Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	1801
Gene name	Diphthamide biosynthesis 1
Gene symbol	DPH1
Synonyms (NCBI Gene)	DEDSSHDPH2LDPH2L1OVCA1
Chromosome	17
Chromosome location	17p13.3
Summary	The protein encoded by this gene is an enzyme involved in the biosynthesis of diphthamide, a modified histidine found only in elongation factor-2 (EEF2). Diphthamide residues in EEF2 are targeted for ADP-ribosylation by diphtheria toxin and Pseudomonas ex

Show/Hide all (5)

SNP ID	Visualize variation	Clinical significance	Consequence
rs200530055	T>C	Likely-pathogenic, uncertain-significance	Non coding transcript variant, intron variant, coding sequence variant, missense variant
rs730882250	T>C,G	Pathogenic, likely-pathogenic	Coding sequence variant, missense variant, non coding transcript variant
rs756128712	G>-	Pathogenic	Coding sequence variant, frameshift variant, 5 prime UTR variant, non coding transcript variant
rs757167361	T>A,C,G	Likely-pathogenic, pathogenic	Coding sequence variant, missense variant, 5 prime UTR variant, initiator codon variant, non coding transcript variant
rs763506909	->T	Likely-pathogenic	Coding sequence variant, frameshift variant, non coding transcript variant

Show/Hide all (38)

miRTarBase ID	miRNA	Experiments	Reference
MIRT004180	hsa-miR-197-3p	Microarray	16822819
MIRT041212	hsa-miR-193b-3p	CLASH	23622248
MIRT038600	hsa-miR-106b-3p	CLASH	23622248
MIRT943845	hsa-miR-4649-3p	CLIP-seq
MIRT1979507	hsa-miR-374a	CLIP-seq
MIRT1979508	hsa-miR-374b	CLIP-seq
MIRT2518866	hsa-miR-1255a	CLIP-seq
MIRT2518867	hsa-miR-1255b	CLIP-seq
MIRT2518868	hsa-miR-1343	CLIP-seq
MIRT2518869	hsa-miR-1913	CLIP-seq
MIRT2518870	hsa-miR-3125	CLIP-seq
MIRT2518871	hsa-miR-3174	CLIP-seq
MIRT2518872	hsa-miR-3192	CLIP-seq
MIRT2518873	hsa-miR-3197	CLIP-seq
MIRT2518874	hsa-miR-324-3p	CLIP-seq
MIRT2518875	hsa-miR-3616-3p	CLIP-seq
MIRT2518876	hsa-miR-3622b-5p	CLIP-seq
MIRT2518877	hsa-miR-3689a-3p	CLIP-seq
MIRT2518878	hsa-miR-3689c	CLIP-seq
MIRT2518879	hsa-miR-3916	CLIP-seq
MIRT2518880	hsa-miR-4253	CLIP-seq
MIRT2518881	hsa-miR-4299	CLIP-seq
MIRT2518882	hsa-miR-4316	CLIP-seq
MIRT2518883	hsa-miR-4456	CLIP-seq
MIRT2518884	hsa-miR-4481	CLIP-seq
MIRT2518885	hsa-miR-4519	CLIP-seq
MIRT2518886	hsa-miR-4710	CLIP-seq
MIRT2518887	hsa-miR-4728-5p	CLIP-seq
MIRT2518888	hsa-miR-4745-5p	CLIP-seq
MIRT2518889	hsa-miR-4749-3p	CLIP-seq
MIRT2518890	hsa-miR-4758-5p	CLIP-seq
MIRT2518891	hsa-miR-4761-3p	CLIP-seq
MIRT2518892	hsa-miR-4792	CLIP-seq
MIRT2518893	hsa-miR-485-5p	CLIP-seq
MIRT2518894	hsa-miR-490-5p	CLIP-seq
MIRT2518895	hsa-miR-548q	CLIP-seq
MIRT2518896	hsa-miR-582-3p	CLIP-seq
MIRT2518897	hsa-miR-877	CLIP-seq

Show/Hide all (19)

GO ID	Ontology	Definition	Evidence	Reference
GO:0005515	Function	Protein binding	IPI	25416956
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0005737	Component	Cytoplasm	IEA
GO:0005829	Component	Cytosol	TAS
GO:0016740	Function	Transferase activity	IEA
GO:0017183	Process	Protein histidyl modification to diphthamide	IBA
GO:0017183	Process	Protein histidyl modification to diphthamide	IEA
GO:0017183	Process	Protein histidyl modification to diphthamide	ISS
GO:0030054	Component	Cell junction	IDA
GO:0032991	Component	Protein-containing complex	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0048144	Process	Fibroblast proliferation	IEA
GO:0051536	Function	Iron-sulfur cluster binding	IEA
GO:0051539	Function	4 iron, 4 sulfur cluster binding	ISS
GO:0090560	Function	2-(3-amino-3-carboxypropyl)histidine synthase activity	IEA
GO:0090560	Function	2-(3-amino-3-carboxypropyl)histidine synthase activity	ISS
GO:0120513	Component	2-(3-amino-3-carboxypropyl)histidine synthase complex	IEA
GO:0120513	Component	2-(3-amino-3-carboxypropyl)histidine synthase complex	ISS

