ACSM3

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

Basic information

Region (hg38): 16:20610242-20797581

Previous symbols: [ "SAH" ]

Links

ENSG00000005187

∙ NCBI:6296 ∙ OMIM:145505 ∙ HGNC:10522 ∙ Uniprot:Q53FZ2 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ACSM3 gene.

Inborn genetic diseases (36 variants)
Neurodevelopmental disorder (9 variants)
Neurodevelopmental disorder with speech delay and variable ocular anomalies (5 variants)
not provided (3 variants)

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.

Variant type	Pathogenic	Likely pathogenic	VUS	Likely benign	Benign	Sum
synonymous						0
missense			14			14
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice variant						0
non coding	6	2	22	2	2	34
Total	6	2	36	2	2

Highest pathogenic variant AF is 0.0000131

Variants in ACSM3

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

Position	Phenotype	Significance	ClinVar
16-20623511-C-T	Inborn genetic diseases	Uncertain significance (Apr 24, 2023)	link
16-20623529-A-G	Inborn genetic diseases	Uncertain significance (Jan 04, 2022)	link
16-20624112-T-C	Inborn genetic diseases	Likely benign (Sep 14, 2023)	link
16-20624155-T-A	Inborn genetic diseases	Uncertain significance (Jul 12, 2023)	link
16-20624188-G-A	Inborn genetic diseases	Uncertain significance (Dec 03, 2021)	link
16-20627192-G-A	Inborn genetic diseases	Uncertain significance (Apr 06, 2022)	link
16-20627270-T-C	Inborn genetic diseases	Uncertain significance (Aug 02, 2021)	link
16-20636755-A-G	Inborn genetic diseases	Uncertain significance (Apr 18, 2023)	link
16-20636767-C-T	Inborn genetic diseases	Likely benign (Feb 06, 2023)	link
16-20636776-T-C	Inborn genetic diseases	Uncertain significance (Oct 27, 2021)	link
16-20636813-G-A	Inborn genetic diseases	Uncertain significance (May 30, 2023)	link
16-20637445-T-G	Inborn genetic diseases	Uncertain significance (Mar 20, 2023)	link
16-20640532-G-A	Inborn genetic diseases	Uncertain significance (May 05, 2023)	link
16-20640534-A-G	Inborn genetic diseases	Uncertain significance (Apr 27, 2022)	link
16-20640570-G-A	Inborn genetic diseases	Uncertain significance (Aug 13, 2021)	link
16-20661846-A-C	Inborn genetic diseases	Uncertain significance (Sep 12, 2023)	link
16-20661849-G-T	Inborn genetic diseases	Uncertain significance (Feb 03, 2022)	link
16-20669867-A-G	Inborn genetic diseases	Uncertain significance (Feb 15, 2023)	link
16-20669910-A-T	Inborn genetic diseases	Uncertain significance (Nov 15, 2021)	link
16-20669958-C-T	Inborn genetic diseases	Uncertain significance (Oct 20, 2021)	link
16-20669966-T-C		Benign (May 24, 2018)	link
16-20669971-G-C	Inborn genetic diseases	Uncertain significance (Apr 12, 2022)	link
16-20682264-C-T		Likely benign (May 24, 2018)	link
16-20682268-C-T	Inborn genetic diseases	Uncertain significance (Feb 23, 2023)	link
16-20682329-G-C	Inborn genetic diseases	Uncertain significance (Jul 07, 2022)	link

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
ghis

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