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PHYHD1 phytanoyl-CoA dioxygenase domain containing 1 [ Homo sapiens (human) ]

Gene ID: 254295, updated on 8-Mar-2025

Summary

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Official Symbol
PHYHD1provided by HGNC
Official Full Name
phytanoyl-CoA dioxygenase domain containing 1provided by HGNC
Primary source
HGNC:HGNC:23396
See related
Ensembl:ENSG00000175287 MIM:620042; AllianceGenome:HGNC:23396
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
Summary
Enables 2-oxoglutarate-dependent dioxygenase activity. [provided by Alliance of Genome Resources, Mar 2025]
Expression
Ubiquitous expression in kidney (RPKM 11.6), thyroid (RPKM 9.8) and 23 other tissues See more
Orthologs
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Genomic context

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See PHYHD1 in Genome Data Viewer
Location:
9q34.11
Exon count:
13
Annotation release Status Assembly Chr Location
RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (128920982..128942041)
RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (141125761..141145449)
RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (131683261..131704320)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene KYAT1-SPOUT1 readthrough Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131600611-131601111 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:131607420-131607646 Neighboring gene kynurenine aminotransferase 1 Neighboring gene Sharpr-MPRA regulatory region 9337 Neighboring gene Sharpr-MPRA regulatory region 7409 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29094 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20355 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131647725-131648487 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:131654523-131655130 Neighboring gene leucine rich repeat containing 8 VRAC subunit A Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29095 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:131666020-131666192 Neighboring gene uncharacterized LOC101929291 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131672021-131672804 Neighboring gene Sharpr-MPRA regulatory region 12425 Neighboring gene ReSE screen-validated silencer GRCh37_chr9:131704025-131704223 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131708642-131709204 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:131709205-131709766 Neighboring gene H3K27ac hESC enhancer GRCh37_chr9:131709767-131710328 Neighboring gene nucleoporin 188 Neighboring gene dolichol kinase Neighboring gene uncharacterized LOC101929314

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: Tissue-specific circular RNA induction during human fetal development
  • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
  • BioProject: PRJNA270632
  • Publication: PMID 26076956
  • Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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Related articles in PubMed

  1. Human phytanoyl-CoA dioxygenase domain-containing 1 (PHYHD1) is a putative oxygen sensor associated with RNA and carbohydrate metabolism. Ala-Nisula T, et al. FEBS Lett, 2023 Jun. PMID 37235702
  2. Crystal structure of PHYHD1A, a 2OG oxygenase related to phytanoyl-CoA hydroxylase. Zhang Z, et al. Biochem Biophys Res Commun, 2011 May 20. PMID 21530488
  3. Prominent use of distal 5' transcription start sites and discovery of a large number of additional exons in ENCODE regions. Denoeud F, et al. Genome Res, 2007 Jun. PMID 17567994, Free PMC Article
  4. Protein array based interactome analysis of amyloid-β indicates an inhibition of protein translation. Virok DP, et al. J Proteome Res, 2011 Apr 1. PMID 21244100
  5. Genome-wide YFP fluorescence complementation screen identifies new regulators for telomere signaling in human cells. Lee OH, et al. Mol Cell Proteomics, 2011 Feb. PMID 21044950, Free PMC Article

See all (13) citations in PubMed

GeneRIFs: Gene References Into Functions

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)

Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Potential readthrough

Included gene: NUP188

Homology

Clone Names

  • MGC16638

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables 2-oxoglutarate-dependent dioxygenase activity IDA
Inferred from Direct Assay
more info
 PubMed 
enables metal ion binding IEA
Inferred from Electronic Annotation
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 

General protein information

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Preferred Names
phytanoyl-CoA dioxygenase domain-containing protein 1
NP_001094346.1
NP_001094347.1
NP_777593.2

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_001100876.2 → NP_001094346.1  phytanoyl-CoA dioxygenase domain-containing protein 1 isoform a

    See identical proteins and their annotated locations for NP_001094346.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (1) represents the longest transcript and encodes isoform a.
    Source sequence(s)
    AK095000, BM689360
    Consensus CDS
    CCDS43885.1
    UniProtKB/Swiss-Prot
    A6PWN9, A6PWP0, B3KT57, B4E3X8, Q5SRE7, Q5SRE9, Q5SRF0, Q7Z623, Q7Z7P9, Q96GM4
    Related
    ENSP00000361673.3, ENST00000372592.8
    Conserved Domains (1) summary
    pfam05721
    Location:12 → 259
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)

  2. NM_001100877.1 → NP_001094347.1  phytanoyl-CoA dioxygenase domain-containing protein 1 isoform c

    See identical proteins and their annotated locations for NP_001094347.1

    Status: VALIDATED

    Description
    Transcript Variant: This variant (3) lacks an alternate in-frame coding exon, compared to variant 1. The resulting protein (isoform c) is shorter than isoform a.
    Source sequence(s)
    AK095000, BC051300, BM689360
    Consensus CDS
    CCDS43886.1
    UniProtKB/Swiss-Prot
    Q5SRE7
    Related
    ENSP00000409928.2, ENST00000421063.6
    Conserved Domains (1) summary
    pfam05721
    Location:12 → 238
    PhyH; Phytanoyl-CoA dioxygenase (PhyH)

  3. NM_174933.4 → NP_777593.2  phytanoyl-CoA dioxygenase domain-containing protein 1 isoform b

    See identical proteins and their annotated locations for NP_777593.2

    Status: VALIDATED

    Description
    Transcript Variant: This variant (2) lacks an alternate coding exon, compared to variant 1, that causes a frameshift. The resulting protein (isoform b) has a longer and distinct C-terminus, compared to isoform a.
    Source sequence(s)
    AK095000, BC009373, BM689360
    Consensus CDS
    CCDS6914.1
    Related
    ENSP00000309515.5, ENST00000308941.9
    Conserved Domains (1) summary
    cl21496
    Location:12 → 147
    2OG-FeII_Oxy; 2OG-Fe(II) oxygenase superfamily

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_000009.12 Reference GRCh38.p14 Primary Assembly

    Range
    128920982..128942041
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060933.1 Alternate T2T-CHM13v2.0

    Range
    141125761..141145449
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q5SRE7.2 GenPept UniProtKB/Swiss-Prot:Q5SRE7

Gene LinkOut

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