DPH5

gene
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Also known as CGI-30

Summary

DPH5 (diphthamide biosynthesis 5, HGNC:24270) is a protein-coding gene on chromosome 1p21.2, encoding Diphthine methyl ester synthase (Q9H2P9). S-adenosyl-L-methionine-dependent methyltransferase that catalyzes four methylations of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine methyl ester.

This gene encodes a component of the diphthamide synthesis pathway. Diphthamide is a post-translationally modified histidine residue found only on translation elongation factor 2. It is conserved from archaebacteria to humans, and is targeted by diphtheria toxin and Pseudomonas exotoxin A to halt cellular protein synthesis. The yeast and Chinese hamster homologs of this protein catalyze the trimethylation of the histidine residue on elongation factor 2, resulting in a diphthine moiety that is subsequently amidated to yield diphthamide. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 51611 — RefSeq curated summary.

At a glance

  • Gene–disease (curated): neurodevelopmental disorder with short stature, prominent forehead, and feeding difficulties (Strong, GenCC)
  • GWAS associations: 2
  • Clinical variants (ClinVar): 49 total — 2 pathogenic, 1 likely-pathogenic
  • Phenotypes (HPO): 51
  • MANE Select transcript: NM_015958

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24270
Approved symbolDPH5
Namediphthamide biosynthesis 5
Location1p21.2
Locus typegene with protein product
StatusApproved
AliasesCGI-30
Ensembl geneENSG00000117543
Ensembl biotypeprotein_coding
OMIM611075
Entrez51611

Gene structure

Transcript identifiers

Ensembl transcripts: 31 — 19 protein_coding, 11 protein_coding_CDS_not_defined, 1 retained_intron

ENST00000342173, ENST00000370105, ENST00000370109, ENST00000427040, ENST00000464270, ENST00000466807, ENST00000476507, ENST00000477293, ENST00000481871, ENST00000481982, ENST00000488176, ENST00000488789, ENST00000490732, ENST00000492067, ENST00000498372, ENST00000690716, ENST00000889720, ENST00000889721, ENST00000889722, ENST00000889723, ENST00000889724, ENST00000889725, ENST00000889726, ENST00000889727, ENST00000934681, ENST00000934682, ENST00000934683, ENST00000934684, ENST00000934685, ENST00000934686, ENST00000950006

RefSeq mRNA: 3 — MANE Select: NM_015958 NM_001077394, NM_001077395, NM_015958

CCDS: CCDS41358, CCDS41359

Canonical transcript exons

ENST00000370109 — 8 exons

ExonStartEnd
ENSE00001884314101025683101025784
ENSE00003463741100989623100990631
ENSE00003483636101025309101025466
ENSE00003564931100995110100995149
ENSE00003575411101021641101021765
ENSE00003603023101001467101001587
ENSE00003659612101013710101013818
ENSE00003694217100992637100992740

Expression profiles

Bgee: expression breadth ubiquitous, 286 present calls, max score 94.96.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.9390 / max 823.0704, expressed in 1800 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter IDTPM avgSamples expressed
1353525.99771795
135361.0130671
135340.5552287
135370.3319162
135380.041111

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
body of pancreasUBERON:000115094.96gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099194.63gold quality
left ovaryUBERON:000211994.42gold quality
buccal mucosa cellCL:000233694.36gold quality
ovaryUBERON:000099294.19gold quality
right adrenal glandUBERON:000123393.94gold quality
ganglionic eminenceUBERON:000402393.85gold quality
cortical plateUBERON:000534393.74gold quality
right adrenal gland cortexUBERON:003582793.73gold quality
right ovaryUBERON:000211892.94gold quality
tibialis anteriorUBERON:000138592.87silver quality
ventricular zoneUBERON:000305392.84gold quality
left adrenal glandUBERON:000123492.58gold quality
pancreasUBERON:000126492.58gold quality
left adrenal gland cortexUBERON:003582592.39gold quality
myocardiumUBERON:000234992.16gold quality
adrenal cortexUBERON:000123592.15gold quality
left ventricle myocardiumUBERON:000656692.08gold quality
islet of LangerhansUBERON:000000691.89gold quality
adrenal glandUBERON:000236991.74gold quality
stromal cell of endometriumCL:000225591.70gold quality
embryoUBERON:000092291.52gold quality
adrenal tissueUBERON:001830391.48gold quality
upper leg skinUBERON:000426291.44gold quality
cardiac muscle of right atriumUBERON:000337991.36gold quality
mucosa of urinary bladderUBERON:000125991.34gold quality
deltoidUBERON:000147691.33gold quality
heart left ventricleUBERON:000208491.25gold quality
granulocyteCL:000009491.22gold quality
cardiac ventricleUBERON:000208291.19gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes5.32
E-MTAB-6524no198.12

