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Mitochondrial disorders v3.6 XPNPEP3 Achchuthan Shanmugasundram changed review comment from: After NHS Genomic Medicine Service consideration, the rating of this gene has not been changed and remains Amber.; to: After NHS Genomic Medicine Service consideration, the rating of this gene has not been changed and remains Amber.

Note from GMS reviewers: The phenotype arising from mutation of this gene is not that of mitochondrial disease. Not sure there is sufficient evidence that this can be classified as primary mitochondrial disease, but may be appropriate to include elsewhere in white matter disorders panel (C&S).
Mitochondrial disorders v3.6 XPNPEP3 Achchuthan Shanmugasundram Tag Q2_21_rating was removed from gene: XPNPEP3.
Tag Q2_21_phenotype was removed from gene: XPNPEP3.
Tag Q2_21_expert_review was removed from gene: XPNPEP3.
Mitochondrial disorders v3.6 XPNPEP3 Achchuthan Shanmugasundram reviewed gene: XPNPEP3: Rating: AMBER; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance:
Mitochondrial disorders v2.177 XPNPEP3 Eleanor Williams Tag Q1_22_rating was removed from gene: XPNPEP3.
Tag Q2_21_rating tag was added to gene: XPNPEP3.
Mitochondrial disorders v2.107 XPNPEP3 Eleanor Williams Tag Q2_21_expert_review tag was added to gene: XPNPEP3.
Mitochondrial disorders v2.84 XPNPEP3 Sarah Leigh Deleted their comment
Mitochondrial disorders v2.84 XPNPEP3 Sarah Leigh changed review comment from: Associated with relevant phenotype in OMIM and as limited Gen2Phen gene. At least three variants reported in three unrelated cases (PMID: 32660933; 20179356). Two of the variants were terminating (RCV000000069, RCV001554332) and the third variant 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).; to: 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).
Mitochondrial disorders v2.84 XPNPEP3 Sarah Leigh changed review comment from: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review, however, Zornitza Stark (Australian Genomics) has commented that the phenotype is not strickly a mitochondrial disorder.; to: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review, however, Zornitza Stark (Australian Genomics) has commented that the phenotype is not strictly a mitochondrial disorder.
Mitochondrial disorders v2.84 XPNPEP3 Sarah Leigh changed review comment from: Associated with relevant phenotype in OMIM and as limited Gen2Phen gene. At least three variants reported in three unrelated cases (PMID: 32660933; 20179356). Two of the variants were terminating (RCV000000069, RCV001554332) and the third variant 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.; to: Associated with relevant phenotype in OMIM and as limited Gen2Phen gene. At least three variants reported in three unrelated cases (PMID: 32660933; 20179356). Two of the variants were terminating (RCV000000069, RCV001554332) and the third variant 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).
Mitochondrial disorders v2.84 XPNPEP3 Sarah Leigh edited their review of gene: XPNPEP3: Added comment: Associated with relevant phenotype in OMIM and as limited Gen2Phen gene. At least three variants reported in three unrelated cases (PMID: 32660933; 20179356). Two of the variants were terminating (RCV000000069, RCV001554332) and the third variant 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.; Changed rating: AMBER
Mitochondrial disorders v2.84 XPNPEP3 Sarah Leigh Classified gene: XPNPEP3 as Amber List (moderate evidence)
Mitochondrial disorders v2.84 XPNPEP3 Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review, however, Zornitza Stark (Australian Genomics) has commented that the phenotype is not strickly a mitochondrial disorder.
Mitochondrial disorders v2.84 XPNPEP3 Sarah Leigh Gene: xpnpep3 has been classified as Amber List (Moderate Evidence).
Mitochondrial disorders v2.84 XPNPEP3 Sarah Leigh Classified gene: XPNPEP3 as Amber List (moderate evidence)
Mitochondrial disorders v2.84 XPNPEP3 Sarah Leigh Added comment: Comment on list classification: There is enough evidence for this gene to be rated GREEN at the next major review, however, Zornitza Stark (Australian Genomics) has commented that the phenotype is not strickly a mitochondrial disorder.
Mitochondrial disorders v2.84 XPNPEP3 Sarah Leigh Gene: xpnpep3 has been classified as Amber List (Moderate Evidence).
Mitochondrial disorders v2.83 XPNPEP3 Sarah Leigh Tag Q2_21_phenotype tag was added to gene: XPNPEP3.
Tag Q1_22_rating tag was added to gene: XPNPEP3.
Mitochondrial disorders v2.83 XPNPEP3 Sarah Leigh Phenotypes for gene: XPNPEP3 were changed from nephronophthisis-like nephropathy to Nephronophthisis-like nephropathy 1 OMIM:613159; nephronophthisis-like nephropathy 1 MONDO:0013163
Mitochondrial disorders v2.82 XPNPEP3 Sarah Leigh Publications for gene: XPNPEP3 were set to 20179356
Mitochondrial disorders v2.81 XPNPEP3 Sarah Leigh Publications for gene: XPNPEP3 were set to PMID: 20179356
Mitochondrial disorders v2.5 XPNPEP3 Zornitza Stark reviewed gene: XPNPEP3: Rating: RED; Mode of pathogenicity: None; Publications: 20179356; Phenotypes: Nephronophthisis-like nephropathy 1, MIM#613159; Mode of inheritance: BIALLELIC, autosomal or pseudoautosomal