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    CRISPLD2 cysteine rich secretory protein LCCL domain containing 2 [ Homo sapiens (human) ]

    Gene ID: 83716, updated on 10-Dec-2024

    Summary

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    Official Symbol
    CRISPLD2provided by HGNC
    Official Full Name
    cysteine rich secretory protein LCCL domain containing 2provided by HGNC
    Primary source
    HGNC:HGNC:25248
    See related
    Ensembl:ENSG00000103196 MIM:612434; AllianceGenome:HGNC:25248
    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
    LGL1; CRISP11; LCRISP2
    Summary
    Predicted to enable glycosaminoglycan binding activity. Involved in face morphogenesis. Located in transport vesicle. [provided by Alliance of Genome Resources, Dec 2024]
    Expression
    Broad expression in gall bladder (RPKM 67.9), placenta (RPKM 54.3) and 20 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CRISPLD2 in Genome Data Viewer
    Location:
    16q24.1
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 16 NC_000016.10 (84819985..84909508)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 16 NC_060940.1 (90886255..90975767)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 16 NC_000016.9 (84853591..84943114)

    Chromosome 16 - NC_000016.10Genomic Context describing neighboring genes Neighboring gene ubiquitin specific peptidase 10 Neighboring gene uncharacterized LOC124903737 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84769037-84770002 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84770003-84770968 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11254 Neighboring gene Sharpr-MPRA regulatory region 6565 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11255 Neighboring gene Sharpr-MPRA regulatory region 1784 Neighboring gene uncharacterized LOC105371378 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84828009-84828510 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84837954-84838454 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84839622-84840200 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84840201-84840777 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 11256 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 7795 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84869778-84870346 Neighboring gene NANOG-H3K4me1 hESC enhancer GRCh37_chr16:84878477-84879206 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:84879989-84880225 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr16:84884617-84885118 Neighboring gene CDK7 strongly-dependent group 2 enhancer GRCh37_chr16:84913207-84914406 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84918435-84919058 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84919059-84919684 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84919685-84920308 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr16:84920309-84920933 Neighboring gene ReSE screen-validated silencer GRCh37_chr16:84943761-84943876 Neighboring gene interferon induced transmembrane protein pseudogene Neighboring gene long intergenic non-protein coding RNA 2176

    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. CRISPLD2 polymorphisms are associated with non-syndromic cleft lip with or without cleft palate in a northern Chinese population. Shi J, et al. Eur J Oral Sci, 2010 Aug. PMID 20662919
    2. The CRISPLD2 gene is involved in cleft lip and/or cleft palate in a Chinese population. Shen X, et al. Birth Defects Res A Clin Mol Teratol, 2011 Oct. PMID 21800413
    3. No evidence for a role of CRISPLD2 in non-syndromic cleft lip with or without cleft palate in an Italian population. Girardi A, et al. Eur J Oral Sci, 2011 Feb. PMID 21244519
    4. CRISPLD2 variants including a C471T silent mutation may contribute to nonsyndromic cleft lip with or without cleft palate. Letra A, et al. Cleft Palate Craniofac J, 2011 Jul. PMID 20815724, Free PMC Article
    5. Both LCCL-domains of human CRISPLD2 have high affinity for lipid A. Vásárhelyi V, et al. Biochimie, 2014 Feb. PMID 24090571

    See all (38) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Decreased CRISPLD2 expression impairs osteogenic differentiation of human mesenchymal stem cells during in vitro expansion.
      Title: Decreased CRISPLD2 expression impairs osteogenic differentiation of human mesenchymal stem cells during in vitro expansion.
    2. Identification of Rac guanine nucleotide exchange factors promoting Lgl1 phosphorylation in glioblastoma.
      Title: Identification of Rac guanine nucleotide exchange factors promoting Lgl1 phosphorylation in glioblastoma.
    3. Our findings suggest that using specific asthma characteristics, such as airway hyperresponsiveness, can help identify more genetically homogeneous asthma subgroups with genotype-phenotype associations that may not be observed in all children with asthma. CRISPLD2 also may be important for baseline lung function in individuals with asthma who also may have airway hyperresponsiveness.
      Title: Whole Genome Sequencing Identifies CRISPLD2 as a Lung Function Gene in Children With Asthma.
    4. CRISPLD2 rs4783099 was associated with cleft lip and/or palate (CL/P) statistically (OR = 3.18, P < .01). Compared to genotype TT, genotypes CC and CT were correlated significantly (OR = 2.04, P = .04) with CL/P. No evidence showed an association between genetic variation at the CRISPLD2 locus and cleft palate only (CP).
      Title: Association Between CRISPLD2 Polymorphisms and the Risk of Nonsyndromic Clefts of the Lip and/or Palate: A Meta-analysis.
    5. we demonstrated that knockdown of Crispld2 in zebrafish alters neural crest cell migration patterns resulting in abnormal jaw and palate development. In this study, we performed RNA profiling in zebrafish embryos and identified 249 differentially expressed genes following knockdown of Crispld2.
      Title: Knockdown of Crispld2 in zebrafish identifies a novel network for nonsyndromic cleft lip with or without cleft palate candidate genes.
    6. Our results suggest that CRISPLD2 rs4783099 may represent a risk factor for NSCPO (non-syndromic oral clefts).
      Title: Brazilian multicenter study of association between polymorphisms in CRISPLD2 and JARID2 and non-syndromic oral clefts.
    7. Data suggest that suppression of CRISPLD2 increases the risk of lung inflammation in early life and adulthood.
      Title: CRISPLD2 (LGL1) inhibits proinflammatory mediators in human fetal, adult, and COPD lung fibroblasts and epithelial cells.
    8. Our data suggest that CRISPLD2 may have a unique anti-HMGB1 effect via miRNA155 and play an important role in immune balance.
      Title: HMGB1 induced inflammatory effect is blocked by CRISPLD2 via MiR155 in hepatic fibrogenesis.
    9. CRISPLD2 is a target of progesterone receptor and its expression is decreased in women with endometriosis.
      Title: CRISPLD2 is a target of progesterone receptor and its expression is decreased in women with endometriosis.
    10. Results demonstrate genetic polymorphism of CRISPLD2 gene is associated with an increased risk of non-syndromic cleft lip with or without cleft palate.
      Title: Preliminary evidence of an interaction between the CRISPLD2 gene and non-syndromic cleft lip with or without cleft palate (nsCL/P) in Xinjiang Uyghur population, China.
    Submit: New GeneRIF Correction See all GeneRIFs (22)

