1. Panels
  2. Intellectual disability
  3. BAP1
Genes in panel
Prev Next
Regions in panel
Prev Next

Intellectual disability

Gene: BAP1

Green List (high evidence)
BAP1 (BRCA1 associated protein 1)
EnsemblGeneIds (GRCh38): ENSG00000163930
EnsemblGeneIds (GRCh37): ENSG00000163930
OMIM: 603089, Gene2Phenotype
BAP1 is in 11 panels

3 reviews

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to Green following NHS Genomic Medicine Service approval.
Created: 11 Oct 2023, 9:34 a.m. | Last Modified: 11 Oct 2023, 9:34 a.m.
Panel Version: 5.286

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Created: 11 Oct 2023, 9:34 a.m.
Last Modified: 11 Oct 2023, 9:34 a.m.
Panel version: 5.286

Mafalda Gomes (Genomics England Curator)

Green List (high evidence)

Kry et al. (2022) performed trio-WES in a cohort with a rare syndromic NDD and identified de novo missense variants in 11 unrelated individuals. All individuals had DD or ID characterised notably by speech (11/11) and motor delay (6/11). Additional common characteristics were hypotonia, (7/11), seizures (6/11), and abnormal behaviour (8/10), including ASD, ADHD, and hypersensitivity. Almost all individuals showed dysmorphic facial features (10/11), and more than half (6/11) had skeletal malformations involving the hands, feet, or spine. Functional analysis showed that most of the variants cannot rescue the consequences of BAP1 inactivation, suggesting a loss-of-function mechanism. In T cells isolated from two affected children, H2A deubiquitination was impaired. In summary, this gene should be promoted to GREEN in this panel, with autosomal dominant mode of inheritance.
Created: 20 Jan 2023, 11:16 a.m. | Last Modified: 20 Jan 2023, 11:16 a.m.
Panel Version: 4.46
Küry et al. (2022) performed trio-WES in a cohort with a rare syndromic NDD and identified de novo missense variants in 11 unrelated individuals. All individuals had DD or ID characterised notably by speech (11/11) and motor delay (6/11). Additional common characteristics were hypotonia, (7/11), seizures (6/11), and abnormal behaviour (8/10), including ASD, ADHD, and hypersensitivity. Almost all individuals showed dysmorphic facial features (10/11), and more than half (6/11) had skeletal malformations involving the hands, feet, or spine. Functional analysis showed that most of the variants cannot rescue the consequences of BAP1 inactivation, suggesting a loss-of-function mechanism. In T cells isolated from two affected children, H2A deubiquitination was impaired. In summary, this gene should be promoted to GREEN in this panel, with autosomal dominant mode of inheritance.
Created: 12 Dec 2022, 3:57 p.m. | Last Modified: 12 Dec 2022, 3:57 p.m.
Panel Version: 4.10

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
Kury-Isidor syndrome, OMIM:619762

Publications

Created: 12 Dec 2022, 3:57 p.m.
Last Modified: 12 Dec 2022, 3:57 p.m.
Panel version: 4.46

Rachel Challis (Cambridge University Hospitals NHS Foundation Trust)

Green List (high evidence)

11 de novo BAP1 missense variants identified predominantly in UCH domain. Functional analysis showed that most of the variants cannot rescue the consequences of BAP1 inactivation, suggesting a loss-of-function mechanism. Analysis of blood from affected patients demonstrated impaired H2A deubiquitination compared to controls.
Sources: Literature
Created: 18 Oct 2022, 3:41 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Intellectual disability; short stature; autism spectrum disorder

Publications

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

Created: 18 Oct 2022, 3:41 p.m.

Panel version: 3.1746

History Filter Activity

11 Oct 2023, Gel status: 3

Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag Q1_23_promote_green was removed from gene: BAP1.

11 Oct 2023, Gel status: 3

Added New Source, Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source NHS GMS was added to BAP1. Source Expert Review Green was added to BAP1. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

20 Jan 2023, Gel status: 2

Set Phenotypes

Mafalda Gomes (Genomics England Curator)

Phenotypes for gene: BAP1 were changed from Kury-Isidor syndrome, OMIM:619762 to Kury-Isidor syndrome, OMIM:619762

20 Jan 2023, Gel status: 2

Set Phenotypes

Mafalda Gomes (Genomics England Curator)

Phenotypes for gene: BAP1 were changed from Kury-Isidor syndrome, OMIM:619762 to Kury-Isidor syndrome, OMIM:619762

20 Jan 2023, Gel status: 2

Set Phenotypes

Mafalda Gomes (Genomics England Curator)

Phenotypes for gene: BAP1 were changed from Kury-Isidor syndrome, OMIM:619762 to Kury-Isidor syndrome, OMIM:619762

20 Jan 2023, Gel status: 2

Set Phenotypes

Mafalda Gomes (Genomics England Curator)

Phenotypes for gene: BAP1 were changed from Kury-Isidor syndrome, OMIM:619762 to Kury-Isidor syndrome, OMIM:619762

20 Jan 2023, Gel status: 2

Set Phenotypes

Mafalda Gomes (Genomics England Curator)

Phenotypes for gene: BAP1 were changed from Kury-Isidor syndrome, OMIM:619762 to Kury-Isidor syndrome, OMIM:619762

20 Jan 2023, Gel status: 2

Set Phenotypes

Mafalda Gomes (Genomics England Curator)

Phenotypes for gene: BAP1 were changed from Kury-Isidor syndrome, OMIM:619762 to Kury-Isidor syndrome, OMIM:619762

20 Jan 2023, Gel status: 2

Set Phenotypes

Mafalda Gomes (Genomics England Curator)

Phenotypes for gene: BAP1 were changed from Kury-Isidor syndrome, OMIM:619762 to Kury-Isidor syndrome, OMIM:619762

20 Jan 2023, Gel status: 2

Set Phenotypes

Mafalda Gomes (Genomics England Curator)

Phenotypes for gene: BAP1 were changed from Intellectual disability; short stature; autism spectrum disorder to Kury-Isidor syndrome, OMIM:619762

20 Jan 2023, Gel status: 2

Added Tag

Mafalda Gomes (Genomics England Curator)

Tag Q1_23_promote_green tag was added to gene: BAP1.

20 Jan 2023, Gel status: 2

Added New Source, Set mode of inheritance, Status Update

Mafalda Gomes (Genomics England Curator)

Source Expert Review Amber was added to BAP1. Mode of inheritance for gene BAP1 was changed from MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Rating Changed from No List (delete) to Amber List (moderate evidence)

18 Oct 2022, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes

Rachel Challis (Cambridge University Hospitals NHS Foundation Trust)

gene: BAP1 was added gene: BAP1 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: BAP1 was set to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Publications for gene: BAP1 were set to 35051358 Phenotypes for gene: BAP1 were set to Intellectual disability; short stature; autism spectrum disorder Review for gene: BAP1 was set to GREEN gene: BAP1 was marked as current diagnostic