Hereditary spastic paraplegia - childhood onset

Gene: PI4KA

Amber List (moderate evidence)

PI4KA (phosphatidylinositol 4-kinase alpha)
EnsemblGeneIds (GRCh38): ENSG00000241973
EnsemblGeneIds (GRCh37): ENSG00000241973
OMIM: 600286, Gene2Phenotype
PI4KA is in 11 panels

2 reviews

Evan Reid (University of Cambridge)

Green List (high evidence)

This paper supports the idea that mutations in this gene can cause a relatively pure spastic paraplegia (PMID: 34415322 PMCID: PMC8557332 DOI: 10.1093/brain/awab124), which I think would justify inclusion of the gene on the HSP panel.
Created: 22 Dec 2021, 1:47 p.m. | Last Modified: 22 Dec 2021, 1:47 p.m.
Panel Version: 2.121

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
spastic paraplegia; leukodystrophy; white matter abnromality; seizures; intellectual disability

Publications

Ivone Leong (Genomics England Curator)

I don't know

After consulting with the Genomics England Clinical Team it was decided that this gene should be added to the Hereditary spastic paraplegia - childhood onset panel with an Amber rating.

Helen Brittain:
"I think the spasticity is likely to be secondary to the CNS findings and therefore might opt for amber at this stage, as it is perhaps unlikely to be clearly relevant to the more typical cohort with isolated spasticity that will be targeted by that panel."
Created: 25 Oct 2021, 10:22 a.m. | Last Modified: 25 Oct 2021, 10:22 a.m.
Panel Version: 2.87
This gene is associated with a relevant phenotype in OMIM and Gene2Phenotype.

PMID: 25855803. From OMIM: "3 fetuses were all diagnosed in utero with multiple congenital anomalies resulting in the termination of pregnancy between 16 and 34 weeks' gestation. All fetuses had bilateral perisylvian polymicrogyria and cerebellar hypoplasia or dysplasia. One had a small pons. Additional features included severe talipes equinovarus, externally rotated hips, and variable contractures of the limbs or fingers."

PMID:34415322. 10 patients from 10 unrelated families with biallelic varaints in PI4KA. Patients showed a spectrum of severe global neurodevelopmental delay (8/10 moderate to severe ID), hypomyelination, cerebellar hyoplasia (1/10), cerebellar atrophy (5/10), bilateral perisylvian polymicrogyria (1/10), immunological problems (hypogammaglobulinaemia, lymphopaenia, and autoimmune neutorpaenia - 4/10), bowl dysfunction (4/10). Age of onset ranged from newborn to 17 years.

PMID: 34415310. 7 unrelated families. Family 1: Amish. Severe extensive multiple intestinal atresia, IBD and combined immunodeficiency (2/4). Families 3 - 8 all have 1 affected individual, (Turkish, Indian, German and Italian). Global developmental delay (all), ID (severe to mild), cerebellar and/or brainstem anomalies (3/6), spasticity (all), immature gyral pattern (1/6), leukodystrophy (6/6), multiple intestinal atresia (0/6), IBD (3/6), combined immunodeficiency (2/6). Early age of onset.
Created: 1 Sep 2021, 1:47 p.m. | Last Modified: 25 Oct 2021, 10:16 a.m.
Panel Version: 2.87

Publications

Details

History Filter Activity

4 Jan 2022, Gel status: 2

Added Tag

Arina Puzriakova (Genomics England Curator)

Tag Q1_22_phenotype tag was added to gene: PI4KA.

4 Jan 2022, Gel status: 2

Added Tag, Added Tag

Arina Puzriakova (Genomics England Curator)

Tag Q1_22_expert_review tag was added to gene: PI4KA. Tag Q1_22_NHS_review tag was added to gene: PI4KA.

25 Oct 2021, Gel status: 2

Removed Tag

Ivone Leong (Genomics England Curator)

Tag Q3_21_rating was removed from gene: PI4KA.

25 Oct 2021, Gel status: 2

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

Ivone Leong (Genomics England Curator)

gene: PI4KA was added gene: PI4KA was added to Hereditary spastic paraplegia - childhood onset. Sources: Expert Review Amber Q3_21_rating tags were added to gene: PI4KA. Mode of inheritance for gene: PI4KA was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: PI4KA were set to 25855803; 34415322; 34415310 Phenotypes for gene: PI4KA were set to Polymicrogyria, perisylvian, with cerebellar hypoplasia and arthrogryposis, OMIM:616531