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Intellectual disability

Gene: AGPS

Green List (high evidence)

AGPS (alkylglycerone phosphate synthase)
EnsemblGeneIds (GRCh38): ENSG00000018510
EnsemblGeneIds (GRCh37): ENSG00000018510
OMIM: 603051, Gene2Phenotype
AGPS is in 15 panels

6 reviews

Arina Puzriakova (Genomics England Curator)

I don't know

Comment on list classification: Though some relevant phenotypic features have been reported, the relationship with ID is not clear from literature. Patients are more likely to be recognised in context of the skeletal phenotype.

Therefore, suggesting a rating downgrade from Green to Amber at the next major review.
Created: 23 Sep 2020, 2:04 p.m. | Last Modified: 23 Sep 2020, 2:04 p.m.
Panel Version: 3.333
To date, five unrelated individuals described with rhizomelic chondrodysplasia punctata due to variants in AGPS, but information regarding cognitive development only reported in three:

- PMID: 21990100 (2012) - Patient 6 (age 4) had severe mental retardation, no speech and smiled to parent's voice; however, authors noted high consanguinity and therefore could not define conclusive genotype-phenotype correlations.
Patient 7 (age 7) smiled responsively at 6 months, and at the time of last examination at 27 months, had no head support, could not roll over or hold objects, and had no speech. No information regarding her subsequent development was provided.

- PMID: 11152660 (2001) - Developmental delay, among other features, was noted in Patient 4.
Created: 23 Sep 2020, 1:56 p.m. | Last Modified: 23 Sep 2020, 1:56 p.m.
Panel Version: 3.332

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Rhizomelic chondrodysplasia punctata, type 3, 600121

Publications

Zornitza Stark (Australian Genomics)

Red List (low evidence)

Variants in this gene cause a skeletal dysplasia, intellect typically normal.
Created: 27 Jan 2020, 6:01 a.m. | Last Modified: 27 Jan 2020, 6:01 a.m.
Panel Version: 3.0

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Rhizomelic chondrodysplasia punctata, type 3, MIM#600121

Caroline Wright (Sanger)

I don't know

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
RHIZOMELIC CHONDRODYSPLASIA PUNCTATA TYPE 3 (RCDP3)

Publications

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;in_UKGTN_v12 . Main mutation mechanism : Uncertain
Created: 27 Jul 2017, 5:01 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; UKGTN_v12; GEL_ID_green_20160217; neuro_20160418_strict; Uncertain. 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, 11:56 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

Lu Raymond (university of cambridge )

I don't know

Richard Scott (Genomics England Curator)

Comment on list classification: Confirmed ID gene.
Created: 29 Jan 2016, 5:04 p.m.

History Filter Activity

23 Sep 2020, Gel status: 3

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: AGPS were changed from RHIZOMELIC CHONDRODYSPLASIA PUNCTATA TYPE 3 (RCDP3) to Rhizomelic chondrodysplasia punctata, type 3, 600121

23 Sep 2020, Gel status: 3

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: AGPS were set to 7807941; 11152660

23 Sep 2020, Gel status: 3

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

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

23 Sep 2020, Gel status: 3

Added Tag

Arina Puzriakova (Genomics England Curator)

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

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.

29 Jan 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).

29 Jan 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)

AGPS was created by ellenmcdonagh

13 Nov 2015, Gel status: 0

Added New Source

Ellen McDonagh (Genomics England Curator)

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