Seroatlas · Human Serome Atlas

CLRN1

Clarin-1

Also known as: CLRN1_HUMAN, RP61, USH3, USH3A

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

Protein identityUniProt · HPA

UniProt accession: P58418
Gene: CLRN1
Ensembl: ENSG00000163646
Chromosome: 3
Canonical length: 232 aa
Protein class: Disease related genes, Human disease related genes, Potential drug targets, Predicted intracellular proteins, Predicted membrane proteins, Transporters
Subcellular location: Vesicles,Centrosome,Basal body

OverviewNCBI Gene

This gene encodes a protein that contains a cytosolic N-terminus, multiple helical transmembrane domains, and an endoplasmic reticulum membrane retention signal, TKGH, in the C-terminus. The encoded protein may be important in development and homeostasis of the inner ear and retina. Mutations within this gene have been associated with Usher syndrome type IIIa. Multiple transcript variants encoding distinct isoforms have been identified for this gene. [provided by RefSeq, Jul 2008]

Canonical amino-acid sequenceUniProt

232 residues, UniProt reviewed canonical sequence.

>P58418|CLRN1
     1  MPSQQKKIIF CMAGVFSFAC ALGVVTALGT PLWIKATVLC KTGALLVNAS GQELDKFMGE
    61  MQYGLFHGEG VRQCGLGARP FRFSFFPDLL KAIPVSIHVN VILFSAILIV LTMVGTAFFM
   121  YNAFGKPFET LHGPLGLYLL SFISGSCGCL VMILFASEVK IHHLSEKIAN YKEGTYVYKT
   181  QSEKYTTSFW VIFFCFFVHF LNGLLIRLAG FQFPFAKSKD AETTNVAADL MY

LocalizationUniProt · AlphaFold · HPA

Whether an antibody against CLRN1 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: Cell surface
Secreted: No
Transmembrane segments: 4
Mean surface accessibility (rSASA): 0.3
Highest tissue expression: 12 nTPM

Expression across tissuesHPA

Tissue

retina: 12 nTPM
adrenal gland: 4.7 nTPM
duodenum: 1.2 nTPM
spinal cord: 0.3 nTPM
testis: 0.3 nTPM
pituitary gland: 0.2 nTPM

Single-cell type

müller glia: 102 nCPM
gonadotrophs: 12 nCPM
retinal horizontal cells: 12 nCPM
neutrophils: 7.7 nCPM
adrenal cortex cells: 6.9 nCPM
sertoli cells: 6.7 nCPM

Immune cell

plasmacytoid DC: 0.2 nTPM
neutrophil: 0.1 nTPM
basophil: 0 nTPM
classical monocyte: 0 nTPM
eosinophil: 0 nTPM
gdT-cell: 0 nTPM

Brain region

cerebral cortex: 2.1 nTPM
basal ganglia: 1.8 nTPM
choroid plexus: 1.7 nTPM
white matter: 1.7 nTPM
hippocampal formation: 1.6 nTPM
amygdala: 1.5 nTPM

DiseaseUniProt · ClinVar · IEDB · PubMed

Four sources answering four different questions about CLRN1.

Disease | AllUniProt

Conditions CLRN1 is implicated in, by any mechanism.

Usher syndrome 3A (USH3A) MIM:276902
Retinitis pigmentosa 61 (RP61) MIM:614180

Disease | GeneticClinVar

96 pathogenic / likely-pathogenic of 445 ClinVar records.

Conditions with pathogenic or likely-pathogenic variants.

Retinitis pigmentosa 61
Usher syndrome type 3A
Usher syndrome type 3
Retinal dystrophy
Usher syndrome

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): 1.81
gnomAD pLI: 0
gnomAD missense Z: -0.59
DepMap mean gene effect: 0.03
DepMap dependency class: none

Cancer expressionTCGA

Across TCGA tumor cohorts, this protein is over-expressed in roughly 3% of surveyed tumor types (aggregate summary; per-cohort expression, alteration, and survival load in the interactive view).

OntologyGO

Biological processes

Cellular components

Protein domainsUniProt · Pfam · InterPro

KeywordsUniProt

Antibody and autoantibody relevanceSeroatlas analysis

Seroatlas reads CLRN1 as an antibody target. Whether an autoantibody or antibody against CLRN1 could matter depends on whether native CLRN1 is physically reachable, whether the body needs it intact, and whether it acts in a disease-relevant tissue.

CLRN1 is annotated at the cell surface, where native CLRN1 is exposed to circulating antibodies and is a prime autoantibody target that could block, deplete, or overstimulate it.

Annotation status

The present source text does not explicitly label CLRN1 as an autoantigen. Seroatlas presents hypothesis context only and does not manufacture a known-serology claim.

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