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Protein

PR domain zinc finger protein 12

Gene

PRDM12

Organism
Homo sapiens (Human)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Involved in the positive regulation of histone H3-K9 dimethylation.1 Publication

Regions

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri243 – 265C2H2-type 1PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri271 – 293C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri299 – 323C2H2-type 3PROSITE-ProRule annotationAdd BLAST25

GO - Molecular functioni

GO - Biological processi

  • detection of temperature stimulus involved in sensory perception of pain Source: MGI
  • neuron projection development Source: MGI
  • positive regulation of histone H3-K9 dimethylation Source: UniProtKB
  • positive regulation of histone H3-K9 methylation Source: MGI
  • regulation of transcription, DNA-templated Source: UniProtKB-KW
  • sensory perception of pain Source: MGI
  • transcription, DNA-templated Source: UniProtKB-KW
Complete GO annotation...

Keywords - Molecular functioni

Methyltransferase, Transferase

Keywords - Biological processi

Transcription, Transcription regulation

Keywords - Ligandi

DNA-binding, Metal-binding, S-adenosyl-L-methionine, Zinc

Enzyme and pathway databases

BioCyciZFISH:ENSG00000130711-MONOMER.

Names & Taxonomyi

Protein namesi
Recommended name:
PR domain zinc finger protein 12 (EC:2.1.1.-)
Alternative name(s):
PR domain-containing protein 12
Gene namesi
Name:PRDM12
Synonyms:PFM9
OrganismiHomo sapiens (Human)
Taxonomic identifieri9606 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresPrimatesHaplorrhiniCatarrhiniHominidaeHomo
Proteomesi
  • UP000005640 Componenti: Chromosome 9

Organism-specific databases

HGNCiHGNC:13997. PRDM12.

Subcellular locationi

GO - Cellular componenti

  • nucleus Source: MGI
Complete GO annotation...

Keywords - Cellular componenti

Nucleus

Pathology & Biotechi

Involvement in diseasei

Neuropathy, hereditary sensory and autonomic, 8 (HSAN8)1 Publication
The disease is caused by mutations affecting the gene represented in this entry.
Disease descriptionA form of hereditary sensory and autonomic neuropathy, a genetically and clinically heterogeneous group of disorders characterized by degeneration of dorsal root and autonomic ganglion cells, and by sensory and/or autonomic abnormalities. HSAN8 patients manifest congenital insensitivity to pain resulting in ulceration to the fingers, tongue, lips, and other distal appendages. Some patients may also have decreased sweating and tear production.
See also OMIM:616488
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07461731D → Y in HSAN8; no effect on nuclear localization; not able to induce histone H3-K9 dimethylation. 1 Publication1
Natural variantiVAR_074618102I → N in HSAN8; no effect on nuclear localization; not able to induce histone H3-K9 dimethylation. 1 Publication1
Natural variantiVAR_074619160W → C in HSAN8; no effect on nuclear localization; not able to induce histone H3-K9 dimethylation. 1 Publication1
Natural variantiVAR_074620168R → C in HSAN8; no effect on nuclear localization; not able to induce histone H3-K9 dimethylation. 1 PublicationCorresponds to variant rs767397937dbSNPEnsembl.1
Natural variantiVAR_074621172E → D in HSAN8; no effect on nuclear localization; not able to induce histone H3-K9 dimethylation. 1 Publication1
Natural variantiVAR_074622289H → L in HSAN8; no effect on nuclear localization; not able to induce histone H3-K9 dimethylation. 1 Publication1
Natural variantiVAR_074623352A → AAAAAAAA in HSAN8; reduced protein amount; results in protein aggregation. 1 Publication1

Keywords - Diseasei

Disease mutation, Neurodegeneration, Neuropathy

Organism-specific databases

DisGeNETi59335.
MIMi616488. phenotype.
OpenTargetsiENSG00000130711.
PharmGKBiPA33710.

Polymorphism and mutation databases

BioMutaiPRDM12.
DMDMi25008955.

PTM / Processingi

Molecule processing

Feature keyPosition(s)DescriptionActionsGraphical viewLength
ChainiPRO_00000477691 – 367PR domain zinc finger protein 12Add BLAST367

Proteomic databases

PaxDbiQ9H4Q4.
PeptideAtlasiQ9H4Q4.
PRIDEiQ9H4Q4.

PTM databases

iPTMnetiQ9H4Q4.
PhosphoSitePlusiQ9H4Q4.

Expressioni

Tissue specificityi

Not found in adult tissues except in dorsal root ganglia.1 Publication

Gene expression databases

BgeeiENSG00000130711.
CleanExiHS_PRDM12.
GenevisibleiQ9H4Q4. HS.

Organism-specific databases

HPAiHPA043143.

Interactioni

GO - Molecular functioni

  • histone methyltransferase binding Source: MGI

Protein-protein interaction databases

STRINGi9606.ENSP00000253008.

Structurei

Secondary structure

1367
Legend: HelixTurnBeta strandPDB Structure known for this area
Show more details
Feature keyPosition(s)DescriptionActionsGraphical viewLength
Beta strandi78 – 83Combined sources6
Beta strandi88 – 92Combined sources5
Beta strandi94 – 97Combined sources4
Beta strandi99 – 106Combined sources8
Beta strandi113 – 117Combined sources5
Beta strandi120 – 122Combined sources3
Beta strandi136 – 140Combined sources5
Beta strandi144 – 151Combined sources8
Helixi160 – 163Combined sources4
Turni170 – 172Combined sources3
Beta strandi175 – 180Combined sources6
Beta strandi183 – 190Combined sources8
Beta strandi199 – 202Combined sources4

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3EP0X-ray2.10A/B60-229[»]
ProteinModelPortaliQ9H4Q4.
SMRiQ9H4Q4.
ModBaseiSearch...
MobiDBiSearch...

Miscellaneous databases

EvolutionaryTraceiQ9H4Q4.

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Domaini86 – 203SETPROSITE-ProRule annotationAdd BLAST118

Compositional bias

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Compositional biasi344 – 359Poly-AlaAdd BLAST16

Sequence similaritiesi

Belongs to the class V-like SAM-binding methyltransferase superfamily.PROSITE-ProRule annotation
Contains 3 C2H2-type zinc fingers.PROSITE-ProRule annotation
Contains 1 SET domain.PROSITE-ProRule annotation

Zinc finger

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Zinc fingeri243 – 265C2H2-type 1PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri271 – 293C2H2-type 2PROSITE-ProRule annotationAdd BLAST23
Zinc fingeri299 – 323C2H2-type 3PROSITE-ProRule annotationAdd BLAST25

Keywords - Domaini

Repeat, Zinc-finger

Phylogenomic databases

eggNOGiENOG410KCSB. Eukaryota.
ENOG410YUJ3. LUCA.
GeneTreeiENSGT00830000128284.
HOGENOMiHOG000231554.
HOVERGENiHBG053666.
InParanoidiQ9H4Q4.
OMAiTTGRMRC.
OrthoDBiEOG091G0A5R.
PhylomeDBiQ9H4Q4.
TreeFamiTF332260.

Family and domain databases

Gene3Di3.30.160.60. 3 hits.
InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR017126. Znf_PRDM12.
[Graphical view]
PfamiPF00096. zf-C2H2. 1 hit.
[Graphical view]
PIRSFiPIRSF037163. PRDM12. 1 hit.
SMARTiSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 3 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 3 hits.
PS50157. ZINC_FINGER_C2H2_2. 3 hits.
[Graphical view]

Sequencei

Sequence statusi: Complete.

