PHYHD1

gene
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Also known as MGC16638

Summary

PHYHD1 (phytanoyl-CoA dioxygenase domain containing 1, HGNC:23396) is a protein-coding gene on chromosome 9q34.11, encoding Phytanoyl-CoA dioxygenase domain-containing protein 1 (Q5SRE7). 2-oxoglutarate(2OG)-dependent dioxygenase that catalyzes the conversion of 2-oxoglutarate to succinate and CO(2) in an iron-dependent manner.

Enables 2-oxoglutarate-dependent dioxygenase activity.

Source: NCBI Gene 254295 — RefSeq curated summary.

At a glance

  • GWAS associations: 7
  • Clinical variants (ClinVar): 81 total
  • MANE Select transcript: NM_001100876

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:23396
Approved symbolPHYHD1
Namephytanoyl-CoA dioxygenase domain containing 1
Location9q34.11
Locus typegene with protein product
StatusApproved
AliasesMGC16638
Ensembl geneENSG00000175287
Ensembl biotypeprotein_coding
OMIM620042
Entrez254295

Gene structure

Transcript identifiers

Ensembl transcripts: 35 — 31 protein_coding, 3 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000308941, ENST00000353176, ENST00000372592, ENST00000412476, ENST00000419552, ENST00000419872, ENST00000421063, ENST00000424503, ENST00000426694, ENST00000428610, ENST00000442837, ENST00000451000, ENST00000487504, ENST00000875818, ENST00000875819, ENST00000875820, ENST00000875821, ENST00000875822, ENST00000875823, ENST00000875824, ENST00000875825, ENST00000875826, ENST00000875827, ENST00000875828, ENST00000875829, ENST00000875830, ENST00000875831, ENST00000875832, ENST00000875833, ENST00000916273, ENST00000916274, ENST00000970308, ENST00000970309, ENST00000970310, ENST00000970311

RefSeq mRNA: 3 — MANE Select: NM_001100876 NM_001100876, NM_001100877, NM_174933

CCDS: CCDS43885, CCDS43886, CCDS6914

Canonical transcript exons

ENST00000372592 — 13 exons

ExonStartEnd
ENSE00001404383128920982128921668
ENSE00001412360128922283128922356
ENSE00001426496128921930128922047
ENSE00003479837128936448128936503
ENSE00003504917128940599128940715
ENSE00003545458128937757128937778
ENSE00003556702128941445128941571
ENSE00003586973128940369128940497
ENSE00003588225128933782128933857
ENSE00003610723128934011128934058
ENSE00003620007128941668128942038
ENSE00003678567128936583128936645
ENSE00003788911128927038128927196

Expression profiles

Bgee: expression breadth ubiquitous, 222 present calls, max score 96.51.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 7.7427 / max 100.8505, expressed in 1100 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter IDTPM avgSamples expressed
988617.13621090
988620.2779168
988570.118758
988590.097256
988580.089343
988600.02348

Top tissues by expression

244 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
body of pancreasUBERON:000115096.51gold quality
olfactory segment of nasal mucosaUBERON:000538696.07gold quality
right lobe of liverUBERON:000111495.85gold quality
apex of heartUBERON:000209895.54gold quality
right lobe of thyroid glandUBERON:000111995.45gold quality
left lobe of thyroid glandUBERON:000112095.22gold quality
left ovaryUBERON:000211994.95gold quality
skin of abdomenUBERON:000141694.63gold quality
right ovaryUBERON:000211894.26gold quality
thyroid glandUBERON:000204694.22gold quality
endocervixUBERON:000045894.21gold quality
metanephros cortexUBERON:001053394.21gold quality
peripheral nervous systemUBERON:000001094.11gold quality
tibial nerveUBERON:000132394.11gold quality
minor salivary glandUBERON:000183094.08gold quality
skin of legUBERON:000151194.05gold quality
adult mammalian kidneyUBERON:000008293.74gold quality
saliva-secreting glandUBERON:000104493.58gold quality
descending thoracic aortaUBERON:000234593.57gold quality
right atrium auricular regionUBERON:000663193.51gold quality
body of stomachUBERON:000116193.45gold quality
right uterine tubeUBERON:000130293.41gold quality
amygdalaUBERON:000187693.20gold quality
left uterine tubeUBERON:000130393.15gold quality
kidney epitheliumUBERON:000481993.04silver quality
thoracic aortaUBERON:000151593.03gold quality
popliteal arteryUBERON:000225092.96gold quality
tibial arteryUBERON:000761092.95gold quality
cardiac atriumUBERON:000208192.92gold quality
aortaUBERON:000094792.90gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

