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Aliases for CLIP1 Gene

Aliases for CLIP1 Gene

  • CAP-Gly Domain Containing Linker Protein 1 2 3 5
  • Restin (Reed-Steinberg Cell-Expressed Intermediate Filament-Associated Protein) 2 3
  • Cytoplasmic Linker Protein 170 Alpha-2 3 4
  • Cytoplasmic Linker Protein 1 3 4
  • CLIP-170 3 4
  • Restin 2 4
  • CYLN1 3 4
  • RSN 3 4
  • Reed-Sternberg Intermediate Filament-Associated Protein 4
  • CAP-Gly Domain-Containing Linker Protein 1 3
  • Cytoplasmic Linker Protein CLIP-170 3
  • CLIP170 3
  • CLIP 3

External Ids for CLIP1 Gene

Previous HGNC Symbols for CLIP1 Gene

  • RSN

Previous GeneCards Identifiers for CLIP1 Gene

  • GC12M121322
  • GC12M121205
  • GC12M122755
  • GC12M119716

Summaries for CLIP1 Gene

Entrez Gene Summary for CLIP1 Gene

  • The protein encoded by this gene links endocytic vesicles to microtubules. This gene is highly expressed in Reed-Sternberg cells of Hodgkin disease. Several transcript variants encoding different isoforms have been found for this gene. [provided by RefSeq, Oct 2011]

GeneCards Summary for CLIP1 Gene

CLIP1 (CAP-Gly Domain Containing Linker Protein 1) is a Protein Coding gene. Diseases associated with CLIP1 include Autosomal Recessive Non-Syndromic Intellectual Disability and Extratemporal Epilepsy. Among its related pathways are PAK Pathway and Actin Nucleation by ARP-WASP Complex. Gene Ontology (GO) annotations related to this gene include nucleic acid binding and microtubule binding. An important paralog of this gene is CLIP2.

UniProtKB/Swiss-Prot for CLIP1 Gene

  • Binds to the plus end of microtubules and regulates the dynamics of the microtubule cytoskeleton. Promotes microtubule growth and microtubule bundling. Links cytoplasmic vesicles to microtubules and thereby plays an important role in intracellular vesicle trafficking. Plays a role macropinocytosis and endosome trafficking.

Gene Wiki entry for CLIP1 Gene

Additional gene information for CLIP1 Gene

No data available for CIViC summary , Tocris Summary , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for CLIP1 Gene

Genomics for CLIP1 Gene

GeneHancer (GH) Regulatory Elements for CLIP1 Gene

Promoters and enhancers for CLIP1 Gene
GeneHancer (GH) Identifier GH Type GH
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH12I122419 Promoter/Enhancer 2.6 EPDnew FANTOM5 Ensembl ENCODE dbSUPER 561.6 +0.5 523 4.3 PKNOX1 FOXA2 ARID4B SIN3A FEZF1 SLC30A9 ZNF766 ZNF143 REST ZNF592 CLIP1 PSMD9 KNTC1 ZCCHC8 ENSG00000252192 RSRC2 DIABLO PITPNM2 ARL6IP4 CCDC62
GH12I122398 Promoter/Enhancer 2 EPDnew Ensembl ENCODE dbSUPER 561.8 +21.3 21263 6 PKNOX1 SMAD1 FOXA2 ARNT ARID4B NEUROD1 SIN3A FEZF1 DMAP1 YY1 CLIP1 PSMD9 ZCCHC8 KNTC1 RSRC2 ENSG00000252192 ENSG00000272849 CCDC62 MLXIP CLIP1-AS1
GH12I122365 Enhancer 1.5 Ensembl ENCODE dbSUPER 23.4 +54.7 54747 4.8 PKNOX1 FOXA2 ARNT ARID4B SIN3A FEZF1 DMAP1 ZNF2 ZNF766 ZNF213 CLIP1 ZCCHC8 RSRC2 ENSG00000235423 ANAPC5 SETD1B DIABLO ENSG00000252192 ENSG00000256861 VPS33A
GH12I122394 Enhancer 1.2 Ensembl ENCODE dbSUPER 19.6 +27.2 27216 1.3 ATF1 ZBTB21 JUN INSM2 CEBPG YY1 ZNF335 CTBP1 GATA3 ZNF366 CLIP1-AS1 CLIP1 RPL21P1
GH12I122404 Enhancer 1.4 Ensembl ENCODE dbSUPER 11.8 +16.1 16139 3.1 ATF1 FOXA2 MLX ARID4B SIN3A DMAP1 ZNF48 YY1 ATF7 RXRA CLIP1 ENSG00000252192 CCDC62 CLIP1-AS1
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data dump

