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Intellectual disability

Gene: ZMIZ1

Green List (high evidence)

ZMIZ1 (zinc finger MIZ-type containing 1)
EnsemblGeneIds (GRCh38): ENSG00000108175
EnsemblGeneIds (GRCh37): ENSG00000108175
OMIM: 607159, Gene2Phenotype
ZMIZ1 is in 3 panels

2 reviews

Catherine Snow (Genomics England)

Comment on list classification: Gene ZMIZ1 identified by expert review by Konstantinos Varvagiannis on Carapito et al. (PMID: 30639322) who reported on 19 individuals, 16 unrelated, with variants affecting ZMIZ1. Apart from one family (3 individuals) for whom parental samples were unavailable, all variants were shown to be de novo.
The phenotype is broad and there are few consistent features throughout the subjects, however all individuals are reported to have ID, varying in severity.
ZMIZ1 is probable in Gene2Phenotype although a list of phenotypes have not been assigned to the G2P entry and currently not associated with any phenotypes in OMIM.
As sufficient number of subjects and ID is consistent throughout there is sufficient evidence to class ZMIZ1 as Green.
Created: 23 May 2019, 3 p.m. | Last Modified: 17 Jul 2019, 12:42 p.m.
Panel Version: 0.200

Konstantinos Varvagiannis (Other)

Green List (high evidence)

Carapito et al. (doi.org/10.1016/j.ajhg.2018.12.007 - PMID to add) report on 19 individuals with variants affecting ZMIZ1 (alternative symbols RAI17/KIAA1224/ZIMP10).

Features included DD/ID (19/19), feeding difficulties, growth failure, microcephaly and variable congenital malformations. Seizures were noted in 3 unrelated individuals (with different variants).

Variants included 6 missense SNVs, 5 frameshift variants, 1 splice site variant, 1 synonymous variant with probable impact on splicing (not studied) and 2 translocations.

In all individuals for whom parental studies were possible (n=16), the variants had occurred as de novo events while for 3 sibs harboring a frameshift variant parental samples were unavailable. These subjects however harbored the same variant as a DDD study participant included in the current report.

One translocation disrupted only ZMIZ1 while a second [t(X;10)] did not disrupt the coding sequence of any gene but only a distal enhancer 276 kb upstream of ZMIZ1. A previous study had found recurrent SNVs of the same region in ASD subjects and suggested possible interaction with the ZMIZ1 promoter (Liu et al. - PMID: 29754769).

The deleterious effect of both translocations was confirmed by quantitative RT-PCR. For 4 missense SNVs as well as a splice variant mRNA levels were similar to controls. The splice site (-2) variant was shown to produce 2 new splicing isoforms from utilization of alternative splice site acceptors.

ZMIZ1 belongs to the PIAS-like family of transcriptional coregulators.

Five missense variants were located in an alanine rich domain (aa 280-305). Seven other variants were predicted to shorten or remove the C-terminal transactivation domain.

This gene enhances - among others - the transcriptional activity of androgen receptor (AR). In vitro studies using HEK293T cell lines supported impaired coactivation of the AR for 3 variants studied. In utero electroporation of pathogenic variants in mouse embryos (E14.5) led to impaired neuronal positioning of the electroporated neurons and disruption of the morphology/polarization.

As the authors note previous studies have shown expression of Zimp10 in the developing mouse brain, craniofacial tissue as well as the interdigital region of limbs (PMIDs cited : 18053775 and 17967885) in line with ID, facial phenotype and syndactyly observed in some patients.

Finally the authors cite a previous report on an individual with ID due to a translocation [t(10;19)] disrupting both ZMIZ1 and PRR12 (Córdova-Fletes al. - PMID: 26163108). Although disruption of ZMIZ1 is discussed as a cause, PRR12 has recently been proposed as (also) an ID gene (Leduc et al. - PMID: 29556724). [For details see PRR12 in the current panel].
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One of the variants found in 2 unrelated individuals in the aforementioned study [NM_020338.3:c.899C>T or p.(T300M)] has been reported in a further individual investigated for ID in the context of a bigger cohort (Lelieveld et al. - PMID: 27479843).
[ Details in the denovo-db : http://denovo-db.gs.washington.edu/denovo-db/QueryVariantServlet?searchBy=Gene&target=ZMIZ1 ]
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ZMIZ1 is not associated with any phenotype in OMIM, nor in G2P.
This gene has been included in gene panels for intellectual disability offered by some diagnostic laboratories.
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As a result, ZMIZ1 can be considered for inclusion in the ID panel as green.
Sources: Literature
Created: 12 Jan 2019, 2:50 p.m.

Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown

Phenotypes
Global developmental delay; Intellectual disability; Feeding difficulties; Growth abnormality; Microcephaly; Abnormality of the skeletal system; Abnormality of the urinary system; Abnormality of the cardiovascular system; Abnormality of head or neck

Publications

Variants in this GENE are reported as part of current diagnostic practice

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review
  • Expert Review Green
  • Expert Review
Phenotypes
  • Abnormality of head or neck
  • Microcephaly
  • Abnormality of the cardiovascular system
  • Abnormality of the skeletal system
  • Feeding difficulties
  • Intellectual disability
  • Global developmental delay
  • Abnormality of the urinary system
  • Growth abnormality
  • Global developmental delay, Intellectual disability, Feeding difficulties, Growth abnormality, Microcephaly, Abnormality of the skeletal system, Abnormality of the urinary system, Abnormality of the cardiovascular system, Abnormality of head or neck
OMIM
607159
Clinvar variants
Variants in ZMIZ1
Penetrance
unknown
Publications
Panels with this gene

History Filter Activity

25 Jul 2019, Gel status: 3

Added New Source, Added New Source, Set Phenotypes, Set publications, Status Update

Catherine Snow (Genomics England)

Source Expert Review Green was added to ZMIZ1. Source Expert Review was added to ZMIZ1. Added phenotypes Global developmental delay, Intellectual disability, Feeding difficulties, Growth abnormality, Microcephaly, Abnormality of the skeletal system, Abnormality of the urinary system, Abnormality of the cardiovascular system, Abnormality of head or neck for gene: ZMIZ1 Publications for gene ZMIZ1 were changed from 29754769; 18053775; 17967885; 26163108; 27479843 to 29754769; 18053775; 17967885; 30639322; 26163108; 27479843 Rating Changed from No List (delete) to Green List (high evidence)

12 Jan 2019, Gel status: 0

Created, Added New Source, Set mode of inheritance, Set publications, Set Phenotypes, Set penetrance

Konstantinos Varvagiannis (Other)

gene: ZMIZ1 was added gene: ZMIZ1 was added to Intellectual disability. Sources: Literature Mode of inheritance for gene: ZMIZ1 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: ZMIZ1 were set to 29754769; 18053775; 17967885; 26163108; 27479843 Phenotypes for gene: ZMIZ1 were set to Global developmental delay; Intellectual disability; Feeding difficulties; Growth abnormality; Microcephaly; Abnormality of the skeletal system; Abnormality of the urinary system; Abnormality of the cardiovascular system; Abnormality of head or neck Penetrance for gene: ZMIZ1 were set to unknown Review for gene: ZMIZ1 was set to GREEN gene: ZMIZ1 was marked as current diagnostic