psi-mi:“MI:0915”(physical association)0.370
CUL3PXDNLpsi-mi:“MI:0914”(association)0.350
NS3C15orf61psi-mi:“MI:0914”(association)0.350
NBASpsi-mi:“MI:0914”(association)0.350
CD1EADAM10psi-mi:“MI:0914”(association)0.350
DPAGT1ALOX12Bpsi-mi:“MI:0914”(association)0.350
ARMCX4PRKACBpsi-mi:“MI:0914”(association)0.350
SMPD2A2ML1psi-mi:“MI:0914”(association)0.350

BioGRID (23): DPAGT1 (Affinity Capture-MS), DPAGT1 (Affinity Capture-MS), ST3GAL2 (Affinity Capture-MS), STX4 (Affinity Capture-MS), RAB21 (Affinity Capture-MS), SCCPDH (Affinity Capture-MS), ALOX12B (Affinity Capture-MS), DPAGT1 (Synthetic Lethality), DPAGT1 (Affinity Capture-RNA), ST3GAL2 (Affinity Capture-MS), DPAGT1 (Affinity Capture-MS), ADPGK (Affinity Capture-MS), OLFML3 (Affinity Capture-MS), ALOX12B (Affinity Capture-MS), DPAGT1 (Affinity Capture-MS)

ESM2 similar proteins: A0JNC1, B0BMY1, B7FA90, D2HKB0, D3ZG27, E7FB98, O35052, P23338, P24140, P42867, P49281, P49282, P98191, Q12887, Q17QZ3, Q1LZA0, Q1LZE6, Q28H54, Q28HR4, Q38833, Q5EA65, Q5F3N0, Q5R460, Q5RA57, Q5W6H5, Q5ZHQ5, Q5ZKD1, Q5ZKS8, Q6AXM5, Q6ZP29, Q7ZYQ3, Q8BGS7, Q8C4N4, Q8CFY5, Q8NA29, Q8R070, Q92521, Q92903, Q99P55, Q9BX95

Diamond homologs: P07286, P0CD61, P23338, P24140, P42864, P42867, P42881, Q5EA65, Q5L520, Q821S0, Q9H3H5, A1AVY0, A4XI01, A6LTS6, B5YFT8, B8FT59, B8IZT8, Q24TE3, Q2RK82, Q6AJ51, Q8ER51, A5VJ31, B2G6K3, Q8R9G3, B1I4C7, O34753, A5D148

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

344 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic13
Likely pathogenic20
Uncertain significance149
Likely benign112
Benign10

Top pathogenic / likely-pathogenic (30)

