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Early onset or syndromic epilepsy v2.178 USP7 Arina Puzriakova Publications for gene: USP7 were set to 26365382; 19946331
Early onset or syndromic epilepsy v2.177 USP7 Arina Puzriakova Phenotypes for gene: USP7 were changed from Intellectual disability, autism, epilepsy, aggressive behaviour, hypotonia, and hypogonadism to Hao-Fountain syndrome, 616863
Early onset or syndromic epilepsy v2.122 TMEM106B Konstantinos Varvagiannis gene: TMEM106B was added
gene: TMEM106B was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: TMEM106B was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: TMEM106B were set to 29186371; 29444210; 32595021
Phenotypes for gene: TMEM106B were set to Leukodystrophy, hypomyelinating, 16 (MIM #617964)
Penetrance for gene: TMEM106B were set to Complete
Mode of pathogenicity for gene: TMEM106B was set to Loss-of-function variants (as defined in pop up message) DO NOT cause this phenotype - please provide details in the comments
Review for gene: TMEM106B was set to AMBER
Added comment: 6 unrelated individuals with Leukodystrophy, hypomyelinating, 16 (MIM #617964) due to a recurrent TMEM106B variant have been reported to date in the literature (Simons et al 2017 - PMID: 29186371, Yan et al 2018 - PMID: 29444210, Ikemoto et al 2020 - PMID: 32595021).

While a 3 y.o. female described by Yan et al had DD (eg sitting at 9m, walking at 25m) with normal cognitive functioning, and a 38 y.o. female had borderline intellectual functioning (IQ 76), 4 affected individuals had ID. Among them, a 19 y.o. male with severe ID was also found to harbor a second de novo possibly damaging USP7 variant. Seizures have been reported in 2 unrelated subjects. [Clinical features are also summarized in table 1 - Ikemoto et al].

All harbored NM_001134232.2(TMEM106B):c.754G>A (p.Asp252Asn) which in almost all cases occurred as a de novo event. In a single case this variant was inherited from a mosaic parent with mild DD in infancy but normal cognition (reported by Simons et al).

As discussed by Ito et al (2018 - PMID: 30643851) the encoded protein is a structural component of the lysosomal membrane, playing a role on lysosome acidification. Acidity of the lysosome mediates multiple aspects of lysosomal function. Ito et al, using patient-derived fibroblasts assessed mRNA and protein levels. These were unaltered compared with controls. While TMEM106B had been previously shown to affect lysosome number, morphology and acidification, Ito et al demonstrated increased number of lysosomes in patient cells as well as impaired acidification compared to controls. As commented lysosomes are required for generation of myelin.

Recurrence of this missense variant, the presence of pLoF TMEM106B variants in gnomAD as well as the phenotypically normal Tmem106b null mice suggest that this variant may have a gain-of-function or dominant negative effect.

Genes for other forms of hypomyelinating lipodystrophy (incl. PLP1) have green rating in the ID panel.

