ARPC1A

protein-coding

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

Gene summary

This gene encodes one of seven subunits of the human Arp2/3 protein complex. This subunit is a member of the SOP2 family of proteins and is most similar to the protein encoded by gene ARPC1B. The similarity between these two proteins suggests that they both may function as p41 subunit of the human Arp2/3 complex that has been implicated in the control of actin polymerization in cells. It is possible that the p41 subunit is involved in assembling and maintaining the structure of the Arp2/3 complex. Multiple versions of the p41 subunit may adapt the functions of the complex to different cell types or developmental stages. Alternatively spliced transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Jul 2010]

MANE transcript

NM_006409.4

Inheritance

—

ClinVar variants

U:43B:1

Top phenotype

—

gnomAD constraint

pLI —, LoF o/e 0.18

Max pathogenic AF

—

Genomic locus

chr7:99,325,898-99,366,262

External References & Databases

Ensembl (ENSG00000241685)

Transcript & Mutation Effects

hg38 • Region Span ~40.4 kb

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GenCC 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 ARPC1A variants in ClinVar

1 Conditions Cataloged

not specifiedTotal: 42

ClinVar Variants & Pathogenicity by Type

Statistics based on transcript NM_006409.4. 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			1 clinvar	1 clinvar		2
missense			42 clinvar			42
nonsense						0
start loss						0
frameshift						0
splice donor/acceptor (+/-2bp)						0
Total	0	0	43	1	0	44

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Transcript Catalog

Annotated transcript isoforms across RefSeq and Ensembl databases

Showing 4 of 51 transcripts

Transcript ID	Source	Protein ID	Coding Exons	MANE Status
NM_006409.4	RefSeq	NP_006400.2	9	MANE Select
ENST00000262942.10	Ensembl	ENSP00000262942.5	9	MANE Select
NM_001190996.2	RefSeq	NP_001177925.1	9	Standard
ENST00000432786.5	Ensembl	ENSP00000408711.1	7	Standard

Gene Ontology (GO) Annotations & Pathways

Biological processes, molecular functions, cellular components and pathways

Pathways ConsensusPathDB

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)

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

Molecular Function

actin binding
actin filament binding

Cellular Component

nucleus
cytosol
Arp2/3 protein complex
actin cytoskeleton
site of double-strand break

gnomAD Constraint

Source: gnomAD

Gene type: protein_coding
Transcript type: protein_coding
Transcript: ENST00000262942
Coding exons: 9
Length: 62267
Individuals with no LoFs: 125743
Homozygous LoFs: 0
Heterozygous LoFs: 4
Defined: 125747
p: 0.0000159

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible
Missense	2.65	116	229	0.507	0.0000140	2467
Missense (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

Population LoF Frequency

Population	CAF	p-value	Status
African	0	0.0	absent
Latino/Admixed American	0.000029	0.000029	rare
Ashkenazi Jewish	0	0.0	absent
East Asian	0.000055	0.000054	rare
Finnish	0	0.0	absent
European (Non-Finnish)	0.0000088	0.0000088	rare
South Asian	0.000033	0.000033	rare
Other	0	0.0	absent

dbNSFP Gene Annotations

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}.;

Recessive Scores

pRec: 0.104

Intolerance Scores

LoFtool: 0.384
RVIS EVS: -0.52
RVIS percentile EVS: 21.2

Essentials

Essential (CRISPR): N
Essential (CRISPR2): N
Essential (gene trap): N
Indispensability pred.: E
Indispensability score: 0.876

Gene Damage Prediction

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