Q9H4Q4-1 [UniParc]FASTAAdd to basket

« Hide

        10         20         30         40         50
MMGSVLPAEA LVLKTGLKAP GLALAEVITS DILHSFLYGR WRNVLGEQLF
60 70 80 90 100
EDKSHHASPK TAFTAEVLAQ SFSGEVQKLS SLVLPAEVII AQSSIPGEGL
110 120 130 140 150
GIFSKTWIKA GTEMGPFTGR VIAPEHVDIC KNNNLMWEVF NEDGTVRYFI
160 170 180 190 200
DASQEDHRSW MTYIKCARNE QEQNLEVVQI GTSIFYKAIE MIPPDQELLV
210 220 230 240 250
WYGNSHNTFL GIPGVPGLEE DQKKNKHEDF HPADSAAGPA GRMRCVICHR
260 270 280 290 300
GFNSRSNLRS HMRIHTLDKP FVCRFCNRRF SQSSTLRNHV RLHTGERPYK
310 320 330 340 350
CQVCQSAYSQ LAGLRAHQKS ARHRPPSTAL QAHSPALPAP HAHAPALAAA
360
AAAAAAAAAH HLPAMVL
Length:367
Mass (Da):40,403
Last modified:October 1, 2001 - v2
Checksum:iF2C665E3AE076C76
GO

Polymorphismi

The poly-alanine tract is polymorphic in the general population and contains a maximum of 14 alanines.1 Publication

Natural variant

Feature keyPosition(s)DescriptionActionsGraphical viewLength
Natural variantiVAR_07461731D → Y in HSAN8; no effect on nuclear localization; not able to induce histone H3-K9 dimethylation. 1 Publication1
Natural variantiVAR_074618102I → N in HSAN8; no effect on nuclear localization; not able to induce histone H3-K9 dimethylation. 1 Publication1
Natural variantiVAR_074619160W → C in HSAN8; no effect on nuclear localization; not able to induce histone H3-K9 dimethylation. 1 Publication1
Natural variantiVAR_074620168R → C in HSAN8; no effect on nuclear localization; not able to induce histone H3-K9 dimethylation. 1 PublicationCorresponds to variant rs767397937dbSNPEnsembl.1
Natural variantiVAR_074621172E → D in HSAN8; no effect on nuclear localization; not able to induce histone H3-K9 dimethylation. 1 Publication1
Natural variantiVAR_074622289H → L in HSAN8; no effect on nuclear localization; not able to induce histone H3-K9 dimethylation. 1 Publication1
Natural variantiVAR_074623352A → AAAAAAAA in HSAN8; reduced protein amount; results in protein aggregation. 1 Publication1

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY004252 mRNA. Translation: AAG13447.2.
AL359092 Genomic DNA. Translation: CAM45744.1.
CH471090 Genomic DNA. Translation: EAW87940.1.
CCDSiCCDS6934.1.
RefSeqiNP_067632.2. NM_021619.2.
UniGeneiHs.495311.

Genome annotation databases

EnsembliENST00000253008; ENSP00000253008; ENSG00000130711.
GeneIDi59335.
KEGGihsa:59335.
UCSCiuc004bzt.2. human.

Keywords - Coding sequence diversityi

Triplet repeat expansion

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AY004252 mRNA. Translation: AAG13447.2.
AL359092 Genomic DNA. Translation: CAM45744.1.
CH471090 Genomic DNA. Translation: EAW87940.1.
CCDSiCCDS6934.1.
RefSeqiNP_067632.2. NM_021619.2.
UniGeneiHs.495311.

3D structure databases

Select the link destinations:
PDBei
RCSB PDBi
PDBji
Links Updated
PDB entryMethodResolution (Å)ChainPositionsPDBsum
3EP0X-ray2.10A/B60-229[»]
ProteinModelPortaliQ9H4Q4.
SMRiQ9H4Q4.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

STRINGi9606.ENSP00000253008.

PTM databases

iPTMnetiQ9H4Q4.
PhosphoSitePlusiQ9H4Q4.

