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Intellectual disability
Gene: AGPS

AGPS (alkylglycerone phosphate synthase)
EnsemblGeneIds (GRCh38): ENSG00000018510
EnsemblGeneIds (GRCh37): ENSG00000018510
OMIM: 603051, Gene2Phenotype
AGPS is in 14 panels

7 reviews

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)

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

Created: 23 Sep 2020, 1:56 p.m.
Last Modified: 23 Sep 2020, 1:56 p.m.
Panel version: 3.332

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

Created: 27 Jan 2020, 6:01 a.m.
Last Modified: 27 Jan 2020, 6:01 a.m.
Panel version: 3.0

Caroline Wright (Sanger)

I don't know

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
RHIZOMELIC CHONDRODYSPLASIA PUNCTATA TYPE 3 (RCDP3)

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;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

25529582
Version 12 ukgtn.nhs.uk

Created: 2 Aug 2017, 2:01 p.m.

Panel version: 1.354

Lu Raymond (university of cambridge )

I don't know

Created: 23 Feb 2016, 10:01 a.m.

Panel version: 0.306

Richard Scott (Genomics England Curator)

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

Created: 29 Jan 2016, 5:04 p.m.

Panel version: 0.25

Details

Mode of Inheritance

BIALLELIC, autosomal or pseudoautosomal

Sources

Expert Review Amber

Phenotypes

Rhizomelic chondrodysplasia punctata, type 3, 600121

OMIM

603051

Clinvar variants

Variants in AGPS

Penetrance

Complete

Publications

Panels with this gene