PRDM16
Histone-lysine N-methyltransferase PRDM16
Also known as: KIAA1675, KMT8F, MEL1, MGC166915, PFM13, PRD16_HUMAN
Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene
Protein identityUniProt · HPA
- UniProt accession
- Q9HAZ2
- Gene
- PRDM16
- Ensembl
- ENSG00000142611
- Chromosome
- 1
- Canonical length
- 1276 aa
- Protein class
- Cancer-related genes, Disease related genes, Enzymes, Human disease related genes, Potential drug targets, Predicted intracellular proteins, Transcription factors
- Subcellular location
- Nucleoplasm
OverviewNCBI Gene
The reciprocal translocation t(1;3)(p36;q21) occurs in a subset of myelodysplastic syndrome (MDS) and acute myeloid leukemia (AML). This gene is located near the 1p36.3 breakpoint and has been shown to be specifically expressed in the t(1:3)(p36,q21)-positive MDS/AML. The protein encoded by this gene is a zinc finger transcription factor and contains an N-terminal PR domain. The translocation results in the overexpression of a truncated version of this protein that lacks the PR domain, which may play an important role in the pathogenesis of MDS and AML. Alternatively spliced transcript variants encoding distinct isoforms have been reported. [provided by RefSeq, Jul 2008]
Canonical amino-acid sequenceUniProt
1276 residues, UniProt reviewed canonical sequence.
>Q9HAZ2|PRDM16
1 MRSKARARKL AKSDGDVVNN MYEPNRDLLA SHSAEDEAED SAMSPIPVGP PSPFPTSEDF
61 TPKEGSPYEA PVYIPEDIPI PADFELRESS IPGAGLGVWA KRKMEAGERL GPCVVVPRAA
121 AKETDFGWEQ ILTDVEVSPQ EGCITKISED LGSEKFCVDA NQAGAGSWLK YIRVACSCDD
181 QNLTMCQISE QIYYKVIKDI EPGEELLVHV KEGVYPLGTV PPGLDEEPTF RCDECDELFQ
241 SKLDLRRHKK YTCGSVGAAL YEGLAEELKP EGLGGGSGQA HECKDCERMF PNKYSLEQHM
301 VIHTEEREYK CDQCPKAFNW KSNLIRHQMS HDSGKRFECE NCVKVFTDPS NLQRHIRSQH
361 VGARAHACPD CGKTFATSSG LKQHKHIHST VKPFICEVCH KSYTQFSNLC RHKRMHADCR
421 TQIKCKDCGQ MFSTTSSLNK HRRFCEGKNH YTPGGIFAPG LPLTPSPMMD KAKPSPSLNH
481 ASLGFNEYFP SRPHPGSLPF STAPPTFPAL TPGFPGIFPP SLYPRPPLLP PTSLLKSPLN
541 HTQDAKLPSP LGNPALPLVS AVSNSSQGTT AAAGPEEKFE SRLEDSCVEK LKTRSSDMSD
601 GSDFEDVNTT TGTDLDTTTG TGSDLDSDVD SDPDKDKGKG KSAEGQPKFG GGLAPPGAPN
661 SVAEVPVFYS QHSFFPPPDE QLLTATGAAG DSIKAIASIA EKYFGPGFMG MQEKKLGSLP
721 YHSAFPFQFL PNFPHSLYPF TDRALAHNLL VKAEPKSPRD ALKVGGPSAE CPFDLTTKPK
781 DVKPILPMPK GPSAPASGEE QPLDLSIGSR ARASQNGGGR EPRKNHVYGE RKLGAGEGLP
841 QVCPARMPQQ PPLHYAKPSP FFMDPIYSRV EKRKVTDPVG ALKEKYLRPS PLLFHPQMSA
901 IETMTEKLES FAAMKADSGS SLQPLPHHPF NFRSPPPTLS DPILRKGKER YTCRYCGKIF
961 PRSANLTRHL RTHTGEQPYR CKYCDRSFSI SSNLQRHVRN IHNKEKPFKC HLCNRCFGQQ
1021 TNLDRHLKKH EHENAPVSQH PGVLTNHLGT SASSPTSESD NHALLDEKED SYFSEIRNFI
1081 ANSEMNQAST RTEKRADMQI VDGSAQCPGL ASEKQEDVEE EDDDDLEEDD EDSLAGKSQD
1141 DTVSPAPEPQ AAYEDEEDEE PAASLAVGFD HTRRCAEDHE GGLLALEPMP TFGKGLDLRR
1201 AAEEAFEVKD VLNSTLDSEA LKHTLCRQAK NQAYAMMLSL SEDTPLHTPS QGSLDAWLKV
1261 TGATSESGAF HPINHLLocalizationUniProt · AlphaFold · HPA
Whether an antibody against PRDM16 can act on the native protein depends on physical access: surface and secreted proteins are reachable by circulating antibodies, intracellular proteins usually are not.
