Seroatlas · Human Serome Atlas

PLEKHM1

Pleckstrin homology domain-containing family M member 1

Also known as: KIAA0356, PKHM1_HUMAN

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

Protein identityUniProt · HPA

UniProt accession: Q9Y4G2
Gene: PLEKHM1
Ensembl: ENSG00000225190
Chromosome: 17
Canonical length: 1056 aa
Protein class: Disease related genes, Human disease related genes, Predicted intracellular proteins
Subcellular location: Vesicles

OverviewNCBI Gene

The protein encoded by this gene is essential for bone resorption, and may play a critical role in vesicular transport in the osteoclast. Mutations in this gene are associated with autosomal recessive osteopetrosis type 6 (OPTB6). Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Sep 2009]

Canonical amino-acid sequenceUniProt

1056 residues, UniProt reviewed canonical sequence.

>Q9Y4G2|PLEKHM1
     1  MLSVVENGLD PQAAIPVIKK KLVGSVKALQ KQYVSLDTVV TSEDGDANTM CSALEAVFIH
    61  GLHAKHIRAE AGGKRKKSAH QKPLPQPVFW PLLKAVTHKH IISELEHLTF VNTDVGRCRA
   121  WLRLALNDGL MECYLKLLLQ EQARLHEYYQ PTALLRDAEE GEFLLSFLQG LTSLSFELSY
   181  KSAILNEWTL TPLALSGLCP LSELDPLSTS GAELQRKESL DSISHSSGSE DIEVHHSGHK
   241  IRRNQKLTAS SLSLDTASSS QLSCSLNSDS CLLQENGSKS PDHCEEPMSC DSDLGTANAE
   301  DSDRSLQEVL LEFSKAQVNS VPTNGLSQET EIPTPQASLS LHGLNTSTYL HCEAPAEPLP
   361  AQAASGTQDG VHVQEPRPQA PSPLDLQQPV ESTSGQQPSS TVSETAREVG QGNGLQKAQA
   421  HDGAGLKLVV SSPTSPKNKS WISEDDFYRP SREQPLESAS DHPIASYRGT PGSRPGLHRH
   481  FSQEPRKNCS LGALDQACVP SPGRRQAQAA PSQGHKSFRV VHRRQMGLSN PFRGLMKLGT
   541  VERRGAMGIW KELFCELSPL EFRLYLSNEE HTCVENCSLL RCESVGPAHS DGRFELVFSG
   601  KKLALRASSQ DEAEDWLDRV REALQKVRPQ QEDEWVNVQY PDQPEEPPEA PQGCLSPSDL
   661  LSEPAALQGT QFDWSSAQVP EPDAIKESLL YLYMDRTWMP YIFSLSLEAL KCFRIRNNEK
   721  MLSDSHGVET IRDILPDTSL GGPSFFKIIT AKAVLKLQAG NAEEAALWRD LVRKVLASYL
   781  ETAEEAVTLG GSLDENCQEV LKFATRENGF LLQYLVAIPM EKGLDSQGCF CAGCSRQIGF
   841  SFVRPKLCAF SGLYYCDICH QDDASVIPAR IIHNWDLTKR PICRQALKFL TQIRAQPLIN
   901  LQMVNASLYE HVERMHLIGR RREQLKLLGD YLGLCRSGAL KELSKRLNHR NYLLESPHRF
   961  SVADLQQIAD GVYEGFLKAL IEFASQHVYH CDLCTQRGFI CQICQHHDII FPFEFDTTVR
  1021  CAECKTVFHQ SCQAVVKKGC PRCARRRKYQ EQNIFA

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against PLEKHM1 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: Other membrane
Secreted: No
Transmembrane segments: 0
Mean surface accessibility (rSASA): 0.43
Highest tissue expression: 29 nTPM

Expression across tissuesHPA

Tissue

esophagus: 29 nTPM
bone marrow: 16 nTPM
salivary gland: 13 nTPM
vagina: 13 nTPM
cerebellum: 11 nTPM
skeletal muscle: 11 nTPM

Single-cell type

papillary tip epithelial cells: 44 nCPM
renal collecting duct intercalated cells: 32 nCPM
renal connecting tubule cells: 30 nCPM
distal convoluted tubule cells: 28 nCPM
oligodendrocytes: 28 nCPM
podocytes: 27 nCPM

Immune cell

neutrophil: 10 nTPM
basophil: 2.6 nTPM
memory B-cell: 2.4 nTPM
eosinophil: 2 nTPM
NK-cell: 1.7 nTPM
classical monocyte: 1.2 nTPM

Brain region

cerebellum: 22 nTPM
white matter: 17 nTPM
thalamus: 15 nTPM
cerebral cortex: 14 nTPM
pons: 13 nTPM
medulla oblongata: 12 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about PLEKHM1.

Disease | AllUniProt

Conditions PLEKHM1 is implicated in, by any mechanism.

Osteopetrosis, autosomal recessive 6 (OPTB6) MIM:611497
Osteopetrosis, autosomal dominant 3 (OPTA3) MIM:618107

Disease | GeneticClinVar

4 pathogenic / likely-pathogenic of 198 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Osteopetrosis, autosomal dominant 3
Autosomal recessive osteopetrosis 6

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): 0.47
gnomAD pLI: 0.01
gnomAD missense Z: 1.18
DepMap mean gene effect: -0.42
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

Molecular functions

zinc ion binding

Cellular components

Protein domainsUniProt · Pfam · InterPro

Pleckstrin homology domain
Protein kinase C-like, phorbol ester/diacylglycerol-binding domain
RUN domain
PH-like domain superfamily
Rubicon Homology Domain
RUN domain superfamily
Differentially Expressed in FDCP 8 Homolog
RUN domain
Rubicon Homology Domain
PLEKHM1, PH domain
PLEKHM1, RUN domain

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of PLEKHM1 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 PLEKHM1 as an antibody target. Whether an autoantibody or antibody against PLEKHM1 could matter depends on whether native PLEKHM1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

PLEKHM1 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 PLEKHM1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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