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  1. Artikel ; Online: Homozygous 22q11.2 distal type II microdeletion is associated with syndromic neurodevelopmental delay.

    Salah, Somaya / Jaber, Hiba / Frumkin, Ayala / Harel, Tamar

    American journal of medical genetics. Part A

    2023  Band 191, Heft 10, Seite(n) 2623–2630

    Abstract: Genomic disorders result from heterozygous copy number variants (CNVs). Homozygous deletions spanning numerous genes are rare, despite the potential contribution of consanguinity to such instances. CNVs in the 22q11.2 region are mediated by nonallelic ... ...

    Abstract Genomic disorders result from heterozygous copy number variants (CNVs). Homozygous deletions spanning numerous genes are rare, despite the potential contribution of consanguinity to such instances. CNVs in the 22q11.2 region are mediated by nonallelic homologous recombination between pairs of low copy repeats (LCRs), from amongst eight LCRs designated A-H. Heterozygous distal type II deletions (LCR-E to LCR-F) have incomplete penetrance and variable expressivity, and can lead to neurodevelopmental issues, minor craniofacial anomalies, and congenital abnormalities. We report siblings with global developmental delay, hypotonia, minor craniofacial anomalies, ocular abnormalities, and minor skeletal issues, in whom chromosomal microarray identified a homozygous distal type II deletion. The deletion was brought to homozygosity as a result of a consanguineous marriage between two heterozygous carriers of the deletion. The phenotype of the children was strikingly more severe and complex than that of the parents. This report suggests that the distal type II deletion harbors a dosage-sensitive gene or regulatory element, which leads to a more severe phenotype when deleted on both chromosomes.
    Mesh-Begriff(e) Child ; Humans ; Chromosome Deletion ; Microarray Analysis ; DNA Copy Number Variations/genetics ; Craniofacial Abnormalities ; Phenotype
    Sprache Englisch
    Erscheinungsdatum 2023-06-27
    Erscheinungsland United States
    Dokumenttyp Case Reports
    ZDB-ID 2108614-X
    ISSN 1552-4833 ; 0148-7299 ; 1552-4825
    ISSN (online) 1552-4833
    ISSN 0148-7299 ; 1552-4825
    DOI 10.1002/ajmg.a.63326
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  2. Artikel ; Online: A neurodevelopmental disorder associated with a loss-of-function missense mutation in RAB35.

    Aguila, Adriana / Salah, Somaya / Kulasekaran, Gopinath / Shweiki, Moatasem / Shaul-Lotan, Nava / Mor-Shaked, Hagar / Daana, Muhannad / Harel, Tamar / McPherson, Peter S

    The Journal of biological chemistry

    2024  Band 300, Heft 4, Seite(n) 107124

    Abstract: Rab35 (Ras-associated binding protein) is a small GTPase that regulates endosomal membrane trafficking and functions in cell polarity, cytokinesis, and growth factor signaling. Altered Rab35 function contributes to progression of glioblastoma, defects in ...

