RAP2A
protein-codingRAP2A, member of RAS oncogene family, the group of RAS type GTPase family
Gene summary
Enables G protein activity; guanyl ribonucleotide binding activity; and magnesium ion binding activity. Involved in several processes, including regulation of JNK cascade; regulation of plasma membrane bounded cell projection organization; and regulation of synapse assembly. Acts upstream of or within establishment of protein localization. Located in Golgi apparatus; endosome; and lamellipodium membrane. Is active in Schaffer collateral - CA1 synapse. [provided by Alliance of Genome Resources, Jun 2026]
- RAP2
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~35.0 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 RAP2A variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_021033.7. 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 | 0 | |||||
| missense | 11 | 11 | ||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| Total | 0 | 0 | 11 | 0 | 0 | 11 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_066361.1 | 2 | MANE Select | |
| Ensembl | ENSP00000245304.3 | 2 | MANE Select | |
| Ensembl | ENSP00000436462.1 | 2 | Standard | |
| Ensembl | ENSP00000802366.1 | 2 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Biological Process
- positive regulation of protein phosphorylation
- microvillus assembly
- negative regulation of cell migration
- actin cytoskeleton reorganization
- positive regulation of protein autophosphorylation
Molecular Function
- magnesium ion binding
- GTPase activity
- protein binding
- GTP binding
- GDP binding
Cellular Component
- cytosol
- plasma membrane
- midbody
- recycling endosome
- recycling endosome membrane
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000245304
- Coding exons
- 2
- Length
- 34907
- Individuals with no LoFs
- 125540
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 1
- Defined
- 125541
- p
- 0.00000398
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | 2.56 | 34 | 109 | 0.311 | 0.00000509 | 1208 |
| Missense (PolyPhen) | 10 | 47.817 | 0.20913 | 550 | ||
| Synonymous | -1.04 | 57 | 47.9 | 1.19 | 0.00000260 | 355 |
| Loss of Function | 2.32 | 0 | 6.24 | 0.00 | 2.66e-7 | 73 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0 | 0.0 | absent |
| Latino/Admixed American | 0.000029 | 0.000029 | rare |
| Ashkenazi Jewish | 0 | 0.0 | absent |
| East Asian | 0 | 0.0 | absent |
| Finnish | 0 | 0.0 | absent |
| European (Non-Finnish) | 0 | 0.0 | absent |
| South Asian | 0 | 0.0 | absent |
| Other | 0 | 0.0 | absent |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Small GTP-binding protein which cycles between a GDP- bound inactive and a GTP-bound active form. In its active form interacts with and regulates several effectors including MAP4K4, MINK1 and TNIK. Part of a signaling complex composed of NEDD4, RAP2A and TNIK which regulates neuronal dendrite extension and arborization during development. More generally, it is part of several signaling cascades and may regulate cytoskeletal rearrangements, cell migration, cell adhesion and cell spreading. {ECO:0000269|PubMed:14966141, ECO:0000269|PubMed:15342639, ECO:0000269|PubMed:16246175, ECO:0000269|PubMed:16540189, ECO:0000269|PubMed:18930710, ECO:0000269|PubMed:20159449}.;
Recessive Scores
- pRec
- 0.190
Intolerance Scores
- RVIS EVS
- 0.01
- RVIS percentile EVS
- 54.63
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- E
- Indispensability score
- 0.731
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Low | Low | Low |
| Primary Immunodeficiency | Medium | Low | Medium |
| Cancer | Low | Low | Low |