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Intellectual disability

Gene: SCYL1

Amber List (moderate evidence)

SCYL1 (SCY1 like pseudokinase 1)
EnsemblGeneIds (GRCh38): ENSG00000142186
EnsemblGeneIds (GRCh37): ENSG00000142186
OMIM: 607982, Gene2Phenotype
SCYL1 is in 7 panels

1 review

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.


Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
  • Expert Review Amber
  • Literature
  • Expert Review Amber
  • Literature
  • Spinocerebellar ataxia, autosomal recessive 21, 616719
Clinvar variants
Variants in SCYL1
Panels with this gene

History Filter Activity

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