ACSM3

acyl-CoA synthetase medium chain family member 3, the group of Acyl-CoA synthetase family

Basic information

Region (hg38): 16:20610243-20797581

Previous symbols: [ "SAH" ]

Links

ENSG00000005187 ∙ NCBI:6296 ∙ OMIM:145505 ∙ HGNC:10522 ∙ Uniprot:Q53FZ2 ∙ 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 ACSM3 gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACSM3 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				3		3
missense			48	4		52
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	48	7	0

Variants in ACSM3

This is a list of pathogenic ClinVar variants found in the ACSM3 region.

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

Position	Type	Phenotype	Significance	ClinVar
16-20623507-T-G		not specified	Uncertain significance (Jan 19, 2025)
16-20623511-C-T		not specified	Uncertain significance (Apr 24, 2023)
16-20623529-A-G		not specified	Uncertain significance (Feb 06, 2024)
16-20623556-T-C		not specified	Uncertain significance (Dec 12, 2023)
16-20624112-T-C		not specified	Likely benign (Sep 14, 2023)
16-20624121-G-C		not specified	Uncertain significance (Oct 04, 2024)
16-20624155-T-A		not specified	Uncertain significance (Jul 12, 2023)
16-20624188-G-A		not specified	Uncertain significance (Mar 05, 2025)
16-20625466-G-A		not specified	Uncertain significance (Dec 06, 2024)
16-20625471-C-T		not specified	Likely benign (Jul 10, 2024)
16-20625481-T-G		not specified	Uncertain significance (Jun 10, 2024)
16-20627192-G-A		not specified	Uncertain significance (Apr 06, 2022)
16-20627270-T-C		not specified	Uncertain significance (Aug 02, 2021)
16-20636754-G-T			Likely benign (Mar 01, 2022)
16-20636755-A-G		not specified	Uncertain significance (Apr 18, 2023)
16-20636767-C-T		not specified	Likely benign (Feb 06, 2023)
16-20636776-T-C		not specified	Uncertain significance (Oct 27, 2021)
16-20636813-G-A		not specified	Uncertain significance (May 30, 2023)
16-20636840-C-T		not specified	Likely benign (Apr 23, 2024)
16-20637441-C-A		not specified	Uncertain significance (Dec 06, 2023)
16-20637445-T-G		not specified	Uncertain significance (Mar 20, 2023)
16-20637447-A-G		not specified	Uncertain significance (Apr 15, 2024)
16-20640468-G-A		not specified	Uncertain significance (Dec 19, 2023)
16-20640481-T-C		not specified	Uncertain significance (Nov 15, 2024)
16-20640504-C-T		not specified	Likely benign (Jan 26, 2025)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACSM3	protein_coding	protein_coding	ENST00000289416	13	187339

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.44e-14	0.301	123187	22	2539	125748	0.0102

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	0.456	290	313	0.927	0.0000158	3828
Missense in Polyphen		115	125.21	0.91847		1544
Synonymous	1.14	95	110	0.862	0.00000567	1115
Loss of Function	1.30	26	34.2	0.761	0.00000196	381

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0487	0.0486
Ashkenazi Jewish	0.00784	0.00777
East Asian	0.000771	0.000761
Finnish	0.00180	0.00180
European (Non-Finnish)	0.0104	0.0104
Middle Eastern	0.000771	0.000761
South Asian	0.00876	0.00876
Other	0.00899	0.00900

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Has medium-chain fatty acid:CoA ligase activity with broad substrate specificity (in vitro). Acts on acids from C(4) to C(11) and on the corresponding 3-hydroxy- and 2,3- or 3,4- unsaturated acids (in vitro) (By similarity). {ECO:0000250}.
• Pathway: Butanoate metabolism - Homo sapiens (human);Valproic Acid Pathway, Pharmacokinetics;Metabolism of lipids;Beta oxidation of butanoyl-CoA to acetyl-CoA;mitochondrial fatty acid beta-oxidation of saturated fatty acids;Mitochondrial Fatty Acid Beta-Oxidation;Metabolism;Fatty acid metabolism;γ-linolenate biosynthesis;icosapentaenoate biosynthesis II (metazoa) (Consensus)

Recessive Scores

• pRec: 0.455

Intolerance Scores

• loftool: 0.959
• rvis_EVS: 1.29
• rvis_percentile_EVS: 93.85

Haploinsufficiency Scores

• pHI: 0.259
• hipred: N
• hipred_score: 0.196

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: N
• gene_indispensability_score: 0.276

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Acsm3
• Phenotype: normal phenotype

Gene ontology

• Biological process: fatty acid biosynthetic process;acyl-CoA metabolic process;regulation of blood pressure;cholesterol homeostasis
• Cellular component: cellular_component;mitochondrial matrix
• Molecular function: molecular_function;acyl-CoA ligase activity;fatty-acyl-CoA synthase activity;ATP binding;fatty acid ligase activity;metal ion binding;butyrate-CoA ligase activity