Gene Details | GeDiPNet - Complete Gene Info, Disease Associations & Pathways

Gene Gene information from NCBI Gene database. Gene SNPs miRNA Gene ontology Other IDs Protein Pathways Associated diseases
Entrez ID	197322
Gene name	Acyl-CoA synthetase family member 3
Gene symbol	ACSF3
Synonyms (NCBI Gene)	-
Chromosome	16
Chromosome location	16q24.3
Summary	This gene encodes a member of the acyl-CoA synthetase family of enzymes that activate fatty acids by catalyzing the formation of a thioester linkage between fatty acids and coenzyme A. The encoded protein is localized to mitochondria, has high specificity

Show/Hide all (25)

SNP ID	Visualize variation	Clinical significance	Consequence
rs140986055	C>T	Pathogenic	Genic upstream transcript variant, coding sequence variant, missense variant, non coding transcript variant, 5 prime UTR variant
rs141090143	C>A,T	Pathogenic-likely-pathogenic, conflicting-interpretations-of-pathogenicity	Genic downstream transcript variant, synonymous variant, coding sequence variant, missense variant, non coding transcript variant, 5 prime UTR variant
rs144681140	G>A,C	Conflicting-interpretations-of-pathogenicity, uncertain-significance	Missense variant, downstream transcript variant, genic downstream transcript variant, 5 prime UTR variant, non coding transcript variant, coding sequence variant
rs145583876	G>A	Pathogenic	Stop gained, genic upstream transcript variant, 5 prime UTR variant, non coding transcript variant, coding sequence variant
rs150487794	G>A	Conflicting-interpretations-of-pathogenicity, pathogenic	Missense variant, genic upstream transcript variant, non coding transcript variant, intron variant, upstream transcript variant, coding sequence variant
rs201954387	G>A	Pathogenic	5 prime UTR variant, genic downstream transcript variant, stop gained, coding sequence variant, non coding transcript variant
rs202182978	C>A,T	Likely-pathogenic	Synonymous variant, missense variant, upstream transcript variant, genic upstream transcript variant, coding sequence variant, intron variant, non coding transcript variant
rs370382601	A>G	Pathogenic	Initiator codon variant, missense variant, upstream transcript variant, genic upstream transcript variant, intron variant, non coding transcript variant
rs387907118	C>T	Pathogenic	Non coding transcript variant, stop gained, genic downstream transcript variant, coding sequence variant, 5 prime UTR variant
rs387907119	G>A	Pathogenic	Non coding transcript variant, genic downstream transcript variant, coding sequence variant, missense variant, 5 prime UTR variant, downstream transcript variant
rs387907120	C>A,T	Pathogenic	Non coding transcript variant, genic upstream transcript variant, upstream transcript variant, intron variant, coding sequence variant, missense variant
rs387907121	T>A,G	Pathogenic	Non coding transcript variant, genic upstream transcript variant, intron variant, coding sequence variant, missense variant, 5 prime UTR variant
rs570233664	G>A,T	Pathogenic	Non coding transcript variant, missense variant, 5 prime UTR variant, genic upstream transcript variant, coding sequence variant, stop gained
rs748382994	C>G,T	Pathogenic-likely-pathogenic	Genic downstream transcript variant, 5 prime UTR variant, stop gained, downstream transcript variant, coding sequence variant, missense variant, non coding transcript variant
rs751342087	->G	Likely-pathogenic	Genic downstream transcript variant, 5 prime UTR variant, downstream transcript variant, coding sequence variant, frameshift variant, non coding transcript variant
rs752104014	G>A	Likely-pathogenic	5 prime UTR variant, genic upstream transcript variant, coding sequence variant, missense variant, non coding transcript variant
rs752338222	G>T	Pathogenic	5 prime UTR variant, stop gained, genic upstream transcript variant, coding sequence variant, non coding transcript variant, intron variant
rs760759040	G>-	Pathogenic	Coding sequence variant, non coding transcript variant, frameshift variant, intron variant, upstream transcript variant, genic upstream transcript variant
rs761573352	G>A	Pathogenic	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, intron variant, genic upstream transcript variant, missense variant
rs766764090	C>A,T	Pathogenic	Coding sequence variant, 5 prime UTR variant, non coding transcript variant, synonymous variant, stop gained, genic upstream transcript variant
rs796051924	T>-	Likely-pathogenic	Genic downstream transcript variant, frameshift variant, non coding transcript variant, coding sequence variant, 5 prime UTR variant
rs1064793662	CA>-	Pathogenic	Genic downstream transcript variant, non coding transcript variant, downstream transcript variant, inframe indel, stop gained, 5 prime UTR variant, coding sequence variant
rs1131691498	G>A	Likely-pathogenic	Non coding transcript variant, genic upstream transcript variant, stop gained, coding sequence variant, intron variant, upstream transcript variant
rs1188774860	A>G	Pathogenic	Genic downstream transcript variant, splice acceptor variant
rs1597898076	G>-	Pathogenic	Frameshift variant, non coding transcript variant, coding sequence variant, genic upstream transcript variant, 5 prime UTR variant

