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    CRB1 crumbs cell polarity complex component 1 [ Homo sapiens (human) ]

    Gene ID: 23418, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CRB1provided by HGNC
    Official Full Name
    crumbs cell polarity complex component 1provided by HGNC
    Primary source
    HGNC:HGNC:2343
    See related
    Ensembl:ENSG00000134376 MIM:604210; AllianceGenome:HGNC:2343
    Gene type
    protein coding
    RefSeq status
    REVIEWED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    LCA8; RP12; CRB1-A; CRB1-B; CRB1-C
    Summary
    This gene encodes a protein which is similar to the Drosophila crumbs protein and localizes to the inner segment of mammalian photoreceptors. In Drosophila crumbs localizes to the stalk of the fly photoreceptor and may be a component of the molecular scaffold that controls proper development of polarity in the eye. Mutations in this gene are associated with a severe form of retinitis pigmentosa, RP12, and with Leber congenital amaurosis. Alternate splicing results in multiple transcript variants, some protein coding and some non-protein coding.[provided by RefSeq, Apr 2012]
    Expression
    Biased expression in brain (RPKM 4.0) and testis (RPKM 1.3) See more
    Orthologs
    mouse all
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    Genomic context

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    See CRB1 in Genome Data Viewer
    Location:
    1q31.3
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (197201504..197478455)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (196463303..196740260)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (197170634..197447585)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 1659 Neighboring gene septin 14 pseudogene 12 Neighboring gene assembly factor for spindle microtubules Neighboring gene H3K27ac hESC enhancer GRCh37_chr1:197170170-197170755 Neighboring gene zinc finger and BTB domain containing 41 Neighboring gene ATPase H+ transporting accessory protein 2 pseudogene Neighboring gene uncharacterized LOC124904477 Neighboring gene mitochondrial ribosomal protein S21 pseudogene 3 Neighboring gene DENN domain containing 1B Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr1:197541395-197542594 Neighboring gene MPRA-validated peak643 silencer Neighboring gene eukaryotic translation elongation factor 1 alpha 1 pseudogene 32 Neighboring gene RPL24 pseudogene 5

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: Tissue-specific circular RNA induction during human fetal development
    • Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
    • BioProject: PRJNA270632
    • Publication: PMID 26076956
    • Analysis date: Mon Apr 2 22:54:59 2018

    Bibliography

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    Related articles in PubMed

    1. CRB1 heterozygotes with regional retinal dysfunction: implications for genetic testing of leber congenital amaurosis. Yzer S, et al. Invest Ophthalmol Vis Sci, 2006 Sep. PMID 16936081
    2. DIFFUSE RETINAL VASCULAR LEAKAGE AND CONE-ROD DYSTROPHY IN A FAMILY WITH THE HOMOZYGOUS MISSENSE C.1429G>A (P.GLY477ARG) MUTATION IN CRB1. Alsulaiman HM, et al. Retin Cases Brief Rep, 2020 Spring. PMID 29200130
    3. Role of the Crumbs proteins in ciliogenesis, cell migration and actin organization. Bazellières E, et al. Semin Cell Dev Biol, 2018 Sep. PMID 29056580
    4. The correlation between CRB1 variants and the clinical severity of Brazilian patients with different inherited retinal dystrophy phenotypes. Motta FL, et al. Sci Rep, 2017 Aug 17. PMID 28819299, Free PMC Article
    5. Report of a novel mutation in CRB1 in a Lebanese family presenting retinal dystrophy. Jalkh N, et al. Ophthalmic Genet, 2014 Mar. PMID 23362850

