OXCT2

Summary

OXCT2 (3-oxoacid CoA-transferase 2, HGNC:18606) is a protein-coding gene on chromosome 1p34.2, encoding Succinyl-CoA:3-ketoacid coenzyme A transferase 2, mitochondrial (Q9BYC2). Key enzyme for ketone body catabolism.

The protein encoded by this gene catalyzes the transfer of a CoA group from succinate to acetoacetate and is an important enzyme in ketone body catabolism. The encoded protein localizes to the mitochondrion. This gene is intronless, and a pseudogene of this gene is located elsewhere on chromosome 1.

Source: NCBI Gene 64064 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 1 total
• MANE Select transcript: NM_022120

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:18606
Approved symbol	OXCT2
Name	3-oxoacid CoA-transferase 2
Location	1p34.2
Locus type	gene with protein product
Status	Approved
Aliases	FKSG25, FLJ00030, SCOT-T
Ensembl gene	ENSG00000198754
Ensembl biotype	protein_coding
OMIM	610289
Entrez	64064

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000327582

RefSeq mRNA: 1 — MANE Select: NM_022120 NM_022120

CCDS: CCDS445

Canonical transcript exons

ENST00000327582 — 1 exons

Exon	Start	End
ENSE00001314260	39769523	39771348

Expression profiles

Bgee: expression breadth ubiquitous, 128 present calls, max score 95.90.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	95.90	gold quality
right testis	UBERON:0004534	93.12	gold quality
left testis	UBERON:0004533	92.67	gold quality
testis	UBERON:0000473	92.17	gold quality
sural nerve	UBERON:0015488	81.82	gold quality
apex of heart	UBERON:0002098	77.92	gold quality
right atrium auricular region	UBERON:0006631	75.60	gold quality
tibial nerve	UBERON:0001323	69.86	gold quality
heart left ventricle	UBERON:0002084	67.63	gold quality
heart	UBERON:0000948	67.33	gold quality
right lobe of thyroid gland	UBERON:0001119	64.43	gold quality
left ovary	UBERON:0002119	64.16	gold quality
ovary	UBERON:0000992	64.06	gold quality
right ovary	UBERON:0002118	62.99	gold quality
islet of Langerhans	UBERON:0000006	62.39	gold quality
prefrontal cortex	UBERON:0000451	62.30	gold quality
left lobe of thyroid gland	UBERON:0001120	62.22	gold quality
thyroid gland	UBERON:0002046	62.14	gold quality
bone marrow cell	CL:0002092	61.89	silver quality
frontal cortex	UBERON:0001870	61.56	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	61.23	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	61.17	gold quality
Brodmann (1909) area 9	UBERON:0013540	60.78	gold quality
right frontal lobe	UBERON:0002810	60.57	gold quality
cerebellum	UBERON:0002037	60.41	gold quality
cerebellar cortex	UBERON:0002129	60.32	gold quality
cerebellar hemisphere	UBERON:0002245	60.32	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	60.18	gold quality
mucosa of transverse colon	UBERON:0004991	60.18	gold quality
cerebral cortex	UBERON:0000956	59.89	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.58

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

9 targeting OXCT2, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-4731-5P	99.89	67.23	2537
HSA-MIR-1321	99.84	65.30	1811
HSA-MIR-4739	99.84	65.25	1832
HSA-MIR-4756-5P	99.84	64.98	1809
HSA-MIR-7152-5P	99.60	69.33	2094
HSA-MIR-7106-5P	99.53	67.47	3574
HSA-MIR-766-5P	99.47	67.91	2225
HSA-MIR-517-5P	97.13	68.43	781
HSA-MIR-7108-3P	94.37	64.79	183

Cross-species orthologs

8 orthologs

Organism	Symbol	Gene ID
danio_rerio	oxct1a	ENSDARG00000013063
danio_rerio	oxct1b	ENSDARG00000054319
mus_musculus	Oxct2a	ENSMUSG00000076436
mus_musculus	Oxct2b	ENSMUSG00000076438
rattus_norvegicus	Oxct2b	ENSRNOG00000077785
rattus_norvegicus	Oxct2a	ENSRNOG00000079897
drosophila_melanogaster	SCOT	FBGN0035298
caenorhabditis_elegans		WBGENE00007330

Paralogs (1): OXCT1 (ENSG00000083720)

Protein

Protein identifiers

Succinyl-CoA:3-ketoacid coenzyme A transferase 2, mitochondrial — Q9BYC2 (reviewed: Q9BYC2)

Alternative names: 3-oxoacid CoA-transferase 2A, Testis-specific succinyl-CoA:3-oxoacid CoA-transferase

All UniProt accessions (1): Q9BYC2

UniProt curated annotations — full annotation on UniProt →

Function. Key enzyme for ketone body catabolism. Transfers the CoA moiety from succinate to acetoacetate. Formation of the enzyme-CoA intermediate proceeds via an unstable anhydride species formed between the carboxylate groups of the enzyme and substrate.

Subunit / interactions. Homodimer.

Subcellular location. Mitochondrion.

Tissue specificity. Testis specific.

Pathway. Ketone metabolism; succinyl-CoA degradation; acetoacetyl-CoA from succinyl-CoA: step 1/1.

Similarity. Belongs to the 3-oxoacid CoA-transferase family.

RefSeq proteins (1): NP_071403* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR004163	CoA_transf_BS	Binding_site
IPR004164	CoA_transf_AS	Active_site
IPR004165	CoA_trans_fam_I	Family
IPR012791	3-oxoacid_CoA-transf_B	Domain
IPR012792	3-oxoacid_CoA-transf_A	Domain
IPR014388	3-oxoacid_CoA-transferase	Family
IPR037171	NagB/RpiA_transferase-like	Homologous_superfamily

Pfam: PF01144

Enzyme classification (BRENDA):

• EC 2.8.3.5 — 3-oxoacid CoA-transferase (BRENDA: 20 organisms, 33 substrates, 60 inhibitors, 44 Km, 8 kcat entries)

Substrate kinetics (BRENDA)

5 substrates with measured Km, best-characterized 5. Km ranges are aggregated across organisms/conditions.

Substrate	Km (mM)	Measurements
ACETOACETATE	0.0002–0.44	13
ACETOACETYL-COA	0.006–0.72	10
SUCCINATE	0.025–39	9
SUCCINYL-COA	0.156–8	9
MALEATE	35	1

Catalyzed reactions (Rhea), 1 shown:

• a 3-oxo acid + succinyl-CoA = a 3-oxoacyl-CoA + succinate (RHEA:24564)

UniProt features (9 total): sequence conflict 4, sequence variant 2, transit peptide 1, chain 1, active site 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9BYC2-F1	92.20	0.87

Functional residue map

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

Catalytic / active sites (1): 341 (5-glutamyl coenzyme a thioester intermediate)

Function

Pathways and Gene Ontology

Reactome pathways

4 pathways

ID	Pathway
R-HSA-77108	Utilization of Ketone Bodies
R-HSA-1430728	Metabolism
R-HSA-556833	Metabolism of lipids
R-HSA-74182	Ketone body metabolism

MSigDB gene sets: 48 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_DN, GSE45365_NK_CELL_VS_CD11B_DC_UP, BENPORATH_ES_WITH_H3K27ME3, KEGG_VALINE_LEUCINE_AND_ISOLEUCINE_DEGRADATION, GOBP_GENERATION_OF_PRECURSOR_METABOLITES_AND_ENERGY, chr1p34, GOBP_LIPID_METABOLIC_PROCESS, GOBP_SMALL_MOLECULE_CATABOLIC_PROCESS, SANSOM_APC_TARGETS_UP, GOBP_LIPID_CATABOLIC_PROCESS, GOBP_FATTY_ACID_DERIVATIVE_METABOLIC_PROCESS, GOCC_MOTILE_CILIUM, GOCC_MITOCHONDRIAL_MATRIX, XU_GH1_EXOGENOUS_TARGETS_DN, GOCC_CILIUM

GO Biological Process (2): ketone body catabolic process (GO:0046952), obsolete ketone body metabolic process (GO:1902224)

GO Molecular Function (4): succinyl-CoA:3-oxo-acid CoA-transferase activity (GO:0008260), protein binding (GO:0005515), CoA-transferase activity (GO:0008410), transferase activity (GO:0016740)

GO Cellular Component (3): mitochondrion (GO:0005739), mitochondrial matrix (GO:0005759), motile cilium (GO:0031514)

Reactome top-level categories

Rollup of top-3 pathways:

Category	Pathways
Ketone body metabolism	1
Metabolism	1
Metabolism of lipids	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
small molecule catabolic process	1
fatty acid derivative catabolic process	1
CoA-transferase activity	1
binding	1
transferase activity, transferring sulphur-containing groups	1
catalytic activity	1
cytoplasm	1
intracellular membrane-bounded organelle	1
mitochondrion	1
intracellular organelle lumen	1
cilium	1

Protein interactions and networks

STRING

952 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
OXCT2	BMP8B	P34820	839
OXCT2	ACAT1	P24752	715
OXCT2	HMGCL	P35914	637
OXCT2	HMGCLL1	Q8TB92	581
OXCT2	HMGCS2	P54868	560
OXCT2	BDH1	Q02338	545
OXCT2	ACAT2	Q9BWD1	504
OXCT2	ACAA2	P42765	482
OXCT2	HMGCS1	Q01581	479
OXCT2	ENO1	P06733	432
OXCT2	BDH2	Q9BUT1	419
OXCT2	FAM187B	Q17R55	419
OXCT2	SEC14L6	B5MCN3	419
OXCT2	AACS	Q86V21	413
OXCT2	HADHB	P55084	409

IntAct

15 interactions, top by confidence:

A	B	Type	Score
OXCT2	MCCC1	psi-mi:“MI:0915”(physical association)	0.620
OXCT2	HSPD1	psi-mi:“MI:0914”(association)	0.530
OXCT1	EPS15	psi-mi:“MI:0914”(association)	0.530
SMR3B	OXCT2	psi-mi:“MI:0915”(physical association)	0.400
OXCT1	BCKDHA	psi-mi:“MI:0914”(association)	0.350
OXCT2	SHMT2	psi-mi:“MI:0914”(association)	0.350
OXCT1	SLC25A5	psi-mi:“MI:0914”(association)	0.350
OXCT2	CLPX	psi-mi:“MI:0914”(association)	0.350
OXCT1	COQ9	psi-mi:“MI:0914”(association)	0.350
OXCT2	NME4	psi-mi:“MI:0914”(association)	0.350
OXCT2	BCKDK	psi-mi:“MI:0914”(association)	0.350

BioGRID (39): MCCC1 (Affinity Capture-MS), OXCT2 (Reconstituted Complex), OXCT2 (Affinity Capture-MS), OXCT2 (Affinity Capture-MS), NME4 (Affinity Capture-MS), ECHDC1 (Affinity Capture-MS), BCKDHA (Affinity Capture-MS), PMPCB (Affinity Capture-MS), ECH1 (Affinity Capture-MS), NFS1 (Affinity Capture-MS), ATP5E (Affinity Capture-MS), OXCT1 (Affinity Capture-MS), C1QBP (Affinity Capture-MS), OXCT2 (Affinity Capture-MS), NDUFAF7 (Affinity Capture-MS)

ESM2 similar proteins: A0QMH2, A5W7G2, B0KTX5, B0RVK3, B0RVK4, B0U5G3, B2GV06, B2I9S0, B3EY95, F1CYZ5, O34317, P0C7I7, P0C7I8, P42315, P44875, P52043, P55809, P56006, P63649, P63651, P65155, P75726, P76458, P76459, P9WKJ4, P9WKJ5, P9WPW0, P9WPW1, P9WPW2, P9WPW3, P9WPW4, P9WPW5, Q01103, Q09450, Q20Z21, Q29551, Q43973, Q4CY36, Q4K8M6, Q73TT7

Diamond homologs: B0RVK3, B2GV06, O34466, P0A101, P0A102, P0C7I8, P23673, P42316, P44874, P55809, P56007, P63651, P76459, P9WPW2, P9WPW3, Q09450, Q29551, Q54JD9, Q59091, Q5XIJ9, Q9BYC2, Q9D0K2, Q9ESL0, Q9JJN4, Q9W058, Q9ZLE4, B0RVK4, O34317, P0C7I7, P33752, P42315, P44875, P56006, P63649, P76458, P9WPW4, P9WPW5, Q01103, Q43973, Q9ZLE3

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 12 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Mitochondrial protein degradation	5	51.9×	1e-06

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	0
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

67 predictions. Top by Δscore:

Variant	Effect	Δscore
1:39769710:C:CT	donor_gain	0.9300
1:39769711:C:CT	donor_gain	0.9300
1:39769824:T:TA	donor_gain	0.9200
1:39769803:C:CA	donor_gain	0.8600
1:39769709:G:GC	donor_gain	0.8400
1:39769753:A:T	donor_gain	0.7600
1:39769708:TGCC:T	donor_gain	0.7500
1:39771172:G:GT	acceptor_gain	0.7000
1:39769757:C:A	donor_gain	0.6900
1:39769712:A:AA	donor_gain	0.6500
1:39769757:CCCG:C	donor_gain	0.6500
1:39769778:TCC:T	donor_gain	0.5700
1:39769754:C:T	donor_gain	0.5500
1:39771152:C:CC	acceptor_gain	0.5500
1:39769677:C:CT	donor_gain	0.5400
1:39771151:A:AC	acceptor_gain	0.5200
1:39769716:G:A	donor_gain	0.5000
1:39769756:C:CA	donor_gain	0.5000
1:39771180:G:GT	acceptor_gain	0.4600
1:39770321:T:TA	donor_gain	0.4400
1:39770519:TCC:T	donor_gain	0.4200
1:39769758:C:T	donor_gain	0.3900
1:39769809:G:C	donor_gain	0.3900
1:39769678:C:CT	donor_gain	0.3800
1:39770049:TGGAA:T	donor_gain	0.3800
1:39770063:GCTCC:G	acceptor_gain	0.3800
1:39771265:G:T	acceptor_gain	0.3800
1:39769706:GGTGC:G	donor_gain	0.3300
1:39769749:AGG:A	donor_gain	0.3300
1:39769603:G:GT	acceptor_gain	0.3200

AlphaMissense

3383 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:39771064:G:C	F64L	0.999
1:39771064:G:T	F64L	0.999
1:39771066:A:G	F64L	0.999
1:39770107:G:C	F383L	0.998
1:39770107:G:T	F383L	0.998
1:39770109:A:G	F383L	0.998
1:39770825:C:G	R144P	0.998
1:39770028:A:G	W410R	0.997
1:39770028:A:T	W410R	0.997
1:39770841:C:G	G139R	0.997
1:39770119:G:C	S379R	0.996
1:39770119:G:T	S379R	0.996
1:39770121:T:G	S379R	0.996
1:39769983:C:G	D425H	0.995
1:39770228:C:T	G343E	0.995
1:39770229:C:A	G343W	0.995
1:39770230:G:C	N342K	0.995
1:39770230:G:T	N342K	0.995
1:39770840:C:T	G139D	0.995
1:39770096:C:G	R387P	0.994
1:39770111:G:A	S382F	0.994
1:39770236:A:C	S340R	0.993
1:39770236:A:T	S340R	0.993
1:39770238:T:G	S340R	0.993
1:39770791:G:C	F155L	0.993
1:39770791:G:T	F155L	0.993
1:39770793:A:G	F155L	0.993
1:39770819:C:G	R146P	0.993
1:39770831:G:T	A142D	0.993
1:39770841:C:A	G139C	0.993

dbSNP variants (sampled 300 via entrez): RS1003550307 (1:39771469 G>A,C), RS1003820866 (1:39772666 C>A), RS1004108609 (1:39773111 C>T), RS1005518194 (1:39770784 G>A,T), RS1010964719 (1:39772118 C>G), RS1011139638 (1:39771584 G>A,T), RS1011727670 (1:39769583 G>C), RS1012257834 (1:39770973 C>T), RS1013257119 (1:39769188 AAAAAAAG>A), RS1015928772 (1:39773317 C>T), RS1016535644 (1:39770799 G>A), RS1018216297 (1:39769612 C>G), RS1022159315 (1:39771590 G>A), RS1023669932 (1:39771293 G>A,C), RS1024670746 (1:39769206 G>A)

Disease associations

OMIM: gene MIM:610289 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

17 total (human), top 17 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
methylmercuric chloride	increases expression	1
S-(1,2-dichlorovinyl)cysteine	affects cotreatment, decreases expression	1
CGP 52608	affects binding, increases reaction	1
ICG 001	decreases expression	1
Atrazine	decreases expression	1
Benzo(a)pyrene	decreases expression	1
Diazinon	increases methylation	1
Fenfluramine	decreases expression	1
Lipopolysaccharides	affects cotreatment, decreases expression	1
Smoke	decreases expression	1
Tobacco Smoke Pollution	decreases expression	1
Tretinoin	decreases expression	1
Valproic Acid	increases expression	1
Zinc	increases expression	1
Aflatoxin B1	increases methylation	1
Okadaic Acid	increases expression	1
Particulate Matter	decreases expression	1

Clinical trials (associated diseases)

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