Details for: CLRN1

Gene ID: 7401

Symbol: CLRN1

Ensembl ID: ENSG00000163646

Description: clarin 1

Associated with

Cells (max top 100)

(Cell Significance Index and respective Thresholds are uniquely calculated using our advanced thresholding algorithms to reveal cell-specific gene markers)

  • Cell Name: hematopoietic stem cell (CL0000037)
    Fold Change: 5.8890
    Cell Significance Index: 100.6700
  • Cell Name: megakaryocyte-erythroid progenitor cell (CL0000050)
    Fold Change: 4.6189
    Cell Significance Index: 63.3400
  • Cell Name: cortical cell of adrenal gland (CL0002097)
    Fold Change: 4.1606
    Cell Significance Index: 111.4900
  • Cell Name: transit amplifying cell of colon (CL0009011)
    Fold Change: 2.7187
    Cell Significance Index: 87.0800
  • Cell Name: retinal progenitor cell (CL0002672)
    Fold Change: 1.3474
    Cell Significance Index: 75.6100
  • Cell Name: Mueller cell (CL0000636)
    Fold Change: 1.2556
    Cell Significance Index: 9.6600
  • Cell Name: intestinal tuft cell (CL0019032)
    Fold Change: 1.2013
    Cell Significance Index: 73.6500
  • Cell Name: paneth cell of epithelium of small intestine (CL1000343)
    Fold Change: 1.1426
    Cell Significance Index: 24.7600
  • Cell Name: CD14-low, CD16-positive monocyte (CL0002396)
    Fold Change: 0.8748
    Cell Significance Index: 21.1900
  • Cell Name: uterine smooth muscle cell (CL0002601)
    Fold Change: 0.3781
    Cell Significance Index: 3.6200
  • Cell Name: enteroendocrine cell of colon (CL0009042)
    Fold Change: 0.3447
    Cell Significance Index: 65.5900
  • Cell Name: sensory neuron (CL0000101)
    Fold Change: 0.3272
    Cell Significance Index: 1.8600
  • Cell Name: enterocyte of epithelium of large intestine (CL0002071)
    Fold Change: 0.3266
    Cell Significance Index: 14.8100
  • Cell Name: cytotoxic T cell (CL0000910)
    Fold Change: 0.1942
    Cell Significance Index: 2.8300
  • Cell Name: epidermal Langerhans cell (CL0002457)
    Fold Change: 0.1687
    Cell Significance Index: -0.3700
  • Cell Name: colon goblet cell (CL0009039)
    Fold Change: 0.1654
    Cell Significance Index: 16.3700
  • Cell Name: tuft cell of colon (CL0009041)
    Fold Change: 0.1575
    Cell Significance Index: 142.2100
  • Cell Name: non-pigmented ciliary epithelial cell (CL0002304)
    Fold Change: 0.1401
    Cell Significance Index: 88.9900
  • Cell Name: intestinal crypt stem cell of colon (CL0009043)
    Fold Change: 0.1384
    Cell Significance Index: 15.0500
  • Cell Name: intestinal crypt stem cell of small intestine (CL0009017)
    Fold Change: 0.1322
    Cell Significance Index: 2.8200
  • Cell Name: gut absorptive cell (CL0000677)
    Fold Change: 0.1304
    Cell Significance Index: 7.8300
  • Cell Name: early T lineage precursor (CL0002425)
    Fold Change: 0.1205
    Cell Significance Index: 1.7500
  • Cell Name: epithelial cell of small intestine (CL0002254)
    Fold Change: 0.1119
    Cell Significance Index: 18.2000
  • Cell Name: enterocyte of epithelium of small intestine (CL1000334)
    Fold Change: 0.1104
    Cell Significance Index: 3.1800
  • Cell Name: keratocyte (CL0002363)
    Fold Change: 0.1059
    Cell Significance Index: 1.6800
  • Cell Name: eye photoreceptor cell (CL0000287)
    Fold Change: 0.0849
    Cell Significance Index: 5.3500
  • Cell Name: transit amplifying cell of small intestine (CL0009012)
    Fold Change: 0.0612
    Cell Significance Index: 1.2700
  • Cell Name: microfold cell of epithelium of small intestine (CL1000353)
    Fold Change: 0.0542
    Cell Significance Index: 3.7500
  • Cell Name: secondary lens fiber (CL0002225)
    Fold Change: 0.0522
    Cell Significance Index: 71.0100
  • Cell Name: periportal region hepatocyte (CL0019026)
    Fold Change: 0.0501
    Cell Significance Index: 0.7400
  • Cell Name: obsolete epithelial cell of alveolus of lung (CL0010003)
    Fold Change: 0.0372
    Cell Significance Index: 0.9300
  • Cell Name: lens epithelial cell (CL0002224)
    Fold Change: 0.0145
