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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 cognitive disability. 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 Dystonia 3, Torsion, X-Linked 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

Additional gene information 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

GeneHancer (GH) Regulatory Elements for ZMYM3 Gene

Promoters and enhancers for ZMYM3 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH0XI071250 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 555.6 +1.5 1474 6.1 HDGF PKNOX1 ARNT NEUROD1 SIN3A FEZF1 ZNF2 YY1 ZNF766 ZNF213 ZMYM3 LOC105373247 TAF1 LOC100420758 MED12 NONO OGT ERCC6L ARR3 ENSG00000229601
GH0XI072107 Enhancer 1.5 FANTOM5 Ensembl ENCODE dbSUPER 16.2 -852.7 -852734 1.2 KLF17 RAD21 GLIS2 ATF7 EGR2 CEBPB ZNF398 ZEB2 ZNF781 ZFP69B RTL5 FLJ44635 ZMYM3 NHSL2 HDAC8 OGT PIR32507 PIR46676
GH0XI071530 Promoter/Enhancer 2.3 EPDnew Ensembl ENCODE dbSUPER 10 -278.5 -278484 5.7 FEZF1 DMAP1 IRF4 YY1 ZNF213 E2F8 ZNF143 SP3 NFYC ZC3H11A OGT TAF1 NONO MED12 ERCC6L GCNA LOC100420758 ENSG00000229601 RPS26P11 ZMYM3
GH0XI072238 Promoter/Enhancer 1.9 EPDnew Ensembl ENCODE 12.1 -983.6 -983560 1.6 ATF1 ARID4B SIN3A ZNF48 POLR2B ZNF213 SP3 GTF2B NFYC REST ERCC6L TAF1 PIN4 NONO OGT ZMYM3 ENSG00000229601 RPS26P11 LOC392489 GC0XM072223
GH0XI071145 Promoter/Enhancer 1.7 Ensembl ENCODE dbSUPER 13.5 +109.1 109097 1.9 HDGF ATF1 FOXA2 ARNT ZNF493 TCF12 POLR2B GLIS2 E2F8 KLF7 NLGN3 MED12 LOC392489 TAF1 NONO ZMYM3 LOC100420758 ARR3 P2RY4 OGT
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around ZMYM3 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the ZMYM3 gene promoter:

Genomic Locations for ZMYM3 Gene

Genomic Locations for ZMYM3 Gene
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 posLast=577577, posLast=10721072, posLast=10781078, posLast=10861086, posLast=11001100, isoforms=21251, posLast=12981298, and posLast=13061306

No data available for DME Specific Peptides for ZMYM3 Gene

Domains & Families for ZMYM3 Gene

Gene Families for ZMYM3 Gene

Human Protein Atlas (HPA):
  • Disease related genes
  • Plasma proteins
  • Predicted intracellular proteins

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

Clone Products

No data available for Enzyme Numbers (IUBMB) , Phenotypes From GWAS Catalog , 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

Subcellular locations from the

Human Protein Atlas (HPA)

Gene Ontology (GO) - Cellular Components for ZMYM3 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005634 nucleus IEA --
GO:0005654 nucleoplasm IDA,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 by RNA polymerase II 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

Clone 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 34
  • 97 (a)
(Canis familiaris)
Mammalia ZMYM3 33 34
  • 94.77 (n)
(Bos Taurus)
Mammalia ZMYM3 33 34
  • 94.7 (n)
(Mus musculus)
Mammalia Zmym3 33 16 34
  • 92.51 (n)
(Rattus norvegicus)
Mammalia Zmym3 33
  • 92.37 (n)
(Monodelphis domestica)
Mammalia ZMYM3 34
  • 87 (a)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 35 (a)
(Gallus gallus)
Aves ZMYM3 33 34
  • 73.64 (n)
(Anolis carolinensis)
Reptilia ZMYM3 34
  • 68 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia zmym3 33
  • 69.09 (n)
Str.19029 33
African clawed frog
(Xenopus laevis)
Amphibia Xl.11236 33
fruit fly
(Drosophila melanogaster)
Insecta woc 34
  • 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 Variation AA Info Type
rs1057521196 likely-benign, not specified 71,240,973(-) C/T coding_sequence_variant, genic_downstream_transcript_variant, synonymous_variant
rs587777358 uncertain-significance, not provided 71,249,610(-) G/A coding_sequence_variant, missense_variant
rs139405380 uncertain-significance, not specified 71,253,061(-) G/C coding_sequence_variant, synonymous_variant
rs142437272 uncertain-significance, not specified 71,240,964(-) G/A coding_sequence_variant, genic_downstream_transcript_variant, synonymous_variant
rs375862549 uncertain-significance, not specified 71,242,420(-) C/T coding_sequence_variant, genic_downstream_transcript_variant, synonymous_variant

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

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

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)

Additional Variant Information 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: HGMD and DISEASES

- 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}.

Additional Disease Information for ZMYM3

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 SM … Ropers HH (Human molecular genetics 1996) 3 4 22 58
  2. Identification and characterization of a set of conserved and new regulators of cytoskeletal organization, cell morphology and migration. (PMID: 21834987) Bai SW … Ridley AJ (BMC biology 2011) 3 4 58
  3. Global, in vivo, and site-specific phosphorylation dynamics in signaling networks. (PMID: 17081983) Olsen JV … Mann M (Cell 2006) 3 4 58
  4. The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4 58
  5. A candidate X-linked mental retardation gene is a component of a new family of histone deacetylase-containing complexes. (PMID: 12493763) Hakimi MA … Shiekhattar R (The Journal of biological chemistry 2003) 3 4 58

Products for ZMYM3 Gene

Sources for ZMYM3 Gene

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