Ophthalmological ciliopathies

Gene: SCLT1

Green List (high evidence)

SCLT1 (sodium channel and clathrin linker 1)
EnsemblGeneIds (GRCh38): ENSG00000151466
EnsemblGeneIds (GRCh37): ENSG00000151466
OMIM: 611399, Gene2Phenotype
SCLT1 is in 9 panels

3 reviews

Eleanor Williams (Genomics England Curator)

Comment on list classification: 3 cases plus a mouse model and functional evidence that the protein is a ciliary protein.
Created: 19 Jun 2019, 2:02 p.m.
Not associated with any phenotype in OMIM or Gene2Phenotype.

PMID: 15797711 - this paper does not appear to be about SCLT1 or ciliopathies

PMID: 23348840 - Tanos et al 2013 - identified SCLT1 as a component of distal appendages (DAPs) of centrioles that have been proposed to anchor cilia to the plasma membrane. It is one of five DAP components and is essential for ciliogenesis.

PMID: 24285566 - Adly et al 2014 - 1 case with index patient with consanguineous Saudi parents and a severe ciliopathy phenotype. He had severe midline cleft lip and palate, microcephaly and choanal atresia. He also had significant eye involvement in the form of severe coloboma, and congenital heart disease (ASD and VSD). He had micropenis. Brain imaging revealed pachygyria and absent corpus callosum. He had abnormal inner ear structures. A splicing mutation was identified in SCLT1 (, NM_144643.2:exon5:c.290+2T>C). This mutation completely abolishes the consensus donor site of exon 5 as confirmed by RTPCR, which showed complete skipping of exon 5 resulting in a frameshift and introduction of a premature stop codon (p.Lys79Valfs*4),

PMID: 28005958 - de Castro-Miró et al 2016 - A cohort of 33 pedigrees affected with a variety of retinal disorders was analysed by WES. 1 case with compound heterozygosity (one missense and one splicing altering mutations) in SCLT1 that segregates with the condition in the family (2 affected siblings). Proposed to be causative of early-onset Retinitis Pigmentosa. SCLT1 is a member of the centrosomal/ciliary protein family.

PMID: 28486600 - Li et al 2017 - report a mouse model with mutated Sclt1 gene. The Sclt1-/- mice exhibit typical ciliopathy phenotypes, including cystic kidney, cleft palate and polydactyly.

PMID: 30425282 - Katagiri et al 2018 - a patient with Senior Løken syndrome and her unaffected parents revealed that the patient had infantile-onset retinal dystrophy and juvenile-onset nephronophthisis. Other systemic abnormalities included hepatic dysfunction, megacystis, mild learning disability, autism, obesity, and hyperinsulinemia. Whole-exome sequencing identified compound heterozygous SCLT1 variants (c.1218 + 3insT and c.1631A > G) in the patient. The unaffected parents were heterozygous for each variant. Transcript analysis using reverse transcription PCR demonstrated that the c.1218 + 3insT variant leads to exon 14 skipping (p.V383_M406del), while the other variant (c.1631A > G) primarily leads to exon 17 skipping (p.D480EfsX11) as well as minor amounts of two transcripts. Immunohistochemical analysis demonstrated that the Sclt1 protein was localized to the distal appendage of the photoreceptor basal body, indicating a ciliary protein.

3 cases plus a mouse model and functional evidence that the protein is a ciliary protein.
Created: 19 Jun 2019, 2 p.m.

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Please note two additional individuals reported in these two papers, one with a retinal phenotype, and one with a multi-system phenotype. Also, note animal model data supporting a multi-system ciliopathy.
Created: 7 Aug 2018, 4:40 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal


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

Alice Gardham (Genomics England)

Red List (low evidence)

Mutations only identified in one patient with features of a ciliopathy
Created: 25 Jan 2017, 9:32 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Ciliopathy like disorder



Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
  • Expert Review Green
  • Expert list
  • Radboud University Medical Center, Nijmegen
  • Expert Review Green
  • Oro-facio-digital syndrome type IX (Adly (2014) Hum Mutat 35,36)
  • No OMIM phenotype
Clinvar variants
Variants in SCLT1
Panels with this gene

History Filter Activity

8 May 2022, Gel status: 3

Added Tag

Eleanor Williams (Genomics England Curator)

Tag gene-checked tag was added to gene: SCLT1.

8 Jul 2019, Gel status: 3

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

Ivone Leong (Genomics England Curator)

gene: SCLT1 was added gene: SCLT1 was added to Ophthalmological ciliopathies. Sources: Radboud University Medical Center, Nijmegen,Expert list,Expert Review Green Mode of inheritance for gene: SCLT1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SCLT1 were set to 15797711 Phenotypes for gene: SCLT1 were set to Oro-facio-digital syndrome type IX (Adly (2014) Hum Mutat 35,36); No OMIM phenotype