DHPS

gene
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Also known as MIG13

Summary

DHPS (deoxyhypusine synthase, HGNC:2869) is a protein-coding gene on chromosome 19p13.13, encoding Deoxyhypusine synthase (P49366). Catalyzes the NAD-dependent oxidative cleavage of spermidine and the subsequent transfer of the butylamine moiety of spermidine to the epsilon-amino group of a critical lysine residue of the eIF-5A precursor protein to form the intermediate deoxyhypusine residue. It is a selective cancer dependency (DepMap: 89.1% of cell lines).

This gene encodes a protein that is required for the formation of hypusine, a unique amino acid formed by the posttranslational modification of only one protein, eukaryotic translation initiation factor 5A. The encoded protein catalyzes the first step in hypusine formation by transferring the butylamine moiety of spermidine to a specific lysine residue of the eukaryotic translation initiation factor 5A precursor, forming an intermediate deoxyhypusine residue. Alternatively spliced transcript variants encoding multiple isoforms have been observed for this gene.

Source: NCBI Gene 1725 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): neurodevelopmental disorder with seizures and speech and walking impairment (Strong, GenCC)
  • GWAS associations: 1
  • Clinical variants (ClinVar): 119 total — 4 likely-pathogenic
  • Phenotypes (HPO): 31
  • Druggable target: yes — 1 molecules with ChEMBL bioactivity
  • Cancer dependency (DepMap): dependent in 89.1% of screened cell lines
  • MANE Select transcript: NM_001930

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:2869
Approved symbolDHPS
Namedeoxyhypusine synthase
Location19p13.13
Locus typegene with protein product
StatusApproved
AliasesMIG13
Ensembl geneENSG00000095059
Ensembl biotypeprotein_coding
OMIM600944
Entrez1725

Gene structure

Transcript identifiers

Ensembl transcripts: 34 — 20 protein_coding, 7 nonsense_mediated_decay, 6 retained_intron, 1 protein_coding_CDS_not_defined

ENST00000210060, ENST00000351660, ENST00000593400, ENST00000593423, ENST00000593432, ENST00000593473, ENST00000594424, ENST00000595100, ENST00000595844, ENST00000595912, ENST00000596162, ENST00000596847, ENST00000597152, ENST00000598246, ENST00000598850, ENST00000599481, ENST00000600451, ENST00000600510, ENST00000600639, ENST00000600864, ENST00000601537, ENST00000601639, ENST00000862636, ENST00000862637, ENST00000862638, ENST00000862639, ENST00000862640, ENST00000917713, ENST00000917714, ENST00000917715, ENST00000917716, ENST00000917717, ENST00000949481, ENST00000949482

RefSeq mRNA: 6 — MANE Select: NM_001930 NM_001206974, NM_001369691, NM_001369692, NM_001369693, NM_001930, NM_013406

CCDS: CCDS12276, CCDS12277, CCDS59354

Canonical transcript exons

ENST00000210060 — 9 exons

ExonStartEnd
ENSE000029804451268156012681880
ENSE000031984191267571712675933
ENSE000035295241267601712676142
ENSE000035425201267710812677211
ENSE000035757741267962312679719
ENSE000035988081267980112679922
ENSE000035994701268016112680325
ENSE000036590821267945712679543
ENSE000037893081267729112677396

Expression profiles

Bgee: expression breadth ubiquitous, 145 present calls, max score 98.31.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 59.1627 / max 320.5754, expressed in 1822 samples.

FANTOM5 promoters (4 alternative TSS)

Promoter IDTPM avgSamples expressed
17932854.41231822
1793272.37791335
1793292.03361278
1793260.3390148

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
right hemisphere of cerebellumUBERON:001489098.31gold quality
cerebellumUBERON:000203798.26gold quality
cerebellar cortexUBERON:000212998.26gold quality
cerebellar hemisphereUBERON:000224598.26gold quality
cortical plateUBERON:000534398.18gold quality
ganglionic eminenceUBERON:000402398.06gold quality
embryoUBERON:000092298.05gold quality
primary visual cortexUBERON:000243697.72gold quality
pituitary glandUBERON:000000797.66gold quality
adenohypophysisUBERON:000219697.43gold quality
right uterine tubeUBERON:000130297.42gold quality
left ovaryUBERON:000211997.28gold quality
prostate glandUBERON:000236797.21gold quality
hindlimb stylopod muscleUBERON:000425297.08gold quality
prefrontal cortexUBERON:000045197.07gold quality
right ovaryUBERON:000211897.01gold quality
skeletal muscle tissueUBERON:000113496.98gold quality
ovaryUBERON:000099296.97gold quality
endocervixUBERON:000045896.94gold quality
body of uterusUBERON:000985396.94gold quality
frontal cortexUBERON:000187096.91gold quality
frontal lobeUBERON:001652596.91gold quality
fundus of stomachUBERON:000116096.79gold quality
right frontal lobeUBERON:000281096.76gold quality
muscle layer of sigmoid colonUBERON:003580596.72gold quality
left lobe of thyroid glandUBERON:000112096.71gold quality
body of stomachUBERON:000116196.69gold quality
right lobe of thyroid glandUBERON:000111996.68gold quality
uterine cervixUBERON:000000296.67gold quality
thyroid glandUBERON:000204696.60gold quality

Single-cell (SCXA)

