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DPH1 diphthamide biosynthesis 1 [ Homo sapiens (human) ]

Gene ID: 1801, updated on 5-Mar-2024

Summary

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Official Symbol
DPH1provided by HGNC
Official Full Name
diphthamide biosynthesis 1provided by HGNC
Primary source
HGNC:HGNC:3003
See related
Ensembl:ENSG00000108963 MIM:603527; AllianceGenome:HGNC:3003
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
DPH2L; OVCA1; DEDSSH; DPH2L1
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 exotoxin A. Defects in this gene have been associated with both ovarian cancer and autosomal recessive intellectual disability with short stature, craniofacial, and ectodermal anomalies. [provided by RefSeq, Oct 2016]
Expression
Ubiquitous expression in prostate (RPKM 16.8), thyroid (RPKM 16.0) and 25 other tissues See more
Orthologs
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Genomic context

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Location:
17p13.3
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (2030112..2043898)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (1918050..1931805)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 17 NC_000017.10 (1933406..1947192)

Chromosome 17 - NC_000017.11Genomic Context describing neighboring genes Neighboring gene replication protein A1 Neighboring gene succinate dehydrogenase complex subunit C pseudogene Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7965 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11459 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11460 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1810454-1810962 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1810963-1811470 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:1825407-1825589 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1834946-1835511 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1835512-1836076 Neighboring gene ReSE screen-validated silencer GRCh37_chr17:1846458-1846649 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1849416-1849974 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1851145-1851648 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1851649-1852150 Neighboring gene reticulon 4 receptor like 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1866080-1866746 Neighboring gene MPRA-validated peak2677 silencer Neighboring gene NANOG hESC enhancer GRCh37_chr17:1879245-1879860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1885529-1886370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1886371-1887212 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1889733-1890236 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1890237-1890738 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1894981-1895842 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1895843-1896703 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1903279-1903789 Neighboring gene uncharacterized LOC105371486 Neighboring gene uncharacterized LOC105371485 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11461 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7966 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1927475-1928020 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr17:1929189-1929689 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1933195-1933786 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr17:1933787-1934378 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11462 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7967 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11463 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7968 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7969 Neighboring gene uncharacterized LOC124903896 Neighboring gene OVCA2 serine hydrolase domain containing Neighboring gene microRNA 132 Neighboring gene microRNA 212

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. The functional variant in promoter of OVCA1 was associated with the risk of gastric cancer in the northeast Chinese Han population. Yu L, et al. Pathol Res Pract, 2022 Feb. PMID 34990869
  2. An adult Chinese patient with developmental delay with short stature, dysmorphic features, and sparse hair (Loucks-Innes syndrome). Cheng SSW, et al. Am J Med Genet A, 2021 Jun. PMID 33704902
  3. DPH1 syndrome: two novel variants and structural and functional analyses of seven missense variants identified in syndromic patients. Urreizti R, et al. Eur J Hum Genet, 2020 Jan. PMID 30877278, Free PMC Article
  4. A novel homozygous DPH1 mutation causes intellectual disability and unique craniofacial features. Sekiguchi F, et al. J Hum Genet, 2018 Apr. PMID 29410513
  5. Novel compound heterozygous DPH1 mutations in a patient with the unique clinical features of airway obstruction and external genital abnormalities. Nakajima J, et al. J Hum Genet, 2018 Apr. PMID 29362492

See all (44) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. DPH1 and DPH2 variants that confer susceptibility to diphthamide deficiency syndrome in human cells and yeast models.
    Title: DPH1 and DPH2 variants that confer susceptibility to diphthamide deficiency syndrome in human cells and yeast models.
  2. The functional variant in promoter of OVCA1 was associated with the risk of gastric cancer in the northeast Chinese Han population.
    Title: The functional variant in promoter of OVCA1 was associated with the risk of gastric cancer in the northeast Chinese Han population.
  3. An adult Chinese patient with developmental delay with short stature, dysmorphic features, and sparse hair (Loucks-Innes syndrome).
    Title: An adult Chinese patient with developmental delay with short stature, dysmorphic features, and sparse hair (Loucks-Innes syndrome).
  4. DPH1 syndrome: two novel variants and structural and functional analyses of seven missense variants identified in syndromic patients.
    Title: DPH1 syndrome: two novel variants and structural and functional analyses of seven missense variants identified in syndromic patients.
  5. Identification of the transcription factor Miz1 as an essential regulator of diphthamide biosynthesis using a CRISPR-mediated genome-wide screen.
    Title: Identification of the transcription factor Miz1 as an essential regulator of diphthamide biosynthesis using a CRISPR-mediated genome-wide screen.
  6. novel homozygous DPH1 mutation causes intellectual disability and unique craniofacial features
    Title: A novel homozygous DPH1 mutation causes intellectual disability and unique craniofacial features.
  7. We used WES to identify novel compound heterozygous mutations in DPH1 (c.289delG, p.Glu97Lysfs*8 and c.491T>C, p.Leu164Pro) in a patient from a nonconsanguineous family presenting with intellectual disability, a short stature, craniofacial abnormalities, and external genital abnormalities.
    Title: Novel compound heterozygous DPH1 mutations in a patient with the unique clinical features of airway obstruction and external genital abnormalities.
  8. DPH1 functions as an oncogene in CRC and can be negatively modulated by miR-218-5p to promote CRC tumourigenesis.
    Title: Diphthamide Biosynthesis 1 is a Novel Oncogene in Colorectal Cancer Cells and is Regulated by MiR-218-5p.
  9. Results identified a second homozygous missense variant in DPH1, seen in four members of a founder population, and associated with autosomal recessive intellectual disability with short stature, craniofacial, and ectodermal anomalies.
    Title: Matching two independent cohorts validates DPH1 as a gene responsible for autosomal recessive intellectual disability with short stature, craniofacial, and ectodermal anomalies.
  10. Methylation of the DPH1 promoter causes immunotoxin resistance in acute lymphoblastic leukemia.
    Title: Methylation of the DPH1 promoter causes immunotoxin resistance in acute lymphoblastic leukemia cell line KOPN-8.
Submit: New GeneRIF Correction See all GeneRIFs (11)

