ARPC1A

actin related protein 2/3 complex subunit 1A, the group of Actin related protein 2/3 complex subunits|WD repeat domain containing

Basic information

Region (hg38): 7:99325898-99366262

Links

ENSG00000241685 ∙ NCBI:10552 ∙ OMIM:604220 ∙ HGNC:703 ∙ Uniprot:Q92747 ∙ 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 ARPC1A gene.

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARPC1A 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			15			15
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region						0
non coding						0
Total	0	0	15	0	0

Variants in ARPC1A

This is a list of pathogenic ClinVar variants found in the ARPC1A region.

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

Position	Type	Phenotype	Significance	ClinVar
7-99333416-T-A		not specified	Likely benign (Sep 30, 2024)
7-99338231-G-A		not specified	Uncertain significance (Nov 02, 2021)
7-99338250-C-T		not specified	Uncertain significance (Jul 16, 2024)
7-99338277-A-G		not specified	Uncertain significance (Aug 16, 2022)
7-99344322-A-G		not specified	Uncertain significance (Jun 11, 2021)
7-99344431-A-C		not specified	Uncertain significance (Jul 20, 2022)
7-99348920-A-G		not specified	Uncertain significance (Jun 03, 2022)
7-99353989-T-C		not specified	Uncertain significance (Mar 27, 2023)
7-99354007-G-T		not specified	Uncertain significance (May 27, 2022)
7-99354012-G-A		not specified	Uncertain significance (Nov 27, 2024)
7-99354051-A-G		not specified	Uncertain significance (Aug 04, 2023)
7-99354090-G-A		not specified	Uncertain significance (Jun 13, 2022)
7-99358377-A-T		not specified	Uncertain significance (Mar 02, 2023)
7-99359584-C-T		not specified	Uncertain significance (Jul 26, 2024)
7-99359585-G-A		not specified	Uncertain significance (May 28, 2024)
7-99359642-A-G		not specified	Uncertain significance (Jul 09, 2024)
7-99359669-A-G		not specified	Uncertain significance (Dec 01, 2022)
7-99363581-G-A		not specified	Uncertain significance (Sep 16, 2021)
7-99363613-A-C		not specified	Uncertain significance (Dec 19, 2022)
7-99363619-A-G		not specified	Uncertain significance (May 27, 2022)
7-99365904-C-T		not specified	Uncertain significance (Jul 22, 2024)
7-99365918-C-T		not specified	Uncertain significance (Aug 02, 2022)
7-99365919-G-A		not specified	Uncertain significance (Apr 06, 2024)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARPC1A	protein_coding	protein_coding	ENST00000262942	9	62267

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.740	0.260	125743	0	4	125747	0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.65	116	229	0.507	0.0000140	2467
Missense in Polyphen		2	34.314	0.058286		457
Synonymous	0.586	77	83.8	0.919	0.00000531	682
Loss of Function	3.55	4	22.0	0.182	0.00000130	221

LoF frequencies by population

Ethnicity	Sum of pLOFs	p
African & African-American	0.0000289	0.0000289
Ashkenazi Jewish	0.00	0.00
East Asian	0.0000545	0.0000544
Finnish	0.00	0.00
European (Non-Finnish)	0.00000882	0.00000879
Middle Eastern	0.0000545	0.0000544
South Asian	0.0000327	0.0000327
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: Probably functions as component of the Arp2/3 complex which is involved in regulation of actin polymerization and together with an activating nucleation-promoting factor (NPF) mediates the formation of branched actin networks. {ECO:0000305|PubMed:8978670}.
• 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;Regulation of actin dynamics for phagocytic cup formation;Axon guidance (Consensus)

Recessive Scores

• pRec: 0.104

Intolerance Scores

• loftool: 0.384
• rvis_EVS: -0.52
• rvis_percentile_EVS: 21.2

Haploinsufficiency Scores

• pHI: 0.391
• hipred: Y
• hipred_score: 0.825
• ghis: 0.628

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: N
• essential_gene_gene_trap: N
• gene_indispensability_pred: E
• gene_indispensability_score: 0.876

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arpc1a

Gene ontology

• Biological process: actin cytoskeleton organization;Arp2/3 complex-mediated actin nucleation;Fc-gamma receptor signaling pathway involved in phagocytosis;ephrin receptor signaling pathway;membrane organization
• Cellular component: nucleus;cytosol;Arp2/3 protein complex;actin cytoskeleton;site of double-strand break;extracellular exosome
• Molecular function: actin binding;actin filament binding