    Abstract Rab35 (Ras-associated binding protein) is a small GTPase that regulates endosomal membrane trafficking and functions in cell polarity, cytokinesis, and growth factor signaling. Altered Rab35 function contributes to progression of glioblastoma, defects in primary cilia formation, and altered cytokinesis. Here, we report a pediatric patient with global developmental delay, hydrocephalus, a Dandy-Walker malformation, axial hypotonia with peripheral hypertonia, visual problems, and conductive hearing impairment. Exome sequencing identified a homozygous missense variant in the GTPase fold of RAB35 (c.80G>A; p.R27H) as the most likely candidate. Functional analysis of the R27H-Rab35 variant protein revealed enhanced interaction with its guanine-nucleotide exchange factor, DENND1A and decreased interaction with a known effector, MICAL1, indicating that the protein is in an inactive conformation. Cellular expression of the variant drives the activation of Arf6, a small GTPase under negative regulatory control of Rab35. Importantly, variant expression leads to delayed cytokinesis and altered length, number, and Arl13b composition of primary cilia, known factors in neurodevelopmental disease. Our findings provide evidence of altered Rab35 function as a causative factor of a neurodevelopmental disorder.
    Mesh-Begriff(e) Female ; Humans ; Male ; ADP-Ribosylation Factor 6 ; ADP-Ribosylation Factors/genetics ; ADP-Ribosylation Factors/metabolism ; Cell Line ; Cilia/metabolism ; Cilia/genetics ; Cilia/pathology ; Cytokinesis/genetics ; Guanine Nucleotide Exchange Factors/genetics ; Guanine Nucleotide Exchange Factors/metabolism ; Loss of Function Mutation ; Mutation, Missense ; Neurodevelopmental Disorders/genetics ; Neurodevelopmental Disorders/metabolism ; Neurodevelopmental Disorders/pathology ; Pedigree ; rab GTP-Binding Proteins/genetics ; rab GTP-Binding Proteins/metabolism ; Models, Molecular ; Protein Structure, Tertiary
    Chemische Substanzen ARF6 protein, human ; RAB35 protein, human
    Sprache Englisch
    Erscheinungsdatum 2024-03-01
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural ; Case Reports
    ZDB-ID 2997-x
    ISSN 1083-351X ; 0021-9258
    ISSN (online) 1083-351X
    ISSN 0021-9258
    DOI 10.1016/j.jbc.2024.107124
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  3. Artikel ; Online: Biallelic variants in PAX3 cause Klein syndrome.

    Salah, Somaya / Meiner, Vardiella / Abumayaleh, Abdelrazzaq / Asafra, Ali / Al-Sharif, Taher / Al-Fallah, Orwa / Hasasneh, Belal / Zlotogora, Joël

    Clinical genetics

    2022  Band 102, Heft 3, Seite(n) 223–227

    Abstract: Waardenburg syndrome is a group of genetic conditions that can cause hearing loss and pigmentation deficiency of the hair, skin, and eyes. Klein-Waardenburg syndrome (Waardenburg syndrome type 3) represents a distinct presentation of Waardenburg syndrome ...

    Abstract Waardenburg syndrome is a group of genetic conditions that can cause hearing loss and pigmentation deficiency of the hair, skin, and eyes. Klein-Waardenburg syndrome (Waardenburg syndrome type 3) represents a distinct presentation of Waardenburg syndrome type 1 and includes musculoskeletal abnormalities in addition to dystopia canthorum hearing loss and pigmentary changes. Heterozygous or homozygous variants in the PAX3 gene cause Klein-Waardenburg syndrome. Here we report on a new severely affected child, with a homozygous PAX3 variant (c.251C>T; p.Ser84Phe), review the features of the syndrome, and propose a new classification. The designation of Waardenburg syndrome should be given only to patients with monoallelic pathogenic variants in PAX3 whether or not musculoskeletal abnormalities are present. Patients with biallelic PAX3 variants should be outlined as a distinct group and designated Klein syndrome.
    Mesh-Begriff(e) Child ; Heterozygote ; Humans ; PAX3 Transcription Factor/genetics ; Pedigree ; Waardenburg Syndrome/diagnosis ; Waardenburg Syndrome/genetics
    Chemische Substanzen PAX3 Transcription Factor ; PAX3 protein, human
    Sprache Englisch
    Erscheinungsdatum 2022-06-05
    Erscheinungsland Denmark
    Dokumenttyp Case Reports ; Journal Article ; Research Support, Non-U.S. Gov't
    ZDB-ID 221209-2
    ISSN 1399-0004 ; 0009-9163
    ISSN (online) 1399-0004
    ISSN 0009-9163
    DOI 10.1111/cge.14167
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  4. Artikel ; Online: Biallelic deletion in a minimal CAPN15 intron in siblings with a recognizable syndrome of congenital malformations and developmental delay.

    Mor-Shaked, Hagar / Salah, Somaya / Yanovsky-Dagan, Shira / Meiner, Vardiella / Atawneh, Osama M / Abu-Libdeh, Bassam / Elpeleg, Orly / Harel, Tamar

    Clinical genetics

    2021  Band 99, Heft 4, Seite(n) 577–582

    Abstract: Calpainopathies constitute a heterogeneous group of disorders resulting from deficiencies in calpains, calcium-specific proteases that modulate substrates by limited proteolysis. Clinical manifestations depend on tissue-specific expression of the ... ...