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

ExperimentMarker?Max mean expression
E-ANND-3yes9.96

Regulation

Is transcription factor: no

Upstream regulators (CollecTRI, top): CTCF, E2F4, E2F6

miRNA regulators (miRDB)

18 targeting DHPS, 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-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-4728-5P99.8569.394718
HSA-MIR-3121-3P99.8271.963630
HSA-MIR-6785-5P99.8268.684428
HSA-MIR-149-3P99.7268.223963
HSA-MIR-6883-5P99.6968.053785
HSA-MIR-452799.6667.43714
HSA-MIR-6503-5P99.6266.96597
HSA-MIR-5197-3P98.7167.051905

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 89.1% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 16)

  • deoxyhypusine synthase has a role in generating spermidine or homospermidine (PMID:12788913)
  • deoxyhypusine synthase and its phosphorylation modification may have other independent cellular functions because of versatile roles of deoxyhypusine synthase (PMID:14749535)
  • crystal structure of deoxyhypusine synthase reveals the configuration of the active enzyme and of an enzyme.NAD.inhibitor ternary complex (PMID:15100216)
  • Dhps-437 and dhps-540 are strongly associated with SP treatment failure and should be evaluated further as a method for surveillance of SP-based therapy in DRC. (PMID:19055622)
  • A novel series of cell movements that orient the polarity of Lrp12/Mig13a-expressing neurons and their axons just prior to cortical plate assembly do not occur in reeler mutant mice. (PMID:20439316)
  • DHPS and WDR83 were capable of forming an RNA duplex at overlapping 3’ untranslated regions and this duplex increased their mutual stability, which was required for the bidirectional regulation. (PMID:22491477)
  • eIF-5A as well as the hypusine-forming enzymes deoxyhypusine synthase (DHS) and deoxyhypusine hydroxylase (DOHH) are highly overexpressed in glioblastoma patient sample (PMID:22927971)
  • Whereas, dhps mutation study revealed that triple mutant haplotype AGEAA (S436A+A437G+K540E) associated with Sulphadoxine resistance was found among 26% of P. falciparum field isolates. (PMID:25511211)
  • the use of N1-Guanyl-1,7-diaminoheptane, a DHPS inhibitor, resulted in a significant decrease in tumor formation in vivo. In patients with esophageal squamous cell carcinoma (ESCC), overexpression of DHPS in ESCC tumors was significantly associated with worse recurrence-free survival, and correlated with distant metastasis. (PMID:27041563)
  • data suggest that rare biallelic variants in DHPS result in reduced enzyme activity that limits the hypusination of eIF5A and are associated with a neurodevelopmental disorder (PMID:30661771)
  • DHPS-dependent hypusination of eIF5A1/2 is necessary for TGFbeta/fibronectin-induced breast cancer metastasis and associates with prognostically unfavorable genomic alterations in TP53 (PMID:31558321)
  • Half Way to Hypusine-Structural Basis for Substrate Recognition by Human Deoxyhypusine Synthase. (PMID:32235505)
  • eIF5A-Independent Role of DHPS in p21(CIP1) and Cell Fate Regulation. (PMID:34947982)
  • Cryo-EM structure of human eIF5A-DHS complex reveals the molecular basis of hypusination-associated neurodegenerative disorders. (PMID:36973244)
  • Deoxyhypusine synthase mutations alter the post-translational modification of eukaryotic initiation factor 5A resulting in impaired human and mouse neural homeostasis. (PMID:37333770)
  • Clinical significance of mutations in dihydropteroate synthase in Pneumocystis jirovecii pneumonia among non-HIV-infected patients. (PMID:37925109)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriodhpsENSDARG00000003270
mus_musculusDhpsENSMUSG00000060038
rattus_norvegicusDhpsENSRNOG00000004219
drosophila_melanogasterDhpsFBGN0035854
caenorhabditis_elegansWBGENE00012460

Protein

Protein identifiers

Deoxyhypusine synthaseP49366 (reviewed: P49366)

All UniProt accessions (13): P49366, B4E3M2, M0QX43, M0QXT2, M0QYZ7, M0QZT3, M0R0J4, M0R0V2, M0R1T2, M0R1T4, M0R253, M0R264, Q5J8M5

UniProt curated annotations — full annotation on UniProt →

Function. Catalyzes the NAD-dependent oxidative cleavage of spermidine and the subsequent transfer of the butylamine moiety of spermidine to the epsilon-amino group of a critical lysine residue of the eIF-5A precursor protein to form the intermediate deoxyhypusine residue. This is the first step of the post-translational modification of that lysine into an unusual amino acid residue named hypusine. Hypusination is unique to mature eIF-5A factor and is essential for its function.

Subunit / interactions. Homotetramer formed by a dimer of dimers.

Disease relevance. Neurodevelopmental disorder with seizures and speech and walking impairment (NEDSSWI) [MIM:618480] An autosomal recessive disorder characterized by global developmental delay with intellectual disability and poor speech acquisition, and walking difficulties due to hypotonia, hypertonia, spasticity, or poor coordination. Additional features include seizures, mild dysmorphic features, and variable short stature. The disease is caused by variants affecting the gene represented in this entry.

Pathway. Protein modification; eIF5A hypusination.

Miscellaneous. Inactive.

Similarity. Belongs to the deoxyhypusine synthase family.