MIM	HGNC	e!Ensembl
603527	3003	ENSG00000108963

Q9BZG8

Protein name

2-(3-amino-3-carboxypropyl)histidine synthase subunit 1 (EC 2.5.1.108) (Diphthamide biosynthesis protein 1) (Diphtheria toxin resistance protein 1) (Ovarian cancer-associated gene 1 protein) (S-adenosyl-L-methionine:L-histidine 3-amino-3-carboxypropyltran

Protein function

Catalyzes the first step of diphthamide biosynthesis, a post-translational modification of histidine which occurs in elongation factor 2 (PubMed:30877278). DPH1 and DPH2 transfer a 3-amino-3-carboxypropyl (ACP) group from S-adenosyl-L-methionine

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF01866	Diphthamide_syn	81 → 382	Putative diphthamide synthesis protein	Family

Tissue specificity

TISSUE SPECIFICITY: Expressed in heart, brain, placenta, lung, liver, skeletal muscle, kidney, pancreas, spleen, thymus, mammary gland, colon, small intestine, testis and ovary. Reduced expression in primary breast and ovarian tumors. {ECO:0000269|PubMed:

Sequence

MRRQVMAALVVSGAAEQGGRDGPGRGRAPRGRVANQIPPEILKNPQLQAAIRVLPSNYNF
EIPKTIWRIQQAQAKKVALQMPEGLLLFACTIVDILERFTEAEVMVMGDVTYGACCVDDF
TARALGADFLVHYGHSCLIPMDTSAQDFRVLYVFVDIRIDTTHLLDSLRLTFPPATALAL
VSTIQFVSTLQAAAQELKAEYRVSVPQCKPLSPGEILGCTSPRLSKEVEAVVYLGDGRFH
LESVMIANPNVPAYRYDPYSKVLSREHYDHQRMQAARQEAIATARSAKSWGLILGTLGRQ
GSPKILEHLESRLRALGLSFVRLLLSEIFPSKLSLLPEVDVWVQVACPRLSIDWGTAFPK
PLLTPYEAAVALRDISWQQPYPMDFYAGSSLGPWTVNHGQDRRPHAPGRPARGKVQEGSA
RPPSAVACEDCSCRDEKVAPLAP

Sequence length

443

Interactions

View interactions

	Reactome
			Synthesis of diphthamide-EEF2

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (7)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
Cerebellar vermis hypoplasia	Likely pathogenic; Pathogenic	rs730882250	RCV000162191	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Dandy-Walker syndrome	Likely pathogenic; Pathogenic	rs730882250	RCV000162191	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Developmental delay with short stature, dysmorphic facial features, and sparse hair	Likely pathogenic; Pathogenic	rs2151346853, rs2151347730, rs730882250	RCV001594434 RCV001594435 RCV000210874	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Developmental delay with short stature, dysmorphic facial features, and sparse hair 1	Likely pathogenic; Pathogenic	rs1185902827, rs730882250, rs757167361, rs2151341681, rs756128712, rs2067429826, rs772969956	RCV003147670 RCV003147374 RCV004567447 RCV003479657 RCV004569770 RCV004570672 RCV004570673	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
DPH1-related disorder	Likely pathogenic	rs1185902827	RCV004758196	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Global developmental delay	Likely pathogenic; Pathogenic	rs730882250	RCV000162191	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Hydrocephalus	Likely pathogenic; Pathogenic	rs730882250	RCV000162191	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (4)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
ASTHMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOFACIAL DYSPLASIA, SHORT STATURE, ECTODERMAL ANOMALIES, INTELLECTUAL DISABILITY SYNDROME	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
CRANIOFACIAL DYSPLASIA-SHORT STATURE-ECTODERMAL ANOMALIES-INTELLECTUAL DISABILITY SYNDROME	—	GenCC, Orphanet GenCC, Orphanet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
INTRACEREBRAL HEMORRHAGE	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (10)

Disease Name	Relationship Type	References	Evidence Score
Associations from Text MiningDisease associations identified through Pubtator
3C syndrome	Associate	26220823	★★★★★ ★☆☆☆☆ Found in Text Mining only
Colorectal Neoplasms	Associate	29145210	★★★★★ ★☆☆☆☆ Found in Text Mining only
Congenital Abnormalities	Associate	30877278	★★★★★ ★☆☆☆☆ Found in Text Mining only
Cranioectodermal Dysplasia	Associate	26220823	★★★★★ ★☆☆☆☆ Found in Text Mining only
Craniofacial Abnormalities	Associate	26220823	★★★★★ ★☆☆☆☆ Found in Text Mining only
Developmental Disabilities	Associate	30877278	★★★★★ ★☆☆☆☆ Found in Text Mining only
Growth Disorders	Associate	26220823, 30877278	★★★★★ ★☆☆☆☆ Found in Text Mining only
Intellectual Disability	Associate	26220823	★★★★★ ★☆☆☆☆ Found in Text Mining only
Neoplasms	Associate	29145210	★★★★★ ★☆☆☆☆ Found in Text Mining only
Syndrome	Associate	30877278	★★★★★ ★☆☆☆☆ Found in Text Mining only

DPH1 (diphthamide biosynthesis 1)