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EGLN3 egl-9 family hypoxia inducible factor 3 [ Homo sapiens (human) ]

Gene ID: 112399, updated on 7-Apr-2024

Summary

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Official Symbol
EGLN3provided by HGNC
Official Full Name
egl-9 family hypoxia inducible factor 3provided by HGNC
Primary source
HGNC:HGNC:14661
See related
Ensembl:ENSG00000129521 MIM:606426; AllianceGenome:HGNC:14661
Gene type
protein coding
RefSeq status
VALIDATED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
PHD3; HIFPH3; HIFP4H3
Summary
Enables peptidyl-proline 4-dioxygenase activity. Involved in several processes, including activation of cysteine-type endopeptidase activity involved in apoptotic process; peptidyl-proline hydroxylation to 4-hydroxy-L-proline; and response to hypoxia. Located in cytosol and nucleus. Implicated in renal cell carcinoma. Biomarker of clear cell renal cell carcinoma. [provided by Alliance of Genome Resources, Apr 2022]
Expression
Broad expression in skin (RPKM 31.3), heart (RPKM 27.7) and 16 other tissues See more
Orthologs
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Genomic context

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See EGLN3 in Genome Data Viewer
Location:
14q13.1
Exon count:
5
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 14 NC_000014.9 (33924227..33951074, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 14 NC_060938.1 (28121430..28148293, complement)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 14 NC_000014.8 (34393433..34420280, complement)

Chromosome 14 - NC_000014.9Genomic Context describing neighboring genes Neighboring gene neuronal PAS domain protein 3 Neighboring gene uncharacterized LOC124903300 Neighboring gene Sharpr-MPRA regulatory region 868 Neighboring gene small nucleolar RNA, H/ACA box 89 Neighboring gene Sharpr-MPRA regulatory region 9495 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr14:34366891-34367394 Neighboring gene GATA motif-containing MPRA enhancer 110 Neighboring gene NANOG hESC enhancer GRCh37_chr14:34400622-34401183 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr14:34407170-34408141 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8243 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 5660 Neighboring gene uncharacterized LOC102724945 Neighboring gene uncharacterized LOC105370446 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:34433111-34433612 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8244 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8245 Neighboring gene Sharpr-MPRA regulatory region 12661 Neighboring gene BRD4-independent group 4 enhancer GRCh37_chr14:34512642-34513841 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 8247 Neighboring gene H3K27ac hESC enhancer GRCh37_chr14:34529023-34529524 Neighboring gene EGLN3 antisense RNA 1

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. PHD3 as a Prognosis Marker and its Relationship with Immune Infiltration in Lung Adenocarcinoma. Wang L, et al. Comb Chem High Throughput Screen, 2022. PMID 35088661
  2. Development of a colorimetric α-ketoglutarate detection assay for prolyl hydroxylase domain (PHD) proteins. Wong SJ, et al. J Biol Chem, 2021 Jan-Jun. PMID 33571527, Free PMC Article
  3. Decreased prolyl hydroxylase 3 mRNA expression in oncocytomas compared with clear cell renal cell carcinoma. Kampantais S, et al. Int J Biol Markers, 2020 Dec. PMID 33118406
  4. PHD3 Controls Lung Cancer Metastasis and Resistance to EGFR Inhibitors through TGFα. Dopeso H, et al. Cancer Res, 2018 Apr 1. PMID 29339541
  5. PHD3 affects gastric cancer progression by negatively regulating HIF1A. Xia YJ, et al. Mol Med Rep, 2017 Nov. PMID 28901473

See all (134) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. Low nuclear expression of HIF-hydroxylases PHD2/EGLN1 and PHD3/EGLN3 are associated with poor recurrence-free survival in clear cell renal cell carcinoma.
    Title: Low nuclear expression of HIF-hydroxylases PHD2/EGLN1 and PHD3/EGLN3 are associated with poor recurrence-free survival in clear cell renal cell carcinoma.
  2. EGLN3 attenuates gastric cancer cell malignant characteristics by inhibiting JMJD8/NF-kappaB signalling activation independent of hydroxylase activity.
    Title: EGLN3 attenuates gastric cancer cell malignant characteristics by inhibiting JMJD8/NF-ÎşB signalling activation independent of hydroxylase activity.
  3. E3 ligase MAEA-mediated ubiquitination and degradation of PHD3 promotes glioblastoma progression.
    Title: E3 ligase MAEA-mediated ubiquitination and degradation of PHD3 promotes glioblastoma progression.
  4. PHD3 as a Prognosis Marker and its Relationship with Immune Infiltration in Lung Adenocarcinoma.
    Title: PHD3 as a Prognosis Marker and its Relationship with Immune Infiltration in Lung Adenocarcinoma.
  5. Inactivation of EGLN3 hydroxylase facilitates Erk3 degradation via autophagy and impedes lung cancer growth.
    Title: Inactivation of EGLN3 hydroxylase facilitates Erk3 degradation via autophagy and impedes lung cancer growth.
  6. PHD3 Loss Promotes Exercise Capacity and Fat Oxidation in Skeletal Muscle.
    Title: PHD3 Loss Promotes Exercise Capacity and Fat Oxidation in Skeletal Muscle.
  7. USP9X promotes apoptosis in cholangiocarcinoma by modulation expression of KIF1Bbeta via deubiquitinating EGLN3.
    Title: USP9X promotes apoptosis in cholangiocarcinoma by modulation expression of KIF1Bβ via deubiquitinating EGLN3.
  8. Development of a colorimetric alpha-ketoglutarate detection assay for prolyl hydroxylase domain (PHD) proteins.
    Title: Development of a colorimetric α-ketoglutarate detection assay for prolyl hydroxylase domain (PHD) proteins.
  9. Decreased prolyl hydroxylase 3 mRNA expression in oncocytomas compared with clear cell renal cell carcinoma.
    Title: Decreased prolyl hydroxylase 3 mRNA expression in oncocytomas compared with clear cell renal cell carcinoma.
  10. Prolyl Hydroxylase 3 Knockdown Accelerates VHL-Mutant Kidney Cancer Growth In Vivo.
    Title: Prolyl Hydroxylase 3 Knockdown Accelerates VHL-Mutant Kidney Cancer Growth In Vivo.
Submit: New GeneRIF Correction See all GeneRIFs (86)

