ARPC2
actin related protein 2/3 complex subunit 2, the group of Actin related protein 2/3 complex subunits
Basic information
Region (hg38): 2:218217141-218254356
Links
Phenotypes
GenCC
Source:
No genCC data.
ClinVar
This is a list of variants' phenotypes submitted to
Variants pathogenicity by type
Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARPC2 gene is commonly pathogenic or not.
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.
| Variant type | Pathogenic | Likely pathogenic | VUS | Likely benign | Benign | Sum |
|---|---|---|---|---|---|---|
| synonymous | 1 | |||||
| missense | 7 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 1 | 1 | ||||
| non coding | 0 | |||||
| Total | 0 | 0 | 7 | 0 | 1 |
Variants in ARPC2
This is a list of pathogenic ClinVar variants found in the ARPC2 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 2-218217477-C-T | Benign (Apr 13, 2018) | |||
| 2-218217527-C-A | not specified | Uncertain significance (Sep 01, 2021) | ||
| 2-218225936-G-A | not specified | Uncertain significance (Apr 19, 2023) | ||
| 2-218234370-G-A | not specified | Uncertain significance (Nov 14, 2023) | ||
| 2-218238802-A-G | not specified | Uncertain significance (Mar 07, 2023) | ||
| 2-218239442-T-G | not specified | Uncertain significance (Nov 03, 2023) | ||
| 2-218245465-C-G | not specified | Uncertain significance (Aug 02, 2021) | ||
| 2-218249361-C-T | Benign (Apr 13, 2018) | |||
| 2-218249885-G-A | not specified | Uncertain significance (Jul 20, 2021) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARPC2 | protein_coding | protein_coding | ENST00000295685 | 10 | 37263 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.998 | 0.00231 | 121877 | 0 | 3 | 121880 | 0.0000123 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 2.70 | 79 | 182 | 0.435 | 0.0000104 | 1992 |
| Missense in Polyphen | 13 | 49.353 | 0.26341 | 642 | ||
| Synonymous | 1.40 | 55 | 69.9 | 0.787 | 0.00000429 | 542 |
| Loss of Function | 3.91 | 0 | 17.8 | 0.00 | 9.90e-7 | 207 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.0000875 | 0.0000875 |
| Ashkenazi Jewish | 0.00 | 0.00 |
| East Asian | 0.00 | 0.00 |
| Finnish | 0.00 | 0.00 |
| European (Non-Finnish) | 0.00 | 0.00 |
| Middle Eastern | 0.00 | 0.00 |
| South Asian | 0.00 | 0.00 |
| Other | 0.00 | 0.00 |
dbNSFP
Source:
- Function
- FUNCTION: Actin-binding component of the Arp2/3 complex, a multiprotein complex that mediates actin polymerization upon stimulation by nucleation-promoting factor (NPF) (PubMed:9230079). The Arp2/3 complex mediates the formation of branched actin networks in the cytoplasm, providing the force for cell motility (PubMed:9230079). Seems to contact the mother actin filament (PubMed:9230079). In addition to its role in the cytoplasmic cytoskeleton, the Arp2/3 complex also promotes actin polymerization in the nucleus, thereby regulating gene transcription and repair of damaged DNA (PubMed:29925947). The Arp2/3 complex promotes homologous recombination (HR) repair in response to DNA damage by promoting nuclear actin polymerization, leading to drive motility of double-strand breaks (DSBs) (PubMed:29925947). {ECO:0000269|PubMed:29925947, ECO:0000269|PubMed:9230079}.;
- Pathway
- Fc gamma R-mediated phagocytosis - Homo sapiens (human);Salmonella infection - Homo sapiens (human);Endocytosis - Homo sapiens (human);Regulation of actin cytoskeleton - Homo sapiens (human);Bacterial invasion of epithelial cells - Homo sapiens (human);Shigellosis - Homo sapiens (human);Pathogenic Escherichia coli infection - Homo sapiens (human);Pathogenic Escherichia coli infection;Developmental Biology;Signal Transduction;Vesicle-mediated transport;role of pi3k subunit p85 in regulation of actin organization and cell migration;how does salmonella hijack a cell;Membrane Trafficking;y branching of actin filaments;Fcgamma receptor (FCGR) dependent phagocytosis;EPH-Ephrin signaling;Innate Immune System;Immune System;EPHB-mediated forward signaling;RHO GTPases Activate WASPs and WAVEs;RHO GTPase Effectors;Signaling by Rho GTPases;Clathrin-mediated endocytosis;ErbB1 downstream signaling;Regulation of actin dynamics for phagocytic cup formation;Axon guidance;RAC1 signaling pathway;CDC42 signaling events;PDGFR-beta signaling pathway
(Consensus)
Recessive Scores
- pRec
- 0.178
Intolerance Scores
- loftool
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.42
Haploinsufficiency Scores
- pHI
- 0.480
- hipred
- Y
- hipred_score
- 0.783
- ghis
- 0.654
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- S
- essential_gene_gene_trap
- E
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.801
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Arpc2
- Phenotype
- hematopoietic system phenotype; pigmentation phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); growth/size/body region phenotype; adipose tissue phenotype (the observable morphological and physiological characteristics of mammalian fat tissue that are manifested through development and lifespan);
Gene ontology
- Biological process
- positive regulation of lamellipodium assembly;actin filament polymerization;Arp2/3 complex-mediated actin nucleation;Fc-gamma receptor signaling pathway involved in phagocytosis;ephrin receptor signaling pathway;membrane organization;actin polymerization-dependent cell motility;positive regulation of substrate adhesion-dependent cell spreading
- Cellular component
- nucleus;endosome;cytosol;Arp2/3 protein complex;focal adhesion;actin cytoskeleton;lamellipodium;site of double-strand break;muscle cell projection membrane;neuron projection;extracellular exosome;glutamatergic synapse
- Molecular function
- structural constituent of cytoskeleton;protein binding;actin filament binding