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DPH3 diphthamide biosynthesis 3 [ Homo sapiens (human) ]

Gene ID: 285381, updated on 5-Mar-2024

Summary

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Official Symbol
DPH3provided by HGNC
Official Full Name
diphthamide biosynthesis 3provided by HGNC
Primary source
HGNC:HGNC:27717
See related
Ensembl:ENSG00000154813 MIM:608959; AllianceGenome:HGNC:27717
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
DESR1; DPH3A; KTI11; ZCSL2; DELGIP; DELGIP1
Summary
This gene encodes a CSL zinc finger-containing protein that is required for dipthamide biosynthesis. The encoded protein is necessary for the initial step in the modification of a histidine residue in elongation factor-2 to diphthamide. This modified residue is a target for ADP ribosylation by the bacterial toxins diphtheria toxin and Pseudomonas exotoxin A. Alternative splicing results in multiple transcript variants that encode the same isoform. [provided by RefSeq, Feb 2009]
Expression
Ubiquitous expression in thyroid (RPKM 7.2), small intestine (RPKM 6.5) and 25 other tissues See more
Orthologs
mouse all
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Genomic context

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Location:
3p25.1
Exon count:
3
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 3 NC_000003.12 (16257061..16264943, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 3 NC_060927.1 (16258288..16266169, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 3 NC_000003.11 (16298568..16306450, complement)

Chromosome 3 - NC_000003.12Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC124906216 Neighboring gene uncharacterized LOC124909349 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19539 Neighboring gene polypeptide N-acetylgalactosaminyltransferase 15 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:16285879-16286378 Neighboring gene Sharpr-MPRA regulatory region 8904 Neighboring gene uncharacterized LOC124906218 Neighboring gene H3K27ac hESC enhancer GRCh37_chr3:16297189-16297690 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 19540 Neighboring gene oxidoreductase NAD binding domain containing 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14113 Neighboring gene THAP domain containing 5 pseudogene 2 Neighboring gene uncharacterized LOC107986065 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 14114 Neighboring gene OCT4-NANOG hESC enhancer GRCh37_chr3:16343021-16343602

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. Solution structure of human DESR1, a CSL zinc-binding protein. Wu F, et al. Proteins, 2008 Apr. PMID 18214955
  2. Frequent DPH3 promoter mutations in skin cancers. Denisova E, et al. Oncotarget, 2015 Nov 3. PMID 26416425, Free PMC Article
  3. Dph3, a small protein required for diphthamide biosynthesis, is essential in mouse development. Liu S, et al. Mol Cell Biol, 2006 May. PMID 16648478, Free PMC Article
  4. Retroviral insertional mutagenesis identifies a small protein required for synthesis of diphthamide, the target of bacterial ADP-ribosylating toxins. Liu S, et al. Mol Cell, 2003 Sep. PMID 14527407
  5. Characterisation of an evolutionary conserved protein interacting with the putative guanine nucleotide exchange factor DelGEF and modulating secretion. Sjölinder M, et al. Exp Cell Res, 2004 Mar 10. PMID 14980502

See all (19) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. The results from this study show occurrence of frequent somatic non-coding mutations adjacent to a pre-existing binding site for Ets transcription factors within the directional promoter of DPH3 and OXNAD1 genes in three major skin cancers.
    Title: Frequent DPH3 promoter mutations in skin cancers.
  2. Solution structure of human DESR1, a CSL zinc-binding protein.
    Title: Solution structure of human DESR1, a CSL zinc-binding protein.
  3. DelGIP1is a binding partner of deafness locus putative guanine nucleotide exchange factor; downregulation of DelGIP1 induced increased extracellular secretion of proteoglycans indicating a possible role for DelGIP1 in the secretion process
    Title: Characterisation of an evolutionary conserved protein interacting with the putative guanine nucleotide exchange factor DelGEF and modulating secretion.
Submit: New GeneRIF Correction

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

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

  • MGC20197

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables ferrous iron binding ISS
Inferred from Sequence or Structural Similarity
more info
  
enables iron chaperone activity ISS
Inferred from Sequence or Structural Similarity
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in negative regulation of protein secretion IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in positive regulation of binding IDA
Inferred from Direct Assay
more info
 PubMed 
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
  
involved_in tRNA wobble base 5-methoxycarbonylmethyl-2-thiouridinylation ISS
Inferred from Sequence or Structural Similarity
more info
  
Component Evidence Code Pubs
located_in cytoplasm IDA
Inferred from Direct Assay
more info
 PubMed 
located_in cytosol 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
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
diphthamide biosynthesis protein 3
Names
CSL-type zinc finger-containing protein 2
DPH3 homolog (KTI11, S. cerevisiae)
DPH3, KTI11 homolog
DPH3A, KTI11 homolog A
Del-GEF interacting protein
deafness locus putative guanine nucleotide exchange factor interacting protein 1
delGEF-interacting protein 1
diphtheria toxin and Pseudomonas exotoxin A sensitivity required gene 1
zinc finger, CSL domain containing 2
zinc finger, CSL-type containing 2

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.

mRNA and Protein(s)

  1. NM_001047434.3 → NP_001040899.1  diphthamide biosynthesis protein 3 isoform 2

    See identical proteins and their annotated locations for NP_001040899.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks an exon in the coding region but maintains the reading frame compared to variant 1. This variant encodes isoform 2, which is shorter than isoform 1.
    Source sequence(s)
    AC090953, AK022970
    Consensus CDS
    CCDS43058.1
    UniProtKB/Swiss-Prot
    Q96FX2
    Related
    ENSP00000373285.4, ENST00000383775.4
    Conserved Domains (1) summary
    pfam05207
    Location:6 → 45
    zf-CSL; CSL zinc finger

  2. NM_206831.3 → NP_996662.1  diphthamide biosynthesis protein 3 isoform 1

    See identical proteins and their annotated locations for NP_996662.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AC090953, DA875039
    Consensus CDS
    CCDS2629.1
    UniProtKB/Swiss-Prot
    Q96FX2
    Related
    ENSP00000419599.1, ENST00000488423.2
    Conserved Domains (1) summary
    pfam05207
    Location:6 → 60
    zf-CSL; CSL zinc finger

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_000003.12 Reference GRCh38.p14 Primary Assembly

    Range
    16257061..16264943 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060927.1 Alternate T2T-CHM13v2.0

    Range
    16258288..16266169 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q96FX2.1 GenPept UniProtKB/Swiss-Prot:Q96FX2

Gene LinkOut

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