ExperimentMarker?Max mean expression
E-ANND-3yes13.60

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

10 targeting PHYHD1, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-182799.6368.573265
HSA-MIR-486-3P99.5166.821901
HSA-MIR-4708-3P99.5167.99870
HSA-MIR-425199.4069.193363
HSA-MIR-122B-3P99.2168.901333
HSA-MIR-21-3P99.2168.951312
HSA-MIR-478499.1567.411733
HSA-MIR-447899.0765.162320
HSA-MIR-3150B-3P98.8167.211728
HSA-MIR-6761-5P98.7168.031504

Literature-anchored findings (GeneRIF, showing 2)

  • PHYHD1A has the double-stranded beta-helix fold and Fe(II) and cosubstrate binding residues characteristic of the 2-oxoglutarate dependent oxygenases and catalyzes the conversion of 2-oxoglutarate to succinate and CO(2) in an iron-dependent manner. (PMID:21530488)
  • Human phytanoyl-CoA dioxygenase domain-containing 1 (PHYHD1) is a putative oxygen sensor associated with RNA and carbohydrate metabolism. (PMID:37235702)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriophyhd1ENSDARG00000029905
mus_musculusPhyhd1ENSMUSG00000079484
rattus_norvegicusPhyhd1ENSRNOG00000016794
drosophila_melanogasterPhyhd1FBGN0037819
caenorhabditis_elegansWBGENE00013650

Protein

Protein identifiers

Phytanoyl-CoA dioxygenase domain-containing protein 1Q5SRE7 (reviewed: Q5SRE7)

All UniProt accessions (9): Q5SRE7, F8WCG7, G5E9M0, H7C2Q0, H7C3M4, I7HJS6, X6RCI6, X6RFQ9, X6RJK6

UniProt curated annotations — full annotation on UniProt →

Function. 2-oxoglutarate(2OG)-dependent dioxygenase that catalyzes the conversion of 2-oxoglutarate to succinate and CO(2) in an iron-dependent manner. However, does not couple 2OG turnover to the hydroxylation of acyl-coenzyme A derivatives, implying that it is not directly involved in phytanoyl coenzyme-A metabolism. Does not show detectable activity towards fatty acid CoA thioesters. Isoform 2 probably lacks enzyme activity. Isoform 3 probably lacks enzyme activity.

Activity regulation. Activity is increased by ascorbate. Inhibited by myristoyl-CoA.

Similarity. Belongs to the PhyH family. PHYHD1 subfamily.

Isoforms (3)

UniProt IDNamesCanonical?
Q5SRE7-11, A, PHYHD1Ayes
Q5SRE7-22, C, PHYHD1C
Q5SRE7-33, B, PHYHD1B

RefSeq proteins (3): NP_001094346, NP_001094347, NP_777593 (=MANE)

Domains & families (InterPro)

IDNameType
IPR008775Phytyl_CoA_dOase-likeFamily

Pfam: PF05721

UniProt features (48 total): strand 19, helix 11, binding site 9, turn 3, splice variant 2, chain 1, modified residue 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

2 structures.

PDBMethodResolution (Å)
2OPWX-RAY DIFFRACTION1.9
3OBZX-RAY DIFFRACTION2.15

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q5SRE7-F193.610.83

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Ligand- & substrate-binding residues (9): 102; 141; 156–158; 156; 158; 174; 246; 248; 257

Post-translational modifications (1): 55

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 97 (showing top): GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_PAIRED_DONORS_WITH_INCORPORATION_OR_REDUCTION_OF_MOLECULAR_OXYGEN, SCHAEFFER_PROSTATE_DEVELOPMENT_48HR_UP, GAUSSMANN_MLL_AF4_FUSION_TARGETS_G_UP, GOMF_DIOXYGENASE_ACTIVITY, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MIKKELSEN_MEF_LCP_WITH_H3K4ME3, MIKKELSEN_IPS_LCP_WITH_H3K4ME3, MIKKELSEN_ES_LCP_WITH_H3K4ME3, CHEMNITZ_RESPONSE_TO_PROSTAGLANDIN_E2_DN, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_B, DELACROIX_RARG_BOUND_MEF, chr9q34, HES2_TARGET_GENES, ID1_TARGET_GENES, PRKDC_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (5): 2-oxoglutarate-dependent dioxygenase activity (GO:0016706), metal ion binding (GO:0046872), protein binding (GO:0005515), oxidoreductase activity (GO:0016491), dioxygenase activity (GO:0051213)

