DDG2P
Gene: XPNPEP3 Red List (low evidence)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
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
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
I don't know
Original DDG2P rating: possible.Created: 19 Nov 2018, 11:31 a.m.
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)
Tag Q1_22_rating was removed from gene: XPNPEP3.
Tag Q1_22_rating tag was added to gene: XPNPEP3.
Gene: xpnpep3 has been classified as Amber List (Moderate Evidence).
Publications for gene: XPNPEP3 were set to 20179356
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
Rebecca Foulger: Original DDG2P rating: possibl
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
If promoting or demoting a gene, please provide comments to justify a decision to move it.
Genes included in a Genomics England gene panel for a rare disease category (green list) should fit the criteria A-E outlined below.
These guidelines were developed as a combination of the ClinGen DEFINITIVE evidence for a causal role of the gene in the disease(a), and the Developmental Disorder Genotype-Phenotype (DDG2P) CONFIRMED DD Gene evidence level(b) (please see the original references provided below for full details). These help provide a guideline for expert reviewers when assessing whether a gene should be on the green or the red list of a panel.
A. There are plausible disease-causing mutations(i) within, affecting or encompassing an interpretable functional region(ii) of this gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
B. There are plausible disease-causing mutations(i) within, affecting or encompassing cis-regulatory elements convincingly affecting the expression of a single gene identified in multiple (>3) unrelated cases/families with the phenotype(iii).
OR
C. As definitions A or B but in 2 or 3 unrelated cases/families with the phenotype, with the addition of convincing bioinformatic or functional evidence of causation e.g. known inborn error of metabolism with mutation in orthologous gene which is known to have the relevant deficient enzymatic activity in other species; existence of an animal model which recapitulates the human phenotype.
AND
D. Evidence indicates that disease-causing mutations follow a Mendelian pattern of causation appropriate for reporting in a diagnostic setting(iv).
AND
E. No convincing evidence exists or has emerged that contradicts the role of the gene in the specified phenotype.
(i)Plausible disease-causing mutations: Recurrent de novo mutations convincingly affecting gene function. Rare, fully-penetrant mutations - relevant genotype never, or very rarely, seen in controls. (ii) Interpretable functional region: ORF in protein coding genes miRNA stem or loop. (iii) Phenotype: the rare disease category, as described in the eligibility statement. (iv) Intermediate penetrance genes should not be included.
It’s assumed that loss-of-function variants in this gene can cause the disease/phenotype unless an exception to this rule is known. We would like to collect information regarding exceptions. An example exception is the PCSK9 gene, where loss-of-function variants are not relevant for a hypercholesterolemia phenotype as they are associated with increased LDL-cholesterol uptake via LDLR (PMID: 25911073).
If a curated set of known-pathogenic variants is available for this gene-phenotype, please contact us at [email protected]
We classify loss-of-function variants as those with the following Sequence Ontology (SO) terms:
Term descriptions can be found on the PanelApp homepage and Ensembl.
If you are submitting this evaluation on behalf of a clinical laboratory please indicate whether you report variants in this gene as part of your current diagnostic practice by checking the box
Standardised terms were used to represent the gene-disease mode of inheritance, and were mapped to commonly used terms from the different sources. Below each of the terms is described, along with the equivalent commonly-used terms.
A variant on one allele of this gene can cause the disease, and imprinting has not been implicated.
A variant on the paternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on the maternally-inherited allele of this gene can cause the disease, if the alternate allele is imprinted (function muted).
A variant on one allele of this gene can cause the disease. This is the default used for autosomal dominant mode of inheritance where no knowledge of the imprinting status of the gene required to cause the disease is known. Mapped to the following commonly used terms from different sources: autosomal dominant, dominant, AD, DOMINANT.
A variant on both alleles of this gene is required to cause the disease. Mapped to the following commonly used terms from different sources: autosomal recessive, recessive, AR, RECESSIVE.
The disease can be caused by a variant on one or both alleles of this gene. Mapped to the following commonly used terms from different sources: autosomal recessive or autosomal dominant, recessive or dominant, AR/AD, AD/AR, DOMINANT/RECESSIVE, RECESSIVE/DOMINANT.
A variant on one allele of this gene can cause the disease, however a variant on both alleles of this gene can result in a more severe form of the disease/phenotype.
A variant in this gene can cause the disease in males as they have one X-chromosome allele, whereas a variant on both X-chromosome alleles is required to cause the disease in females. Mapped to the following commonly used term from different sources: X-linked recessive.
A variant in this gene can cause the disease in males as they have one X-chromosome allele. A variant on one allele of this gene may also cause the disease in females, though the disease/phenotype may be less severe and may have a later-onset than is seen in males. X-linked inactivation and mosaicism in different tissues complicate whether a female presents with the disease, and can change over their lifetime. This term is the default setting used for X-linked genes, where it is not known definitately whether females require a variant on each allele of this gene in order to be affected. Mapped to the following commonly used terms from different sources: X-linked dominant, x-linked, X-LINKED, X-linked.
The gene is in the mitochondrial genome and variants within this can cause this disease, maternally inherited. Mapped to the following commonly used term from different sources: Mitochondrial.
Mapped to the following commonly used terms from different sources: Unknown, NA, information not provided.
For example, if the mode of inheritance is digenic, please indicate this in the comments and which other gene is involved.