ACBD3
Basic information
Region (hg38): 1:226144679-226186741
Previous symbols: [ "GOLPH1", "GOCAP1" ]
Links
Transcripts
Transcript IDs starting with ENST are treated as Ensembl, all others as RefSeq. Showing 4 of 20.
| Transcript ID | Protein ID | Coding exons | MANE Select | MANE Plus Clinical |
|---|---|---|---|---|
NM_022735.4 | NP_073572.2 | 8 | yes | - |
ENST00000366812.6 | ENSP00000355777.5 | 8 | yes | - |
ENST00000912077.1 | ENSP00000582136.1 | 8 | - | - |
ENST00000912077.2 | ENSP00000582136.1 | 8 | - | - |
Phenotypes
GenCC
Source:
ClinVar
This is a list of variants' phenotypes submitted to
- not_specified (69 variants)
- not_provided (1 variants)
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACBD3 gene is commonly pathogenic or not. These statistics are base on transcript: NM_022735.4. Only rare variants are included in the table.
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.
| Effect | PathogenicP | Likely pathogenicLP | VUSVUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | 1 | ||||
| missense | 70 | 1 | 71 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 3 | 3 | ||||
| Total | 0 | 0 | 73 | 1 | 1 |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ACBD3 | protein_coding | protein_coding | ENST00000366812 | 8 | 42052 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 125734 | 0 | 13 | 125747 | 0.0000517 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.82 | 184 | 268 | 0.687 | 0.0000145 | 3391 |
| Missense in Polyphen | 37 | 74.289 | 0.49806 | 902 | ||
| Synonymous | 0.465 | 96 | 102 | 0.941 | 0.00000542 | 1010 |
| Loss of Function | 3.46 | 9 | 29.1 | 0.309 | 0.00000173 | 327 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000289 | 0.0000289 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.000110 | 0.000109 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.0000727 | 0.0000703 |
| Middle Eastern | 0.000110 | 0.000109 |
| South Asian | 0.0000664 | 0.0000653 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Involved in the maintenance of Golgi structure by interacting with giantin, affecting protein transport between the endoplasmic reticulum and Golgi (PubMed:11590181). Involved in hormone-induced steroid biosynthesis in testicular Leydig cells (By similarity). Recruits PI4KB to the Golgi apparatus membrane; enhances the enzyme activity of PI4KB activity via its membrane recruitment thereby increasing the local concentration of the substrate in the vicinity of the kinase (PubMed:27009356). {ECO:0000250|UniProtKB:Q8BMP6, ECO:0000269|PubMed:11590181, ECO:0000269|PubMed:27009356}.;
- Pathway
- Benzodiazepine Pathway, Pharmacodynamics;Golgi Associated Vesicle Biogenesis;Clathrin derived vesicle budding;trans-Golgi Network Vesicle Budding;Vesicle-mediated transport;Membrane Trafficking
(Consensus)
Recessive Scores
- pRec
- 0.135
Intolerance Scores
- loftool
- 0.582
- rvis_EVS
- 0.15
- rvis_percentile_EVS
- 64.51
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.664
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Gene ontology
- Biological process
- steroid biosynthetic process
- Cellular component
- Golgi membrane;mitochondrion;Golgi apparatus;membrane
- Molecular function
- fatty-acyl-CoA binding;protein binding;protein kinase A regulatory subunit binding