GO Cellular Component (0):

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen1
dioxygenase activity1
cation binding1
binding1
catalytic activity1
oxidoreductase activity1

Protein interactions and networks

STRING

1196 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
PHYHD1ZNF705BP0CI00419
PHYHD1C16orf86Q6ZW13397
PHYHD1CZIBQ9NWV4385
PHYHD1AASDHQ4L235368
PHYHD1ZNF844Q08AG5368
PHYHD1YRDCQ86U90365
PHYHD1OCEL1Q9H607360
PHYHD1ZNF829Q3KNS6360
PHYHD1TLCD1Q96CP7359
PHYHD1C22orf42Q6IC83356
PHYHD1ALDH18A1P54886353
PHYHD1MTRNR2L3P0CJ70349
PHYHD1TTF2Q9UNY4345
PHYHD1MT-ATP6P00846338
PHYHD1ZNF251Q9BRH9337

IntAct

8 interactions, top by confidence:

ABTypeScore
PHYHD1POT1psi-mi:“MI:0915”(physical association)0.510
PHYHD1psi-mi:“MI:0915”(physical association)0.370
HNRNPLLTBX3psi-mi:“MI:0914”(association)0.350
LGALS9BABCC4psi-mi:“MI:0914”(association)0.350
PHYHD1IPO7psi-mi:“MI:0914”(association)0.350
PHYHD1POT1psi-mi:“MI:0915”(physical association)0.000

BioGRID (9): PHYHD1 (Reconstituted Complex), PHYHD1 (Affinity Capture-MS), PHYHD1 (Affinity Capture-MS), PHYHD1 (Affinity Capture-MS), PHYHD1 (Affinity Capture-MS), PRPS1 (Affinity Capture-MS), IPO7 (Affinity Capture-MS), PHYHD1 (Two-hybrid), APP (Reconstituted Complex)

ESM2 similar proteins: B4G0F3, B5DEQ3, B7ZMP1, B8BKI7, B9SQI7, C1BYA3, C6JS30, E0CSI1, E0CTF3, E9Q4Z2, O00763, O14832, O15229, O18778, O35386, O62515, O88867, O94851, P09925, P0CF52, P28492, P37287, P57093, Q08C93, Q0IIB1, Q0VC74, Q1RLY6, Q2R483, Q571F8, Q5BJP9, Q5F4B3, Q5R5T5, Q5R9W8, Q5SRE7, Q64323, Q6DIZ8, Q6GQI7, Q6IQE9, Q812G0, Q91WN4

Diamond homologs: P0C660, Q0IIB1, Q10E49, Q54XH6, Q5BJP9, Q5SRE7, Q5U3U0, Q65WW7, Q9DB26, Q9NAM7, Q9ZVF6, D0E8I4, Q5MNH2, Q5MNH9, P0DX11, O14832, O18778, O35386, P57093

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

81 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance56
Likely benign14
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1940 predictions. Top by Δscore:

VariantEffectΔscore
9:128922282:GGA:Gacceptor_gain1.0000
9:128922352:AGAAG:Adonor_loss1.0000
9:128922356:GGTAG:Gdonor_loss1.0000
9:128922357:GTAG:Gdonor_loss1.0000
9:128922358:T:Adonor_loss1.0000
9:128936446:A:AGacceptor_gain1.0000
9:128936447:G:GGacceptor_gain1.0000
9:128936447:GCTC:Gacceptor_gain1.0000
9:128936447:GCTCT:Gacceptor_gain1.0000
9:128936499:TGCAG:Tdonor_loss1.0000
9:128936500:GCAGG:Gdonor_loss1.0000
9:128936501:CAGGT:Cdonor_loss1.0000
9:128936502:AGGTG:Adonor_loss1.0000
9:128936504:GTGA:Gdonor_loss1.0000
9:128940498:G:GGdonor_gain1.0000
9:128941439:T:TAacceptor_gain1.0000
9:128941442:CAG:Cacceptor_loss1.0000
9:128941443:A:AGacceptor_gain1.0000
9:128941443:AG:Aacceptor_gain1.0000
9:128941443:AGG:Aacceptor_gain1.0000
9:128941443:AGGG:Aacceptor_gain1.0000
9:128941444:G:Aacceptor_gain1.0000
9:128941444:G:GCacceptor_gain1.0000
9:128941444:GGG:Gacceptor_gain1.0000
9:128941444:GGGG:Gacceptor_gain1.0000
9:128941444:GGGGC:Gacceptor_gain1.0000
9:128921066:C:Gdonor_gain0.9900
9:128922279:CCA:Cacceptor_loss0.9900
9:128922281:A:AGacceptor_gain0.9900
9:128922281:AG:Aacceptor_gain0.9900

