ARCN1

archain 1, the group of COPI coat complex

Basic information

Region (hg38): 11:118572390-118603033

Previous symbols: [ "COPD" ]

Links

ENSG00000095139 ∙ NCBI:372 ∙ OMIM:600820 ∙ HGNC:649 ∙ Uniprot:P48444 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay (Strong), mode of inheritance: AD
• short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay (Strong), mode of inheritance: AD

Clinical Genomic Database

Source: CGD

Condition	Inheritance	Intervention Categories	Intervention/Rationale	Manifestation Categories	References
Short stature-micrognathia syndrome	AD	General	Genetic knowledge may be beneficial related to issues such as selection of optimal supportive care, informed medical decision-making, prognostic considerations, and avoidance of unnecessary testing	Craniofacial; Musculoskeletal; Neurologic	27476655

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARCN1 gene.

• Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay (6 variants)
• not provided (4 variants)
• ARCN1-related disorder (1 variants)
• Inborn genetic diseases (1 variants)
• See cases (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARCN1 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				42	7	49
missense			99	6	2	107
nonsense	7	4				11
start loss						0
frameshift	5	1	1			7
inframe indel		1				1
splice donor/acceptor (+/-2bp)						0
splice region			3	9	4	16
non coding		1	1	22	7	31
Total	12	7	101	70	16

Variants in ARCN1

This is a list of pathogenic ClinVar variants found in the ARCN1 region.

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

Position	Type	Phenotype	Significance	ClinVar
11-118572545-A-G		not specified	Uncertain significance (Jun 21, 2024)
11-118572558-C-T		ARCN1-related disorder	Benign (Mar 01, 2025)
11-118572559-C-A			Likely benign (May 18, 2022)
11-118572566-G-A			Likely benign (Apr 22, 2024)
11-118581186-T-C		Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay	Benign (Dec 05, 2021)
11-118581235-G-A			Likely benign (Nov 18, 2024)
11-118581238-C-A			Likely benign (Dec 17, 2024)
11-118581238-C-G			Likely benign (Oct 14, 2023)
11-118581238-C-T			Likely benign (Oct 12, 2024)
11-118581250-T-C			Uncertain significance (Nov 01, 2024)
11-118581251-G-A		not specified	Likely benign (Feb 04, 2025)
11-118581258-G-T		ARCN1-related disorder	Benign (Mar 01, 2025)
11-118581263-G-A			Likely benign (Jan 05, 2025)
11-118581263-G-T			Likely benign (Jan 05, 2024)
11-118581268-G-A			Uncertain significance (Apr 08, 2022)
11-118581288-A-G			Uncertain significance (Nov 08, 2022)
11-118581297-C-T		Short stature, rhizomelic, with microcephaly, micrognathia, and developmental delay	Likely pathogenic (Oct 09, 2024)
11-118581298-G-A		Inborn genetic diseases	Uncertain significance (Jun 17, 2024)
11-118581315-A-G			Uncertain significance (Apr 20, 2023)
11-118581318-C-T		Inborn genetic diseases	Pathogenic (Feb 23, 2021)
11-118581325-G-A		Inborn genetic diseases	Conflicting classifications of pathogenicity (Jan 06, 2025)
11-118581327-A-G		Inborn genetic diseases	Uncertain significance (Aug 14, 2024)
11-118581356-G-A			Likely benign (Jul 19, 2022)
11-118581378-C-A		Inborn genetic diseases	Uncertain significance (Aug 31, 2022)
11-118581382-C-T			Uncertain significance (Aug 10, 2023)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARCN1	protein_coding	protein_coding	ENST00000264028	10	30644

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
1.00	0.0000273	0	0	0	0	0.00

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.08	186	285	0.653	0.0000151	3361
Missense in Polyphen		37	95.982	0.38549		1216
Synonymous	-0.0879	105	104	1.01	0.00000563	976
Loss of Function	5.05	0	29.6	0.00	0.00000199	306

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: Component of the coatomer, a cytosolic protein complex that binds to dilysine motifs and reversibly associates with Golgi non-clathrin-coated vesicles, which further mediate biosynthetic protein transport from the ER, via the Golgi up to the trans Golgi network. The coatomer complex is required for budding from Golgi membranes, and is essential for the retrograde Golgi-to-ER transport of dilysine-tagged proteins. In mammals, the coatomer can only be recruited by membranes associated to ADP-ribosylation factors (ARFs), which are small GTP-binding proteins; the complex also influences the Golgi structural integrity, as well as the processing, activity, and endocytic recycling of LDL receptors (By similarity). {ECO:0000250}.
• Pathway: miR-targeted genes in epithelium - TarBase;miR-targeted genes in leukocytes - TarBase;miR-targeted genes in lymphocytes - TarBase;miR-targeted genes in muscle cell - TarBase;miR-targeted genes in squamous cell - TarBase;miR-517 relationship with ARCN1 and USP1;Vesicle-mediated transport;Membrane Trafficking;Glycosphingolipid biosynthesis - neolactoseries;Post-translational protein modification;Metabolism of proteins;Tyrosine metabolism;Proteoglycan biosynthesis;Androgen and estrogen biosynthesis and metabolism;Glycosphingolipid biosynthesis - ganglioseries;Glycosphingolipid biosynthesis - globoseries;Purine metabolism;Pyrimidine metabolism;Glycosphingolipid metabolism;Phosphatidylinositol phosphate metabolism;Prostaglandin formation from arachidonate;Methionine and cysteine metabolism;Aminosugars metabolism;Galactose metabolism;O-Glycan biosynthesis;C21-steroid hormone biosynthesis and metabolism;Glycerophospholipid metabolism;Vitamin B9 (folate) metabolism;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;N-Glycan biosynthesis;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Recessive Scores

• pRec: 0.176

Intolerance Scores

• loftool: 0.125
• rvis_EVS: -0.63
• rvis_percentile_EVS: 17.03

Haploinsufficiency Scores

• pHI: 0.314
• hipred: Y
• hipred_score: 0.785
• ghis: 0.546

Essentials

• essential_gene_CRISPR: E
• essential_gene_CRISPR2: E
• essential_gene_gene_trap: E
• gene_indispensability_pred: N
• gene_indispensability_score: 0.482

Gene Damage Prediction

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

Mouse Genome Informatics

• Gene name: Arcn1
• Phenotype: pigmentation phenotype; behavior/neurological phenotype (the observable actions or reactions of mammalian organisms that are manifested through development and lifespan); nervous system phenotype (the observable morphological and physiological characteristics of the extensive, intricate network of electochemical structures in the body that is comprised of the brain, spinal cord, nerves, ganglia and parts of the receptor organs that are manifested through development and lifespan); growth/size/body region phenotype; integument phenotype (the observable morphological and physiological characteristics of the skin and its associated structures, such as the hair, nails, sweat glands, sebaceous glands and other secretory glands that are manifested through development and lifespan); cellular phenotype

Gene ontology

• Biological process: intracellular protein transport;endoplasmic reticulum to Golgi vesicle-mediated transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;adult locomotory behavior;cerebellar Purkinje cell layer maturation;pigmentation;Golgi localization
• Cellular component: Golgi membrane;endoplasmic reticulum membrane;cytosol;membrane;COPI vesicle coat;transport vesicle;COPI-coated vesicle
• Molecular function: RNA binding