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Fetal anomalies

Gene: PI4KA

Green List (high evidence)
PI4KA (phosphatidylinositol 4-kinase alpha)
EnsemblGeneIds (GRCh38): ENSG00000241973
EnsemblGeneIds (GRCh37): ENSG00000241973
OMIM: 600286, Gene2Phenotype
PI4KA is in 13 panels

4 reviews

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

There is sufficient evidence to promote this gene to Green at the next GMS panel update, inline with the recent review by the R21 Clinical Oversight Group.
Created: 5 Sep 2025, 4:41 p.m. | Last Modified: 5 Sep 2025, 4:41 p.m.
Panel Version: 6.29
Created: 5 Sep 2025, 4:41 p.m.
Last Modified: 5 Sep 2025, 4:41 p.m.
Panel version: 6.29

Anna de Burca (Oxford University Hospitals NHS Foundation Trust)

Green List (high evidence)

This gene and phenotype were reviewed during meetings in June & July 2025. 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 & Elizabeth Scotchman (North Thames GLH), Natalie Bibb, Stephanie Allen & Sarah Graham (Central & South GLH) and Alice Gardham, Esther Kinning, Vicki Harrison, Anna DeBurca, Natalie Canham, Elizabeth Wall, Sunayna Best, Soo-Mi Park & Sahar Mansour (R21 Clinical Oversight Group).
Created: 5 Sep 2025, 4:31 p.m. | Last Modified: 5 Sep 2025, 4:31 p.m.
Panel Version: 6.28
Thin CC, ventriculomegaly, cerebellar hypoplasia, potine hypoplasia, perisylvian polymicrogyria, arthrogryposis, micrognathia.
Created: 5 Sep 2025, 2:55 p.m. | Last Modified: 5 Sep 2025, 2:55 p.m.
Panel Version: 6.24

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis

Publications

Created: 5 Sep 2025, 2:55 p.m.
Last Modified: 5 Sep 2025, 2:55 p.m.
Panel version: 6.28

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: 12 Dec 2025, 3:10 p.m. | Last Modified: 12 Dec 2025, 3:10 p.m.
Panel Version: 6.120
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.
Created: 29 Aug 2024, 8:33 p.m. | Last Modified: 29 Aug 2024, 8:33 p.m.
Panel Version: 4.36
Created: 29 Aug 2024, 8:33 p.m.
Last Modified: 29 Aug 2024, 8:33 p.m.
Panel version: 6.120

Natalie Bibb (C&S GLH)

I don't know

Variable AR phenotypes, Gastrointestinal defects and immunodeficiency syndrome 2 OMIM:619708. Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis OMIM:616531. Spastic paraplegia 84, OMIM:619621. PMID:34415310 - 12 affected infants from large Amish family,Biallelic PI4KA variants segregated with disease (Gastrointestinal defects and immunodeficiency syndrome , presenting after birth with clinical signs of bowel obstruction died of intestinal atresia in the first weeks of life, although no antenatal scanning clinical history compatible with 3rd trimester polyhydraminos. PMID:25855803 - 1 family 3 affected fetus (+3 early miscarriages) diagnosed in utero with multiple congenital abnormalities including severe bilateral talipes, micrognathia. Post mortems showed polymicrogyria, cerebellar hypoplasia, joint contractures. In vitro functional expression assays in COS-7 cells showed that the D1854N mutant enzyme had no detectable catalytic activity, consistent with a loss of function. Wide phenotypic spectrum but green as evidence of prenatal phenotype with suggestion that loss-of-function variants and may represent the most severe disease. Amber - need more evidence of presenting prenatally consistently.
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
Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis MONDO:0014679; Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, OMIM:616531

Publications

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

History Filter Activity

16 Dec 2025, Gel status: 3

Removed Tag, Removed Tag

Achchuthan Shanmugasundram (Genomics England Curator)

Tag Q3_25_promote_green was removed from gene: PI4KA. Tag Q3_25_NHS_review was removed from gene: PI4KA.

12 Dec 2025, Gel status: 3

Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source Expert Review Green was added to PI4KA. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

8 Sep 2025, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: PI4KA were changed from Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, OMIM:616531; Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis MONDO:0014679; Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis to Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, OMIM:616531

8 Sep 2025, Gel status: 2

Added Tag, Added Tag

Arina Puzriakova (Genomics England Curator)

Tag Q3_25_promote_green tag was added to gene: PI4KA. Tag Q3_25_NHS_review tag was added to gene: PI4KA.

5 Sep 2025, Gel status: 2

Set Phenotypes, Set publications

Arina Puzriakova (Genomics England Curator)

Added phenotypes Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis for gene: PI4KA Publications for gene: PI4KA were updated from 34415310 to 34415310; 39891418

29 Aug 2024, Gel status: 2

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

Achchuthan Shanmugasundram (Genomics England Curator)

gene: PI4KA was added gene: PI4KA was added to Fetal anomalies. Sources: Expert Review Amber,NHS GMS Mode of inheritance for gene: PI4KA was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PI4KA were set to 34415310 Phenotypes for gene: PI4KA were set to Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis MONDO:0014679; Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, OMIM:616531