PRDM12 (PR/SET domain 12)

Gene

• Entrez ID: 59335
• Gene name: PR/SET domain 12
• Gene symbol: PRDM12
• Synonyms (NCBI Gene): HSAN8, PFM9
• Chromosome: 9
• Chromosome location: 9q34.12
• 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 f

SNPs

SNP ID	Visualize variation	Clinical significance	Consequence
rs755205487	G>A,C	Pathogenic	Coding sequence variant, missense variant, synonymous variant
rs768643868	T>A,G	Likely-pathogenic	Coding sequence variant, missense variant
rs879255636	T>A	Pathogenic	Coding sequence variant, missense variant
rs879255637	G>C,T	Pathogenic	Coding sequence variant, missense variant
rs879255638	A>T	Pathogenic	Coding sequence variant, missense variant
rs1554752857	GTGGTAC>CA	Likely-pathogenic	Coding sequence variant, frameshift variant

miRNA

miRTarBase ID	miRNA	Experiments	Reference
MIRT719793	hsa-miR-6733-3p	HITS-CLIP	19536157
MIRT719792	hsa-miR-4302	HITS-CLIP	19536157
MIRT719791	hsa-miR-3126-5p	HITS-CLIP	19536157
MIRT719790	hsa-miR-6875-5p	HITS-CLIP	19536157
MIRT719789	hsa-miR-4419a	HITS-CLIP	19536157
MIRT719788	hsa-miR-4510	HITS-CLIP	19536157
MIRT719787	hsa-miR-6127	HITS-CLIP	19536157
MIRT719786	hsa-miR-6129	HITS-CLIP	19536157
MIRT719785	hsa-miR-6130	HITS-CLIP	19536157
MIRT719784	hsa-miR-6133	HITS-CLIP	19536157
MIRT719783	hsa-miR-4632-3p	HITS-CLIP	19536157
MIRT719782	hsa-miR-4710	HITS-CLIP	19536157
MIRT719781	hsa-miR-6834-5p	HITS-CLIP	19536157
MIRT719793	hsa-miR-6733-3p	HITS-CLIP	19536157
MIRT719792	hsa-miR-4302	HITS-CLIP	19536157
MIRT719791	hsa-miR-3126-5p	HITS-CLIP	19536157
MIRT719790	hsa-miR-6875-5p	HITS-CLIP	19536157
MIRT719789	hsa-miR-4419a	HITS-CLIP	19536157
MIRT719788	hsa-miR-4510	HITS-CLIP	19536157
MIRT719787	hsa-miR-6127	HITS-CLIP	19536157
MIRT719786	hsa-miR-6129	HITS-CLIP	19536157
MIRT719785	hsa-miR-6130	HITS-CLIP	19536157
MIRT719784	hsa-miR-6133	HITS-CLIP	19536157
MIRT719783	hsa-miR-4632-3p	HITS-CLIP	19536157
MIRT719782	hsa-miR-4710	HITS-CLIP	19536157
MIRT719781	hsa-miR-6834-5p	HITS-CLIP	19536157
MIRT1259915	hsa-miR-1284	CLIP-seq
MIRT1259916	hsa-miR-145	CLIP-seq
MIRT1259917	hsa-miR-1538	CLIP-seq
MIRT1259918	hsa-miR-1908	CLIP-seq
MIRT1259919	hsa-miR-2110	CLIP-seq
MIRT1259920	hsa-miR-2277-5p	CLIP-seq
MIRT1259921	hsa-miR-3136-3p	CLIP-seq
MIRT1259922	hsa-miR-3157-3p	CLIP-seq
MIRT1259923	hsa-miR-3183	CLIP-seq
MIRT1259924	hsa-miR-3940-3p	CLIP-seq
MIRT1259925	hsa-miR-4271	CLIP-seq
MIRT1259926	hsa-miR-4290	CLIP-seq
MIRT1259927	hsa-miR-431	CLIP-seq
MIRT1259928	hsa-miR-4649-3p	CLIP-seq
MIRT1259929	hsa-miR-4667-3p	CLIP-seq
MIRT1259930	hsa-miR-4699-3p	CLIP-seq
MIRT1259931	hsa-miR-4723-3p	CLIP-seq
MIRT1259932	hsa-miR-4725-3p	CLIP-seq
MIRT1259933	hsa-miR-4738-3p	CLIP-seq
MIRT1259934	hsa-miR-4745-3p	CLIP-seq
MIRT1259935	hsa-miR-4760-5p	CLIP-seq
MIRT1259936	hsa-miR-4761-5p	CLIP-seq
MIRT1259937	hsa-miR-577	CLIP-seq
MIRT1259938	hsa-miR-583	CLIP-seq
MIRT1259939	hsa-miR-624	CLIP-seq
MIRT1259940	hsa-miR-663	CLIP-seq
MIRT1259941	hsa-miR-665	CLIP-seq
MIRT1259942	hsa-miR-744	CLIP-seq
MIRT1259943	hsa-miR-874	CLIP-seq
MIRT2076571	hsa-miR-1273	CLIP-seq
MIRT1259916	hsa-miR-145	CLIP-seq
MIRT1259922	hsa-miR-3157-3p	CLIP-seq
MIRT1259923	hsa-miR-3183	CLIP-seq
MIRT1259926	hsa-miR-4290	CLIP-seq
MIRT1259927	hsa-miR-431	CLIP-seq
MIRT1259929	hsa-miR-4667-3p	CLIP-seq
MIRT1259931	hsa-miR-4723-3p	CLIP-seq
MIRT2076572	hsa-miR-720	CLIP-seq
MIRT1259943	hsa-miR-874	CLIP-seq
MIRT1259916	hsa-miR-145	CLIP-seq
MIRT2303181	hsa-miR-205	CLIP-seq
MIRT1259920	hsa-miR-2277-5p	CLIP-seq
MIRT1259922	hsa-miR-3157-3p	CLIP-seq
MIRT1259923	hsa-miR-3183	CLIP-seq
MIRT1259926	hsa-miR-4290	CLIP-seq
MIRT1259927	hsa-miR-431	CLIP-seq
MIRT1259929	hsa-miR-4667-3p	CLIP-seq
MIRT1259931	hsa-miR-4723-3p	CLIP-seq
MIRT1259943	hsa-miR-874	CLIP-seq
MIRT1259916	hsa-miR-145	CLIP-seq
MIRT1259922	hsa-miR-3157-3p	CLIP-seq
MIRT1259923	hsa-miR-3183	CLIP-seq
MIRT1259926	hsa-miR-4290	CLIP-seq
MIRT1259927	hsa-miR-431	CLIP-seq
MIRT1259929	hsa-miR-4667-3p	CLIP-seq
MIRT1259931	hsa-miR-4723-3p	CLIP-seq
MIRT2076572	hsa-miR-720	CLIP-seq
MIRT1259943	hsa-miR-874	CLIP-seq