    See all (114) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Quality of life in patients with CRB1-associated retinal dystrophies: A longitudinal study.
      Title: Quality of life in patients with CRB1-associated retinal dystrophies: A longitudinal study.
    2. Genotype-phenotype associations in CRB1 bi-allelic patients: a novel mutation, a systematic review and meta-analysis.
      Title: Genotype-phenotype associations in CRB1 bi-allelic patients: a novel mutation, a systematic review and meta-analysis.
    3. Human CRB1 and CRB2 form homo- and heteromeric protein complexes in the retina.
      Title: Human CRB1 and CRB2 form homo- and heteromeric protein complexes in the retina.
    4. A novel pathogenic CRB1 variant presenting as Leber Congenital Amaurosis 8 and evaluation of gene editing feasibility.
      Title: A novel pathogenic CRB1 variant presenting as Leber Congenital Amaurosis 8 and evaluation of gene editing feasibility.
    5. Foveal Hypoplasia in CRB1-Related Retinopathies.
      Title: Foveal Hypoplasia in CRB1-Related Retinopathies.
    6. CRB1 is required for recycling by RAB11A+ vesicles in human retinal organoids.
      Title: CRB1 is required for recycling by RAB11A+ vesicles in human retinal organoids.
    7. CRB1-Associated Retinal Dystrophies: Genetics, Clinical Characteristics, and Natural History.
      Title: CRB1-Associated Retinal Dystrophies: Genetics, Clinical Characteristics, and Natural History.
    8. A novel nonsense variant (c.1499C>G) in CRB1 caused Leber congenital amaurosis-8 in a Chinese family and a literature review.
      Title: A novel nonsense variant (c.1499C>G) in CRB1 caused Leber congenital amaurosis-8 in a Chinese family and a literature review.
    9. CRB1-associated retinal dystrophies in a Belgian cohort: genetic characteristics and long-term clinical follow-up.
      Title: CRB1-associated retinal dystrophies in a Belgian cohort: genetic characteristics and long-term clinical follow-up.
    10. In Silico Analysis of Pathogenic CRB1 Single Nucleotide Variants and Their Amenability to Base Editing as a Potential Lead for Therapeutic Intervention.
      Title: In Silico Analysis of Pathogenic CRB1 Single Nucleotide Variants and Their Amenability to Base Editing as a Potential Lead for Therapeutic Intervention.
    Submit: New GeneRIF Correction See all GeneRIFs (77)

    Phenotypes

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    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    Lupus nephritis susceptibility Loci in women with systemic lupus erythematosus.
    EBI GWAS Catalog
    Variants of DENND1B associated with asthma in children.
    EBI GWAS Catalog

    Variation

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    See variants in ClinVar

    See studies and variants in dbVar

    See Variation Viewer (GRCh37.p13)

    See Variation Viewer (GRCh38)

    Pathways from PubChem

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    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables calcium ion binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    Process Evidence Code Pubs
    involved_in blood vessel remodeling IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in cell-cell signaling TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in cellular response to light stimulus IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in detection of light stimulus involved in visual perception IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in establishment of bipolar cell polarity involved in cell morphogenesis IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in establishment or maintenance of cell polarity TAS
    Traceable Author Statement
    more info
    		 PubMed 
    involved_in establishment or maintenance of epithelial cell apical/basal polarity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in establishment or maintenance of epithelial cell apical/basal polarity NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    involved_in eye photoreceptor cell development IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in gene expression IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in glial cell differentiation IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in heterophilic cell-cell adhesion via plasma membrane cell adhesion molecules IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in photoreceptor cell maintenance IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in photoreceptor cell outer segment organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in plasma membrane organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in post-embryonic retina morphogenesis in camera-type eye IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in protein localization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in retina layer formation IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in adherens junction IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    located_in apical junction complex NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in apical plasma membrane NAS
    Non-traceable Author Statement
    more info
    		 PubMed 
    located_in extracellular region IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in glial cell projection IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in microvillus IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in photoreceptor inner segment IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in photoreceptor outer segment IEA
    Inferred from Electronic Annotation
    more info
    		  
    is_active_in plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of protein-containing complex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of protein-containing complex IDA
    Inferred from Direct Assay
    more info
    		 PubMed 
    part_of subapical complex IEA
    Inferred from Electronic Annotation
    more info
    		  

    General protein information

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    Preferred Names
    protein crumbs homolog 1
    Names
    crumbs 1, cell polarity complex component
    crumbs family member 1, photoreceptor morphogenesis associated

    NCBI Reference Sequences (RefSeq)

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    RefSeqs maintained independently of Annotated Genomes

