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Intellectual disability

Gene: PIK3CA

Green List (high evidence)
PIK3CA (phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha)
EnsemblGeneIds (GRCh38): ENSG00000121879
EnsemblGeneIds (GRCh37): ENSG00000121879
OMIM: 171834, Gene2Phenotype
PIK3CA is in 21 panels

5 reviews

Rebecca Foulger (Genomics England curator)

Comment on mode of inheritance: Changed MOI from 'Unknown' in order to capture appropriate variants within this gene in our current tiering pipeline.
Created: 1 Nov 2018, 3:33 p.m.
Created: 1 Nov 2018, 3:33 p.m.

Panel version: 2.529

Sarah Leigh (Genomics England Curator)

Comment on mode of inheritance: Somatic (post-zygotic) variants in this gene can cause Megalencephaly-capillary malformation-polymicrogyria syndrome, a feature of which is variable ID.
Created: 4 Jan 2018, 11:06 a.m.
Comment on phenotypes: Gene2Phenotype confirmed gene with ID related disease – Megalencephaly-capillary malformation-polymicrogyria syndrome, somatic 3
Created: 4 Jan 2018, 10:55 a.m.
Created: 4 Jan 2018, 10:55 a.m.

Panel version: Imported from Intellectual disability update Dec 2017 panel version 0.122

Helen Brittain (Genomics England Curator)

Comment when marking as ready: Somatic (post-zygotic) variants in this gene can cause Megalencephaly-capillary malformation-polymicrogyria syndrome, a feature of which is variable ID. The phenotype is appropriate for inclusion, however the reliability of pick-up is questionable given the somatic mosaic nature. Green rating in line with other related panels (e.g. Regional overgrowth disorders).
Created: 21 Dec 2017, 1:39 p.m.
Created: 21 Dec 2017, 1:39 p.m.

Panel version: Imported from Intellectual disability update Dec 2017 panel version 0.88

BRIDGE consortium (NIHRBR-RD)

Green List (high evidence)

This is a pertinent gene from the NIHR BioResource - Rare Diseases Study (NIHRBR-RD) BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene is on the SPEED_NEURO_20170705 gene list. Evidences used for SPEED NEURO gene list: in_ddg2p_20141118_conf;in_ddg2p_20141118_conf;in_ddg2p_201507;in_ddg2p_201507_conf;in_ddg2p_2_4_2017;in_ddg2p_2_4_2017_conf;in_UKGTN_v12 . Main mutation mechanism : Activating
Created: 27 Jul 2017, 8:01 p.m.
Evidences key, gene present in following gene lists and main mutation mechanism : ddg2p_20141118; ddg2p_20141118_conf; ddg2p_201507; ddg2p_201507_conf; UKGTN_v12; Nijmegen_ID_candidates; neuro_20160418_strict; Activating. This is a pertinent gene from the BRIDGE Study : SPEED (Specialist Pathology: Evaluating Exomes in Diagnostics) which covers epilepsies, movement and microcephaly disorders, this gene comes from the SPEED_NEURO_v3.0_20170404 gene list. The following experts from the BRIDGE consortium NIHRBR-RD contributed to this panel: - Professor F. Lucy Raymond, Cambridge Institute for Medical Research, University of Cambridge - Manju Kurian, Paediatric neurologist, Great Ormond Street Hosptial - Keren Carss, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Alba Sanchis-Juan, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Marie Erwood NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust - Louise Daugherty, NIHR BioResource - Rare Diseases, Cambridge University Hospitals NHS Foundation Trust
Created: 19 Jul 2017, 1:06 p.m.

Mode of inheritance
Unknown

Publications

Mode of pathogenicity
Other

Created: 2 Aug 2017, 9:32 p.m.

Panel version: 1.354

Louise Daugherty (Genomics England Curator)

Comment on list classification: Changed rating of gene from Amber to Green. This gene was rated as Green in v2.467 and incorrectly automatically demoted to Amber in v2.468. This was due to a defect in the automatic PanelApp uploading tool where a reference gene list was added as a new Source (Victorian Clinical Genetics Services), and under certain conditions associated to previous sources listed, resulted in the rating of the gene being automatically changed when it should not have been.
Created: 29 Sep 2018, 7:14 p.m.
Approximately 170 patients have been reported in the literature without significant sex predominance (ORPHA:6004)
Created: 12 Jan 2018, 11:34 a.m.
Comment on phenotypes: added OMIM phenotype
Created: 12 Jan 2018, 11:29 a.m.
Comment on phenotypes: removed : Ovarian cancer, somatic, 167000; Breast cancer, somatic, 114480; Colorectal cancer, somatic, 114500; Gastric cancer, somatic, 613659; Hepatocellular carcinoma, somatic, 114550; Nonsmall cell lung cancer, somatic, 211980; Keratosis, seborrheic, somatic, 182000; Nevus, epidermal, somatic, 162900; CLOVE syndrome, somatic, 612918;
Created: 21 Dec 2017, 4:47 p.m.
added somatic and mosaicism tag
Created: 21 Dec 2017, 4:46 p.m.
Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to assess inclusion and pertinence to this panel.
Created: 20 Jul 2017, 1:16 p.m.
Created: 20 Jul 2017, 1:16 p.m.

Panel version: 1.638

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
  • Victorian Clinical Genetics Services
Phenotypes
  • Megalencephaly-capillary malformation-polymicrogyria syndrome, somatic, 602501
  • Megalencephaly-capillary malformation-polymicrogyria syndrome, Orphanet:60040
Tags
mosaicism somatic
OMIM
171834
Clinvar variants
Variants in PIK3CA
Penetrance
Complete
Mode of Pathogenicity
Other - please provide details in the comments
Panels with this gene

History Filter Activity

1 Nov 2018, Gel status: 3

Set mode of inheritance

Rebecca Foulger (Genomics England curator)

Mode of inheritance for gene: PIK3CA was changed from Unknown to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

29 Sep 2018, Gel status: 3

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: pik3ca has been classified as Green List (High Evidence).

29 Sep 2018, Gel status: 2

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to PIK3CA.

12 Mar 2018, Gel status: 4

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.

12 Jan 2018, Gel status: 4

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for PIK3CA were set to Megalencephaly-capillary malformation-polymicrogyria syndrome, somatic, 602501; Megalencephaly-capillary malformation-polymicrogyria syndrome, Orphanet:60040

4 Jan 2018, Gel status: 4

Added New Source, Set mode of inheritance

Sarah Leigh (Genomics England Curator)

Expert Review Green was added to PIK3CA. Panel: Intellectual disability Model of inheritance for gene PIK3CA was set to Unknown

21 Dec 2017, Gel status: 2

Set Phenotypes

Louise Daugherty (Genomics England Curator)

Phenotypes for PIK3CA were set to Megalencephaly-capillary malformation-polymicrogyria syndrome, somatic, 602501

20 Jul 2017, Gel status: 2

Gene classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

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

19 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

PIK3CA was created by BRIDGE

19 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

PIK3CA was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene