CAKUT

Gene: ZMYM2

Green List (high evidence)

ZMYM2 (zinc finger MYM-type containing 2)
EnsemblGeneIds (GRCh38): ENSG00000121741
EnsemblGeneIds (GRCh37): ENSG00000121741
OMIM: 602221, Gene2Phenotype
ZMYM2 is in 2 panels

1 review

Ivone Leong (Genomics England Curator)

Green List (high evidence)

Review by Konstantinos Varvagiannis on the Intellectual disability panel:
"Heterozygous pathogenic (pLoF) ZMYM2 variants have been reported in individuals with syndromic presentation including CAKUT (in several cases) and variable neurological manifestations among extra-renal features. DD and ID were reported in some of the families described to date as summarized below. You might consider inclusion with green/amber rating in the ID panel and green in the panel for CAKUT.

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Connaughton et al (2020 - PMID: 32891193) report on 19 individuals (from 15 unrelated families) with heterozygous pathogenic ZMYM2 variants. [Article not reviewed in detail].

Affected individuals from 7 families presented with CAKUT while all of them displayed extra-renal features. Neurological manifestations were reported in 16 individuals from 14 families (data not available for 1 fam), among others hypotonia (3/14 fam), speech delay (4/14 fam), global DD (9/14 fam), ID (4/14 fam), microcephaly (4/14 fam). ASD was reported in 4 fam (4 indiv). Seizures were reported in 2 fam (2 indiv). Variable other features included cardiac defects, facial dysmorphisms, small hands and feet with dys-/hypo-plastic nails and clinodactyly.

14 pLoF variants were identified, in most cases as de novo events (8 fam). In 2 families the variant was inherited from an affected parent. Germline mosaicism occurred in 1 family.

The human disease features were recapitulated in a X. tropicalis morpholino knockdown, with expression of truncating variants failing to rescue renal and craniofacial defects. Heterozygous Zmym2-deficient mice also recapitulated the features of CAKUT.

ZMYM2 (previously ZNF198) encodes a nuclear zinc finger protein localizing to the nucleus (and PML nuclear body).

It has previously been identified as transcriptional corepressor interacting with nuclear receptors and the LSD1-CoREST-HDAC1 complex. It has also been shown to interact with FOXP transcription factors.

The authors provide evidence for loss of interaction of the truncated ZMYM2 with FOXP1 (mutations in the latter having recently been reported in syndromic CAKUT).
Sources: Literature
Created: 19 Sep 2020, 1:07 a.m."

Based on the expert review and evidence, there is enough evidence to support a gene-disease association. Therefore, this gene has been given a Green rating.
Sources: Expert Review
Created: 12 Nov 2020, 2:50 p.m.

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

Phenotypes
CAKUT; Abnormality of the urinary system; Global developmental delay; Intellectual disability; Microcephaly; Abnormality of the cardiovascular system; Autism; Seizures; Abnormality of the head or neck; Abnormality of the nail; Small hand; Short foot; Clinodactyly

Publications

Details

Mode of Inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Sources
  • Expert Review Green
  • Expert Review
Phenotypes
  • CAKUT
  • Abnormality of the urinary system
  • Global developmental delay
  • Intellectual disability
  • Microcephaly
  • Abnormality of the cardiovascular system
  • Autism
  • Seizures
  • Abnormality of the head or neck
  • Abnormality of the nail
  • Small hand
  • Short foot
  • Clinodactyly
OMIM
602221
Clinvar variants
Variants in ZMYM2
Penetrance
None
Publications
Panels with this gene

History Filter Activity

12 Nov 2020, Gel status: 3

Entity classified by Genomics England curator

Ivone Leong (Genomics England Curator)

Gene: zmym2 has been classified as Green List (High Evidence).

12 Nov 2020, Gel status: 1

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

Ivone Leong (Genomics England Curator)

gene: ZMYM2 was added gene: ZMYM2 was added to CAKUT. Sources: Expert Review Mode of inheritance for gene: ZMYM2 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: ZMYM2 were set to 32891193 Phenotypes for gene: ZMYM2 were set to CAKUT; Abnormality of the urinary system; Global developmental delay; Intellectual disability; Microcephaly; Abnormality of the cardiovascular system; Autism; Seizures; Abnormality of the head or neck; Abnormality of the nail; Small hand; Short foot; Clinodactyly Review for gene: ZMYM2 was set to GREEN