OXSM

protein-coding

3-oxoacyl-ACP synthase, mitochondrial

Gene summary

This gene encodes a beta-ketoacyl synthetase. The encoded enzyme is required for elongation of fatty acid chains in the mitochondria. Alternatively spliced transcript variants have been described.[provided by RefSeq, Feb 2009]

MANE transcript

NM_017897.3

Inheritance

—

ClinVar variants

P:1U:59B:3

Top phenotype

Hypercholesterolemia, familial, 1

gnomAD constraint

pLI —, LoF o/e 0.66

Max pathogenic AF

—

Genomic locus

chr3:25,782,917-25,794,534

External References & Databases

Ensembl (ENSG00000151093)

Transcript & Mutation Effects

hg38 • Region Span ~11.6 kb

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GenCC Phenotypes & Disease Associations

Curated gene-disease validity assertions and inheritance patterns

No GenCC data available for this gene.

ClinVar Associated Diseases & Phenotypes

Reported disease conditions connected to OXSM variants in ClinVar

2 Conditions Cataloged

not specifiedTotal: 61

Hypercholesterolemia, familial, 1Total: 1

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_017897.3. Only rare variants are included.

We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.

Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.

Effect	PathogenicP	Likely pathogenicLP	VUS	Likely benignLB	BenignB	Sum
synonymous						0
missense	1 clinvar		58 clinvar	3 clinvar		62
nonsense			1 clinvar			1
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	1	0	59	3	0	63

Loading ClinVar variants...

Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 25 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_017897.3	RefSeq	NP_060367.1	2	MANE Select
ENST00000280701.8	Ensembl	ENSP00000280701.3	2	MANE Select
NM_001145391.2	RefSeq	NP_001138863.1	3	Standard
ENST00000420173.2	Ensembl	ENSP00000411303.2	3	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

Fatty acid biosynthesis - Homo sapiens (human)
Biotin metabolism - Homo sapiens (human)
palmitate biosynthesis
Phosphatidylinositol phosphate metabolism

Biological Process

acyl-CoA metabolic process
short-chain fatty acid biosynthetic process
medium-chain fatty acid biosynthetic process

Molecular Function

3-oxoacyl-[acyl-carrier-protein] synthase activity

Cellular Component

mitochondrion
cytosol

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000280701
Coding exons: 2
Length: 11618
Individuals with no LoFs: 125687
Homozygous LoFs: 0
Heterozygous LoFs: 60
Defined: 125747
p: 0.000239

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	-0.0216	244	243	1.00	0.0000117	2948
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0.00025	0.00025	rare
Latino/Admixed American	0.00023	0.00023	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.00043	0.00044	rare
Finnish	0.00013	0.000092	rare
European (Non-Finnish)	0.00030	0.00030	rare
South Asian	0.00016	0.00013	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.488

Intolerance Scores

LoFtool: 0.246
RVIS EVS: 0.15
RVIS percentile EVS: 64.51

Essentials

Essential (CRISPR): E
Essential (CRISPR2): E
Essential (gene trap): N
Indispensability pred.: N
Indispensability score: 0.0277

Gene Damage Prediction

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