Seroatlas · Human Serome Atlas

CRNKL1

Crooked neck-like protein 1

Also known as: CLF, Clf1, CRN, CRNL1_HUMAN, SYF3

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

Protein identityUniProt · HPA

UniProt accession: Q9BZJ0
Gene: CRNKL1
Ensembl: ENSG00000101343
Chromosome: 20
Canonical length: 848 aa
Protein class: Plasma proteins, Predicted intracellular proteins

OverviewNCBI Gene

The crooked neck (crn) gene of Drosophila is essential for embryogenesis and is thought to be involved in cell cycle progression and pre-mRNA splicing. A protein encoded by this human locus has been found to localize to pre-mRNA splicing complexes in the nucleus and is necessary for pre-mRNA splicing. Alternatively spliced transcript variants have been described. [provided by RefSeq, Jul 2013]

Canonical amino-acid sequenceUniProt

848 residues, UniProt reviewed canonical sequence.

>Q9BZJ0|CRNKL1
     1  MTATVENLTF QKDTLGNAVD KNTSRLELRS YSLAGRHGST EPLVLAWSSQ FRRLTWGCAL
    61  DALHRSPCVA ASQHGVTHLI RSSRTPHSTR CRKEDAQPGH HGNGAASVTA QARGQRSVLQ
   121  VPLPVPRSCL FSESFVVSVS SQSRFLASVP GTGVQRSTAA DMAASTAAGK QRIPKVAKVK
   181  NKAPAEVQIT AEQLLREAKE RELELLPPPP QQKITDEEEL NDYKLRKRKT FEDNIRKNRT
   241  VISNWIKYAQ WEESLKEIQR ARSIYERALD VDYRNITLWL KYAEMEMKNR QVNHARNIWD
   301  RAITTLPRVN QFWYKYTYME EMLGNVAGAR QVFERWMEWQ PEEQAWHSYI NFELRYKEVD
   361  RARTIYERFV LVHPDVKNWI KYARFEEKHA YFAHARKVYE RAVEFFGDEH MDEHLYVAFA
   421  KFEENQKEFE RVRVIYKYAL DRISKQDAQE LFKNYTIFEK KFGDRRGIED IIVSKRRFQY
   481  EEEVKANPHN YDAWFDYLRL VESDAEAEAV REVYERAIAN VPPIQEKRHW KRYIYLWINY
   541  ALYEELEAKD PERTRQVYQA SLELIPHKKF TFAKMWILYA QFEIRQKNLS LARRALGTSI
   601  GKCPKNKLFK VYIELELQLR EFDRCRKLYE KFLEFGPENC TSWIKFAELE TILGDIDRAR
   661  AIYELAISQP RLDMPEVLWK SYIDFEIEQE ETERTRNLYR RLLQRTQHVK VWISFAQFEL
   721  SSGKEGSLTK CRQIYEEANK TMRNCEEKEE RLMLLESWRS FEEEFGTASD KERVDKLMPE
   781  KVKKRRKVQT DDGSDAGWEE YFDYIFPEDA ANQPNLKLLA MAKLWKKQQQ EKEDAEHHPD
   841  EDVDESES

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CRNKL1 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): 0.4
Highest tissue expression: 22 nTPM

Expression across tissuesHPA

Tissue

bone marrow: 22 nTPM
skeletal muscle: 16 nTPM
breast: 15 nTPM
tongue: 14 nTPM
parathyroid gland: 14 nTPM
prostate: 13 nTPM

Single-cell type

esophageal apical cells: 104 nCPM
tuft cells: 81 nCPM
endometrial glandular cells: 69 nCPM
early primary spermatocytes: 68 nCPM
oocytes: 65 nCPM
neutrophils: 57 nCPM

Immune cell

neutrophil: 38 nTPM
basophil: 37 nTPM
eosinophil: 32 nTPM
non-classical monocyte: 24 nTPM
NK-cell: 23 nTPM
T-reg: 18 nTPM

Brain region

cerebellum: 27 nTPM
white matter: 27 nTPM
basal ganglia: 21 nTPM
medulla oblongata: 19 nTPM
spinal cord: 19 nTPM
hypothalamus: 19 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CRNKL1.

Disease | GeneticClinVar

3 pathogenic / likely-pathogenic of 99 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Microcephaly, progressive, with simplified gyral pattern and cerebellar 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): 0.55
gnomAD pLI: 0
gnomAD missense Z: 0.88
DepMap mean gene effect: -1.8
DepMap dependency class: pan

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 14% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Molecular functions

RNA binding

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

InteractionsUniProt · HPA

Protein binding partners of CRNKL1 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 CRNKL1 as an antibody target. Whether an autoantibody or antibody against CRNKL1 could matter depends on whether native CRNKL1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CRNKL1 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 CRNKL1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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