GeneHancers around CLIP1 on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the CLIP1 gene promoter:

Genomic Locations for CLIP1 Gene

Genomic Locations for CLIP1 Gene
151,201 bases
Minus strand

Genomic View for CLIP1 Gene

Genes around CLIP1 on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
CLIP1 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for CLIP1 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for CLIP1 Gene

Proteins for CLIP1 Gene

  • Protein details for CLIP1 Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    Recommended name:
    CAP-Gly domain-containing linker protein 1
    Protein Accession:
    Secondary Accessions:
    • A0AVD3
    • Q17RS4
    • Q29RG0

    Protein attributes for CLIP1 Gene

    1438 amino acids
    Molecular mass:
    162246 Da
    Quaternary structure:
    • Interacts with MTOR; phosphorylates and regulates CLIP1 (PubMed:12231510). Interacts (via CAP-Gly domains) with tubulin (PubMed:17563362, PubMed:17889670). Interacts with SLAIN2 (PubMed:21646404). Interacts (via zinc finger) with DCTN1 (PubMed:17828275, PubMed:20679239). Interacts with TUBA1B, MAPRE1 and MAPRE3 (PubMed:17563362). Binds preferentially to tyrosinated microtubules, and only marginally to detyrosinated microtubules (By similarity).

    Three dimensional structures from OCA and Proteopedia for CLIP1 Gene

    Alternative splice isoforms for CLIP1 Gene


neXtProt entry for CLIP1 Gene

Post-translational modifications for CLIP1 Gene

  • Phosphorylated. Phosphorylation induces conformational changes by increasing the affinity of the N-terminus for C-terminus, resulting in inhibition of its function thus decreasing its binding to microtubules and DCTN1. Exhibits a folded, autoinhibited conformation when phosphorylated and an open conformation when dephosphorylated with increased binding affinity to microtubules and DCTN1. Phosphorylation regulates its recruitment to tyrosinated microtubules and the recruitment of vesicular cargo to microtubules in neurons (By similarity). Phosphorylation by MTOR may positively regulate CLIP1 association with microtubules (PubMed:12231510).
  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for CLIP1 Gene

Domains & Families for CLIP1 Gene

Gene Families for CLIP1 Gene

Human Protein Atlas (HPA):
  • Cancer-related genes
  • Plasma proteins
  • Predicted intracellular proteins

Protein Domains for CLIP1 Gene

Graphical View of Domain Structure for InterPro Entry



  • Intramolecular interaction between the zinc finger domain and the CAP-Gly domains may inhibit interaction with tubulin.
  • Intramolecular interaction between the zinc finger domain and the CAP-Gly domains may inhibit interaction with tubulin.
genes like me logo Genes that share domains with CLIP1: view

Function for CLIP1 Gene

Molecular function for CLIP1 Gene

UniProtKB/Swiss-Prot Function:
Binds to the plus end of microtubules and regulates the dynamics of the microtubule cytoskeleton. Promotes microtubule growth and microtubule bundling. Links cytoplasmic vesicles to microtubules and thereby plays an important role in intracellular vesicle trafficking. Plays a role macropinocytosis and endosome trafficking.

