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Severe microcephaly

Gene: ARF3

Red List (low evidence)

ARF3 (ADP ribosylation factor 3)
EnsemblGeneIds (GRCh38): ENSG00000134287
EnsemblGeneIds (GRCh37): ENSG00000134287
OMIM: 103190, Gene2Phenotype
ARF3 is in 3 panels

2 reviews

Ivone Leong (Genomics England Curator)

Comment on list classification: Demoted from Amber to Red as per my review.
Created: 1 Oct 2021, 1:44 p.m. | Last Modified: 1 Oct 2021, 1:44 p.m.
Panel Version: 2.255
Comment on list classification: New gene added by Konstantinos Varvagiannis (Other). This gene is not associated with a phenotype in OMIM or Gene2Phenotype.

PMID:34346499, individual 1 also has severe microcephaly (-3.3SD), spasticity, cerebellum atrophy and brainstem atrophy. Individual 2 does not have microcephaly, but has cerebellar hypoplasia.

As only 1 patient has severe microcephaly. This gene has been given a Red rating.
Created: 1 Oct 2021, 1:40 p.m. | Last Modified: 1 Oct 2021, 1:44 p.m.
Panel Version: 2.254

Konstantinos Varvagiannis (Other)

I don't know

Sakamoto et al (2021 - PMID: 34346499) provide some evidence that monoallelic ARF3 pathogenic variants may be associated with a NDD with brain abnormality.

Using trio exome sequencing, the authors identified 2 individuals with NDD harboring de novo ARF3 variants, namely: NM_001659.2:c.200A>T / p.Asp67Val and c.296G>T / p.Arg99Leu.

Individual 1 (with Asp67Val / age : 4y10m), appeared to be more severelely affected with prenatal onset progressive microcephaly, severe global DD, epilepsy. Upon MRI there was cerebellar and brainstem atrophy. Individual 2 (Arg99Leu / 14y) had severe DD and ID (IQ of 23), epilepsy and upon MRI cerebellar hypoplasia. This subject did not exhibit microcephaly. Common facial features incl. broad nose, full cheeks, small philtrum, strabismus, thin upper lips and abnormal jaw. There was no evidence of systemic involvement in both.

ARF3 encodes ADP-ribosylation factor 3. Adenosine diphosphate ribosylation factors (ARFs) are key proteins for regulation of cargo sorting at the Golgi network, with ARF3 mainly working at the trans-Golgi network. ARFs belong to the small GTP-binding protein (G protein) superfamily. ARF3 switches between an active GTP-bound form and an inactive GDP-bound form, regulated by guanine nucleotide exchange factors (GEFs) and GTPase activating proteins (GAPs) respectively.

Members of the ARF superfamily regulate various aspects of membrane traffic, among others in neurons.

There are 5 homologs of ARF families, divided in 3 classes. ARF3 and ARF1 belong to class I. Monoallelic ARF1 mutations are associated with Periventricular nodular heterotopia 8 (MIM 618185).

In vivo, in vitro and in silico studies for the 2 variants suggest that both impair the Golgi transport system although each variant most likely exerts a different effect (gain-of-function for Arg99Leu vs loss-of-function/dominant-negative for Asp67Val).

This was also reflected in somewhat different phenotype of the subjects with the respective variants. Common features included severe DD, epilepsy and brain abnormalities although Asp67Val was associated with diffuse brain atrophy as well as congenital microcephaly and Arg99Leu with cerebellar hypoplasia.

Evidence to support the effect of each variant include:

Had identical Golgi localization to that of wt
Had increased binding activity with GGA1, a protein recruited by the GTP-bound active form of ARF3 to the TGN membrane (supporting GoF)
In silico structural analysis suggested it may fail to stabilize the conformation of Asp26, resulting in impaired GTP hydrolysis (GoF).
In transgenic fruit flies, evaluation of the ARF3 variant toxicity using the rough eye phenotype this variant was associated with increased severity of the r-e phenotype similar to a previously studied GoF variant (Gln71Leu)

Did not show a Golgi-like pattern of localization (similar to Thr31Asn a previously studied dominant-negative variant)
Displayed decreased protein stability
In silico structural analysis suggested that Asp67Val may lead to compromised binding of GTP or GDP (suggestive of LoF)
In transgenic Drosophila eye-specific expression of Asp67Val (similar to Thr31Asn, a known dominant-negative variant) was lethal possibly due to high toxicity in very small amounts in tissues outside the eye.

There is no associated phenotype in OMIM, G2P or SysID.
Sources: Literature
Created: 15 Aug 2021, 6:49 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Global developmental delay; Intellectual disability; Seizures; Morphological abnormality of the central nervous system



Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
  • Expert Review Red
  • Literature
  • Global developmental delay
  • Intellectual disability, MONDO:0001071
  • Seizures
  • Morphological abnormality of the central nervous system
  • microcephaly, MONDO:0001149
Clinvar variants
Variants in ARF3
Panels with this gene

History Filter Activity

1 Oct 2021, Gel status: 1

Removed Tag

Ivone Leong (Genomics England Curator)

Tag watchlist was removed from gene: ARF3.

1 Oct 2021, Gel status: 1

Entity classified by Genomics England curator

Ivone Leong (Genomics England Curator)

Gene: arf3 has been classified as Red List (Low Evidence).

1 Oct 2021, Gel status: 2

Created, Added New Source, Added Tag, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance

Ivone Leong (Genomics England Curator)

gene: ARF3 was added gene: ARF3 was added to Severe microcephaly. Sources: Expert Review Amber,Literature watchlist tags were added to gene: ARF3. Mode of inheritance for gene: ARF3 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: ARF3 were set to 34346499 Phenotypes for gene: ARF3 were set to Global developmental delay; Intellectual disability, MONDO:0001071; Seizures; Morphological abnormality of the central nervous system; microcephaly, MONDO:0001149 Penetrance for gene: ARF3 were set to unknown