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

41 targeting DPH5, 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-56899.9869.862084
HSA-MIR-806899.9873.852376
HSA-MIR-548AA99.9670.643753
HSA-MIR-548AP-3P99.9670.643753
HSA-MIR-548T-3P99.9670.643753
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-15A-5P99.9072.802787
HSA-MIR-15B-5P99.9072.782798
HSA-MIR-16-5P99.9072.802780
HSA-MIR-195-5P99.9072.812805
HSA-MIR-4697-3P99.8967.091123
HSA-MIR-2681-5P99.7567.641655
HSA-MIR-6885-3P99.7570.363187
HSA-MIR-29B-2-5P99.6768.981726
HSA-MIR-452799.6667.43714
HSA-MIR-6503-5P99.6266.96597
HSA-MIR-4743-3P99.6268.122095
HSA-MIR-3682-3P99.5867.63865
HSA-MIR-5584-5P99.4968.222814
HSA-MIR-889-5P99.4168.751025
HSA-MIR-135A-5P99.3671.851601
HSA-MIR-135B-5P99.3671.631613
HSA-MIR-4652-3P99.3370.022742
HSA-MIR-450599.2767.812678
HSA-MIR-578799.2267.862628
HSA-MIR-5587-5P99.0768.58838
HSA-MIR-10B-3P99.0466.98988
HSA-MIR-989899.0067.89500
HSA-MIR-4755-3P98.7765.591915

Literature-anchored findings (GeneRIF, showing 1)

  • The yeast and Chinese hamster homologs of human DPH5 catalyze the trimethylation step in the biosynthesis of diphthamide (PMID:15485916)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriodph5ENSDARG00000100242
mus_musculusDph5ENSMUSG00000033554
rattus_norvegicusDph5ENSRNOG00000013719
drosophila_melanogasterDph5FBGN0024558
caenorhabditis_elegansWBGENE00007194

Protein

Protein identifiers

Diphthine methyl ester synthaseQ9H2P9 (reviewed: Q9H2P9)

Alternative names: Diphthamide biosynthesis methyltransferase

All UniProt accessions (2): Q9H2P9, Q96DC6

UniProt curated annotations — full annotation on UniProt →

Function. S-adenosyl-L-methionine-dependent methyltransferase that catalyzes four methylations of the modified target histidine residue in translation elongation factor 2 (EF-2), to form an intermediate called diphthine methyl ester. The four successive methylation reactions represent the second step of diphthamide biosynthesis.

Disease relevance. Neurodevelopmental disorder with short stature, prominent forehead, and feeding difficulties (NEDSFF) [MIM:620070] An autosomal recessive disorder characterized by distinct craniofacial features, multisystem dysfunction, profound neurodevelopmental delays, and neonatal death. The disease is caused by variants affecting the gene represented in this entry.

Pathway. Protein modification; peptidyl-diphthamide biosynthesis.

Similarity. Belongs to the diphthine synthase family.

Isoforms (6)

UniProt IDNamesCanonical?
Q9H2P9-11yes
Q9H2P9-22
Q9H2P9-33
Q9H2P9-44
Q9H2P9-55
Q9H2P9-66

RefSeq proteins (3): NP_001070862, NP_001070863, NP_057042* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR0008784pyrrol_MeaseDomain
IPR004551Dphthn_synthaseFamily
IPR0147764pyrrole_Mease_sub2Homologous_superfamily
IPR0147774pyrrole_Mease_sub1Homologous_superfamily
IPR0359964pyrrol_Methylase_sfHomologous_superfamily

Pfam: PF00590

Enzyme classification (BRENDA):

  • EC 2.1.1.314 — diphthine methyl ester synthase (BRENDA: 5 organisms, 9 substrates, 0 inhibitors, 0 Km, 0 kcat entries)

