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Intellectual disability

Gene: TBC1D2B

Green List (high evidence)
TBC1D2B (TBC1 domain family member 2B)
EnsemblGeneIds (GRCh38): ENSG00000167202
EnsemblGeneIds (GRCh37): ENSG00000167202
TBC1D2B is in 3 panels

4 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to green following NHS Genomic Medicine Service approval.
Created: 26 Sep 2024, 2:57 p.m. | Last Modified: 26 Sep 2024, 2:57 p.m.
Panel Version: 7.41

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Created: 26 Sep 2024, 2:57 p.m.
Last Modified: 26 Sep 2024, 2:57 p.m.
Panel version: 7.41

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review.
Created: 11 Apr 2024, 11:24 a.m. | Last Modified: 11 Apr 2024, 11:24 a.m.
Panel Version: 5.519
TBC1D2B variants have been associated with Neurodevelopmental disorder with seizures and gingival overgrowth (OMIM:619323) and as definitive Gen2Phen gene for TBC1D2B-related neurodevelopmental disorder. So far, 11 TBC1D2B variants have been reported in 8 unrelated families. Global developmental delay (HP:0001263) was reported in 5/8 families, mental deterioration (HP:0001268) was seen in 5/8 families and seizures (HP:0001250) were reported in 8/8 families (four of these were controlled with medication)(PMID: 38374468).
Created: 11 Apr 2024, 11:23 a.m. | Last Modified: 11 Apr 2024, 11:23 a.m.
Panel Version: 5.518
Created: 11 Apr 2024, 11:23 a.m.
Last Modified: 11 Apr 2024, 11:23 a.m.
Panel version: 5.518

Arina Puzriakova (Genomics England Curator)

Comment on list classification: New gene added by Konstantinos Varvagiannis. Updating rating from Grey to Amber based on one publication (PMID:32623794). Manifestation of ID is variable amongst cases, but is mostly within the mild range. Additional cases would help determine the relevance of ID to the overall disease presentation (added 'watchlist' tag)
Created: 16 Nov 2020, 2:28 p.m. | Last Modified: 16 Nov 2020, 2:28 p.m.
Panel Version: 3.536
Created: 16 Nov 2020, 2:28 p.m.
Last Modified: 16 Nov 2020, 2:28 p.m.
Panel version: 3.536

Konstantinos Varvagiannis (Other)

I don't know

Harms et al (2020 - PMID: 32623794) report on 3 unrelated individuals with biallelic pLoF TBC1D2B variants.

Features included cognitive impairment (mild ID in one case, regression at the age of 12y in another, hypotonia and delayed milestones in a third aged 8m), seizures (3/3 - variable age of onset) and/or gingival overgrowth (2/3 - prior to initiation of AEDs). Other findings included behavioral abnormalities, mandibular anomalies, abnormal brain imaging and ophthalmologic or (rarely) audiometric evaluations.

All were born to non-consanguineous couples and additional investigations were performed in some.

Variants were identified by WES or trio WGS, with Sanger confirmation/compatible segregation analyses.

In line with the pLoF variants, mRNA studies in fibroblasts from 2 unrelated affected individuals demonstrated significantly reduced (~80-90%) TBC1C2D mRNA levels compared to controls, restored following cycloheximide treatment. Protein was absent in patient fibroblasts.

TBC-domain containing GTPase activating proteins are known as key regulators of RAB GTPase activity. TBC1D2B was shown to colocalize with RAB5-positive endocytic vesicles. CRISPR/Cas9-mediated ko of TBC1D2B in HeLa cells suggested a role in EGF receptor endocytosis and decreased cell viability of TBC1D2B-deficient HeLa cells upon serum deprivation.

Genes encoding other TBC domain-containg GTPase-activating proteins, e.g. TBC1D7 and TBC1D20, TBC1D24 are associated with recessive neurodevelopmental disorders (with ID and/or seizures) and the pathophysiological defect in TBC1D2B-related disorder (deficit in vesicle trafficking and/or cell survival) is proposed to be similar to that of TBC1D24.

Overall this gene can be considered for inclusion with amber/green rating in the ID panel and green in epilepsy panel.
Sources: Literature
Created: 13 Jul 2020, 7:04 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Global developmental delay; Intellectual disability; Seizures; Gingival overgrowth; Behavioral abnormality; Abnormality of the mandible; Abnormality of brain morphology; Abnormality of the eye; Hearing abnormality

Publications

Created: 13 Jul 2020, 7:04 p.m.

Panel version: 3.170

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
Phenotypes
  • Neurodevelopmental disorder with seizures and gingival overgrowth, OMIM:619323
  • neurodevelopmental disorder with seizures and gingival overgrowth, MONDO:0859148
Tags
gene-checked
Clinvar variants
Variants in TBC1D2B
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

26 Sep 2024, Gel status: 3

Removed Tag, Removed Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q2_24_promote_green was removed from gene: TBC1D2B. Tag Q2_24_NHS_review was removed from gene: TBC1D2B.

26 Sep 2024, Gel status: 3

Added New Source, Added New Source, Status Update

Achchuthan Shanmugasundram (Genomics England Curator)

Source NHS GMS was added to TBC1D2B. Source Expert Review Green was added to TBC1D2B. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

11 Apr 2024, Gel status: 2

Removed Tag, Added Tag, Added Tag

Sarah Leigh (Genomics England Curator)

Tag watchlist was removed from gene: TBC1D2B. Tag Q2_24_promote_green tag was added to gene: TBC1D2B. Tag Q2_24_NHS_review tag was added to gene: TBC1D2B.

11 Apr 2024, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: tbc1d2b has been classified as Amber List (Moderate Evidence).

11 Apr 2024, Gel status: 2

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: TBC1D2B were set to 32623794

11 Apr 2024, Gel status: 2

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: TBC1D2B were changed from Global developmental delay; Intellectual disability; Seizures; Gingival overgrowth; Behavioral abnormality; Abnormality of the mandible; Abnormality of brain morphology; Abnormality of the eye; Hearing abnormality to Neurodevelopmental disorder with seizures and gingival overgrowth, OMIM:619323; neurodevelopmental disorder with seizures and gingival overgrowth, MONDO:0859148

8 May 2022, Gel status: 2

Added Tag

Eleanor Williams (Genomics England Curator)

Tag gene-checked tag was added to gene: TBC1D2B.

16 Nov 2020, Gel status: 2

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag watchlist tag was added to gene: TBC1D2B.

16 Nov 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: tbc1d2b has been classified as Amber List (Moderate Evidence).

13 Jul 2020, Gel status: 0

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

Konstantinos Varvagiannis (Other)

gene: TBC1D2B was added gene: TBC1D2B was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: TBC1D2B was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TBC1D2B were set to 32623794 Phenotypes for gene: TBC1D2B were set to Global developmental delay; Intellectual disability; Seizures; Gingival overgrowth; Behavioral abnormality; Abnormality of the mandible; Abnormality of brain morphology; Abnormality of the eye; Hearing abnormality Penetrance for gene: TBC1D2B were set to Complete Review for gene: TBC1D2B was set to AMBER