Seroatlas · Human Serome Atlas

PRDM6

Putative histone-lysine N-methyltransferase PRDM6

Also known as: KMT8C, PRDM6_HUMAN, PRISM

Cross-references: UniProt · Ensembl · Human Protein Atlas · GeneCards · NCBI Gene

Protein identityUniProt · HPA

UniProt accession: Q9NQX0
Gene: PRDM6
Ensembl: ENSG00000061455
Chromosome: 5
Canonical length: 595 aa
Protein class: Disease related genes, Enzymes, Human disease related genes, Potential drug targets, Predicted intracellular proteins, Transcription factors
Subcellular location: Nucleoplasm

OverviewNCBI Gene

The protein encoded by this gene is a transcriptional repressor and a member of the PRDM family. Family members contain a PR domain and multiple zinc-finger domains. The encoded protein is involved in regulation of vascular smooth muscle cells (VSMC) contractile proteins. Mutations in this gene result in patent ductus arteriosus 3 (PDA3). [provided by RefSeq, Apr 2017]

Canonical amino-acid sequenceUniProt

595 residues, UniProt reviewed canonical sequence.

>Q9NQX0|PRDM6
     1  MLKPGDPGGS AFLKVDPAYL QHWQQLFPHG GAGPLKGSGA AGLLSAPQPL QPPPPPPPPE
    61  RAEPPPDSLR PRPASLSSAS STPASSSTSA SSASSCAAAA AAAALAGLSA LPVSQLPVFA
   121  PLAAAAVAAE PLPPKELCLG ATSGPGPVKC GGGGGGGGEG RGAPRFRCSA EELDYYLYGQ
   181  QRMEIIPLNQ HTSDPNNRCD MCADNRNGEC PMHGPLHSLR RLVGTSSAAA AAPPPELPEW
   241  LRDLPREVCL CTSTVPGLAY GICAAQRIQQ GTWIGPFQGV LLPPEKVQAG AVRNTQHLWE
   301  IYDQDGTLQH FIDGGEPSKS SWMRYIRCAR HCGEQNLTVV QYRSNIFYRA CIDIPRGTEL
   361  LVWYNDSYTS FFGIPLQCIA QDENLNVPST VMEAMCRQDA LQPFNKSSKL APTTQQRSVV
   421  FPQTPCSRNF SLLDKSGPIE SGFNQINVKN QRVLASPTST SQLHSEFSDW HLWKCGQCFK
   481  TFTQRILLQM HVCTQNPDRP YQCGHCSQSF SQPSELRNHV VTHSSDRPFK CGYCGRAFAG
   541  ATTLNNHIRT HTGEKPFKCE RCERSFTQAT QLSRHQRMPN ECKPITESPE SIEVD

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PRDM6 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): 0.49
Highest tissue expression: 15 nTPM

Expression across tissuesHPA

Tissue

blood vessel: 15 nTPM
urinary bladder: 8.8 nTPM
colon: 4.7 nTPM
placenta: 3.9 nTPM
gallbladder: 3.1 nTPM
lung: 2.8 nTPM

Single-cell type

smooth muscle cells: 79 nCPM
fibro-adipogenic progenitors: 50 nCPM
fibroblasts: 45 nCPM
mesothelial cells: 43 nCPM
undifferentiated spermatogonia: 39 nCPM
endometrial stromal cells: 39 nCPM

Immune cell

basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM
intermediate monocyte: 0 nTPM
MAIT T-cell: 0 nTPM

Brain region

choroid plexus: 1.3 nTPM
pons: 1 nTPM
medulla oblongata: 0.8 nTPM
white matter: 0.7 nTPM
cerebral cortex: 0.6 nTPM
midbrain: 0.6 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PRDM6.

Disease | AllUniProt

Conditions PRDM6 is implicated in, by any mechanism.

Patent ductus arteriosus 3 (PDA3) MIM:617039

Disease | GeneticClinVar

3 pathogenic / likely-pathogenic of 149 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Patent ductus arteriosus 3

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): 0.42
gnomAD pLI: 0.61
gnomAD missense Z: 1.13
DepMap mean gene effect: 0.05
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 5% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

nucleus

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of PRDM6 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 PRDM6 as an antibody target. Whether an autoantibody or antibody against PRDM6 could matter depends on whether native PRDM6 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PRDM6 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 PRDM6 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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