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Aliases for ZMYM3 Gene

Aliases for ZMYM3 Gene

  • Zinc Finger MYM-Type Containing 3 2 3 5
  • Zinc Finger Protein 261 2 3 4
  • DXS6673E 3 4
  • ZNF261 3 4
  • Zinc Finger MYM-Type Protein 3 3
  • Zinc Finger, MYM-Type 3 3
  • ZNF198L2 3
  • KIAA0385 4
  • XFIM 3
  • MYM 3

External Ids for ZMYM3 Gene

Previous HGNC Symbols for ZMYM3 Gene

  • ZNF261

Previous GeneCards Identifiers for ZMYM3 Gene

  • GC0XM070243
  • GC0XM070376
  • GC0XM070459
  • GC0XM064255

Summaries for ZMYM3 Gene

Entrez Gene Summary for ZMYM3 Gene

  • 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. A chromosomal translocation (X;13) involving this gene is associated with X-linked mental retardation. Several alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Jan 2010]

GeneCards Summary for ZMYM3 Gene

ZMYM3 (Zinc Finger MYM-Type Containing 3) is a Protein Coding gene. Diseases associated with ZMYM3 include Allan-Herndon-Dudley Syndrome and Myasthenic Syndrome, Congenital, 6, Presynaptic. An important paralog of this gene is ZMYM4.

UniProtKB/Swiss-Prot for ZMYM3 Gene

  • Plays a role in the regulation of cell morphology and cytoskeletal organization.

Gene Wiki entry for ZMYM3 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for ZMYM3 Gene

Genomics for ZMYM3 Gene

Regulatory Elements for ZMYM3 Gene

Enhancers for ZMYM3 Gene
GeneHancer Identifier Enhancer Score Enhancer Sources Gene-Enhancer Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor Binding Sites within enhancer Gene Targets for Enhancer
GH0XG071224 1 ENCODE dbSUPER 20.5 +29.7 29722 2.3 MXI1 SAP130 RARA ZFHX2 ZBTB48 NR2F6 EZH2 GATAD2A MAZ FOXA3 ZMYM3 GJB1 NONO GC0XP071223 PIR53282 GC0XM071249
GH0XG071227 1.2 ENCODE dbSUPER 13.3 +27.3 27285 1.8 ELF3 TBP FOXA2 MLX ARID4B RAD21 RARA YY1 GATA4 CREM ZMYM3 GJB1 GC0XP071223 PIR53282 GC0XM071249
GH0XG071300 1 Ensembl ENCODE 13 -46.7 -46697 2.0 FOXA2 JUN YY1 FOSL1 POLR2A PATZ1 HNF4G FOS PAF1 FOXA3 ZMYM3 ENSG00000228427 TAF1 MED12 IL2RG ITGB1BP2 LOC100131556
GH0XG071213 1.3 ENCODE dbSUPER 4.9 +39.3 39303 4.1 FOXA2 CREB3L1 ZFP64 ARID4B SIN3A DMAP1 ZNF2 YY1 SLC30A9 ZNF143 ZMYM3 GJB1 GC0XP071223
GH0XG071145 1.2 ENCODE dbSUPER 5.1 +108.9 108852 1.4 HDGF ATF1 FOXA2 ARNT ZNF493 TCF12 GLIS2 KLF7 SP3 MCM3 ZMYM3 NLGN3 ENSG00000228427
- Elite enhancer and/or Elite enhancer-gene association Download GeneHancer data dump

Enhancers around ZMYM3 on UCSC Golden Path with GeneCards custom track

Promoters for ZMYM3 Gene
Ensembl Regulatory Elements (ENSRs) TSS Distance (bp) Size (bp) Binding Sites for Transcription Factors within promoters

Genomic Location for ZMYM3 Gene

71,239,624 bp from pter
71,255,261 bp from pter
15,638 bases
Minus strand

Genomic View for ZMYM3 Gene

Genes around ZMYM3 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
ZMYM3 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for ZMYM3 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for ZMYM3 Gene

Proteins for ZMYM3 Gene

  • Protein details for ZMYM3 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    Zinc finger MYM-type protein 3
    Protein Accession:
    Secondary Accessions:
    • D3DVV3
    • O15089
    • Q96E26

    Protein attributes for ZMYM3 Gene

    1370 amino acids
    Molecular mass:
    152379 Da
    Quaternary structure:
    • May be a component of a BHC histone deacetylase complex that contains HDAC1, HDAC2, HMG20B/BRAF35, KDM1A, RCOR1/CoREST, PHF21A/BHC80, ZMYM2, ZNF217, ZMYM3, GSE1 and GTF2I.
    • Sequence=BAA20839.2; Type=Erroneous initiation; Evidence={ECO:0000305};

    Alternative splice isoforms for ZMYM3 Gene


neXtProt entry for ZMYM3 Gene

Post-translational modifications for ZMYM3 Gene

  • Ubiquitination at isoforms=2577, posLast=10721072, isoforms=21078, posLast=10861086, isoforms=21100, posLast=12511251, isoforms=21298, and isoforms=21306
  • Modification sites at PhosphoSitePlus

No data available for DME Specific Peptides for ZMYM3 Gene

Domains & Families for ZMYM3 Gene

Gene Families for ZMYM3 Gene

Protein Domains for ZMYM3 Gene

Suggested Antigen Peptide Sequences for ZMYM3 Gene

Graphical View of Domain Structure for InterPro Entry

genes like me logo Genes that share domains with ZMYM3: view

No data available for UniProtKB/Swiss-Prot for ZMYM3 Gene

Function for ZMYM3 Gene

Molecular function for ZMYM3 Gene

UniProtKB/Swiss-Prot Function:
Plays a role in the regulation of cell morphology and cytoskeletal organization.

Gene Ontology (GO) - Molecular Function for ZMYM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000981 RNA polymerase II transcription factor activity, sequence-specific DNA binding IBA --
GO:0003677 DNA binding TAS 10486218
GO:0008270 zinc ion binding IEA --
GO:0046872 metal ion binding IEA --
genes like me logo Genes that share ontologies with ZMYM3: view
genes like me logo Genes that share phenotypes with ZMYM3: view

Animal Model Products

CRISPR Products

miRNA for ZMYM3 Gene

Inhibitory RNA Products

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for ZMYM3 Gene

Localization for ZMYM3 Gene

Subcellular locations from UniProtKB/Swiss-Prot for ZMYM3 Gene

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for ZMYM3 gene
Compartment Confidence
nucleus 5
plasma membrane 1
extracellular 1
mitochondrion 1
peroxisome 1
endoplasmic reticulum 1
cytosol 1

Gene Ontology (GO) - Cellular Components for ZMYM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IBA --
GO:0005737 cytoplasm IBA --
genes like me logo Genes that share ontologies with ZMYM3: view

Pathways & Interactions for ZMYM3 Gene

SuperPathways for ZMYM3 Gene

No Data Available

Gene Ontology (GO) - Biological Process for ZMYM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0006357 regulation of transcription from RNA polymerase II promoter IEA --
GO:0007010 cytoskeleton organization IMP 21834987
GO:0007275 multicellular organism development TAS 10486218
GO:0022604 regulation of cell morphogenesis IMP 21834987
genes like me logo Genes that share ontologies with ZMYM3: view

No data available for Pathways by source and SIGNOR curated interactions for ZMYM3 Gene

Drugs & Compounds for ZMYM3 Gene

No Compound Related Data Available

Transcripts for ZMYM3 Gene

Unigene Clusters for ZMYM3 Gene

Zinc finger, MYM-type 3:
Representative Sequences:

CRISPR Products

Inhibitory RNA Products

Alternative Splicing Database (ASD) splice patterns (SP) for ZMYM3 Gene

ExUns: 1a · 1b ^ 2 ^ 3a · 3b ^ 4 ^ 5 ^ 6a · 6b ^ 7a · 7b ^ 8 ^ 9a · 9b ^ 10 ^ 11 ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^ 17 ^ 18 ^ 19a · 19b ^ 20a ·
SP1: - - -
SP2: - -
SP4: - - - - - - - - - -

ExUns: 20b · 20c ^ 21 ^ 22a · 22b ^ 23a · 23b ^ 24 ^ 25
SP1: - -
SP5: -

Relevant External Links for ZMYM3 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for ZMYM3 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for ZMYM3 Gene

Protein differential expression in normal tissues from HIPED for ZMYM3 Gene

This gene is overexpressed in Platelet (19.5), Fetal ovary (10.1), Blymphocyte (9.8), and Fetal Brain (7.8).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for ZMYM3 Gene

Protein tissue co-expression partners for ZMYM3 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of ZMYM3 Gene:


SOURCE GeneReport for Unigene cluster for ZMYM3 Gene:


mRNA Expression by UniProt/SwissProt for ZMYM3 Gene:

Tissue specificity: Most abundant in brain, moderate in muscle and heart, low in other tissues except placenta.

Evidence on tissue expression from TISSUES for ZMYM3 Gene

  • Nervous system(4.7)
  • Liver(4.2)
  • Muscle(4.2)
genes like me logo Genes that share expression patterns with ZMYM3: view

Primer Products

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues and Phenotype-based relationships between genes and organs from Gene ORGANizer for ZMYM3 Gene

Orthologs for ZMYM3 Gene

This gene was present in the common ancestor of animals.

