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Intellectual disability

Gene: ARF1

Green List (high evidence)
ARF1 (ADP ribosylation factor 1)
EnsemblGeneIds (GRCh38): ENSG00000143761
EnsemblGeneIds (GRCh37): ENSG00000143761
OMIM: 103180, Gene2Phenotype
ARF1 is in 5 panels

5 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

Comment on publications: PMID:36345169 reported a paediatric patient identified with a monoallelic de novo missense variant (c.296 G > A; p.R99H) in the ARF1 gene, associated with developmental delay, hypotonia, intellectual disability and motor stereotypies. This patient did not exhibit periventricular heterotopias previously observed in other patients with ARF1 variants (including p.R99H). Functional analysis shows that the pathogenetic mechanism of the R99H-ARF1 variant involves constitutive activation with resultant Golgi and endosomal alterations.
Created: 23 Mar 2023, 5:03 p.m. | Last Modified: 23 Mar 2023, 5:03 p.m.
Panel Version: 5.5
Comment on publications: PMID:36345169 reported a paediatric patient identified with a monoallelic de novo missense variant (c.296 G > A; p.R99H) in the ARF1 gene, associated with developmental delay, hypotonia, intellectual disability and motor stereotypies. This patient did not exhibit periventricular heterotopias previously observed in other patients with ARF1 variants (including p.R99H). Functional analysis shows that the pathogenetic mechanism of the R99H-ARF1 variant involves constitutive activation with resultant Golgi and endosomal alterations.
Created: 23 Mar 2023, 5:02 p.m. | Last Modified: 23 Mar 2023, 5:02 p.m.
Panel Version: 5.5
Comment on publications: PMID:36345169 reported a paediatric patient identified with a monoallelic de novo missense variant (c.296 G > A; p.R99H) in the ARF1 gene, associated with developmental delay, hypotonia, intellectual disability and motor stereotypies. This patient did not exhibit periventricular heterotopias previously observed in other patients with ARF1 variants (including p.R99H). Functional analysis shows that the pathogenetic mechanism of the R99H-ARF1 variant involves constitutive activation with resultant Golgi and endosomal alterations.
Created: 23 Mar 2023, 5:02 p.m. | Last Modified: 23 Mar 2023, 5:02 p.m.
Panel Version: 5.4
Comment on publications: PMID:36345169 reported a paediatric patient identified with a monoallelic de novo missense variant (c.296 G > A; p.R99H) in the ARF1 gene, associated with developmental delay, hypotonia, intellectual disability and motor stereotypies. This patient did not exhibit periventricular heterotopias previously observed in other patients with ARF1 variants (including p.R99H). Functional analysis shows that the pathogenetic mechanism of the R99H-ARF1 variant involves constitutive activation with resultant Golgi and endosomal alterations.
Created: 23 Mar 2023, 5:02 p.m. | Last Modified: 23 Mar 2023, 5:02 p.m.
Panel Version: 5.4
Created: 23 Mar 2023, 5:02 p.m.
Last Modified: 23 Mar 2023, 5:02 p.m.
Panel version: 5.4

Sarah Leigh (Genomics England Curator)

The rating of this gene has been updated following NHS Genomic Medicine Service approval.
Created: 14 Mar 2022, 2:22 p.m. | Last Modified: 14 Mar 2022, 2:22 p.m.
Panel Version: 3.1519
Created: 14 Mar 2022, 2:22 p.m.
Last Modified: 14 Mar 2022, 2:22 p.m.
Panel version: 3.1519

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

Added to ID panel as developmental delay (especially in speech) is a reported feature in all cases (except for one individuals for which only limited clinical information was available). Although only one patient has been reported with a moderate ID diagnosis, developmental delay is likely to be noticed earlier in the course of disease than cortical malformations and may prompt genetic investigation. Inclusion on this panel could increase the likelihood of detecting cases and therefore a Green rating is warranted.
Created: 3 Sep 2021, 2:38 p.m. | Last Modified: 3 Sep 2021, 2:38 p.m.
Panel Version: 3.1252
Comment on publications: Gana et al., 2021 (PMID: 34353862) - additional family identified with a 5-year-old girl who inherited a heterozygous nonsense variant in the ARF1 gene (c.234G>A; p.Trp78Ter) from her father. Both displayed periventricular nodular heterotopia on brain MRI but with milder clinical expression in the father.
Created: 3 Sep 2021, 2:24 p.m. | Last Modified: 3 Sep 2021, 2:24 p.m.
Panel Version: 2.62

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Periventricular nodular heterotopia 8, OMIM:618185

Publications

Created: 3 Sep 2021, 2:24 p.m.
Last Modified: 3 Sep 2021, 2:24 p.m.
Copied from panel: Malformations of cortical development v2.62

Ivone Leong (Genomics England Curator)

Comment on list classification: New gene added by Zornitza Stark (Australian Genomics). This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype. There is enough evidence to support a gene-disease association. This gene should be rated Green at the next review.
Created: 17 Aug 2021, 1:42 p.m. | Last Modified: 17 Aug 2021, 1:42 p.m.
Panel Version: 2.55
Created: 17 Aug 2021, 1:42 p.m.
Last Modified: 17 Aug 2021, 1:42 p.m.
Copied from panel: Malformations of cortical development v2.62

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Three unrelated individuals reported with de novo missense in this gene.
Sources: Expert list
Created: 24 Aug 2020, 11:02 a.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Periventricular nodular heterotopia 8, MIM# 618185

Publications

Variants in this GENE are reported as part of current diagnostic practice

Created: 24 Aug 2020, 11:02 a.m.

Copied from panel: Malformations of cortical development v2.62

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Sources
  • Expert Review Green
  • Expert list
Phenotypes
  • Periventricular nodular heterotopia 8, OMIM:618185
OMIM
103180
Clinvar variants
Variants in ARF1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

23 Mar 2023, Gel status: 3

Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Publications for gene: ARF1 were set to 28868155; 34353862; 36345169

23 Mar 2023, Gel status: 3

Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Publications for gene: ARF1 were set to 28868155; 34353862; 36345169

23 Mar 2023, Gel status: 3

Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Publications for gene: ARF1 were set to 28868155; 34353862; 36345169

23 Mar 2023, Gel status: 3

Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Publications for gene: ARF1 were set to 28868155; 34353862

14 Mar 2022, Gel status: 3

Removed Tag

Ivone Leong (Genomics England Curator)

Tag Q3_21_rating was removed from gene: ARF1.

14 Mar 2022, Gel status: 3

Added New Source, Status Update

Ivone Leong (Genomics England Curator)

Source Expert Review Green was added to ARF1. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

3 Sep 2021, Gel status: 2

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

Arina Puzriakova (Genomics England Curator)

gene: ARF1 was added gene: ARF1 was added to Intellectual disability. Sources: Expert list,Expert Review Amber Q3_21_rating tags were added to gene: ARF1. Mode of inheritance for gene: ARF1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: ARF1 were set to 28868155; 34353862 Phenotypes for gene: ARF1 were set to Periventricular nodular heterotopia 8, OMIM:618185