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

Gene ID: 7461, updated on 2-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
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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 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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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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Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

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

Clone Names

  • KIAA0291, MGC11333

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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