Phenotypes From GWAS Catalog for CLIP1 Gene

Gene Ontology (GO) - Molecular Function for CLIP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0003676 nucleic acid binding IEA --
GO:0005515 protein binding IPI 11940666
GO:0008017 microtubule binding IEA,IDA 17889670
GO:0008270 zinc ion binding IDA 17828275
GO:0015631 tubulin binding IDA 17889670
genes like me logo Genes that share ontologies with CLIP1: view
genes like me logo Genes that share phenotypes with CLIP1: view

Animal Models for CLIP1 Gene

MGI Knock Outs for CLIP1:

Animal Model Products

miRNA for CLIP1 Gene

miRTarBase miRNAs that target CLIP1

Clone Products

  • Addgene plasmids for CLIP1

No data available for Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Transcription Factor Targets and HOMER Transcription for CLIP1 Gene

Localization for CLIP1 Gene

Subcellular locations from UniProtKB/Swiss-Prot for CLIP1 Gene

Cytoplasm. Cytoplasm, cytoskeleton. Cytoplasmic vesicle membrane; Peripheral membrane protein; Cytoplasmic side. Cell projection, ruffle. Note=Localizes to microtubule plus ends (PubMed:21646404, PubMed:17889670). Localizes preferentially to the ends of tyrosinated microtubules (By similarity). Accumulates in plasma membrane regions with ruffling and protrusions. Associates with the membranes of intermediate macropinocytic vesicles (PubMed:12433698). {ECO:0000250 UniProtKB:Q922J3, ECO:0000269 PubMed:12433698, ECO:0000269 PubMed:17889670, ECO:0000269 PubMed:21646404}.

Subcellular locations from

Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for CLIP1 gene
Compartment Confidence
cytoskeleton 5
cytosol 5
endosome 5
nucleus 4
golgi apparatus 1

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (3)
  • Microtubule ends (3)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for CLIP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000776 kinetochore TAS 15928712
GO:0001726 ruffle IEA --
GO:0005635 nuclear envelope IEA --
GO:0005737 cytoplasm IEA --
GO:0005768 endosome TAS 1356075
genes like me logo Genes that share ontologies with CLIP1: view

Pathways & Interactions for CLIP1 Gene

genes like me logo Genes that share pathways with CLIP1: view

Pathways by source for CLIP1 Gene

SIGNOR curated interactions for CLIP1 Gene

Is activated by:
Is inactivated by:

Gene Ontology (GO) - Biological Process for CLIP1 Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0000278 mitotic cell cycle TAS 15928712
GO:0001578 microtubule bundle formation IMP 17889670
GO:0006810 transport IEA --
GO:0007062 sister chromatid cohesion TAS --
GO:0031116 positive regulation of microtubule polymerization IMP 15262990
genes like me logo Genes that share ontologies with CLIP1: view

Drugs & Compounds for CLIP1 Gene

(5) Drugs for CLIP1 Gene - From: Novoseek

Name Status Disease Links Group Role Mechanism of Action Clinical Trials

(2) Additional Compounds for CLIP1 Gene - From: Novoseek

Name Synonyms Role CAS Number PubChem IDs PubMed IDs
genes like me logo Genes that share compounds with CLIP1: view

Transcripts for CLIP1 Gene

Unigene Clusters for CLIP1 Gene

CAP-GLY domain containing linker protein 1:
Representative Sequences:

Clone Products

  • Addgene plasmids for CLIP1

Alternative Splicing Database (ASD) splice patterns (SP) for CLIP1 Gene

ExUns: 1 ^ 2 ^ 3 ^ 4 ^ 5a · 5b ^ 6a · 6b ^ 7 ^ 8 ^ 9 ^ 10 ^ 11a · 11b · 11c ^ 12 ^ 13 ^ 14 ^ 15a · 15b ^ 16a · 16b ^ 17a · 17b ^ 18 ^ 19 ^
SP1: - - - -
SP2: - - - - -
SP3: - - -
SP6: - -

ExUns: 20 ^ 21 ^ 22a · 22b ^ 23 ^ 24a · 24b ^ 25 ^ 26a · 26b ^ 27a · 27b · 27c · 27d
SP1: - - -
SP2: - - -
SP4: - - -

Relevant External Links for CLIP1 Gene

GeneLoc Exon Structure for
ECgene alternative splicing isoforms for

Expression for CLIP1 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for CLIP1 Gene

mRNA expression in embryonic tissues and stem cells from LifeMap Discovery

mRNA differential expression in normal tissues according to GTEx for CLIP1 Gene

This gene is overexpressed in Muscle - Skeletal (x8.4).