Catalyzed reactions (Rhea), 1 shown:

  • 2-[(3S)-amino-3-carboxypropyl]-L-histidyl-[translation elongation factor 2] + 4 S-adenosyl-L-methionine = diphthine methyl ester-[translation elongation factor 2] + 4 S-adenosyl-L-homocysteine + 3 H(+) (RHEA:42652)

UniProt features (19 total): binding site 7, splice variant 5, sequence variant 3, sequence conflict 2, chain 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H2P9-F192.200.81

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 (7): 9; 84; 87; 112–113; 163; 225; 250

Post-translational modifications (1): 171

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-5358493Synthesis of diphthamide-EEF2

MSigDB gene sets: 319 (showing top): CREIGHTON_ENDOCRINE_THERAPY_RESISTANCE_1, BLALOCK_ALZHEIMERS_DISEASE_UP, OCT1_03, WTGAAAT_UNKNOWN, ZHOU_INFLAMMATORY_RESPONSE_LIVE_DN, DODD_NASOPHARYNGEAL_CARCINOMA_UP, GATA2_01, GRYDER_PAX3FOXO1_ENHANCERS_IN_TADS, ACEVEDO_LIVER_CANCER_UP, GOBP_METHYLATION, IVANOVA_HEMATOPOIESIS_EARLY_PROGENITOR, chr1p21, OSMAN_BLADDER_CANCER_DN, NUYTTEN_EZH2_TARGETS_DN, GRYDER_PAX3FOXO1_TOP_ENHANCERS

GO Biological Process (2): protein histidyl modification to diphthamide (GO:0017183), methylation (GO:0032259)

GO Molecular Function (4): diphthine methyl ester synthase activity (GO:0141133), diphthine synthase activity (GO:0004164), methyltransferase activity (GO:0008168), transferase activity (GO:0016740)

GO Cellular Component (1): 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 methyltransferase activity2
S-adenosylmethionine-dependent methyltransferase activity2
peptidyl-histidine modification1
metabolic process1
transferase activity, transferring one-carbon groups1
catalytic activity1
cytoplasm1
cellular anatomical structure1

Protein interactions and networks

STRING

1548 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
DPH5DPH2Q9BQC3994
DPH5DPH1Q9BZG8980
DPH5EEF2P13639930
DPH5DPH7Q9BTV6874
DPH5DPH3Q96FX2856
DPH5DPH6Q7L8W6839
DPH5DNAJC24Q6P3W2810
DPH5RTCAO00442614
DPH5ENOSF1Q7L5Y1579
DPH5ARMC9Q7Z3E5569
DPH5ELP5Q8TE02551
DPH5LRRC39Q96DD0537
DPH5RIDAP52758493
DPH5MOB3CQ70IA8493
DPH5TMEM14CQ9P0S9458

IntAct

5 interactions, top by confidence:

ABTypeScore
NHERF1psi-mi:“MI:0914”(association)0.530
LRRK2psi-mi:“MI:0914”(association)0.350

BioGRID (34): DPH5 (Affinity Capture-RNA), DPH5 (Affinity Capture-RNA), DPH5 (Affinity Capture-RNA), C12orf10 (Co-fractionation), CD2AP (Co-fractionation), DPH5 (Co-fractionation), DPH5 (Co-fractionation), DPH5 (Co-fractionation), GCLC (Co-fractionation), NMD3 (Co-fractionation), PARVA (Co-fractionation), SPG20 (Co-fractionation), ZYX (Co-fractionation), DPH5 (Synthetic Lethality), DPH5 (Proximity Label-MS)

ESM2 similar proteins: A0A0K9RL25, A0A0U1WZ18, A0A1S4A695, B9N1F9, O15305, O35621, O80840, O88958, O97555, O97556, P21856, P31150, P46926, P50396, P50398, P50399, P60028, P78330, Q16HW7, Q1W374, Q1W375, Q1W376, Q1W377, Q259G4, Q2KHU0, Q3SZJ9, Q3UFY7, Q4R7R3, Q5E982, Q5R8T8, Q5RB83, Q5ZID6, Q5ZKF6, Q60HD6, Q61598, Q64422, Q6AYP7, Q6Q7J2, Q7SYN4, Q7XPW5