    Abstract Calpainopathies constitute a heterogeneous group of disorders resulting from deficiencies in calpains, calcium-specific proteases that modulate substrates by limited proteolysis. Clinical manifestations depend on tissue-specific expression of the defective calpain and substrate specificity. CAPN15, encoding the Drosophila small optic lobes (sol) homolog, was recently found to cause various eye defects in individuals carrying bi-allelic missense variants. Here we report on two siblings with manifestations reminiscent of Johanson-Blizzard syndrome including failure to thrive, microcephaly, global developmental delay, dysmorphic features, endocrine abnormalities and congenital malformations, in addition to eye abnormalities. Exome sequencing identified a homozygous 47 base-pair deletion in a minimal intron of CAPN15, including the splice donor site. Sequencing of cDNA revealed single exon skipping, resulting in an out-of-frame deletion with a predicted premature termination codon. These findings expand the phenotypic spectrum associated with CAPN15 variants, and suggest that complete loss-of-function is associated with a recognizable syndrome of congenital malformations and developmental delay, overlapping Johanson-Blizzard syndrome and the recently observed brain defects in Capn15 knockout (KO) mice. Moreover, the data highlight the unique opportunity for indel detection in minimal introns.
    Mesh-Begriff(e) Abnormalities, Multiple/genetics ; Alleles ; Anus, Imperforate/genetics ; Base Pairing ; Calpain/genetics ; Codon, Nonsense ; Consanguinity ; Developmental Disabilities/genetics ; Ectodermal Dysplasia/genetics ; Eye Abnormalities/genetics ; Genetic Association Studies ; Growth Disorders/genetics ; Hearing Loss, Sensorineural/genetics ; Humans ; Hypothyroidism/genetics ; INDEL Mutation ; Intellectual Disability/genetics ; Introns/genetics ; Male ; Microphthalmos/genetics ; Muscle Hypotonia/genetics ; Nose/abnormalities ; Pancreatic Diseases/genetics ; Pedigree ; RNA Splice Sites/genetics ; Sequence Deletion ; Steatorrhea/genetics
    Chemische Substanzen Codon, Nonsense ; RNA Splice Sites ; CAPN15 protein, human (EC 3.4.22.-) ; Calpain (EC 3.4.22.-)
    Sprache Englisch
    Erscheinungsdatum 2021-01-13
    Erscheinungsland Denmark
    Dokumenttyp Comparative Study ; Journal Article
    ZDB-ID 221209-2
    ISSN 1399-0004 ; 0009-9163
    ISSN (online) 1399-0004
    ISSN 0009-9163
    DOI 10.1111/cge.13920
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  5. Artikel ; Online: Unbiased phenotype and genotype matching maximizes gene discovery and diagnostic yield.

    Rips, Jonathan / Halstuk, Orli / Fuchs, Adina / Lang, Ziv / Sido, Tal / Gershon-Naamat, Shiri / Abu-Libdeh, Bassam / Edvardson, Simon / Salah, Somaya / Breuer, Oded / Hadhud, Mohamad / Eden, Sharon / Simon, Itamar / Slae, Mordechai / Damseh, Nadirah S / Abu-Libdeh, Abdulsalam / Eskin-Schwartz, Marina / Birk, Ohad S / Varga, Julia /
    Schueler-Furman, Ora / Rosenbluh, Chaggai / Elpeleg, Orly / Yanovsky-Dagan, Shira / Mor-Shaked, Hagar / Harel, Tamar

    Genetics in medicine : official journal of the American College of Medical Genetics

    2024  Band 26, Heft 4, Seite(n) 101068

    Abstract: Purpose: Widespread application of next-generation sequencing, combined with data exchange platforms, has provided molecular diagnoses for countless families. To maximize diagnostic yield, we implemented an unbiased semi-automated genematching algorithm ...