Variant IDHGVSClassification
1451203NM_001382.4(DPAGT1):c.762_765del (p.Cys255fs)Pathogenic
2927002NM_001382.4(DPAGT1):c.732C>A (p.Tyr244Ter)Pathogenic
3233256NM_001382.4(DPAGT1):c.1133A>T (p.Asn378Ile)Pathogenic
36920NM_001382.4(DPAGT1):c.699dup (p.Thr234fs)Pathogenic
36921NM_001382.4(DPAGT1):c.358C>A (p.Leu120Met)Pathogenic
36922NM_001382.4(DPAGT1):c.791T>G (p.Val264Gly)Pathogenic
3752613NM_001382.4(DPAGT1):c.980_981del (p.Ser327fs)Pathogenic
39774NM_001382.4(DPAGT1):c.161+5G>APathogenic
4785074NM_001382.4(DPAGT1):c.172C>T (p.Gln58Ter)Pathogenic
4786678NM_001382.4(DPAGT1):c.737C>A (p.Ser246Ter)Pathogenic
565496NM_001382.4(DPAGT1):c.360G>C (p.Leu120=)Pathogenic
640003NM_001382.4(DPAGT1):c.398C>G (p.Ser133Ter)Pathogenic
65471NM_001382.4(DPAGT1):c.503T>C (p.Leu168Pro)Pathogenic
1299537NM_001382.4(DPAGT1):c.1097T>C (p.Leu366Ser)Likely pathogenic
1333389NM_001382.4(DPAGT1):c.457A>T (p.Lys153Ter)Likely pathogenic
1480366NM_001382.4(DPAGT1):c.644-1G>TLikely pathogenic
1685304NM_001382.4(DPAGT1):c.643+1G>ALikely pathogenic
2445686NC_000011.9:g.(118971849_118972204)(118972786?)delLikely pathogenic
2499560NM_001382.4(DPAGT1):c.742G>A (p.Val248Met)Likely pathogenic
2954181NM_001382.4(DPAGT1):c.1005+1G>ALikely pathogenic
3382969NM_001382.4(DPAGT1):c.728+1delLikely pathogenic
36918NM_001382.4(DPAGT1):c.349G>A (p.Val117Ile)Likely pathogenic
429774NM_001382.4(DPAGT1):c.1123C>T (p.His375Tyr)Likely pathogenic
4786262NM_001382.4(DPAGT1):c.282+1G>ALikely pathogenic
4845787NM_001382.4(DPAGT1):c.698dup (p.Thr234fs)Likely pathogenic
65469NM_001382.4(DPAGT1):c.341C>G (p.Ala114Gly)Likely pathogenic
802807NM_001382.4(DPAGT1):c.574G>C (p.Gly192Arg)Likely pathogenic
807593NM_001382.4(DPAGT1):c.698T>C (p.Phe233Ser)Likely pathogenic
996651NM_001382.4(DPAGT1):c.1197T>A (p.Tyr399Ter)Likely pathogenic
996692NM_001382.4(DPAGT1):c.419A>G (p.Tyr140Cys)Likely pathogenic

SpliceAI

3383 predictions. Top by Δscore:

VariantEffectΔscore
11:119097294:CCAC:Cacceptor_gain1.0000
11:119097295:CACC:Cacceptor_gain1.0000
11:119097297:CCTGG:Cacceptor_loss1.0000
11:119097298:C:CCacceptor_gain1.0000
11:119097299:T:Aacceptor_loss1.0000
11:119097309:A:Tacceptor_gain1.0000
11:119098399:TTA:Tdonor_loss1.0000
11:119098400:TA:Tdonor_loss1.0000
11:119098401:A:ACdonor_gain1.0000
11:119098401:A:Cdonor_loss1.0000
11:119098402:C:CCdonor_gain1.0000
11:119098486:ACCTT:Aacceptor_loss1.0000
11:119098487:CCTT:Cacceptor_gain1.0000
11:119098489:T:Aacceptor_loss1.0000
11:119098490:T:Cacceptor_gain1.0000
11:119098490:T:TCacceptor_gain1.0000
11:119098497:C:CTacceptor_gain1.0000
11:119098498:A:Tacceptor_gain1.0000
11:119100257:CCTA:Cdonor_loss1.0000
11:119100259:TACCT:Tdonor_loss1.0000
11:119100260:ACCT:Adonor_loss1.0000
11:119108091:ACGGG:Adonor_gain1.0000
11:119108092:CGGG:Cdonor_gain1.0000
11:119108093:GGG:Gdonor_gain1.0000
11:119108093:GGGG:Gdonor_gain1.0000
11:119108094:GG:Gdonor_gain1.0000
11:119108094:GGG:Gdonor_gain1.0000
11:119108095:GG:Gdonor_gain1.0000
11:119108096:G:GAdonor_loss1.0000
11:119108096:G:GGdonor_gain1.0000