Isoforms (3)

UniProt IDNamesCanonical?
P49366-1Longyes
P49366-2Short
P49366-33

RefSeq proteins (6): NP_001193903, NP_001356620, NP_001356621, NP_001356622, NP_001921, NP_037538 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002773Deoxyhypusine_synthaseFamily
IPR029035DHS-like_NAD/FAD-binding_domHomologous_superfamily
IPR036982Deoxyhypusine_synthase_sfHomologous_superfamily

Pfam: PF01916

Enzyme classification (BRENDA):

  • EC 2.5.1.46 — deoxyhypusine synthase (BRENDA: 37 organisms, 87 substrates, 98 inhibitors, 39 Km, 9 kcat entries)

Substrate kinetics (BRENDA)

10 substrates with measured Km, best-characterized 10. Km ranges are aggregated across organisms/conditions.

SubstrateKm (mM)Measurements
SPERMIDINE0.0006–0.3714
NAD+0.0012–0.817
[EIF5A-PRECURSOR]-L-LYSINE0.0001–1.125
[EIF5A-PRECURSOR]-LYSINE0.0007–0.00183
1,3-DIAMINOPROPANE0.0954–0.10582
PUTRESCINE0.0015–0.2032
[EIF5A-PRECURSOR]-DEOXYHYPUSINE0.0066–0.00862
HOMOSPERMINE0.01931
[EIF5A-1-PRECURSOR]-LYSINE0.00151
[EIF5A-2-PRECURSOR]-LYSINE0.00831

Catalyzed reactions (Rhea), 1 shown:

  • [eIF5A protein]-L-lysine + spermidine = [eIF5A protein]-deoxyhypusine + propane-1,3-diamine (RHEA:33299)

UniProt features (76 total): helix 20, mutagenesis site 15, binding site 12, sequence conflict 9, strand 7, turn 5, sequence variant 3, splice variant 2, chain 1, active site 1, modified residue 1

Structure

Experimental structures (PDB)

89 structures, top 30 by resolution.

PDBMethodResolution (Å)
9IEGX-RAY DIFFRACTION1.27
9IE3X-RAY DIFFRACTION1.3
9IEAX-RAY DIFFRACTION1.3
9IDTX-RAY DIFFRACTION1.33
9IDVX-RAY DIFFRACTION1.33
9IDUX-RAY DIFFRACTION1.34
9IDWX-RAY DIFFRACTION1.34
9IE4X-RAY DIFFRACTION1.34
9IE1X-RAY DIFFRACTION1.35
9IDYX-RAY DIFFRACTION1.37
9IENX-RAY DIFFRACTION1.37
9ID3X-RAY DIFFRACTION1.39
9IDOX-RAY DIFFRACTION1.39
9IDQX-RAY DIFFRACTION1.39
9IE2X-RAY DIFFRACTION1.39
9IE9X-RAY DIFFRACTION1.39
9IEMX-RAY DIFFRACTION1.39
9IEDX-RAY DIFFRACTION1.4
6XXJX-RAY DIFFRACTION1.41
9IDAX-RAY DIFFRACTION1.41
9IEQX-RAY DIFFRACTION1.41
9IE7X-RAY DIFFRACTION1.42
9IDFX-RAY DIFFRACTION1.43
9IDMX-RAY DIFFRACTION1.43
9IDNX-RAY DIFFRACTION1.43
9IE5X-RAY DIFFRACTION1.43
9ID6X-RAY DIFFRACTION1.44
9IDRX-RAY DIFFRACTION1.44
9IDZX-RAY DIFFRACTION1.44
9IETX-RAY DIFFRACTION1.44

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P49366-F193.950.89

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 (1): 329 (nucleophile)

Ligand- & substrate-binding residues (12): 308–309; 314–316; 323–329; 342–343; 105–109; 131–133; 136–137; 137; 238; 243; 283; 288

Post-translational modifications (1): 78

Mutagenesis-validated functional residues (15):

PositionPhenotype
106strongly reduced nad and spermidine binding. reduced activity.
109strongly reduced spermidine binding. reduced activity.
137strongly reduced nad binding. strongly reduced formation of covalent intermediate.
238strongly reduced nad binding. strongly reduced formation of covalent intermediate.
243reduces spermidine binding by 98%. strongly reduced formation of covalent intermediate.
287reduces covalent intermediate formation and deoxyhypusine synthesis by 99.5%. retains low spermidine cleavage activity.
288reduces spermidine binding by 98%. strongly reduced nad binding. strongly reduced formation of covalent intermediate.
305strongly reduced nad binding. no effect on enzyme activity.
313strongly reduced nad binding.
316reduces spermidine binding by 98%. loss of covalent intermediate formation and deoxyhypusine synthesis.
317strongly reduced nad binding. no effect on enzyme activity.
323reduces spermidine binding by 98%. strongly reduced formation of covalent intermediate.
327reduces spermidine binding by 98%. loss of covalent intermediate formation and deoxyhypusine synthesis.
329loss of covalent intermediate formation and deoxyhypusine synthesis.
342strongly reduced nad binding. strongly reduced activity.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-204626Hypusine synthesis from eIF5A-lysine

