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DDG2P

Gene: XPNPEP3

Red List (low evidence)
XPNPEP3 (X-prolyl aminopeptidase 3)
EnsemblGeneIds (GRCh38): ENSG00000196236
EnsemblGeneIds (GRCh37): ENSG00000196236
OMIM: 613553, Gene2Phenotype
XPNPEP3 is in 18 panels

4 reviews

Achchuthan Shanmugasundram (Genomics England Curator)

Red List (low evidence)

The DDG2P confidence category for the disease NEPHRONOPHTHISIS-LIKE NEPHROPATHY TYPE 1, OMIM:613159 is limited. The allelic requirement and mutation consequence are biallelic_autosomal and absent gene product (PMID:20179356).
Created: 4 Oct 2023, 5:08 p.m. | Last Modified: 4 Oct 2023, 5:08 p.m.
Panel Version: 3.12

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
NEPHRONOPHTHISIS-LIKE NEPHROPATHY TYPE 1, OMIM:613159

Publications

Created: 4 Oct 2023, 5:08 p.m.
Last Modified: 4 Oct 2023, 5:08 p.m.
Panel version: 3.12

Eleanor Williams (Genomics England Curator)

The GMS review tag has been removed. This gene is tagged for green rating on the renal ciliopathies panel which is part of the Paediatric disorders superpanel so should be made green shortly on the super panel.

The DDG2P panel as a whole will also be shortly updated to reflect the current DDG2P panel in the Gene2Phenotype resource.
Created: 3 Aug 2022, 4:37 p.m. | Last Modified: 3 Aug 2022, 4:37 p.m.
Panel Version: 2.76
Created: 3 Aug 2022, 4:37 p.m.
Last Modified: 3 Aug 2022, 4:37 p.m.
Panel version: 2.76

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

Associated with relevant phenotype in OMIM and as limited Gen2Phen gene. At least three variants were reported in three unrelated cases (PMID: 32660933; 20179356). Two of the variants were terminating (RCV000000069, RCV001554332) and the third was a missense variant (RCV000000068), that seems to activate a cryptic splice site; RT-PCR of lymphoblastoid cells showed that this resulted in the inclusion of intronic bases and a frameshift. Cilia-related function was examined by the suppression of zebrafish xpnpep3, resulting in phenotypes reminiscent of ciliopathy morphants, this effect was rescued by human XPNPEP3 that was devoid of a mitochondrial localization signal (PMID: 20179356).
Created: 11 Jan 2022, 5:27 p.m. | Last Modified: 11 Jan 2022, 5:27 p.m.
Panel Version: 2.60
Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review.
Created: 11 Jan 2022, 3:53 p.m. | Last Modified: 11 Jan 2022, 3:53 p.m.
Panel Version: 2.60
Created: 11 Jan 2022, 3:53 p.m.
Last Modified: 11 Jan 2022, 3:53 p.m.
Panel version: 2.60

Rebecca Foulger (Genomics England curator)

I don't know

Original DDG2P rating: possible.
Created: 19 Nov 2018, 11:31 a.m.
Created: 19 Nov 2018, 11:31 a.m.

Panel version: 0.2

History Filter Activity

4 Oct 2023, Gel status: 1

Added New Source, Set publications, Status Update

Achchuthan Shanmugasundram (Genomics England Curator)

Source Expert Review Red was added to XPNPEP3. Publications for gene: XPNPEP3 were updated from 20179356; 32660933 to 20179356; 32660933 Rating Changed from Amber List (moderate evidence) to Red List (low evidence)

3 Aug 2022, Gel status: 2

Removed Tag

Eleanor Williams (Genomics England Curator)

Tag Q1_22_rating was removed from gene: XPNPEP3.

11 Jan 2022, Gel status: 2

Added Tag

Sarah Leigh (Genomics England Curator)

Tag Q1_22_rating tag was added to gene: XPNPEP3.

11 Jan 2022, Gel status: 2

Entity classified by Genomics England curator

Sarah Leigh (Genomics England Curator)

Gene: xpnpep3 has been classified as Amber List (Moderate Evidence).

11 Jan 2022, Gel status: 1

Set publications

Sarah Leigh (Genomics England Curator)

Publications for gene: XPNPEP3 were set to 20179356

11 Jan 2022, Gel status: 1

Set Phenotypes

Sarah Leigh (Genomics England Curator)

Phenotypes for gene: XPNPEP3 were changed from NEPHRONOPHTHISIS-LIKE NEPHROPATHY TYPE 1 613159 to Nephronophthisis-like nephropathy 1 OMIM:613159; nephronophthisis-like nephropathy 1 MONDO:0013163

29 Jan 2019, Gel status: 1

Panel promoted to version 1.0

Rebecca Foulger (Genomics England curator)

Rebecca Foulger: Original DDG2P rating: possibl

19 Nov 2018, Gel status: 1

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

Rebecca Foulger (Genomics England curator)

gene: XPNPEP3 was added gene: XPNPEP3 was added to DDG2P. Sources: Expert Review Red,DD-Gene2Phenotype Mode of inheritance for gene: XPNPEP3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene: XPNPEP3 were set to 20179356 Phenotypes for gene: XPNPEP3 were set to NEPHRONOPHTHISIS-LIKE NEPHROPATHY TYPE 1 613159