OXCT2

3-oxoacid CoA-transferase 2

Basic information

Region (hg38): 1:39769523-39771348

Links

ENSG00000198754 ∙ NCBI:64064 ∙ OMIM:610289 ∙ HGNC:18606 ∙ Uniprot:Q9BYC2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the OXCT2 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OXCT2 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						0
missense			29	4		33
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	29	4	0

Variants in OXCT2

This is a list of pathogenic ClinVar variants found in the OXCT2 region.

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

Position	Type	Phenotype	Significance	ClinVar
1-39769737-G-A		not specified	Uncertain significance (Jul 06, 2021)
1-39769746-C-G		not specified	Uncertain significance (Jan 02, 2024)
1-39769839-A-G		not specified	Uncertain significance (Jun 30, 2022)
1-39769857-T-C		not specified	Uncertain significance (Apr 19, 2024)
1-39769864-G-T		not specified	Uncertain significance (Jun 06, 2023)
1-39769869-C-G		not specified	Uncertain significance (Feb 28, 2024)
1-39769881-C-T		not specified	Uncertain significance (Jun 17, 2022)
1-39769919-G-A		not specified	Likely benign (Jan 26, 2022)
1-39769997-A-G		not specified	Uncertain significance (Oct 26, 2022)
1-39770049-T-C		not specified	Uncertain significance (Sep 30, 2021)
1-39770205-G-C		not specified	Uncertain significance (Dec 06, 2022)
1-39770249-A-G		not specified	Uncertain significance (Mar 20, 2024)
1-39770292-T-C		not specified	Uncertain significance (Jan 08, 2024)
1-39770319-C-A		not specified	Uncertain significance (Dec 07, 2021)
1-39770350-G-C		not specified	Uncertain significance (May 23, 2024)
1-39770352-T-C		not specified	Uncertain significance (Jan 04, 2024)
1-39770423-C-A		not specified	Uncertain significance (Oct 10, 2023)
1-39770462-T-C		not specified	Uncertain significance (Nov 13, 2023)
1-39770586-T-C		not specified	Uncertain significance (Feb 28, 2024)
1-39770589-A-T		not specified	Uncertain significance (Sep 16, 2021)
1-39770595-C-T		not specified	Uncertain significance (Mar 07, 2024)
1-39770621-C-A		not specified	Uncertain significance (Dec 15, 2022)
1-39770649-T-C			Likely benign (Nov 01, 2022)
1-39770696-C-T		not specified	Uncertain significance (May 24, 2024)
1-39770712-G-C		not specified	Uncertain significance (Dec 18, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OXCT2	protein_coding	protein_coding	ENST00000327582	1	1826

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
2.73e-7	0.0497	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.639	233	262	0.889	0.0000156	3304
Missense in Polyphen		90	95.223	0.94515		1283
Synonymous	1.86	96	122	0.786	0.00000867	1103
Loss of Function	-1.56	8	4.44	1.80	2.74e-7	63

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.00	0.00
Ashkenazi Jewish	0.00	0.00
East Asian	0.00	0.00
Finnish	0.00	0.00
European (Non-Finnish)	0.00	0.00
Middle Eastern	0.00	0.00
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 (By similarity). {ECO:0000250}.
• Pathway: Butanoate metabolism - Homo sapiens (human);Synthesis and degradation of ketone bodies - Homo sapiens (human);Valine, leucine and isoleucine degradation - Homo sapiens (human);Metabolism of lipids;Metabolism;Utilization of Ketone Bodies;Ketone body metabolism;Butanoate metabolism (Consensus)

Haploinsufficiency Scores

• pHI: 0.254
• ghis: 0.524

Essentials

• essential_gene_CRISPR: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.402

Gene Damage Prediction

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

Gene ontology

• Biological process: ketone body catabolic process
• Cellular component: mitochondrion;mitochondrial matrix;motile cilium
• Molecular function: 3-oxoacid CoA-transferase activity