MSigDB gene sets: 263 (showing top): GOBP_REGULATION_OF_CELL_ACTIVATION, GOBP_REGULATION_OF_LEUKOCYTE_PROLIFERATION, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, HSIAO_HOUSEKEEPING_GENES, GOBP_POSITIVE_REGULATION_OF_CELL_ADHESION, GOBP_POSITIVE_REGULATION_OF_LEUKOCYTE_PROLIFERATION, GOBP_TRANSLATION, GCM_PRKCG, GOBP_CELL_CELL_ADHESION, GOBP_POLYAMINE_METABOLIC_PROCESS, GOBP_PROTEIN_MATURATION, GOBP_LEUKOCYTE_PROLIFERATION, CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, GOBP_POSITIVE_REGULATION_OF_CELL_ACTIVATION

GO Biological Process (8): translation (GO:0006412), spermidine metabolic process (GO:0008216), positive regulation of cell population proliferation (GO:0008284), positive regulation of T cell proliferation (GO:0042102), glucose homeostasis (GO:0042593), spermidine catabolic process (GO:0046203), protein maturation (GO:0051604), peptidyl-hypusine biosynthetic process (GO:0008612)

GO Molecular Function (4): deoxyhypusine synthase activity (GO:0034038), identical protein binding (GO:0042802), protein binding (GO:0005515), transferase activity (GO:0016740)

GO Cellular Component (2): cytoplasm (GO:0005737), cytosol (GO:0005829)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
Gamma carboxylation, hypusinylation, hydroxylation, and arylsulfatase activation1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
protein metabolic process2
cellular anatomical structure2
peptidyltransferase activity1
translational initiation1
translational elongation1
translational termination1
macromolecule biosynthetic process1
protein biosynthetic process1
polyamine metabolic process1
cell population proliferation1
regulation of cell population proliferation1
positive regulation of cellular process1
T cell proliferation1
regulation of T cell proliferation1
positive regulation of lymphocyte proliferation1
positive regulation of T cell activation1
carbohydrate homeostasis1
polyamine catabolic process1
spermidine metabolic process1
gene expression1
biosynthetic process1
protein maturation1
transferase activity, transferring alkyl or aryl (other than methyl) groups1
protein binding1
binding1
catalytic activity1
intracellular anatomical structure1
cytoplasm1

Protein interactions and networks

STRING

1889 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DHPSDOHHQ9BU89997
DHPSEIF5AP10159994
DHPSEIF5AL1Q6IS14837
DHPSEIF5A2Q9GZV4793
DHPSDHFRP00374789
DHPSODC1P11926698
DHPSSRMP19623691
DHPSSMSP52788667
DHPSSH3BP5O60239637
DHPSAGMATQ9BSE5544
DHPSXPO4Q9C0E2531
DHPSPAOXQ6QHF9527
DHPSATP2B4P23634526
DHPSSMOXQ9NWM0526
DHPSWDR83Q9BRX9518

IntAct

160 interactions, top by confidence:

ABTypeScore
MAPK3DHPSpsi-mi:“MI:0915”(physical association)0.920
RPL9DHPSpsi-mi:“MI:0915”(physical association)0.870
DHPSRPL9psi-mi:“MI:0915”(physical association)0.870
RPL9DHPSpsi-mi:“MI:0914”(association)0.870
EIF5A2DHPSpsi-mi:“MI:0915”(physical association)0.830
DHPSEIF5A2psi-mi:“MI:0915”(physical association)0.830
EIF5A2DHPSpsi-mi:“MI:0914”(association)0.830
MAPK1MAPK3psi-mi:“MI:0914”(association)0.770
MAPK3MAPK1psi-mi:“MI:0914”(association)0.770
RAB27BDHPSpsi-mi:“MI:0915”(physical association)0.720
DHPSEIF5Apsi-mi:“MI:0915”(physical association)0.720
DHPSRAB27Bpsi-mi:“MI:0915”(physical association)0.720
EIF5ADHPSpsi-mi:“MI:0915”(physical association)0.720
DHPSDHPSpsi-mi:“MI:0915”(physical association)0.670

BioGRID (156): DHPS (Two-hybrid), EIF5A (Two-hybrid), PTPRH (Two-hybrid), RAB27B (Two-hybrid), REL (Two-hybrid), RPL9 (Two-hybrid), ZNF138 (Two-hybrid), VASH1 (Two-hybrid), WDYHV1 (Two-hybrid), EIF5A2 (Two-hybrid), BRCA1 (Two-hybrid), DHPS (Affinity Capture-MS), DHPS (Affinity Capture-MS), DHPS (Affinity Capture-MS), DHPS (Affinity Capture-MS)

ESM2 similar proteins: A2RRU1, A7MB78, A8XKV0, G3ISL7, J9VTK7, O06983, O08739, O09178, O31041, O34823, O34872, O93869, P05033, P0A1Z0, P0A1Z1, P0A9H3, P0A9H4, P0ABE9, P0ABF0, P0DUG1, P0DUM8, P10759, P13807, P13834, P17625, P23109, P23337, P27134, P27472, P28345, P45148, P49366, P52095, P54840, P61517, P61518, P9WEN1, Q01432, Q09580, Q22460

Diamond homologs: A3MVC9, A4YHK6, A6URC0, A8AA61, B0R5L2, B5APK2, B6YVB1, C3MPN8, C3MYN2, C3N5B4, C3NDW8, C3NHT5, C4KGY0, C5A5L0, O26230, O27984, O28088, O50105, O94337, P38791, P49365, P49366, P60038, Q38BX0, Q3TXU5, Q4J978, Q54MQ7, Q58224, Q5JEY0, Q6AY53, Q6CG56, Q6CNG7, Q6EWQ6, Q6FRN2, Q6KZL5, Q6RJS2, Q75EW4, Q8PV89, Q8Q051, Q8SQN2

SIGNOR signaling

5 interactions.

