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    LRRC7 leucine rich repeat containing 7 [ Homo sapiens (human) ]

    Gene ID: 57554, updated on 5-May-2024

    Summary

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    Official Symbol
    LRRC7provided by HGNC
    Official Full Name
    leucine rich repeat containing 7provided by HGNC
    Primary source
    HGNC:HGNC:18531
    See related
    Ensembl:ENSG00000033122 MIM:614453; AllianceGenome:HGNC:18531
    Gene type
    protein coding
    RefSeq status
    VALIDATED
    Organism
    Homo sapiens
    Lineage
    Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
    Also known as
    DENSIN
    Summary
    Predicted to be involved in several processes, including establishment or maintenance of epithelial cell apical/basal polarity; positive regulation of neuron projection development; and receptor clustering. Located in several cellular components, including centrosome; cytosol; and nucleoplasm. [provided by Alliance of Genome Resources, Apr 2022]
    Expression
    Biased expression in brain (RPKM 2.3), testis (RPKM 0.6) and 2 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See LRRC7 in Genome Data Viewer
    Location:
    1p31.1
    Exon count:
    31
    Annotation release Status Assembly Chr Location
    RS_2023_10 current GRCh38.p14 (GCF_000001405.40) 1 NC_000001.11 (69567922..70144364)
    RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) 1 NC_060925.1 (69444558..70022853)
    105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) 1 NC_000001.10 (70033605..70610047)

    Chromosome 1 - NC_000001.11Genomic Context describing neighboring genes Neighboring gene uncharacterized LOC105378789 Neighboring gene long intergenic non-protein coding RNA 1758 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 987 Neighboring gene shugoshin 1 pseudogene 1 Neighboring gene uncharacterized LOC124904199 Neighboring gene RNA, 7SL, cytoplasmic 538, pseudogene Neighboring gene peptidylprolyl cis/trans isomerase, NIMA-interacting 1 pseudogene 1 Neighboring gene NANOG hESC enhancer GRCh37_chr1:70503542-70504181 Neighboring gene ReSE screen-validated silencer GRCh37_chr1:70534982-70535190 Neighboring gene LRRC7 antisense RNA 1 Neighboring gene Sharpr-MPRA regulatory region 9273 Neighboring gene NANOG hESC enhancer GRCh37_chr1:70606447-70606948 Neighboring gene Sharpr-MPRA regulatory region 3760 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr1:70626481-70626982 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1186 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 1187 Neighboring gene leucine rich repeat containing 40 Neighboring gene RNA, 7SL, cytoplasmic 242, pseudogene Neighboring gene NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr1:70686957-70687502 Neighboring gene serine and arginine rich splicing factor 11

    Genomic regions, transcripts, and products

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    Go to nucleotide: Graphics FASTA GenBank

    Expression

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    • Project title: HPA RNA-seq normal tissues
    • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
    • BioProject: PRJEB4337
    • Publication: PMID 24309898
    • Analysis date: Wed Apr 4 07:08:55 2018

    Bibliography

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    Related articles in PubMed

    1. Genetic variant analysis of the putative regulatory regions of the LRRC7 gene in bipolar disorder. Fiorentino A, et al. Psychiatr Genet, 2016 Apr. PMID 26901794, Free PMC Article
    2. A novel protein, densin, expressed by glomerular podocytes. Ahola H, et al. J Am Soc Nephrol, 2003 Jul. PMID 12819232
    3. Cloning and characterization of a novel splice variant of the brain-specific protein densin-180. Wang L, et al. Int J Mol Med, 2003 Feb. PMID 12525888
    4. Densin and beta-catenin form a complex and co-localize in cultured podocyte cell junctions. Heikkilä E, et al. Mol Cell Biochem, 2007 Nov. PMID 17581699
    5. Densin is a novel cell membrane protein of Sertoli cells in the testis. Lassila M, et al. Mol Reprod Dev, 2007 May. PMID 17039495

