GOLGA4
protein-codinggolgin A4, the group of Golgins
Gene summary
The Golgi apparatus, which participates in glycosylation and transport of proteins and lipids in the secretory pathway, consists of a series of stacked cisternae (flattened membrane sacs). Interactions between the Golgi and microtubules are thought to be important for the reorganization of the Golgi after it fragments during mitosis. This gene encodes one of the golgins, a family of proteins localized to the Golgi. This protein has been postulated to play a role in Rab6-regulated membrane-tethering events in the Golgi apparatus. Alternatively spliced transcript variants encoding different isoforms have been identified in this gene. [provided by RefSeq, Feb 2010]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~123.7 kbGenCC Phenotypes & Disease Associations
Curated gene-disease validity assertions and inheritance patterns
No GenCC data available for this gene.
ClinVar Associated Diseases & Phenotypes
Reported disease conditions connected to GOLGA4 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_002078.5. Only rare variants are included.
We include only reliable ClinVar variants with their consequences to MANE Select, MANE Plus Clinical transcripts, or transcripts with TSL equal to 1. Click a count to filter the variants table below.
Slight differences between displayed counts and ClinVar may occur due to a different transcript/consequence chosen by our variant effect predictor, or because we classify Benign/Likely benign as Likely benign and Pathogenic/Likely pathogenic as Likely pathogenic.
| Effect | PathogenicP | Likely pathogenicLP | VUS | Likely benignLB | BenignB | Sum |
|---|---|---|---|---|---|---|
| synonymous | 2 | 1 | 3 | |||
| missense | 297 | 26 | 5 | 328 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 7 | 7 | ||||
| Total | 0 | 0 | 306 | 27 | 5 | 338 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_002069.2 | 23 | MANE Select | |
| Ensembl | ENSP00000354486.2 | 23 | MANE Select | |
| RefSeq | NP_001166184.1 | 23 | Standard | |
| RefSeq | NP_001397650.1 | 24 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Vesicle-mediated transport
- Membrane Trafficking
- Retrograde transport at the Trans-Golgi-Network
- Intra-Golgi and retrograde Golgi-to-ER traffic
Biological Process
- vesicle-mediated transport
- Golgi to plasma membrane protein transport
- positive regulation of axon extension
Molecular Function
- protein binding
- GTPase binding
Cellular Component
- Golgi membrane
- cytoplasm
- Golgi apparatus
- trans-Golgi network
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000356847
- Coding exons
- 23
- Length
- 123575
- Individuals with no LoFs
- 125531
- Homozygous LoFs
- 1
- Heterozygous LoFs
- 216
- Defined
- 125748
- p
- 0.000863
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.103 | 1081 | 1.07e+3 | 1.01 | 0.0000534 | 14924 |
| Missense (PolyPhen) | 319 | 344.42 | 0.9262 | 5150 | ||
| Synonymous | -0.594 | 400 | 385 | 1.04 | 0.0000188 | 3793 |
| Loss of Function | 5.95 | 47 | 116 | 0.404 | 0.00000613 | 1530 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.00076 | 0.00074 | rare |
| Latino/Admixed American | 0.00039 | 0.00038 | rare |
| Ashkenazi Jewish | 0.00032 | 0.00030 | rare |
| East Asian | 0.00061 | 0.00060 | rare |
| Finnish | 0.00032 | 0.00032 | rare |
| European (Non-Finnish) | 0.00051 | 0.00050 | rare |
| South Asian | 0.0042 | 0.0035 | notable |
| Other | 0.0012 | 0.0011 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Involved in vesicular trafficking at the Golgi apparatus level. May play a role in delivery of transport vesicles containing GPI-linked proteins from the trans-Golgi network through its interaction with MACF1. Involved in endosome-to-Golgi trafficking (PubMed:29084197). {ECO:0000269|PubMed:15265687, ECO:0000269|PubMed:29084197}.;
Recessive Scores
- pRec
- 0.191
Intolerance Scores
- LoFtool
- 0.918
- RVIS EVS
- 0.07
- RVIS percentile EVS
- 59.05
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.649
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |