Seroatlas · Human Serome Atlas

CLRN3

Clarin-3

Also known as: CLRN3_HUMAN, MGC32871, TMEM12, USH3AL1

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

Protein identityUniProt · HPA

UniProt accession: Q8NCR9
Gene: CLRN3
Ensembl: ENSG00000180745
Chromosome: 10
Canonical length: 226 aa
Protein class: Predicted membrane proteins, Transporters

OverviewNCBI Gene

Predicted to be involved in sensory perception of sound. Located in extracellular exosome. [provided by Alliance of Genome Resources, Jul 2025]

Canonical amino-acid sequenceUniProt

226 residues, UniProt reviewed canonical sequence.

>Q8NCR9|CLRN3
     1  MPTTKKTLMF LSSFFTSLGS FIVICSILGT QAWITSTIAV RDSASNGSIF ITYGLFRGES
    61  SEELSHGLAE PKKKFAVLEI LNNSSQKTLH SVTILFLVLS LITSLLSSGF TFYNSISNPY
   121  QTFLGPTGVY TWNGLGASFV FVTMILFVAN TQSNQLSEEL FQMLYPATTS KGTTHSYGYS
   181  FWLILLVILL NIVTVTIIIF YQKARYQRKQ EQRKPMEYAP RDGILF

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CLRN3 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: Unknown
Secreted: No
Transmembrane segments: 4
Mean surface accessibility (rSASA): 0.3
Highest tissue expression: 84 nTPM

Expression across tissuesHPA

Tissue

small intestine: 84 nTPM
liver: 75 nTPM
duodenum: 69 nTPM
colon: 67 nTPM
rectum: 66 nTPM
kidney: 41 nTPM

Single-cell type

tuft cells: 196 nCPM
enterocytes: 157 nCPM
colonocytes: 109 nCPM
goblet cells: 97 nCPM
epididymal efferent duct absorptive cells: 62 nCPM
enteric transient amplifying cells: 53 nCPM

Immune cell

myeloid DC: 0.1 nTPM
non-classical monocyte: 0.1 nTPM
plasmacytoid DC: 0.1 nTPM
basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM

Brain region

cerebral cortex: 0.3 nTPM
hippocampal formation: 0.3 nTPM
hypothalamus: 0.3 nTPM
pons: 0.3 nTPM
white matter: 0.3 nTPM
amygdala: 0.2 nTPM

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): 1.18
gnomAD pLI: 0.04
gnomAD missense Z: -0.54
DepMap mean gene effect: 0.15
DepMap dependency class: none

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

sensory perception of sound

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads CLRN3 as an antibody target. Whether an autoantibody or antibody against CLRN3 could matter depends on whether native CLRN3 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CLRN3 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 CLRN3 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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