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

Gene ID: 57554, updated on 11-Apr-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
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Genomic context

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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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