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Intellectual disability

Gene: UPB1

Amber List (moderate evidence)

UPB1 (beta-ureidopropionase 1)
EnsemblGeneIds (GRCh38): ENSG00000100024
EnsemblGeneIds (GRCh37): ENSG00000100024
OMIM: 606673, Gene2Phenotype
UPB1 is in 3 panels

5 reviews

Ellen McDonagh (Genomics England Curator)

Comment when marking as ready: Updated based on the latest reviews displayed here from the Intellectual disability update Oct 2017 panel.
Created: 29 Nov 2017, 4:03 p.m.

Helen Brittain (Genomics England Curator)

Comment when marking as ready: Further evidence needed as to the phenotype with biallelic variants in this gene.
Created: 14 Nov 2017, 1:50 p.m.
Comment on list classification: Phenotypic variability reported is broad (normal through to significant ID). The significant ID is in consanguinous Turkish population, where there could be a second cause. One patient had normal development but congenital malformations of the GI/GU systems.

I am not clear that there is a single phenotype in the described cases and am concerned that the broad phenotypic spectrum may reflect other diagnoses or not support causation for UPB1. Further evidence is needed as to the phenotype before re-classification.
Created: 14 Nov 2017, 1:50 p.m.

Caroline Wright (Sanger)

Red List (low evidence)

Rebecca Foulger (Genomics England curator)

Green List (high evidence)

Beta-ureidopropionase deficiency phenotype has wide phenotypic variability and can range from ID and seizures to normal neurologic development. >3 unrelated cases (PMIDs:27553092, 25638458, 15385443, 22525402, 25445412) where DD/ID is reported alongside a homozygous UPB1 variant, supporting causation. Note that one disease-causing variant (c.977G>A) of beta-ureidopropionase deficiency, is highly prevalent in the Chinese population.
Created: 31 Oct 2017, 11:36 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Beta-ureidopropionase deficiency, 613161 (can include mental retardation; developmental delay)

Publications

Lu Raymond (university of cambridge )

Red List (low evidence)

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Beta-ureidopropionase deficiency, 613161 (can include mental retardation, developmental delay)
OMIM
606673
Clinvar variants
Variants in UPB1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

29 Sep 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to UPB1.

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

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

29 Nov 2017, Gel status: 2

Gene classified by Genomics England curator

Ellen McDonagh (Genomics England Curator)

This gene has been classified as Amber List (Moderate Evidence).

29 Nov 2017, Gel status: 1

Set mode of inheritance, Set publications

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene UPB1 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene UPB1 was set to ['27553092', ' 22525402', ' 25638458', ' 15385443', ' 25445412']

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: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

UPB1 was added to Intellectual disabilitypanel. Source: Expert Review Red

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

UPB1 was added to Intellectual disabilitypanel. Sources: Radboud University Medical Center, Nijmegen