CLIP3

gene
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Also known as CLIPR-59RSNL1

Summary

CLIP3 (CAP-Gly domain containing linker protein 3, HGNC:24314) is a protein-coding gene on chromosome 19q13.12, encoding CAP-Gly domain-containing linker protein 3 (Q96DZ5). Functions as a cytoplasmic linker protein.

This gene encodes a member of the cytoplasmic linker protein 170 family. Members of this protein family contain a cytoskeleton-associated protein glycine-rich domain and mediate the interaction of microtubules with cellular organelles. The encoded protein plays a role in T cell apoptosis by facilitating the association of tubulin and the lipid raft ganglioside GD3. The encoded protein also functions as a scaffold protein mediating membrane localization of phosphorylated protein kinase B. Alternatively spliced transcript variants have been observed for this gene.

Source: NCBI Gene 25999 — RefSeq curated summary.

At a glance

  • Clinical variants (ClinVar): 77 total
  • MANE Select transcript: NM_015526

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:24314
Approved symbolCLIP3
NameCAP-Gly domain containing linker protein 3
Location19q13.12
Locus typegene with protein product
StatusApproved
AliasesCLIPR-59, RSNL1
Ensembl geneENSG00000105270
Ensembl biotypeprotein_coding
OMIM607382
Entrez25999

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 7 protein_coding, 2 retained_intron

ENST00000360535, ENST00000585466, ENST00000586457, ENST00000590559, ENST00000592017, ENST00000593074, ENST00000904679, ENST00000904680, ENST00000923666

RefSeq mRNA: 2 — MANE Select: NM_015526 NM_001199570, NM_015526

CCDS: CCDS12486

Canonical transcript exons

ENST00000360535 — 14 exons

ExonStartEnd
ENSE000010573483601917136019306
ENSE000010573513601889836019026
ENSE000011514123601690736016979
ENSE000011514183601738636017450
ENSE000011514253601765536017778
ENSE000011514323601784836017991
ENSE000011514513602614736026265
ENSE000011514573602658636026747
ENSE000012659003602439636024632
ENSE000014301683601466036016212
ENSE000025023993602713236027271
ENSE000026959343603219236032415
ENSE000029594853603272436032873
ENSE000037892883602695236027045

Expression profiles

Bgee: expression breadth ubiquitous, 231 present calls, max score 99.08.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 31.7782 / max 990.3994, expressed in 1244 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter IDTPM avgSamples expressed
18064431.56541244
1806430.164969
1806420.047914

Top tissues by expression

279 total, by Bgee expression score (0-100, higher = more expressed):

TissueAnatomy IDExpression scoreQuality
cortical plateUBERON:000534399.08gold quality
ganglionic eminenceUBERON:000402398.99gold quality
prefrontal cortexUBERON:000045198.94gold quality
lateral nuclear group of thalamusUBERON:000273698.89gold quality
right hemisphere of cerebellumUBERON:001489098.89gold quality
substantia nigra pars reticulataUBERON:000196698.87gold quality
cerebellar hemisphereUBERON:000224598.86gold quality
cerebellar cortexUBERON:000212998.82gold quality
Brodmann (1909) area 46UBERON:000648398.82gold quality
right frontal lobeUBERON:000281098.80gold quality
substantia nigra pars compactaUBERON:000196598.78gold quality
entorhinal cortexUBERON:000272898.78gold quality
postcentral gyrusUBERON:000258198.77gold quality
cerebellumUBERON:000203798.76gold quality
parietal lobeUBERON:000187298.72gold quality
frontal cortexUBERON:000187098.68gold quality
ventricular zoneUBERON:000305398.66gold quality
dorsolateral prefrontal cortexUBERON:000983498.56gold quality
neocortexUBERON:000195098.47gold quality
lateral globus pallidusUBERON:000247698.35gold quality
temporal lobeUBERON:000187198.34gold quality
Brodmann (1909) area 9UBERON:001354098.34gold quality
cerebral cortexUBERON:000095698.33gold quality
amygdalaUBERON:000187698.17gold quality
superior frontal gyrusUBERON:000266198.08gold quality
cingulate cortexUBERON:000302798.08gold quality
anterior cingulate cortexUBERON:000983598.07gold quality
superior vestibular nucleusUBERON:000722798.05gold quality
hypothalamusUBERON:000189898.03gold quality
ponsUBERON:000098897.98gold quality

Single-cell (SCXA)

Detected in 6 experiment(s), a significant marker in 3.

