Annotation inferences using phylogenetic trees

PAINT target assertions identify PTN002834949; the historical tree placement was not reconstructed.

Gene Ontology annotation based on UniProtKB/Swiss-Prot Subcellular Location vocabulary mapping, accompanied by conservative changes to GO terms applied by UniProt

The source maps a curated UniProt cell-membrane location to GO.

GO_REF:0000107

Automatic transfer of experimentally verified manual GO annotation data to orthologs using Ensembl Compara

The donor is mouse Q8K445; direct compartment premises were checked against its source records and PMID:19539019.

GO_REF:0000117

Electronic Gene Ontology annotations created by ARBA machine learning models

The current ARBA rule has a matching Metazoa/IPR026748 route to hearing.

PMID:15521980

Mutation screening of USH3 gene (clarin-1) in Spanish patients with Usher syndrome: low prevalence and phenotypic variability.

Spanish CLRN1 mutation families show heterogeneous auditory and retinal disease in the Usher syndrome context.

PMID:15650299

Serial audiometry and speech recognition findings in Finnish Usher syndrome type III patients.

Serial audiometry in 59 Finnish patients and speech testing in 31 document variable progressive hearing impairment.

PMID:19423712

Clarin-1, encoded by the Usher Syndrome III causative gene, forms a membranous microdomain: possible role of clarin-1 in organizing the actin cytoskeleton.

Human 232-residue CLRN1 in HEK293 cells reaches the surface, concentrates in protrusions and changes cortical actin organization; direct actin partners remain unresolved.

PMID:21310491

CLRN1 mutations cause nonsyndromic retinitis pigmentosa.

P31L and L154W segregate with nonsyndromic retinal disease; the reported localization comparison places wild type at the membrane and mutants in the ER.

PMID:29985171

Clarin-1 gene transfer rescues auditory synaptopathy in model of Usher syndrome.

Mouse deletion and rescue distinguish congenital bundle defects from synaptic actin/calcium-channel disorganization; mouse CLRN1 associates with CaVβ2 and harmonin in tagged assays.

PMID:32296183

A reference map of the human binary protein interactome.

HuRI records positive binary CLRN1 interactions with diverse proteins, supporting assay-scoped binding annotations.

file:human/CLRN1/CLRN1-deep-research-falcon.md

Deep research on CLRN1 function

Clarin-1 acts at two hair-cell membrane sites, the apical stereociliary bundle and the basolateral inner-hair-cell ribbon synapse
At the ribbon synapse clarin-1 organizes cortical F-actin and the CaV1.3 calcium-channel complex for exocytosis and afferent transmission
In the retina, Muller glia are the best-supported site of CLRN1 action, implying non-cell-autonomous photoreceptor support

PMID:19414487

Usher syndrome IIIA gene clarin-1 is essential for hair cell function and associated neural activation.

Mouse Clrn1 deletion produces progressive hearing and vestibular evoked-potential defects, early bundle disorganization and later hair-cell loss.

PMID:19539019

Localization and expression of clarin-1, the Clrn1 gene product, in auditory hair cells and photoreceptors.

Controlled mouse immunolabeling places clarin-1 in developing stereocilia and basal hair-cell regions; UB/OC-1 experiments associate it with microtubules and post-Golgi trafficking.

"shows complete colocalization"
Endogenous mouse UB/OC-1 clarin-1 staining is spatially separate from phalloidin-labeled actin, while tubulin staining overlaps and both filamentous patterns are lost after nocodazole.

"does not co-localize with actin"

PMID:26180195

Zebrafish Models for the Mechanosensory Hair Cell Dysfunction in Usher Syndrome 3 Reveal That Clarin-1 Is an Essential Hair Bundle Protein.

Zebrafish loss impairs hearing/balance behavior and mechanically evoked hair-cell responses; native and human-tagged clarin-1 localize to bundles under appropriate fixation.

PMID:31625146

Clarin-1 expression in adult mouse and human retina highlights a role of Müller glia in Usher syndrome.

Human and animal retinal transcript data favor Müller-glial expression, and biochemical assays detect retinal clarin-1 protein.

PMID:40067805

The USH3A causative gene clarin1 functions in Müller glia to maintain retinal photoreceptors.

Zebrafish cell-specific rescue supports a Müller-glial contribution to actin-rich apical structures and protection against light-induced photoreceptor loss.

PMID:42390169

Müller Glia-Exclusive CLRN1 Expression Drives Non-Cell-Autonomous Photoreceptor Degeneration in Usher Syndrome Type 3A.

A CLRN1-null rabbit model develops auditory and late retinal abnormalities, with Müller-glial expression and altered retinal cell profiles.

file:human/CLRN1/CLRN1-source-evidence.json

CLRN1 source reconciliation and evidence index