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    ZMYM3 zinc finger MYM-type containing 3 [ Homo sapiens (human) ]

    Gene ID: 9203, updated on 27-Nov-2024

    Summary

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    Official Symbol
    ZMYM3provided by HGNC
    Official Full Name
    zinc finger MYM-type containing 3provided by HGNC
    Primary source
    HGNC:HGNC:13054
    See related
    Ensembl:ENSG00000147130 MIM:300061; AllianceGenome:HGNC:13054
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    MYM; XFIM; ZNF261; XLID112; DXS6673E; ZNF198L2
    Summary
    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]
    Expression
    Ubiquitous expression in ovary (RPKM 15.3), testis (RPKM 11.9) and 25 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See ZMYM3 in Genome Data Viewer
    Location:
    Xq13.1
    Exon count:
    28
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (71239624..71255290, complement)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (69673728..69689295, complement)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) X NC_000023.10 (70459474..70475047, complement)

    Chromosome X - NC_000023.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC107985688 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29740 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29741 Neighboring gene gap junction protein beta 1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20895 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20896 Neighboring gene uncharacterized LOC105373247 Neighboring gene non-POU domain containing octamer binding Neighboring gene BRD4-independent group 4 enhancer GRCh37_chrX:70523398-70524597 Neighboring gene integrin subunit beta 1 binding protein 2

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Disease-only alleles at the extreme ends of the human ZMYM3 exceptionally long 5' UTR short tandem repeat in bipolar disorder: A pilot study. Alizadeh F, et al. J Affect Disord, 2019 May 15. PMID 30909162
    2. Skewing of the genetic architecture at the ZMYM3 human-specific 5' UTR short tandem repeat in schizophrenia. Alizadeh F, et al. Mol Genet Genomics, 2018 Jun. PMID 29332164
    3. Evolving evidence on a link between the ZMYM3 exceptionally long GA-STR and human cognition. Afshar H, et al. Sci Rep, 2020 Nov 10. PMID 33173136, Free PMC Article
    4. Deleterious, protein-altering variants in the transcriptional coregulator ZMYM3 in 27 individuals with a neurodevelopmental delay phenotype. Hiatt SM, et al. Am J Hum Genet, 2023 Feb 2. PMID 36586412, Free PMC Article
    5. Methylation of ZNF261 as an assay for determining X chromosome inactivation patterns. Beever C, et al. Am J Med Genet A, 2003 Jul 30. PMID 12838571

    See all (82) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Deleterious, protein-altering variants in the transcriptional coregulator ZMYM3 in 27 individuals with a neurodevelopmental delay phenotype.
      Title: Deleterious, protein-altering variants in the transcriptional coregulator ZMYM3 in 27 individuals with a neurodevelopmental delay phenotype.
    2. Evolving evidence on a link between the ZMYM3 exceptionally long GA-STR and human cognition.
      Title: Evolving evidence on a link between the ZMYM3 exceptionally long GA-STR and human cognition.
    3. AGS mutations in this cluster impair the interaction of RNase H2 with several members of the CoREST chromatin-silencing complex that include the histone deacetylase HDAC2 and the demethylase KDM1A, the transcriptional regulators RCOR1 and GTFII-I as well as ZMYM3, an MYM-type zinc finger protein.
      Title: Aicardi-Goutières Syndrome associated mutations of RNase H2B impair its interaction with ZMYM3 and the CoREST histone-modifying complex.
    4. The ZMYM3 "exceptionally long" 5' UTR STR findings may alter our perspective of disease pathogenesis in psychiatric disorders, and set an example in which the low frequency alleles at the extreme short and long ends of the human STRs are, at least in part, a result of natural selection against these alleles and their unambiguous link to major human disorders.
      Title: Disease-only alleles at the extreme ends of the human ZMYM3 exceptionally long 5' UTR short tandem repeat in bipolar disorder: A pilot study.
    5. Data found skewing of the genetic architecture at the ZMYM3 short tandem repeats (STR) in schizophrenia. Further, results found a bell-shaped distribution of alleles and selection against alleles at the extreme ends of this STR.
      Title: Skewing of the genetic architecture at the ZMYM3 human-specific 5' UTR short tandem repeat in schizophrenia.
    Submit: New GeneRIF Correction

