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Intellectual disability

Gene: SLC35A1

Green List (high evidence)

SLC35A1 (solute carrier family 35 member A1)
EnsemblGeneIds (GRCh38): ENSG00000164414
EnsemblGeneIds (GRCh37): ENSG00000164414
OMIM: 605634, Gene2Phenotype
SLC35A1 is in 10 panels

7 reviews

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Kauskot et al. (PMID: 30115659) reported recently on 2 affected sibs with "delayed psychomotor development" (the article focuses on the hematological phenotype). These individuals were homozygous for a missense variant (NM_006416.4:c.439T>C / p.Ser147Pro).

This gene is included in the DD panel of G2P, associated with CDG (disease confidence:probable).

It is also included in gene panels for ID offered by diagnostic laboratories (incl. Radboudumc).

As a result, SLC35A1 could possibly be considered for upgrade to green.
Created: 23 Dec 2018, 11:31 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Congenital disorder of glycosylation, type IIf (MIM 603585)

Publications

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

Louise Daugherty (Genomics England Curator)

I don't know

After external review comment on 21 Jun 2018, I have reviewed the publications again. However, the evidence remains the same, there are three unrelated families with congenital disorder of glycosylation,but only two of the three had intellectual disability the other case report is rather haematological (PMID:15576474). Gene Amber until there is an additional case to support gene-disease association for ID and rating of this gene to Green.
Created: 19 Jul 2018, 12:05 p.m.
added watchlist tag
Created: 16 Jul 2018, 9:48 a.m.
Comment on list classification: Red to Amber and added watchlist tag. Current evidence in the literature is that there are three families, however only two of the three had ID, the other case report is rather haematological. These are the same publications referenced by external expert review. Not enough evidence to make Green at present.
Created: 16 Jul 2018, 9:45 a.m.
Comment on publications: 23873973, 15576474, 28856833 there are now three families
Created: 16 Jul 2018, 9:42 a.m.

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Please note additional report by Ng et al, bringing the total up to 3 families.
Created: 21 Jun 2018, 11:23 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

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

Caroline Wright (Sanger)

I don't know

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
CONGENITAL DISORDERS OF GLYCOSYLATION

Publications

Rebecca Foulger (Genomics England curator)

Red List (low evidence)

Removed watchlist tag following promotion of SLC35A1 to Green.
Created: 18 Feb 2019, 2:55 p.m.
Comment on list classification: Updated rating from Amber to Green following clinical agreement from Helen Brittain: Green review by Konstantinos Varvagiannis, and currently 3 SLC35A1 cases with ID and seizures (PMIDs: 23873973, 28856833, 30115659).
Created: 18 Feb 2019, 2:53 p.m.
Summary of evidence: There are 2 existing cases of ID and SLC35A1 variants (a Turkish patient in PMID:23873973, and a German patient in PMID:28856833). There is a further paper linking SLC35A1 to a glycosylation disorder (PMID:15576474) but without an ID or epilepsy phenotype. As noted by Konstantinos Varvagiannis, a 2018 paper (PMID:30115659) now reports 2 siblings with a haematological phenotype and a homozygous p.Ser147Pro variant in SLC35A1. The authors say that the siblings' phenotypes included delayed psychomotor development, epilepsy, ataxia, microcephaly, choreiform movements, and macrothrombocytopenia.
Created: 18 Feb 2019, 2:43 p.m.
Only 1 family reporting ID in a patient with SLC35A1 variant (PMID:23873973, 2013). Phenotypes taken from PMID:23873973. Probable DD-G2P gene for 'congenital disorder of glycosylation'.
Created: 31 Oct 2017, 9:24 a.m.

Phenotypes
Congenital disorder of glycosylation, type Iif, 603585; intellectual disability, ataxia, seizures, bleeding diathesis and proteinuria

Publications

Lu Raymond (university of cambridge )

I don't know

Richard Scott (Genomics England Curator)

Comment on list classification: SIngle family reported to date
Created: 8 Feb 2016, 1:06 a.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
Phenotypes
  • Congenital disorder of glycosylation, type IIf, 603585
  • intellectual disability, ataxia, seizures, bleeding diathesis and proteinuria
OMIM
605634
Clinvar variants
Variants in SLC35A1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

18 Feb 2019, Gel status: 3

Removed Tag

Rebecca Foulger (Genomics England curator)

Tag watchlist was removed from gene: SLC35A1.

18 Feb 2019, Gel status: 3

Entity classified by Genomics England curator

Rebecca Foulger (Genomics England curator)

Gene: slc35a1 has been classified as Green List (High Evidence).

18 Feb 2019, Gel status: 2

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: SLC35A1 were set to 23873973, 15576474, 28856833; 30115659

18 Feb 2019, Gel status: 2

Set Phenotypes

Rebecca Foulger (Genomics England curator)

Phenotypes for gene: SLC35A1 were changed from Congenital disorder of glycosylation, type Iif, 603585; intellectual disability, ataxia, seizures, bleeding diathesis and proteinuria to Congenital disorder of glycosylation, type IIf, 603585; intellectual disability, ataxia, seizures, bleeding diathesis and proteinuria

18 Feb 2019, Gel status: 2

Set publications

Rebecca Foulger (Genomics England curator)

Publications for gene: SLC35A1 were set to 23873973, 15576474, 28856833

29 Sep 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to SLC35A1.

16 Jul 2018, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: slc35a1 has been classified as Amber List (Moderate Evidence).

16 Jul 2018, Gel status: 1

Set publications

Louise Daugherty (Genomics England Curator)

Publications for gene: SLC35A1 were set to 23873973, 15576474, 28856833

12 Mar 2018, Gel status: 1

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.

29 Nov 2017, Gel status: 1

Set publications

Ellen McDonagh (Genomics England Curator)

Publications for gene SLC35A1 was set to ['23873973']

8 Feb 2016, Gel status: 1

Gene classified by Genomics England curator

Richard Scott (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

8 Feb 2016, Gel status: 1

Gene classified by Genomics England curator

Richard Scott (Genomics England Curator)

This gene has been classified as Red List (Low 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)

SLC35A1 was created by ellenmcdonagh

13 Nov 2015, Gel status: 0

Added New Source

Ellen McDonagh (Genomics England Curator)

SLC35A1 was added to Intellectual disabilitypanel. Sources: Expert Review Amber