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Intellectual disability

Gene: XPNPEP3

Red List (low evidence)

XPNPEP3 (X-prolyl aminopeptidase 3)
EnsemblGeneIds (GRCh38): ENSG00000196236
EnsemblGeneIds (GRCh37): ENSG00000196236
OMIM: 613553, Gene2Phenotype
XPNPEP3 is in 15 panels

4 reviews

Sarah Leigh (Genomics England Curator)

Red List (low evidence)

Associated with 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).
So far only one case of Nephronophthisis-like nephropathy 1 OMIM:613159 has displayed intellectual disability (PMID: 20179356).
Created: 11 Jan 2022, 5:34 p.m. | Last Modified: 11 Jan 2022, 5:34 p.m.
Panel Version: 3.1493

Caroline Wright (Sanger)

Red List (low evidence)

Phenotypes
NEPHRONOPHTHISIS-LIKE NEPHROPATHY TYPE 1 (NPHPL1)

Rebecca Foulger (Genomics England curator)

Red List (low evidence)

Mental retardation reported in 1 family (PMID:20179356): no further recent studies so insufficient cases to support causation.
Created: 31 Oct 2017, 9:24 a.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Nephronophthisis-like nephropathy 1, 613159

Publications

Lu Raymond (university of cambridge )

Red List (low evidence)

History Filter Activity

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 1, 613159 to Nephronophthisis-like nephropathy 1 OMIM:613159; nephronophthisis-like nephropathy 1 MONDO:0013163

29 Sep 2018, Gel status: 1

Added New Source

Louise Daugherty (Genomics England Curator)

Source Victorian Clinical Genetics Services was added to XPNPEP3.

12 Mar 2018, Gel status: 1

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: 1

Set mode of inheritance, Set publications

Ellen McDonagh (Genomics England Curator)

Model of inheritance for gene XPNPEP3 was set to BIALLELIC, autosomal or pseudoautosomal Publications for gene XPNPEP3 was set to ['20179356']

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)

XPNPEP3 was added to Intellectual disabilitypanel. Source: Expert Review Red

24 Jun 2015, Gel status: 1

Added New Source

Ellen McDonagh (Genomics England Curator)

XPNPEP3 was added to Intellectual disabilitypanel. Sources: Radboud University Medical Center, Nijmegen