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Intellectual disability

Gene: PRUNE1

Green List (high evidence)
PRUNE1 (prune exopolyphosphatase 1)
EnsemblGeneIds (GRCh38): ENSG00000143363
EnsemblGeneIds (GRCh37): ENSG00000143363
OMIM: 617413, Gene2Phenotype
PRUNE1 is in 4 panels

4 reviews

Eleanor Williams (Genomics England Curator)

Green List (high evidence)

Further clinical analysis of previously reported patients and functional analysis of some of the variants in PMID:33105479 - Nistala et al 2020 - detailed phenotypic analysis of a previously reported family (SZ51, Karaca et al 2015) plus detailed literature and clinical review of all 35 NMIHBA patients reported to date. They also characterized 4 variants (p.D30N, p.D106N, p.R128Q and p.G174*) within the conserved N-terminal domain. Wild type or mutant proteins were transfected into HEK293 cells. Cells showed either no protein expression (p.G174*) or loss of PRUNE1 function due to impaired protein stability or loss of enzymatic function (3 missense variants). Prune1−/− mice show midgestational lethality, associated with changes in embryonic growth and vascular development.
Created: 3 Feb 2021, 12:01 p.m. | Last Modified: 3 Feb 2021, 12:01 p.m.
Panel Version: 3.756

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies OMIM:617481; neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies MONDO:0060490

Publications

Created: 3 Feb 2021, 12:01 p.m.
Last Modified: 3 Feb 2021, 12:01 p.m.
Panel version: 3.756

Helen Brittain (Genomics England Curator)

Comment when marking as ready: Appropriate phenotype, sufficient cases
Created: 13 Nov 2017, 1:46 p.m.
Created: 13 Nov 2017, 1:46 p.m.

Panel version: Imported from Intellectual disability update Oct 2017 panel version 0.73

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_manual . Main mutation mechanism : Loss of function/missense
Created: 27 Jul 2017, 8:09 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Publications

  • Manual assessment of Genes of interest from literature searches and personal communication

Created: 2 Aug 2017, 9:54 p.m.

Panel version: 1.354

Louise Daugherty (Genomics England Curator)

Green List (high evidence)

Promoted gene status from Amber to Green due to expert review and evidence more than three unrelated individuals. PRUNE1 previous symbol is PRUNE
Created: 29 Nov 2017, 2:10 p.m.
Comment on list classification: This gene is from an expert list and needs further assessment by the Genomics England curation team to access inclusion and pertinence to this panel.
Created: 28 Jul 2017, 3:49 p.m.
added new-gene-name tag, new approved HGNC gene symbol is PRUNE1
Created: 28 Jul 2017, 3:46 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies, 617481; NMIHBA; Complex neurological syndrome

Publications

Created: 28 Jul 2017, 3:46 p.m.

Panel version: 1.465

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Green
  • Expert Review Green
Phenotypes
  • Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies OMIM:617481
  • neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies MONDO:0060490
  • NMIHBA
  • Complex neurological syndrome
OMIM
617413
Clinvar variants
Variants in PRUNE1
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

11 Feb 2021, Gel status: 3

Clear Sources

Catherine Snow (Genomics England)

Source: Expert Review Amber was removed from gene: PRUNE1

3 Feb 2021, Gel status: 3

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for gene: PRUNE1 were changed from Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies, 617481; NMIHBA; Complex neurological syndrome to Neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies OMIM:617481; neurodevelopmental disorder with microcephaly, hypotonia, and variable brain anomalies MONDO:0060490; NMIHBA; Complex neurological syndrome

3 Feb 2021, Gel status: 3

Set publications

Eleanor Williams (Genomics England Curator)

Publications for gene: PRUNE1 were set to 26539891; 28334956

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.

29 Nov 2017, Gel status: 4

Added New Source, Set publications

Ellen McDonagh (Genomics England Curator)

Expert Review Green was added to PRUNE1. Panel: Intellectual disability Publications for gene PRUNE1 was set to ['26539891', '28334956']

5 Nov 2017, Gel status: 2

Changed Gene Name

GEL ()

PRUNE was changed to PRUNE1

5 Nov 2017, Gel status: 2

Removed Tag

GEL ()

new-gene-name was removed from PRUNE. Panel: Intellectual disability

28 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).

28 Jul 2017, Gel status: 0

Changed Gene Name

Louise Daugherty (Genomics England Curator)

PRUNE1* was changed to PRUNE

27 Jul 2017, Gel status: 0

Added New Source

BRIDGE consortium (NIHRBR-RD)

PRUNE1* was added to Intellectual disabilitypanel. Sources: BRIDGE study SPEED NEURO Tier1 Gene

27 Jul 2017, Gel status: 0

Created

BRIDGE consortium (NIHRBR-RD)

PRUNE1* was created by BRIDGE