    These reference sequences exist independently of genome builds. Explain

    These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

    Genomic

    1. NG_008483.3 RefSeqGene

      Range
      71750..281953
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_001193640.2 → NP_001180569.1  protein crumbs homolog 1 isoform 2 precursor

      See identical proteins and their annotated locations for NP_001180569.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks two in-frame exons compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.
      Source sequence(s)
      AL136322, AL139136, AL513325
      Consensus CDS
      CCDS53454.1
      UniProtKB/TrEMBL
      A8K118
      Related
      ENSP00000356369.2, ENST00000367399.6
      Conserved Domains (3) summary
      smart00179
      Location:285 → 326
      EGF_CA; Calcium-binding EGF-like domain
      cd00054
      Location:148 → 183
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam02210
      Location:402 → 537
      Laminin_G_2; Laminin G domain

    2. NM_001257965.2 → NP_001244894.1  protein crumbs homolog 1 isoform 3

      Status: REVIEWED

      Description
      Transcript Variant: This variant (3) contains three noncoding exons in place of the first exon and contains an alternate in-frame exon compared to variant 1. The resulting isoform (3) is shorter at the N- terminus and contains an alternate internal segment compared to isoform 1.
      Source sequence(s)
      AL136322, AL139136, AL356315, AL513325
      Consensus CDS
      CCDS58053.1
      UniProtKB/TrEMBL
      B7Z826, F5H0L2
      Related
      ENSP00000438786.1, ENST00000535699.5
      Conserved Domains (3) summary
      smart00179
      Location:328 → 369
      EGF_CA; Calcium-binding EGF-like domain
      cd00054
      Location:79 → 114
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam02210
      Location:445 → 580
      Laminin_G_2; Laminin G domain

    3. NM_001257966.2 → NP_001244895.1  protein crumbs homolog 1 isoform 4 precursor

      See identical proteins and their annotated locations for NP_001244895.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (4) lacks an alternate in-frame segment of two coding exons and most of a third compared to variant 1. The resulting isoform (4) has the same N- and C-termini but lacks an alternate internal segment compared to isoform 1.
      Source sequence(s)
      AL136322, AL139136, AL513325
      Consensus CDS
      CCDS58052.1
      UniProtKB/TrEMBL
      A0A7D6VMU1
      Related
      ENSP00000438091.1, ENST00000538660.5
      Conserved Domains (3) summary
      smart00179
      Location:397 → 438
      EGF_CA; Calcium-binding EGF-like domain
      cd00054
      Location:148 → 183
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam02210
      Location:514 → 649
      Laminin_G_2; Laminin G domain

    4. NM_201253.3 → NP_957705.1  protein crumbs homolog 1 isoform 1 precursor

      See identical proteins and their annotated locations for NP_957705.1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longest isoform (1).
      Source sequence(s)
      AL136322, AL139136, AL513325
      Consensus CDS
      CCDS1390.1
      UniProtKB/Swiss-Prot
      A2A308, B7Z5T2, B9EG71, P82279, Q5K3A6, Q5TC28, Q5VUT1, Q6N027, Q8WWY0, Q8WWY1
      UniProtKB/TrEMBL
      A0A7D6VM04, A8K118
      Related
      ENSP00000356370.3, ENST00000367400.8
      Conserved Domains (3) summary
      smart00179
      Location:397 → 438
      EGF_CA; Calcium-binding EGF-like domain
      cd00054
      Location:148 → 183
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam02210
      Location:514 → 649
      Laminin_G_2; Laminin G domain

    RNA

    1. NR_047563.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (5) lacks an alternate internal segment of a coding exon compared to variant 1, that causes a frameshift. The resulting transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is thought to be non-protein coding.
      Source sequence(s)
      AL136322, AL139136, AL513325

    2. NR_047564.2 RNA Sequence

      Status: REVIEWED

      Description
      Transcript Variant: This variant (6) uses an alternate splice junction at the 3' end of a coding exon compared to variant 1, that causes a frameshift. The resulting transcript is a candidate for nonsense-mediated mRNA decay (NMD) and is thought to be non-protein coding.
      Source sequence(s)
      AL136322, AL139136, AL513325
      Related
      ENST00000484075.5

