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    DPH1 diphthamide biosynthesis 1 [ Homo sapiens (human) ]

    Gene ID: 1801, updated on 3-Nov-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
    mouse all
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    Genomic context

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    See DPH1 in Genome Data Viewer
    Location:
    17p13.3
    Exon count:
    13
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 17 NC_000017.11 (2030112..2043898)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 17 NC_060941.1 (1918050..1931805)
    RS_2024_09 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 SDHC pseudogene 5 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 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. 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
    2. A novel homozygous DPH1 mutation causes intellectual disability and unique craniofacial features. Sekiguchi F, et al. J Hum Genet, 2018 Apr. PMID 29410513
    3. 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
    4. Diphthamide Biosynthesis 1 is a Novel Oncogene in Colorectal Cancer Cells and is Regulated by MiR-218-5p. Liu M, et al. Cell Physiol Biochem, 2017. PMID 29145210
    5. Matching two independent cohorts validates DPH1 as a gene responsible for autosomal recessive intellectual disability with short stature, craniofacial, and ectodermal anomalies. Loucks CM, et al. Hum Mutat, 2015 Oct. PMID 26220823, Free PMC Article

    See all (47) 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
    part_of 2-(3-amino-3-carboxypropyl)histidine synthase complex ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    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
    		  

    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_2024_08

    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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