AlphaMissense

2669 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
11:119100350:A:CN185K1.000
11:119100350:A:TN185K1.000
11:119097917:G:CN285K0.999
11:119097917:G:TN285K0.999
11:119098020:C:AG251V0.999
11:119100731:G:TA132D0.999
11:119100751:C:AK125N0.999
11:119100751:C:GK125N0.999
11:119100760:C:AW122C0.999
11:119100760:C:GW122C0.999
11:119100762:A:GW122R0.999
11:119100762:A:TW122R0.999
11:119100779:T:AD116V0.999
11:119100779:T:CD116G0.999
11:119100779:T:GD116A0.999
11:119100780:C:GD116H0.999
11:119100781:A:CD115E0.999
11:119100781:A:TD115E0.999
11:119100782:T:AD115V0.999
11:119100782:T:GD115A0.999
11:119100783:C:GD115H0.999
11:119100791:C:TG112D0.999
11:119100792:C:GG112R0.999
11:119097976:C:GG266R0.998
11:119097984:G:TA263D0.998
11:119097996:C:TG259D0.998
11:119097997:C:GG259R0.998
11:119098007:A:CC255W0.998
11:119098017:T:AD252V0.998
11:119098017:T:CD252G0.998

dbSNP variants (sampled 300 via entrez): RS1000213032 (11:119102476 T>C,G), RS1000265564 (11:119102674 T>C), RS1000700484 (11:119095205 G>A,T), RS1000809642 (11:119095563 T>C), RS1001422022 (11:119100150 C>T), RS1001541110 (11:119095607 C>T), RS1001596868 (11:119095883 C>T), RS1001996468 (11:119094079 CG>C), RS1002225361 (11:119103052 C>T), RS1002443737 (11:119098882 T>C), RS1003061278 (11:119101911 A>G), RS1003269168 (11:119097530 T>G), RS1004257036 (11:119102697 G>A), RS1004776855 (11:119102113 A>C), RS1004877876 (11:119095460 A>C,G)

Disease associations

OMIM: gene MIM:191350 | disease phenotypes: MIM:608093, MIM:614750, MIM:160565, MIM:232220, MIM:232240

GenCC curated gene-disease

DiseaseClassificationInheritance
DPAGT1-congenital disorder of glycosylationDefinitiveAutosomal recessive
congenital myasthenic syndrome 13DefinitiveAutosomal recessive
congenital myasthenic syndromes with glycosylation defectSupportiveAutosomal recessive

ClinGen Gene-Disease Validity (1)

Expert-panel classifications — Definitive > Strong > Moderate > Limited > Disputed > Refuted.

DiseaseClassificationInheritance
DPAGT1-congenital disorder of glycosylationDefinitiveAR

Mondo (7): DPAGT1-congenital disorder of glycosylation (MONDO:0011964), congenital myasthenic syndrome 13 (MONDO:0013883), congenital disorder of glycosylation (MONDO:0015286), tubular aggregate myopathy (MONDO:0008051), neurodevelopmental disorder (MONDO:0700092), glycogen storage disease Ib (MONDO:0009288), (MONDO:0018144)

Orphanet (7): Congenital myasthenic syndrome with glycosylation defect (Orphanet:353327), Congenital myasthenic syndrome (Orphanet:590), DPAGT1-CDG (Orphanet:86309), Congenital disorder of glycosylation (Orphanet:137), Tubular aggregate myopathy (Orphanet:2593), Glycogen storage disease due to glucose-6-phosphatase deficiency (Orphanet:364), Glycogen storage disease due to glucose-6-phosphatase deficiency type Ib (Orphanet:79259)

HPO phenotypes

123 total (30 of 123 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000028Cryptorchidism
HP:0000218High palate
HP:0000252Microcephaly
HP:0000347Micrognathia
HP:0000365Hearing impairment
HP:0000483Astigmatism
HP:0000486Strabismus
HP:0000508Ptosis
HP:0000510Rod-cone dystrophy
HP:0000518Cataract
HP:0000519Developmental cataract
HP:0000577Exotropia
HP:0000639Nystagmus
HP:0000648Optic atrophy
HP:0000662Nyctalopia
HP:0000717Autism
HP:0000718Aggressive behavior
HP:0000750Delayed speech and language development
HP:0000939Osteoporosis
HP:0000952Jaundice
HP:0000954Single transverse palmar crease
HP:0000998Hypertrichosis
HP:0001072Thickened skin
HP:0001166Arachnodactyly
HP:0001249Intellectual disability
HP:0001250Seizure
HP:0001251Ataxia
HP:0001252Hypotonia
HP:0001263Global developmental delay