    Abstract Purpose: Widespread application of next-generation sequencing, combined with data exchange platforms, has provided molecular diagnoses for countless families. To maximize diagnostic yield, we implemented an unbiased semi-automated genematching algorithm based on genotype and phenotype matching.
    Methods: Rare homozygous variants identified in 2 or more affected individuals, but not in healthy individuals, were extracted from our local database of ∼12,000 exomes. Phenotype similarity scores (PSS), based on human phenotype ontology terms, were assigned to each pair of individuals matched at the genotype level using HPOsim.
    Results: 33,792 genotype-matched pairs were discovered, representing variants in 7567 unique genes. There was an enrichment of PSS ≥0.1 among pathogenic/likely pathogenic variant-level pairs (94.3% in pathogenic/likely pathogenic variant-level matches vs 34.75% in all matches). We highlighted founder or region-specific variants as an internal positive control and proceeded to identify candidate disease genes. Variant-level matches were particularly helpful in cases involving inframe indels and splice region variants beyond the canonical splice sites, which may otherwise have been disregarded, allowing for detection of candidate disease genes, such as KAT2A, RPAIN, and LAMP3.
    Conclusion: Semi-automated genotype matching combined with PSS is a powerful tool to resolve variants of uncertain significance and to identify candidate disease genes.
    Mesh-Begriff(e) Humans ; Genotype ; Phenotype ; Mutation ; Homozygote ; Genetic Association Studies
    Sprache Englisch
    Erscheinungsdatum 2024-01-06
    Erscheinungsland United States
    Dokumenttyp Journal Article
    ZDB-ID 1455352-1
    ISSN 1530-0366 ; 1098-3600
    ISSN (online) 1530-0366
    ISSN 1098-3600
    DOI 10.1016/j.gim.2024.101068
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  6. Artikel ; Online: Biallelic variants in AGTPBP1, involved in tubulin deglutamylation, are associated with cerebellar degeneration and motor neuropathy.

    Sheffer, Ruth / Gur, Michal / Brooks, Rebecca / Salah, Somaya / Daana, Muhannad / Fraenkel, Nitay / Eisenstein, Eli / Rabie, Malcolm / Nevo, Yoram / Jalas, Chaim / Elpeleg, Orly / Edvardson, Shimon / Harel, Tamar

    European journal of human genetics : EJHG

    2019  Band 27, Heft 9, Seite(n) 1419–1426

    Abstract: The ATP/GTP-Binding Protein 1 (AGTPBP1) gene (OMIM *606830) catalyzes deglutamylation of polyglutamylated proteins, and its deficiency manifests by cerebellar ataxia and peripheral neuropathy in mice and lower motor neuron-like disease in sheep. In the ... ...

    Abstract The ATP/GTP-Binding Protein 1 (AGTPBP1) gene (OMIM *606830) catalyzes deglutamylation of polyglutamylated proteins, and its deficiency manifests by cerebellar ataxia and peripheral neuropathy in mice and lower motor neuron-like disease in sheep. In the mutant mice, cerebellar atrophy due to Purkinje cell degeneration is observed, likely due to increased tubulin polyglutamylation in affected brain areas. We report two unrelated individuals who presented with early onset cerebellar atrophy, developmental arrest with progressive muscle weakness, and feeding and respiratory difficulties, accompanied by severe motor neuronopathy. Whole exome sequencing followed by segregation analysis in the families and cDNA studies revealed deleterious biallelic variants in the AGTPBP1 gene. We conclude that complete loss-of-function of AGTPBP1 in humans, just like in mice and sheep, is associated with cerebellar and motor neuron disease, reminiscent of Pontocerebellar Hypoplasia Type 1 (PCH1).
    Mesh-Begriff(e) Alleles ; Amino Acid Substitution ; Child, Preschool ; Consanguinity ; DNA Mutational Analysis ; Female ; GTP-Binding Proteins/genetics ; Humans ; Infant ; Magnetic Resonance Imaging ; Male ; Motor Neuron Disease/diagnostic imaging ; Motor Neuron Disease/etiology ; Motor Neuron Disease/metabolism ; Motor Neuron Disease/pathology ; Mutation ; Neurodegenerative Diseases/diagnostic imaging ; Neurodegenerative Diseases/etiology ; Neurodegenerative Diseases/metabolism ; Neurodegenerative Diseases/pathology ; Serine-Type D-Ala-D-Ala Carboxypeptidase/genetics ; Spinocerebellar Degenerations/diagnostic imaging ; Spinocerebellar Degenerations/etiology ; Spinocerebellar Degenerations/metabolism ; Spinocerebellar Degenerations/pathology ; Tubulin/metabolism ; Whole Exome Sequencing
    Chemische Substanzen Tubulin ; AGTPBP1 protein, human (EC 3.4.16.4) ; Serine-Type D-Ala-D-Ala Carboxypeptidase (EC 3.4.16.4) ; GTP-Binding Proteins (EC 3.6.1.-)
    Sprache Englisch
    Erscheinungsdatum 2019-04-11
    Erscheinungsland England
    Dokumenttyp Journal Article
    ZDB-ID 1141470-4
    ISSN 1476-5438 ; 1018-4813
    ISSN (online) 1476-5438
    ISSN 1018-4813
    DOI 10.1038/s41431-019-0400-y
    Datenquelle MEDical Literature Analysis and Retrieval System OnLINE

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  7. Artikel ; Online: Pathogenic Variants in NUP214 Cause "Plugged" Nuclear Pore Channels and Acute Febrile Encephalopathy.

    Fichtman, Boris / Harel, Tamar / Biran, Nitzan / Zagairy, Fadia / Applegate, Carolyn D / Salzberg, Yuval / Gilboa, Tal / Salah, Somaya / Shaag, Avraham / Simanovsky, Natalia / Ayoubieh, Houriya / Sobreira, Nara / Punzi, Giuseppe / Pierri, Ciro Leonardo / Hamosh, Ada / Elpeleg, Orly / Harel, Amnon / Edvardson, Simon

    American journal of human genetics

    2019  Band 105, Heft 1, Seite(n) 48–64

    Abstract: We report biallelic missense and frameshift pathogenic variants in the gene encoding human nucleoporin NUP214 causing acute febrile encephalopathy. Clinical symptoms include neurodevelopmental regression, seizures, myoclonic jerks, progressive ... ...

    Abstract We report biallelic missense and frameshift pathogenic variants in the gene encoding human nucleoporin NUP214 causing acute febrile encephalopathy. Clinical symptoms include neurodevelopmental regression, seizures, myoclonic jerks, progressive microcephaly, and cerebellar atrophy. NUP214 and NUP88 protein levels were reduced in primary skin fibroblasts derived from affected individuals, while the total number and density of nuclear pore complexes remained normal. Nuclear transport assays exhibited defects in the classical protein import and mRNA export pathways in affected cells. Direct surface imaging of fibroblast nuclei by scanning electron microscopy revealed a large increase in the presence of central particles (known as "plugs") in the nuclear pore channels of affected cells. This observation suggests that large transport cargoes may be delayed in passage through the nuclear pore channel, affecting its selective barrier function. Exposure of fibroblasts from affected individuals to heat shock resulted in a marked delay in their stress response, followed by a surge in apoptotic cell death. This suggests a mechanistic link between decreased cell survival in cell culture and severe fever-induced brain damage in affected individuals. Our study provides evidence by direct imaging at the single nuclear pore level of functional changes linked to a human disease.
    Mesh-Begriff(e) Active Transport, Cell Nucleus ; Acute Febrile Encephalopathy/etiology ; Acute Febrile Encephalopathy/metabolism ; Acute Febrile Encephalopathy/pathology ; Apoptosis ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; Cell Proliferation ; Cells, Cultured ; Child ; Child, Preschool ; Female ; Fibroblasts/metabolism ; Fibroblasts/pathology ; Frameshift Mutation ; Humans ; Infant ; Ion Channels/physiology ; Male ; Mutation, Missense ; Nuclear Pore/genetics ; Nuclear Pore/metabolism ; Nuclear Pore/pathology ; Nuclear Pore Complex Proteins/chemistry ; Nuclear Pore Complex Proteins/genetics ; Nuclear Pore Complex Proteins/metabolism ; Pedigree ; Protein Conformation
    Chemische Substanzen Ion Channels ; NUP214 protein, human ; Nuclear Pore Complex Proteins
    Sprache Englisch
    Erscheinungsdatum 2019-06-06
    Erscheinungsland United States
    Dokumenttyp Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
    ZDB-ID 219384-x
    ISSN 1537-6605 ; 0002-9297
    ISSN (online) 1537-6605
    ISSN 0002-9297
    DOI 10.1016/j.ajhg.2019.05.003
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