Genes in panel
STRs in panel
Prev Next

Fetal anomalies

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

Arina Puzriakova (Genomics England Curator)

The rating of this gene has been updated following NHS Genomic Medicine Service approval.
Created: 3 Mar 2022, 11:19 a.m. | Last Modified: 3 Mar 2022, 11:19 a.m.
Panel Version: 1.836

Ivone Leong (Genomics England Curator)

Comment on list classification: New gene added by Rhiannon Mellis (Great Ormond Street Hospital).

Following curation and clinical review at GOSH it has been agreed that the associated phenotype is fetally-relevant. Therefore this gene should be promoted to Green at the next GMS panel update (added 'for-review' tag).
Created: 1 Feb 2021, 4:26 p.m. | Last Modified: 1 Feb 2021, 4:26 p.m.
Panel Version: 1.529

Rhiannon Mellis (Great Ormond Street Hospital)

Green List (high evidence)

This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in October 2020. This gene has a Green evidence rating on at least one other related PanelApp panel. Clinical review and curation was performed by Lyn Chitty, Rhiannon Mellis, and Richard Scott. Outcome of review: Confirmed that phenotype is fetally-relevant: add to the Fetal anomalies panel as a Green gene.

Green on related panel(s): Rare multisystem ciliopathy Super panel

Copied from rare multisystem ciliopathies panel:
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.
Sources: Literature
Created: 28 Jan 2021, 3:29 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

No OMIM phenotype; Oro-facio-digital syndrome type IX; Senior-Løken Syndrome


Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
  • Expert Review Green
  • No OMIM phenotype
  • Oro-facio-digital syndrome type IX
  • Senior-Løken Syndrome
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.

3 Mar 2022, Gel status: 3

Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag for-review was removed from gene: SCLT1.

3 Mar 2022, Gel status: 3

Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source Expert Review Green was added to SCLT1. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

4 Feb 2021, Gel status: 2

Added Tag

Ivone Leong (Genomics England Curator)

Tag for-review tag was added to gene: SCLT1.

1 Feb 2021, Gel status: 2

Entity classified by Genomics England curator

Ivone Leong (Genomics England Curator)

Gene: sclt1 has been classified as Amber List (Moderate Evidence).

1 Feb 2021, Gel status: 0

Set publications

Ivone Leong (Genomics England Curator)

Publications for gene: SCLT1 were set to

28 Jan 2021, Gel status: 0

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

Rhiannon Mellis (Great Ormond Street Hospital)

gene: SCLT1 was added gene: SCLT1 was added to Fetal anomalies. Sources: Literature Mode of inheritance for gene: SCLT1 was set to BIALLELIC, autosomal or pseudoautosomal Phenotypes for gene: SCLT1 were set to No OMIM phenotype; Oro-facio-digital syndrome type IX; Senior-Løken Syndrome Review for gene: SCLT1 was set to GREEN