AEffectBMechanism
ERK1/2“up-regulates activity”DHPSphosphorylation
DHPS“up-regulates activity”EIF5A“post translational modification”

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic4
Uncertain significance81
Likely benign13
Benign4

Top pathogenic / likely-pathogenic (4)

Variant IDHGVSClassification
1331656NM_001930.4(DHPS):c.216_217dup (p.Lys73fs)Likely pathogenic
2506774NM_001930.4(DHPS):c.785-1G>CLikely pathogenic
4526968NM_001930.4(DHPS):c.709dup (p.Thr237fs)Likely pathogenic
560195NM_001930.4(DHPS):c.912_917del (p.Tyr305_Ile306del)Likely pathogenic

SpliceAI

1514 predictions. Top by Δscore:

VariantEffectΔscore
19:12675513:C:CAacceptor_gain1.0000
19:12675521:A:AGacceptor_gain1.0000
19:12675521:AG:Aacceptor_gain1.0000
19:12675522:G:GAacceptor_loss1.0000
19:12675522:G:GGacceptor_gain1.0000
19:12675522:GG:Gacceptor_gain1.0000
19:12675522:GGGT:Gacceptor_gain1.0000
19:12675895:C:CTacceptor_gain1.0000
19:12675929:TAGAC:Tacceptor_gain1.0000
19:12675931:GACCT:Gacceptor_loss1.0000
19:12675934:C:CCacceptor_gain1.0000
19:12676012:CTTA:Cdonor_loss1.0000
19:12676013:TTA:Tdonor_loss1.0000
19:12676014:TA:Tdonor_loss1.0000
19:12676015:A:ACdonor_gain1.0000
19:12676015:AC:Adonor_gain1.0000
19:12676016:C:CTdonor_gain1.0000
19:12676016:CC:Cdonor_gain1.0000
19:12676138:TTCCG:Tacceptor_gain1.0000
19:12676139:TCCG:Tacceptor_gain1.0000
19:12676140:CCG:Cacceptor_gain1.0000
19:12676140:CCGC:Cacceptor_gain1.0000
19:12676141:CG:Cacceptor_gain1.0000
19:12676141:CGC:Cacceptor_gain1.0000
19:12676143:C:CCacceptor_gain1.0000
19:12676145:G:Cacceptor_gain1.0000
19:12676154:C:CTacceptor_gain1.0000
19:12677102:ACTC:Adonor_loss1.0000
19:12677103:CTCA:Cdonor_loss1.0000
19:12677104:TCACC:Tdonor_loss1.0000

AlphaMissense

2435 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:12676050:C:AW327C0.999
19:12676050:C:GW327C0.999
19:12676052:A:GW327R0.999
19:12676052:A:TW327R0.999
19:12677348:C:GD243H0.999
19:12677359:C:TG239D0.999
19:12677362:T:AD238V0.999
19:12677363:C:GD238H0.999
19:12679534:A:GW201R0.999
19:12679534:A:TW201R0.999
19:12679719:C:AR165S0.999
19:12679719:C:GR165S0.999
19:12679801:C:AR165M0.999
19:12679882:T:AD138V0.999
19:12679882:T:GD138A0.999
19:12679883:C:GD138H0.999
19:12679885:T:AE137V0.999
19:12680206:A:CS109R0.999
19:12680206:A:TS109R0.999
19:12680208:T:GS109R0.999
19:12676110:G:CN307K0.998
19:12676110:G:TN307K0.998
19:12677134:G:CH288D0.998
19:12677135:C:AK287N0.998
19:12677135:C:GK287N0.998
19:12677291:C:GD262H0.998
19:12677347:T:AD243V0.998
19:12677347:T:GD243A0.998
19:12677350:C:TG242D0.998
19:12677351:C:GG242R0.998

dbSNP variants (sampled 300 via entrez): RS1000133427 (19:12678027 T>A,C,G), RS1000217733 (19:12682860 C>G), RS1000308722 (19:12678753 A>G,T), RS1000433971 (19:12682965 A>C), RS1000465152 (19:12683124 T>C), RS1000624419 (19:12673587 T>C), RS1000718066 (19:12677654 T>C), RS1000730248 (19:12672374 T>C), RS1001158984 (19:12675208 C>G), RS1001400495 (19:12674983 G>A,T), RS1001847921 (19:12683797 C>T), RS1001871017 (19:12673542 T>A,C), RS1001883433 (19:12680288 T>C), RS1002165997 (19:12673912 C>G), RS1002400255 (19:12673711 C>T)

Disease associations

OMIM: gene MIM:600944 | disease phenotypes: MIM:618480

GenCC curated gene-disease

DiseaseClassificationInheritance
neurodevelopmental disorder with seizures and speech and walking impairmentStrongAutosomal recessive

Mondo (1): neurodevelopmental disorder with seizures and speech and walking impairment (MONDO:0032775)

Orphanet (0):

HPO phenotypes

31 total (30 of 31 shown, HPO-id order):

HPOTerm
HP:0000007Autosomal recessive inheritance
HP:0000218High palate
HP:0000219Thin upper lip vermilion
HP:0000319Smooth philtrum
HP:0000369Low-set ears
HP:0000426Prominent nasal bridge
HP:0000490Deeply set eye
HP:0000750Delayed speech and language development
HP:0000960Sacral dimple
HP:0001250Seizure
HP:0001252Hypotonia
HP:0001257Spasticity
HP:0001263Global developmental delay
HP:0001562Oligohydramnios
HP:0001622Premature birth
HP:0002019Constipation
HP:0002317Unsteady gait
HP:0002353EEG abnormality
HP:0002509Limb hypertonia
HP:0003593Infantile onset
HP:0004209Clinodactyly of the 5th finger
HP:0004322Short stature
HP:0008936Axial hypotonia
HP:0010880Increased nuchal translucency
HP:0011856Pica
HP:0031936Delayed ability to walk
HP:0034210Fetal intraventricular hemorrhage
HP:0100023Recurrent hand flapping
HP:0100602Preeclampsia
HP:0100876Infra-orbital crease

GWAS associations

1 associations (top):

StudyTraitp-value
GCST90002401_250Platelet distribution width3.000000e-09

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0007984platelet component distribution width

Drugs & pharmacology

Drug and pharmacology data

Is drug target: yes

ChEMBL targets (1): CHEMBL4415 (SINGLE PROTEIN)

Molecules with ChEMBL bioactivity

1 molecules (phase ≥1), by development phase (incl. off-target/promiscuous compounds). Patent mentions across the top 20 by phase: 16,499 (via chembl_molecule»patent_compound — counts attach to the compound, not the gene–compound relationship, so off-target/promiscuous molecules can dominate).

MoleculeNamePhasePatents
CHEMBL957BOSENTAN416,499

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

ChEMBL bioactivities

51 potent at pChembl≥5 of 76 total, top 50 by pChembl (potency: 10 = 0.1 nM, 6 = 1 µM).

pChemblTypeValueUnitMolecule
8.04IC509.2nMCHEMBL5281395
7.96IC5011nMCHEMBL5265996
7.92IC5012nMCHEMBL5288132
7.85IC5014nMCHEMBL5091313
7.85IC5014nMCHEMBL5269564
7.75IC5018nMCHEMBL5274333
7.58IC5026nMCHEMBL5268272
7.54IC5029nMCHEMBL5267547
7.52IC5030nMCHEMBL5278471
7.40IC5040nMCHEMBL5079375
7.30IC5050nMCHEMBL5074971
7.21IC5062nMCHEMBL4555677
7.16IC5069nMCHEMBL5281395
7.04IC5092nMCHEMBL4543218
7.00IC50100nMCHEMBL5075342
6.96IC50110nMCHEMBL5282634
6.92IC50120nMCHEMBL4462702
6.85IC50140nMCHEMBL229457
6.82IC50150nMCHEMBL5281552
6.80IC50160nMCHEMBL5287156
6.77IC50170nMCHEMBL5288132
6.75IC50180nMCHEMBL5084409
6.75IC50180nMCHEMBL5091281
6.64IC50230nMCHEMBL5265996
6.50IC50320nMCHEMBL5090481
6.48IC50330nMCHEMBL5078063
6.39IC50410nMCHEMBL5269564
6.37IC50430nMCHEMBL4442298
6.36IC50440nMCHEMBL5283409
6.30IC50500nMCHEMBL229457
6.28IC50530nMCHEMBL5091279
6.25IC50560nMCHEMBL5070084
6.24IC50580nMCHEMBL5278471
6.20IC50630nMCHEMBL5267547
6.19IC50640nMCHEMBL5081296
6.10IC50790nMCHEMBL5268272
6.08IC50840nMCHEMBL4447948
5.93IC501170nMCHEMBL5075319
5.76IC501720nMCHEMBL229457
5.64IC502300nMCHEMBL4470208
5.64IC502290nMCHEMBL5089864
5.62IC502380nMCHEMBL5080635
5.37IC504310nMCHEMBL5080971
5.36IC504420nMCHEMBL5073964
5.27IC505400nMCHEMBL4572958
5.26IC505430nMCHEMBL5078229
5.20IC506300nMCHEMBL5269301
5.16IC506900nMCHEMBL4555677
5.09IC508200nMCHEMBL5281757
5.06IC508700nMCHEMBL5274695

PubChem BioAssay actives

51 with measured affinity, of 184 total; 40 most potent distinct compounds. Largely complementary to BindingDB; screening values are coarse (µM, 4 dp), so sub-nM hits tie at the floor.

