Gene
clrn1
- ID
- ZDB-GENE-040718-420
- Name
- clarin 1
- Symbol
- clrn1 Nomenclature History
- Previous Names
-
- zgc:91933
- Type
- protein_coding_gene
- Location
- Chr: 15 Mapping Details/Browsers
- Description
- Acts upstream of or within several processes, including plasma membrane bounded cell projection organization; sensory perception of sound; and synaptic vesicle recycling via endosome. Located in ciliary transition zone and stereocilium bundle. Is expressed in auditory epithelial support cell; brain; hair cell; and sensory system. Used to study Usher syndrome. Human ortholog(s) of this gene implicated in Usher syndrome type 3A and retinitis pigmentosa 61. Orthologous to human CLRN1 (clarin 1).
- Genome Resources
- Note
- None
- Comparative Information
-
- All Expression Data
- 11 figures from 4 publications
- Cross-Species Comparison
- High Throughput Data
- Thisse Expression Data
-
- MGC:91933 (1 image)
Wild Type Expression Summary
- All Phenotype Data
- 11 figures from 3 publications
- Cross-Species Comparison
- Alliance
Phenotype Summary
Mutations
| Allele | Type | Localization | Consequence | Mutagen | Supplier |
|---|---|---|---|---|---|
| cwr1001 | Allele with one deletion | Exon 0 | Frameshift, Premature Stop | zinc finger nuclease | |
| cwr1002 | Allele with one deletion | Exon 0 | Frameshift, Premature Stop | zinc finger nuclease | |
| cwr1003 | Allele with one deletion | Exon 0 | Frameshift, Premature Stop | zinc finger nuclease | |
| cwr1004 | Allele with one deletion | Exon 0 | Frameshift, Premature Stop | zinc finger nuclease | |
| la011760Tg | Transgenic insertion | Unknown | Unknown | DNA | |
| mw99 | Allele with one deletion | Unknown | Unknown | CRISPR |
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| Targeting Reagent | Created Alleles | Citations |
|---|---|---|
| MO1-clrn1 | N/A | Ogun et al., 2014 |
| MO2-clrn1 | N/A | Ogun et al., 2014 |
| MO3-clrn1 | N/A | Ogun et al., 2014 |
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Human Disease
| Disease Ontology Term | Multi-Species Data | OMIM Term | OMIM Phenotype ID |
|---|---|---|---|
| retinitis pigmentosa 61 | Alliance | Retinitis pigmentosa 61 | 614180 |
| Usher syndrome type 3A | Alliance | Usher syndrome, type 3A | 276902 |
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| Human Disease | Fish | Conditions | Citations |
|---|---|---|---|
| Usher syndrome | clrn1cwr1001/cwr1001 | control | Gopal et al., 2015 |
| Usher syndrome | clrn1cwr1004/cwr1004 | control | Gopal et al., 2015 |
| Usher syndrome | clrn1cwr1003/cwr1003 | control | Gopal et al., 2015 |
| Usher syndrome | clrn1cwr1002/cwr1002 | control | Gopal et al., 2015 |
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Domain, Family, and Site Summary
| Type | InterPro ID | Name |
|---|---|---|
| Family | IPR026748 | Clarin |
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Domain Details Per Protein
| Protein | Additional Resources | Length | Clarin |
|---|---|---|---|
| UniProtKB:Q6DGA8 | InterPro | 232 |
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Interactions and Pathways
No data available
| Name | Type | Antigen Genes | Isotype | Host Organism | Assay | Source | Citations |
|---|---|---|---|---|---|---|---|
| Ab2-clrn1 | polyclonal | Rabbit |
|
Proteintech
|
2 | ||
| Ab1-clrn1 | polyclonal | Rabbit |
|
Novus Biologicals, LLC
|
4 |
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Plasmids
No data available
| Construct | Regulatory Region | Coding Sequence | Species | Tg Lines | Citations |
|---|---|---|---|---|---|
| Tg2(gfap:clrn1-2A-GFP) |
| 1 | Nonarath et al., 2025 | ||
| Tg(gfap:clrn1-2A-GFP) |
| 1 | Nonarath et al., 2025 | ||
| Tg(gnat2:clrn1-2A-mCherry) |
| 1 | Nonarath et al., 2025 | ||
| Tg(rho:clrn1-2A-mCherry) |
| 1 | Nonarath et al., 2025 |
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| Relationship | Marker Type | Marker | Accession Numbers | Citations |
|---|---|---|---|---|
| Contained in | Fosmid | CH1073-270L17 | ZFIN Curated Data | |
