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Ataxia and cerebellar anomalies - narrow panel

Gene: SLC44A1

Green List (high evidence)
SLC44A1 (solute carrier family 44 member 1)
EnsemblGeneIds (GRCh38): ENSG00000070214
EnsemblGeneIds (GRCh37): ENSG00000070214
OMIM: 606105, Gene2Phenotype
SLC44A1 is in 3 panels

3 reviews

Eleanor Williams (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to green following NHS Genomic Medicine Service approval.
Created: 5 Feb 2023, 5:18 p.m. | Last Modified: 5 Feb 2023, 5:18 p.m.
Panel Version: 3.30
Created: 5 Feb 2023, 5:18 p.m.
Last Modified: 5 Feb 2023, 5:18 p.m.
Panel version: 3.30

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There is sufficient evidence to rate this gene Green at the next GMS panel update - at least 3 unrelated families reported with distinct SLC44A1 variants and this neurodegenerative disorder, including progressive cerebellar ataxia (PMID: 31855247)
Created: 1 Mar 2021, 12:48 p.m. | Last Modified: 1 Mar 2021, 12:56 p.m.
Panel Version: 2.49
Associated with relevant phenotype in OMIM (MIM# 618868), but not yet in Gene2Phenotype.

- PMID: 31855247 (2020) - Four individuals from three families with different homozygous frameshift variants (Asp517Metfs*19, Ser126Metfs*8, and Lys90Metfs*18) in SLC44A1. Clinical features in all affected individuals included progressive ataxia, tremor, cognitive decline, optic atrophy, dysarthria, as well as urinary and bowel incontinence. Brain MRI demonstrated cerebellar atrophy and leukoencephalopathy. Functional studies indicate choline transporter deficiency as the underlying pathological mechanism.
Created: 1 Mar 2021, 12:47 p.m. | Last Modified: 1 Mar 2021, 12:47 p.m.
Panel Version: 2.48

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline, OMIM:618868; Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline, MONDO:0030028

Publications

Created: 1 Mar 2021, 12:47 p.m.
Last Modified: 1 Mar 2021, 12:56 p.m.
Panel version: 2.48

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Childhood neurodegenerative condition. Four affected individuals from three families with homozygous frameshift variants reported. Functional evidence points to impaired choline transporter function yet unchanged membrane phosphatidylcholine content. Choline treatments may be beneficial. Suggest adding to optic neuropathy and possibly other panels, including severe paediatric disorders.
Sources: Literature
Created: 23 Apr 2020, 4:18 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
progressive ataxia; tremor; cognitive decline; dysphagia; optic atrophy; dysarthria

Publications

Created: 23 Apr 2020, 4:18 a.m.

Panel version: 2.6

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • NHS GMS
  • Expert Review Green
Phenotypes
  • Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline, OMIM:618868
  • Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline, MONDO:0030028
OMIM
606105
Clinvar variants
Variants in SLC44A1
Penetrance
None
Publications
Panels with this gene

History Filter Activity

5 Feb 2023, Gel status: 3

Removed Tag

Eleanor Williams (Genomics England Curator)

Tag Q2_21_rating was removed from gene: SLC44A1.

5 Feb 2023, Gel status: 3

Added New Source, Added New Source, Status Update

Eleanor Williams (Genomics England Curator)

Source Expert Review Green was added to SLC44A1. Source NHS GMS was added to SLC44A1. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

1 Mar 2021, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: slc44a1 has been classified as Amber List (Moderate Evidence).

1 Mar 2021, Gel status: 0

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag Q2_21_rating tag was added to gene: SLC44A1.

11 Feb 2021, Gel status: 0

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: SLC44A1 were changed from progressive ataxia; tremor; cognitive decline; dysphagia; optic atrophy; dysarthria to Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline, OMIM:618868; Neurodegeneration, childhood-onset, with ataxia, tremor, optic atrophy, and cognitive decline, MONDO:0030028

23 Apr 2020, Gel status: 0

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

Zornitza Stark (Australian Genomics)

gene: SLC44A1 was added gene: SLC44A1 was added to Ataxia and cerebellar anomalies - narrow panel. Sources: Literature Mode of inheritance for gene: SLC44A1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: SLC44A1 were set to 31855247 Phenotypes for gene: SLC44A1 were set to progressive ataxia; tremor; cognitive decline; dysphagia; optic atrophy; dysarthria Review for gene: SLC44A1 was set to GREEN