AP1AR
protein-codingadaptor related protein complex 1 associated regulatory protein
Gene summary
Enables AP-1 adaptor complex binding activity and kinesin binding activity. Involved in negative regulation of receptor recycling and vesicle targeting, trans-Golgi to endosome. Acts upstream of or within negative regulation of substrate adhesion-dependent cell spreading. Located in Golgi apparatus and transport vesicle. [provided by Alliance of Genome Resources, Jul 2025]
- C4orf16
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~41.4 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 AP1AR variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_018569.6. 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 | 1 | 1 | ||||
| missense | 33 | 1 | 34 | |||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 39 | 1 | 1 | 41 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_061039.3 | 10 | MANE Select | |
| Ensembl | ENSP00000274000.5 | 10 | MANE Select | |
| RefSeq | NP_001121898.1 | 9 | Standard | |
| Ensembl | ENSP00000309023.6 | 9 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- negative regulation of receptor recycling
- protein transport
- regulation of Arp2/3 complex-mediated actin nucleation
- cellular protein localization
- vesicle targeting, trans-Golgi to endosome
Molecular Function
- kinesin binding
- AP-1 adaptor complex binding
Cellular Component
- endosome
- early endosome
- late endosome
- Golgi apparatus
- cytosol
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000274000
- Coding exons
- 10
- Length
- 38311
- Individuals with no LoFs
- 125712
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 18
- Defined
- 125730
- p
- 0.0000716
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 1.19 | 103 | 143 | 0.719 | 0.00000718 | 1969 |
| Missense (PolyPhen) | 44 | 66.585 | 0.66081 | 969 | ||
| Synonymous | 0.184 | 48 | 49.7 | 0.967 | 0.00000260 | 521 |
| Loss of Function | 2.95 | 5 | 18.8 | 0.266 | 9.42e-7 | 253 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000030 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0.00022 | 0.00022 | rare |
| Finnish | 0.00019 | 0.00018 | rare |
| European (Non-Finnish) | 0.000063 | 0.000062 | rare |
| South Asian | 0.000033 | 0.000033 | rare |
| Other | 0.00016 | 0.00016 | rare |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Necessary for adaptor protein complex 1 (AP-1)-dependent transport between the trans-Golgi network and endosomes. Regulates the membrane association of AP1G1/gamma1-adaptin, one of the subunits of the AP-1 adaptor complex. The direct interaction with AP1G1/gamma1-adaptin attenuates the release of the AP-1 complex from membranes. Regulates endosomal membrane traffic via association with AP-1 and KIF5B thus linking kinesin-based plus- end-directed microtubular transport to AP-1-dependent membrane traffic. May act as effector of AP-1 in calcium-induced endo- lysosome secretion. Inhibits Arp2/3 complex function; negatively regulates cell spreading, size and motility via intracellular sequestration of the Arp2/3 complex. {ECO:0000269|PubMed:15775984, ECO:0000269|PubMed:19706427, ECO:0000269|PubMed:21525240, ECO:0000269|PubMed:22689987}.;
Recessive Scores
- pRec
- 0.141
Intolerance Scores
- LoFtool
- 0.760
- RVIS EVS
- 0.33
- RVIS percentile EVS
- 73.27
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.114
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |