Human Gene Module / Chromosome X / ZMYM3

ZMYM3zinc finger MYM-type containing 3

SFARI Gene Score
S
Syndromic Syndromic
Autism Reports / Total Reports
2 / 8
Rare Variants / Common Variants
27 / 0
Aliases
-
Associated Syndromes
-
Chromosome Band
Xq13.1
Associated Disorders
-
Relevance to Autism

ZMYM3 was initially identified as a neurodevelopmental disorder candidate gene in a female with intellectual disability who had a balanced translocation affecting the 5'UTR of one isoform of ZMYM3 (van der Maarel et al., 1996) and in three affected brothers with intellectual disability, ADHD, and syndromic features who had a maternally-inherited ZMYM3 missense variant (Philips et al., 2014). Hiatt et al., 2022 utilized the MatchMaker Exchange to assemble a cohort of 27 individuals with rare, protein-altering variation in the ZMYM3 gene; 24 of these individuals were male and presented with overlapping features including developmental delay (23/23 individuals), intellectual disability (17/20 individuals), behavioral abnormalities (including a diagnosis of autism or a report of autistic traits in 15/21 individuals), and a specific facial gestalt, whereas the three affected females in this cohort displayed a more variable phenotype of developmental delay and some facial dysmorphism. Several studies have suggested a link between allelic variation in an exceptionally long short tandem repeat in the 5'UTR of the ZMYM3 gene and schizophrenia, bipolar disorder, and late-onset neurocognitive disorder (Alizadeh et al., 2018; Alizadeh et al., 2019; Afshar et al., 2020).

Molecular Function

This gene is located on the X chromosome and is subject to X inactivation. It is highly conserved in vertebrates and most abundantly expressed in the brain. The encoded protein is a component of histone deacetylase-containing multiprotein complexes that function through modifying chromatin structure to keep genes silent. Plays a role in the regulation of cell morphology and cytoskeletal organization.

SFARI Genomic Platforms
Reports related to ZMYM3 (8 Reports)
# Type Title Author, Year Autism Report Associated Disorders
1 Support - Philips AK et al. (2014) No ADHD
2 Positive Association - Alizadeh F et al. (2018) No -
3 Positive Association - Alizadeh F et al. (2019) No -
4 Support Large-Scale Exome Sequencing Study Implicates Both Developmental and Functional Changes in the Neurobiology of Autism Satterstrom FK et al. (2020) Yes -
5 Positive Association - Afshar H et al. (2020) No -
6 Primary - Hiatt SM et al. (2023) Yes ADHD
7 Support - Giovenino C et al. (2023) No -
8 Support - van der Maarel SM et al. (1996) No -
Rare Variants   (27)
Status Allele Change Residue Change Variant Type Inheritance Pattern Parental Transmission Family Type PubMed ID Author, Year
- - translocation Unknown - - 8817323 van der Maarel SM et al. (1996)
c.507A>T p.Arg169Ser missense_variant Unknown - Simplex 36586412 Hiatt SM et al. (2023)
c.2255A>G p.Tyr752Cys missense_variant De novo - Simplex 36586412 Hiatt SM et al. (2023)
c.3192T>C p.Tyr1064= synonymous_variant De novo - - 31981491 Satterstrom FK et al. (2020)
c.3605T>A p.Val1202Asp missense_variant De novo - Simplex 36586412 Hiatt SM et al. (2023)
c.3638T>C p.Met1213Thr missense_variant Unknown - Simplex 36586412 Hiatt SM et al. (2023)
c.3820C>T p.Arg1274Trp missense_variant De novo - Simplex 36586412 Hiatt SM et al. (2023)
c.3880C>T p.Arg1294Cys missense_variant De novo - Simplex 36586412 Hiatt SM et al. (2023)
c.1321C>T p.Arg441Trp missense_variant Unknown - Multiplex 36586412 Hiatt SM et al. (2023)
c.1360T>C p.Cys454Arg missense_variant De novo - Multiplex 36586412 Hiatt SM et al. (2023)
c.905G>A p.Arg302His missense_variant Familial Maternal Simplex 36586412 Hiatt SM et al. (2023)
c.1322G>A p.Arg441Gln missense_variant Familial Maternal Simplex 36586412 Hiatt SM et al. (2023)
c.2794A>G p.Ile932Val missense_variant Familial Maternal Simplex 36586412 Hiatt SM et al. (2023)
c.3409T>A p.Tyr1137Asn missense_variant Familial Maternal Simplex 36586412 Hiatt SM et al. (2023)
c.3970C>T p.Arg1324Trp missense_variant Familial Maternal Simplex 36586412 Hiatt SM et al. (2023)
c.4029G>A p.Met1343Ile missense_variant Familial Maternal Simplex 36586412 Hiatt SM et al. (2023)
c.721G>A p.Glu241Lys missense_variant Familial Maternal Multiplex 36586412 Hiatt SM et al. (2023)
c.1183C>A p.Arg395Ser missense_variant Familial Maternal Multiplex 36586412 Hiatt SM et al. (2023)
c.1192C>T p.Pro398Ser missense_variant Familial Maternal Multiplex 36586412 Hiatt SM et al. (2023)
c.1322G>A p.Arg441Gln missense_variant Familial Maternal Multiplex 36586412 Hiatt SM et al. (2023)
c.2193G>C p.Glu731Asp missense_variant Familial Maternal Multiplex 36586412 Hiatt SM et al. (2023)
c.1321C>T p.Arg441Trp missense_variant Familial Maternal Multiplex 24721225 Philips AK et al. (2014)
c.1322G>A p.Arg441Gln missense_variant Familial Maternal Multiplex 36879111 Giovenino C et al. (2023)
c.205G>A p.Asp69Asn missense_variant Familial Maternal Extended multiplex 36586412 Hiatt SM et al. (2023)
c.3371G>A p.Arg1124Gln missense_variant Familial Maternal Extended multiplex 36586412 Hiatt SM et al. (2023)
c.3518G>A p.Ser1173Asn missense_variant Familial Maternal Extended multiplex 36586412 Hiatt SM et al. (2023)
c.671_672insATGG p.Asp224GlufsTer10 frameshift_variant Familial Maternal Simplex 36586412 Hiatt SM et al. (2023)
Common Variants  

No common variants reported.

SFARI Gene score
S

Syndromic

Score Delta: Score remained at S

The syndromic category includes mutations that are associated with a substantial degree of increased risk and consistently linked to additional characteristics not required for an ASD diagnosis. If there is independent evidence implicating a gene in idiopathic ASD, it will be listed as "#S" (e.g., 2S, 3S, etc.). If there is no such independent evidence, the gene will be listed simply as "S."

Krishnan Probability Score

Score 0.49119380669097

Ranking 5722/25841 scored genes


[Show Scoring Methodology]
Krishnan and colleagues generated probability scores genome-wide by using a machine learning approach on a human brain-specific gene network. The method was first presented in Nat Neurosci 19, 1454-1462 (2016), and scores for more than 25,000 RefSeq genes can be accessed in column G of supplementary table 3 (see: http://www.nature.com/neuro/journal/v19/n11/extref/nn.4353-S5.xlsx). A searchable browser, with the ability to view networks of associated ASD risk genes, can be found at asd.princeton.edu.
ExAC Score

Score 0.99996681593756

Ranking 553/18225 scored genes


[Show Scoring Methodology]
The Exome Aggregation Consortium (ExAC) is a summary database of 60,706 exomes that has been widely used to estimate 'constraint' on mutation for individual genes. It was introduced by Lek et al. Nature 536, 285-291 (2016), and the ExAC browser can be found at exac.broadinstitute.org. The pLI score was developed as measure of intolerance to loss-of- function mutation. A pLI > 0.9 is generally viewed as highly constrained, and thus any loss-of- function mutations in autism in such a gene would be more likely to confer risk. For a full list of pLI scores see: ftp://ftp.broadinstitute.org/pub/ExAC_release/release0.3.1/functional_gene_constraint/fordist_cle aned_exac_nonTCGA_z_pli_rec_null_data.txt
Sanders TADA Score

Score 0.94474774516919

Ranking 16197/18665 scored genes


[Show Scoring Methodology]
The TADA score ('Transmission and De novo Association') was introduced by He et al. PLoS Genet 9(8):e1003671 (2013), and is a statistic that integrates evidence from both de novo and transmitted mutations. It forms the basis for the claim of 65 individual genes being strongly associated with autism risk at a false discovery rate of 0.1 (Sanders et al. Neuron 87, 1215-1233 (2015)). The calculated TADA score for 18,665 RefSeq genes can be found in column P of Supplementary Table 6 in the Sanders et al. paper (the column headed 'tadaFdrAscSscExomeSscAgpSmallDel'), which represents a combined analysis of exome data and small de novo deletions (see www.cell.com/cms/attachment/2038545319/2052606711/mmc7.xlsx).
Zhang D Score

Score 0.29649314646553

Ranking 2795/20870 scored genes


[Show Scoring Methodology]
The DAMAGES score (disease-associated mutation analysis using gene expression signatures), or D score, was developed to combine evidence from de novo loss-of- function mutation with evidence from cell-type- specific gene expression in the mouse brain (specifically translational profiles of 24 specific mouse CNS cell types isolated from 6 different brain regions). Genes with positive D scores are more likely to be associated with autism risk, with higher-confidence genes having higher D scores. This statistic was first presented by Zhang & Shen (Hum Mutat 38, 204- 215 (2017), and D scores for more than 20,000 RefSeq genes can be found in column M in supplementary table 2 from that paper.
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