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    Associated conditions

    Description Tests
    Intellectual developmental disorder, X-linked 112
    MedGen: C5829589 OMIM: 301111 GeneReviews: Not available
    		not available

    Copy number response

    Description
    Copy number response
    Haploinsufficency

    No evidence available (Last evaluated 2012-07-25)

    ClinGen Genome Curation Page
    Triplosensitivity

    No evidence available (Last evaluated 2012-07-25)

    ClinGen Genome Curation Page

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA0385

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding TAS
    Traceable Author Statement
    more info
    		 PubMed 
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables zinc ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in cytoskeleton organization IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in regulation of cell morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    located_in nucleus IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    zinc finger MYM-type protein 3
    Names
    zinc finger protein 261
    zinc finger, MYM-type 3

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_016407.2 RefSeqGene

      Range
      6150..20666
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001171162.1 → NP_001164633.1  zinc finger MYM-type protein 3 isoform 2

      See identical proteins and their annotated locations for NP_001164633.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains an alternate 5' non-coding exon, and uses an alternate in-frame donor splice site at an internal coding exon compared to variant 1. This results in a shorter isoform (2) missing a 12 aa protein segment compared to isoform 1.
      Source sequence(s)
      CB305871, DA331402, X95808
      Consensus CDS
      CCDS55444.1
      UniProtKB/TrEMBL
      A6NHB5
      Related
      ENSP00000363110.1, ENST00000373998.5
      Conserved Domains (4) summary
      smart00746
      Location:311 → 347
      TRASH; metallochaperone-like domain
      PHA03307
      Location:2 → 305
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam06467
      Location:493 → 532
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam12012
      Location:1173 → 1341
      DUF3504; Domain of unknown function (DUF3504)

    2. NM_001171163.1 → NP_001164634.1  zinc finger MYM-type protein 3 isoform 3

      See identical proteins and their annotated locations for NP_001164634.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) contains an alternate 5' non-coding exon and an additional segment at its 3' end compared to variant 1. This results in a frame-shift and a much shorter isoform (3) compared to isoform 1. This isoform retains four Zn finger domains at the C-terminus, and is supported by homologs in mouse and rat.
      Source sequence(s)
      AK290762, BC013009
      Consensus CDS
      CCDS55443.1
      UniProtKB/TrEMBL
      A6NL54, A8K3Z7
      Related
      ENSP00000363093.1, ENST00000373981.5
      Conserved Domains (3) summary
      smart00746
      Location:311 → 347
      TRASH; metallochaperone-like domain
      PHA03307
      Location:2 → 304
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam06467
      Location:446 → 488
      zf-FCS; MYM-type Zinc finger with FCS sequence motif

    3. NM_005096.3 → NP_005087.1  zinc finger MYM-type protein 3 isoform 1

      See identical proteins and their annotated locations for NP_005087.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) contains an alternate 5' non-coding exon compared to variant 1. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AB002383, AK290762, BC013009, CB305871
      Consensus CDS
      CCDS14409.1
      UniProtKB/Swiss-Prot
      D3DVV3, O15089, Q14202, Q96E26
      UniProtKB/TrEMBL
      A6NHB5
      Conserved Domains (4) summary
      smart00746
      Location:311 → 347
      TRASH; metallochaperone-like domain
      PHA03307
      Location:2 → 305
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam06467
      Location:493 → 532
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam12012
      Location:1185 → 1353
      DUF3504; Domain of unknown function (DUF3504)