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2024_08

    The following sections contain reference sequences that belong to a specific genome build. Explain

    Reference GRCh38.p14 Primary Assembly

    Genomic

    1. NC_000001.11 Reference GRCh38.p14 Primary Assembly

      Range
      197201504..197478455
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047416573.1 → XP_047272529.1  protein crumbs homolog 1 isoform X2

      UniProtKB/TrEMBL
      B7Z826

    2. XM_017000852.2 → XP_016856341.1  protein crumbs homolog 1 isoform X7

      UniProtKB/TrEMBL
      A8K118

    3. XM_011509367.2 → XP_011507669.1  protein crumbs homolog 1 isoform X3

      UniProtKB/TrEMBL
      A8K118
      Conserved Domains (3) summary
      smart00179
      Location:397 → 438
      EGF_CA; Calcium-binding EGF-like domain
      cd00054
      Location:148 → 183
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam02210
      Location:514 → 649
      Laminin_G_2; Laminin G domain

    4. XM_047416574.1 → XP_047272530.1  protein crumbs homolog 1 isoform X4

      UniProtKB/TrEMBL
      A8K118

    5. XM_011509365.3 → XP_011507667.1  protein crumbs homolog 1 isoform X1

      UniProtKB/TrEMBL
      A8K118
      Related
      ENSP00000491102.1, ENST00000638467.1
      Conserved Domains (3) summary
      smart00179
      Location:397 → 438
      EGF_CA; Calcium-binding EGF-like domain
      cd00054
      Location:148 → 183
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam02210
      Location:514 → 649
      Laminin_G_2; Laminin G domain

    6. XM_047416572.1 → XP_047272528.1  protein crumbs homolog 1 isoform X2

      UniProtKB/TrEMBL
      B7Z826

    7. XM_047416575.1 → XP_047272531.1  protein crumbs homolog 1 isoform X5

      UniProtKB/TrEMBL
      A0A7D6VLH9
      Related
      ENSP00000505267.1, ENST00000681519.1

    8. XM_011509369.3 → XP_011507671.1  protein crumbs homolog 1 isoform X6

      See identical proteins and their annotated locations for XP_011507671.1

      UniProtKB/TrEMBL
      B7Z824
      Conserved Domains (2) summary
      cd00054
      Location:627 → 656
      EGF_CA; Calcium-binding EGF-like domain, present in a large number of membrane-bound and extracellular (mostly animal) proteins. Many of these proteins require calcium for their biological function and calcium-binding sites have been found to be located at the ...
      pfam02210
      Location:461 → 586
      Laminin_G_2; Laminin G domain

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      196463303..196740260
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054335671.1 → XP_054191646.1  protein crumbs homolog 1 isoform X2

      UniProtKB/TrEMBL
      B7Z826

    2. XM_054335676.1 → XP_054191651.1  protein crumbs homolog 1 isoform X7

      UniProtKB/TrEMBL
      A8K118

    3. XM_054335672.1 → XP_054191647.1  protein crumbs homolog 1 isoform X3

      UniProtKB/TrEMBL
      A8K118

    4. XM_054335673.1 → XP_054191648.1  protein crumbs homolog 1 isoform X4

      UniProtKB/TrEMBL
      A8K118

    5. XM_054335669.1 → XP_054191644.1  protein crumbs homolog 1 isoform X1

      UniProtKB/TrEMBL
      A8K118

    6. XM_054335670.1 → XP_054191645.1  protein crumbs homolog 1 isoform X2

      UniProtKB/TrEMBL
      B7Z826

    7. XM_054335674.1 → XP_054191649.1  protein crumbs homolog 1 isoform X5

      UniProtKB/TrEMBL
      A0A7D6VLH9

    8. XM_054335675.1 → XP_054191650.1  protein crumbs homolog 1 isoform X6

      UniProtKB/TrEMBL
      B7Z824

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_012076.2: Suppressed sequence

      Description
      NM_012076.2: This RefSeq was permanently suppressed because it is a nonsense-mediated mRNA decay (NMD) candidate.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    P82279.2 GenPept UniProtKB/Swiss-Prot:P82279

    Gene LinkOut

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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