ARPC5
actin related protein 2/3 complex subunit 5, the group of Actin related protein 2/3 complex subunits
Basic information
Region (hg38): 1:183620846-183635783
Links
Phenotypes
GenCC
Source:
- immunodeficiency 113 with autoimmunity and autoinflammation (Moderate), mode of inheritance: AR
Clinical Genomic Database
Source:
| Condition | Inheritance | Intervention Categories | Intervention/Rationale | Manifestation Categories | References |
|---|---|---|---|---|---|
| Immunodeficiency 113 with autoimmunity and autoinflammation | AR | Allergy/Immunology/Infectious | Among other findings, the condition can immunologic abnormalities including immunodeficiency and diagnosis may allow preventative measures and early and prompt treatment of infections | Allergy/Immunology/Infectious; Craniofacial; Dermatologic; Hematologic; Neurologic | 37349293 |
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 ARPC5 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 | 9 | |||||
| nonsense | 0 | |||||
| start loss | 0 | |||||
| frameshift | 0 | |||||
| inframe indel | 0 | |||||
| splice donor/acceptor (+/-2bp) | 0 | |||||
| splice region | 0 | |||||
| non coding | 0 | |||||
| Total | 0 | 0 | 9 | 0 | 1 |
Variants in ARPC5
This is a list of pathogenic ClinVar variants found in the ARPC5 region.
You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.
| Position | Type | Phenotype | Significance | ClinVar |
|---|---|---|---|---|
| 1-183627553-C-G | Inborn genetic diseases | Uncertain significance (Oct 13, 2023) | ||
| 1-183630484-T-G | Inborn genetic diseases | Uncertain significance (Aug 12, 2021) | ||
| 1-183630503-C-T | Benign (May 04, 2021) | |||
| 1-183630552-T-C | Inborn genetic diseases | Uncertain significance (Dec 26, 2023) | ||
| 1-183630604-T-G | Inborn genetic diseases | Uncertain significance (Aug 05, 2024) | ||
| 1-183630622-T-C | Inborn genetic diseases | Uncertain significance (Sep 25, 2024) | ||
| 1-183633116-T-C | Inborn genetic diseases | Uncertain significance (Dec 03, 2021) | ||
| 1-183633138-C-T | Inborn genetic diseases | Uncertain significance (Nov 25, 2024) | ||
| 1-183635564-G-T | Inborn genetic diseases | Uncertain significance (May 05, 2023) | ||
| 1-183635637-G-T | Immunodeficiency 113 with autoimmunity and autoinflammation | Pathogenic (Nov 17, 2023) | ||
| 1-183635648-G-GCA | Immunodeficiency 113 with autoimmunity and autoinflammation | Pathogenic (Nov 17, 2023) | ||
| 1-183635655-G-C | Inborn genetic diseases | Uncertain significance (Feb 21, 2024) |
GnomAD
Source:
| Gene | Type | Bio Type | Transcript | Coding Exons | Length |
|---|---|---|---|---|---|
| ARPC5 | protein_coding | protein_coding | ENST00000294742 | 4 | 12492 |
| pLI Probability LOF Intolerant | pRec Probability LOF Recessive | Individuals with no LOFs | Individuals with Homozygous LOFs | Individuals with Heterozygous LOFs | Defined | p |
|---|---|---|---|---|---|---|
| 0.822 | 0.175 | 0 | 0 | 0 | 0 | 0.00 |
| Z-Score | Observed | Expected | Observed/Expected | Mutation Rate | Total Possible in Transcript | |
|---|---|---|---|---|---|---|
| Missense | 1.63 | 45 | 87.9 | 0.512 | 0.00000422 | 1003 |
| Missense in Polyphen | 10 | 28.832 | 0.34684 | 360 | ||
| Synonymous | -1.21 | 42 | 33.1 | 1.27 | 0.00000151 | 302 |
| Loss of Function | 2.21 | 0 | 5.69 | 0.00 | 2.39e-7 | 73 |
LoF frequencies by population
| Ethnicity | Sum of pLOFs | p |
|---|---|---|
| African & African-American | 0.00 | 0.00 |
| 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: 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). 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;Regulation of Actin Cytoskeleton;Developmental Biology;Neutrophil degranulation;Signal Transduction;Vesicle-mediated transport;Membrane Trafficking;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)
Intolerance Scores
- loftool
- rvis_EVS
- -0.25
- rvis_percentile_EVS
- 35.42
Haploinsufficiency Scores
- pHI
- 0.0916
- hipred
- Y
- hipred_score
- 0.675
- ghis
- 0.690
Essentials
- essential_gene_CRISPR
- N
- essential_gene_CRISPR2
- N
- essential_gene_gene_trap
- N
- gene_indispensability_pred
- E
- gene_indispensability_score
- 0.813
Gene Damage Prediction
| All | Recessive | Dominant | |
|---|---|---|---|
| Mendelian | Medium | Medium | Medium |
| Primary Immunodeficiency | Medium | Medium | Medium |
| Cancer | Medium | Medium | Medium |
Mouse Genome Informatics
- Gene name
- Arpc5
- Phenotype
Gene ontology
- Biological process
- smooth muscle cell migration;cell migration;orbitofrontal cortex development;maintenance of cell polarity;actin cytoskeleton organization;Arp2/3 complex-mediated actin nucleation;Fc-gamma receptor signaling pathway involved in phagocytosis;neutrophil degranulation;ephrin receptor signaling pathway;actin filament network formation;membrane organization;microtubule organizing center localization;lamellipodium organization
- Cellular component
- extracellular region;nucleus;cytoplasm;endosome;cytosol;Arp2/3 protein complex;focal adhesion;actin cytoskeleton;lamellipodium;growth cone;secretory granule lumen;site of double-strand break;extracellular exosome;ficolin-1-rich granule lumen
- Molecular function
- structural constituent of cytoskeleton;protein binding;actin filament binding