OXSM

3-oxoacyl-ACP synthase, mitochondrial

Basic information

Region (hg38): 3:25782916-25794534

Links

ENSG00000151093 ∙ NCBI:54995 ∙ OMIM:610324 ∙ HGNC:26063 ∙ Uniprot:Q9NWU1 ∙ 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 OXSM gene.

• Inborn genetic diseases (16 variants)
• not provided (3 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the OXSM 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			15	1		16
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding				2	1	3
Total	0	0	15	3	1

Variants in OXSM

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

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

Position	Type	Phenotype	Significance	ClinVar
3-25783222-C-T			Likely benign (Jul 05, 2019)
3-25783242-G-C		Congenital disorder of deglycosylation	Likely benign (Jan 08, 2023)
3-25783245-C-A		Congenital disorder of deglycosylation	Likely benign (Sep 19, 2023)
3-25783247-C-G		Congenital disorder of deglycosylation	Likely benign (May 26, 2023)
3-25783248-G-A		Congenital disorder of deglycosylation	Likely benign (Jan 17, 2024)
3-25783249-T-C		not specified • Congenital disorder of deglycosylation	Likely benign (Jan 10, 2024)
3-25783250-T-C		Congenital disorder of deglycosylation	Likely benign (Jun 03, 2022)
3-25783252-C-T		Congenital disorder of deglycosylation	Likely benign (Nov 15, 2023)
3-25783263-AG-A		Congenital disorder of deglycosylation	Pathogenic (Aug 09, 2023)
3-25783265-G-A		Congenital disorder of deglycosylation	Likely benign (Jan 16, 2024)
3-25783268-G-A		Congenital disorder of deglycosylation	Benign (Jan 29, 2024)
3-25783269-T-C		Congenital disorder of deglycosylation	Uncertain significance (May 25, 2022)
3-25783271-G-C		Congenital disorder of deglycosylation	Uncertain significance (Sep 01, 2021)
3-25783283-G-A		Congenital disorder of deglycosylation	Likely benign (Jan 08, 2021)
3-25783287-A-T		Congenital disorder of deglycosylation	Uncertain significance (May 16, 2022)
3-25783295-G-A		Congenital disorder of deglycosylation	Likely benign (Sep 13, 2023)
3-25783295-G-C		Congenital disorder of deglycosylation	Likely benign (Nov 23, 2020)
3-25783298-G-A		Congenital disorder of deglycosylation	Likely benign (Aug 04, 2023)
3-25783300-C-T		Congenital disorder of deglycosylation	Uncertain significance (Aug 09, 2022)
3-25783303-C-T		Congenital disorder of deglycosylation	Uncertain significance (Aug 22, 2019)
3-25783313-C-A		Congenital disorder of deglycosylation	Uncertain significance (Jan 04, 2022)
3-25783313-C-G		Congenital disorder of deglycosylation	Uncertain significance (Jun 03, 2022)
3-25783325-C-G		Congenital disorder of deglycosylation	Uncertain significance (May 17, 2022)
3-25783328-G-T		Congenital disorder of deglycosylation	Pathogenic (Jul 13, 2023)
3-25783334-C-T		Congenital disorder of deglycosylation	Likely benign (Dec 19, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
OXSM	protein_coding	protein_coding	ENST00000280701	2	11618

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.0000247	0.766	125687	0	60	125747	0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	-0.0216	244	243	1.00	0.0000117	2948
Missense in Polyphen		105	103.27	1.0167		1216
Synonymous	1.20	73	87.3	0.836	0.00000409	986
Loss of Function	1.15	9	13.6	0.662	7.88e-7	180

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.000478	0.000477
Ashkenazi Jewish	0.00	0.00
East Asian	0.000435	0.000435
Finnish	0.000126	0.0000924
European (Non-Finnish)	0.000299	0.000299
Middle Eastern	0.000435	0.000435
South Asian	0.000163	0.000131
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: May play a role in the biosynthesis of lipoic acid as well as longer chain fatty acids required for optimal mitochondrial function. {ECO:0000269|PubMed:15668256}.
• Pathway: Fatty acid biosynthesis - Homo sapiens (human);Biotin metabolism - Homo sapiens (human);palmitate biosynthesis;Phosphatidylinositol phosphate metabolism (Consensus)

Recessive Scores

• pRec: 0.488

Intolerance Scores

• loftool: 0.246
• rvis_EVS: 0.15
• rvis_percentile_EVS: 64.51

Haploinsufficiency Scores

• pHI: 0.0434
• hipred: N
• hipred_score: 0.292
• ghis: 0.518

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.0277

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Oxsm

Gene ontology

• Biological process: acyl-CoA metabolic process;short-chain fatty acid biosynthetic process;medium-chain fatty acid biosynthetic process
• Cellular component: mitochondrion;cytosol
• Molecular function: 3-oxoacyl-[acyl-carrier-protein] synthase activity