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GeneBe

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

ENSG00000005187NCBI:6296OMIM:145505HGNC:10522Uniprot:Q53FZ2AlphaFoldGenCCjaxSfariGnomADPubmed

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 Type 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

GeneTypeBio TypeTranscript Coding Exons Length
ACSM3protein_codingprotein_codingENST00000289416 13187339
pLI Probability
LOF Intolerant
pRec Probability
LOF Recessive
Individuals with
no LOFs
Individuals with
Homozygous LOFs
Individuals with
Heterozygous LOFs
Defined p
1.44e-140.3011231872225391257480.0102
Z-Score Observed Expected Observed/Expected Mutation Rate Total Possible in Transcript
Missense0.4562903130.9270.00001583828
Missense in Polyphen115125.210.918471544
Synonymous1.14951100.8620.000005671115
Loss of Function1.302634.20.7610.00000196381

LoF frequencies by population

EthnicitySum of pLOFs p
African & African-American0.04870.0486
Ashkenazi Jewish0.007840.00777
East Asian0.0007710.000761
Finnish0.001800.00180
European (Non-Finnish)0.01040.0104
Middle Eastern0.0007710.000761
South Asian0.008760.00876
Other0.008990.00900

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

AllRecessiveDominant
MendelianMediumMediumMedium
Primary ImmunodeficiencyMediumMediumMedium
CancerMediumMediumMedium

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