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
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
- 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) | ||
16-20623529-A-G | Inborn genetic diseases | Uncertain significance (Jan 04, 2022) | ||
16-20624112-T-C | Inborn genetic diseases | Likely benign (Sep 14, 2023) | ||
16-20624155-T-A | Inborn genetic diseases | Uncertain significance (Jul 12, 2023) | ||
16-20624188-G-A | Inborn genetic diseases | Uncertain significance (Dec 03, 2021) | ||
16-20627192-G-A | Inborn genetic diseases | Uncertain significance (Apr 06, 2022) | ||
16-20627270-T-C | Inborn genetic diseases | Uncertain significance (Aug 02, 2021) | ||
16-20636755-A-G | Inborn genetic diseases | Uncertain significance (Apr 18, 2023) | ||
16-20636767-C-T | Inborn genetic diseases | Likely benign (Feb 06, 2023) | ||
16-20636776-T-C | Inborn genetic diseases | Uncertain significance (Oct 27, 2021) | ||
16-20636813-G-A | Inborn genetic diseases | Uncertain significance (May 30, 2023) | ||
16-20637445-T-G | Inborn genetic diseases | Uncertain significance (Mar 20, 2023) | ||
16-20640532-G-A | Inborn genetic diseases | Uncertain significance (May 05, 2023) | ||
16-20640534-A-G | Inborn genetic diseases | Uncertain significance (Apr 27, 2022) | ||
16-20640570-G-A | Inborn genetic diseases | Uncertain significance (Aug 13, 2021) | ||
16-20661846-A-C | Inborn genetic diseases | Uncertain significance (Sep 12, 2023) | ||
16-20661849-G-T | Inborn genetic diseases | Uncertain significance (Feb 03, 2022) | ||
16-20669867-A-G | Inborn genetic diseases | Uncertain significance (Feb 15, 2023) | ||
16-20669910-A-T | Inborn genetic diseases | Uncertain significance (Nov 15, 2021) | ||
16-20669958-C-T | Inborn genetic diseases | Uncertain significance (Oct 20, 2021) | ||
16-20669966-T-C | Benign (May 24, 2018) | |||
16-20669971-G-C | Inborn genetic diseases | Uncertain significance (Apr 12, 2022) | ||
16-20682264-C-T | Likely benign (May 24, 2018) | |||
16-20682268-C-T | Inborn genetic diseases | Uncertain significance (Feb 23, 2023) | ||
16-20682329-G-C | Inborn genetic diseases | Uncertain significance (Jul 07, 2022) |
GnomAD
Source:
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:
- 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