AlphaMissense

1915 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
9:128927161:T:CF53L0.997
9:128927163:C:AF53L0.997
9:128927163:C:GF53L0.997
9:128936628:A:CS140R0.996
9:128936630:C:AS140R0.996
9:128936630:C:GS140R0.996
9:128940392:T:CF161L0.993
9:128940394:C:AF161L0.993
9:128940394:C:GF161L0.993
9:128934048:A:CK102N0.992
9:128934048:A:TK102N0.992
9:128936645:G:CK145N0.992
9:128936645:G:TK145N0.992
9:128941477:C:GH246D0.992
9:128941528:C:GH263D0.991
9:128941569:C:AN276K0.991
9:128941569:C:GN276K0.991
9:128936629:G:TS140I0.990
9:128941570:T:AW277R0.990
9:128941570:T:CW277R0.990
9:128940377:C:GH156D0.989
9:128940383:G:CD158H0.988
9:128941555:T:AW272R0.988
9:128941555:T:CW272R0.988
9:128933806:A:CS73R0.987
9:128933808:T:AS73R0.987
9:128933808:T:GS73R0.987
9:128934047:A:TK102I0.987
9:128940431:T:AW174R0.987
9:128940431:T:CW174R0.987

dbSNP variants (sampled 300 via entrez): RS1000077209 (9:128929565 TG>T), RS1000179391 (9:128922626 C>G), RS1000248876 (9:128935732 T>C), RS1000332648 (9:128929072 T>C), RS1000383433 (9:128928692 G>A), RS1000424899 (9:128929343 A>T), RS1000664744 (9:128927255 G>A,C), RS1000804415 (9:128924520 G>C), RS1000857088 (9:128936215 G>A), RS1000914492 (9:128921459 C>A,T), RS1001031964 (9:128930732 A>G), RS1001078279 (9:128919282 G>A), RS1001289316 (9:128935873 G>T), RS1001506845 (9:128928074 G>A,T), RS1001666661 (9:128921931 T>C,G)

Disease associations

OMIM: gene MIM:620042 | disease phenotypes: MIM:143890

GenCC curated gene-disease

Mondo (1): hypercholesterolemia, familial, 1 (MONDO:0007750)

Orphanet (1): Homozygous familial hypercholesterolemia (Orphanet:391665)

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

7 associations (top):

StudyTraitp-value
GCST009733_143Urinary metabolite levels in chronic kidney disease1.000000e-55
GCST009733_144Urinary metabolite levels in chronic kidney disease3.000000e-37
GCST012020_22Serum metabolite levels4.000000e-189
GCST012020_406Serum metabolite levels2.000000e-230
GCST012020_407Serum metabolite levels2.000000e-38
GCST012353_3Serum metabolite concentrations in chronic kidney disease2.000000e-12
GCST012353_36Serum metabolite concentrations in chronic kidney disease2.000000e-42

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0005116urinary metabolite measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

33 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Aciddecreases expression, affects expression, affects cotreatment7
Benzo(a)pyrenedecreases expression, increases methylation2
Tetrachlorodibenzodioxindecreases expression2
Cyclosporinedecreases expression, increases expression2
Aflatoxin B1affects expression, decreases expression2
aristolochic acid Iincreases expression1
methylmercuric chloridedecreases expression1
methyleugenoldecreases expression1
pirinixic acidaffects binding, decreases expression, increases activity1
bisphenol Aincreases expression1
ethyl-p-hydroxybenzoatedecreases expression1
arseniteincreases methylation1
tris(1,3-dichloro-2-propyl)phosphatedecreases expression1
di-n-butylphosphoric acidaffects expression1
perfluorooctane sulfonic acidincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
licochalcone Bincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Sunitinibdecreases expression1
Acetaminophendecreases expression1
Cadmiumdecreases expression, increases abundance1
Ivermectindecreases expression1
Nickeldecreases expression1
Plant Extractsaffects cotreatment, decreases expression1
Quercetindecreases expression1
Silicon Dioxideincreases expression1
Smokedecreases expression1
Tobacco Smoke Pollutiondecreases expression1
Urethanedecreases expression1

Clinical trials (associated diseases)

28 trials via MONDO — disease-level, not drug-specific.

