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    PRDM12 PR/SET domain 12 [ Homo sapiens (human) ]

    Gene ID: 59335, updated on 2-Nov-2024

    Summary

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    Official Symbol
    PRDM12provided by HGNC
    Official Full Name
    PR/SET domain 12provided by HGNC
    Primary source
    HGNC:HGNC:13997
    See related
    Ensembl:ENSG00000130711 MIM:616458; AllianceGenome:HGNC:13997
    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
    PFM9; HSAN8
    Summary
    This gene encodes a transcriptional regulator of sensory neuronal specification that plays a critical role in pain perception. The encoded protein contains an N-terminal PRDI-BF1 and RIZ homology (PR) domain, a SET domain, and three C-terminal C2H2 zinc finger DNA-binding domains. Naturally occurring mutations in this gene are associated with congenital insensitivity to pain (CIP), and hereditary sensory and autonomic neuropathies (HSAN's) affecting peripheral sensory and autonomic neurons. Deregulation of this gene is associated with solid cancers and hematological malignancies including chronic myeloid leukaemia. [provided by RefSeq, Mar 2017]
    Expression
    Low expression observed in reference dataset See more
    Orthologs
    mouse all
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    Genomic context

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    See PRDM12 in Genome Data Viewer
    Location:
    9q34.12
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (130664594..130682983)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (142869556..142887937)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (133539981..133558370)

    Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene far upstream element binding protein 3 Neighboring gene Sharpr-MPRA regulatory region 1186 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133507597-133508347 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133513639-133514234 Neighboring gene microRNA 6856 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133538423-133539264 Neighboring gene VISTA enhancer hs876 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr9:133541982-133543181 Neighboring gene ribosomal protein L19 pseudogene 15 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 20403 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr9:133556829-133557504 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 29157 Neighboring gene ABL breakpoint recombination region Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133587784-133588460 Neighboring gene uncharacterized LOC128092248 Neighboring gene exosome component 2 Neighboring gene ABL proto-oncogene 1, non-receptor tyrosine kinase

    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 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. Midface toddler excoriation syndrome (MiTES) can be caused by autosomal recessive biallelic mutations in a gene for congenital insensitivity to pain, PRDM12. Moss C, et al. Br J Dermatol, 2018 Nov. PMID 29949203
    2. Quantitative PCR identifies a minimal deleted region of 120 kb extending from the Philadelphia chromosome ABL translocation breakpoint in chronic myeloid leukemia with poor outcome. Kolomietz E, et al. Leukemia, 2003 Jul. PMID 12835719
    3. Hereditary Sensory Polyneuropathy, Pain Insensitivity and Global Developmental Delay due to Novel Mutation in PRDM12 Gene. Saini AG, et al. Indian J Pediatr, 2017 Apr. PMID 28050684
    4. A potential role for PRDM12 in the pathogenesis of chronic myeloid leukaemia with derivative chromosome 9 deletion. Reid AG, et al. Leukemia, 2004 Jan. PMID 14523459
    5. Clinical features for diagnosis and management of patients with PRDM12 congenital insensitivity to pain. Zhang S, et al. J Med Genet, 2016 Aug. PMID 26975306, Free PMC Article

    See all (21) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Ocular manifestations among patients with congenital insensitivity to pain due to variants in PRDM12 and SCN9A genes.
      Title: Ocular manifestations among patients with congenital insensitivity to pain due to variants in PRDM12 and SCN9A genes.
    2. PRDM12 in Health and Diseases.
      Title: PRDM12 in Health and Diseases.
    3. Study in five further children, from four families, with facial lesions typical of midface toddler excoriation syndrome (MiTES) found autosomal recessive mutations in PRDM12 in four of five patients and extended the phenotypic spectrum of PRDM12 mutations, which usually cause hereditary sensory and autonomic neuropathy type VIII, characterized by mutilating self-inflicted wounds of the extremities, lips and tongue.
      Title: Midface toddler excoriation syndrome (MiTES) can be caused by autosomal recessive biallelic mutations in a gene for congenital insensitivity to pain, PRDM12.
    4. The natural history of the PRDM12-CIP disorder.
      Title: Clinical features for diagnosis and management of patients with PRDM12 congenital insensitivity to pain.
    5. PRDM12 and its functional fly homolog Hamlet are evolutionary conserved master regulators of sensory neuronal specification and play a critical role in pain perception
      Title: The evolutionarily conserved transcription factor PRDM12 controls sensory neuron development and pain perception.
    6. Prdm12 is a key factor in the orchestration of sensory neurogenesis.
      Title: Transcriptional regulator PRDM12 is essential for human pain perception.
    7. Down-regulation of PRDM12 is associated with the pathogenesis of chronic myeloid leukaemia with derivative chromosome 9 deletion
      Title: A potential role for PRDM12 in the pathogenesis of chronic myeloid leukaemia with derivative chromosome 9 deletion.
    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

    EBI GWAS Catalog

    Description
    Fraction of exhaled nitric oxide values in childhood are associated with 17q11.2-q12 and 17q12-q21 variants.
    EBI GWAS Catalog

    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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    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables DNA binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables histone chaperone activity IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables histone methyltransferase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables histone methyltransferase binding IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    enables metal ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables methyltransferase activity IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    acts_upstream_of_or_within detection of temperature stimulus involved in sensory perception of pain IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in negative regulation of transcription by RNA polymerase II ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    involved_in neurogenesis IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within neuron projection development IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    acts_upstream_of_or_within protein methylation IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    involved_in regulation of gene expression IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    acts_upstream_of_or_within sensory perception of pain IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    Component Evidence Code Pubs
    located_in nucleoplasm IDA
    Inferred from Direct Assay
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    		 PubMed 

    General protein information

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    Preferred Names
    PR domain zinc finger protein 12
    Names
    PR domain containing 12

    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_053081.1 RefSeqGene

      Range
      5001..23390
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_021619.3 → NP_067632.2  PR domain zinc finger protein 12

      See identical proteins and their annotated locations for NP_067632.2

      Status: REVIEWED

      Source sequence(s)
      AY004252
      Consensus CDS
      CCDS6934.1
      UniProtKB/Swiss-Prot
      A3KFK9, Q9H4Q4
      Related
      ENSP00000253008.2, ENST00000253008.3
      Conserved Domains (5) summary
      COG5048
      Location:244 → 294
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:245 → 265
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:244 → 265
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:99 → 203
      SET; SET domain
      pfam13465
      Location:257 → 282
      zf-H2C2_2; Zinc-finger double domain

    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_000009.12 Reference GRCh38.p14 Primary Assembly

      Range
      130664594..130682983
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060933.1 Alternate T2T-CHM13v2.0

      Range
      142869556..142887937
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H4Q4.2 GenPept UniProtKB/Swiss-Prot:Q9H4Q4

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

    Chemical Information
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