110

Show/Hide all (110)

miRTarBase ID	miRNA	Experiments	Reference
MIRT024911	hsa-miR-215-5p	Microarray	19074876
MIRT026799	hsa-miR-192-5p	Microarray	19074876
MIRT763350	hsa-miR-4277	CLIP-seq
MIRT763351	hsa-miR-526b	CLIP-seq
MIRT763352	hsa-miR-1207-5p	CLIP-seq
MIRT763353	hsa-miR-1273	CLIP-seq
MIRT763354	hsa-miR-1293	CLIP-seq
MIRT763355	hsa-miR-1827	CLIP-seq
MIRT763356	hsa-miR-1915	CLIP-seq
MIRT763357	hsa-miR-192	CLIP-seq
MIRT763358	hsa-miR-203	CLIP-seq
MIRT763359	hsa-miR-215	CLIP-seq
MIRT763360	hsa-miR-2467-3p	CLIP-seq
MIRT763361	hsa-miR-3065-3p	CLIP-seq
MIRT763362	hsa-miR-3148	CLIP-seq
MIRT763363	hsa-miR-3151	CLIP-seq
MIRT763364	hsa-miR-3665	CLIP-seq
MIRT763365	hsa-miR-3675-5p	CLIP-seq
MIRT763366	hsa-miR-3683	CLIP-seq
MIRT763367	hsa-miR-3690	CLIP-seq
MIRT763368	hsa-miR-4254	CLIP-seq
MIRT763369	hsa-miR-4257	CLIP-seq
MIRT763370	hsa-miR-4268	CLIP-seq
MIRT763371	hsa-miR-4316	CLIP-seq
MIRT763372	hsa-miR-4446-3p	CLIP-seq
MIRT763373	hsa-miR-4446-5p	CLIP-seq
MIRT763374	hsa-miR-4447	CLIP-seq
MIRT763375	hsa-miR-4453	CLIP-seq
MIRT763376	hsa-miR-4459	CLIP-seq
MIRT763377	hsa-miR-4472	CLIP-seq
MIRT763378	hsa-miR-4483	CLIP-seq
MIRT763379	hsa-miR-4488	CLIP-seq
MIRT763380	hsa-miR-4492	CLIP-seq
MIRT763381	hsa-miR-4498	CLIP-seq
MIRT763382	hsa-miR-4505	CLIP-seq
MIRT763383	hsa-miR-4514	CLIP-seq
MIRT763384	hsa-miR-4538	CLIP-seq
MIRT763385	hsa-miR-4640-5p	CLIP-seq
MIRT763386	hsa-miR-4645-5p	CLIP-seq
MIRT763387	hsa-miR-4649-5p	CLIP-seq
MIRT763388	hsa-miR-4673	CLIP-seq
MIRT763389	hsa-miR-4692	CLIP-seq
MIRT763390	hsa-miR-4697-5p	CLIP-seq
MIRT763391	hsa-miR-4710	CLIP-seq
MIRT763392	hsa-miR-4726-3p	CLIP-seq
MIRT763393	hsa-miR-4726-5p	CLIP-seq
MIRT763394	hsa-miR-4731-5p	CLIP-seq
MIRT763395	hsa-miR-4733-3p	CLIP-seq
MIRT763396	hsa-miR-4736	CLIP-seq
MIRT763397	hsa-miR-4763-3p	CLIP-seq
MIRT763398	hsa-miR-4779	CLIP-seq
MIRT763399	hsa-miR-486-3p	CLIP-seq
MIRT763400	hsa-miR-513a-3p	CLIP-seq
MIRT763401	hsa-miR-541	CLIP-seq
