Send feedback

HTD2

gene
On this page

Summary

HTD2 (hydroxyacyl-thioester dehydratase type 2, HGNC:53111) is a protein-coding gene on chromosome 3p14.3, encoding Hydroxyacyl-thioester dehydratase type 2, mitochondrial (P86397). Mitochondrial 3-hydroxyacyl-thioester dehydratase, which may be involved in fatty acid biosynthesis.

This gene encodes a protein that localizes to the mitochondria and can function as a 3-hydroxyacyl thioester dehydratase. This gene is located just downstream of the gene for ribonuclease P/MRP subunit p14 (RPP14) in a genomic context that is conserved among animals. The upstream RPP14 gene is thought to be co-transcribed with this gene, and bicistronic transcripts may include open reading frames for both proteins.

Source: NCBI Gene 109703458 — RefSeq curated summary.

At a glance

  • Expression (HPA): Tissue enhanced — highest in skeletal muscle, hippocampal formation, dorsal hippocampus
  • GTEx eGene: eQTL in 0 tissues, sQTL in 10 (q < 0.05)
  • MANE Select transcript: NM_001348712

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:53111
Approved symbolHTD2
Namehydroxyacyl-thioester dehydratase type 2
Location3p14.3
Locus typegene with protein product
StatusApproved
Ensembl geneENSG00000255154
Ensembl biotypeprotein_coding
OMIM620769
Entrez109703458

Gene structure

Transcript identifiers

Ensembl transcripts: 15 — 14 protein_coding, 1 protein_coding_CDS_not_defined

MANE Select: ENST00000461393

Transcript support level (Ensembl TSL; 1 = fully mRNA-supported): TSL 1: 1, TSL 2: 3, TSL 3: 1, TSL 4: 1, TSL 5: 1

ENST00000461393, ENST00000474660, ENST00000475412, ENST00000476007, ENST00000477305, ENST00000481972, ENST00000498618, ENST00000992408, ENST00000992409, ENST00000992410, ENST00000992411, ENST00001035799, ENST00001035800, ENST00001035801, ENST00001144259

RefSeq mRNA: 4 — MANE Select: NM_001348712 NM_001348712, NM_001348713, NM_001348714, NM_001348715

CCDS: CCDS87096

Canonical transcript exons

ENST00000461393 — 5 exons

ExonStartEnd
ENSE000018497755831744058320193
ENSE000018971165830652058306651
ENSE000037240725831651558316591
ENSE000037417115831691558316993
ENSE000037466565831050758310591

Expression profiles

Bgee: expression breadth ubiquitous, 134 present calls, max score 90.13.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 8.0521 / max 110.7990, expressed in 1774 samples.

Highest expression (Bgee): primordial germ cell in gonad, male germ line stem cell (sensu Vertebrata) in testis, muscle of leg, gastrocnemius, skeletal muscle tissue.

Genetic regulation across tissues (GTEx eQTL / sQTL)

HTD2 is an eGene in GTEx v10 — its expression is genetically regulated (eQTL) in 0 tissues and its splicing (sQTL) in 10 (q < 0.05). Strongest associations first; slope = normalized effect of the lead variant’s alternative allele.

10 significant tissue × QTL associations:

TissueQTLq-valueSlopeLead variant
Muscle Skeletalsqtl4.2e-06+0.553:58315733:A:G
Esophagus Mucosasqtl5.7e-05-0.423:58398516:A:C
Adipose Visceral Omentumsqtl2.4e-03-0.403:58274433:C:T
Cells EBV-transformed lymphocytessqtl2.5e-03-0.713:58370859:T:TGTG
Testissqtl2.7e-03+0.703:58306798:T:G
Lungsqtl9.0e-03-0.303:58343535:G:A
Esophagus Gastroesophageal Junctionsqtl1.7e-02+0.623:58315733:A:G
Breast Mammary Tissuesqtl2.9e-02-0.353:58450761:C:T
Esophagus Muscularissqtl4.0e-02-0.343:58289968:C:T
Artery Tibialsqtl4.7e-02+0.573:58197351:C:T

FANTOM5 promoters

2 alternative TSS:

Promoter IDTPM avgSamples expressed
370398.05211774
370406.99401740

Top tissues by expression

showing 100 of 134 tissues by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099190.13gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047388.50gold quality
muscle of legUBERON:000138384.85gold quality
gastrocnemiusUBERON:000138884.43gold quality
skeletal muscle tissueUBERON:000113483.98gold quality
muscle tissueUBERON:000238582.70gold quality
duodenumUBERON:000211481.44gold quality
islet of LangerhansUBERON:000000680.96gold quality
heart left ventricleUBERON:000208480.83gold quality
hindlimb stylopod muscleUBERON:000425280.60gold quality
rectumUBERON:000105280.16gold quality
smooth muscle tissueUBERON:000113580.01gold quality
heartUBERON:000094879.47gold quality
apex of heartUBERON:000209878.84gold quality
right atrium auricular regionUBERON:000663178.63gold quality
stromal cell of endometriumCL:000225578.41gold quality
prefrontal cortexUBERON:000045178.02gold quality
adrenal tissueUBERON:001830377.93gold quality
placentaUBERON:000198777.72gold quality
mucosa of transverse colonUBERON:000499177.57gold quality
ventricular zoneUBERON:000305377.56gold quality
gall bladderUBERON:000211077.27gold quality
leukocyteCL:000073877.13gold quality
monocyteCL:000057676.90gold quality
vermiform appendixUBERON:000115476.54gold quality
granulocyteCL:000009476.53gold quality
lymph nodeUBERON:000002976.47gold quality
endometriumUBERON:000129576.37gold quality
adult mammalian kidneyUBERON:000008276.22gold quality
adrenal glandUBERON:000236976.10gold quality
urinary bladderUBERON:000125575.95gold quality
right adrenal glandUBERON:000123375.94gold quality
left adrenal glandUBERON:000123475.79gold quality
fallopian tubeUBERON:000388975.71gold quality
right adrenal gland cortexUBERON:003582775.67gold quality
omental fat padUBERON:001041475.63gold quality
cortical plateUBERON:000534375.54gold quality
esophagus mucosaUBERON:000246975.47gold quality
left adrenal gland cortexUBERON:003582575.44gold quality
ovaryUBERON:000099275.25gold quality
left ovaryUBERON:000211975.21gold quality
left uterine tubeUBERON:000130375.17gold quality
pancreasUBERON:000126475.14gold quality
adipose tissueUBERON:000101375.07gold quality
esophagusUBERON:000104375.02gold quality
mucosa of stomachUBERON:000119974.99gold quality
frontal cortexUBERON:000187074.96gold quality
colonUBERON:000115574.80gold quality
ganglionic eminenceUBERON:000402374.72gold quality
lower esophagusUBERON:001347374.71gold quality
lower esophagus muscularis layerUBERON:003583374.71gold quality
muscle layer of sigmoid colonUBERON:003580574.64gold quality
subcutaneous adipose tissueUBERON:000219074.56gold quality
transverse colonUBERON:000115774.55gold quality
esophagogastric junction muscularis propriaUBERON:003584174.48gold quality
intestineUBERON:000016074.21gold quality
skin of legUBERON:000151174.17gold quality
kidneyUBERON:000211374.02gold quality
tonsilUBERON:000237273.97gold quality
cortex of kidneyUBERON:000122573.92gold quality
left coronary arteryUBERON:000162673.88gold quality
popliteal arteryUBERON:000225073.86gold quality
tibial arteryUBERON:000761073.83gold quality
zone of skinUBERON:000001473.82gold quality
right ovaryUBERON:000211873.82gold quality
descending thoracic aortaUBERON:000234573.82gold quality
vaginaUBERON:000099673.81gold quality
multicellular organismUBERON:000046873.74gold quality
body of stomachUBERON:000116173.67gold quality
liverUBERON:000210773.62gold quality
adenohypophysisUBERON:000219673.62gold quality
body of uterusUBERON:000985373.55gold quality
right lobe of liverUBERON:000111473.53gold quality
skin of abdomenUBERON:000141673.36gold quality
bloodUBERON:000017873.17gold quality
pituitary glandUBERON:000000773.09gold quality
thoracic mammary glandUBERON:000520073.08gold quality
bone marrowUBERON:000237173.07gold quality
saliva-secreting glandUBERON:000104473.03gold quality
ectocervixUBERON:001224972.93gold quality
myometriumUBERON:000129672.92gold quality
right coronary arteryUBERON:000162572.83gold quality
lower esophagus mucosaUBERON:003583472.82gold quality
endocervixUBERON:000045872.76gold quality
superior frontal gyrusUBERON:000266172.76gold quality
thoracic aortaUBERON:000151572.72gold quality
olfactory segment of nasal mucosaUBERON:000538672.70gold quality
thyroid glandUBERON:000204672.63gold quality
minor salivary glandUBERON:000183072.55gold quality
ascending aortaUBERON:000149672.52gold quality
calcaneal tendonUBERON:000370172.46gold quality
fundus of stomachUBERON:000116072.41gold quality
stomachUBERON:000094572.39gold quality
left lobe of thyroid glandUBERON:000112072.28gold quality
cerebral cortexUBERON:000095672.17gold quality
body of pancreasUBERON:000115072.10gold quality
small intestineUBERON:000210872.08gold quality
lungUBERON:000204871.85gold quality
right lobe of thyroid glandUBERON:000111971.84gold quality
metanephros cortexUBERON:001053371.74gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

ExperimentMarker?Max mean expression
E-ANND-3no1.12

HPA expression

RNA tissue specificity: Tissue enhanced

showing 60 of 78 HPA tissues / cells by nTPM:

Tissue / cellAxisnTPMProtein (IHC)
Skeletal muscletissue41.0low
Hippocampal formationtissue38.5
Frontal cortextissue37.1
Caudate putamentissue35.5
Tonguetissue35.1
Cerebral cortextissue29.1low
Somatosensory cortextissue29.1
Thalamustissue28.5
Motor cortextissue28.3
Occipital cortextissue27.9
Ponstissue27.6
Midbraintissue27.6
Superior colliculitissue26.7
Retrosplenial and cingulate cortextissue26.3
Prefrontal cortextissue26.1
Entorhinal cortextissue26.1
Putamentissue26.0
Septumtissue25.7
Spinal cordtissue25.6
Cerebellumtissue25.3not detected
Corpus callosumtissue25.3
Medulla oblongatatissue25.2
Hypothalamustissue25.0
Substantia nigratissue24.7
Ventral forebraintissue24.4
Temporal cortextissue24.4
Retrosplenial cortextissue24.2
Insular cortextissue23.5
Periaqueductal graytissue23.1
Olfactory bulbtissue23.1
Amygdalatissue21.9
Basal gangliatissue21.5medium
Livertissue14.2medium
Choroid plexustissue12.5
Postcentral gyrustissue12.3
Nucleus accumbenstissue12.2
Heart muscletissue11.7high
Parathyroid glandtissue11.3
Duodenumtissue11.2high
Locus coeruleustissue10.6
Kidneytissue10.2high
Hippocampustissue9.9medium
Thyroid glandtissue9.7medium
Ovarytissue9.3medium
Retinatissue8.5
Rectumtissue8.5high
Colontissue8.3medium
Small intestinetissue8.2high
Breasttissue8.1low
Esophagustissue8.1not detected
Seminal vesicletissue8.0low
Endometrium 1tissue7.8low
Tonsiltissue7.5medium
Skin 1tissue7.4not detected
Fallopian tubetissue7.3not detected
Pituitary glandtissue7.2
Adipose tissuetissue7.2not detected
Smooth muscletissue7.1not detected
Testistissue7.0high
Salivary glandtissue7.0high

Brain sub-regions (HPA Brain Atlas): detected in 191; highest nTPM — Dorsal hippocampus (38.5), Ventral hippocampus (31.4), Ventral spinal cord (25.6), Subiculum (25.3), White matter (25.3).

Regulation

Is transcription factor: no

Functional genomics

Regional missense constraint (gnomAD RMC): no regional variation along ENST00000461393 — one region, missense o/e 1.88.

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusHtd2ENSMUSG00000144287
rattus_norvegicusRpp14ENSRNOG00000063660

Additional cross-species homologs

Sequence homologs in species beyond Ensembl Compara’s model organisms, by Diamond local protein alignment (% sequence identity; best hit per species). Lower-identity rows are more distant homologs. The matched accessions’ gene symbols aren’t in biobtree yet, so each row shows the UniProt accession.

OrganismUniProtIdentityMethod
Aeromonas caviaeO3247257.1%Diamond
Methylorubrum extorquens AM1C5AZ7453.0%Diamond
Rhodospirillum rubrum ATCC 11170Q2RQ3651.8%Diamond

Genomic neighbors (locus context)

Genes flanking this one on the chromosome (NCBI/Entrez gene neighborhood). Positional context only — some neighbors share regulatory elements (bidirectional promoters, antisense/overlapping transcripts), but chromosomal adjacency is not itself a functional relationship (see Interactions for that).