TrialPhaseStatusTitle
NCT06231459PHASE4COMPLETEDExpression of Pro- and Anti-inflammatory Cytokines During Anti-PCSK9 in Familial Hypercholesterolemia
NCT00000594PHASE3COMPLETEDNHLBI Type II Coronary Intervention Study
NCT00092833PHASE3TERMINATEDInvestigational Drug in Patients With Hypercholesterolemia or in Patients With Sitosterolemia (0653-026)(COMPLETED)
NCT00134485PHASE3COMPLETEDStudy To Evaluate The Safety And Efficacy Of Torcetrapib/Atorvastatin In Subjects With Familial Hypercholerolemia
NCT00134511PHASE3COMPLETEDStudy To Evaluate The Effect Of Torcetrapib/Atorvastatin In Patients With Genetic High Cholesterol Disorder
NCT00136981PHASE3COMPLETEDCarotid B-Mode Ultrasound Study to Compare Anti-Atherosclerotic Effect of Torcetrpib/Atorvastatin to Atorvastatin Alone.
NCT00384293PHASE3TERMINATEDCarotid IMT (Intima Media Thickening) Study (0524A-041)(TERMINATED)
NCT01524289PHASE3COMPLETEDStudy to Assess the Tolerability and Efficacy of Anacetrapib (MK-0859) Co-Administered With Statin in Participants With Heterozygous Familial Hypercholesterolemia (MK-0859-020)
NCT00280995PHASE2COMPLETEDDose-escalating Safety Study of ISIS 301012 in Homozygous Familial Hypercholesterolemia Subjects on Lipid Lowering Therapy
NCT00281008PHASE2COMPLETEDStudy of ISIS 301012 (Mipomersen) in Heterozygous Familial Hypercholesterolemia Subjects on Lipid Lowering Therapy
NCT01375751PHASE2COMPLETEDReduction of Low-Density Lipoprotein Cholesterol (LDL-C) With PCSK9 Inhibition in Heterozygous Familial Hypercholesterolemia Disorder Study
NCT00515307PHASE1COMPLETEDBone Marrow Stem Cells as a Source of Allogenic Hepatocyte Transplantation in Homozygous Familial Hypercholesterolemia
NCT01583647PHASE1TERMINATEDA Study of Extended-release (ER) Niacin/Laropiprant in Adolescents With Heterozygous Familial Hypercholesterolemia (MK-0524A-158)
NCT00005168Not specifiedCOMPLETEDHyperapo B and Coronary Heart Disease
NCT01753232Not specifiedCOMPLETEDSafety and Efficacy of the DALI LDL-adsorber and MONET Lipoprotein Filter
NCT03018678Not specifiedCOMPLETEDScreening Protocol for a Gene Therapy Trial in Subjects With Homozygous Familial Hypercholesterolemia
NCT03110432Not specifiedCOMPLETEDProspective German Very High Cardiovascular Risk Patients Dyslipidemia Treatment Indication Registry
NCT03795038Not specifiedCOMPLETEDComparison of the Plasma Lipoprotein Apheresis Systems DIAMED and MONET vs. the Whole Blood Apheresis System DALI
NCT03989167Not specifiedRECRUITINGClinical Decision Support for Familial Hypercholesterolemia
NCT04073797Not specifiedRECRUITINGPET Imaging of Inflammation and Lipid Lowering Study
NCT04118348Not specifiedCOMPLETEDEvaluating the Efficacy of Pediatric Lipid Screening Alerts
NCT04313270Not specifiedUNKNOWNSubclinical Atherosclerosis in Patients With Familial Hypercholesterolemia Treated With Evolocumab®
NCT04526457Not specifiedCOMPLETEDIs Family Screening Improved by Genetic Testing of Familial Hypercholesterolemia
NCT04656028Not specifiedACTIVE_NOT_RECRUITINGGenetic Testing and Motivational Counseling for FH
NCT04722068Not specifiedCOMPLETEDRegeneron 1331 Kinetics Sub-Study HoFH
NCT04837638Not specifiedUNKNOWNDiet Quality and Coronary Artery Calcification in Adults With Heterozygous Familial Hypercholesterolemia
NCT06555120Not specifiedRECRUITINGScreening for Familial Hypercholesterolemia in Children
NCT07543731Not specifiedNOT_YET_RECRUITINGA Real-World Study of Long-Term Adherence and Persistence to Inclisiran, Evolocumab, and Alirocumab
  • Disease cohort memberships (association, not causation — diseases whose associated-gene cohort lists this gene; a subset are also under Associated diseases): hypercholesterolemia, familial, 1