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

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: mouse all
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Genomic context

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_000009.12 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

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.
PRDM12 in Health and Diseases.
Title: PRDM12 in Health and Diseases.
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.
The natural history of the PRDM12-CIP disorder.
Title: Clinical features for diagnosis and management of patients with PRDM12 congenital insensitivity to pain.
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.
Prdm12 is a key factor in the orchestration of sensory neurogenesis.
Title: Transcriptional regulator PRDM12 is essential for human pain perception.
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.

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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
Congenital insensitivity to pain-hypohidrosis syndrome MedGen: C4225308 OMIM: 616488 GeneReviews: Congenital Insensitivity to Pain Overview	not available

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 EBI GWAS CatalogPubMed

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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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

NG_053081.1 RefSeqGene

Range

5001..23390

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

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