Protein differential expression in normal tissues from HIPED for CLIP1 Gene

This gene is overexpressed in Peripheral blood mononuclear cells (15.1).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB, PaxDb, MaxQB, and MOPED for CLIP1 Gene

Protein tissue co-expression partners for CLIP1 Gene

- Elite partner

NURSA nuclear receptor signaling pathways regulating expression of CLIP1 Gene:


SOURCE GeneReport for Unigene cluster for CLIP1 Gene:


mRNA Expression by UniProt/SwissProt for CLIP1 Gene:

Tissue specificity: Detected in dendritic cells (at protein level). Highly expressed in the Reed-Sternberg cells of Hodgkin disease.

Evidence on tissue expression from TISSUES for CLIP1 Gene

  • Blood(4.4)
  • Intestine(4.3)
  • Liver(4.3)
  • Nervous system(3.9)
  • Muscle(2.8)
  • Heart(2.2)
  • Kidney(2.2)

Phenotype-based relationships between genes and organs from Gene ORGANizer for CLIP1 Gene

Germ Layers:
  • ectoderm
  • endoderm
  • mesoderm
  • cardiovascular
  • integumentary
  • nervous
  • respiratory
  • skeletal muscle
  • skeleton
Head and neck:
  • brain
  • cerebellum
  • cheek
  • chin
  • cranial nerve
  • ear
  • eye
  • eyelid
  • face
  • forehead
  • head
  • jaw
  • lip
  • mandible
  • maxilla
  • mouth
  • neck
  • nose
  • outer ear
  • pharynx
  • skull
  • tooth
  • chest wall
  • heart
  • abdominal wall
  • foot
  • lower limb
  • blood vessel
  • hair
  • peripheral nerve
  • peripheral nervous system
  • skin
  • spinal column
  • spinal cord
genes like me logo Genes that share expression patterns with CLIP1: view

Orthologs for CLIP1 Gene

This gene was present in the common ancestor of animals.

Orthologs for CLIP1 Gene

Organism Taxonomy Gene Similarity Type Details
(Pan troglodytes)
Mammalia CLIP1 33 34
  • 98.97 (n)
(Ornithorhynchus anatinus)
Mammalia -- 34
  • 91 (a)
-- 34
  • 81 (a)
(Canis familiaris)
Mammalia CLIP1 33 34
  • 89.7 (n)
(Bos Taurus)
Mammalia CLIP1 33 34
  • 89.39 (n)
(Mus musculus)
Mammalia Clip1 33 16 34
  • 87.11 (n)
(Monodelphis domestica)
Mammalia CLIP1 34
  • 84 (a)
(Gallus gallus)
Aves CLIP1 33 34
  • 75.1 (n)
(Anolis carolinensis)
Reptilia CLIP1 34
  • 70 (a)
tropical clawed frog
(Silurana tropicalis)
Amphibia clip1 33
  • 63.72 (n)
(Danio rerio)
Actinopterygii CLIP1 (2 of 2) 34
  • 60 (a)
clip1a 33 34
  • 55.52 (n)
fruit fly
(Drosophila melanogaster)
Insecta CLIP-190 34
  • 23 (a)
sea squirt
(Ciona savignyi)
Ascidiacea -- 34
  • 29 (a)
Species where no ortholog for CLIP1 was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya gossypii)
  • Actinobacteria (Mycobacterium tuberculosis)
  • African clawed frog (Xenopus laevis)
  • African malaria mosquito (Anopheles gambiae)
  • Alicante grape (Vitis vinifera)
  • alpha proteobacteria (Wolbachia pipientis)
  • amoeba (Dictyostelium discoideum)
  • Archea (Pyrococcus horikoshii)
  • baker's yeast (Saccharomyces cerevisiae)
  • barley (Hordeum vulgare)
  • beta proteobacteria (Neisseria meningitidis)
  • bread mold (Neurospora crassa)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • green algae (Chlamydomonas reinhardtii)
  • honey bee (Apis mellifera)
  • K. lactis yeast (Kluyveromyces lactis)
  • loblloly pine (Pinus taeda)
  • malaria parasite (Plasmodium falciparum)
  • medicago trunc (Medicago Truncatula)
  • moss (Physcomitrella patens)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rat (Rattus norvegicus)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea urchin (Strongylocentrotus purpuratus)
  • sorghum (Sorghum bicolor)
  • soybean (Glycine max)
  • stem rust fungus (Puccinia graminis)
  • sugarcane (Saccharum officinarum)
  • thale cress (Arabidopsis thaliana)
  • tomato (Lycopersicon esculentum)
  • toxoplasmosis (Toxoplasma gondii)
  • Trichoplax (Trichoplax adhaerens)
  • wheat (Triticum aestivum)
  • worm (Caenorhabditis elegans)