- Antibody reachability
- Intracellular
- Secreted
- No
- Transmembrane segments
- 0
- Mean surface accessibility (rSASA)
- 0.61
- Highest tissue expression
- 18 nTPM
Expression across tissuesHPA
Tissue
- blood vessel: 18 nTPM
- stomach: 8.7 nTPM
- thyroid gland: 7.6 nTPM
- duodenum: 7 nTPM
- kidney: 6.8 nTPM
- choroid plexus: 5.6 nTPM
Single-cell type
- choroid plexus epithelial cells: 859 nCPM
- renal connecting tubule cells: 383 nCPM
- retinal pigment epithelial cells: 320 nCPM
- renal collecting duct principal cells: 316 nCPM
- renal collecting duct intercalated cells: 308 nCPM
- distal convoluted tubule cells: 278 nCPM
Immune cell
- NK-cell: 2.4 nTPM
- naive B-cell: 0.1 nTPM
- naive CD8 T-cell: 0.1 nTPM
- basophil: 0 nTPM
- classical monocyte: 0 nTPM
- eosinophil: 0 nTPM
Brain region
- choroid plexus: 42 nTPM
- cerebral cortex: 18 nTPM
- basal ganglia: 18 nTPM
- thalamus: 16 nTPM
- amygdala: 15 nTPM
- hippocampal formation: 13 nTPM
DiseaseUniProt · ClinVar · IEDB · PubMed
Four sources answering four different questions about PRDM16.
Disease | AllUniProt
Conditions PRDM16 is implicated in, by any mechanism.
- Left ventricular non-compaction 8 (LVNC8) MIM:615373
- Cardiomyopathy, dilated, 1LL (CMD1LL) MIM:615373
Disease | GeneticClinVar
17 pathogenic / likely-pathogenic of 1,559 ClinVar records.
Conditions with pathogenic or likely-pathogenic variants.
- Left ventricular noncompaction 8
- Left ventricular noncompaction cardiomyopathy
- Cardiomyopathy, dilated, 1LL
- Inborn genetic diseases
- PRDM16-related congenital heart disease
Genetic constraint and essentialitygnomAD · DepMap
Does the body need this protein intact? Low LOEUF or a strong DepMap dependency means loss or blockade of the protein is likely to be felt.
- gnomAD LOEUF (loss-of-function intolerance)
- 0.19
- gnomAD pLI
- 1
- gnomAD missense Z
- 1.35
- DepMap mean gene effect
- -0.13
- DepMap dependency class
- selective
Cancer expressionTCGA
Across TCGA tumor cohorts, this protein is over-expressed in roughly 4% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).
OntologyGO
Biological processes
- beige fat cell differentiation
- brown fat cell differentiation
- heterochromatin organization
- methylation
- negative regulation of DNA-templated transcription
- negative regulation of granulocyte differentiation
- negative regulation of muscle cell differentiation
- negative regulation of transcription by RNA polymerase II
- negative regulation of transforming growth factor beta receptor signaling pathway
- negative regulation of white fat cell differentiation
- positive regulation of cold-induced thermogenesis
- positive regulation of DNA-templated transcription
- protein localization to chromatin
- protein maturation
- regulation of cellular respiration
- regulation of transcription by RNA polymerase II
- regulatory T cell differentiation
- tolerance induction in gut-associated lymphoid tissue
Molecular functions
- chromatin-protein adaptor activity
- DNA-binding transcription activator activity, RNA polymerase II-specific
- DNA-binding transcription factor binding
- DNA-binding transcription repressor activity, RNA polymerase II-specific
- histone H3 methyltransferase activity
- histone H3K9 methyltransferase activity
- histone H3K9 monomethyltransferase activity
- RNA polymerase II cis-regulatory region sequence-specific DNA binding
- sequence-specific DNA binding
- transcription cis-regulatory region binding
- transcription coactivator activity
- transcription coregulator activity
- transcription corepressor activity
- zinc ion binding
Cellular components
Protein domainsUniProt · Pfam · InterPro
KeywordsUniProt
InteractionsUniProt · HPA
Protein binding partners of PRDM16 in the human serome: UniProt-annotated complex subunits plus reported interactors. Each links to its own Seroatlas record.
Antibody and autoantibody relevanceSeroatlas analysis
Seroatlas reads PRDM16 as an antibody target. Whether an autoantibody or antibody against PRDM16 could matter depends on whether native PRDM16 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.
PRDM16 is annotated as predominantly intracellular. Intracellular proteins are common autoantibody markers, becoming visible to the immune system after cell injury or altered processing, but are usually markers of disease rather than direct drivers.
Annotation status
The present source text does not explicitly label PRDM16 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.
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