    Cell Significance Index: 22.3000
  • Cell Name: L2/3-6 intratelencephalic projecting glutamatergic neuron (CL4023040)
    Fold Change: 0.0103
    Cell Significance Index: 2.0600
  • Cell Name: skeletal muscle fiber (CL0008002)
    Fold Change: 0.0084
    Cell Significance Index: 0.2200
  • Cell Name: enteroendocrine cell of small intestine (CL0009006)
    Fold Change: 0.0080
    Cell Significance Index: 0.2000
  • Cell Name: small intestine goblet cell (CL1000495)
    Fold Change: 0.0037
    Cell Significance Index: 0.1300
  • Cell Name: intestinal epithelial cell (CL0002563)
    Fold Change: 0.0029
    Cell Significance Index: 0.0300
  • Cell Name: anterior lens cell (CL0002223)
    Fold Change: 0.0004
    Cell Significance Index: 0.7100
  • Cell Name: pigmented epithelial cell (CL0000529)
    Fold Change: -0.0004
    Cell Significance Index: -0.7900
  • Cell Name: corneal endothelial cell (CL0000132)
    Fold Change: -0.0007
    Cell Significance Index: -0.0100
  • Cell Name: pancreatic A cell (CL0000171)
    Fold Change: -0.0062
    Cell Significance Index: -4.5900
  • Cell Name: ciliary muscle cell (CL1000443)
    Fold Change: -0.0063
    Cell Significance Index: -2.8700
  • Cell Name: obsolete caudal ganglionic eminence derived GABAergic cortical interneuron (CL4023070)
    Fold Change: -0.0063
    Cell Significance Index: -2.2500
  • Cell Name: neoplastic cell (CL0001063)
    Fold Change: -0.0068
    Cell Significance Index: -1.3500
  • Cell Name: basal cell of epidermis (CL0002187)
    Fold Change: -0.0073
    Cell Significance Index: -0.1100
  • Cell Name: type B pancreatic cell (CL0000169)
    Fold Change: -0.0081
    Cell Significance Index: -4.5900
  • Cell Name: dopaminergic neuron (CL0000700)
    Fold Change: -0.0102
    Cell Significance Index: -2.9300
  • Cell Name: indirect pathway medium spiny neuron (CL4023029)
    Fold Change: -0.0136
    Cell Significance Index: -0.6000
  • Cell Name: basal epithelial cell of tracheobronchial tree (CL0002329)
    Fold Change: -0.0146
    Cell Significance Index: -0.4100
  • Cell Name: pigmented ciliary epithelial cell (CL0002303)
    Fold Change: -0.0150
    Cell Significance Index: -2.1800
  • Cell Name: direct pathway medium spiny neuron (CL4023026)
    Fold Change: -0.0166
    Cell Significance Index: -0.6300
  • Cell Name: glycinergic neuron (CL1001509)
    Fold Change: -0.0166
    Cell Significance Index: -0.8700
  • Cell Name: medial ganglionic eminence derived interneuron (CL4023063)
    Fold Change: -0.0175
    Cell Significance Index: -0.2500
  • Cell Name: precursor B cell (CL0000817)
    Fold Change: -0.0193
    Cell Significance Index: -0.2500
  • Cell Name: progenitor cell (CL0011026)
    Fold Change: -0.0198
    Cell Significance Index: -0.2100
  • Cell Name: pancreatic acinar cell (CL0002064)
    Fold Change: -0.0239
    Cell Significance Index: -4.0800
  • Cell Name: smooth muscle cell of sphincter of pupil (CL0002243)
    Fold Change: -0.0245
    Cell Significance Index: -2.5500
  • Cell Name: intermediate cell of urothelium (CL4030055)
    Fold Change: -0.0250
    Cell Significance Index: -4.5200
  • Cell Name: smooth muscle cell of prostate (CL1000487)
    Fold Change: -0.0292
    Cell Significance Index: -0.3400
  • Cell Name: photoreceptor cell (CL0000210)
    Fold Change: -0.0306
    Cell Significance Index: -0.4300
  • Cell Name: luminal cell of prostate epithelium (CL0002340)
    Fold Change: -0.0315
    Cell Significance Index: -0.3300
  • Cell Name: BEST4+ enteroycte (CL4030026)
    Fold Change: -0.0319
    Cell Significance Index: -0.4800
  • Cell Name: erythrocyte (CL0000232)
    Fold Change: -0.0357
    Cell Significance Index: -0.9100
  • Cell Name: pancreatic ductal cell (CL0002079)
    Fold Change: -0.0378
    Cell Significance Index: -4.3400
  • Cell Name: neuron associated cell (CL0000095)
    Fold Change: -0.0399
    Cell Significance Index: -1.6300
  • Cell Name: fibro/adipogenic progenitor cell (CL0009099)
    Fold Change: -0.0423
