Renal ciliopathies

Gene: XPNPEP3

Green List (high evidence)

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

3 reviews

Sarah Leigh (Genomics England Curator)

Green List (high evidence)

The rating of this gene has been updated to Green following NHS Genomic Medicine Service approval.
Created: 30 Jan 2023, 3:08 p.m. | Last Modified: 30 Jan 2023, 4:06 p.m.
Panel Version: 2.3
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, 5:15 p.m. | Last Modified: 11 Jan 2022, 5:15 p.m.
Panel Version: 1.49
Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review.
Created: 11 Jan 2022, 3:37 p.m. | Last Modified: 11 Jan 2022, 3:37 p.m.
Panel Version: 1.49

Zornitza Stark (Australian Genomics)

Green List (high evidence)

PMID 20179356: two families with 5 individuals reported. Functional data, including animal models, supportive evidence for involvement in ciliary function.

PMID 32660933: Additional case reported.
Created: 10 May 2021, 10:09 a.m. | Last Modified: 10 May 2021, 10:09 a.m.
Panel Version: 1.41

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Nephronophthisis-like nephropathy 1, OMIM #613159

Publications

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

Alice Gardham (Genomics England)

Red List (low evidence)

Mutations only identified in 2 families. Not offered on GOS ciliopathy panel. Possible DD on G2P
Created: 19 Jan 2017, 3:44 p.m.

Mode of inheritance
BIALLELIC, autosomal or pseudoautosomal

Phenotypes
Nephronophthisis-like nephropathy 1 613159

Publications

Details

Mode of Inheritance
BIALLELIC, autosomal or pseudoautosomal
Sources
  • NHS GMS
  • Expert Review Green
  • Illumina TruGenome Clinical Sequencing Services
  • Orphanet
  • Emory Genetics Laboratory
  • Radboud University Medical Center, Nijmegen
Phenotypes
  • Nephronophthisis-like nephropathy 1 OMIM:613159
  • nephronophthisis-like nephropathy 1 MONDO:0013163
OMIM
613553
Clinvar variants
Variants in XPNPEP3
Penetrance
None
Publications
Panels with this gene

History Filter Activity

30 Jan 2023, Gel status: 3

Removed Tag

Sarah Leigh (Genomics England Curator)

Tag Q1_22_rating was removed from gene: XPNPEP3.

30 Jan 2023, Gel status: 3

Added New Source, Added New Source, Status Update

Sarah Leigh (Genomics England Curator)

Source Expert Review Green was added to XPNPEP3. Source NHS GMS was added to XPNPEP3. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)

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

10 Jul 2019, Gel status: 1

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

Eleanor Williams (Genomics England Curator)

gene: XPNPEP3 was added gene: XPNPEP3 was added to Renal ciliopathies. Sources: Radboud University Medical Center, Nijmegen,Emory Genetics Laboratory,Orphanet,Expert Review Red,Illumina TruGenome Clinical Sequencing Services 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; Ciliopathies; Nephronophthisis-like nephropathy 1, 613159