Intellectual disabilityGene: ZNF292
Comment on list classification: Gene added by external reviewer. Promoted from grey to Amber due to the evidence presented, and reflecting the rating of 'probable' in Gene2Phenotype for ZNF292-related developmental disorder. At this stage, this has not been made Green due to uncertainty regarding the penetrance and the comment from the reviewer regarding manual review of some relevant LoF variants in gnomAD suggested that they represent false positive calls.
Created: 27 Nov 2019, 4:55 p.m. | Last Modified: 27 Nov 2019, 4:55 p.m.
Panel Version: 2.1125
Correction to the phrase "Manual review of some relevant LoF variants in gnomAD suggested that they represent false positive calls":
Irrespective of the variants identified in their cohort, Mirzaa et al. reviewed many pLoF variants which are listed in gnomAD. The authors suggested that some of these variants may not represent true LoF variants.
Eg. NM_015021.3:c.2690C>A ( https://gnomad.broadinstitute.org/variant/6-87966037-C-A ) which appears to be a stopgain variant (Ser[TCA]>Ter[TAA]) is probably not a true LoF variant. It always occurred in cis (/the same reads) with NM_015021.3:c.2689T>C (Ser[TCA] to Pro[CCA]). This is visible in the IGV graph of gnomAD (url above).
Thus, gnomAD lists 2 single-nucleotide variants affecting the same codon, one next to the other. However, as the 2 SNVs always occurred in cis, this represents a single missense multi-nucleotide variant (Ser[TCA]>Gln[CAA]) [ NM_015021.3(ZNF292_v001):c.2689_2690delinsCA ].
Similar observations were made for other variants seen in gnomAD.
Created: 12 Jan 2020, 6:45 p.m. | Last Modified: 12 Jan 2020, 6:45 p.m.
Panel Version: 3.0
Mirzaa et al. (2019 - PMID: 31723249) report on 28 individuals (from 27 families) with putatively pathogenic ZNF292 variants.
Main features consisted of DD and ID (27/28 - mild in 40%, moderate in 22%, severe in 11%) with or without ASD and ADHD. A single individual had no evidence of ID but had speech delay and ASD at the age of 6. Additional features (by diminishing order of frequency) included presence of non-specific dysmorphic features (~45%), abnormal tone, brain MRI abnormalities, growth failure, feeding difficulties, skeletal and cardiac anomalies, microcephaly and epilepsy (~11%).
As the authors comment, ZNF292 encodes a zinc finger protein, acting as a transcription factor.
Evidence is provided that gene has high expression in the developing human brain, with its expression being higher in prenatal development and diminishing postnatally. Znf292 is also expressed in adult mouse brain (highest in hippocampus/Purkinje cells).
Variants were identified by exome or targeted panel sequencing (targeted capture/molecular inversion probes). Previous investigations (eg. aCGH, analysis of relevant genes) had probably ruled out alternative causes in most with few having VUS or possibly relevant additional variants (eg. a KDM5C stopgain variant in a male).
24 putatively pathogenic variants were observed in this cohort, all predicting LoF (stopgain, frameshift or splice variants). All were de novo with the exception of one family where the variant was inherited from an affected parent. Almost all were absent from gnomAD and had CADD scores > 35.
Most variants lied within the last and largest exon that encodes a DNA binding domain. RT-PCR on RNA from 2 individuals harboring such variants confirmed that NMD does not apply. This exon however represents ~88% of the total coding length so the distribution of variants in this (NMD escaping) region was consistent with what would also be expected by chance.
ZNF292 has a pLI of 1 in gnomAD. Manual review of some relevant LoF variants in gnomAD suggested that they represent false positive calls.
As a result, the effect of variants is not clear although haploinsufficiency is still possible based also on phenotype of (larger) deletions spanning this gene (cited: Engwerda et al - PMID: 29904178 / The study focuses on deletions of the broader 6q. A possible role of ZNF292 is discussed as autism was present in 4/10 individuals with deletions encompassing this gene).
Based on the aforementioned cohort with one individual being diagnosed with mild ID only as an adult and/or presence of 5 pLoF variants in gnomAD the authors propose that some variants may be incompletely penetrant or associated with only mild features.
Finally, 15 additional individuals (belonging to 12 families) harbored variants for which pathogenicity was suspected (but could not be concluded) due to insufficient phenotypic information, lack of sufficient parental studies or missense variants. In this cohort variants were mostly pLoF, while 3 individuals (incl. 2 sibs) had a de novo missense SNV.
Other studies were not here reviewed as some of the individuals reported were published previously in larger cohorts.
There is no associated phenotype in OMIM / G2P. SysID includes this gene among the candidate ID ones.
ZNF292 is included in gene panels for ID offered by some diagnostic laboratories (incl. Radboudumc and GeneDx).
Overall ZNF292 could be added to the ID panel probably with green (or amber) rating.
[Please consider inclusion in other possibly relevant panels eg. autism, epilepsy]
Sources: Radboud University Medical Center, Nijmegen, Literature
Created: 16 Nov 2019, 9:23 a.m.
Mode of inheritance
MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown
Intellectual disability; Autism; Attention deficit hyperactivity disorder; Abnormality of the face; Abnormal muscle tone; Abnormality of nervous system morphology; Growth abnormality; Feeding difficulties; Abnormality of the skeletal system; Abnormality of the cardiovascular system; Microcephaly; Seizures
Variants in this GENE are reported as part of current diagnostic practice
Gene: znf292 has been classified as Amber List (Moderate Evidence).
gene: ZNF292 was added gene: ZNF292 was added to Intellectual disability. Sources: Radboud University Medical Center, Nijmegen,Literature Mode of inheritance for gene: ZNF292 was set to MONOALLELIC, autosomal or pseudoautosomal, imprinted status unknown Publications for gene: ZNF292 were set to 31723249; 29904178 Phenotypes for gene: ZNF292 were set to Intellectual disability; Autism; Attention deficit hyperactivity disorder; Abnormality of the face; Abnormal muscle tone; Abnormality of nervous system morphology; Growth abnormality; Feeding difficulties; Abnormality of the skeletal system; Abnormality of the cardiovascular system; Microcephaly; Seizures Penetrance for gene: ZNF292 were set to Incomplete Review for gene: ZNF292 was set to GREEN gene: ZNF292 was marked as current diagnostic