Seroatlas · Human Serome Atlas

CLP1

Polyribonucleotide 5'-hydroxyl-kinase Clp1

Also known as: CLP1_HUMAN, hClp1, HEAB

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

Protein identityUniProt · HPA

UniProt accession: Q92989
Gene: CLP1
Ensembl: ENSG00000172409
Chromosome: 11
Canonical length: 425 aa
Protein class: Disease related genes, Enzymes, Human disease related genes, Potential drug targets, Predicted intracellular proteins
Subcellular location: Nucleoplasm,Cytosol

OverviewNCBI Gene

This gene encodes a member of the Clp1 family. The encoded protein is a multifunctional kinase which is a component of the tRNA splicing endonuclease complex and a component of the pre-mRNA cleavage complex II. This protein is implicated in tRNA, mRNA, and siRNA maturation. Mutations in this gene are associated with pontocerebellar hypoplasia type 10 (PCH10). Alternatively splice transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Sep 2014]

Canonical amino-acid sequenceUniProt

425 residues, UniProt reviewed canonical sequence.

>Q92989|CLP1
     1  MGEEANDDKK PTTKFELERE TELRFEVEAS QSVQLELLTG MAEIFGTELT RNKKFTFDAG
    61  AKVAVFTWHG CSVQLSGRTE VAYVSKDTPM LLYLNTHTAL EQMRRQAEKE EERGPRVMVV
   121  GPTDVGKSTV CRLLLNYAVR LGRRPTYVEL DVGQGSVSIP GTMGALYIER PADVEEGFSI
   181  QAPLVYHFGS TTPGTNIKLY NKITSRLADV FNQRCEVNRR ASVSGCVINT CGWVKGSGYQ
   241  ALVHAASAFE VDVVVVLDQE RLYNELKRDL PHFVRTVLLP KSGGVVERSK DFRRECRDER
   301  IREYFYGFRG CFYPHAFNVK FSDVKIYKVG APTIPDSCLP LGMSQEDNQL KLVPVTPGRD
   361  MVHHLLSVST AEGTEENLSE TSVAGFIVVT SVDLEHQVFT VLSPAPRPLP KNFLLIMDIR
   421  FMDLK

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CLP1 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): 0.26
Highest tissue expression: 25 nTPM

Expression across tissuesHPA

Tissue

bone marrow: 25 nTPM
tonsil: 12 nTPM
thymus: 10 nTPM
lymph node: 10 nTPM
appendix: 9.5 nTPM
liver: 9.5 nTPM

Single-cell type

early spermatids: 48 nCPM
cytotrophoblasts: 21 nCPM
migrating cytotrophoblasts: 20 nCPM
basal keratinocytes: 19 nCPM
extravillous trophoblasts: 19 nCPM
decidual stromal cells: 17 nCPM

Immune cell

basophil: 31 nTPM
neutrophil: 22 nTPM
eosinophil: 20 nTPM
classical monocyte: 19 nTPM
myeloid DC: 19 nTPM
MAIT T-cell: 19 nTPM

Brain region

choroid plexus: 6 nTPM
cerebellum: 4.9 nTPM
pons: 4.5 nTPM
white matter: 4.4 nTPM
cerebral cortex: 4.3 nTPM
basal ganglia: 4.1 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CLP1.

Disease | AllUniProt

Conditions CLP1 is implicated in, by any mechanism.

Pontocerebellar hypoplasia 10 (PCH10) MIM:615803

Disease | GeneticClinVar

4 pathogenic / likely-pathogenic of 132 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Pontocerebellar hypoplasia type 10
Pontoneocerebellar hypoplasia

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): 0.59
gnomAD pLI: 0.2
gnomAD missense Z: 2.25
DepMap mean gene effect: -1.76
DepMap dependency class: pan

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 6% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

Cellular components

Protein domainsUniProt · Pfam · InterPro

P-loop containing nucleoside triphosphate hydrolase
Clp1, P-loop domain
Clp1/Grc3
mRNA cleavage and polyadenylation factor CLP1 P-loop
Clp1, C-terminal
Clp1
Clp1, N-terminal
Clp1, C-terminal domain superfamily
Clp1, N-terminal domain superfamily
Pre-mRNA cleavage complex II protein Clp1
N-terminal beta-sandwich domain of polyadenylation factor

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of CLP1 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 CLP1 as an antibody target. Whether an autoantibody or antibody against CLP1 could matter depends on whether native CLP1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CLP1 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 CLP1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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