ACTR3

actin related protein 3, the group of Actin related protein 2/3 complex subunits|Actin related proteins

Basic information

Region (hg38): 2:113890062-113962596

Links

ENSG00000115091 ∙ NCBI:10096 ∙ OMIM:604222 ∙ HGNC:170 ∙ Uniprot:P61158 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

No genCC data.

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ACTR3 gene.

• Inborn genetic diseases (5 variants)
• not provided (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ACTR3 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						0
missense			5			5
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding					1	1
Total	0	0	5	0	1

Variants in ACTR3

This is a list of pathogenic ClinVar variants found in the ACTR3 region.

You can filter this list by clicking the number of variants in the Variants pathogenicity by type table.

Position	Type	Phenotype	Significance	ClinVar
2-113913172-G-T		not specified	Likely benign (Jan 04, 2024)
2-113916982-A-G		not specified	Uncertain significance (Jan 23, 2023)
2-113927358-A-G		not specified	Uncertain significance (Jul 11, 2023)
2-113940101-A-T		not specified	Uncertain significance (Aug 08, 2022)
2-113942280-A-G		not specified	Uncertain significance (Jul 14, 2021)
2-113942312-G-A		not specified	Uncertain significance (Jun 02, 2023)
2-113942363-A-AT			Benign (Dec 13, 2017)
2-113951528-T-C		not specified	Uncertain significance (Dec 30, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ACTR3	protein_coding	protein_coding	ENST00000263238	12	72637

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.000144	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	3.61	76	230	0.330	0.0000120	2730
Missense in Polyphen		20	94.725	0.21114		1122
Synonymous	0.429	70	74.7	0.937	0.00000373	776
Loss of Function	4.65	0	25.2	0.00	0.00000133	310

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: dbNSFP

• Function: FUNCTION: ATP-binding component of the Arp2/3 complex, a multiprotein complex that mediates actin polymerization upon stimulation by nucleation-promoting factor (NPF) (PubMed:9000076). The Arp2/3 complex mediates the formation of branched actin networks in the cytoplasm, providing the force for cell motility (PubMed:9000076). Seems to contact the pointed end of the daughter actin filament (PubMed:9000076). 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:17220302, 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). Plays a role in ciliogenesis (PubMed:20393563). {ECO:0000269|PubMed:17220302, ECO:0000269|PubMed:20393563, ECO:0000269|PubMed:29925947, ECO:0000269|PubMed:9000076}.
• Pathway: Tight junction - Homo sapiens (human);Association Between Physico-Chemical Features and Toxicity Associated Pathways;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;EGFR1;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: 0.142

Intolerance Scores

• loftool: 0.0643
• rvis_EVS: 0.13
• rvis_percentile_EVS: 62.74

Haploinsufficiency Scores

• pHI: 0.692
• hipred: Y
• hipred_score: 0.739
• ghis: 0.526

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: E
• gene_indispensability_score: 0.937

Gene Damage Prediction

	All	Recessive	Dominant
Mendelian	Medium	Medium	Medium
Primary Immunodeficiency	Medium	Medium	Medium
Cancer	Medium	Medium	Medium

Mouse Genome Informatics

• Gene name: Actr3
• Phenotype: embryo phenotype; mortality/aging (the observable characteristics related to the ability of a mammalian organism to live and age that are manifested throughout development and life span)

Gene ontology

• Biological process: establishment or maintenance of cell polarity;asymmetric cell division;meiotic chromosome movement towards spindle pole;meiotic cytokinesis;Arp2/3 complex-mediated actin nucleation;Fc-gamma receptor signaling pathway involved in phagocytosis;positive regulation of transcription by RNA polymerase II;ephrin receptor signaling pathway;spindle localization;cilium assembly;membrane organization;actin polymerization-dependent cell motility;cellular response to interferon-gamma
• Cellular component: nucleus;cytoplasm;cytosol;Arp2/3 protein complex;brush border;cell-cell junction;focal adhesion;actin cytoskeleton;membrane;lamellipodium;site of double-strand break;extracellular exosome
• Molecular function: structural constituent of cytoskeleton;protein binding;ATP binding;actin filament binding