ACSM3
Basic information
Region (hg38): 16:20610242-20797581
Previous symbols: [ "SAH" ]
Links
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
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 | |||||
missense | 32 | 35 | ||||
nonsense | 0 | |||||
start loss | 0 | |||||
frameshift | 0 | |||||
inframe indel | 0 | |||||
splice donor/acceptor (+/-2bp) | 0 | |||||
splice region ? | 0 | |||||
non coding ? | 0 | |||||
Total | 0 | 0 | 32 | 6 | 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 | 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) | ||
16-20624155-T-A | not specified | Uncertain significance (Jul 12, 2023) | ||
16-20624188-G-A | not specified | Uncertain significance (Dec 03, 2021) | ||
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) | ||
16-20640516-T-A | not specified | Uncertain significance (Nov 03, 2023) | ||
16-20640532-G-A | not specified | Uncertain significance (May 05, 2023) | ||
16-20640534-A-G | not specified | Uncertain significance (Apr 27, 2022) | ||
16-20640570-G-A | not specified | Uncertain significance (Aug 13, 2021) | ||
16-20661846-A-C | not specified | Uncertain significance (Sep 12, 2023) | ||
16-20661849-G-T | not specified | Uncertain significance (Feb 03, 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