Gene ontology (GO)

GO ID	Ontology	Definition	Evidence	Reference
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	IEA
GO:0000122	Process	Negative regulation of transcription by RNA polymerase II	ISS
GO:0000981	Function	DNA-binding transcription factor activity, RNA polymerase II-specific	IEA
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA
GO:0001227	Function	DNA-binding transcription repressor activity, RNA polymerase II-specific	ISS
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	IEA
GO:0001228	Function	DNA-binding transcription activator activity, RNA polymerase II-specific	ISS
GO:0003677	Function	DNA binding	IEA
GO:0005634	Component	Nucleus	IBA
GO:0005634	Component	Nucleus	IDA	26005867
GO:0005634	Component	Nucleus	IEA
GO:0005654	Component	Nucleoplasm	IDA
GO:0006479	Process	Protein methylation	IDA	26005867
GO:0008270	Function	Zinc ion binding	IEA
GO:0010468	Process	Regulation of gene expression	IBA
GO:0019233	Process	Sensory perception of pain	IEA
GO:0019233	Process	Sensory perception of pain	IMP	26005867
GO:0019233	Process	Sensory perception of pain	ISS
GO:0022008	Process	Neurogenesis	IBA
GO:0022008	Process	Neurogenesis	IEA
GO:0022008	Process	Neurogenesis	IEA
GO:0031175	Process	Neuron projection development	IMP	26005867
GO:0045944	Process	Positive regulation of transcription by RNA polymerase II	IEA
GO:0046872	Function	Metal ion binding	IEA
GO:0048665	Process	Neuron fate specification	IEA
GO:0048665	Process	Neuron fate specification	ISS
GO:0050965	Process	Detection of temperature stimulus involved in sensory perception of pain	IMP	26005867
GO:0140713	Function	Histone chaperone activity	IDA	26005867
GO:0140713	Function	Histone chaperone activity	IEA
GO:1990226	Function	Histone methyltransferase binding	IBA
GO:1990226	Function	Histone methyltransferase binding	IDA	26005867

Other IDs

• MIM: 616458
• HGNC: 13997
• e!Ensembl: ENSG00000130711

Protein

• UniProt ID: Q9H4Q4
• Protein name: PR domain zinc finger protein 12 (PR domain-containing protein 12)
• Protein function: Transcriptional regulator necessary for the development of nociceptive neurons, playing a key role in determining the nociceptive lineage from neural crest cell progenitors. Initiates neurogenesis and activates downstream pro-neuronal transcript
• PDB: 3EP0
• Family and domains:

  Pfam

  Accession	ID	Position in sequence	Description	Type
  PF00096	zf-C2H2	243 → 265	Zinc finger, C2H2 type	Domain
  PF00096	zf-C2H2	271 → 293	Zinc finger, C2H2 type	Domain

• Tissue specificity: TISSUE SPECIFICITY: Not found in adult tissues except in dorsal root ganglia. {ECO:0000269|PubMed:26005867}.
• Sequence:

  MMGSVLPAEALVLKTGLKAPGLALAEVITSDILHSFLYGRWRNVLGEQLFEDKSHHASPK
  TAFTAEVLAQSFSGEVQKLSSLVLPAEVIIAQSSIPGEGLGIFSKTWIKAGTEMGPFTGR
  VIAPEHVDICKNNNLMWEVFNEDGTVRYFIDASQEDHRSWMTYIKCARNEQEQNLEVVQI
  GTSIFYKAIEMIPPDQELLVWYGNSHNTFLGIPGVPGLEEDQKKNKHEDFHPADSAAGPA
  GRMRCVICHRGFNSRSNLRSHMRIHTLDKPFVCRFCNRRFSQSSTLRNHVRLHTGERPYK
  CQVCQSAYSQLAGLRAHQKSARHRPPSTALQAHSPALPAPHAHAPALAAAAAAAAAAAAH
  HLPAMVL

• Sequence length: 367

Associated diseases

Evidence Score:

• ★☆☆☆☆  Gene-disease association found in Text Mining only
• ★★☆☆☆  Found in Text Mining and Unknown/Other Associations
• ★★★☆☆  Reported in Unknown/Other Associations across ≥2 Sources
• ★★★★☆  ClinVar: Pathogenic/Likely Pathogenic (<5 Variants)
• ★★★★★  ClinVar: Pathogenic/Likely Pathogenic (≥5 Variants)

Causal
Phenotype Name	Clinical Significance	dbSNP ID	RCV Accession	Evidence Score
Congenital insensitivity to pain-hypohidrosis syndrome	Pathogenic; Likely pathogenic	rs2132588902, rs2132586619, rs2132608070, rs2132607877, rs1410327797, rs879255636, rs879255637, rs755205487, rs879255638, rs2490743581, rs752427775	RCV001385116 RCV001784875 RCV001805751 RCV001843830 RCV003016068 RCV000239476 RCV000239529 RCV000239564 RCV000239481 RCV003592614 RCV001051882	★★★★★ ClinVar: Pathogenic / Likely Pathogenic (≥5 Variants)

Unknown / Other Associations
Phenotype Name	Clinical Significance	Source	Evidence Score
CONGENITAL PAIN INSENSITIVITY	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Familial cancer of breast	Likely benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
HEREDITARY SENSORY AND AUTONOMIC NEUROPATHIES	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary sensory and autonomic neuropathy	Uncertain significance	ClinVar Disgenet	★★★☆☆ Reported in Unknown/Other Associations (≥2 sources)
HEREDITARY SENSORY AND AUTONOMIC NEUROPATHY TYPE 8	—	Disgenet	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE VIII	—	CTD, HPO CTD, HPO	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
PRDM12-related disorder	Likely benign; Benign	ClinVar	★★☆☆☆ Found in Text Mining + Unknown/Other Associations

Associations from Text Mining
Disease Name	Disease (Merged)	Source	PMID	Relationship Type	Evidence Score
Congenital Pain Insensitivity	Congenital Pain Insensitivity	CTD_human_DG	26005867		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Congenital Pain Insensitivity	Congenital Pain Insensitivity	BEFREE	26975306		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Corneal Opacity	Corneal opacity	Pubtator	36111846	Associate	★☆☆☆☆ Found in Text Mining only
Corneal Ulcer	Corneal Ulcer	HPO_DG			★☆☆☆☆ Found in Text Mining only
Hereditary Sensory and Autonomic Neuropathies	Hereditary sensory and autonomic neuropathy	BEFREE	25891934, 29949203		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary Sensory and Autonomic Neuropathies	Hereditary sensory and autonomic neuropathy	Pubtator	35263888	Associate	★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hereditary sensory and autonomic neuropathy type 8	Hereditary Sensory And Autonomic Neuropathy	Orphanet			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Hypohidrosis	Hypohidrosis	HPO_DG			★☆☆☆☆ Found in Text Mining only
Neoplasms	Neoplasms	BEFREE	12835719		★☆☆☆☆ Found in Text Mining only
NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE VIII	Hereditary Motor And Sensory Neuropathy	GENOMICS_ENGLAND_DG	25891934, 26005867		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE VIII	Hereditary Motor And Sensory Neuropathy	ORPHANET_DG	26005867, 26975306, 28050684		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE VIII	Hereditary Motor And Sensory Neuropathy	UNIPROT_DG	26005867		★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE VIII	Hereditary Motor And Sensory Neuropathy	CTD_human_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
NEUROPATHY, HEREDITARY SENSORY AND AUTONOMIC, TYPE VIII	Hereditary Motor And Sensory Neuropathy	CLINVAR_DG			★★☆☆☆ Found in Text Mining + Unknown/Other Associations
Pain Insensitivity Congenital	Congenital pain insensitivity	Pubtator	26975306, 36111846, 38591490	Associate	★☆☆☆☆ Found in Text Mining only
Peritoneal Neoplasms	Peritoneal neoplasm	Pubtator	36111846	Associate	★☆☆☆☆ Found in Text Mining only
Prostatic Neoplasms	Prostatic neoplasm	Pubtator	30616239	Associate	★☆☆☆☆ Found in Text Mining only
Pruritus	Pruritus	Pubtator	38591490	Associate	★☆☆☆☆ Found in Text Mining only