ExperimentMarker?Max mean expression
E-GEOD-84465yes22.73
E-ANND-3yes9.10
E-GEOD-93593yes6.89
E-MTAB-7037no34.47
E-CURD-112no2.44
E-MTAB-9543no2.43

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

120 targeting CLIP3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNAMax scoreAvg scoremiRNA target_count
HSA-MIR-4283100.0066.422097
HSA-MIR-450A-1-3P100.0069.331837
HSA-MIR-6740-5P100.0065.64932
HSA-MIR-449A99.9971.051776
HSA-MIR-806899.9873.852376
HSA-MIR-3688-3P99.9772.022834
HSA-MIR-449B-5P99.9770.261580
HSA-MIR-60799.9773.625593
HSA-MIR-211099.9666.681930
HSA-MIR-6825-5P99.9669.813431
HSA-MIR-6753-3P99.9366.57637
HSA-MIR-7107-3P99.9366.73627
HSA-MIR-449299.8768.253611
HSA-MIR-6857-5P99.8765.32985
HSA-MIR-444799.8567.812900
HSA-MIR-130B-5P99.8368.501888
HSA-MIR-684499.8270.692423
HSA-MIR-7110-5P99.8067.841712
HSA-MIR-6842-5P99.8067.541587
HSA-MIR-4659A-3P99.8072.624248
HSA-MIR-4659B-3P99.8072.624248
HSA-MIR-3913-5P99.7867.26968
HSA-MIR-3150A-3P99.7664.441640
HSA-MIR-6763-5P99.7664.681767
HSA-MIR-6885-3P99.7570.363187
HSA-MIR-58699.6570.402051
HSA-MIR-570099.6469.882280
HSA-MIR-651-5P99.6468.491104
HSA-MIR-6861-3P99.6068.46444
HSA-MIR-6752-5P99.5967.321243

Literature-anchored findings (GeneRIF, showing 8)

  • play an important role in membrane-microtubule interactions. (PMID:11854307)
  • CLIPR-59 prevents microtubule-raft interactions (PMID:15262990)
  • CLIPR-59 may act as a typical chaperone, allowing a prompt interaction between tubulin and the raft component GD3 during cell apoptosis triggered by CD95/Fas (PMID:20052288)
  • CLIPR-59 modulates ubiquitination of RIP1, resulting in the formation of Complex-II and thus promoting Caspase-8 activation to induce apoptosis by TNF-alpha. (PMID:22297296)
  • DHHC17 is a ClipR-59 palmitoyltransferase that modulates ClipR-59 plasma membrane binding. (PMID:24001771)
  • CLIPR-59 interacts with Spy1 resulting in its decreased association with a de-ubiquitinating enzyme in glioblastoma cells. (PMID:26017671)
  • this study indicates that inhibition of miRNA-593-3p by insulin promotes glucose metabolism through the regulation of Slc38a1 and CLIP3 expression, and provides a new insight into the role and mechanism of insulin-induced glycolysis. (PMID:27613819)
  • Downregulated CLIP3 induces radioresistance by enhancing stemness and glycolytic flux in glioblastoma. (PMID:34488821)

Cross-species orthologs

3 orthologs

OrganismSymbolGene ID
danio_rerioclip3ENSDARG00000054456
mus_musculusClip3ENSMUSG00000013921
rattus_norvegicusClip3ENSRNOG00000050104

Paralogs (4): CLIP2 (ENSG00000106665), CLIP4 (ENSG00000115295), CLIP1 (ENSG00000130779), DCTN1 (ENSG00000204843)

Protein

Protein identifiers

CAP-Gly domain-containing linker protein 3Q96DZ5 (reviewed: Q96DZ5)

Alternative names: Cytoplasmic linker protein 170-related 59 kDa protein

All UniProt accessions (2): Q96DZ5, K7ESF3

UniProt curated annotations — full annotation on UniProt →

Function. Functions as a cytoplasmic linker protein. Involved in TGN-endosome dynamics. May modulate the cellular compartmentalization of AKT kinase family and promote its cell membrane localization, thereby playing a role in glucose transport in adipocytes.

