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    CLIP2 CAP-Gly domain containing linker protein 2 [ Homo sapiens (human) ]

    Gene ID: 7461, updated on 26-Nov-2024

    Summary

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    Official Symbol
    CLIP2provided by HGNC
    Official Full Name
    CAP-Gly domain containing linker protein 2provided by HGNC
    Primary source
    HGNC:HGNC:2586
    See related
    Ensembl:ENSG00000106665 MIM:603432; AllianceGenome:HGNC:2586
    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
    CLIP; CYLN2; WSCR3; WSCR4; WBSCR3; WBSCR4; CLIP-115
    Summary
    The protein encoded by this gene belongs to the family of cytoplasmic linker proteins, which have been proposed to mediate the interaction between specific membranous organelles and microtubules. This protein was found to associate with both microtubules and an organelle called the dendritic lamellar body. This gene is hemizygously deleted in Williams syndrome, a multisystem developmental disorder caused by the deletion of contiguous genes at 7q11.23. Alternative splicing of this gene generates 2 transcript variants. [provided by RefSeq, Jul 2008]
    Expression
    Ubiquitous expression in brain (RPKM 29.5), colon (RPKM 11.1) and 21 other tissues See more
    Orthologs
    mouse all
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    Genomic context

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    See CLIP2 in Genome Data Viewer
    Location:
    7q11.23
    Exon count:
    17
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) 7 NC_000007.14 (74289407..74405935)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) 7 NC_060931.1 (75491680..75608201)
    RS_2024_09 previous assembly GRCh37.p13 (GCF_000001405.25) 7 NC_000007.13 (73703737..73820265)

    Chromosome 7 - NC_000007.14Genomic Context describing neighboring genes Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73667761-73668363 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:73668364-73668966 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:73668967-73669569 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26149 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26150 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26151 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73676953-73677454 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73677455-73677954 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26152 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26153 Neighboring gene replication factor C subunit 2 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26155 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26154 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26156 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26157 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73693216-73693846 Neighboring gene uncharacterized LOC107986742 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73696998-73697628 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26158 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18277 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73704091-73704735 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73704736-73705379 Neighboring gene Sharpr-MPRA regulatory region 1083 Neighboring gene NFE2L2 motif-containing MPRA enhancer 193 Neighboring gene H3K27ac hESC enhancer GRCh37_chr7:73722243-73722881 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73778293-73779164 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73779165-73780034 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73786483-73787481 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73794630-73795130 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73795131-73795631 Neighboring gene Sharpr-MPRA regulatory region 11240 Neighboring gene ReSE screen-validated silencer GRCh37_chr7:73810181-73810370 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73818996-73819860 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73819861-73820723 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18279 Neighboring gene OCT4-NANOG-H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73843950-73844923 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73848492-73849112 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73849734-73850353 Neighboring gene CAGE-defined high expression enhancer upstream of GTF2IRD1 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18280 Neighboring gene ATAC-STARR-seq lymphoblastoid silent region 18281 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26159 Neighboring gene GTF2I repeat domain containing 1 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73892244-73892825 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73892826-73893408 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26160 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26161 Neighboring gene ATAC-STARR-seq lymphoblastoid active region 26162 Neighboring gene H3K27ac-H3K4me1 hESC enhancer GRCh37_chr7:73909445-73910043 Neighboring gene RNA, 5S ribosomal pseudogene 233 Neighboring gene H3K4me1 hESC enhancer GRCh37_chr7:73919312-73919812 Neighboring gene Williams-Beuren syndrome chromosome region 23

    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. Gain of chromosome band 7q11 in papillary thyroid carcinomas of young patients is associated with exposure to low-dose irradiation. Hess J, et al. Proc Natl Acad Sci U S A, 2011 Jun 7. PMID 21606360, Free PMC Article
    2. CLIP2 as radiation biomarker in papillary thyroid carcinoma. Selmansberger M, et al. Oncogene, 2015 Jul 23. PMID 25284583
    3. Dose-dependent expression of CLIP2 in post-Chernobyl papillary thyroid carcinomas. Selmansberger M, et al. Carcinogenesis, 2015 Jul. PMID 25957251, Free PMC Article
    4. Integration of a radiation biomarker into modeling of thyroid carcinogenesis and post-Chernobyl risk assessment. Kaiser JC, et al. Carcinogenesis, 2016 Dec. PMID 27729373, Free PMC Article
    5. CILP-2 is a novel secreted protein and associated with insulin resistance. Wu T, et al. J Mol Cell Biol, 2019 Dec 19. PMID 30896018, Free PMC Article

