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

Gene ID: 9203, updated on 11-Apr-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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Location:
Xq13.1
Exon count:
28
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) X NC_000023.11 (71239624..71255290, complement)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) X NC_060947.1 (69673728..69689295, complement)
105.20220307 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. 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
  2. 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
  3. 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
  4. 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
  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 (75) 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 Variation Viewer (GRCh37.p13)

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_2023_10

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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