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Hearing loss

Gene: SLC52A3

Green List (high evidence)

SLC52A3 (solute carrier family 52 member 3)
EnsemblGeneIds (GRCh38): ENSG00000101276
EnsemblGeneIds (GRCh37): ENSG00000101276
OMIM: 613350, Gene2Phenotype
SLC52A3 is in 17 panels

1 review

Eleanor Williams (Genomics England Curator)

Comment on list classification: More than 3 cases reported with variants in SLC52A3 in patients Brown-Vialetto-van Laere syndrome. Sensorineural deafness is a feature of this syndrome and often presents first.
Created: 11 May 2020, 11:34 a.m. | Last Modified: 11 May 2020, 11:34 a.m.
Panel Version: 2.11
Associated with Brown-Vialetto-Van Laere syndrome 1 #211530 (AR) in OMIM, a form of progressive bulbar palsy with sensorineural deafness.

Multiple cases of variants in this gene have been found in patients with Brown-Vialetto-Van Laere syndrome 1:

PMID: 20206331 Green et al 2010 - identified homozygous or compound heterozygous variants in C20orf54 (SLC52A3) in individuals with Brown-Vialetto-Van Laere syndrome from 7 families of European, Pakistani and Arabic ancestry. Nonsense and missense variants were found. Used homozgyosity mapping in the first family and then candidate gene analysis. They also report that 58 cases have been documented in the literature, with the age at onset ranged from infancy to early in the third decade, with the majority presenting in the second decade. Hearing loss preceded the onset of neurological signs in most cases. C20ORF54 is thought to play a role in riboflavin transport.

PMID: 20920669 Johnson et al 2010 - performed exome sequencing in patients with Brown-Vialetto-van Laere syndrome. In one patient in common with Green et al 2010 they found compound heterozygous variants in C20orf54 (patient 2008-410) rather than the homozygous variant Green et al reported (case 4). The results were confirmed by Sanger sequence and the parents were found to each have 1 heterozygous variant. They also report an additional family (DZ) from Eastern Turkey with a homozygous variant in affected individuals.
Created: 11 May 2020, 11:32 a.m. | Last Modified: 11 May 2020, 11:32 a.m.
Panel Version: 2.10
Gene suggested for panel by Dr Julia Rankin (Royal Devon and Exeter NHS Foundation Trust). Sensorineural deafness is the presenting feature in cases presenting after infancy with other neurology a year or 2 later – treatment with Riboflavin can be effective.
Sources: Expert list
Created: 11 May 2020, 10:02 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

History Filter Activity

12 May 2020, Gel status: 3

Added Tag

Eleanor Williams (Genomics England Curator)

Tag for-review tag was added to gene: SLC52A3.

11 May 2020, Gel status: 3

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for gene: SLC52A3 were changed from to Brown-Vialetto-Van Laere syndrome 1 #211530

11 May 2020, Gel status: 3

Set publications

Eleanor Williams (Genomics England Curator)

Publications for gene: SLC52A3 were set to

11 May 2020, Gel status: 3

Added Tag

Eleanor Williams (Genomics England Curator)

Tag treatable tag was added to gene: SLC52A3.

11 May 2020, Gel status: 3

Set mode of inheritance

Eleanor Williams (Genomics England Curator)

Mode of inheritance for gene: SLC52A3 was changed from Unknown to BIALLELIC, autosomal or pseudoautosomal

11 May 2020, Gel status: 3

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: slc52a3 has been classified as Green List (High Evidence).

11 May 2020, Gel status: 1

Created, Added New Source, Set mode of inheritance

Eleanor Williams (Genomics England Curator)

gene: SLC52A3 was added gene: SLC52A3 was added to Hearing loss. Sources: Expert list Mode of inheritance for gene: SLC52A3 was set to Unknown