DPH3 diphthamide biosynthesis 3 [Homo sapiens (human)] - Gene

Summary

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

Location:: 3p25.1

Exon count:: 3

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	3	NC_000003.12 (16257061..16264943, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	3	NC_060927.1 (16258288..16266169, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	3	NC_000003.11 (16298568..16306450, complement)

Chromosome 3 - NC_000003.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
Solution structure of human DESR1, a CSL zinc-binding protein.
Title: Solution structure of human DESR1, a CSL zinc-binding protein.
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.

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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 Variation Viewer (GRCh37.p13)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

SHGC-30634 (e-PCR)
- UniSTS:35587

SHGC-76745 (e-PCR)
- UniSTS:69933

G42949 (e-PCR)
- UniSTS:94837

RH102557 (e-PCR)
- UniSTS:96891

A008J21 (e-PCR)
- UniSTS:64893

D3S2963E (e-PCR)
- UniSTS:150947

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)

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
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