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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:Q53FZ2AlphaFoldGenCCjaxSfariGnomADPubmedClinVar

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 (24 variants)
  • not provided (2 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.

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
2
clinvar
2
missense
23
clinvar
1
clinvar
24
nonsense
0
start loss
0
frameshift
0
inframe indel
0
splice donor/acceptor (+/-2bp)
0
splice region
0
non coding
0
Total 0 0 23 3 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
16-20623511-C-T Inborn genetic diseases Uncertain significance (Apr 24, 2023)2569250
16-20623529-A-G Inborn genetic diseases Uncertain significance (Jan 04, 2022)2335819
16-20624112-T-C Inborn genetic diseases Likely benign (Sep 14, 2023)2624154
16-20624155-T-A Inborn genetic diseases Uncertain significance (Jul 12, 2023)2611479
16-20624188-G-A Inborn genetic diseases Uncertain significance (Dec 03, 2021)2264142
16-20627192-G-A Inborn genetic diseases Uncertain significance (Apr 06, 2022)2281262
16-20627270-T-C Inborn genetic diseases Uncertain significance (Aug 02, 2021)2371887
16-20636754-G-T Likely benign (Mar 01, 2022)2646284
16-20636755-A-G Inborn genetic diseases Uncertain significance (Apr 18, 2023)2537798
16-20636767-C-T Inborn genetic diseases Likely benign (Feb 06, 2023)2470376
16-20636776-T-C Inborn genetic diseases Uncertain significance (Oct 27, 2021)2227032
16-20636813-G-A Inborn genetic diseases Uncertain significance (May 30, 2023)2552557
16-20637445-T-G Inborn genetic diseases Uncertain significance (Mar 20, 2023)2526887
16-20640532-G-A Inborn genetic diseases Uncertain significance (May 05, 2023)2544025
16-20640534-A-G Inborn genetic diseases Uncertain significance (Apr 27, 2022)2286272
16-20640570-G-A Inborn genetic diseases Uncertain significance (Aug 13, 2021)2244738
16-20661846-A-C Inborn genetic diseases Uncertain significance (Sep 12, 2023)2591282
16-20661849-G-T Inborn genetic diseases Uncertain significance (Feb 03, 2022)2399140
16-20669867-A-G Inborn genetic diseases Uncertain significance (Feb 15, 2023)2484403
16-20669910-A-T Inborn genetic diseases Uncertain significance (Nov 15, 2021)2261651
16-20669958-C-T Inborn genetic diseases Uncertain significance (Oct 20, 2021)2255840
16-20669966-T-C Benign (May 24, 2018)786939
16-20669971-G-C Inborn genetic diseases Uncertain significance (Apr 12, 2022)2407933
16-20682264-C-T Likely benign (May 24, 2018)747986
16-20682268-C-T Inborn genetic diseases Uncertain significance (Feb 23, 2023)2472570

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