1. Panels
  2. Intellectual disability
  3. STT3A
Genes in panel
Prev Next
Regions in panel
Prev Next

Intellectual disability

Gene: STT3A

Green List (high evidence)
STT3A (STT3A, catalytic subunit of the oligosaccharyltransferase complex)
EnsemblGeneIds (GRCh38): ENSG00000134910
EnsemblGeneIds (GRCh37): ENSG00000134910
OMIM: 601134, Gene2Phenotype
STT3A is in 7 panels

7 reviews

Tracy Lester (Genetics laboratory, Oxford UK)

Green List (high evidence)

This gene should be changed to both monoallelic and biallelic inheritance following publication of a new paper showing missense variants in the active site cause an AD form
Created: 3 Aug 2022, 11:43 a.m. | Last Modified: 3 Aug 2022, 11:43 a.m.
Panel Version: 3.1648

Mode of inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal

Phenotypes
short stature; skeletal defects; intellectual disability; speech delay

Publications

Created: 3 Aug 2022, 11:43 a.m.
Last Modified: 3 Aug 2022, 11:43 a.m.
Panel version: 3.1648

Sarah Leigh (Genomics England Curator)

The rating of this gene has been updated following NHS Genomic Medicine Service approval.
Created: 9 Mar 2022, 3:40 p.m. | Last Modified: 9 Mar 2022, 3:40 p.m.
Panel Version: 3.1510
Created: 9 Mar 2022, 3:40 p.m.
Last Modified: 9 Mar 2022, 3:40 p.m.
Panel version: 3.1510

Arina Puzriakova (Genomics England Curator)

The mode of inheritance of this gene has been updated to 'BOTH monoallelic and biallelic, autosomal or pseudoautosomal' following NHS Genomic Medicine Service approval.
Created: 30 Jan 2023, 5:50 p.m. | Last Modified: 30 Jan 2023, 5:50 p.m.
Panel Version: 4.53
Comment on mode of inheritance: Should be updated from 'biallelic' to 'both mono- and biallelic'. Congenital disorder of glycosylation due to monoallelic variants in STT3A has been identified in at least 16 patients from 9 families (PMID: 34653363). Phenotypes included mild-moderate ID/DD in 10/16 subjects.
Created: 19 Jul 2022, 10:03 a.m. | Last Modified: 19 Jul 2022, 10:03 a.m.
Panel Version: 3.1632
Comment on list classification: There is enough evidence to support a gene-disease association, and so STT3A should be promoted from Amber to Green at the next GMS panel update (added 'for-review' tag).

ID/DD reported in all cases (at least 7 individuals from 3 unrelated families, with 2 different homozygous variants in STT3A)
Created: 15 Oct 2020, 3:14 p.m. | Last Modified: 15 Oct 2020, 3:14 p.m.
Panel Version: 3.451
Removed 'watchlist' tag as now the number of unrelated cases reaches threshold for a Green rating on this panel
Created: 15 Oct 2020, 3:01 p.m. | Last Modified: 15 Oct 2020, 3:01 p.m.
Panel Version: 3.450
Created: 15 Oct 2020, 3:01 p.m.
Last Modified: 15 Oct 2020, 3:01 p.m.
Panel version: 4.53

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Three unrelated families reported now, DD/ID is part of the phenotype.
Created: 29 Feb 2020, 3:26 a.m. | Last Modified: 29 Feb 2020, 3:26 a.m.
Panel Version: 3.3

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Congenital disorder of glycosylation, type Iw; OMIM #615596

Publications

Created: 29 Feb 2020, 3:26 a.m.
Last Modified: 29 Feb 2020, 3:26 a.m.
Panel version: 3.3

Caroline Wright (Sanger)

Red List (low evidence)

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
CONGENITAL DISORDER OF GLYCOSYLATION, TYPE IW

Publications

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

Panel version: 0

Rebecca Foulger (Genomics England curator)

PMID:28424003 (Ghosh et al., 2017) describe 5 related individuals with a likely pathogenic variant in STT3A, 2 of whom also had variants in TUSC3. Common phenotypic features in all symptomatic individuals include developmental delay, intellectual disability, with absent speech and seizures.
Created: 25 Sep 2017, 9:39 a.m.
Created: 25 Sep 2017, 9:39 a.m.

Panel version: 1.424

Lu Raymond (university of cambridge )

Red List (low evidence)

Created: 23 Feb 2016, 11:08 a.m.

Panel version: 0.306

Details

Mode of Inheritance
BOTH monoallelic and biallelic, autosomal or pseudoautosomal
Sources
  • NHS GMS
  • Expert Review Green
Phenotypes
  • Congenital disorder of glycosylation, type Iw, autosomal dominant, OMIM:619714
  • Congenital disorder of glycosylation, type Iw, autosomal recessive, OMIM:615596
OMIM
601134
Clinvar variants
Variants in STT3A
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

30 Jan 2023, Gel status: 3

Removed Tag, Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag Q3_22_MOI was removed from gene: STT3A. Tag Q3_22_NHS_review was removed from gene: STT3A.

30 Jan 2023, Gel status: 3

Added New Source, Set mode of inheritance

Arina Puzriakova (Genomics England Curator)

Source NHS GMS was added to STT3A. Mode of inheritance for gene STT3A was changed from BIALLELIC, autosomal or pseudoautosomal to BOTH monoallelic and biallelic, autosomal or pseudoautosomal

10 Aug 2022, Gel status: 3

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag Q3_22_NHS_review tag was added to gene: STT3A.

19 Jul 2022, Gel status: 3

Set mode of inheritance

Arina Puzriakova (Genomics England Curator)

Mode of inheritance for gene: STT3A was changed from BIALLELIC, autosomal or pseudoautosomal to BIALLELIC, autosomal or pseudoautosomal

19 Jul 2022, Gel status: 3

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag Q3_22_MOI tag was added to gene: STT3A.

19 Jul 2022, Gel status: 3

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: STT3A were changed from Congenital disorder of glycosylation, type Iw, 615596 to Congenital disorder of glycosylation, type Iw, autosomal dominant, OMIM:619714; Congenital disorder of glycosylation, type Iw, autosomal recessive, OMIM:615596

19 Jul 2022, Gel status: 3

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: STT3A were set to 23842455; 28424003; 30701557

9 Mar 2022, Gel status: 3

Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag for-review was removed from gene: STT3A.

9 Mar 2022, Gel status: 3

Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source Expert Review Green was added to STT3A. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

15 Oct 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: stt3a has been classified as Amber List (Moderate Evidence).

15 Oct 2020, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: STT3A were changed from ?Congenital disorder of glycosylation, type Iw, 615596; developmental delay; intellectual disability to Congenital disorder of glycosylation, type Iw, 615596

15 Oct 2020, Gel status: 2

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: STT3A were set to 28424003; 23842455

15 Oct 2020, Gel status: 2

Removed Tag, Added Tag

Arina Puzriakova (Genomics England Curator)

Tag watchlist was removed from gene: STT3A. Tag for-review tag was added to gene: STT3A.

12 Mar 2018, Gel status: 2

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: 2

Added New Source, Set publications

Ellen McDonagh (Genomics England Curator)

Expert Review Amber was added to STT3A. Panel: Intellectual disability Publications for gene STT3A was set to ['28424003', ' 23842455']

13 Nov 2015, Gel status: 1

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)

STT3A was created by ellenmcdonagh

13 Nov 2015, Gel status: 0

Added New Source

Ellen McDonagh (Genomics England Curator)

STT3A was added to Intellectual disabilitypanel. Sources: Expert Review Red