    Cell Significance Index: -2.1400
  • Cell Name: preadipocyte (CL0002334)
    Fold Change: -0.0459
    Cell Significance Index: -0.9000
  • Cell Name: fast muscle cell (CL0000190)
    Fold Change: -0.0469
    Cell Significance Index: -0.6100
  • Cell Name: lens fiber cell (CL0011004)
    Fold Change: -0.0490
    Cell Significance Index: -1.5500
  • Cell Name: mesothelial cell of epicardium (CL0011019)
    Fold Change: -0.0522
    Cell Significance Index: -0.4500
  • Cell Name: ependymal cell (CL0000065)
    Fold Change: -0.0560
    Cell Significance Index: -0.6600
  • Cell Name: forebrain neuroblast (CL1000042)
    Fold Change: -0.0570
    Cell Significance Index: -3.5100
  • Cell Name: eukaryotic cell (CL0000255)
    Fold Change: -0.0583
    Cell Significance Index: -2.5400
  • Cell Name: cardiac muscle myoblast (CL0000513)
    Fold Change: -0.0607
    Cell Significance Index: -4.6600
  • Cell Name: hepatic stellate cell (CL0000632)
    Fold Change: -0.0611
    Cell Significance Index: -0.6300
  • Cell Name: hippocampal granule cell (CL0001033)
    Fold Change: -0.0617
    Cell Significance Index: -4.1500
  • Cell Name: skeletal muscle fibroblast (CL0011027)
    Fold Change: -0.0618
    Cell Significance Index: -0.4200
  • Cell Name: plasmacytoid dendritic cell (CL0000784)
    Fold Change: -0.0646
    Cell Significance Index: -0.8500
  • Cell Name: vascular leptomeningeal cell (CL4023051)
    Fold Change: -0.0668
    Cell Significance Index: -1.0000
  • Cell Name: L5/6 near-projecting glutamatergic neuron (CL4030067)
    Fold Change: -0.0668
    Cell Significance Index: -0.3500
  • Cell Name: L5 extratelencephalic projecting glutamatergic cortical neuron (CL4023041)
    Fold Change: -0.0705
    Cell Significance Index: -2.4700
  • Cell Name: cerebral cortex GABAergic interneuron (CL0010011)
    Fold Change: -0.0745
    Cell Significance Index: -0.7500
  • Cell Name: fibroblast of mammary gland (CL0002555)
    Fold Change: -0.0774
    Cell Significance Index: -2.2200
  • Cell Name: neural cell (CL0002319)
    Fold Change: -0.0780
    Cell Significance Index: -0.9100
  • Cell Name: subcutaneous adipocyte (CL0002521)
    Fold Change: -0.0839
    Cell Significance Index: -0.3700
  • Cell Name: basal epithelial cell of prostatic duct (CL0002236)
    Fold Change: -0.0863
    Cell Significance Index: -0.7700
  • Cell Name: corticothalamic-projecting glutamatergic cortical neuron (CL4023013)
    Fold Change: -0.0867
    Cell Significance Index: -2.7600
  • Cell Name: type I muscle cell (CL0002211)
    Fold Change: -0.0873
    Cell Significance Index: -2.1300
  • Cell Name: CD4-positive, alpha-beta thymocyte (CL0000810)
    Fold Change: -0.0934
    Cell Significance Index: -1.6100
  • Cell Name: nasal mucosa goblet cell (CL0002480)
    Fold Change: -0.0941
    Cell Significance Index: -0.9600
  • Cell Name: bronchus fibroblast of lung (CL2000093)
    Fold Change: -0.0952
    Cell Significance Index: -1.0200
  • Cell Name: macroglial cell (CL0000126)
    Fold Change: -0.0963
    Cell Significance Index: -1.1200
  • Cell Name: L6b glutamatergic cortical neuron (CL4023038)
    Fold Change: -0.0990
    Cell Significance Index: -3.2400
  • Cell Name: luminal adaptive secretory precursor cell of mammary gland (CL4033057)
    Fold Change: -0.1018
    Cell Significance Index: -4.7900
  • Cell Name: respiratory basal cell (CL0002633)
    Fold Change: -0.1034
    Cell Significance Index: -1.0200
  • Cell Name: decidual natural killer cell, human (CL0002343)
    Fold Change: -0.1054
    Cell Significance Index: -1.0900
  • Cell Name: epithelial cell of prostate (CL0002231)
    Fold Change: -0.1148
    Cell Significance Index: -0.7100
  • Cell Name: midzonal region hepatocyte (CL0019028)
    Fold Change: -0.1163
    Cell Significance Index: -0.6700
  • Cell Name: erythroid progenitor cell (CL0000038)
    Fold Change: -0.1208
    Cell Significance Index: -1.5800
  • Cell Name: skin fibroblast (CL0002620)
    Fold Change: -0.1213
    Cell Significance Index: -0.2800

