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Intellectual disability

Gene: PRODH

Amber List (moderate evidence)
PRODH (proline dehydrogenase 1)
EnsemblGeneIds (GRCh38): ENSG00000100033
EnsemblGeneIds (GRCh37): ENSG00000100033
OMIM: 606810, Gene2Phenotype
PRODH is in 5 panels

5 reviews

Arina Puzriakova (Genomics England Curator)

I don't know

The rating of this gene has been updated to Amber following NHS Genomic Medicine Service approval. Additional comments from reviewing GLHs: 'Agree to downgrade on ID panel. Gene is green on R98 and this is appropriate (East); No pathogenic variants found in Sheffield (NEY); Agree for this gene to be amber. More evidence needed to link with intellectual disability phenotype (C&S)'
Created: 30 Jan 2023, 5:50 p.m. | Last Modified: 30 Jan 2023, 5:50 p.m.
Panel Version: 4.53
Created: 30 Jan 2023, 5:50 p.m.
Last Modified: 30 Jan 2023, 5:50 p.m.
Panel version: 4.53

Tracy Lester (Genetics laboratory, Oxford UK)

I don't know

I am not convinced that there is sufficient evidence for this gene to be green on the intellectual disability panel. Many of the variants listed in HGMDpro are listed as functional polys, and some of those listed as pathogenic are high frequency in gnomad (with homozygotes listed) - eg L441P. Most of the variants listed as pathogenic were identified as being of increased freq in a schizophrenia cohort compared to controls, but with little other supporting evidence. The cohorts used were small (approx 300). I think the gene should be amber in relation to the Intellectual disability.
Created: 25 Apr 2022, 3:58 p.m. | Last Modified: 25 Apr 2022, 3:58 p.m.
Panel Version: 3.1561

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Intellectual disabilty

Created: 25 Apr 2022, 3:58 p.m.
Last Modified: 25 Apr 2022, 3:58 p.m.
Panel version: 3.1561

Caroline Wright (Sanger)

Red List (low evidence)

Created: 5 Nov 2017, 2:42 a.m.

Panel version: 0

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

Evidence for the association of PRODH variants with Hyperprolinemia, type I, OMIM; 239500 has been classified as Definitive by ClinGen Aminoacidopathy Gene Curation Expert Panel on 04/27/2021
(https://search.clinicalgenome.org/kb/gene-validity/CGGV:assertion_5f28c677-a9b4-4bb3-9aed-14af97ad9896-2021-04-27T160000.000Z)
Created: 19 May 2022, 3 p.m. | Last Modified: 19 May 2022, 3 p.m.
Panel Version: 3.1578
Comment on list classification: Associated with phenotype in OMIM, not in G2P. At least 9 variants reported
Created: 28 Feb 2017, 2:58 p.m.

Phenotypes
Hyperprolinemia, type I, OMIM; 239500; hyperprolinemia type 1, MONDO:0009400

Created: 28 Feb 2017, 2:58 p.m.

Panel version: 3.1578

Lu Raymond (university of cambridge )

Red List (low evidence)

Created: 23 Feb 2016, 11:31 a.m.

Panel version: 0.306

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • NHS GMS
  • Expert Review Amber
  • Victorian Clinical Genetics Services
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Hyperprolinemia, type I, OMIM:239500
  • {Schizophrenia, susceptibility to, OMIM:4}, 600850
OMIM
606810
Clinvar variants
Variants in PRODH
Penetrance
Complete
Publications
Panels with this gene

History Filter Activity

24 Jan 2024, Gel status: 2

Set Phenotypes

Arina Puzriakova (Genomics England Curator)

Phenotypes for gene: PRODH were changed from Hyperprolinemia, type I, OMIM; 239500; {Schizophrenia, susceptibility to, OMIM:4}, 600850 to Hyperprolinemia, type I, OMIM:239500; {Schizophrenia, susceptibility to, OMIM:4}, 600850

31 Jan 2023, Gel status: 2

Removed Tag, Removed Tag, Removed Tag

Arina Puzriakova (Genomics England Curator)

Tag Q2_22_rating was removed from gene: PRODH. Tag Q2_22_expert_review was removed from gene: PRODH. Tag Q2_22_NHS_review was removed from gene: PRODH.

30 Jan 2023, Gel status: 2

Added New Source, Added New Source, Status Update

Arina Puzriakova (Genomics England Curator)

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

19 May 2022, Gel status: 3

Added Tag

Sarah Leigh (Genomics England Curator)

Tag Q2_22_NHS_review tag was added to gene: PRODH.

19 May 2022, Gel status: 3

Added Tag, Added Tag

Sarah Leigh (Genomics England Curator)

Tag Q2_22_rating tag was added to gene: PRODH. Tag Q2_22_expert_review tag was added to gene: PRODH.

19 May 2022, Gel status: 3

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: PRODH were changed from Hyperprolinemia, type I, 239500; {Schizophrenia, susceptibility to, 4}, 600850 to Hyperprolinemia, type I, OMIM; 239500; {Schizophrenia, susceptibility to, OMIM:4}, 600850

19 May 2022, Gel status: 3

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: PRODH were set to 12217952

29 Sep 2018, Gel status: 4

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to PRODH.

12 Mar 2018, Gel status: 3

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.

28 Feb 2017, Gel status: 4

Set publications

Sarah Leigh (Genomics England Curator)

Publications for PRODH were set to 12217952

28 Feb 2017, Gel status: 4

Set Mode of Inheritance

Sarah Leigh (Genomics England Curator)

Mode of inheritance for PRODH was changed to BIALLELIC, autosomal or pseudoautosomal

28 Feb 2017, Gel status: 4

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for PRODH were set to Hyperprolinemia, type I, 239500;{Schizophrenia, susceptibility to, 4}, 600850

28 Feb 2017, Gel status: 4

Gene classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

28 Feb 2017, Gel status: 4

Gene classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

This gene has been classified as Green List (High Evidence).

13 Nov 2015, Gel status: 1

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: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

PRODH was added to Intellectual disabilitypanel. Source: Expert Review Red

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

PRODH was added to Intellectual disabilitypanel. Sources: Radboud University Medical Center, Nijmegen