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

    Gene ID: 59335, updated on 7-Sep-2023

    Summary

    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
    NEW
    Try the new Gene table
    Try the new Transcript table

    Genomic context

    See PRDM12 in Genome Data Viewer
    Location:
    9q34.12
    Exon count:
    5
    Annotation release Status Assembly Chr Location
    RS_2023_03 current GRCh38.p14 (GCF_000001405.40) 9 NC_000009.12 (130664594..130682983)
    RS_2023_03 current T2T-CHM13v2.0 (GCF_009914755.1) 9 NC_060933.1 (142869556..142887937)
    105.20220307 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 H3K4me1 hESC enhancer GRCh37_chr9:133556829-133557504 Neighboring gene ABL breakpoint recombination region Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr9:133587784-133588460 Neighboring gene umcharacterized LOC128092248 Neighboring gene exosome component 2 Neighboring gene ABL proto-oncogene 1, non-receptor tyrosine kinase

    Genomic regions, transcripts, and products

    Expression

    • 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

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?

    Phenotypes

    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

    Interactions

    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

    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
    PubMed 
    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
     
    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
    PubMed 
    located_in nucleus IDA
    Inferred from Direct Assay
    more info
    PubMed 

    General protein information

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

    NCBI Reference Sequences (RefSeq)

    NEW Try the new Transcript table

    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_021619.3NP_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:244294
      COG5048; FOG: Zn-finger [General function prediction only]
      sd00017
      Location:245265
      ZF_C2H2; C2H2 Zn finger [structural motif]
      pfam00096
      Location:244265
      zf-C2H2; Zinc finger, C2H2 type
      pfam00856
      Location:99203
      SET; SET domain
      pfam13465
      Location:257282
      zf-H2C2_2; Zinc-finger double domain

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_03

    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)