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this specific cell.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Cell ID: Standard Cell Ontology term used for mapping and comparing cells across experiments. Ensures consistency in analyzing cellular functions across tissues.
Fold Change: Represents the ratio of the current Cell Significance Index to the Cell Significance Index Threshold, indicating how much the gene expression has changed compared to a baseline.
Cell Significance Index: Reflects how strongly a gene is expressed in this cell type. Calculated using techniques like effect size estimation and bootstrapping for reliability.

Other Information

**Key Characteristics:** 1. **Cellular localization:** CLRN1 is widely expressed in various cell types, including erythrocytes, thymocytes, hematopoietic stem cells, T cells, megakaryocytes, enterocytes, Mueller cells, colon goblet cells, and precursor B cells. 2. **Protein structure:** The CLRN1 protein is a cytoplasmic protein with a long N-terminus and a shorter C-terminus, which may interact with microtubules and actin filaments. 3. **Functional domains:** CLRN1 contains multiple functional domains, including a protein-binding domain, a microtubule-binding domain, and a lamellipodium assembly domain. 4. **Regulatory mechanisms:** CLRN1 is involved in the regulation of lamellipodium assembly, a process critical for cell motility and sensory perception. **Pathways and Functions:** 1. **Actin filament organization:** CLRN1 regulates the organization of actin filaments, which is essential for cellular motility, shape, and structure. 2. **Microtubule cytoskeleton:** CLRN1 interacts with microtubules, which are critical for maintaining cellular shape, polarity, and motility. 3. **Protein binding:** CLRN1 binds to various proteins, including actin-binding proteins, microtubule-binding proteins, and signaling molecules, which modulate its activity and function. 4. **Sensory perception:** CLRN1 is involved in the maintenance of sensory receptor cells, including photoreceptor cells and auditory receptor cells, which are essential for sensory perception. 5. **Cell motility:** CLRN1 regulates the assembly of lamellipodia, a process critical for cell motility and migration. **Clinical Significance:** 1. **Usher syndrome:** Mutations in the CLRN1 gene have been associated with Usher syndrome, a genetic disorder characterized by deafness and vision loss. 2. **Retinitis pigmentosa:** CLRN1 mutations have also been linked to retinitis pigmentosa, a group of genetic disorders affecting the retina and leading to progressive vision loss. 3. **Hearing loss:** CLRN1 mutations have been associated with hearing loss, particularly in individuals with Usher syndrome. 4. **Immunological disorders:** CLRN1 may also play a role in immunological disorders, such as autoimmune diseases and immunodeficiency disorders, due to its involvement in regulating immune cell function and signaling. In conclusion, CLRN1 is a novel gene that plays a critical role in maintaining cellular architecture, sensory perception, and cellular motility. Its dysregulation has been implicated in various genetic disorders, including Usher syndrome, retinitis pigmentosa, and hearing loss. Further research is needed to fully understand the mechanisms of CLRN1 function and its role in human disease.

