OXCT1

3-oxoacid CoA-transferase 1

Basic information

Region (hg38): 5:41730065-41870425

Previous symbols: [ "OXCT" ]

Links

ENSG00000083720 ∙ NCBI:5019 ∙ OMIM:601424 ∙ HGNC:8527 ∙ Uniprot:P55809 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• succinyl-CoA:3-ketoacid CoA transferase deficiency (Definitive), mode of inheritance: AR
• succinyl-CoA:3-ketoacid CoA transferase deficiency (Strong), mode of inheritance: AR
• succinyl-CoA:3-ketoacid CoA transferase deficiency (Strong), mode of inheritance: AR
• succinyl-CoA:3-ketoacid CoA transferase deficiency (Strong), mode of inheritance: AR
• succinyl-CoA:3-ketoacid CoA transferase deficiency (Definitive), mode of inheritance: AR
• succinyl-CoA:3-ketoacid CoA transferase deficiency (Supportive), mode of inheritance: AR

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Succinyl CoA:3-oxoacid CoA transferase deficiency	AR	Biochemical	Diagnosis may allow prompt recognition and treatment of ketoacidotic episodes (eg, with IV glucose and sodium bicarbonate), which may be beneficial to reduce morbidity and mortality	Biochemical	4258782; 1405472; 8751852; 9521962; 10964512; 11286388; 11757586; 20652411

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OXCT1 gene.

• Succinyl-CoA acetoacetate transferase deficiency (5 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OXCT1 gene is commonly pathogenic or not.

In the table, we include only reliable ClinVar variants with their consequences to MANE Select, Mane Plus Clinical transcripts, or transcripts with TSL equals 1. Click the count to view the source variants.

Warning: slight differences between displayed counts and the number of variants in ClinVar may occur, primarily due to (1) the application of a different transcript and/or consequence by our variant effect predictor or (2) differences in clinical significance: we classify Benign/Likely benign variants as Likely benign and Pathogenic/Likely pathogenic variants as Likely pathogenic.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous			2	31	1	34
missense	2	2	55	4	1	64
nonsense	1	1				2
start loss						0
frameshift		3				3
inframe indel						0
splice donor/acceptor (+/-2bp)	2	2				4
splice region			5	6	3	14
non coding			24	20	26	70
Total	5	8	81	55	28

Highest pathogenic variant AF is 0.00000658

Variants in OXCT1

This is a list of pathogenic ClinVar variants found in the OXCT1 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
5-41730113-T-C		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 13, 2018)
5-41730256-C-A		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 13, 2018)
5-41730285-C-A		Succinyl-CoA acetoacetate transferase deficiency	Benign (Jan 12, 2018)
5-41730295-C-G		Succinyl-CoA acetoacetate transferase deficiency	Benign (Jan 13, 2018)
5-41730384-T-C		Succinyl-CoA acetoacetate transferase deficiency	Likely benign (Jan 13, 2018)
5-41730463-T-A		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 12, 2018)
5-41730500-G-A		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 13, 2018)
5-41730651-G-GT		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jun 14, 2016)
5-41730657-T-C		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 13, 2018)
5-41730688-C-T		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 13, 2018)
5-41730706-C-T		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 13, 2018)
5-41730718-A-G		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 13, 2018)
5-41730764-A-G		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 13, 2018)
5-41730773-A-G		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 12, 2018)
5-41730794-T-C		Succinyl-CoA acetoacetate transferase deficiency	Benign (Jan 12, 2018)
5-41731146-C-A		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 13, 2018)
5-41731162-G-A		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 12, 2018)
5-41731367-G-T		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 12, 2018)
5-41731538-T-C		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 13, 2018)
5-41731541-T-C		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 13, 2018)
5-41731572-C-T		Succinyl-CoA acetoacetate transferase deficiency	Likely benign (Jan 13, 2018)
5-41731591-G-T		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 12, 2018)
5-41731635-T-C		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 13, 2018)
5-41731703-C-T		Succinyl-CoA acetoacetate transferase deficiency	Uncertain significance (Jan 13, 2018)
5-41731728-T-C		OXCT1-related disorder	Likely benign (Dec 29, 2021)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OXCT1	protein_coding	protein_coding	ENST00000196371	17	140455

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.00473	0.995	125723	0	25	125748	0.0000994

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.57	169	293	0.578	0.0000153	3390
Missense in Polyphen		24	94.938	0.2528		1158
Synonymous	-0.841	111	100	1.11	0.00000546	1004
Loss of Function	3.53	10	31.3	0.319	0.00000172	372

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000174	0.000174
Ashkenazi Jewish	0.0000992	0.0000992
East Asian	0.0000544	0.0000544
Finnish	0.0000924	0.0000924
European (Non-Finnish)	0.000132	0.000132
Middle Eastern	0.0000544	0.0000544
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: 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.
• Pathway: Butanoate metabolism - Homo sapiens (human);Synthesis and degradation of ketone bodies - Homo sapiens (human);Valine, leucine and isoleucine degradation - Homo sapiens (human);3-Methylglutaconic Aciduria Type I;Valine, Leucine and Isoleucine Degradation;2-Methyl-3-Hydroxybutryl CoA Dehydrogenase Deficiency;Isovaleric Aciduria;3-Methylcrotonyl Coa Carboxylase Deficiency Type I;Propionic Acidemia;Maple Syrup Urine Disease;3-Hydroxy-3-Methylglutaryl-CoA Lyase Deficiency;Isobutyryl-coa dehydrogenase deficiency;3-hydroxyisobutyric aciduria;3-hydroxyisobutyric acid dehydrogenase deficiency;Isovaleric acidemia;Methylmalonate Semialdehyde Dehydrogenase Deficiency;Succinyl CoA: 3-ketoacid CoA transferase deficiency;Methylmalonic Aciduria;3-Methylglutaconic Aciduria Type IV;3-Methylglutaconic Aciduria Type III;Ketone Body Metabolism;Butyrate Metabolism;Beta-Ketothiolase Deficiency;Synthesis and Degradation of Ketone Bodies;ketolysis;Butanoate metabolism;Metabolism of lipids;Metabolism;Utilization of Ketone Bodies;Ketone body metabolism;Butanoate metabolism;Valine Leucine Isoleucine degradation (Consensus)

Intolerance Scores

• loftool: 0.212
• rvis_EVS: -0.2
• rvis_percentile_EVS: 38.82

Haploinsufficiency Scores

• pHI: 0.100
• hipred: N
• hipred_score: 0.471
• ghis: 0.492

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.375

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Oxct1
• Phenotype: mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); muscle phenotype; cellular phenotype; homeostasis/metabolism phenotype

Gene ontology

• Biological process: brain development;heart development;response to nutrient;response to hormone;response to activity;positive regulation of insulin secretion involved in cellular response to glucose stimulus;ketone catabolic process;response to starvation;response to ethanol;cellular ketone body metabolic process;ketone body catabolic process;adipose tissue development
• Cellular component: nucleoplasm;mitochondrion;mitochondrial matrix
• Molecular function: 3-oxoacid CoA-transferase activity;protein homodimerization activity