    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
    Many sequence variants affecting diversity of adult human height.
    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)

    Interactions

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    Products Interactant Other Gene Complex Source Pubs Description

    General gene information

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    Markers

    Homology

    Clone Names

    • MGC74865, DKFZp434B044

    Gene Ontology Provided by GOA

    Function Evidence Code Pubs
    enables glycosaminoglycan binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    enables heparin binding IEA
    Inferred from Electronic Annotation
    more info
    		  
    Process Evidence Code Pubs
    involved_in extracellular matrix organization IEA
    Inferred from Electronic Annotation
    more info
    		  
    involved_in face morphogenesis IMP
    Inferred from Mutant Phenotype
    more info
    		 PubMed 
    involved_in lung development IEA
    Inferred from Electronic Annotation
    more info
    		  
    Component Evidence Code Pubs
    located_in extracellular exosome HDA PubMed 
    located_in extracellular matrix IEA
    Inferred from Electronic Annotation
    more info
    		  
    located_in extracellular region TAS
    Traceable Author Statement
    more info
    		  
    is_active_in extracellular space IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in ficolin-1-rich granule lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in secretory granule lumen TAS
    Traceable Author Statement
    more info
    		  
    located_in transport vesicle IDA
    Inferred from Direct Assay
    more info
    		  

    General protein information

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    Preferred Names
    cysteine-rich secretory protein LCCL domain-containing 2
    Names
    CRISP-11
    LCCL domain-containing cysteine-rich secretory protein 2
    cysteine-rich secretory protein 11
    late gestation lung 1
    testis secretory sperm-binding protein Li 207a
    trypsin inhibitor

    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_031476.4 → NP_113664.1  cysteine-rich secretory protein LCCL domain-containing 2 precursor

      See identical proteins and their annotated locations for NP_113664.1

      Status: VALIDATED

      Source sequence(s)
      AC025280, AL136861, BQ015624, DA325436, DB095807, DB260709
      Consensus CDS
      CCDS10949.1
      UniProtKB/Swiss-Prot
      D3DUM0, Q6P590, Q6UWH0, Q6UXC6, Q96IB1, Q96K61, Q9H0B8
      UniProtKB/TrEMBL
      A0A140VK80, H3BTI0
      Related
      ENSP00000262424.5, ENST00000262424.10
      Conserved Domains (2) summary
      smart00603
      Location:286 → 370
      LCCL; LCCL domain
      cd05380
      Location:56 → 201
      SCP_euk; SCP_euk: SCP-like extracellular protein domain, as found mainly in eukaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5 from vespid venom. It has been proposed ...

    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_000016.10 Reference GRCh38.p14 Primary Assembly

      Range
      84819985..84909508
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_005256190.2 → XP_005256247.1  cysteine-rich secretory protein LCCL domain-containing 2 isoform X1

      See identical proteins and their annotated locations for XP_005256247.1

      UniProtKB/Swiss-Prot
      D3DUM0, Q6P590, Q6UWH0, Q6UXC6, Q96IB1, Q96K61, Q9H0B8
      UniProtKB/TrEMBL
      A0A140VK80, H3BTI0
      Conserved Domains (2) summary
      smart00603
      Location:286 → 370
      LCCL; LCCL domain
      cd05380
      Location:56 → 201
      SCP_euk; SCP_euk: SCP-like extracellular protein domain, as found mainly in eukaryotes. This family includes plant pathogenesis-related protein 1 (PR-1), CRISPs, mammalian cysteine-rich secretory proteins, and allergen 5 from vespid venom. It has been proposed ...

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060940.1 Alternate T2T-CHM13v2.0

      Range
      90886255..90975767
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054314093.1 → XP_054170068.1  cysteine-rich secretory protein LCCL domain-containing 2 isoform X1

      UniProtKB/TrEMBL
      H3BTI0

    2. XM_054314094.1 → XP_054170069.1  cysteine-rich secretory protein LCCL domain-containing 2 isoform X2

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9H0B8.1 GenPept UniProtKB/Swiss-Prot:Q9H0B8

    Gene LinkOut

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