Diamond homologs: A0B879, A1RU15, A2SQF6, A3CWF9, A3DLV7, A4FYP1, A4YHI8, A6US81, A6UU49, A6VJP1, A7IA21, A9A6D8, B0R4W9, B1YAU2, B6YXP9, B8GIF8, B9LV13, C3MPQ5, C3MYP9, C3N5D1, C3NDY5, C3NHR8, C4KGZ7, C5A3K4, O27902, O29866, O58456, O74898, O81769, P0CU37, P32469, Q0W085, Q12XB4, Q18JS3, Q2FQ45, Q2NFJ8, Q3IS55, Q467Z4, Q4HZI0, Q58670

SIGNOR signaling

1 interactions.

AEffectBMechanism
DPH5“down-regulates activity”EEF2methylation

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic2
Likely pathogenic1
Uncertain significance33
Likely benign0
Benign0

Top pathogenic / likely-pathogenic (3)

Variant IDHGVSClassification
1708533NM_015958.3(DPH5):c.619C>T (p.Arg207Ter)Pathogenic
1708534NM_015958.3(DPH5):c.329A>G (p.Asn110Ser)Pathogenic
4849473NM_015958.3(DPH5):c.260+1G>TLikely pathogenic

SpliceAI

1371 predictions. Top by Δscore:

VariantEffectΔscore
1:101021634:GACTT:Gdonor_loss1.0000
1:101021635:ACTTA:Adonor_loss1.0000
1:101021636:CTTAC:Cdonor_loss1.0000
1:101021637:TTA:Tdonor_loss1.0000
1:101021638:T:TGdonor_loss1.0000
1:101021640:C:Tdonor_loss1.0000
1:101021781:CAA:Cacceptor_gain1.0000
1:101021782:A:Tacceptor_gain1.0000
1:101025316:T:TAdonor_gain1.0000
1:101025321:C:Adonor_gain1.0000
1:100990629:CTG:Cacceptor_gain0.9900
1:100995103:AACT:Aacceptor_loss0.9900
1:100995104:ACTT:Aacceptor_loss0.9900
1:100995105:CTT:Cacceptor_loss0.9900
1:100995106:TTAC:Tacceptor_loss0.9900
1:100995107:TACT:Tacceptor_loss0.9900
1:100995108:A:ACdonor_gain0.9900
1:100995108:ACTT:Aacceptor_loss0.9900
1:100995109:C:CCdonor_gain0.9900
1:100995109:C:Tacceptor_loss0.9900
1:100995146:ATGTC:Aacceptor_loss0.9900
1:100995147:TGT:Tacceptor_gain0.9900
1:100995148:GT:Gacceptor_gain0.9900
1:100995149:TC:Tacceptor_loss0.9900
1:100995150:C:Aacceptor_loss0.9900
1:100995150:C:CCacceptor_gain0.9900
1:100995151:T:Gacceptor_loss0.9900
1:101001583:TATAA:Tacceptor_gain0.9900
1:101001585:TAA:Tacceptor_gain0.9900
1:101001588:C:CCacceptor_gain0.9900

AlphaMissense

1863 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
1:101001476:A:GC161R0.998
1:101013741:A:TI113K0.997
1:101001472:A:GL162S0.996
1:101025349:T:AE32V0.996
1:100995149:T:AD164V0.995
1:101001467:C:GD164H0.995
1:101013733:C:GA116P0.995
1:101013745:A:GS112P0.995
1:101013749:A:CN110K0.995
1:101013749:A:TN110K0.995
1:101013808:G:CH91D0.995
1:100990607:A:TV220D0.994
1:100992681:A:GL197P0.994
1:101001562:G:TS132Y0.994
1:101001574:C:AG128V0.994
1:101001574:C:TG128E0.994
1:101013741:A:CI113R0.994
1:101025427:C:TG6E0.994
1:101025428:C:AG6W0.994
1:100995149:T:GD164A0.993
1:101001562:G:AS132F0.993
1:101021653:C:TG83D0.993
1:101021654:C:GG83R0.993
1:101021662:A:TL80H0.993
1:101025389:C:GG19R0.993
1:101025404:C:GD14H0.993
1:101025428:C:GG6R0.993
1:101025428:C:TG6R0.993
1:100990604:C:TG221D0.992
1:100995148:G:CD164E0.992

