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  3. SCAF4
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Intellectual disability

Gene: SCAF4

Green List (high evidence)
SCAF4 (SR-related CTD associated factor 4)
EnsemblGeneIds (GRCh38): ENSG00000156304
EnsemblGeneIds (GRCh37): ENSG00000156304
OMIM: 616023, Gene2Phenotype
SCAF4 is in 5 panels

5 reviews

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

In repsonse to Ian Berry's (Leeds Genetics Laboratory) review, which also reports an additional patient with a de novo truncating variant, there is sufficient evidence for SCAF4 to be green on this panel.
Created: 24 May 2022, 9:34 a.m. | Last Modified: 24 May 2022, 9:34 a.m.
Panel Version: 3.1581
Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review.
Created: 24 May 2022, 9:27 a.m. | Last Modified: 24 May 2022, 9:27 a.m.
Panel Version: 3.1581
Created: 24 May 2022, 9:27 a.m.
Last Modified: 24 May 2022, 9:27 a.m.
Panel version: 3.1581

Ian Berry (Leeds Genetics Laboratory)

Green List (high evidence)

Fleidner et al. 2020, satisfies standard requirements for green gene. Also identified in GMS WGS patient (de novo truncation) referred under ID clinical indication, with Seizures & moderate ID.
Created: 19 May 2022, 8:42 p.m. | Last Modified: 19 May 2022, 8:42 p.m.
Panel Version: 3.1580

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Seizures; intellectual disability (mild)

Publications

Created: 19 May 2022, 8:42 p.m.
Last Modified: 19 May 2022, 8:42 p.m.
Panel version: 3.1580

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to Green following NHS Genomic Medicine Service approval.
Created: 30 Jan 2023, 5:50 p.m. | Last Modified: 30 Jan 2023, 5:50 p.m.
Panel Version: 4.53
Comment on list classification: At least 8 unrelated individuals reported in PMID:32730804 with a neurodevelopmental disorder characterised by DD/ID, mostly in the mild range (severe in only one individual).

Rating Amber in view of the mild ID presentation. This may be reviewed if further cases are reported with more severe manifestations of relevant phenotypes.
Created: 9 Oct 2020, 11:17 a.m. | Last Modified: 9 Oct 2020, 11:17 a.m.
Panel Version: 3.412
Currently not associated with any phenotype in OMIM (last edited on 23/09/2014), but is a probable gene SCAF4-related Neurodevelopmental Disorder in Gen2Phen.
Created: 9 Oct 2020, 11 a.m. | Last Modified: 9 Oct 2020, 11 a.m.
Panel Version: 3.411
Created: 9 Oct 2020, 11 a.m.
Last Modified: 9 Oct 2020, 11 a.m.
Panel version: 4.53

Zornitza Stark (Australian Genomics)

Green List (high evidence)

> 5 variants reported in individuals with variable neurodevelopmental disorder characterized by intellectual disability, seizures, behavioral abnormalities, and various skeletal and structural anomalies. Suggest also adding to epilepsy panel.
Created: 4 Aug 2020, 10:55 a.m. | Last Modified: 4 Aug 2020, 10:55 a.m.
Panel Version: 3.226

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
intellectual disability; seizures; behavioral abnormalities

Publications

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

Created: 4 Aug 2020, 10:55 a.m.
Last Modified: 4 Aug 2020, 10:55 a.m.
Panel version: 3.226

Eleanor Williams (Genomics England Curator)

Conference talk/abstract from ESHG2020 - C02.1 - SCAF4 loss of function in humans and Drosophila implicates mRNA transcriptional termination in neurodevelopmental disorders - Fliedner et al - report 9 unrelated patients with likely pathogenic variants in SCAF4 and mild developmental delay and intellectual disability. 8 de novo. 1 inherited. Seizures, skeletal, renal and cardiac anomalies were also seen.
Sources: Literature
Created: 12 Jun 2020, 7:44 p.m. | Last Modified: 13 Jun 2020, 7:24 a.m.
Panel Version: 3.90

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

Created: 12 Jun 2020, 7:44 p.m.
Last Modified: 13 Jun 2020, 7:24 a.m.
Panel version: 3.90

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
  • NHS GMS
  • Literature
Phenotypes
  • Fliedner-Zweier syndrome, OMIM:620511
OMIM
616023
Clinvar variants
Variants in SCAF4
Penetrance
None
Publications
Panels with this gene

History Filter Activity

16 Oct 2023, Gel status: 3

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: SCAF4 were changed from SCAF4-related Neurodevelopmental Disorder; Intellectual disability; Seizures; Behavioural abnormalities to Fliedner-Zweier syndrome, OMIM:620511

16 Oct 2023, Gel status: 3

Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag gene-checked was removed from gene: SCAF4.

7 Feb 2023, Gel status: 3

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag gene-checked tag was added to gene: SCAF4.

31 Jan 2023, Gel status: 3

Removed Tag, Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag Q2_22_rating was removed from gene: SCAF4. Tag Q2_22_NHS_review was removed from gene: SCAF4.

30 Jan 2023, Gel status: 3

Added New Source, Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source NHS GMS was added to SCAF4. Source Expert Review Green was added to SCAF4. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

24 May 2022, Gel status: 2

Removed Tag, Added Tag, Added Tag

Sarah Leigh (Genomics England Curator)

Tag watchlist was removed from gene: SCAF4. Tag Q2_22_rating tag was added to gene: SCAF4. Tag Q2_22_NHS_review tag was added to gene: SCAF4.

24 May 2022, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: scaf4 has been classified as Amber List (Moderate Evidence).

9 Oct 2020, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: SCAF4 were changed from to SCAF4-related Neurodevelopmental Disorder; Intellectual disability; Seizures; Behavioural abnormalities

9 Oct 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: scaf4 has been classified as Amber List (Moderate Evidence).

9 Oct 2020, Gel status: 1

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: SCAF4 were set to

23 Jun 2020, Gel status: 1

Added Tag

Eleanor Williams (Genomics England Curator)

Tag watchlist tag was added to gene: SCAF4.

12 Jun 2020, Gel status: 1

Created, Added New Source, Set mode of inheritance

Eleanor Williams (Genomics England Curator)

gene: SCAF4 was added gene: SCAF4 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: SCAF4 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown