ACOD1
Basic information
Region (hg38): 13:76948511-76958638
Previous symbols: [ "IRG1" ]
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 ACOD1 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 | 1 | |||||
| missense | 3 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 0 | 1 | 3 |
Variants in ACOD1
This is a list of pathogenic ClinVar variants found in the ACOD1 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 13-76953608-T-G | Likely benign (Mar 01, 2023) | |||
| 13-76953656-G-T | Benign (Aug 21, 2018) | |||
| 13-76955316-C-T | Benign (Apr 26, 2018) | |||
| 13-76955509-A-G | Benign (Aug 21, 2018) | |||
| 13-76957357-G-A | Benign (Jul 10, 2017) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ACOD1 | protein_coding | protein_coding | ENST00000377462 | 5 | 10146 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.00000457 | 0.647 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.57 | 186 | 257 | 0.724 | 0.0000126 | 3134 |
| Missense in Polyphen | 57 | 105.16 | 0.54203 | 1323 | ||
| Synonymous | 3.03 | 62 | 101 | 0.615 | 0.00000528 | 993 |
| Loss of Function | 0.976 | 10 | 13.9 | 0.718 | 6.72e-7 | 179 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the inhibition of the inflammatory response. Acts as a negative regulator of the Toll-like receptors (TLRs)- mediated inflammatory innate response by stimulating the tumor necrosis factor alpha-induced protein TNFAIP3 expression via reactive oxygen species (ROS) in LPS-tolerized macrophages. Involved in antimicrobial response of innate immune cells; ACOD1- mediated itaconic acid production contributes to the antimicrobial activity of macrophages. Plays a role in the embryo implantation. {ECO:0000269|PubMed:23609450, ECO:0000269|PubMed:23610393}.;
Recessive Scores
- pRec
- 0.132
Haploinsufficiency Scores
- pHI
- 0.124
- hipred
- Y
- hipred_score
- 0.706
- ghis
- 0.414
Mouse Genome Informatics
- Gene name
- Acod1
- Phenotype
- hematopoietic system phenotype; immune system phenotype;
Gene ontology
- Biological process
- positive regulation of antimicrobial humoral response;defense response;inflammatory response;embryo implantation;propionate metabolic process, methylcitrate cycle;negative regulation of NF-kappaB transcription factor activity;negative regulation of type I interferon production;negative regulation of toll-like receptor 2 signaling pathway;negative regulation of toll-like receptor 4 signaling pathway;cellular response to interferon-beta;negative regulation of innate immune response;negative regulation of inflammatory response;cellular response to molecule of bacterial origin;cellular response to lipopolysaccharide;cellular response to interferon-gamma;cellular response to interleukin-1;cellular response to tumor necrosis factor;cellular response to progesterone stimulus;tolerance induction to lipopolysaccharide;positive regulation of reactive oxygen species metabolic process
- Cellular component
- mitochondrion
- Molecular function
- 2-methylcitrate dehydratase activity;aconitate decarboxylase activity