Subunit / interactions. Homodimer. Interacts with AKT1 and AKT2; when AKT1 and AKT2 are phosphorylated and activated, affinity is higher for AKT2. Interacts with ZDHHC13 (via ANK repeats). Interacts with ZDHHC17 (via ANK repeats).

Subcellular location. Cell membrane. Cytoplasm. Golgi apparatus. Golgi stack.

Post-translational modifications. Palmitoylation by ZDHHC17 regulates association with the plasma membrane.

Domain organisation. Microtubule association is inhibited by the ANK repeats and the Golgi localization region (GoLD).

Miscellaneous. The N-terminal half is dispensable for proper Golgi targeting, whereas the GoLD region is required.

RefSeq proteins (2): NP_001186499, NP_056341* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR000938CAP-Gly_domainDomain
IPR002110Ankyrin_rptRepeat
IPR036770Ankyrin_rpt-contain_sfHomologous_superfamily
IPR036859CAP-Gly_dom_sfHomologous_superfamily

Pfam: PF01302, PF12796

UniProt features (31 total): strand 8, compositionally biased region 4, repeat 3, region of interest 3, modified residue 2, lipid moiety-binding region 2, mutagenesis site 2, helix 2, domain 2, chain 1, sequence variant 1, turn 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2CP0SOLUTION NMR

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q96DZ5-F174.930.43

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (4): 374, 401, 534, 535

Mutagenesis-validated functional residues (2):

PositionPhenotype
509inhibits interaction with zdhhc13 and zdhhc17.
534–535strongly reduced plasma membrane association and decrease in the levels of akt at the plasma membrane.

Function

Pathways and Gene Ontology

Reactome pathways

1 pathways

IDPathway
R-HSA-5357905Regulation of TNFR1 signaling

MSigDB gene sets: 273 (showing top): GCACCTT_MIR18A_MIR18B, VERHAAK_AML_WITH_NPM1_MUTATED_DN, GOBP_NEGATIVE_REGULATION_OF_PROTEIN_CONTAINING_COMPLEX_ASSEMBLY, GNF2_RTN1, GCM_MAP4K4, GOBP_CARBOHYDRATE_TRANSPORT, GOBP_REGULATION_OF_PROTEIN_POLYMERIZATION, GOBP_CYTOPLASMIC_MICROTUBULE_ORGANIZATION, GOBP_POSITIVE_REGULATION_OF_ENDOCYTOSIS, YAGI_AML_WITH_INV_16_TRANSLOCATION, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, TGCGCANK_UNKNOWN, GOBP_REGULATION_OF_PHOSPHORYLATION, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_LIPOPROTEIN_METABOLIC_PROCESS

GO Biological Process (11): positive regulation of protein phosphorylation (GO:0001934), positive regulation of D-glucose transmembrane transport (GO:0010828), peptidyl-L-cysteine S-palmitoylation (GO:0018230), negative regulation of microtubule polymerization (GO:0031115), cytoplasmic microtubule organization (GO:0031122), positive regulation of apoptotic process (GO:0043065), membrane biogenesis (GO:0044091), fat cell differentiation (GO:0045444), positive regulation of endocytosis (GO:0045807), protein transport along microtubule (GO:0098840), positive regulation of protein localization to plasma membrane (GO:1903078)

GO Molecular Function (4): microtubule binding (GO:0008017), ganglioside binding (GO:0035594), microtubule plus-end binding (GO:0051010), protein binding (GO:0005515)

GO Cellular Component (14): nucleus (GO:0005634), Golgi stack (GO:0005795), trans-Golgi network (GO:0005802), cytosol (GO:0005829), plasma membrane (GO:0005886), cell cortex (GO:0005938), early endosome membrane (GO:0031901), trans-Golgi network membrane (GO:0032588), microtubule plus-end (GO:0035371), membrane raft (GO:0045121), recycling endosome membrane (GO:0055038), cytoplasm (GO:0005737), Golgi apparatus (GO:0005794), membrane (GO:0016020)

Reactome top-level categories

Rollup of top-1 pathways:

CategoryPathways
TNF signaling1

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cytoplasm3
cellular anatomical structure3
intracellular membrane-bounded organelle2
Golgi apparatus subcompartment2
cell periphery2
endosome membrane2
regulation of protein phosphorylation1
protein phosphorylation1
positive regulation of protein modification process1
positive regulation of phosphorylation1
regulation of D-glucose transmembrane transport1
positive regulation of transmembrane transport1
D-glucose transmembrane transport1
peptidyl-S-diacylglycerol-L-cysteine biosynthetic process from peptidyl-cysteine1
protein palmitoylation1
negative regulation of microtubule polymerization or depolymerization1
regulation of microtubule polymerization1
negative regulation of protein polymerization1
microtubule polymerization1
negative regulation of supramolecular fiber organization1
microtubule cytoskeleton organization1
supramolecular fiber organization1
apoptotic process1
regulation of apoptotic process1
positive regulation of programmed cell death1
cellular component biogenesis1
cell differentiation1
endocytosis1
regulation of endocytosis1
positive regulation of transport1
positive regulation of cellular component organization1
intracellular protein transport1
transport along microtubule1
microtubule-based protein transport1
protein localization to plasma membrane1
regulation of protein localization to plasma membrane1
positive regulation of protein localization to cell periphery1
positive regulation of protein localization to membrane1
tubulin binding1
glycosphingolipid binding1

Protein interactions and networks

STRING

1133 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CLIP3ANK1P16157518
CLIP3ANK3Q12955511
CLIP3ANK2Q01484510
CLIP3ZDHHC17Q8IUH5505
CLIP3TOR1AO14656475
CLIP3ZDHHC13Q8IUH4473
CLIP3MALRD1Q5VYJ5462
CLIP3CHST8Q9H2A9443
CLIP3ZBTB7CA1YPR0443
CLIP3ZDHHC22Q8N966436
CLIP3TTC38Q5R3I4432
CLIP3PHKBQ93100426
CLIP3TBC1D4O60343416
CLIP3PACSIN1Q9BY11409
CLIP3PIP5K1AQ99755407

IntAct

29 interactions, top by confidence:

ABTypeScore
GOLGA2CLIP3psi-mi:“MI:0915”(physical association)0.560
CLIP3CEP83psi-mi:“MI:0915”(physical association)0.560
TLE5CLIP3psi-mi:“MI:0915”(physical association)0.560
GRNCLIP3psi-mi:“MI:0915”(physical association)0.560
CLIP3HSPB1psi-mi:“MI:0915”(physical association)0.560
CLIP3WFS1psi-mi:“MI:0915”(physical association)0.560
CLIP3KIF1Bpsi-mi:“MI:0915”(physical association)0.560
RNF11CLIP3psi-mi:“MI:0915”(physical association)0.560
PB2psi-mi:“MI:0914”(association)0.350
DLK1PLPP3psi-mi:“MI:0914”(association)0.350
MICBLGALS8psi-mi:“MI:0914”(association)0.350
FMR1CLIP3psi-mi:“MI:0915”(physical association)0.000
CLIP3GOLGA2psi-mi:“MI:0915”(physical association)0.000
CEP83CLIP3psi-mi:“MI:0915”(physical association)0.000
TLE5CLIP3psi-mi:“MI:0915”(physical association)0.000

BioGRID (23): AKT1 (Affinity Capture-Western), AKT2 (Affinity Capture-Western), CLIP3 (Affinity Capture-Western), CLIP3 (Affinity Capture-Western), AKT2 (Reconstituted Complex), AKT1 (Reconstituted Complex), SPDYA (Affinity Capture-Western), CLIP3 (Affinity Capture-Western), CLIP3 (Affinity Capture-Western), CYLD (Affinity Capture-Western), CLIP3 (Biochemical Activity), CLIP3 (Two-hybrid), GOLGA2 (Two-hybrid), CEP83 (Two-hybrid), CLIP3 (Affinity Capture-RNA)

ESM2 similar proteins: A0A0D1E2P6, A0A0D2XVZ5, A0A0P0VG31, A0A0P1AAU8, A0A287B8J2, A2WYG9, A4QP73, B9EHT4, B9F2Y7, D0NCC1, J9VKM5, O08788, O59739, P0C7L7, P0CP26, P0CP27, P14725, P28023, P39742, P82874, P92792, Q10MW6, Q13217, Q14203, Q149L6, Q27968, Q28I38, Q54M21, Q54NS3, Q58DR2, Q5JJI4, Q5JNB5, Q5R686, Q5R6H3, Q5ZI13, Q6PCJ1, Q6YUL8, Q7ZXQ8, Q8TBM8, Q91YW3