SymbolTypeEntrez
RPP14protein-coding11102
PDHBprotein-coding5162
PXKprotein-coding54899
ABHD6protein-coding57406
DNASE1L3protein-coding1776
KCTD6protein-coding200845

Protein

Protein identifiers

Hydroxyacyl-thioester dehydratase type 2, mitochondrial — P86397 (reviewed: P86397)

Alternative names: 3-hydroxyacyl-[acyl-carrier-protein] dehydratase

All UniProt accessions (5): A0A087WTC8, A0A087WUW1, A0A087WYB6, L0R6P0, P86397

UniProt curated annotations — full annotation on UniProt →

Function. Mitochondrial 3-hydroxyacyl-thioester dehydratase, which may be involved in fatty acid biosynthesis.

Subcellular location. Mitochondrion.

Tissue specificity. Highly expressed in heart and liver. Expressed at lower levels in skeletal muscle, spleen, kidney and placenta.

Miscellaneous. This protein is produced by a bicistronic gene which also produces the RPP14 protein from an overlapping reading frame.

Similarity. Belongs to the HTD2 family.

RefSeq proteins (4): NP_001335641, NP_001335642, NP_001335643, NP_001335644 (=MANE)

Domains & families (InterPro)

IDNameType
IPR002539MaoC-like_domDomain
IPR029069HotDog_dom_sfHomologous_superfamily
IPR050965UPF0336/Enoyl-CoA_hydrataseFamily

Pfam: PF01575

Catalyzed reactions (Rhea)

  • a (3R)-hydroxyacyl-[ACP] = a (2E)-enoyl-[ACP] + H2O (RHEA:13097)
  • (3R)-hydroxyhexanoyl-[ACP] = (2E)-hexenoyl-[ACP] + H2O (RHEA:41828)
  • (3R)-hydroxydecanoyl-[ACP] = (2E)-decenoyl-[ACP] + H2O (RHEA:41860)

UniProt features (15 total): strand 5, helix 4, mutagenesis site 2, transit peptide 1, chain 1, turn 1, domain 1

Structure

Experimental structures (PDB)

1 structure by resolution:

PDBTitleMethodResolution (Å)
3IR3Crystal structure of human 3-hydroxyacyl-thioester dehydratase 2 (HTD2)X-RAY DIFFRACTION1.99

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-P86397-F184.540.74

Human Protein Atlas

Protein class: Enzymes, ENZYME proteins, Lyases, Predicted intracellular proteins

Protein evidence: Evidence at protein level

Subcellular location (HPA, imaging): mitochondria; nucleoli

Antibody reliability (HPA): IH approved · IF supported

Functional residue map

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

Mutagenesis-validated functional residues (2)

PositionPhenotype
62abolishes ability to complement a htd2-delta mutant yeast.
67abolishes ability to complement a htd2-delta mutant yeast.

Function

Pathways and Gene Ontology

Reactome pathways

0 curated (TAS) of 4; 0 disease pathways. Curated-first; evidence = TAS (manually curated) vs IEA (electronic inference).

4 pathways:

IDPathwayEvidence
R-HSA-8978868Fatty acid metabolism—
R-HSA-75105Fatty acyl-CoA biosynthesis—
R-HSA-1430728Metabolism—
R-HSA-556833Metabolism of lipids—

MSigDB gene sets: 67 (showing top): GOBP_ORGANOPHOSPHATE_METABOLIC_PROCESS, GOBP_NUCLEOSIDE_PHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_MONOCARBOXYLIC_ACID_METABOLIC_PROCESS, GOBP_ORGANOPHOSPHATE_BIOSYNTHETIC_PROCESS, GOBP_ORGANIC_ACID_BIOSYNTHETIC_PROCESS, GOBP_NUCLEOBASE_CONTAINING_SMALL_MOLECULE_METABOLIC_PROCESS, GOBP_SMALL_MOLECULE_BIOSYNTHETIC_PROCESS, GOBP_FATTY_ACYL_COA_METABOLIC_PROCESS, GOBP_SULFUR_COMPOUND_BIOSYNTHETIC_PROCESS, GOBP_AMIDE_METABOLIC_PROCESS, GOBP_AMIDE_BIOSYNTHETIC_PROCESS, GOBP_FATTY_ACID_BIOSYNTHETIC_PROCESS, GOBP_MONOCARBOXYLIC_ACID_BIOSYNTHETIC_PROCESS, GOBP_LIPID_METABOLIC_PROCESS, GOBP_ORGANIC_ACID_METABOLIC_PROCESS

GO Biological Process (4): fatty acid biosynthetic process (GO:0006633), fatty-acyl-CoA biosynthetic process (GO:0046949), lipid metabolic process (GO:0006629), fatty acid metabolic process (GO:0006631)

GO Molecular Function (4): 3-hydroxyacyl-CoA dehydratase activity (GO:0018812), (3R)-hydroxyacyl-[acyl-carrier-protein] dehydratase activity (GO:0019171), lyase activity (GO:0016829), hydro-lyase activity (GO:0016836)

GO Cellular Component (2): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759)

Reactome top-level categories

3 top-level categories:

CategoryPathways
Fatty acid metabolism1
Metabolism1
Metabolism of lipids1

GO top-level categories

17 GO namespaces:

CategoryTerms
fatty acid metabolic process1
lipid biosynthetic process1
monocarboxylic acid biosynthetic process1
fatty-acyl-CoA metabolic process1
acyl-CoA biosynthetic process1
fatty acid derivative biosynthetic process1
primary metabolic process1
lipid metabolic process1
monocarboxylic acid metabolic process1
enoyl-CoA hydratase activity1
hydro-lyase activity1
catalytic activity1
carbon-oxygen lyase activity1
cytoplasm1
intracellular membrane-bounded organelle1
mitochondrion1
intracellular organelle lumen1

Experimentally-supported GO annotations

GO terms backed by direct experimental evidence (ECO experimental codes) — 1 of 10 annotations. The rest are phylogenetic / computational / electronic (IEA).

1 experimentally-supported GO terms:

GO termNSEvidence
mitochondrionCCdirect assay

Protein interactions and networks

STRING

showing 15 of 768 interactions by confidence (×1000):

Protein AProtein BPartner UniProtScore
HTD2OXSMQ9NWU1412
HTD2CHCHD1Q96BP2407
HTD2MCATQ8IVS2406
HTD2DMAC2Q9NW81394
HTD2PPP4R4Q6NUP7386
HTD2MRPL42Q9Y6G3379
HTD2MECRQ9BV79375
HTD2UQCC3Q6UW78372
HTD2SCP2P22307370
HTD2SLC35A4Q96G79364
HTD2POP1Q99575348
HTD2NEURL3Q96EH8345
HTD2UQCC1Q9NVA1332
HTD2ACOT8O14734331
HTD2MYO19Q96H55323

Disease & clinical

Genetic variants

ClinVar

No ClinVar records for this gene.

SpliceAI

Top 10 splice-impact sites by Δscore (adjacent positions with the same effect merged into one range; 27 predictions of 343):

Position(s)EffectΔscoreSites
3:58310497acceptor_gain1.0000
3:58310505–58310506acceptor_loss1.00006
3:58310589donor_gain1.0000
3:58310592–58310593donor_loss1.00004
3:58310592donor_loss0.9900
3:58317438–58317439acceptor_loss0.99004
3:58317548acceptor_gain0.9900
3:58313438donor_gain0.9800
3:58316592–58316593donor_loss0.98006
3:58317438–58317439acceptor_loss0.98002

AlphaMissense

336 missense substitutions predicted likely pathogenic (of 1,092 scored), across 91 residues. Top 20 hotspot residues, ranked by the number of likely-pathogenic substitutions (of those reachable by a single-nucleotide change), then by mean score:

ResidueLikely-pathogenic substitutionsMean am_pathogenicityMax am_pathogenicity
D6280.9720.986
H6780.9040.982
F4880.8780.989
D5280.7560.893
F11470.9840.996
F5670.9610.994
F7870.9010.983
N6470.8940.982
H8470.8820.958
C14470.8690.984
F7270.8130.967
F10770.8120.953
G10260.9420.966
G15660.9230.984
M15460.8950.957
P10160.8670.952
Q11060.8620.954
V13060.7830.941
M10060.7750.962
G6160.7290.912

HPA cancer prognostics

RNA cancer specificity: Low cancer specificity

Human Protein Atlas survival analysis — favorable = higher expression predicts better survival.

2 prognostic cancer types:

CancerPrognosticp-value
Kidney Renal Clear Cell Carcinoma (TCGA)favorable3.46e-05
Kidney Renal Clear Cell Carcinoma (validation)favorable8.11e-05

Disease associations

OMIM: gene MIM:620769 | disease phenotypes:

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (CPIC guideline: no)

CTD chemical–gene interactions

3 total (human), top 3 by PubMed support.

ChemicalActions (top 5)PubMed papers
Smokedecreases expression1
Okadaic Aciddecreases expression1
S-Nitrosoglutathionedecreases expression1

Clinical trials (associated diseases)

Via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.