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Intellectual disability

Gene: PET100

Amber List (moderate evidence)

PET100 (PET100 homolog)
EnsemblGeneIds (GRCh38): ENSG00000229833
EnsemblGeneIds (GRCh37): ENSG00000229833
OMIM: 614770, Gene2Phenotype
PET100 is in 13 panels

6 reviews

Eleanor Williams (Genomics England Curator)

Green List (high evidence)

Comment on list classification: Leaving this gene rating as amber until the next GMS review, but as reviewer Zornitza Stark notes there are 8 Lebanese familes with the same variant, plus an Asian British family with a similar phenotype and a different variant, plus functional data to support the disease causation, so would recommend Green rating.
Created: 12 Nov 2020, 9:59 p.m. | Last Modified: 12 Nov 2020, 9:59 p.m.
Panel Version: 3.531
Comment on phenotypes: Removing MIM# 220110 as this is associated with variants in SURF1
Created: 12 Nov 2020, 9:57 p.m. | Last Modified: 12 Nov 2020, 9:57 p.m.
Panel Version: 3.530
PMID: 24462369 - Lim et al 2014 - report 8 complex IV-deficient Leigh Syndrome individuals from six families of Lebanese origin and identify a homozygous c.3G>C (p.Met1?) mutation in C19orf79 (renamed PET100). Infants presented with developmental delay and seizures.

PMID: 25293719 - Oláhová et al 2015 - report a child born to consanguineous, first-cousin British Pakistani parents with fatal, neonatal-onset isolated complex IV deficiency associated with multiorgan involvement. Exome sequencing revealed a homozygous truncating variant (c.142C>T, p.(Gln48*)) in the PET100 gene. Functional experiments with patient fibroblasts showed that the truncation of the proteinresults in a complete loss of enzyme activity and assembly of the holocomplex.

PMID: 31406627 - Mansour et al 2019 - report another 2 Lebanese families, of which one is consanguineous, with two affected siblings each. In both a missense mutation in exon 1 of the PET100 gene (c.3G > C; [p.Met1?]) was identified by exome sequencing. In both families the probands presented in infancy with developmental delay and seizures along with lactic acidosis.
Created: 12 Nov 2020, 9:53 p.m. | Last Modified: 12 Nov 2020, 9:53 p.m.
Panel Version: 3.528

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Mitochondrial complex IV deficiency, nuclear type 12 OMIM:619055; Leigh syndrome

Publications

Zornitza Stark (Australian Genomics)

Green List (high evidence)

We have rated this gene Green as: large number of Lebanese families reported (now 8); good functional data to support gene-disease association; non-Lebanese family with different variants reported.
Created: 10 Feb 2020, 3:48 a.m. | Last Modified: 10 Feb 2020, 3:48 a.m.
Panel Version: 3.0

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Mitochondrial complex IV deficiency, MIM# 220110

Publications

Variants in this GENE are reported as part of current diagnostic practice

Louise Daugherty (Genomics England Curator)

Changed rating of gene from Red to Amber. This gene was rated as Amber in v2.467 and incorrectly automatically demoted to Red 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, 10:39 p.m.
added founder-effect tag PMID:24462369.
Then removed tag due to subsequent paper of a girl born to consanguineous, first-cousin British Asian parents, confirming PET100 mutation as an important cause of isolated complex IV deficiency outside of the Lebanese population, extending the phenotypic spectrum associated with abnormalities within this gene.
Created: 8 Dec 2017, 6:11 p.m.

Caroline Wright (Sanger)

I don't know

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
MITOCHONDRIAL COMPLEX IV DEFICIENCY

Publications

  • 0

Lu Raymond (university of cambridge )

I don't know

Richard Scott (Genomics England Curator)

Comment on list classification: Single ancestral allele reported to date. Requires further data before diagnostic grade
Created: 7 Feb 2016, 11:53 p.m.

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • Expert Review Amber
  • Victorian Clinical Genetics Services
Phenotypes
  • Intellectual disability
  • Complex IV-deficient Leigh syndrome
  • Mitochondrial complex IV deficiency, nuclear type 12 OMIM:619055
Tags
for-review
OMIM
614770
Clinvar variants
Variants in PET100
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

12 Nov 2020, Gel status: 2

Entity classified by Genomics England curator

Eleanor Williams (Genomics England Curator)

Gene: pet100 has been classified as Amber List (Moderate Evidence).

12 Nov 2020, Gel status: 2

Added Tag

Eleanor Williams (Genomics England Curator)

Tag for-review tag was added to gene: PET100.

12 Nov 2020, Gel status: 2

Set Phenotypes

Eleanor Williams (Genomics England Curator)

Phenotypes for gene: PET100 were changed from Mitochondrial complex IV deficiency,220110; Intellectual disability; Complex IV-deficient Leigh syndrome to Intellectual disability; Complex IV-deficient Leigh syndrome; Mitochondrial complex IV deficiency, nuclear type 12 OMIM:619055

12 Nov 2020, Gel status: 2

Set publications

Eleanor Williams (Genomics England Curator)

Publications for gene: PET100 were set to 26425749; 24462369; 25293719

29 Sep 2018, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: pet100 has been classified as Amber List (Moderate Evidence).

29 Sep 2018, Gel status: 2

Entity classified by Genomics England curator

Louise Daugherty (Genomics England Curator)

Gene: pet100 has been classified as Amber List (Moderate Evidence).

29 Sep 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to PET100.

12 Mar 2018, Gel status: 2

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.

5 Jan 2018, Gel status: 2

Added New Source, Set publications

Ellen McDonagh (Genomics England Curator)

Expert Review Amber was added to PET100. Panel: Intellectual disability Publications for gene PET100 was set to ['26425749', ' 24462369', '25293719']

8 Feb 2016, Gel status: 1

Gene classified by Genomics England curator

Richard Scott (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

7 Feb 2016, Gel status: 1

Gene classified by Genomics England curator

Richard Scott (Genomics England Curator)

This gene has been classified as Red List (Low Evidence).

13 Nov 2015, Gel status: 2

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 2

gel status update

GEL ()

The Gel status was updated for this whole panel

13 Nov 2015, Gel status: 0

Created

Ellen McDonagh (Genomics England Curator)

PET100 was created by ellenmcdonagh

13 Nov 2015, Gel status: 0

Added New Source

Ellen McDonagh (Genomics England Curator)

PET100 was added to Intellectual disabilitypanel. Sources: Expert Review Amber