CompoundAssayTypeValueUnit
6-[(2R)-1-amino-4-methylpentan-2-yl]-3-pyridin-3-yl-4,5-dihydrothieno[2,3-c]pyridin-7-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic500.0092uM
6-[(2R)-1-amino-3,3-dimethylbutan-2-yl]-3-pyridin-3-yl-4,5-dihydrothieno[2,3-c]pyridin-7-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic500.0110uM
6-[(1R)-2-amino-1-cyclohexylethyl]-3-pyridin-3-yl-4,5-dihydrothieno[2,3-c]pyridin-7-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic500.0120uM
6-[(1R)-2-amino-1-phenylethyl]-3-pyridin-3-yl-4,5-dihydrothieno[2,3-c]pyridin-7-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic500.0140uM
2-(4-bromophenyl)-6-chloro-5-(2-methoxyphenoxy)pyrimidin-4-amine1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic500.0140uM
6-(2-amino-1-phenylethyl)-3-pyridin-3-yl-4,5-dihydrothieno[2,3-c]pyridin-7-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic500.0180uM
6-(1-aminopentan-2-yl)-3-pyridin-3-yl-4,5-dihydrothieno[2,3-c]pyridin-7-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic500.0260uM
6-[2-amino-1-(1-benzothiophen-3-yl)ethyl]-3-pyridin-3-yl-4,5-dihydrothieno[2,3-c]pyridin-7-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic500.0290uM
6-(1-aminooctan-2-yl)-3-pyridin-3-yl-4,5-dihydrothieno[2,3-c]pyridin-7-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic500.0300uM
6-chloro-5-(2-methoxyphenoxy)-2-(3-methoxyphenyl)pyrimidin-4-amine1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic500.0400uM
2-benzyl-6-chloro-5-(2-methoxyphenoxy)pyrimidin-4-amine1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic500.0500uM
6-bromo-N-(1H-indol-4-yl)-1-benzothiophene-2-carboxamide1561253: Inhibition of human N-terminal His6-tagged TEV protease site linked DHPS expressed in Escherichia coli BL21 (DE3) assessed as reduction in radiolabelled amino-butylidene incorporation in eIF5A using [3H]Spermidine trichloride as substrate after 90 to 120 mins in presence of eIF5A and 14 uM NAD+ by Topcount scintillation counting methodic500.0620uM
N-(1H-indol-4-yl)-6-iodo-1-benzothiophene-2-carboxamide1561253: Inhibition of human N-terminal His6-tagged TEV protease site linked DHPS expressed in Escherichia coli BL21 (DE3) assessed as reduction in radiolabelled amino-butylidene incorporation in eIF5A using [3H]Spermidine trichloride as substrate after 90 to 120 mins in presence of eIF5A and 14 uM NAD+ by Topcount scintillation counting methodic500.0920uM
6-chloro-2-(4-chlorophenyl)-5-(2-methoxyphenoxy)pyrimidin-4-amine1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic500.1000uM
6-[2-amino-1-(1H-indol-3-yl)ethyl]-3-pyridin-3-yl-4,5-dihydrothieno[2,3-c]pyridin-7-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic500.1100uM
6-chloro-N-(1H-indol-4-yl)-1-benzothiophene-2-carboxamide1561253: Inhibition of human N-terminal His6-tagged TEV protease site linked DHPS expressed in Escherichia coli BL21 (DE3) assessed as reduction in radiolabelled amino-butylidene incorporation in eIF5A using [3H]Spermidine trichloride as substrate after 90 to 120 mins in presence of eIF5A and 14 uM NAD+ by Topcount scintillation counting methodic500.1200uM
2-(7-aminoheptyl)guanidine1561253: Inhibition of human N-terminal His6-tagged TEV protease site linked DHPS expressed in Escherichia coli BL21 (DE3) assessed as reduction in radiolabelled amino-butylidene incorporation in eIF5A using [3H]Spermidine trichloride as substrate after 90 to 120 mins in presence of eIF5A and 14 uM NAD+ by Topcount scintillation counting methodic500.1400uM
6-(2-hydroxy-1-phenylethyl)-3-pyridin-3-yl-4,5-dihydrothieno[2,3-c]pyridin-7-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic500.1500uM
6-[(1S)-2-amino-1-phenylethyl]-3-pyridin-3-yl-4,5-dihydrothieno[2,3-c]pyridin-7-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic500.1600uM
2-[6-amino-5-(2-methoxyphenoxy)-2-(4-methylphenyl)pyrimidin-4-yl]oxyethanol1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic500.1800uM
6-chloro-2-(4-iodophenyl)-5-(2-methoxyphenoxy)pyrimidin-4-amine1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic500.1800uM
2-[6-amino-2-benzyl-5-(2-methoxyphenoxy)pyrimidin-4-yl]oxyethanol1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic500.3200uM
2-[6-amino-2-(3-fluorophenyl)-5-(2-methoxyphenoxy)pyrimidin-4-yl]oxyethanol1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic500.3300uM
6-cyano-N-(1H-indol-4-yl)-1-benzothiophene-2-carboxamide1561253: Inhibition of human N-terminal His6-tagged TEV protease site linked DHPS expressed in Escherichia coli BL21 (DE3) assessed as reduction in radiolabelled amino-butylidene incorporation in eIF5A using [3H]Spermidine trichloride as substrate after 90 to 120 mins in presence of eIF5A and 14 uM NAD+ by Topcount scintillation counting methodic500.4300uM
6-(3-amino-1-phenylpropyl)-3-pyridin-3-yl-4,5-dihydrothieno[2,3-c]pyridin-7-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic500.4400uM
6-chloro-5-(2-methoxyphenoxy)-2-phenylpyrimidin-4-amine1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic500.5300uM
2-[6-amino-2-(3-iodophenyl)-5-(2-methoxyphenoxy)pyrimidin-4-yl]oxyethanol1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic500.5600uM
6-chloro-2-(4-fluorophenyl)-5-(2-methoxyphenoxy)pyrimidin-4-amine1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic500.6400uM
4-tert-butyl-N-(1H-indol-4-yl)benzamide1561253: Inhibition of human N-terminal His6-tagged TEV protease site linked DHPS expressed in Escherichia coli BL21 (DE3) assessed as reduction in radiolabelled amino-butylidene incorporation in eIF5A using [3H]Spermidine trichloride as substrate after 90 to 120 mins in presence of eIF5A and 14 uM NAD+ by Topcount scintillation counting methodic500.8400uM
2-[6-amino-5-(2-methoxyphenoxy)-2-(3-methylphenyl)pyrimidin-4-yl]oxyethanol1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic501.1700uM
2-[6-amino-2-(4-iodophenyl)-5-(2-methoxyphenoxy)pyrimidin-4-yl]oxyethanol1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic502.2900uM
N-(1H-indol-4-yl)-1-benzothiophene-2-carboxamide1561253: Inhibition of human N-terminal His6-tagged TEV protease site linked DHPS expressed in Escherichia coli BL21 (DE3) assessed as reduction in radiolabelled amino-butylidene incorporation in eIF5A using [3H]Spermidine trichloride as substrate after 90 to 120 mins in presence of eIF5A and 14 uM NAD+ by Topcount scintillation counting methodic502.3000uM
2-[6-amino-2-(4-fluorophenyl)-5-(2-methoxyphenoxy)pyrimidin-4-yl]oxyethanol1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic502.3800uM
2-[6-amino-2-(3-bromophenyl)-5-(2-methoxyphenoxy)pyrimidin-4-yl]oxyethanol1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic504.3100uM
2-[6-amino-2-(3-chlorophenyl)-5-(2-methoxyphenoxy)pyrimidin-4-yl]oxyethanol1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic504.4200uM
6-tert-butyl-N-(1H-indol-4-yl)-1-benzothiophene-2-carboxamide1561253: Inhibition of human N-terminal His6-tagged TEV protease site linked DHPS expressed in Escherichia coli BL21 (DE3) assessed as reduction in radiolabelled amino-butylidene incorporation in eIF5A using [3H]Spermidine trichloride as substrate after 90 to 120 mins in presence of eIF5A and 14 uM NAD+ by Topcount scintillation counting methodic505.4000uM
2-[6-amino-2-(2-fluorophenyl)-5-(2-methoxyphenoxy)pyrimidin-4-yl]oxyethanol1820366: Inhibition of DHPS (unknown origin ) incubated for 30 mins by NAD/NADH-Glow assayic505.4300uM
6-benzyl-3-pyridin-3-yl-4,5-dihydrothieno[2,3-c]pyridin-7-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic506.3000uM
2-benzyl-5-pyridin-3-yl-3,4-dihydroisoquinolin-1-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic508.2000uM
2-benzyl-5-pyridin-3-ylisoquinolin-1-one1943588: Displacement of [3H]spermidine trihydrochloride from N-terminal 6his tagged TEV fused human DHPS expressed in Escherichia coli BL21 (DE3) incubated for 120 mins in the presence of 14 uM NAD+ by radiometric assayic508.7000uM

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
decabromobiphenyl etheraffects expression, increases expression2
Tretinoindecreases expression, increases expression2
Valproic Acidaffects expression, decreases expression2
FR900359increases phosphorylation1
TAK-243increases sumoylation1
triphenyl phosphateaffects expression1
alpha-pineneaffects cotreatment, increases expression, increases abundance1
bisphenol Adecreases expression1
beta-lapachoneincreases expression1
sodium arsenitedecreases expression1
cobaltous chloridedecreases expression1
tetrabromobisphenol Adecreases expression1
methacrylaldehydeaffects cotreatment, increases expression, increases abundance1
corosolic acidincreases expression1
2,2’,4,4’-tetrabromodiphenyl etherincreases expression1
pentabrominated diphenyl ether 100increases expression1
Temozolomidedecreases expression1
Sunitinibdecreases expression1
Acroleinaffects cotreatment, increases expression, increases abundance1
Air Pollutantsaffects cotreatment, increases abundance, increases expression1
Benzo(a)pyreneaffects methylation1
Carbamazepineaffects expression1
Dinitrochlorobenzeneaffects binding1
Doxorubicinincreases expression1
Ivermectindecreases expression1
Leaddecreases expression1
Methyl Methanesulfonatedecreases expression1
Nicotinedecreases expression1
Ozoneaffects cotreatment, increases expression, increases abundance1
Rotenoneincreases expression1

ChEMBL screening assays

12 unique, capped per target: 7 binding, 5 functional

Representative assays (with source publication via chembl_document):

Assay IDTypeDescriptionSource paper
CHEMBL4358945BindingInhibition of human N-terminal His6-tagged TEV protease site linked DHPS expressed in Escherichia coli BL21 (DE3) assessed as reduction in radiolabelled amino-butylidene incorporation in eIF5A using [3H]Spermidine trichloride as substrate aDiscovery of Novel Allosteric Inhibitors of Deoxyhypusine Synthase. — J Med Chem
CHEMBL653163FunctionalEffect on hypusine synthesis in CHO cells at concentration 10 uM.Diamine and triamine analogs and derivatives as inhibitors of deoxyhypusine synthase: synthesis and biological activity. — J Med Chem

Clinical trials (associated diseases)

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