GWAS associations

4 associations (top):

StudyTraitp-value
GCST008059_151Estimated glomerular filtration rate1.000000e-11
GCST90002389_371Lymphocyte percentage of white cells1.000000e-14
GCST90002396_509Mean reticulocyte volume2.000000e-80
GCST90002397_405Mean spheric corpuscular volume2.000000e-15

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0007993lymphocyte percentage of leukocytes
EFO:0010701mean reticulocyte volume

MeSH disease descriptors (4)

DescriptorNameTree numbers
D018981Congenital Disorders of GlycosylationC16.320.565.202.125; C18.452.648.202.125
D065886Neurodevelopmental DisordersF03.625
C535748Congenital disorder of glycosylation type 1J (supp.)
C562594Glycogen Storage Disease IB (supp.)

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4739704 (SINGLE PROTEIN)

PharmGKB: 1 entry (VIP=true, CPIC=false)

ChEMBL bioactivities

4 potent at pChembl≥5 of 6 total, top 4 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.00IC5010nMCHEMBL4776441
6.70IC50200nMCHEMBL4753142
6.22IC50600nMCHEMBL4752744
5.35IC504500nMCHEMBL4797442

PubChem BioAssay actives

4 with measured affinity, of 17 total; 4 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
4-[[(2S,3S)-1-amino-3-[(2S,3R,4S,5R)-5-(aminomethyl)-3,4-dihydroxyoxolan-2-yl]oxy-3-[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dihydroxyoxolan-2-yl]-1-oxopropan-2-yl]amino]-N-[[4-[4-[4-(trifluoromethoxy)phenoxy]piperidin-1-yl]phenyl]methyl]butanamide1696848: Inhibition of human DPAGT1 expressed in HEK293 (Expi293) cells incubated for 2 hrs using UDP-GlcN-Cg-FITC and alpha-dihydroundecap-renyl phosphate by reversed-phase HPLC analysisic500.0100uM
(2S,3S,4S)-2-[(1R)-2-amino-1-[(2S,3S,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-4-hydroxy-3-methoxyoxolan-2-yl]-2-oxoethoxy]-3,4-dihydroxy-N-[[4-[4-[4-(trifluoromethoxy)phenoxy]piperidin-1-yl]phenyl]methyl]-3,4-dihydro-2H-pyran-6-carboxamide1696848: Inhibition of human DPAGT1 expressed in HEK293 (Expi293) cells incubated for 2 hrs using UDP-GlcN-Cg-FITC and alpha-dihydroundecap-renyl phosphate by reversed-phase HPLC analysisic500.2000uM
(2S,3S,4S)-2-[(1R)-2-amino-1-[(2S,3R,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3-hydroxy-4-methoxyoxolan-2-yl]-2-oxoethoxy]-3,4-dihydroxy-N-[[4-[4-[4-(trifluoromethoxy)phenoxy]piperidin-1-yl]phenyl]methyl]-3,4-dihydro-2H-pyran-6-carboxamide1696848: Inhibition of human DPAGT1 expressed in HEK293 (Expi293) cells incubated for 2 hrs using UDP-GlcN-Cg-FITC and alpha-dihydroundecap-renyl phosphate by reversed-phase HPLC analysisic500.6000uM
(2S,3S,4S)-2-[(1R)-2-amino-1-[(2S,3R,4R,5R)-5-(2,4-dioxopyrimidin-1-yl)-3,4-dimethoxyoxolan-2-yl]-2-oxoethoxy]-3,4-dihydroxy-N-[(3S)-2-oxoazepan-3-yl]-3,4-dihydro-2H-pyran-6-carboxamide1696848: Inhibition of human DPAGT1 expressed in HEK293 (Expi293) cells incubated for 2 hrs using UDP-GlcN-Cg-FITC and alpha-dihydroundecap-renyl phosphate by reversed-phase HPLC analysisic504.5000uM

