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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
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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)

Genotypes

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

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Chemical Information
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