Biallelic variants in TMEM222 cause a new autosomal recessive neurodevelopmental disorder

Polla, Daniel L.; Fard, Mohammad Ali Farazi; Tabatabaei, Zahra; Habibzadeh, Parham; Levchenko, Olga A.; Nikuei, Pooneh; Hussain, Mureed; Hardenberg, Sandra von; Zeinali, Sirous; Fallah, Mohammad; Schuurs-Hoeijmakers, Janneke; Shahzad, Mohsin; Fareeha, Fatima; Fatima, Naz; Kaat, Laura Donker; Brüggenwirth, Hennie T.; Fleming, Leah; Condie, John; Płoski, Rafał; Pollak, Agnieszka; Pilch, Jacek; Демина, Н. А.; Чухрова, А. Л.; Sergeeva, Vasilina S.; Venselaar, Hanka; Masri, Amira; Hamamy, Hanan; Santoni, Federico; Linda, Katrin; Ahmed, Zubair M.; Kasri, Nael Nadif; Brouwer, Arjan P.M. de; Bergmann, Anke; Hethey, Sven; Yavarian, Majid; Ansar, Muhammad; Riazuddin, Saima; Riazuddin, Sheikh; Silawi, Mohammad; Ruggeri, Gaia; Pirozzi, Filomena; Eftekhar, Ebrahim; Sheshdeh, Afsaneh Taghipour; Bahramjahan, Shima; Mirzaa, Ghayda; Лавров, А. В.; Antonarakis, Stylianos E.; Faghihi, Mohammad Ali; Bokhoven, Hans van

doi:10.1038/s41436-021-01133-w

Cited by 6 publications

(5 citation statements)

References 38 publications

(42 reference statements)

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“…For instance, C14orf28 (dopamine receptor–interacting protein, DRIP1 ( 178 )) retains papain-like deubiquitinase domain with additional, second “fingers”-like domain. DUF7788, a family of uncharacterized transmembrane proteins, includes not only A. thaliana RTE1 (ethylene signaling ( 179 , 180 , 181 )) but also human TMEM222 (C1orf160) predominantly found in brain ( 182 ), and deleterious variants of which correlate with neurodevelopmental disorders ( 183 ). Human CEP76 and DRC7 from KOG3639 family contain potentially active papain-like domain and might be involved in altering centriole dynamics.…”

Section: Resultsmentioning

confidence: 99%

Identification and classification of papain-like cysteine proteinases

Ozhelvaci

Steczkiewicz

2023

Journal of Biological Chemistry

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Section: Resultsmentioning

confidence: 99%

Identification and classification of papain-like cysteine proteinases

Ozhelvaci

Steczkiewicz

2023

Journal of Biological Chemistry

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“…Matching to multiple other cases reported in GeneMatcher enabled establishment of novel causative gene–disease associations, namely TMEM222 (FAM_60), ZNFX1 (FAM_75) and GAD1 (FAM_116). Biallelic p/lp variants in TMEM222 cause an autosomal recessive neurodevelopmental disorder ( 25 ), biallelic p/lp variants in ZNFX1 lead to multisystem inflammation and susceptibility to viral infections ( 26 ) and biallelic p/lp variants in GAD1 are causal for an early-infantile onset epilepsy and developmental delay ( 27 , 28 ). GeneMatcher matches were obtained for five additional genes; these genes are currently subject of further investigation (data not shown).…”

Section: Resultsmentioning

confidence: 99%

“…The combination of a thorough analysis of the sequencing data (and CNV data), including literature search of candidate genes and the use of GeneMatcher seems to be very effective. In this study, a diagnosis was established in three cases using GeneMatcher ( 25 , 26 , 28 ) and another five cases are currently subject of further analysis after identification of further patients via GeneMatcher (data not shown). This corresponds to a rate of 1.9% (3/157) of definitely and an additional 3.2% (5/157) of potentially solved cases using GeneMatcher in all analysed 157 tWES families with an initially negative or inconclusive diagnostic report.…”

Section: Discussionmentioning

confidence: 99%

A holistic approach to maximise diagnostic output in trio exome sequencing

Hardenberg

Wallaschek

et al. 2023

Front. Pediatr.

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IntroductionRare genetic diseases are a major cause for severe illness in children. Whole exome sequencing (WES) is a powerful tool for identifying genetic causes of rare diseases. For a better and faster assessment of the vast number of variants that are identified in the index patient in WES, parental sequencing can be applied (“trio WES”).MethodsWe assessed the diagnostic rate of routine trio WES including analysis of copy number variants in 224 pediatric patients during an evaluation period of three years.ResultsTrio WES provided a diagnosis in 67 (30%) of all 224 analysed children. The turnaround time of trio WES analysis has been reduced significantly from 41 days in 2019 to 23 days in 2021. Copy number variants could be identified to be causative in 10 cases (4.5%), underlying the importance of copy number variant analysis. Variants in three genes which were previously not associated with a clinical condition (GAD1, TMEM222 and ZNFX1) were identified using the matching tool GeneMatcher and were part of the first description of a new syndrome.DiscussionTrio WES has proven to have a high diagnostic yield and to shorten the process of identifying the correct diagnosis in paediatric patients. Re-evaluation of all 224 trio WES 1–3 years after initial analysis did not establish new diagnoses. Initiating (trio) WES as a first-tier diagnostics including copy number variant detection should be considered as early as possible, especially for children treated in ICU, if a monogenetic disease is suspected.

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“…Among these targets, none was a protein kinase or previously identified by ABP-1 as targets, which suggested these proteins may be more detectable in the breast cancer cell line in use here. Some of these targets, such as TMEM222 and CALR, have poorly annotated function but are known to reside in lipid-bound environments such as the early endosomes or endoplasmic reticulum. − …”

Section: Resultsmentioning

confidence: 99%

Precision Targeting of Endogenous Epidermal Growth Factor Receptor (EGFR) by Structurally Aligned Dual-Modifier Labeling

Salazar-Estrada

Kamath

Liu

2022

ACS Pharmacol. Transl. Sci.

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Covalent modification of endogenous proteins by chemical probes is used for proteome-wide profiling of cellular protein function and drug discovery. However, probe selectivity in the complex cellular environment is a challenge, and new probes with better target selectivity are continuously needed. On the basis of the success of monocovalent activity-based and reactivity-based probes, an approach of structurally aligned dual-modifier labeling (SADL) was investigated here on its potential in improving target precision. Two reactive groups, based on the acrylamide and NHS ester chemistry, were linked with structural alignment to be under the same anilinoquinazoline ligand-directive for targeting the epidermal growth factor receptor (EGFR) protein kinase as the model system for proteome-wide profiling. The SADL approach was compared with its monocovalent precursors in a label-free MaxLFQ workflow using MDA-MB-468 triple negative breast cancer cells. The dual-modifier probe consistently showed labeling of EGFR with improved precision over both monocovalent precursors under various controls. The workflow also labeled endogenous USP34 and PKMYT1 with high selectivity. Precision labeling with two covalent modifiers under a common ligand directive may broaden protein identification opportunities in the native environment to complement genetic and antibody-based approaches for elucidating biological or disease mechanisms, as well as accelerating drug target discovery.

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Biallelic variants in TMEM222 cause a new autosomal recessive neurodevelopmental disorder

Cited by 6 publications

References 38 publications

Identification and classification of papain-like cysteine proteinases

Identification and classification of papain-like cysteine proteinases

A holistic approach to maximise diagnostic output in trio exome sequencing

Precision Targeting of Endogenous Epidermal Growth Factor Receptor (EGFR) by Structurally Aligned Dual-Modifier Labeling

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