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

  • FLJ21620, MGC125998, MGC125999

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 2-oxoglutarate-dependent dioxygenase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables L-ascorbic acid binding IEA
Inferred from Electronic Annotation
more info
  
enables ferrous iron binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables hypoxia-inducible factor-proline dioxygenase activity IEA
Inferred from Electronic Annotation
more info
  
enables peptidyl-proline 4-dioxygenase activity IBA
Inferred from Biological aspect of Ancestor
more info
  
enables peptidyl-proline 4-dioxygenase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
Process Evidence Code Pubs
involved_in DNA damage response IEA
Inferred from Electronic Annotation
more info
  
involved_in activation of cysteine-type endopeptidase activity involved in apoptotic process IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in apoptotic process IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in cellular response to hypoxia IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in peptidyl-proline hydroxylation to 4-hydroxy-L-proline IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in peptidyl-proline hydroxylation to 4-hydroxy-L-proline IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in protein hydroxylation IDA
Inferred from Direct Assay
more info
 PubMed 
involved_in regulation of cell population proliferation IEP
Inferred from Expression Pattern
more info
 PubMed 
involved_in regulation of neuron apoptotic process ISS
Inferred from Sequence or Structural Similarity
more info
  
involved_in response to hypoxia IEP
Inferred from Expression Pattern
more info
 PubMed 
Component Evidence Code Pubs
is_active_in cytoplasm IBA
Inferred from Biological aspect of Ancestor
more info
  
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 TAS
Traceable Author Statement
more info
  
is_active_in nucleus IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in nucleus IDA
Inferred from Direct Assay
more info
 PubMed 

General protein information

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Preferred Names
prolyl hydroxylase EGLN3
Names
HIF-PH3
HIF-prolyl hydroxylase 3
HPH-1
HPH-3
hypoxia-inducible factor prolyl hydroxylase 3
prolyl hydroxylase domain-containing protein 3
NP_001295032.1
NP_071356.1

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_001308103.2 → NP_001295032.1  prolyl hydroxylase EGLN3 isoform 2

    See identical proteins and their annotated locations for NP_001295032.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) uses an alternate in-frame splice site in the 5' coding region compared to variant 1. It encodes isoform 2, which lacks a portion of the 5' coding region compared to isoform 1.
    Source sequence(s)
    AJ310545, AK123350, AL358340, BC102030, BX091357
    Consensus CDS
    CCDS76671.1
    UniProtKB/TrEMBL
    F8W1G2, Q3T1B0
    Related
    ENSP00000447470.1, ENST00000553215.5
    Conserved Domains (1) summary
    smart00702
    Location:24 → 119
    P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

  2. NM_022073.4 → NP_071356.1  prolyl hydroxylase EGLN3 isoform 1

    See identical proteins and their annotated locations for NP_071356.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).
    Source sequence(s)
    AK025273, AL358340
    Consensus CDS
    CCDS9646.1
    UniProtKB/Swiss-Prot
    Q2TA79, Q3B8N4, Q6P1R2, Q9H6Z9
    UniProtKB/TrEMBL
    B3KVT0
    Related
    ENSP00000250457.4, ENST00000250457.9
    Conserved Domains (1) summary
    smart00702
    Location:36 → 213
    P4Hc; Prolyl 4-hydroxylase alpha subunit homologues

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_000014.9 Reference GRCh38.p14 Primary Assembly

    Range
    33924227..33951074 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060938.1 Alternate T2T-CHM13v2.0

    Range
    28121430..28148293 complement
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q9H6Z9.1 GenPept UniProtKB/Swiss-Prot:Q9H6Z9

Gene LinkOut

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