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Fetal anomalies

Gene: DEPDC5

Green List (high evidence)
DEPDC5 (DEP domain containing 5)
EnsemblGeneIds (GRCh38): ENSG00000100150
EnsemblGeneIds (GRCh37): ENSG00000100150
OMIM: 614191, Gene2Phenotype
DEPDC5 is in 5 panels

5 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, 11:09 a.m. | Last Modified: 26 Sep 2024, 11:09 a.m.
Panel Version: 4.192
This gene and phenotype were reviewed during meetings between November 2023 & July 2024. The meetings included representatives of the North Thames and Central & South R21 testing GLHs and from the R21 Clinical Oversight Group. Clinical review and curation was performed by Natalie Chandler, Alison Male and Lyn Chitty (North Thames GLH), Stephanie Allen, Natalie Bibb, Esther Kinning and Denise Williams (Central & South GLH) and Natalie Canham, Anna De Burca and Samantha Doyle R21 Clinical Oversight Group. Outcome of review: Confirmed that the phenotype is fetally relevant, support adding to the Fetal anomalies panel as a Green gene.
Created: 29 Aug 2024, 8:33 p.m. | Last Modified: 29 Aug 2024, 8:33 p.m.
Panel Version: 4.36

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Created: 29 Aug 2024, 8:33 p.m.
Last Modified: 29 Aug 2024, 8:33 p.m.
Panel version: 4.192

Natalie Chandler (North Thames GLH)

Green List (high evidence)

Amber review in 2021 as not felt enough evidence of fetal phenotype at time. Noted amber on cortical maformation panel. PMID:32848577 reported a child with a homozygous missense variant (p.Pro1031His) who presented with cortical dysplasia and childhood onset epilepsy. PMID:36067010 reported homozygous missense variants in five unrelated families (three Irish Traveller families with same variant - p.Thr337Arg; and one Tunisian and one Lebanese families with the same variant - p.Arg806Cys). All nine children from these five families presented with consistent phenotypic features including extensive bilateral polymicrogyria, congenital macrocephaly, early onset refractory epilepsy and severe psychomotor developmental delay. Polymicrogyria is one of the most common malformations of cortical development, characterized by abnormal cortical lamination and excessive folding of the cortical surface. Skin biopsy immunohistochemistry suggested hyperactivation of the mTOR pathway. The disease mechanism is suggested as 'loss of function' as DEPDC5 is a repressor/inhibitor within the mTOR pathway. Green
Created: 29 Aug 2024, 8:07 p.m. | Last Modified: 29 Aug 2024, 8:07 p.m.
Panel Version: 4.35

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Epilepsy, familial focal, with variable foci 1 MIM#604364 biallelic only

Publications

Created: 29 Aug 2024, 8:07 p.m.
Last Modified: 29 Aug 2024, 8:07 p.m.
Panel version: 4.35

Arina Puzriakova (Genomics England Curator)

Comment on list classification: Updated rating from Red to Amber inline with this recent Amber review by Rhiannon Mellis (GOSH), awaiting further evidence supporting that this gene can cause a fetal phenotype.
Created: 19 Aug 2022, 3:21 p.m. | Last Modified: 19 Aug 2022, 3:21 p.m.
Panel Version: 1.930
Created: 19 Aug 2022, 3:21 p.m.
Last Modified: 19 Aug 2022, 3:21 p.m.
Panel version: 1.930

Rhiannon Mellis (Great Ormond Street Hospital)

I don't know

This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs.

Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH).

Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene.

Currently rated Green on the following other PanelApp panel(s): Intellectual disability, Genetics epilepsies. Amber on cortical malformations panel.

Details of review:
Previously reviewed as Red because only associated with familial epilepsy without structural brain anomalies (AD - caused by het LOF variants) but data presented by Dr Lara Menzies at CGS Spring Meeting 2021 suggests that there may also be a biallelic phenotype with hypomorphic variants. 5 cases presented from 3 unrelated Irish traveller families with significant polymicrogyria and macrocephaly as well as seizures and severe dev delay. At least 2 of the cases had prenatal features: ventriculomegaly, macrocephaly and IUGR for one, polymicrogyria on MRI for another - fetal MRI done because of FHx of affected child. (Unpublished data)

Liu et al 2020 (PMID: 32848577) report one case with homozygous missense variants in this gene, who had focal cortical dysplasia and seizures from 3yo
Created: 11 Aug 2022, 2:16 p.m. | Last Modified: 11 Aug 2022, 2:16 p.m.
Panel Version: 1.900
This gene and phenotype were reviewed during a meeting on 21st October 2021 between representatives of the North Thames and Central & South R21 testing GLHs.

