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Intellectual disability

Gene: TUBGCP2

Amber List (moderate evidence)
TUBGCP2 (tubulin gamma complex associated protein 2)
EnsemblGeneIds (GRCh38): ENSG00000130640
EnsemblGeneIds (GRCh37): ENSG00000130640
TUBGCP2 is in 6 panels

2 reviews

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

PMID: 40017707 (2025) - reports a 6-year-old girl with lissencephaly caused by compound heterozygous variants in TUBGCP2 (two paternal missense variants: c.178 C>T, c.538T>C and one maternal exon variant: 2–14 deletion). The patient presented with microcephaly, developmental delay, intellectual disability, and seizures. A literature review of 8 patients (including the reported case) with TUBGCP2 variants showed that all exhibited lissencephaly, microcephaly and developmental delay, with most having intellectual disability, seizures, and dysmorphic facial features.

This publication supports inclusion of the TUBGCP2 gene on the intellectual disability panel at the next GMS panel update.
Created: 17 Mar 2025, 5:03 p.m. | Last Modified: 17 Mar 2025, 5:03 p.m.
Panel Version: 8.152
Comment on publications: PMID: 40017707 was identified by the Genomics England Applied Machine Learning (ML) team in a Biocuration-ML project for identifying new gene-disease associations using Natural Language Processing (NLP) and Generative AI techniques.
Created: 17 Mar 2025, 4:58 p.m. | Last Modified: 17 Mar 2025, 4:58 p.m.
Panel Version: 8.152
Comment on list classification: Although the phenotype is relevant for this panel, additional cases would help determine the aetiology of the ID presentation. This gene has been added to other panels (Malformations of cortical development/Epilepsy/Microcephaly), in view of which these patients are more likely to be recognised.

Rating Amber, awaiting further publications (added to watchlist).
Created: 27 Aug 2020, 10:34 a.m. | Last Modified: 27 Aug 2020, 10:46 a.m.
Panel Version: 3.268
Associated with phenotype in OMIM, and a probable gene for Microcephaly and Lissencephaly Spectrum Disorders in G2P.

PMID: 31630790 (2019) - Five patients from four families with biallelic variants in the TUBGCP2 gene. Affected individuals shared phenotypic features that included progressive microcephaly (4/4), developmental delay (5/5, mild-severe), seizures (4/5). All patients exhibited lissencephaly-spectrum phenotypes with varying degrees of cortical malformations on brain imaging including pachygyria and subcortical band heterotopia.

Difficult to determine whether DD is an independent feature. In the two most severely delayed patients, seizures were an early feature and developmental regression was coupled with the onset of seizures in one patient. Intrafamilial clinical variability was observed across two affected male cousins of Family 1: one patient had no seizures and only displayed some language delay, while the more severely delayed cousin also harboured a de novo 2q23.1 duplication (includes the dosage-dependent gene, MBD5, linked to ID, dysmorphism, motor and language delay, hypotonia, and autistic features - all features observed in the individual).

All variants segregated with disease in each family. Analysis of fibroblasts derived from one patient with a splice site variant revealed several abnormal transcripts, predicted to result in LoF. No further functional studies of other variants or patient cells were performed.
Created: 27 Aug 2020, 10:24 a.m. | Last Modified: 27 Aug 2020, 10:24 a.m.
Panel Version: 3.267

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures, 618737

Publications

Created: 27 Aug 2020, 10:24 a.m.
Last Modified: 27 Aug 2020, 10:46 a.m.
Panel version: 8.152

Zornitza Stark (Australian Genomics)

Green List (high evidence)

Four unrelated families reported.
Sources: Expert list
Created: 2 Mar 2020, 4:25 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Lissencephaly; pachygyria; subcortical band heterotopia; microcephaly; intellectual disability

Publications

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

Created: 2 Mar 2020, 4:25 a.m.

Panel version: 3.3

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
Phenotypes
  • Pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures, OMIM:618737
Tags
gene-checked Q1_25_ promote_green
Clinvar variants
Variants in TUBGCP2
Penetrance
None
Publications
Panels with this gene

History Filter Activity

17 Mar 2025, Gel status: 2

Removed Tag, Added Tag

Arina Puzriakova (Genomics England Curator)

Tag watchlist was removed from gene: TUBGCP2. Tag Q1_25_ promote_green tag was added to gene: TUBGCP2.

17 Mar 2025, Gel status: 2

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: TUBGCP2 were set to 31630790

3 Oct 2024, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: TUBGCP2 were changed from Lissencephaly; pachygyria; subcortical band heterotopia; microcephaly; intellectual disability to Pachygyria, microcephaly, developmental delay, and dysmorphic facies, with or without seizures, OMIM:618737

17 Oct 2023, Gel status: 2

Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag gene-checked tag was added to gene: TUBGCP2.

27 Aug 2020, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: tubgcp2 has been classified as Amber List (Moderate Evidence).

27 Aug 2020, Gel status: 0

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: tubgcp2 has been removed from the panel.

27 Aug 2020, Gel status: 0

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag watchlist tag was added to gene: TUBGCP2.

2 Mar 2020, Gel status: 0

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

Zornitza Stark (Australian Genomics)

gene: TUBGCP2 was added gene: TUBGCP2 was added to Intellectual disability. Sources: Expert list Mode of inheritance for gene: TUBGCP2 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: TUBGCP2 were set to 31630790 Phenotypes for gene: TUBGCP2 were set to Lissencephaly; pachygyria; subcortical band heterotopia; microcephaly; intellectual disability Review for gene: TUBGCP2 was set to GREEN gene: TUBGCP2 was marked as current diagnostic