Orthologs for ZMYM3 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia ZMYM3 35
  • 97 (a)
(Canis familiaris)
Mammalia ZMYM3 34 35
  • 94.77 (n)
(Bos Taurus)
Mammalia ZMYM3 34 35
  • 94.7 (n)
(Mus musculus)
Mammalia Zmym3 34 16 35
  • 92.51 (n)
(Rattus norvegicus)
Mammalia Zmym3 34
  • 92.37 (n)
(Monodelphis domestica)
Mammalia ZMYM3 35
  • 87 (a)
(Ornithorhynchus anatinus)
Mammalia -- 35
  • 35 (a)
(Gallus gallus)
Aves ZMYM3 34 35
  • 73.64 (n)
(Anolis carolinensis)
Reptilia ZMYM3 35
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia zmym3 34
  • 69.09 (n)
Str.19029 34
African clawed frog
(Xenopus laevis)
Amphibia Xl.11236 34
fruit fly
(Drosophila melanogaster)
Insecta woc 35
  • 22 (a)
Species where no ortholog for ZMYM3 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (Ciona intestinalis)
  • sea squirt (Ciona savignyi)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)
  • zebrafish (Danio rerio)

Evolution for ZMYM3 Gene

Gene Tree for ZMYM3 (if available)
Gene Tree for ZMYM3 (if available)

Paralogs for ZMYM3 Gene

Paralogs for ZMYM3 Gene

(2) SIMAP similar genes for ZMYM3 Gene using alignment to 7 proteins:

genes like me logo Genes that share paralogs with ZMYM3: view

Variants for ZMYM3 Gene

Sequence variations from dbSNP and Humsavar for ZMYM3 Gene

SNP ID Clin Chr 0X pos Sequence Context AA Info Type
rs139405380 Uncertain significance 71,253,061(+) TCCAG(C/G)CCAGC upstream-variant-2KB, reference, synonymous-codon
rs142437272 Uncertain significance 71,240,964(+) ATCTC(A/G)CGCAC reference, synonymous-codon
rs375862549 Uncertain significance 71,242,420(+) AACAC(C/T)GTATC reference, synonymous-codon
rs587777358 Uncertain significance 71,249,610(+) GGCCC(A/G)GAATT reference, missense
rs879255361 Uncertain significance 71,241,267(-) CCCTC(C/T)GCTGC reference, missense

Structural Variations from Database of Genomic Variants (DGV) for ZMYM3 Gene

Variant ID Type Subtype PubMed ID
esv1584074 OTHER inversion 17803354
esv33082 CNV loss 17666407
nsv508781 CNV insertion 20534489

Variation tolerance for ZMYM3 Gene

Residual Variation Intolerance Score: 6.95% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 1.41; 27.79% of all genes are more intolerant (likely to be disease-causing)

Relevant External Links for ZMYM3 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for ZMYM3 Gene

Disorders for ZMYM3 Gene

MalaCards: The human disease database

(3) MalaCards diseases for ZMYM3 Gene - From: DISEASES and GeneCards

Disorder Aliases PubMed IDs
allan-herndon-dudley syndrome
  • allan-herndon syndrome
myasthenic syndrome, congenital, 6, presynaptic
  • cms1a
non-syndromic x-linked intellectual disability
  • non-specific x-linked mental retardation
- elite association - COSMIC cancer census association via MalaCards
Search ZMYM3 in MalaCards View complete list of genes associated with diseases


  • Note=A chromosomal aberration involving ZMYM3 may be a cause of X-linked mental retardation in Xq13.1. Translocation t(X;13)(q13.1;?). {ECO:0000269 PubMed:8817323}.

Relevant External Links for ZMYM3

Atlas of Genetics and Cytogenetics in Oncology and Haematology:
genes like me logo Genes that share disorders with ZMYM3: view

No data available for Genatlas for ZMYM3 Gene

Publications for ZMYM3 Gene

  1. Cloning and characterization of DXS6673E, a candidate gene for X- linked mental retardation in Xq13.1. (PMID: 8817323) van der Maarel S.M. … Ropers H.-H. (Hum. Mol. Genet. 1996) 3 4 22 64
  2. Identification and characterization of a set of conserved and new regulators of cytoskeletal organisation, cell morphology and migration. (PMID: 21834987) Bai S.W. … Ridley A.J. (BMC Biol. 2011) 3 4 64
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen J.V. … Mann M. (Cell 2006) 3 4 64
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard D.S. … Malek J. (Genome Res. 2004) 3 4 64
  5. A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes. (PMID: 12493763) Hakimi M.-A. … Shiekhattar R. (J. Biol. Chem. 2003) 3 4 64

Products for ZMYM3 Gene

Sources for ZMYM3 Gene

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