    See all (41) citations in PubMed

    GeneRIFs: Gene References Into Functions

    What's a GeneRIF?
    1. Clinical, pathologic, and genomic characteristics of two pediatric glioneuronal tumors with a CLIP2::MET fusion.
      Title: Clinical, pathologic, and genomic characteristics of two pediatric glioneuronal tumors with a CLIP2::MET fusion.
    2. Whole exome sequencing identifies three novel gene mutations in patients with the triad of diabetic ketoacidosis, hypertriglyceridemia, and acute pancreatitis.
      Title: Whole exome sequencing identifies three novel gene mutations in patients with the triad of diabetic ketoacidosis, hypertriglyceridemia, and acute pancreatitis.
    3. CILP-2 is a novel secreted protein and demonstrated that circulating CILP-2 levels were elevated in both IGT and nT2DM subjects and associated with IR. CILP-2 overexpression promoted hepatic IR in HFD-fed mice, increased PEPCK expression and suppressed insulin signaling in hepatocytes.
      Title: CILP-2 is a novel secreted protein and associated with insulin resistance.
    4. Cross checking with epidemiological estimates and model validation suggests that CLIP2 is a marker of high precision. CLIP2 leaves an imprint in the epidemiological incidence data which is typical for a driver gene.
      Title: Integration of a radiation biomarker into modeling of thyroid carcinogenesis and post-Chernobyl risk assessment.
    5. CLIP2 protein expression is elevated in papillary thyroid carcinomas from patients exposed to radioiodine fallout compared with a nonexposed control group.
      Title: CLIP2 as radiation biomarker in papillary thyroid carcinoma.
    6. A clear radiation dose-response relationship for the CLIP2 marker expression in post-Chernobyl papillary thyroid carcinomas
      Title: Dose-dependent expression of CLIP2 in post-Chernobyl papillary thyroid carcinomas.
    7. CLIP2 haploinsufficiency by itself does not lead to the physical or cognitive characteristics of the Williams-Beuren syndrome; GTF2IRD1 and GTF2I are the main genes causing the cognitive defects
      Title: The contribution of CLIP2 haploinsufficiency to the clinical manifestations of the Williams-Beuren syndrome.
    8. Data show that gene CLIP2 was specifically overexpressed in the exposed cases.
      Title: Gain of chromosome band 7q11 in papillary thyroid carcinomas of young patients is associated with exposure to low-dose irradiation.
    9. 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.
    Submit: New GeneRIF Correction

    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

    Variation

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    See Variation Viewer (GRCh37.p13)

    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 microtubule binding ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    enables microtubule plus-end binding IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Process Evidence Code Pubs
    involved_in cytoplasmic microtubule organization IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    Component Evidence Code Pubs
    is_active_in cell cortex IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    part_of microtubule associated complex TAS
    Traceable Author Statement
    more info
    		 PubMed 
    is_active_in microtubule plus-end IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  
    located_in microtubule plus-end ISS
    Inferred from Sequence or Structural Similarity
    more info
    		  
    is_active_in nucleus IBA
    Inferred from Biological aspect of Ancestor
    more info
    		  

    General protein information

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    Preferred Names
    CAP-Gly domain-containing linker protein 2
    Names
    Williams-Beuren syndrome chromosome region 3
    Williams-Beuren syndrome chromosome region 4
    cytoplasmic linker 2
    cytoplasmic linker protein 115
    cytoplasmic linker protein 2
    testicular tissue protein Li 40
    williams-Beuren syndrome chromosomal region 3 protein
    williams-Beuren syndrome chromosomal region 4 protein

    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_011830.2 RefSeqGene

      Range
      5002..121530
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. NM_003388.5 → NP_003379.4  CAP-Gly domain-containing linker protein 2 isoform 1

      Status: REVIEWED

      Description
      Transcript Variant: This variant (1) encodes the longer isoform (1).
      Source sequence(s)
      AC005015
      Consensus CDS
      CCDS5569.1
      UniProtKB/Swiss-Prot
      O14527, O43611, Q9UDT6
      UniProtKB/TrEMBL
      A0A140VJG6
      Related
      ENSP00000223398.6, ENST00000223398.11
      Conserved Domains (2) summary
      COG1196
      Location:357 → 971
      Smc; Chromosome segregation ATPase [Cell cycle control, cell division, chromosome partitioning]
      pfam01302
      Location:221 → 285
      CAP_GLY; CAP-Gly domain

    2. NM_032421.3 → NP_115797.2  CAP-Gly domain-containing linker protein 2 isoform 2

      Status: REVIEWED

      Description
      Transcript Variant: This variant (2) lacks an exon within the coding region, as compared to variant 1. Isoform 2 encoded by this variant is thus missing an internal aa fragment as compared to isoform 1.
      Source sequence(s)
      AC005015
      Consensus CDS
      CCDS5570.1
      UniProtKB/TrEMBL
      A7E2F7
      Related
      ENSP00000355151.5, ENST00000361545.9
      Conserved Domains (2) summary
      TIGR02168
      Location:357 → 975
      SMC_prok_B; chromosome segregation protein SMC, common bacterial type
      pfam01302
      Location:221 → 285
      CAP_GLY; CAP-Gly domain

    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_000007.14 Reference GRCh38.p14 Primary Assembly

      Range
      74289407..74405935
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_047420800.1 → XP_047276756.1  CAP-Gly domain-containing linker protein 2 isoform X1

    Alternate T2T-CHM13v2.0

    Genomic

    1. NC_060931.1 Alternate T2T-CHM13v2.0

      Range
      75491680..75608201
      Download
      GenBank, FASTA, Sequence Viewer (Graphics)

    mRNA and Protein(s)

    1. XM_054358938.1 → XP_054214913.1  CAP-Gly domain-containing linker protein 2 isoform X1

    Nucleotide Protein
    Heading Accession and Version
    Protein Accession Links
    GenPept Link UniProtKB Link
    Q9UDT6.1 GenPept UniProtKB/Swiss-Prot:Q9UDT6

    Gene LinkOut

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

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