ARF3

ADP ribosylation factor 3, the group of ARF GTPase family

Basic information

Region (hg38): 12:48935723-48957487

Links

ENSG00000134287 ∙ NCBI:377 ∙ OMIM:103190 ∙ HGNC:654 ∙ Uniprot:P61204 ∙ AlphaFold ∙ GenCC ∙ jax ∙ Sfari ∙ GnomAD ∙ Pubmed ∙ ClinVar

Phenotypes

GenCC

Source: genCC

• complex neurodevelopmental disorder (Strong), mode of inheritance: AD

ClinVar

This is a list of variants' phenotypes submitted to ClinVar and linked to the ARF3 gene.

• Intellectual disability;Kyphosis;Atrophy/Degeneration affecting the central nervous system (1 variants)
• 7 conditions (1 variants)
• Microcephaly;Intellectual disability;Scoliosis;Dystonic disorder;Atrophy/Degeneration affecting the central nervous system (1 variants)

Variants pathogenicity by type

Statistics on ClinVar variants can assist in determining whether a specific variant type in the ARF3 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					1	1
missense	3	2	3			8
nonsense						0
start loss						0
frameshift						0
inframe indel						0
splice donor/acceptor (+/-2bp)						0
splice region					1	1
non coding						0
Total	3	2	3	0	1

Variants in ARF3

This is a list of pathogenic ClinVar variants found in the ARF3 region.

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

Position	Type	Phenotype	Significance	ClinVar
12-48939041-C-T			Uncertain significance (Mar 13, 2023)
12-48939087-C-T		Inborn genetic diseases	Uncertain significance (Jun 30, 2023)
12-48939660-T-C		7 conditions	Pathogenic (-)
12-48939689-C-T		Inborn genetic diseases	Uncertain significance (Apr 15, 2024)
12-48939762-C-T		Hypotonia;Atrophy/Degeneration affecting the central nervous system;Pectus excavatum;Microcephaly;Intellectual disability • 12 conditions • See cases	Pathogenic/Likely pathogenic (Mar 27, 2024)
12-48940016-G-A			Benign (Jun 29, 2021)
12-48940056-T-A		Microcephaly;Intellectual disability;Scoliosis;Dystonic disorder;Atrophy/Degeneration affecting the central nervous system	Pathogenic (-)
12-48940113-G-GA			Benign (Aug 27, 2020)
12-48940957-G-A		Seizure;Intellectual disability;Atrophy/Degeneration affecting the central nervous system	Conflicting classifications of pathogenicity (May 27, 2022)
12-48941001-G-T		Intellectual disability;Kyphosis;Atrophy/Degeneration affecting the central nervous system	Pathogenic (-)
12-48941037-A-G			Uncertain significance (Feb 04, 2024)
12-48941040-C-T			Uncertain significance (May 19, 2022)
12-48941062-G-C		Microcephaly;Intellectual disability;Scoliosis;Dystonic disorder;Atrophy/Degeneration affecting the central nervous system	Likely pathogenic (-)

GnomAD

Source: gnomAD

Gene	Type	Bio Type	Transcript	Coding Exons	Length
ARF3	protein_coding	protein_coding	ENST00000256682	4	21829

pLI Probability LOF Intolerant	pRec Probability LOF Recessive	Individuals with no LOFs	Individuals with Homozygous LOFs	Individuals with Heterozygous LOFs	Defined	p
0.353	0.636	125738	0	2	125740	0.00000795

	Z-Score	Observed	Expected	Observed/Expected	Mutation Rate	Total Possible in Transcript
Missense	2.82	28	112	0.250	0.00000664	1193
Missense in Polyphen		3	30.769	0.097499		381
Synonymous	1.19	34	44.1	0.771	0.00000269	351
Loss of Function	2.12	2	8.79	0.227	5.25e-7	87

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)	0.0000180	0.0000176
Middle Eastern	0.00	0.00
South Asian	0.00	0.00
Other	0.00	0.00

dbNSFP

Source: dbNSFP

• Function: FUNCTION: GTP-binding protein that functions as an allosteric activator of the cholera toxin catalytic subunit, an ADP- ribosyltransferase. Involved in protein trafficking; may modulate vesicle budding and uncoating within the Golgi apparatus.
• Pathway: Endocytosis - Homo sapiens (human);Vesicle-mediated transport;Membrane Trafficking;Metabolism of lipids;Post-translational protein modification;Metabolism of proteins;Metabolism;Transport to the Golgi and subsequent modification;Asparagine N-linked glycosylation;Synthesis of PIPs at the Golgi membrane;COPI-dependent Golgi-to-ER retrograde traffic;Golgi-to-ER retrograde transport;COPI-mediated anterograde transport;PI Metabolism;Phospholipid metabolism;ER to Golgi Anterograde Transport;Intra-Golgi and retrograde Golgi-to-ER traffic (Consensus)

Intolerance Scores

• loftool: 0.297
• rvis_EVS: -0.03
• rvis_percentile_EVS: 51.04

Haploinsufficiency Scores

• pHI: 0.874
• hipred: Y
• hipred_score: 0.694
• ghis: 0.652

Essentials

• essential_gene_CRISPR: N
• essential_gene_CRISPR2: S
• essential_gene_gene_trap: H
• gene_indispensability_pred: E
• gene_indispensability_score: 0.955

Mouse Genome Informatics

• Gene name: Arf3
• Phenotype: immune system phenotype; vision/eye phenotype

Gene ontology

• Biological process: phosphatidylinositol biosynthetic process;intracellular protein transport;retrograde vesicle-mediated transport, Golgi to endoplasmic reticulum;Golgi to plasma membrane transport;vesicle-mediated transport
• Cellular component: Golgi membrane;cytoplasm;Golgi apparatus;plasma membrane;perinuclear region of cytoplasm;extracellular exosome
• Molecular function: GTPase activity;GTP binding