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

Gene ID: 83716, updated on 2-Nov-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, Nov 2024]
Expression
Broad expression in gall bladder (RPKM 67.9), placenta (RPKM 54.3) and 20 other tissues See more
Orthologs
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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

  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

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