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Associated conditions

Description Tests
Developmental delay with short stature, dysmorphic facial features, and sparse hair 1
MedGen: CN323360 OMIM: 616901 GeneReviews: Not available
not available

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • FLJ33211

Gene Ontology Provided by GOA

Function Evidence Code Pubs
contributes_to 2-(3-amino-3-carboxypropyl)histidine synthase activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables 4 iron, 4 sulfur cluster binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in fibroblast proliferation IEA
Inferred from Electronic Annotation
more info
  
involved_in protein histidyl modification to diphthamide IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in protein histidyl modification to diphthamide IEA
Inferred from Electronic Annotation
more info
  
involved_in protein histidyl modification to diphthamide ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in cell junction IDA
Inferred from Direct Assay
more info
  
located_in cytosol TAS
Traceable Author Statement
more info
  
located_in nucleoplasm IDA
Inferred from Direct Assay
more info
  
part_of protein-containing complex ISS
Inferred from Sequence or Structural Similarity
more info
  

General protein information

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Preferred Names
2-(3-amino-3-carboxypropyl)histidine synthase subunit 1
Names
DPH-like 1
DPH1 homolog
DPH2-like 1
S-adenosyl-L-methionine:L-histidine 3-amino-3-carboxypropyltransferase 1
candidate tumor suppressor in ovarian cancer 1
diphthamide biosynthesis protein 1
diphthamide biosynthesis protein 2 homolog-like 1
diphtheria toxin resistance protein 1
diptheria toxin resistance protein required for diphthamide biosynthesis (Saccharomyces)-like 1
ovarian cancer-associated gene 1 protein
ovarian tumor suppressor candidate 1
NP_001333503.1
NP_001333504.1
NP_001333505.1
NP_001374.4

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_051946.1 RefSeqGene

    Range
    5042..18787
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001346574.1 → NP_001333503.1  2-(3-amino-3-carboxypropyl)histidine synthase subunit 1 isoform 2

    Status: REVIEWED

    Source sequence(s)
    AC090617, AC099684
    UniProtKB/TrEMBL
    I3L1H5

  2. NM_001346575.1 → NP_001333504.1  2-(3-amino-3-carboxypropyl)histidine synthase subunit 1 isoform 3

    Status: REVIEWED

    Source sequence(s)
    AC090617, AC099684
    UniProtKB/TrEMBL
    I3L1H5

  3. NM_001346576.2 → NP_001333505.1  2-(3-amino-3-carboxypropyl)histidine synthase subunit 1 isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC090617, AF321876, BC096088, U34880
    UniProtKB/TrEMBL
    B2RA29

  4. NM_001383.6 → NP_001374.4  2-(3-amino-3-carboxypropyl)histidine synthase subunit 1 isoform 1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longest isoform (1).
    Source sequence(s)
    AC090617, AF321876, U34880
    Consensus CDS
    CCDS42228.2
    UniProtKB/Swiss-Prot
    A0A6Q8JGF9, D3DTI3, Q16439, Q4VBA2, Q9BTW7, Q9BZG8, Q9UCY0
    UniProtKB/TrEMBL
    I3L1H5
    Related
    ENSP00000263083.7, ENST00000263083.12
    Conserved Domains (1) summary
    pfam01866
    Location:76 → 377
    Diphthamide_syn; Putative diphthamide synthesis protein

RNA

  1. NR_144474.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC090617, AC099684
    Related
    ENST00000575667.6

  2. NR_144475.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC090617, AC099684

  3. NR_144476.2 RNA Sequence

    Status: REVIEWED

    Source sequence(s)
    AC090617, AC099684

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000017.11 Reference GRCh38.p14 Primary Assembly

    Range
    2030112..2043898
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060941.1 Alternate T2T-CHM13v2.0

    Range
    1918050..1931805
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9BZG8.3 GenPept UniProtKB/Swiss-Prot:Q9BZG8

Gene LinkOut

The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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