1. Panels
  2. Intellectual disability
  3. SCYL1
Genes in panel
Prev Next
Regions in panel
Prev Next

Intellectual disability

Gene: SCYL1

Green List (high evidence)
SCYL1 (SCY1 like pseudokinase 1)
EnsemblGeneIds (GRCh38): ENSG00000142186
EnsemblGeneIds (GRCh37): ENSG00000142186
OMIM: 607982, Gene2Phenotype
SCYL1 is in 8 panels

2 reviews

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

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
Associated with relevant phenotype in OMIM and as probable Gen2Phen gene. At least six variants reported in five cases of OMIM:616719 with mild to severe intellectual disability (PMID: 26581903, 29419818, 30531813). Together with supportive functional and animal data (PMID: 17571074, 26581903)
Created: 26 May 2021, 11:42 a.m. | Last Modified: 26 May 2021, 11:42 a.m.
Panel Version: 3.1097
Created: 26 May 2021, 11:42 a.m.
Last Modified: 26 May 2021, 11:42 a.m.
Panel version: 3.1519

Catherine Snow (Genomics England)

Comment on list classification: Gene identified in literature PMID:30914295 as missing in PanelApp compared to other curated gene list for ID genes.

Schmidt et al (PMID: 26581903) reported on two families with three individuals affected by a previously unsubscribed ataxia syndrome. Siblings, born to unrelated healthy parents of white European descent with British and German roots and an individual born to non-consanguineous parents with at least three generations of Cuban family history.

Both affected siblings were found to harbour two mutations within SCYL1 (SCY1-like, kinase-like [MIM: 607982]), c.937delG (p.Val313Cysfs*6) in exon 7 and c.1509_1510delTG (p.Ala504Profs*15) in exon 11 (GenBank: NM_020680.3. One sib had normal cognition; the other had mild intellectual disability.

The other unrelated individual was reported to have SCYL1 variant with a splice-site mutation (c.1230+1G>A [p.?]) affecting the invariable +1 nucleotide of intron 9 (causing disruption of correct mRNA splicing by inducing skipping of exon 9, which encodes part of the HEAT repeat domain) and a premature termination mutation (c.1636C>T [p. Gln546*]) in exon 12.They were also reported to have mild learning disability.

SCYL1 is probable in Gene2Phenotype but no phenotypes assigned to the entry. SCYL1 in OMIM as Spinocerebellar ataxia, autosomal recessive 21.

As only two unrelated cases have been identified and ID has been classed as mild and not in all individuals, SCYL1 will be classified as Amber and added to the watchlist.
Created: 30 May 2019, 3:02 p.m.
Created: 30 May 2019, 3:02 p.m.

Panel version: Imported from Intellectual disability update May 2019 panel version 0.126

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Literature
  • Literature
Phenotypes
  • Spinocerebellar ataxia, autosomal recessive 21 OMIM:616719
  • acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome MONDO:0014744
OMIM
607982
Clinvar variants
Variants in SCYL1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

14 Mar 2022, Gel status: 3

Removed Tag

Ivone Leong (Genomics England Curator)

Tag Q2_21_rating was removed from gene: SCYL1.

14 Mar 2022, Gel status: 3

Added New Source, Status Update

Ivone Leong (Genomics England Curator)

Source Expert Review Green was added to SCYL1. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

26 May 2021, Gel status: 2

Removed Tag, Added Tag

Sarah Leigh (Genomics England Curator)

Tag watchlist was removed from gene: SCYL1. Tag Q2_21_rating tag was added to gene: SCYL1.

26 May 2021, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: SCYL1 were set to 26581903; 30914295

26 May 2021, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: SCYL1 were changed from Spinocerebellar ataxia, autosomal recessive 21, 616719 to Spinocerebellar ataxia, autosomal recessive 21 OMIM:616719; acute infantile liver failure-cerebellar ataxia-peripheral sensory motor neuropathy syndrome MONDO:0014744

25 Jul 2019, Gel status: 2

Added Tag

Catherine Snow (Genomics England)

Tag watchlist tag was added to gene: SCYL1.

25 Jul 2019, Gel status: 2

Set mode of inheritance

Catherine Snow (Genomics England)

Mode of inheritance for gene SCYL1 was changed from to BIALLELIC, autosomal or pseudoautosomal

25 Jul 2019, Gel status: 2

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

Catherine Snow (Genomics England)

gene: SCYL1 was added gene: SCYL1 was added to Intellectual disability. Sources: Literature,Expert Review Amber Mode of inheritance for gene: SCYL1 was set to Publications for gene: SCYL1 were set to 26581903; 30914295 Phenotypes for gene: SCYL1 were set to Spinocerebellar ataxia, autosomal recessive 21, 616719