Clinical review and curation was performed by Lyn Chitty, Alison Male, Rowenna Roberts, Rhiannon Mellis (North Thames GLH) and Stephanie Allen, Denise Williams and Esther Kinning (Central & South GLH).

Outcome of review: May be fetally relevant but currently limited evidence, support adding to the Fetal anomalies panel as Amber gene.

Currently rated Green on the following other PanelApp panel(s): Intellectual disability, Genetics epilepsies. Amber on cortical malformations panel.

Details of review:
Previously reviewed as Red because only associated with familial epilepsy without structural brain anomalies (AD - caused by het LOF variants) but data presented by Dr Lara Menzies at CGS Spring Meeting 2021 suggests that there may also be a biallelic phenotype with hypomorphic variants. 5 cases presented from 3 unrelated Irish traveller families with significant polymicrogyria and macrocephaly as well as seizures and severe dev delay. At least 2 of the cases had prenatal features: ventriculomegaly, macrocephaly and IUGR for one, polymicrogyria on MRI for another - fetal MRI done because of FHx of affected child. (Unpublished data)

Liu et al 2020 (PMID: 32848577) report one case with homozygous missense variants in this gene, who had focal cortical dysplasia and seizures from 3yo
Created: 11 Aug 2022, 2:16 p.m. | Last Modified: 11 Aug 2022, 2:16 p.m.
Panel Version: 1.900

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Epilepsy; Structural brain malformations

Publications

Created: 11 Aug 2022, 2:16 p.m.
Last Modified: 11 Aug 2022, 2:16 p.m.
Panel version: 1.900

Rebecca Foulger (Genomics England curator)

Red List (low evidence)

This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Phenotype is not fetally-relevant. Additional notes from clinical review: Epilepsy but no structural brain defects, so probably not detectable prenatally. Action taken: Demoted DEPDC5 gene rating from Green to Red.
Created: 24 Mar 2019, 4:30 p.m.
DDG2P rating in original PAGE list: Confirmed for FAMILIAL FOCAL EPILEPSY WITH VARIABLE FOCI
Created: 11 Dec 2018, 9:04 a.m.
Created: 11 Dec 2018, 9:04 a.m.

Panel version: 0.134

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • NHS GMS
  • PAGE DD-Gene2Phenotype
Phenotypes
  • Developmental and epileptic encephalopathy 111, OMIM:620504
OMIM
614191
Clinvar variants
Variants in DEPDC5
Penetrance
None
Publications
Panels with this gene

History Filter Activity

26 Sep 2024, Gel status: 3

Removed Tag, Removed Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q3_24_promote_green was removed from gene: DEPDC5. Tag Q3_24_NHS_review was removed from gene: DEPDC5.

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 DEPDC5. Source Expert Review Green was added to DEPDC5. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

30 Aug 2024, Gel status: 2

Set Phenotypes

Achchuthan Shanmugasundram (Genomics England Curator)

Phenotypes for gene: DEPDC5 were changed from Epilepsy; Structural brain malformations to Developmental and epileptic encephalopathy 111, OMIM:620504

30 Aug 2024, Gel status: 2

Set publications

Achchuthan Shanmugasundram (Genomics England Curator)

Publications for gene: DEPDC5 were set to 32848577

30 Aug 2024, Gel status: 2

Added Tag, Added Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q3_24_promote_green tag was added to gene: DEPDC5. Tag Q3_24_NHS_review tag was added to gene: DEPDC5.

19 Aug 2022, Gel status: 2

Entity classified by Genomics England curator

Arina Puzriakova (Genomics England Curator)

Gene: depdc5 has been classified as Amber List (Moderate Evidence).

19 Aug 2022, Gel status: 1

Set publications

Arina Puzriakova (Genomics England Curator)

Publications for gene: DEPDC5 were set to

19 Aug 2022, Gel status: 1

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: DEPDC5 were changed from FAMILIAL FOCAL EPILEPSY WITH VARIABLE FOCI to Epilepsy; Structural brain malformations

19 Aug 2022, Gel status: 1

Set mode of inheritance

Arina Puzriakova (Genomics England Curator)

Mode of inheritance for gene: DEPDC5 was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to BIALLELIC, autosomal or pseudoautosomal

24 Mar 2019, Gel status: 1

Added New Source, Status Update

Rebecca Foulger (Genomics England curator)

Source Expert Review Red was added to DEPDC5. Rating Changed from Green List (high evidence) to Red List (low evidence)

8 Nov 2018, Gel status: 4

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

Rebecca Foulger (Genomics England curator)

gene: DEPDC5 was added gene: DEPDC5 was added to Fetal anomalies. Sources: Expert Review Green,PAGE DD-Gene2Phenotype Mode of inheritance for gene: DEPDC5 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Phenotypes for gene: DEPDC5 were set to FAMILIAL FOCAL EPILEPSY WITH VARIABLE FOCI