FARP2
protein-codingFERM, ARH/RhoGEF and pleckstrin domain protein 2, the group of Dbl family Rho GEFs|FERM domain containing|Pleckstrin homology domain containing|MicroRNA protein coding host genes
Gene summary
Enables guanyl-nucleotide exchange factor activity. Acts upstream of or within Rac protein signal transduction and neuron remodeling. Located in cytoplasm. [provided by Alliance of Genome Resources, Jul 2025]
MANE transcript
Inheritance
ClinVar variants
Top phenotype
gnomAD constraint
Max pathogenic AF
Genomic locus
External References & Databases
Transcript & Mutation Effects
hg38 • Region Span ~138.6 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 FARP2 variants in ClinVar
ClinVar Variants & Pathogenicity by Type
Statistics based on transcript NM_014808.4. 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 | 11 | 2 | 13 | |||
| missense | 204 | 20 | 4 | 228 | ||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| splice donor/acceptor (+/-2bp) | 6 | 6 | ||||
| Total | 0 | 0 | 210 | 31 | 6 | 247 |
Transcript Catalog
Annotated transcript isoforms across RefSeq and Ensembl databases
| Transcript ID | Source | Protein ID | Coding Exons | MANE Status |
|---|---|---|---|---|
| RefSeq | NP_055623.1 | 26 | MANE Select | |
| Ensembl | ENSP00000264042.3 | 26 | MANE Select | |
| RefSeq | NP_001269912.1 | 17 | Standard | |
| RefSeq | NP_001269913.1 | 17 | Standard |
Gene Ontology (GO) Annotations & Pathways
Biological processes, molecular functions, cellular components and pathways
Pathways ConsensusPathDB
- Adherens junction - Homo sapiens (human)
- Rap1 signaling pathway - Homo sapiens (human)
- Developmental Biology
- SEMA3A-Plexin repulsion signaling by inhibiting Integrin adhesion
- Semaphorin interactions
Biological Process
- cell adhesion
- neuron remodeling
- Rac protein signal transduction
- hair cycle process
- osteoclast differentiation
Molecular Function
- Rho guanyl-nucleotide exchange factor activity
- cytoskeletal protein binding
- Rac guanyl-nucleotide exchange factor activity
Cellular Component
- cytoplasm
- cytosol
- cytoskeleton
gnomAD Constraint
Source:
- Gene type
- protein_coding
- Transcript type
- protein_coding
- Transcript
- ENST00000264042
- Coding exons
- 26
- Length
- 138599
- Individuals with no LoFs
- 125462
- Homozygous LoFs
- 0
- Heterozygous LoFs
- 286
- Defined
- 125748
- p
- 0.00114
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible | |
|---|---|---|---|---|---|---|
| Missense | -0.331 | 639 | 616 | 1.04 | 0.0000372 | 6872 |
| Missense (PolyPhen) | 250 | 246.42 | 1.0145 | 3009 | ||
| Synonymous | -0.336 | 254 | 247 | 1.03 | 0.0000157 | 2057 |
| Loss of Function | 0.377 | 56 | 59.1 | 0.947 | 0.00000304 | 665 |
Population LoF Frequency
| Population | CAF | p-value | Status |
|---|---|---|---|
| African | 0.0011 | 0.00074 | notable |
| Latino/Admixed American | 0.0012 | 0.0012 | notable |
| Ashkenazi Jewish | 0.00060 | 0.00060 | rare |
| East Asian | 0.0027 | 0.0027 | notable |
| Finnish | 0.00028 | 0.00028 | rare |
| European (Non-Finnish) | 0.0012 | 0.0012 | notable |
| South Asian | 0.0011 | 0.0010 | notable |
| Other | 0.0013 | 0.0013 | notable |
dbNSFP Gene Annotations
Source:
- Function
- FUNCTION: Functions as guanine nucleotide exchange factor that activates RAC1. May have relatively low activity. Plays a role in the response to class 3 semaphorins and remodeling of the actin cytoskeleton. Plays a role in TNFSF11-mediated osteoclast differentiation, especially in podosome rearrangement and reorganization of the actin cytoskeleton. Regulates the activation of ITGB3, integrin signaling and cell adhesion (By similarity). {ECO:0000250}.;
Recessive Scores
- pRec
- 0.192
Intolerance Scores
- LoFtool
- 0.735
- RVIS EVS
- 0.37
- RVIS percentile EVS
- 75.31
Essentials
- Essential (CRISPR)
- N
- Essential (CRISPR2)
- N
- Essential (gene trap)
- N
- Indispensability pred.
- N
- Indispensability score
- 0.277
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |