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

Gene ID: 59335, updated on 27-Oct-2018

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; Vega:OTTHUMG00000020808
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

Genomic context

See PRDM12 in Genome Data Viewer
Location:
9q34.12
Exon count:
5
Annotation release Status Assembly Chr Location
109 current GRCh38.p12 (GCF_000001405.38) 9 NC_000009.12 (130664594..130682997)
105 previous assembly GRCh37.p13 (GCF_000001405.25) 9 NC_000009.11 (133539981..133558384)

Chromosome 9 - NC_000009.12Genomic Context describing neighboring genes Neighboring gene far upstream element binding protein 3 Neighboring gene microRNA 6856 Neighboring gene VISTA enhancer hs876 Neighboring gene ribosomal protein L19 pseudogene 15 Neighboring gene ABL breakpoint recombination region Neighboring gene exosome component 2 Neighboring gene ribosomal protein L37 pseudogene 17 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 Jun 15 11:32:44 2016

Bibliography

GeneRIFs: Gene References Into FunctionsWhat's a GeneRIF?

Phenotypes

NHGRI GWAS Catalog

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

General gene information

Homology

Gene Ontology Provided by GOA

Function Evidence Code Pubs
DNA-binding transcription factor activity, RNA polymerase II-specific ISM
Inferred from Sequence Model
more info
PubMed 
RNA polymerase II regulatory region sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
chromatin DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone methyltransferase binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
histone methyltransferase binding IDA
Inferred from Direct Assay
more info
PubMed 
metal ion binding IEA
Inferred from Electronic Annotation
more info
 
methyltransferase activity IEA
Inferred from Electronic Annotation
more info
 
sequence-specific DNA binding IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
Process Evidence Code Pubs
detection of temperature stimulus involved in sensory perception of pain IMP
Inferred from Mutant Phenotype
more info
PubMed 
methylation IEA
Inferred from Electronic Annotation
more info
 
neurogenesis IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
neuron projection development IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of histone H3-K9 dimethylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of histone H3-K9 dimethylation IMP
Inferred from Mutant Phenotype
more info
PubMed 
positive regulation of histone H3-K9 methylation IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
positive regulation of histone H3-K9 methylation IDA
Inferred from Direct Assay
more info
PubMed 
regulation of transcription by RNA polymerase II IEA
Inferred from Electronic Annotation
more info
 
sensory perception of pain IMP
Inferred from Mutant Phenotype
more info
PubMed 
Component Evidence Code Pubs
nucleus IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
NP_067632.2

NCBI Reference Sequences (RefSeq)

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..23404
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_021619.2NP_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
    Q9H4Q4
    Related
    ENSP00000253008.2, OTTHUMP00000022367, ENST00000253008.2, OTTHUMT00000054664
    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: Homo sapiens Annotation Release 109 details...Open this link in a new tab

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

Reference GRCh38.p12 Primary Assembly

Genomic

  1. NC_000009.12 Reference GRCh38.p12 Primary Assembly

    Range
    130664594..130682997
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)
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