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GeneE
25 sources retrieved Β· Most recent: April 2026 Β· Index updated 15 days ago
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ARCN1
archain 1 coat protein complex I subunit delta
Chromosome 11 Β· 11q23.3
NCBI Gene: 372Ensembl: ENSG00000095139.16HGNC: HGNC:649UniProt: B0YIW5
198PubMed Papers
21Diseases
0Drugs
29Pathogenic Variants
FUNCTIONAL ROLE
Highly ConstrainedTransporter
CLINICAL
OMIM Disease Gene
DATA QUALITY
βœ“ Experimental GO Evidenceβœ“ Swiss-Prot Reviewed
RNA bindingmembraneprotein bindingGolgi localizationshort stature, rhizomelic, with microcephaly, micrognathia, and developmental delaygenetic disordermicrocephalyGriscelli disease
✦AI Summary

ARCN1 encodes archain 1, the delta subunit of the COPI (coat protein complex I) coatomer, a cytosolic protein complex essential for vesicular trafficking 1. The protein functions as a core component of COPI-coated vesicles, mediating retrograde Golgi-to-ER transport of dilysine-tagged proteins and anterograde ER-to-Golgi biosynthetic transport 2. ARCN1 recognizes dilysine motifs and associates reversibly with Golgi membranes in an ARF-dependent manner, maintaining Golgi structural integrity and regulating protein processing and endocytic recycling 3. Beyond classical vesicular trafficking, ARCN1 has emerged as a key regulator of innate immunity and viral infection. ARCN1 suppresses anti-RSV immune responses by promoting STUB1-mediated degradation of IKKΞ΅, an essential kinase for type I interferon production 4. Similarly, miR-33a inhibits influenza A virus replication partly by downregulating ARCN1 expression, indicating the protein's importance in viral trafficking 5. Clinically, ARCN1 mutations cause a rare syndromic disorder characterized by intrauterine growth restriction, micrognathia, short stature, developmental delay (71.4% of patients), microcephaly, and genitourinary malformations 6. Severe manifestations include hepatoblastoma, cataracts, and lethal skeletal abnormalities, with phenotype severity correlating with COPI trafficking dysfunction and ER stress responses 3. This constellation defines ARCN1-related syndrome, a disorder spanning from embryonic lethality to milder presentations.

Sources cited
1
ARCN1 is a novel human gene encoding a 57 kDa archain protein with highly conserved homologs across species, located at chromosome 11q23.3
PMID: 7782067
2
ARCN1 suppresses anti-RSV innate immune responses by promoting STUB1-mediated IKKΞ΅ degradation and reducing type I interferon production
PMID: 41343552
3
ARCN1 mutations cause syndromic disorder with intrauterine growth restriction, micrognathia, short stature, developmental delay (71.4%), microcephaly (80%), and genitourinary malformations
PMID: 35300924
4
ARCN1 encodes the delta subunit of COPI complex, required for intracellular collagen trafficking and involved in ER stress response; mutations cause rhizomelic short stature with microretrognathia
PMID: 38044464
5
miR-33a inhibits influenza A virus replication by targeting and downregulating ARCN1, which is required for efficient viral internalization
PMID: 26498766
6
ARCN1 variants are associated with ARCN1-related syndrome, characterized by microcephaly, global developmental delay, and multiple congenital abnormalities, caused by splicing defects
PMID: 33154040
Disease Associationsβ“˜21
short stature, rhizomelic, with microcephaly, micrognathia, and developmental delayOpen Targets
0.77Strong
genetic disorderOpen Targets
0.41Moderate
microcephalyOpen Targets
0.11Weak
Griscelli diseaseOpen Targets
0.09Suggestive
Griscelli disease type 3Open Targets
0.09Suggestive
Griscelli syndrome type 3Open Targets
0.09Suggestive
uncombable hair syndromeOpen Targets
0.07Suggestive
infectionOpen Targets
0.07Suggestive
Respiratory Syncytial Virus InfectionOpen Targets
0.07Suggestive
Microcephaly - albinism - digital anomaliesOpen Targets
0.06Suggestive
microcephaly-albinism-digital anomalies syndromeOpen Targets
0.06Suggestive
Dysequilibrium syndromeOpen Targets
0.06Suggestive
Rare hereditary ataxiaOpen Targets
0.06Suggestive
oculocutaneous albinism type 3Open Targets
0.06Suggestive
ringed hair diseaseOpen Targets
0.06Suggestive
Griscelli disease type 1Open Targets
0.06Suggestive
Griscelli syndrome type 1Open Targets
0.06Suggestive
pili bifurcatiOpen Targets
0.06Suggestive