Overall TMEM106B can be considered for the ID panel with green rating and the epilepsy panel with amber rating.
Sources: Literature
Early onset or syndromic epilepsy v1.331 USP7 Rebecca Foulger Source Wessex and West Midlands GLH was added to USP7.
Early onset or syndromic epilepsy v1.330 USP7 Rebecca Foulger Source NHS GMS was added to USP7.
Early onset or syndromic epilepsy v1.307 USP7 Rebecca Foulger Marked gene: USP7 as ready
Early onset or syndromic epilepsy v1.307 USP7 Rebecca Foulger Gene: usp7 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v1.307 USP7 Rebecca Foulger commented on gene: USP7: Kept rating as Amber based on two post-Webex Amber reviews from Helen Lord and Alison Callaway.
Early onset or syndromic epilepsy v1.262 USP7 Rebecca Foulger edited their review of gene: USP7: Added comment: Review and rating collated by Helen Lord (Oxford University Hospitals NHS Foundation Trust, 2019_08_30) on behalf of West Midlands, Oxford and Wessex GLH for GMS Neurology specialist test group. This gene was added to the Genetic epilepsy syndromes panel after the initial panel was reviewed by West Midlands, Oxford and Wessex GLH: this gene was therefore reviewed following the group Webex call on 2019_08_08 for Clinical Indication R59 Early onset or syndromic epilepsy.; Changed rating: AMBER
Early onset or syndromic epilepsy v1.261 USP7 Helen Lord reviewed gene: USP7: Rating: AMBER; Mode of pathogenicity: ; Publications: ; Phenotypes: ; Mode of inheritance: MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Early onset or syndromic epilepsy v1.256 USP7 Alison Callaway reviewed gene: USP7: Rating: AMBER; Mode of pathogenicity: None; Publications: ; Phenotypes: ; Mode of inheritance: None
Early onset or syndromic epilepsy v1.101 USP7 Rebecca Foulger Classified gene: USP7 as Amber List (moderate evidence)
Early onset or syndromic epilepsy v1.101 USP7 Rebecca Foulger Added comment: Comment on list classification: USP7 was added to the panel and rated Green by Konstantinos Varvagiannis. Not currently associated with a disorder in OMIM, but has a 'possible' Disease confidence in Gene2Phenotype for the disorder: Intellectual disability, autism, epilepsy, aggressive behaviour, hypotonia, and hypogonadism (based on PMID:26365382). There is now a 2019 paper in addition to PMID:26365382 (PMID:30679821). In total, nearly half (10/22) individuals have a seizure phenotype. However, the Tyr143Ter variant described by both PMID:26365382 and PMID:30679821 is a VUS, and the microdeletions in other patients cover additional genes (PMID:26365382 Figure 5). Plus three patients in PMID:30679821 harbour variants in additional genes. Rated Amber until there is more evidence that USP7 variants are causative for the seizure phenotype.
Early onset or syndromic epilepsy v1.101 USP7 Rebecca Foulger Gene: usp7 has been classified as Amber List (Moderate Evidence).
Early onset or syndromic epilepsy v1.100 USP7 Rebecca Foulger commented on gene: USP7: PMID:30679821: Fountain et al., 2019 report on the clinical and genetic spectrum of 16 new and 7 previously reported (by PMID:26365382) individuals with USP7 heterozygous de novo variants. The variants include 2 deletions, 3 nonsense, 3 splice site variants and 8 missense variants. Seizures are recorded in 10/22 patients. Note that Patients 18 and 20 harbor additional variants in TMEM106B and SLC2A1, Patient 19 also has a de novo heterozygous 102.5-kb mosaic loss of uncertain significance at 10q21.1.
Early onset or syndromic epilepsy v1.100 USP7 Rebecca Foulger commented on gene: USP7
Early onset or syndromic epilepsy v1.100 USP7 Rebecca Foulger Phenotypes for gene: USP7 were changed from Intellectual disability, autism, epilepsy, aggressive behaviour, hypotonia, and hypogonadism to Intellectual disability, autism, epilepsy, aggressive behaviour, hypotonia, and hypogonadism
Early onset or syndromic epilepsy v1.100 USP7 Rebecca Foulger Phenotypes for gene: USP7 were changed from Global developmental delay; Delayed speech and language development; Intellectual disability; Behavioral abnormality; Seizures; Abnormality of brain morphology; Hypogonadism to Intellectual disability, autism, epilepsy, aggressive behaviour, hypotonia, and hypogonadism
Early onset or syndromic epilepsy v1.13 USP7 Konstantinos Varvagiannis gene: USP7 was added
gene: USP7 was added to Genetic epilepsy syndromes. Sources: Literature
Mode of inheritance for gene: USP7 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: USP7 were set to 26365382; 19946331
Phenotypes for gene: USP7 were set to Global developmental delay; Delayed speech and language development; Intellectual disability; Behavioral abnormality; Seizures; Abnormality of brain morphology; Hypogonadism
Penetrance for gene: USP7 were set to unknown
Review for gene: USP7 was set to GREEN
Added comment: Fountain et al. (2019 - doi.org/10.1038/s41436-019-0433-1 - PMID: NA) report on 23 individuals, all of whom harbored pathogenic de novo variants affecting USP7.

Variants included 8 deletions spanning USP7 (and other proximal genes - the gene is located at 16p13.2), 4 nonsense, 8 missense and 3 splice site mutations.

Haploinsufficiency appears to be the underlying mechanism (as suggested by the type of variants reported).

The common phenotype consisted of DD/ID (almost universal feature - 22/23) with prominent speech delay (23/23). Other features included seizures (10/22 - seen in all categories of USP7 variants), variable behavioral anomalies (incl. aggressive behavior, temper tantrums, ASD, ADHD), brain MRI abnormalities, as well as hypogonadism in some.

7 of these (23) individuals (6 with deletions, 1 with nonsense variant) were previously reported by the same group (2015 - Hao et al. - PMID: 26365382). In this study, the authors provided evidence that USP7 encodes a deubiquitinating enzyme, component of the MAGEL2/TRIM27 ubiquitin ligase complex. USP7 is involved in fine-tuning of the WASH activity - a protein involved in endosomal actin assembly and protein recycling - by promoting or limiting WASH ubiquitination (the former achieved by preventing TRIM27 autoubiquitination and degradation and the latter by direct WASH deubiquitination).

Overlap to some extent of the USP7-related phenotype with Schaaf-Yang syndrome (due to MAGEL2 mutations - MIM615547) is suggested.

In mice, Usp7 (or Hausp - herpesvirus-associated ubiquitin-specific protease) conditional knockout in brain results in neonatal lethality (PMID cited: 19946331).
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USP7 is not associated with any phenotype in OMIM.
This gene is part of the DD panel of G2P, associated with "Intellectual disability, autism, epilepsy, aggressive behaviour, hypotonia, and hypogonadism" (Disease confidence: possible).
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As a result, this gene can be considered for inlusion in this panel as green (or amber).
Sources: Literature