ARPC1A

Chr 7

actin related protein 2/3 complex subunit 1A

Also known as: Arc40, HEL-68, HEL-S-307, SOP2Hs, SOP2L

NCBI Gene: 10552ENSG00000241685UniProt: Q92747

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]

67
ClinVar variants
18
Pathogenic / LP
0.74
pLI score
0
Active trials
Clinical Summary— ARPC1A
⚡
Population Constraint (gnomAD)
Moderately constrained gene (pLI 0.74) — some intolerance to loss-of-function variants.
📋
ClinVar Variants
18 Pathogenic / Likely Pathogenic· 47 VUS of 67 total submissions
Some data sources returned errors (1)

clinvar: Error: NCBI fetch failed: 429 https://eutils.ncbi.nlm.nih.gov/entrez/eutils/esummary.fcgi

Population Genetics & Constraint

gnomAD v4 — loss-of-function & missense intolerance

gnomAD
Moderate LoF intolerance
LoF Constraint?LOEUF (Loss-of-function Observed/Expected Upper bound Fraction) is the upper bound of the 90% CI for LoF OE — the preferred gnomAD v4 metric. Lower = more intolerant to LoF. LOEUF < 0.35 = highly constrained.
0.42LOEUF
pLI 0.740
Z-score 3.55
OE 0.18 (0.09–0.42)
Moderately constrained

More LoF-intolerant than ~75% of genes

Missense Constraint?Missense Z-score: standard deviations fewer missense variants observed vs. expected. Z > 3.09 (p < 0.001) = gene does not tolerate missense variation. OE missense < 0.6 is also considered constrained.
2.65Z-score
OE missense 0.51 (0.43–0.59)
116 obs / 228.9 exp
Mild constraint

Moderately missense-constrained (top ~2.5%)

Observed / Expected Ratios?Shaded band = 90% confidence interval. Vertical tick = point estimate. Grey threshold line = gnomAD constraint cutoff for that variant class.
LoF OE?Ratio of observed to expected LoF variants. Upper CI bound (LOEUF) ≤ 0.35 = strong LoF constraint signal.0.18 (0.09–0.42)
0≤0.351.4
Missense OE?Ratio of observed to expected missense variants. OE ≤ 0.6 = fewer missense variants than expected by chance.0.51 (0.43–0.59)
0≤0.61.4
Synonymous OE?Control metric — synonymous variants are largely neutral and expected near OE = 1.0. Significant deviation may indicate annotation issues.0.92
0≤1.21.6
LoF obs/exp: 4 / 22.0Missense obs/exp: 116 / 228.9Syn Z: 0.59

ClinVar Variant Classifications

67 submitted variants in ClinVar

ClinVar

Classification Summary

Pathogenic17
Likely Pathogenic1
VUS47
Likely Benign2
17
Pathogenic
1
Likely Pathogenic
47
VUS
2
Likely Benign

Curated Variants Distribution

Classified variants from ClinVar · 5 ACMG categories

ClassificationLoFMissense + InframeNon-codingSynonymousTotal
Pathogenic
0
0
17
0
17
Likely Pathogenic
0
0
1
0
1
VUS
0
41
6
0
47
Likely Benign
0
1
1
0
2
Benign
0
0
0
0
0
Total04225067

LoF = frameshift, stop gained/lost, canonical splice · Counts from ClinVar esearch · Updated hourly

View in ClinVar →

Protein Context — Lollipop Plot

ARPC1A · protein map & ClinVar variants

Showing all ClinVar variants across the protein. Search a specific variant to highlight its position.

OMIM — Genotype-Phenotype Relationships

1 OMIM entry

OMIM
Clinical Literature
Landmark / reviewRecent case evidence
Key Publications
Landmark & review papers · by relevance
PubMed
The N6-methyladenosine Epitranscriptomic Landscape of Lung Adenocarcinoma.
Wang S et al.·Cancer Discov
2024
Prognostic relevance and validation of ARPC1A in the progression of low-grade glioma.
Dai J et al.·Aging (Albany NY)
2024
Pan-cancer analysis of Arp2/3 complex subunits: focusing on ARPC1A's role and validating the ARPC1A/c-Myc axis in non-small cell lung cancer.
Zhou C et al.·Front Immunol
2025
Machine learning-assisted multi-dimensional transcriptomic analysis of cytoskeleton-related molecules and their relationship with prognosis in hepatocellular carcinoma.
Li Y et al.·Sci Rep
2025
Inactivating negative regulators of cortical branched actin enhances persistence of single cell migration.
Fokin AI et al.·J Cell Sci
2024
Prenatal diagnosis and molecular cytogenetic characterization of a de novo interstitial deletion of 7q (7q22.1→q31.1).
Chen CP et al.·Gene
2013Case report
Top 10 resultsSearch PubMed ↗
Recent Gene-Specific Literature
Gene in title · MEDLINE · newest first
Europe PMC
Top 5 resultsSearch Europe PMC ↗

Clinical Trials

Active and recruiting trials from ClinicalTrials.gov

ClinicalTrials.gov

No active trials found for this gene.

Search ClinicalTrials.gov →

External Resources

Links to major genomics databases and tools