Adult-onset autosomal recessive cerebellar ataxiaOpen Targets
0.06Suggestive
Childhood-onset autosomal recessive slowly progressive spinocerebellar ataxiaOpen Targets
0.05Suggestive
Short stature-micrognathia syndromeUniProt
Pathogenic Variants29
NM_001655.5(ARCN1):c.508C>T (p.Arg170Ter)Pathogenic
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay
β˜…β˜…β˜†β˜†2025β†’ Residue 170
NM_001655.5(ARCN1):c.231AGA[1] (p.Glu78del)Likely pathogenic
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay|not provided
β˜…β˜…β˜†β˜†2025β†’ Residue 78
NM_001655.5(ARCN1):c.654-15A>GPathogenic
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay|not provided
β˜…β˜…β˜†β˜†2024
NM_001655.5(ARCN1):c.1303C>T (p.Arg435Ter)Pathogenic
not provided|ARCN1-related disorder
β˜…β˜…β˜†β˜†2023β†’ Residue 435
NM_001655.5(ARCN1):c.934C>T (p.Arg312Ter)Pathogenic
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay
β˜…β˜…β˜†β˜†2023β†’ Residue 312
NM_001655.5(ARCN1):c.174C>G (p.Tyr58Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2025β†’ Residue 58
NM_001655.5(ARCN1):c.1288C>T (p.Arg430Ter)Pathogenic
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay
β˜…β˜†β˜†β˜†2025β†’ Residue 430
NM_001655.5(ARCN1):c.1142G>A (p.Trp381Ter)Pathogenic
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay
β˜…β˜†β˜†β˜†2025β†’ Residue 381
NM_001655.5(ARCN1):c.462del (p.Ala155fs)Pathogenic
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay
β˜…β˜†β˜†β˜†2025β†’ Residue 155
NM_001655.5(ARCN1):c.55C>T (p.Arg19Ter)Likely pathogenic
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay
β˜…β˜†β˜†β˜†2024β†’ Residue 19
NM_001655.5(ARCN1):c.886dup (p.Glu296fs)Pathogenic
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay
β˜…β˜†β˜†β˜†2024β†’ Residue 296
NM_001655.5(ARCN1):c.526C>T (p.Gln176Ter)Likely pathogenic
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay
β˜…β˜†β˜†β˜†2023β†’ Residue 176
NM_001655.5(ARCN1):c.711del (p.Phe238fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 238
NM_001655.5(ARCN1):c.1099C>T (p.Gln367Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2023β†’ Residue 367
NM_001655.5(ARCN1):c.1207G>T (p.Glu403Ter)Pathogenic
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay
β˜…β˜†β˜†β˜†2023β†’ Residue 403
NM_001655.5(ARCN1):c.862C>T (p.Arg288Ter)Pathogenic
See cases|ARCN1-related disorder
β˜…β˜†β˜†β˜†2022β†’ Residue 288
NM_001655.5(ARCN1):c.941del (p.Arg314fs)Pathogenic
not provided
β˜…β˜†β˜†β˜†2022β†’ Residue 314
NM_001655.5(ARCN1):c.522_525del (p.Glu174fs)Likely pathogenic
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay
β˜…β˜†β˜†β˜†2022β†’ Residue 174
NM_001655.5(ARCN1):c.814G>T (p.Glu272Ter)Likely pathogenic
Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay
β˜…β˜†β˜†β˜†2022β†’ Residue 272
NM_001655.5(ARCN1):c.553G>T (p.Gly185Ter)Pathogenic
not provided
β˜…β˜†β˜†β˜†2021β†’ Residue 185
View on ClinVar β†—
Related Genes
STX5Protein interaction100%COPZ1Protein interaction100%ARF1Protein interaction99%USO1Protein interaction98%ARFGAP3Protein interaction96%KDELR1Protein interaction96%
Tissue Expression6 tissues
Heart
100%
Brain
93%
Lung
69%
Liver
67%
Ovary
60%
Bone Marrow
32%
Gene Interaction Network
Click a node to explore
ARCN1STX5COPZ1ARF1USO1ARFGAP3KDELR1
PROTEIN STRUCTURE
Preparing viewer…
AlphaFoldAI-predicted Β· UniProt P48444
View on AlphaFold β†—
Constraintβ“˜
LOEUFβ“˜
0.14Highly Constrained
pLIβ“˜
1.00Intolerant
Observed/Expected LoF0.06 [0.03–0.14]
RankingsWhere ARCN1 stands among ~20K protein-coding genes
  • #2,135of 20,598
    Most Researched198 Β· top quartile
  • #1,835of 5,498
    Most Pathogenic Variants29
  • #192of 17,882
    Most Constrained (LOEUF)0.14 Β· top 5%
Genes detectedARCN1
Sources retrieved25 papers
Response timeβ€”
πŸ“„ Sources
25β–Ό
1
The human archain gene, ARCN1, has highly conserved homologs in rice and Drosophila.
PMID: 7782067
Genomics Β· 1995
1.00
2
ARCN1 suppresses innate immune responses against respiratory syncytial virus by promoting STUB1-mediated IKKΞ΅ degradation.
PMID: 41343552
PLoS Pathog Β· 2025
0.90
3
Shared genetic risk between major orofacial cleft phenotypes in an African population.
PMID: 38634654
Genet Epidemiol Β· 2024
0.84
4
Expanding the phenotypic spectrum of ARCN1-related syndrome.
PMID: 35300924
Genet Med Β· 2022
0.80
5
Identification and characterization of human LL5A gene and mouse Ll5a gene in silico.
PMID: 14532993
Int J Oncol Β· 2003
0.70