    4. NM_201599.3 → NP_963893.1  zinc finger MYM-type protein 3 isoform 1

      See identical proteins and their annotated locations for NP_963893.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) represents the predominant transcript. Variants 1 and 2 encode the same isoform (1).
      Source sequence(s)
      AB002383, CB305871, DA539831
      Consensus CDS
      CCDS14409.1
      UniProtKB/Swiss-Prot
      D3DVV3, O15089, Q14202, Q96E26
      UniProtKB/TrEMBL
      A6NHB5
      Related
      ENSP00000322845.5, ENST00000314425.9
      Conserved Domains (4) summary
      smart00746
      Location:311 → 347
      TRASH; metallochaperone-like domain
      PHA03307
      Location:2 → 305
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam06467
      Location:493 → 532
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam12012
      Location:1185 → 1353
      DUF3504; Domain of unknown function (DUF3504)

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000023.11 Reference GRCh38.p14 Primary Assembly

      Range
      71239624..71255290 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047442633.1 → XP_047298589.1  zinc finger MYM-type protein 3 isoform X2

    2. XM_005262309.5 → XP_005262366.1  zinc finger MYM-type protein 3 isoform X1

      See identical proteins and their annotated locations for XP_005262366.1

      UniProtKB/Swiss-Prot
      D3DVV3, O15089, Q14202, Q96E26
      UniProtKB/TrEMBL
      A6NHB5
      Conserved Domains (4) summary
      smart00746
      Location:311 → 347
      TRASH; metallochaperone-like domain
      PHA03307
      Location:2 → 305
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam06467
      Location:493 → 532
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam12012
      Location:1185 → 1353
      DUF3504; Domain of unknown function (DUF3504)

    3. XM_011531062.4 → XP_011529364.1  zinc finger MYM-type protein 3 isoform X1

      See identical proteins and their annotated locations for XP_011529364.1

      UniProtKB/Swiss-Prot
      D3DVV3, O15089, Q14202, Q96E26
      UniProtKB/TrEMBL
      A6NHB5
      Related
      ENSP00000363100.1, ENST00000373988.5
      Conserved Domains (4) summary
      smart00746
      Location:311 → 347
      TRASH; metallochaperone-like domain
      PHA03307
      Location:2 → 305
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam06467
      Location:493 → 532
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam12012
      Location:1185 → 1353
      DUF3504; Domain of unknown function (DUF3504)

    4. XM_047442634.1 → XP_047298590.1  zinc finger MYM-type protein 3 isoform X2

    5. XM_005262310.4 → XP_005262367.1  zinc finger MYM-type protein 3 isoform X2

      See identical proteins and their annotated locations for XP_005262367.1

      UniProtKB/TrEMBL
      A6NHB5
      Conserved Domains (4) summary
      smart00746
      Location:311 → 347
      TRASH; metallochaperone-like domain
      PHA03307
      Location:2 → 305
      PHA03307; transcriptional regulator ICP4; Provisional
      pfam06467
      Location:493 → 532
      zf-FCS; MYM-type Zinc finger with FCS sequence motif
      pfam12012
      Location:1173 → 1341
      DUF3504; Domain of unknown function (DUF3504)

    6. XM_047442632.1 → XP_047298588.1  zinc finger MYM-type protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DVV3, O15089, Q14202, Q96E26

    7. XM_047442635.1 → XP_047298591.1  zinc finger MYM-type protein 3 isoform X2

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060947.1 Alternate T2T-CHM13v2.0

      Range
      69673728..69689295 complement
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054328112.1 → XP_054184087.1  zinc finger MYM-type protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DVV3, O15089, Q14202, Q96E26

    2. XM_054328115.1 → XP_054184090.1  zinc finger MYM-type protein 3 isoform X2

    3. XM_054328111.1 → XP_054184086.1  zinc finger MYM-type protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DVV3, O15089, Q14202, Q96E26

    4. XM_054328116.1 → XP_054184091.1  zinc finger MYM-type protein 3 isoform X2

    5. XM_054328114.1 → XP_054184089.1  zinc finger MYM-type protein 3 isoform X2

    6. XM_054328113.1 → XP_054184088.1  zinc finger MYM-type protein 3 isoform X1

      UniProtKB/Swiss-Prot
      D3DVV3, O15089, Q14202, Q96E26

    7. XM_054328117.1 → XP_054184092.1  zinc finger MYM-type protein 3 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q14202.2 GenPept UniProtKB/Swiss-Prot:Q14202

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