dbSNP variants (sampled 300 via entrez): RS1000000812 (1:100996675 C>T), RS1000150437 (1:101007620 C>G,T), RS1000181166 (1:101001978 C>T), RS1000399962 (1:101006162 C>T), RS1000440778 (1:100998976 G>A), RS1000444728 (1:101019874 T>C), RS1000471588 (1:100998793 G>T), RS1000507079 (1:101014214 A>G,T), RS1000771063 (1:101005925 G>A,C,T), RS1000777338 (1:101000321 A>C), RS1000808483 (1:101000071 C>T), RS1001105871 (1:101009177 G>C), RS1001148887 (1:101010690 T>C), RS1001281964 (1:100989211 G>A), RS1001341500 (1:100993553 AATATAAATATATATAT>A)

Disease associations

OMIM: gene MIM:611075 | disease phenotypes: MIM:620070

GenCC curated gene-disease

DiseaseClassificationInheritance
neurodevelopmental disorder with short stature, prominent forehead, and feeding difficultiesStrongAutosomal recessive

ClinGen Gene-Disease Validity (1)

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

DiseaseClassificationInheritance
neurodevelopmental disorder with short stature, prominent forehead, and feeding difficultiesLimitedAR

Mondo (1): neurodevelopmental disorder with short stature, prominent forehead, and feeding difficulties (MONDO:0859295)

Orphanet (0):

HPO phenotypes

51 total (30 of 51 shown, HPO-id order):

HPOTerm
HP:0000006Autosomal dominant inheritance
HP:0000020Urinary incontinence
HP:0000218High palate
HP:0000286Epicanthus
HP:0000337Broad forehead
HP:0000341Narrow forehead
HP:0000347Micrognathia
HP:0000348High forehead
HP:0000431Wide nasal bridge
HP:0000490Deeply set eye
HP:0000582Upslanted palpebral fissure
HP:0000637Long palpebral fissure
HP:0000653Sparse eyelashes
HP:0000670Carious teeth
HP:0001182Tapered finger
HP:0001252Hypotonia
HP:0001263Global developmental delay
HP:0001320Cerebellar vermis hypoplasia
HP:0001344Absent speech
HP:0001522Death in infancy
HP:0001558Decreased fetal movement
HP:0001561Polyhydramnios
HP:0001631Atrial septal defect
HP:0001698Pericardial effusion
HP:0001763Pes planus
HP:0001838Rocker bottom foot
HP:0002020Gastroesophageal reflux
HP:0002069Bilateral tonic-clonic seizure
HP:0002187Profound intellectual disability
HP:0002280Enlarged cisterna magna

GWAS associations

2 associations (top):

StudyTraitp-value
GCST001890_9QT interval (drug interaction)3.000000e-06
GCST006535_2Irritable bowel syndrome3.000000e-06

EFO canonical traits (2, from GWAS)

EFO IDTrait name
EFO:0004682QT interval
EFO:0007916response to tricyclic antidepressant

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
sodium arsenitedecreases expression, affects cotreatment, increases abundance, increases expression3
Valproic Aciddecreases expression, increases expression, affects expression3
Tretinoindecreases expression2
Cadmium Chloridedecreases expression2
dicrotophosdecreases expression1
methylmercuric chloridedecreases expression1
bisphenol Aincreases expression1
cobaltous chlorideincreases expression1
manganese chlorideaffects cotreatment, increases abundance, increases expression1
beta-methylcholineaffects expression1
perfluorooctane sulfonic acidincreases expression1
CGP 52608affects binding, increases reaction1
JP8 aviation fueldecreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
Acetaminophendecreases expression1
Air Pollutantsaffects expression, increases abundance1
Arsenicaffects cotreatment, increases abundance, increases expression1
Manganeseincreases expression, affects cotreatment, increases abundance1
Ozoneaffects expression, increases abundance1
Phenylmercuric Acetateaffects cotreatment, decreases expression1
Thiramdecreases expression1
Tobacco Smoke Pollutionincreases methylation1
Tunicamycinincreases expression1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxidedecreases expression1
Cyclosporineincreases expression1
Antirheumatic Agentsincreases expression1
Thapsigarginincreases expression1
Okadaic Aciddecreases expression1
Copper Sulfatedecreases expression1

Clinical trials (associated diseases)

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