Evolution for CLIP1 Gene

Gene Tree for CLIP1 (if available)
Gene Tree for CLIP1 (if available)

Paralogs for CLIP1 Gene

Paralogs for CLIP1 Gene

genes like me logo Genes that share paralogs with CLIP1: view

Variants for CLIP1 Gene

Sequence variations from dbSNP and Humsavar for CLIP1 Gene

SNP ID Clin Chr 12 pos Variation AA Info Type
VAR_036446 A breast cancer sample p.Met1213Ile
rs137857498 likely-benign, not specified 122,336,647(-) T/C coding_sequence_variant, intron_variant, synonymous_variant
rs138064731 likely-benign, not specified 122,355,163(-) C/A/G/T coding_sequence_variant, synonymous_variant
rs141383610 likely-benign, not specified 122,377,749(-) G/A coding_sequence_variant, synonymous_variant
rs549426099 likely-benign, not specified 122,341,590(-) A/G coding_sequence_variant, synonymous_variant

Structural Variations from Database of Genomic Variants (DGV) for CLIP1 Gene

Variant ID Type Subtype PubMed ID
dgv324e199 CNV deletion 23128226
esv2672169 CNV deletion 23128226
esv3630973 CNV gain 21293372
esv3630974 CNV loss 21293372
esv3630975 CNV loss 21293372
nsv1138177 CNV deletion 24896259
nsv1138178 CNV deletion 24896259
nsv476982 CNV novel sequence insertion 20440878
nsv973131 CNV duplication 23825009

Variation tolerance for CLIP1 Gene

Residual Variation Intolerance Score: 4.49% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 19.86; 98.97% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for CLIP1 Gene

Human Gene Mutation Database (HGMD)
SNPedia medical, phenotypic, and genealogical associations of SNPs for

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for CLIP1 Gene

Disorders for CLIP1 Gene

MalaCards: The human disease database

(5) MalaCards diseases for CLIP1 Gene - From: HGMD, Orphanet, DISEASES, and GeneCards

- elite association - COSMIC cancer census association via MalaCards
Search CLIP1 in MalaCards View complete list of genes associated with diseases

Additional Disease Information for CLIP1

genes like me logo Genes that share disorders with CLIP1: view

No data available for UniProtKB/Swiss-Prot and Genatlas for CLIP1 Gene

Publications for CLIP1 Gene

  1. Structural basis for tubulin recognition by cytoplasmic linker protein 170 and its autoinhibition. (PMID: 17563362) Mishima M … Hakoshima T (Proceedings of the National Academy of Sciences of the United States of America 2007) 3 4 22 58
  2. Structure-function relationship of CAP-Gly domains. (PMID: 17828277) Weisbrich A … Steinmetz MO (Nature structural & molecular biology 2007) 3 4 22 58
  3. The FKBP12-rapamycin-associated protein (FRAP) is a CLIP-170 kinase. (PMID: 12231510) Choi JH … Zheng XF (EMBO reports 2002) 3 4 22 58
  4. Localization of the gene (RSN) coding for restin, a marker for Reed-Sternberg cells in Hodgkin's disease, to human chromosome band 12q24.3 and YAC cloning of the locus. (PMID: 8222754) Hilliker C … Van den Berghe H (Cytogenetics and cell genetics 1994) 2 3 22 58
  5. SLAIN2 links microtubule plus end-tracking proteins and controls microtubule growth in interphase. (PMID: 21646404) van der Vaart B … Akhmanova A (The Journal of cell biology 2011) 3 4 58

Products for CLIP1 Gene

  • Addgene plasmids for CLIP1

Sources for CLIP1 Gene

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