Polymorphism and mutation databases

BioMutaiPRDM12.
DMDMi25008955.

Proteomic databases

PaxDbiQ9H4Q4.
PeptideAtlasiQ9H4Q4.
PRIDEiQ9H4Q4.

Protocols and materials databases

DNASUi59335.
Structural Biology KnowledgebaseSearch...

Genome annotation databases

EnsembliENST00000253008; ENSP00000253008; ENSG00000130711.
GeneIDi59335.
KEGGihsa:59335.
UCSCiuc004bzt.2. human.

Organism-specific databases

CTDi59335.
DisGeNETi59335.
GeneCardsiPRDM12.
HGNCiHGNC:13997. PRDM12.
HPAiHPA043143.
MIMi616458. gene.
616488. phenotype.
neXtProtiNX_Q9H4Q4.
OpenTargetsiENSG00000130711.
PharmGKBiPA33710.
GenAtlasiSearch...

Phylogenomic databases

eggNOGiENOG410KCSB. Eukaryota.
ENOG410YUJ3. LUCA.
GeneTreeiENSGT00830000128284.
HOGENOMiHOG000231554.
HOVERGENiHBG053666.
InParanoidiQ9H4Q4.
OMAiTTGRMRC.
OrthoDBiEOG091G0A5R.
PhylomeDBiQ9H4Q4.
TreeFamiTF332260.

Enzyme and pathway databases

BioCyciZFISH:ENSG00000130711-MONOMER.

Miscellaneous databases

ChiTaRSiPRDM12. human.
EvolutionaryTraceiQ9H4Q4.
GenomeRNAii59335.
PROiQ9H4Q4.
SOURCEiSearch...

Gene expression databases

BgeeiENSG00000130711.
CleanExiHS_PRDM12.
GenevisibleiQ9H4Q4. HS.

Family and domain databases

Gene3Di3.30.160.60. 3 hits.
InterProiIPR001214. SET_dom.
IPR007087. Znf_C2H2.
IPR015880. Znf_C2H2-like.
IPR013087. Znf_C2H2/integrase_DNA-bd.
IPR017126. Znf_PRDM12.
[Graphical view]
PfamiPF00096. zf-C2H2. 1 hit.
[Graphical view]
PIRSFiPIRSF037163. PRDM12. 1 hit.
SMARTiSM00317. SET. 1 hit.
SM00355. ZnF_C2H2. 3 hits.
[Graphical view]
PROSITEiPS50280. SET. 1 hit.
PS00028. ZINC_FINGER_C2H2_1. 3 hits.
PS50157. ZINC_FINGER_C2H2_2. 3 hits.
[Graphical view]
ProtoNetiSearch...

Entry informationi

Entry nameiPRD12_HUMAN
AccessioniPrimary (citable) accession number: Q9H4Q4
Secondary accession number(s): A3KFK9
Entry historyi
Integrated into UniProtKB/Swiss-Prot: November 8, 2002
Last sequence update: October 1, 2001
Last modified: November 2, 2016
This is version 133 of the entry and version 2 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program
DisclaimerAny medical or genetic information present in this entry is provided for research, educational and informational purposes only. It is not in any way intended to be used as a substitute for professional medical advice, diagnosis, treatment or care.

Miscellaneousi

Keywords - Technical termi

3D-structure, Complete proteome, Reference proteome

Documents

  1. Human chromosome 9
    Human chromosome 9: entries, gene names and cross-references to MIM
  2. Human entries with polymorphisms or disease mutations
    List of human entries with polymorphisms or disease mutations
  3. Human polymorphisms and disease mutations
    Index of human polymorphisms and disease mutations
  4. MIM cross-references
    Online Mendelian Inheritance in Man (MIM) cross-references in UniProtKB/Swiss-Prot
  5. PDB cross-references
    Index of Protein Data Bank (PDB) cross-references
  6. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.