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Intellectual disability

Gene: SLC22A5

Red List (low evidence)
SLC22A5 (solute carrier family 22 member 5)
EnsemblGeneIds (GRCh38): ENSG00000197375
EnsemblGeneIds (GRCh37): ENSG00000197375
OMIM: 603377, Gene2Phenotype
SLC22A5 is in 15 panels

7 reviews

Sarah Leigh (Genomics England Curator)

Comment on mode of inheritance: The mode of inheritance for SLC22A5 variants should be BIALLELIC, autosomal or pseudoautosomal. Although, heterozygous SLC22A5 variants have been seen in a few cases, these are detectable biochemically and are not associated with clear clinical presentation (PMID: 10545605; 11261427).
Created: 1 Aug 2023, 2:49 p.m. | Last Modified: 8 Aug 2023, 9:39 a.m.
Panel Version: 5.233
Created: 1 Aug 2023, 2:49 p.m.
Last Modified: 8 Aug 2023, 9:39 a.m.
Panel version: 5.227

Louise Daugherty (Genomics England Curator)

Red List (low evidence)

Comment on list classification: Changed from Green to Red until more info to support gene-disease association to ID. Rated red due to current information in the literature and external expert and internal clinical review, this is gene is not associated to ID phenotype
Created: 24 Jul 2018, 10:39 a.m.
This gene was rated as Green in 2016, probably due to being a confirmed DD feb 2016, however this phenotype is not relevant for the ID panel but is a relevant phenotype to the metabolic and neuromuscular panels, so will be downgraded to Red as suggested by external expert review comment and current internal clinical review.
Created: 24 Jul 2018, 10:37 a.m.
Past onto internal clinical team for further review and consideration to downgrade rating.
Created: 19 Jul 2018, 2:14 p.m.
Created: 19 Jul 2018, 2:14 p.m.

Panel version: 2.211

Zornitza Stark (Australian Genomics)

Red List (low evidence)

Not convinced this causes intellectual disability. It causes episodes of hypoglycaemia (I suppose if untreated could cause intellectual impairment but it's a stretch) and a muscle phenotype.
Created: 21 Jun 2018, 10:57 a.m.
Created: 21 Jun 2018, 10:57 a.m.

Panel version: 2.108

Caroline Wright (Sanger)

I don't know

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
SYSTEMIC PRIMARY CARNITINE DEFICIENCY

Publications

Created: 5 Nov 2017, 2:42 a.m.

Panel version: 0

BRIDGE consortium (NIHRBR-RD)

Green List (high evidence)

This is a pertinent gene from the NIHR BioResource - Rare Diseases Study (NIHRBR-RD) BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene is on the SPEED_NEURO_20170705 gene list. Evidences used for SPEED NEURO gene list: in_ddg2p_20141118_conf;in_ddg2p_20141118_conf;in_ddg2p_201507;in_ddg2p_201507_conf;in_ddg2p_2_4_2017;in_ddg2p_2_4_2017_conf . Main mutation mechanism : Loss of function
Created: 27 Jul 2017, 8:25 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; GEL_ID_green_20160217; neuro_20160418_strict; Loss of function. This is a pertinent gene from the BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene comes from the SPEED_NEURO_v3.0_20170404 gene list. The following experts from the BRIDGE consortium NIHRBR-RD contributed to this panel: - Professor F. Lucy Raymond, Cambridge Institute for Medical Research, University of Cambridge - Manju Kurian, Paediatric neurologist, Great Ormond Street Hosptial - Keren Carss, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Alba Sanchis-Juan, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Marie Erwood NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Louise Daugherty, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust
Created: 19 Jul 2017, 1:22 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

Created: 2 Aug 2017, 10:34 p.m.

Panel version: 1.354

Lu Raymond (university of cambridge )

I don't know

Created: 23 Feb 2016, 10:11 a.m.

Panel version: 0.306

Richard Scott (Genomics England Curator)

Comment on list classification: Confirmed DD gene
Created: 8 Feb 2016, 1 a.m.
Created: 8 Feb 2016, 1 a.m.

Panel version: 0.241

History Filter Activity

8 Aug 2023, Gel status: 1

Set mode of inheritance

Sarah Leigh (Genomics England Curator)

Mode of inheritance for gene: SLC22A5 was changed from BOTH monoallelic and biallelic, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal

1 Aug 2023, Gel status: 1

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: SLC22A5 were set to 9916797; 10425211; 15714519; 10480371; 9700603; 2235122; 20027113; 9634512; 11058897; 3974805; 10051646

1 Aug 2023, Gel status: 1

Set mode of inheritance

Sarah Leigh (Genomics England Curator)

Mode of inheritance for gene: SLC22A5 was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

1 Aug 2023, Gel status: 1

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: SLC22A5 were changed from Carnitine deficiency, systemic primary, 212140 to Carnitine deficiency, systemic primary, OMIM:212140; systemic primary carnitine deficiency disease, MONDO:0008919

24 Jul 2018, Gel status: 1

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: slc22a5 has been classified as Red List (Low Evidence).

19 Jul 2018, Gel status: 3

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for gene: SLC22A5 were set to Carnitine deficiency, systemic primary, 212140

12 Mar 2018, Gel status: 3

Panel promoted to version 2.0

Ellen McDonagh (Genomics England Curator)

12.03.2018: Due to major updates completed (Phase 1, 2 and 3), this panel was promoted to Version 2 in order to reflect the major updates since November 2017 which have resulted in reviews for 836 genes added by Genomics England Curators and the Clinical Team, 130 new Green genes added to the interpretation pipeline (from 751 to 881 Green genes), and the gene total has increased from 1879 to 1927.

8 Feb 2016, Gel status: 4

Gene classified by Genomics England curator

Richard Scott (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

8 Feb 2016, Gel status: 4

Gene classified by Genomics England curator

Richard Scott (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

13 Nov 2015, Gel status: 2

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 2

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 0

Created

Ellen McDonagh (Genomics England Curator)

SLC22A5 was created by ellenmcdonagh

13 Nov 2015, Gel status: 0

Added New Source

Ellen McDonagh (Genomics England Curator)

SLC22A5 was added to Intellectual disabilitypanel. Sources: Expert Review Amber