Genular Protein ID: 3953887590

Symbol: CLRN1_HUMAN

Name: Clarin-1

UniProtKB Accession Codes:

P58418 D3DNJ3 E1ACU9 Q8N6A9

Database IDs:

AGR 1 AlphaFoldDB 1 Antibodypedia 1 Bgee 1 BioGRID 1 BioGRID-ORCS 1 BioMuta 1 CCDS 3 CTD 1 ChiTaRS 1 DMDM 1 DNASU 1 DisGeNET 1 EMBL 9 Ensembl 3 ExpressionAtlas 1 GO 16 GeneCards 1 GeneReviews 1 GeneTree 1 GeneWiki 1 GenomeRNAi 1 GlyCosmos 1 GlyGen 1 HGNC 1 HOGENOM 1 HPA 1 InParanoid 1 IntAct 1 InterPro 1 KEGG 1 MANE-Select 1 MIM 5 MalaCards 1 NCBI Taxonomy 1 OMA 1 OpenTargets 1 Orphanet 2 OrthoDB 1 PANTHER 2 PRO 1 PathwayCommons 1 PaxDb 1 PharmGKB 1 Pharos 1 PhosphoSitePlus 1 PhylomeDB 1 Proteomes 1 ProteomicsDB 1 RNAct 1 RefSeq 3 STRING 1 SignaLink 1 TCDB 1 TreeFam 1 UCSC 1 VEuPathDB 1 eggNOG 1 iPTMnet 1 neXtProt 1

Citations:

PubMed ID: 11524702

Title: Mutations in a novel gene with transmembrane domains underlie Usher syndrome type 3.

PubMed ID: 11524702

DOI: 10.1086/323610

PubMed ID: 12145752

Title: Usher syndrome type III: revised genomic structure of the USH3 gene and identification of novel mutations.

PubMed ID: 12145752

DOI: 10.1086/342098

PubMed ID: 12080385

Title: USH3A transcripts encode clarin-1, a four-transmembrane-domain protein with a possible role in sensory synapses.

PubMed ID: 12080385

DOI: 10.1038/sj.ejhg.5200831

PubMed ID: 20717163

Title: Alternative splice variants of the USH3A gene Clarin 1 (CLRN1).

PubMed ID: 20717163

DOI: 10.1038/ejhg.2010.140

PubMed ID: 16641997

Title: The DNA sequence, annotation and analysis of human chromosome 3.

PubMed ID: 16641997

DOI: 10.1038/nature04728

PubMed ID: 15489334

Title: The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC).

PubMed ID: 15489334

DOI: 10.1101/gr.2596504

PubMed ID: 15521980

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

PubMed ID: 15521980

DOI: 10.1111/j.1399-0004.2004.00352.x

PubMed ID: 18273898

Title: Spectrum of USH2A mutations in Scandinavian patients with Usher syndrome type II.

PubMed ID: 18273898

DOI: 10.1002/humu.9524

PubMed ID: 21310491

Title: CLRN1 mutations cause nonsyndromic retinitis pigmentosa.

PubMed ID: 21310491

DOI: 10.1016/j.ophtha.2010.10.047

PubMed ID: 23304067

Title: Two novel disease-causing mutations in the CLRN1 gene in patients with Usher syndrome type 3.

PubMed ID: 23304067

Sequence Information:

  • Length: 232
  • Mass: 25719
  • Checksum: 2713C621FEBE4281
  • Sequence:
    • MPSQQKKIIF CMAGVFSFAC ALGVVTALGT PLWIKATVLC KTGALLVNAS GQELDKFMGE 
MQYGLFHGEG VRQCGLGARP FRFSFFPDLL KAIPVSIHVN VILFSAILIV LTMVGTAFFM 
YNAFGKPFET LHGPLGLYLL SFISGSCGCL VMILFASEVK IHHLSEKIAN YKEGTYVYKT 
QSEKYTTSFW VIFFCFFVHF LNGLLIRLAG FQFPFAKSKD AETTNVAADL MY

Database document:

This is a preview of the gene's schema. Only a few entries are kept for 'singleCellExpressions,' 'mRNAExpressions,' and other large data arrays for visualization purposes. You can zoom in with the mouse wheel for a closer view, and the text will adjust automatically if necessary. For the full schema, download it here.