| Encodes | cDNA | MGC:91933 | ZFIN Curated Data | |
| Encodes | cDNA | MGC:192239 | ZFIN Curated Data |
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| Type | Accession # | Sequence | Length (nt/aa) | Analysis |
|---|---|---|---|---|
| RNA | RefSeq:NM_001002671 (1) | 1459 nt | ||
| Genomic | GenBank:CU929266 (2) | 25758 nt | ||
| Polypeptide | UniProtKB:Q6DGA8 (1) | 232 aa |
- Nonarath, H.J.T., Simpson, S.L., Slobodianuk, T.L., Tran, H., Collery, R.F., Dinculescu, A., Link, B.A. (2025) The USH3A causative gene clarin1 functions in Müller glia to maintain retinal photoreceptors. PLoS Genetics. 21:e1011205e1011205
- Chang, J., Chen, X., Zhang, T., Wang, R., Wang, A., Lan, X., Zhou, Y., Ma, S., Xia, Q. (2020) The novel insight into the outcomes of CRISPR/Cas9 editing intra- and inter-species. International journal of biological macromolecules. 163:711-717
- Gopal, S.R., Lee, Y.T., Stepanyan, R., McDermott, B.M., Alagramam, K.N. (2019) Unconventional secretory pathway activation restores hair cell mechanotransduction in an USH3A model. Proceedings of the National Academy of Sciences of the United States of America. 116(22):11000-11009
- Gopal, S.R., Chen, D.H., Chou, S.W., Zang, J., Neuhauss, S.C., Stepanyan, R., McDermott, B.M., Alagramam, K.N. (2015) Zebrafish Models for the Mechanosensory Hair Cell Dysfunction in Usher Syndrome 3 Reveal That Clarin-1 Is an Essential Hair Bundle Protein. The Journal of neuroscience : the official journal of the Society for Neuroscience. 35:10188-201
- Ogun, O., Zallocchi, M. (2014) Clarin-1 acts as a modulator of mechanotransduction activity and presynaptic ribbon assembly. The Journal of cell biology. 207(3):375-391
- Phillips, J.B., Västinsalo, H., Wegner, J., Clément, A., Sankila, E.M., and Westerfield, M. (2013) The cone-dominant retina and the inner ear of zebrafish express the ortholog of CLRN1, the causative gene of human Usher syndrome type 3A. Gene expression patterns : GEP. 13(8):473-81
- Varshney, G.K., Lu, J., Gildea, D., Huang, H., Pei, W., Yang, Z., Huang, S.C., Schoenfeld, D.S., Pho, N., Casero, D., Hirase, T., Mosbrook-Davis, D.M., Zhang, S., Jao, L.E., Zhang, B., Woods, I.G., Zimmerman, S., Schier, A.F., Wolfsberg, T., Pellegrini, M., Burgess, S.M., and Lin, S. (2013) A large-scale zebrafish gene knockout resource for the genome-wide study of gene function. Genome research. 23(4):727-735
- Wang, D., Jao, L.E., Zheng, N., Dolan, K., Ivey, J., Zonies, S., Wu, X., Wu, K., Yang, H., Meng, Q., Zhu, Z., Zhang, B., Lin, S., and Burgess, S.M. (2007) Efficient genome-wide mutagenesis of zebrafish genes by retroviral insertions. Proceedings of the National Academy of Sciences of the United States of America. 104(30):12428-12433
- Strausberg,R.L., Feingold,E.A., Grouse,L.H., Derge,J.G., Klausner,R.D., Collins,F.S., Wagner,L., Shenmen,C.M., Schuler,G.D., Altschul,S.F., Zeeberg,B., Buetow,K.H., Schaefer,C.F., Bhat,N.K., Hopkins,R.F., Jordan,H., Moore,T., Max,S.I., Wang,J., Hsieh,F., Diatchenko,L., Marusina,K., Farmer,A.A., Rubin,G.M., Hong,L., Stapleton,M., Soares,M.B., Bonaldo,M.F., Casavant,T.L., Scheetz,T.E., Brownstein,M.J., Usdin,T.B., Toshiyuki,S., Carninci,P., Prange,C., Raha,S.S., Loquellano,N.A., Peters,G.J., Abramson,R.D., Mullahy,S.J., Bosak,S.A., McEwan,P.J., McKernan,K.J., Malek,J.A., Gunaratne,P.H., Richards,S., Worley,K.C., Hale,S., Garcia,A.M., Gay,L.J., Hulyk,S.W., Villalon,D.K., Muzny,D.M., Sodergren,E.J., Lu,X., Gibbs,R.A., Fahey,J., Helton,E., Ketteman,M., Madan,A., Rodrigues,S., Sanchez,A., Whiting,M., Madan,A., Young,A.C., Shevchenko,Y., Bouffard,G.G., Blakesley,R.W., Touchman,J.W., Green,E.D., Dickson,M.C., Rodriguez,A.C., Grimwood,J., Schmutz,J., Myers,R.M., Butterfield,Y.S., Krzywinski,M.I., Skalska,U., Smailus,D.E., Schnerch,A., Schein,J.E., Jones,S.J., and Marra,M.A. (2002) Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Proceedings of the National Academy of Sciences of the United States of America. 99(26):16899-903
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