Intellectual disability - microarray and sequencing
Gene: USP7The rating of this gene has been updated following NHS Genomic Medicine Service approval.Created: 9 Mar 2022, 3:40 p.m. | Last Modified: 9 Mar 2022, 3:40 p.m.
Panel Version: 3.1510
Comment on list classification: Based on published evidence and expert reviews, this gene should be promoted from Amber to Green at the next GMS panel update (added 'for-review' tag)Created: 15 Oct 2020, 4:06 p.m. | Last Modified: 15 Oct 2020, 4:06 p.m.
Panel Version: 3.452
USP7 is now associated with Hao-Fountain syndrome (MIM# 616863) in OMIM, and the disease confidence for 'USP7-related developmental disorder' in Gen2Phen has been upgraded from 'possible' to 'probable'.
In total, 23 individuals reported across 3 publications with an ID/DD phenotype, associated with de novo variants in USP7.Created: 15 Oct 2020, 4:02 p.m. | Last Modified: 15 Oct 2020, 4:02 p.m.
Panel Version: 3.451
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes
Hao-Fountain syndrome, 616863
Publications
The number of individuals with de novo variants in this gene is large, even if those with microdeletions +/- ?second diagnostic findings are completely discounted. I am not sure who has assessed the Tyr143Ter variant as a VOUS and what their reasoning was: it is de novo and absent from gnomad, and easily meets criteria for pathogenicity if gene-disease association is considered established. I also note the almost complete absence of LoF variants in this gene in gnomad.Created: 2 Mar 2020, 5:20 a.m. | Last Modified: 2 Mar 2020, 5:20 a.m.
Panel Version: 3.3
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, NOT imprinted
Phenotypes
ID; Autism
Publications
Variants in this GENE are reported as part of current diagnostic practice
Comment on list classification: USP7 was 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, 22/23 individuals have an ID/DD phenotype, and 23/23 have speech delay. 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. Therefore although the phenotype is relevant, I have updated the rating from Red to Amber until there is more evidence that USP7 variants are causative.Created: 2 Jul 2019, 2:26 p.m. | Last Modified: 2 Jul 2019, 2:26 p.m.
Panel Version: 2.935
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. Speech delay was seen in 23/23 patients, and ID/DD was seen in 22/23 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.Created: 2 Jul 2019, 2:21 p.m. | Last Modified: 2 Jul 2019, 2:21 p.m.
Panel Version: 2.933
PMID:26365382: Hao et al., 2015 queried clinical databases to identify 6 cases with de novo heterozygous chromosomal microdeletions (varying from 267kb - 4.74Mb), and one case with a heterozygous nonsense variant in USP7. DD/ID was seen in 7/7 patients. Note that the Tyr143Ter variant described is listed as a VUS in OMIM.Created: 2 Jul 2019, 2:21 p.m. | Last Modified: 2 Jul 2019, 2:21 p.m.
Panel Version: 2.933
Please consider also PMID : 33012787 for Green rating (several cases reported to date).Created: 10 Oct 2020, 10:08 p.m. | Last Modified: 10 Oct 2020, 10:09 p.m.
Panel Version: 3.420
This gene was previously included in the current panel, rated red, though with no reviews (Source : Victorian Clinical Genetics Services).
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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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USP7 is included in gene panels for ID offered by diagnostic laboratories (incl. also Radboudumc).
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As a result, this gene can be considered for upgrade to green.Created: 26 Jan 2019, 11:18 a.m.
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Phenotypes
Global developmental delay; Delayed speech and language development; Intellectual disability; Behavioral abnormality; Seizures; Abnormality of brain morphology; Hypogonadism
Publications
Variants in this GENE are reported as part of current diagnostic practice
Tag for-review was removed from gene: USP7.
Source Expert Review Green was added to USP7. Rating Changed from Amber List (moderate evidence) to Green List (high evidence)
Publications for gene: USP7 were set to 30679821; 26365382; 19946331
Phenotypes for gene: USP7 were changed from Intellectual disability, autism, epilepsy, aggressive behaviour, hypotonia, and hypogonadism to Hao-Fountain syndrome, 616863
Gene: usp7 has been classified as Amber List (Moderate Evidence).
Tag for-review tag was added to gene: USP7.
Phenotypes for gene: USP7 were changed from to Intellectual disability, autism, epilepsy, aggressive behaviour, hypotonia, and hypogonadism
Gene: usp7 has been classified as Amber List (Moderate Evidence).
Gene: usp7 has been classified as Red List (Low Evidence).
Mode of inheritance for gene: USP7 was changed from to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Publications for gene: USP7 were set to
gene: USP7 was added gene: USP7 was added to Intellectual disability. Sources: Victorian Clinical Genetics Services Mode of inheritance for gene: USP7 was set to