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
sodium arseniteaffects methylation, decreases expression, affects cotreatment, increases abundance, increases expression4
Valproic Acidaffects expression, decreases methylation, increases expression4
bisphenol Adecreases expression, affects cotreatment2
cobaltous chloridedecreases expression2
Cisplatinaffects expression, increases expression2
Tunicamycinincreases expression2
dicrotophosincreases expression1
beta-lapachonedecreases expression1
ochratoxin Adecreases expression1
beta-methylcholineaffects expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
perfluoro-n-nonanoic acidaffects methylation1
ICG 001increases expression1
bisphenol Bincreases expression1
abrinedecreases expression1
bisphenol Saffects cotreatment, decreases expression1
Temozolomideincreases expression1
Decitabineaffects expression1
Arsenic Trioxideincreases expression1
Ethanoldecreases expression, increases abundance, affects cotreatment1
Arsenicaffects cotreatment, increases abundance, increases expression1
Benzo(a)pyreneincreases methylation1
Coumestrolincreases expression1
Dexamethasoneaffects cotreatment, decreases expression1
Diurondecreases expression1
Doxorubicindecreases expression1
Ethyl Methanesulfonatedecreases expression1
Fluorouracilaffects response to substance1

ChEMBL screening assays

7 unique, capped per target: 7 binding

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4701670BindingInhibition of human DPAGT1 expressed in HEK293 (Expi293) cells incubated for 2 hrs using UDP-GlcN-Cg-FITC and alpha-dihydroundecap-renyl phosphate by reversed-phase HPLC analysisDPAGT1 Inhibitors of Capuramycin Analogues and Their Antimigratory Activities of Solid Tumors. — J Med Chem

Cellosaurus cell lines

1 cell lines: 1 transformed cell line

First 10 cell lines (id-ordered, not curated):

CellosaurusNameCategorySex
CVCL_DB02GM20941Transformed cell lineFemale

Clinical trials (associated diseases)

