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Xp21.2 region (includes NR0B1) Gain
ISCA-46302-Gain 2

Fetal anomalies
Gene: PTEN

PTEN (phosphatase and tensin homolog)
EnsemblGeneIds (GRCh38): ENSG00000171862
EnsemblGeneIds (GRCh37): ENSG00000171862
OMIM: 601728, Gene2Phenotype
PTEN is in 54 panels

4 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to green and the mode of inheritance updated to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted 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

Created: 12 Dec 2025, 3:10 p.m.
Last Modified: 12 Dec 2025, 3:10 p.m.
Panel version: 6.120

Arina Puzriakova (Genomics England Curator)

Green List (high evidence)

Upgraded from Red to Amber but there is sufficient evidence to make 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

Sunayna Best (Leeds Teaching Hospitals NHS 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

Yu et al, 2025. 14 fetal cases with a PTEN variant, 5 detected in 2nd trimester: three presented with macrocephaly, one showed mild ventriculomegaly, and another had cardiac defects (coarctation of the aorta and ventricular septal defect). Nine additional cases were identified during the third trimester six displayed macrocephaly with or without polyhydramnios and ventriculomegaly; one case had mild ventriculomegaly; another presented only with mild polyhydramnios; and one was characterized by macrosomia. Lynch et al 2025: further case report, fetus with macrosomia, TOP 25/40.
Created: 5 Sep 2025, 2:55 p.m. | Last Modified: 5 Sep 2025, 2:55 p.m.

Panel Version: 6.24

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Phenotypes
Cowden syndrome 1

Publications

40261085

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

Rebecca Foulger (Genomics England curator)

Red List (low evidence)

This gene was re-reviewed in a consistency check by Anna de Burca (Genomics England Clinical Team), and at a Fetal Working Group call on July 19th 2019 by Lyn Chitty, Anna de Burca, Richard Scott, Rhiannon Mellis, Rebecca Foulger and Ellen McDonagh. Outcome of review: Hydrocephalus is very unusual, and PTEN is on the Hydrocephalus panel because of the macrocephaly phenotype. Demote from Green to Red.
Created: 25 Jul 2019, 8:04 a.m. | Last Modified: 12 Aug 2019, 10:37 a.m.

Panel Version: 0.329

This gene and phenotype were reviewed during meetings at Great Ormond Street hospital in March and April 2019. Clinical review and curation was performed by Lyn Chitty, Anna de Burca, Rhiannon Mellis, Richard Scott, Ellen McDonagh and Rebecca Foulger. Outcome of review: Confirmed that phenotype is fetally-relevant: include on the Fetal anomalies panel as a Green gene. Additional notes from clinical review: Although caution was taken when considering PTEN for the Fetal anomalies panel because of the cancer association (and therefore a potential incidental finding), macrocephaly presents at birth and PTEN is Green on the Hydrocephalus panel. Therefore after group review, it was decided to include PTEN on the Fetal anomalies panel.
Created: 29 Apr 2019, 12:28 p.m.

In original PAGE file (and in DD-G2P), mode of inheritance is 'Monoallelic' for MACROCEPHALY/AUTISM SYNDROME; BANNAYAN-ZONANA SYNDROME; COWDEN DISEASE; VACTERL ASSOCIATION WITH HYDROCEPHALUS; LHERMITTE-DUCLOS DISEASE. Mode of inheritance in original PAGE file (and in DD-G2P) is mosaic for PROTEUS SYNDROME.
Created: 27 Apr 2019, 10:41 a.m.

DDG2P rating in original PAGE list: Confirmed for BANNAYAN-ZONANA SYNDROME, Confirmed for COWDEN DISEASE, Confirmed for VACTERL ASSOCIATION WITH HYDROCEPHALUS, Confirmed for LHERMITTE-DUCLOS DISEASE, Confirmed for PROTEUS SYNDROME and Confirmed for MACROCEPHALY/AUTISM SYNDROME.
Created: 11 Dec 2018, 9:05 a.m.

Mosaicism tag added based on original PAGE file which records Mosaic MOI for PROTEUS SYNDROME.
Created: 8 Nov 2018, 4:54 p.m.

In the original PAGE file, listed as Mosaic for PROTEUS SYNDROME. In the original PAGE file, MOP listed as LOF for BANNAYAN-ZONANA SYNDROME, COWDEN DISEASE, LHERMITTE-DUCLOS DISEASE, PROTEUS SYNDROME and listed as Uncertain for VACTERL ASSOCIATION WITH HYDROCEPHALUS and MACROCEPHALY/AUTISM SYNDROME.
Created: 8 Nov 2018, 4:45 p.m.

Created: 8 Nov 2018, 4:45 p.m.
Last Modified: 12 Aug 2019, 10:37 a.m.
Panel version: 0.311

Details

Mode of Inheritance

MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted

Sources

NHS GMS
Expert Review Green
PAGE DD-Gene2Phenotype

Phenotypes

Cowden syndrome 1, OMIM:158350

Tags

mosaicism

OMIM

601728

Clinvar variants

Variants in PTEN

Penetrance

None

Publications

40261085

Panels with this gene

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: PTEN. Tag Q3_25_NHS_review was removed from gene: PTEN.

12 Dec 2025, Gel status: 3

Added New Source, Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

Source Expert Review Green was added to PTEN. Source NHS GMS was added to PTEN. 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: PTEN were changed from COWDEN DISEASE; Cowden syndrome 1; LHERMITTE-DUCLOS DISEASE; PROTEUS SYNDROME; MACROCEPHALY/AUTISM SYNDROME; BANNAYAN-ZONANA SYNDROME; VACTERL ASSOCIATION WITH HYDROCEPHALUS to Cowden syndrome 1, OMIM:158350

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: PTEN. Tag Q3_25_NHS_review tag was added to gene: PTEN.

5 Sep 2025, Gel status: 2

Added New Source, Set mode of inheritance, Set Phenotypes, Set publications, Status Update

Arina Puzriakova (Genomics England Curator)

Source Expert Review Amber was added to PTEN. Mode of inheritance for gene PTEN was changed from MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown to MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted Added phenotypes Cowden syndrome 1 for gene: PTEN Publications for gene: PTEN were updated from to 40261085 Rating Changed from Red List (low evidence) to Amber List (moderate evidence)

25 Jul 2019, Gel status: 1