MIRT763402	hsa-miR-570	CLIP-seq
MIRT763403	hsa-miR-637	CLIP-seq
MIRT763404	hsa-miR-654-5p	CLIP-seq
MIRT763405	hsa-miR-665	CLIP-seq
MIRT763406	hsa-miR-762	CLIP-seq
MIRT763407	hsa-miR-875-3p	CLIP-seq
MIRT763408	hsa-miR-940	CLIP-seq
MIRT1545054	hsa-miR-128	CLIP-seq
MIRT1545055	hsa-miR-4300	CLIP-seq
MIRT1545056	hsa-miR-920	CLIP-seq
MIRT2166345	hsa-miR-2113	CLIP-seq
MIRT2166346	hsa-miR-4265	CLIP-seq
MIRT2166347	hsa-miR-4296	CLIP-seq
MIRT2166348	hsa-miR-4322	CLIP-seq
MIRT2166349	hsa-miR-4648	CLIP-seq
MIRT2166350	hsa-miR-4654	CLIP-seq
MIRT2166351	hsa-miR-4769-5p	CLIP-seq
MIRT2464822	hsa-miR-146b-3p	CLIP-seq
MIRT2464823	hsa-miR-3173-5p	CLIP-seq
MIRT2464824	hsa-miR-3192	CLIP-seq
MIRT2464825	hsa-miR-326	CLIP-seq
MIRT2464826	hsa-miR-330-5p	CLIP-seq
MIRT2464827	hsa-miR-3649	CLIP-seq
MIRT763368	hsa-miR-4254	CLIP-seq
MIRT2464828	hsa-miR-4308	CLIP-seq
MIRT2464829	hsa-miR-4314	CLIP-seq
MIRT2464830	hsa-miR-4646-5p	CLIP-seq
MIRT2464831	hsa-miR-492	CLIP-seq
MIRT2464832	hsa-miR-874	CLIP-seq
MIRT2468889	hsa-miR-1538	CLIP-seq
MIRT2468890	hsa-miR-193a-3p	CLIP-seq
MIRT2468891	hsa-miR-193b	CLIP-seq
MIRT2468892	hsa-miR-3144-5p	CLIP-seq
MIRT2468893	hsa-miR-3160-3p	CLIP-seq
MIRT2468894	hsa-miR-3191	CLIP-seq
MIRT2468895	hsa-miR-4487	CLIP-seq
MIRT763382	hsa-miR-4505	CLIP-seq
MIRT2468896	hsa-miR-4652-5p	CLIP-seq
MIRT2468897	hsa-miR-4667-5p	CLIP-seq
MIRT2468898	hsa-miR-4700-5p	CLIP-seq
MIRT2468899	hsa-miR-4717-3p	CLIP-seq
MIRT763394	hsa-miR-4731-5p	CLIP-seq
MIRT763395	hsa-miR-4733-3p	CLIP-seq
MIRT2468900	hsa-miR-4745-3p	CLIP-seq
MIRT2468901	hsa-miR-4772-3p	CLIP-seq
MIRT2468902	hsa-miR-485-5p	CLIP-seq
MIRT2468903	hsa-miR-558	CLIP-seq
MIRT2468889	hsa-miR-1538	CLIP-seq
MIRT2468890	hsa-miR-193a-3p	CLIP-seq
MIRT2468891	hsa-miR-193b	CLIP-seq
MIRT2468893	hsa-miR-3160-3p	CLIP-seq
MIRT2468895	hsa-miR-4487	CLIP-seq
MIRT763395	hsa-miR-4733-3p	CLIP-seq
MIRT2468900	hsa-miR-4745-3p	CLIP-seq
MIRT2468901	hsa-miR-4772-3p	CLIP-seq
MIRT2468903	hsa-miR-558	CLIP-seq