    See all (41) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. The important role of this gene in the synapse and mental illness endophenotypes observed in animal models suggests that LRRC7 may play a role in susceptibility to bipolar disorder.
      Title: Genetic variant analysis of the putative regulatory regions of the LRRC7 gene in bipolar disorder.
    2. Characterization of a central Ca2+/calmodulin-dependent protein kinase IIalpha/beta binding domain in densin that selectively modulates glutamate receptor subunit phosphorylation.
      Title: Characterization of a central Ca2+/calmodulin-dependent protein kinase IIalpha/beta binding domain in densin that selectively modulates glutamate receptor subunit phosphorylation.
    3. We found no genome-wide statistically significant associations but identified several plausible candidate genes among findings at p < 5E-05: LRRC7, TMEM132D, SEMA3A, ALK, and STIP1.
      Title: Genome-wide association study of the child behavior checklist dysregulation profile.
    4. Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
      Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.
    5. common variants in LRRC7, KIRREL, NPHS2 and ACTN4 do not appeear to contribute to susceptibility to diabetic nephropathy in Finnish patients with type 1 diabetes
      Title: Association analysis of podocyte slit diaphragm genes as candidates for diabetic nephropathy.
    6. Observational study of gene-disease association. (HuGE Navigator)
      Title: Association analysis of podocyte slit diaphragm genes as candidates for diabetic nephropathy.
    7. Densin may associate with the cadherin-catenin and nephrin complex(es), and may be involved in the formation of the cell-cell contacts.
      Title: Densin and beta-catenin form a complex and co-localize in cultured podocyte cell junctions.
    8. expressed by glomerular podocytes and has a role in associating with the nephrin interacting protein complex at the slit diaphragm
      Title: A novel protein, densin, expressed by glomerular podocytes.
    9. A novel splice variant, LRRC7, of densin-180 is located on 1p31 and consists of 8 exons. Unlike wild type, not brain-specific.
      Title: Cloning and characterization of a novel splice variant of the brain-specific protein densin-180.
    10. Densin-180 co-localized with delta-catenin/NPRAP at synapses in delta-catenin/NPRAP and may be involved in organization of the synaptic cell-cell junction through interaction with the delta-catenin/NPRAP-N-cadherin complex
      Title: Densin-180 interacts with delta-catenin/neural plakophilin-related armadillo repeat protein at synapses.
    Submit: New GeneRIF Correction See all GeneRIFs (12)

    Phenotypes

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    Find tests for this gene in the NIH Genetic Testing Registry (GTR)

    Review eQTL and phenotype association data in this region using PheGenI

    EBI GWAS Catalog

    Description
    EMR-linked GWAS study: investigation of variation landscape of loci for body mass index in children.
    EBI GWAS Catalog
    Genetic association of short sleep duration with hypertension incidence--a 6-year follow-up in the Korean genome and epidemiology study.
    EBI GWAS Catalog
    Genome wide study of maternal and parent-of-origin effects on the etiology of orofacial clefts.
    EBI GWAS Catalog
    Genome-wide association study of the child behavior checklist dysregulation profile.
    EBI GWAS Catalog
    Novel genetic loci identified for the pathophysiology of childhood obesity in the Hispanic population.
    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)

    Genotypes

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • KIAA1365, MGC144918, DKFZp686I1147

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables protein binding IPI
    Inferred from Physical Interaction
    more info
    		 PubMed 
    enables protein kinase binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cell-cell adhesion IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in embryo development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in establishment or maintenance of epithelial cell apical/basal polarity IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neurotransmitter receptor transport postsynaptic membrane to endosome IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in neurotransmitter receptor transport, endosome to postsynaptic membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in positive regulation of neuron projection development IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    involved_in receptor clustering IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in adherens junction IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in axon initial segment IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    is_active_in basolateral plasma membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in cytosol TAS
    Traceable Author Statement
    more info
    		  
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    is_active_in postsynaptic density IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    colocalizes_with postsynaptic membrane IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in specific granule lumen TAS
    Traceable Author Statement
    more info
    		  

    General protein information

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    Preferred Names
    leucine-rich repeat-containing protein 7
    Names
    densin-180

    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.

    mRNA and Protein(s)

    1. NM_001330635.3 → NP_001317564.1  leucine-rich repeat-containing protein 7 isoform 2

      Status: VALIDATED

      Source sequence(s)
      AL117353, AL157948, AL158840, AL353771, AL359412, AL359894, AL391728
      Consensus CDS
      CCDS81341.1
      UniProtKB/Swiss-Prot
      Q5VXC2, Q5VXC3, Q68D07, Q86VE8, Q8WX20, Q96NW7, Q9P2I2
      UniProtKB/TrEMBL
      A0A075B6E9
      Related
      ENSP00000309245.4, ENST00000310961.9
      Conserved Domains (4) summary
      COG4886
      Location:97 → 407
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      cd00992
      Location:1405 → 1490
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      sd00033
      Location:31 → 52
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:51 → 107
      LRR_8; Leucine rich repeat

    2. NM_001350216.3 → NP_001337145.1  leucine-rich repeat-containing protein 7 isoform 3

      Status: VALIDATED

      Source sequence(s)
      AL117353, AL157948, AL158840, AL353771, AL359412, AL359894, AL391728
      UniProtKB/Swiss-Prot
      Q5VXC2, Q5VXC3, Q68D07, Q86VE8, Q8WX20, Q96NW7, Q9P2I2
      Conserved Domains (3) summary
      COG4886
      Location:131 → 441
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:65 → 86
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:85 → 141
      LRR_8; Leucine rich repeat

    3. NM_001366836.3 → NP_001353765.1  leucine-rich repeat-containing protein 7 isoform 4

      Status: VALIDATED

      Source sequence(s)
      AL117353, AL359412, AL359894, AL391728
      Consensus CDS
      CCDS90974.1
      UniProtKB/TrEMBL
      B1AKT2
      Related
      ENSP00000359997.1, ENST00000370958.5
      Conserved Domains (2) summary
      COG4886
      Location:62 → 217
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:64 → 85
      LRR_RI; leucine-rich repeat [structural motif]

    4. NM_001366837.3 → NP_001353766.1  leucine-rich repeat-containing protein 7 isoform 5

      Status: VALIDATED

      Source sequence(s)
      AL117353, AL359412, AL359894, AL391728
      Conserved Domains (2) summary
      COG4886
      Location:29 → 184
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:31 → 52
      LRR_RI; leucine-rich repeat [structural motif]

    5. NM_001366838.3 → NP_001353767.1  leucine-rich repeat-containing protein 7 isoform 6

      Status: VALIDATED

      Source sequence(s)
      AL117353, AL157948, AL158840, AL353771, AL359412, AL359894, AL391728
      UniProtKB/Swiss-Prot
      Q5VXC2, Q5VXC3, Q68D07, Q86VE8, Q8WX20, Q96NW7, Q9P2I2
      Conserved Domains (4) summary
      COG4886
      Location:130 → 440
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      cd00992
      Location:1438 → 1523
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      sd00033
      Location:64 → 85
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:84 → 140
      LRR_8; Leucine rich repeat

    6. NM_001366839.3 → NP_001353768.1  leucine-rich repeat-containing protein 7 isoform 7

      Status: VALIDATED

      Source sequence(s)
      AL117353, AL157948, AL158840, AL353771, AL359412, AL359894, AL391728
      UniProtKB/Swiss-Prot
      Q5VXC2, Q5VXC3, Q68D07, Q86VE8, Q8WX20, Q96NW7, Q9P2I2
      Conserved Domains (4) summary
      COG4886
      Location:97 → 407
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      cd00992
      Location:1345 → 1430
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      sd00033
      Location:31 → 52
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:51 → 107
      LRR_8; Leucine rich repeat

    7. NM_001366840.1 → NP_001353769.1  leucine-rich repeat-containing protein 7 isoform 8

      Status: VALIDATED

      Source sequence(s)
      AL117353, AL359412, AL359894, AL391728
      Conserved Domains (2) summary
      COG4886
      Location:63 → 218
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:65 → 86
      LRR_RI; leucine-rich repeat [structural motif]

    8. NM_001366841.1 → NP_001353770.1  leucine-rich repeat-containing protein 7 isoform 9

      Status: VALIDATED

      Source sequence(s)
      AL117353, AL157948, AL158840, AL353771, AL359412, AL359894, AL391728
      UniProtKB/Swiss-Prot
      Q5VXC2, Q5VXC3, Q68D07, Q86VE8, Q8WX20, Q96NW7, Q9P2I2
      Conserved Domains (3) summary
      COG4886
      Location:97 → 407
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:31 → 52
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:51 → 107
      LRR_8; Leucine rich repeat

    9. NM_001366842.1 → NP_001353771.1  leucine-rich repeat-containing protein 7 isoform 10

      Status: VALIDATED

      Source sequence(s)
      AL117353, AL359412, AL359894, AL391728
      Conserved Domains (2) summary
      COG4886
      Location:81 → 236
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      sd00033
      Location:83 → 104
      LRR_RI; leucine-rich repeat [structural motif]

    10. NM_001370785.2 → NP_001357714.1  leucine-rich repeat-containing protein 7 isoform 11

      Status: VALIDATED

      Source sequence(s)
      AL117353, AL157948, AL158840, AL353771, AL359412, AL359894, AL391728
      Consensus CDS
      CCDS90975.1
      UniProtKB/Swiss-Prot
      Q5VXC2, Q5VXC3, Q68D07, Q86VE8, Q8WX20, Q96NW7, Q9P2I2
      UniProtKB/TrEMBL
      A0A494C1A4
      Related
      ENSP00000498937.2, ENST00000651989.2
      Conserved Domains (4) summary
      COG4886
      Location:130 → 440
      LRR; Leucine-rich repeat (LRR) protein [Transcription]
      cd00992
      Location:1485 → 1570
      PDZ_signaling; PDZ domain found in a variety of Eumetazoan signaling molecules, often in tandem arrangements. May be responsible for specific protein-protein interactions, as most PDZ domains bind C-terminal polypeptides, and binding to internal (non-C-terminal) ...
      sd00033
      Location:64 → 85
      LRR_RI; leucine-rich repeat [structural motif]
      pfam13855
      Location:85 → 140
      LRR_8; Leucine rich repeat

    RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

    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
      69567922..70144364
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060925.1 Alternate T2T-CHM13v2.0

      Range
      69444558..70022853
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    Suppressed Reference Sequence(s)

    The following Reference Sequences have been suppressed. Explain

    1. NM_020794.2: Suppressed sequence

      Description
      NM_020794.2: This RefSeq has been removed because currently there is insufficient support for the transcript and protein.
    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q96NW7.1 GenPept UniProtKB/Swiss-Prot:Q96NW7

    Gene LinkOut

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

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