217 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT04586348PHASE4UNKNOWNPrenatal Iodine Supplementation and Early Childhood Neurodevelopment
NCT04873115PHASE4UNKNOWNDouble-blind, Placebo-controlled, Randomized Clinical Trial Comparing the Efficacy and Safety of Sialanar Plus orAl rehabiLitation Against Placebo Plus Oral Rehabilitation for chIldren and Adolescents With seVere Sialorrhoea and Neurodisabilties,
NCT02559102PHASE3COMPLETEDDexmedetomidine Sedation Versus General Anaesthesia for Inguinal Hernia Surgery in Infants
NCT02757079PHASE3COMPLETEDStudy of the Efficacy and Safety of NPC-15 for Sleep Disorders of Children With Neurodevelopmental Disorders
NCT06915480PHASE3RECRUITINGReducing Missed Appointments
NCT07377032PHASE3RECRUITINGTAP-GRIN: Interventional Study on Patients With GRIN-related Neurodevelopmental Disorders
NCT02909959PHASE2COMPLETEDSulforaphane for the Treatment of Young Men With Autism Spectrum Disorder
NCT06081348PHASE2RECRUITINGSertraline vs. Placebo in the Treatment of Anxiety in Children and AdoLescents With NeurodevelopMental Disorders
NCT06352372PHASE2COMPLETEDSafety and Efficacy of tPBM for Epileptiform Activity in Autism
NCT05960617PHASE2UNKNOWNEfficacy and Safety of Empagliflozin in GSD-Ib Patients
NCT07572825PHASE1NOT_YET_RECRUITINGAssessing the Safety and Tolerability of NMN in DHDDS-CDG
NCT00503191PHASE1COMPLETEDNeuroModulation Technique Treatment of Autism
NCT04475848PHASE1COMPLETEDA Study to Investigate the Safety, Tolerability, Pharmacokinetics, Pharmacodynamics and Food Effect of RO6953958 in Healthy Participants
NCT06300398PHASE1COMPLETEDIAMA-6 Oral Dose Study in Healthy Adults
NCT02089789Not specifiedRECRUITINGClinical and Basic Investigations Into Known and Suspected Congenital Disorders of Glycosylation
NCT02503267Not specifiedUNKNOWNIncidence and Consequences of Disorders of Glycosylation in Patients With Conotruncal and Septal Heart Defects
NCT02955264Not specifiedCOMPLETEDUsing D-Galactose as a Food Supplement in Congenital Disorders of Glycosylation
NCT03250728Not specifiedCOMPLETEDRole of the Endothelium in Stroke-like Episode Among CDG Patients
NCT03560570Not specifiedCOMPLETEDStudy of Hemostasis in Patients With Congenital Disorder of Glycosylation
NCT04198987Not specifiedCOMPLETEDDietary Monosaccharide Supplementation in Patients With Congenital Disorders of Glycosylation
NCT04199000Not specifiedRECRUITINGClinical and Basic Investigations Into Congenital Disorders of Glycosylation
NCT04201067Not specifiedCOMPLETEDLarge-Scale Metabolomic Profiling for the Diagnosis of Inborn Errors of Metabolism
NCT01783041PHASE2/PHASE3COMPLETEDEffect of Early L-Carnitine Supplementation on Neurodevelopmental Outcomes in Very Preterm Infants
NCT05767385PHASE2/PHASE3RECRUITINGFetal Cerebrovascular Autoregulation in Congenital Heart Disease and Association With Neonatal Neurobehavior
NCT05675098EARLY_PHASE1NOT_YET_RECRUITINGCentral Nervous System Stimulants and Physical Function in Children With Cerebral Palsy
NCT00783783Not specifiedCOMPLETEDCYP2D6 Pharmacogenetics in Risperidone-Treated Children
NCT01778504Not specifiedRECRUITINGStudying Childhood-onset Behavioral, Psychiatric, and Developmental Disorders
NCT01850784Not specifiedUNKNOWNHigh Energy Formula Feeding in Infants With Congenital Heart Disease
NCT01922791Not specifiedCOMPLETEDNutrition and Pregnancy Intervention Study
NCT01942525Not specifiedUNKNOWNInfluence of Intrauterine Growth Restriction on Amplitude-integrated EEG in Preterm Infants
NCT02003170Not specifiedCOMPLETEDEtiology and Early Diagnosis of Neurodevelopmental Disorders
NCT02118649Not specifiedACTIVE_NOT_RECRUITINGEnhancing Behavior and Brain Response to Visual Targets Using a Computer Game
NCT02557191Not specifiedTERMINATEDBiomarkers, Neurodevelopment and Preterm Infants
NCT02690675Not specifiedCOMPLETEDIron Supplement Effect on Child Development
NCT02694003Not specifiedCOMPLETEDBetter Nights, Better Days for Children With Neurodevelopment Disorders
NCT02792894Not specifiedCOMPLETEDFamily Networks (FaNs) for Children With Developmental Disorders and Delays
NCT02871674Not specifiedUNKNOWNGood Night Project: Behavioural Sleep Interventions for Children With ADHD: A Randomised Controlled Trial
NCT02887157Not specifiedCOMPLETEDAnalyzing Retinal Microanatomy in ROP
NCT02898298Not specifiedCOMPLETEDPositive Emotion Regulation Training in Children, Adolescents and Young Adults With and Without Developmental Disorder
NCT02912780Not specifiedUNKNOWNIntroduction of Microsystems in a Level 3 Neonatal Intensive Care Unit