Show/Hide all (23)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000166	Function	Nucleotide binding	IEA
GO:0005515	Function	Protein binding	IPI	28514442, 32296183, 33961781
GO:0005524	Function	ATP binding	IEA
GO:0005739	Component	Mitochondrion	HTP	34800366
GO:0005739	Component	Mitochondrion	IBA
GO:0005739	Component	Mitochondrion	IDA	21846720
GO:0005739	Component	Mitochondrion	IEA
GO:0005759	Component	Mitochondrial matrix	TAS
GO:0006629	Process	Lipid metabolic process	IEA
GO:0006631	Process	Fatty acid metabolic process	IDA	17762044
GO:0006631	Process	Fatty acid metabolic process	IEA
GO:0006633	Process	Fatty acid biosynthetic process	IBA
GO:0006633	Process	Fatty acid biosynthetic process	IDA	21846720
GO:0006633	Process	Fatty acid biosynthetic process	IEA
GO:0016405	Function	CoA-ligase activity	IBA
GO:0016874	Function	Ligase activity	IEA
GO:0031957	Function	Very long-chain fatty acid-CoA ligase activity	IDA	17762044
GO:0031957	Function	Very long-chain fatty acid-CoA ligase activity	TAS
GO:0035338	Process	Long-chain fatty-acyl-CoA biosynthetic process	TAS
GO:0090409	Function	Malonyl-CoA synthetase activity	IDA	21642549, 21846720
GO:0090409	Function	Malonyl-CoA synthetase activity	IEA
GO:0090410	Process	Malonate catabolic process	IDA	21642549, 21846720
GO:0090410	Process	Malonate catabolic process	IEA

MIM	HGNC	e!Ensembl
614245	27288	ENSG00000176715

Q4G176

Protein name

Malonate--CoA ligase ACSF3, mitochondrial (EC 6.2.1.76) (Acyl-CoA synthetase family member 3)

Protein function

Catalyzes the initial reaction in intramitochondrial fatty acid synthesis, by activating malonate and methylmalonate, but not acetate, into their respective CoA thioester (PubMed:21841779, PubMed:21846720). May have some preference toward very-l

Family and domains

Pfam

Accession	ID	Position in sequence	Description	Type
PF00501	AMP-binding	46 → 480	AMP-binding enzyme	Family
PF13193	AMP-binding_C	488 → 563	AMP-binding enzyme C-terminal domain	Domain

Sequence

MLPHVVLTFRRLGCALASCRLAPARHRGSGLLHTAPVARSDRSAPVFTRALAFGDRIALV
DQHGRHTYRELYSRSLRLSQEICRLCGCVGGDLREERVSFLCANDASYVVAQWASWMSGG
VAVPLYRKHPAAQLEYVICDSQSSVVLASQEYLELLSPVVRKLGVPLLPLTPAIYTGAVE
EPAEVPVPEQGWRNKGAMIIYTSGTTGRPKGVLSTHQNIRAVVTGLVHKWAWTKDDVILH
VLPLHHVHGVVNALLCPLWVGATCVMMPEFSPQQVWEKFLSSETPRINVFMAVPTIYTKL
MEYYDRHFTQPHAQDFLRAVCEEKIRLMVSGSAALPLPVLEKWKNITGHTLLERYGMTEI
GMALSGPLTTAVRLPGSVGTPLPGVQVRIVSENPQREACSYTIHAEGDERGTKVTPGFEE
KEGELLVRGPSVFREYWNKPEETKSAFTLDGWFKTGDTVVFKDGQYWIRGRTSVDIIKTG
GYKVSALEVEWHLLAHPSITDVAVIGVPDMTWGQRVTAVVTLREGHSLSHRELKEWARNV
LAPYAVPSELVLVEEIPRNQMGKIDKKALIRHFHPS

Sequence length

576

Interactions

View interactions

	KEGG		Reactome
	Fatty acid biosynthesis Valine, leucine and isoleucine degradation Metabolic pathways Fatty acid metabolism		Synthesis of very long-chain fatty acyl-CoAs

Evidence Score: ★☆☆☆☆ Gene-disease association found in Text Mining only ★★☆☆☆ Found in Text Mining and Unknown/Other Associations ★★★☆☆ Reported in Unknown/Other Associations across ≥2 Sources ★★★★☆ ClinVar: Pathogenic/Likely Pathogenic (<5 Variants) ★★★★★ ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Show/Hide Causal Diseases (4)

Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Causal Diseases associated with Pathogenic or Likely Pathogenic variants in ClinVar
ACSF3-related disorder	Likely pathogenic; Pathogenic	rs138156311, rs141090143	RCV003399204 RCV003407360	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Combined malonic and methylmalonic acidemia	Likely pathogenic; Pathogenic	rs1912700120, rs1025201214, rs756599931, rs150487794, rs916461556, rs745684193, rs1776373606, rs138156311, rs771558691, rs1567685802, rs1975494455, rs2151416957, rs750594210, rs2151444797, rs775794698 View all (134 more)	RCV001330531 RCV001330534 RCV001378316 RCV001378855 RCV001377030 View all (154 more)	★★★★★ ★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)
Methylmalonic acidemia	Pathogenic; Likely pathogenic	rs1064793662, rs142575695	RCV001274023 RCV001274015	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)
Sarcoma	Likely pathogenic	rs373322510	RCV005928307	★★★★★ ★★★★☆ ClinVar: Pathogenic / Likely Pathogenic (<5 Variants)

Show/Hide Unknown Diseases (27)

Phenotype Name	Clinical Significance	Source	Evidence Score
Unknown / Other Associations ClinVar entries with uncertain/conflicting evidence, and associations from other databases (OMIM, Orphanet, GWAS, etc.) where the gene is not established as causal.
Acute myeloid leukemia	Benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cervical cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Cholangiocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COLOR VISION DISORDER	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Colorectal cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
COMBINED MALONIC AND METHYLMALONIC ACIDURIA	—	CTD, Disgenet, HPO CTD, Disgenet, HPO CTD, Disgenet, HPO	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Gastric cancer	Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Global developmental delay	Uncertain significance	ClinVar Disgenet	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Hepatocellular carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lung cancer	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Lymphoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant lymphoma, large B-cell, diffuse	Benign; Likely benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Malignant tumor of esophagus	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MALONIC ACIDURIA	—	CTD, Disgenet CTD, Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Melanoma	Benign	ClinVar GWAS catalog	★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
METHYLMALONIC ACIDURIA	—	Disgenet	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
MULTIPLE SCLEROSIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NON-MELANOMA SKIN CARCINOMA	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Nonpapillary renal cell carcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Ovarian serous cystadenocarcinoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
RHEUMATOID ARTHRITIS	—	GWAS catalog	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thymoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Thyroid cancer, nonmedullary, 1	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine carcinosarcoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uterine corpus endometrial carcinoma	Benign; Uncertain significance	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Uveal melanoma	Benign	ClinVar	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Show/Hide Text Mining Associations (15)

Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Associations from Text Mining Disease associations identified through text mining
B-Cell Lymphomas	B-Cell Lymphoma	BEFREE	22420028		★★★★★ ★☆☆☆☆ Found in Text Mining only
Cardiovascular Diseases	Cardiovascular disease	Pubtator	31882500	Associate	★★★★★ ★☆☆☆☆ Found in Text Mining only
Combined Malonic and Methylmalonic Aciduria	Combined malonic and methylmalonic aciduria	Pubtator	21841779, 33625768, 37987109	Associate	★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Complex partial seizure with impairment of consciousness	Dyscognitive seizures	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Complex partial seizures	Seizure	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Encephalopathies	Epileptic encephalopathy	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Generalized clonic seizures	Clonic Seizures	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Global developmental delay	Developmental Delay	HPO_DG			★★★★★ ★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
Hypoglycemia	Hypoglycemia	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Inborn Errors of Metabolism	Inborn Errors Of Metabolism	BEFREE	31376476		★★★★★ ★☆☆☆☆ Found in Text Mining only
Ketosis	Ketosis	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Lymphoma	Lymphoma	BEFREE	22420028		★★★★★ ★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Metabolic Diseases	Metabolic Diseases	BEFREE	21841779		★★★★★ ★☆☆☆☆ Found in Text Mining only
Microcephaly	Microcephaly	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only
Migraine Disorders	Migraine	HPO_DG			★★★★★ ★☆☆☆☆ Found in Text Mining only

ACSF3 (acyl-CoA synthetase family member 3)