Diamond homologs: A0A287B8J2, B9EHT4, O08788, O42184, O42667, O55156, P28023, P30622, P33420, P35458, Q10235, Q14203, Q20728, Q54Z01, Q5E951, Q5R686, Q5U243, Q66HD5, Q6PCJ1, Q8CI96, Q8N3C7, Q922J3, Q96DZ5, Q99426, Q9D1E6, Q9JK25, Q9NQT8, Q9UDT6, Q9VJE5, Q9Z0H8, E9Q309, P13496, P34531, Q01397, Q15813, Q32KS0, Q55CN0, Q5FVQ9, Q5RBD9, Q5U378

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

77 variants total. Per-class counts are floors (≥ shown; pagination cap):

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance64
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1524 predictions. Top by Δscore:

VariantEffectΔscore
19:36016210:AACCT:Aacceptor_loss1.0000
19:36016212:CCT:Cacceptor_loss1.0000
19:36016213:C:CGacceptor_loss1.0000
19:36016214:T:Aacceptor_loss1.0000
19:36016975:CGTCA:Cacceptor_gain1.0000
19:36016977:TCA:Tacceptor_gain1.0000
19:36016978:CA:Cacceptor_gain1.0000
19:36016978:CAC:Cacceptor_gain1.0000
19:36016978:CACT:Cacceptor_loss1.0000
19:36016979:AC:Aacceptor_loss1.0000
19:36016980:C:CCacceptor_gain1.0000
19:36016980:C:CGacceptor_loss1.0000
19:36016981:T:Cacceptor_loss1.0000
19:36017380:A:Cdonor_gain1.0000
19:36017381:CTCA:Cdonor_gain1.0000
19:36017382:TCA:Tdonor_loss1.0000
19:36017383:CA:Cdonor_loss1.0000
19:36017384:A:ACdonor_gain1.0000
19:36017385:C:CTdonor_gain1.0000
19:36017385:CT:Cdonor_gain1.0000
19:36017385:CTTG:Cdonor_gain1.0000
19:36017385:CTTGT:Cdonor_gain1.0000
19:36017386:TTGT:Tdonor_gain1.0000
19:36017387:TGTC:Tdonor_gain1.0000
19:36017446:CAATC:Cacceptor_gain1.0000
19:36017447:AATC:Aacceptor_gain1.0000
19:36017448:ATC:Aacceptor_gain1.0000
19:36017448:ATCC:Aacceptor_loss1.0000
19:36017449:TC:Tacceptor_gain1.0000
19:36017449:TCC:Tacceptor_loss1.0000

AlphaMissense

3542 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
19:36017678:G:CF476L1.000
19:36017678:G:TF476L1.000
19:36017679:A:CF476C1.000
19:36017679:A:GF476S1.000
19:36017680:A:GF476L1.000
19:36017682:A:TV475D1.000
19:36017685:C:TG474E1.000
19:36017686:C:AG474W1.000
19:36017686:C:GG474R1.000
19:36017686:C:TG474R1.000
19:36017699:G:CC469W1.000
19:36017700:C:TC469Y1.000
19:36017705:G:CF467L1.000
19:36017705:G:TF467L1.000
19:36017706:A:GF467S1.000
19:36017707:A:GF467L1.000
19:36017710:A:CY466D1.000
19:36017724:A:TV461D1.000
19:36017728:A:GS460P1.000
19:36017730:C:AG459V1.000
19:36017730:C:TG459D1.000
19:36017731:C:AG459C1.000
19:36017731:C:GG459R1.000
19:36017742:C:AG455V1.000
19:36017742:C:TG455D1.000
19:36017743:C:GG455R1.000
19:36017757:A:GL450P1.000
19:36017766:C:TG447D1.000
19:36017767:C:GG447R1.000
19:36017771:C:AW445C1.000

dbSNP variants (sampled 300 via entrez): RS1000028536 (19:36032921 G>A,C,T), RS1000105680 (19:36029821 T>C), RS1000210396 (19:36026492 C>G,T), RS1000496667 (19:36028111 C>T), RS1000582183 (19:36029431 A>G), RS1000613564 (19:36014695 T>A), RS1000737033 (19:36014488 G>A), RS1001190810 (19:36023075 C>A), RS1001267171 (19:36025212 A>C), RS1001616869 (19:36025366 A>G), RS1001987694 (19:36029891 C>A), RS1002050116 (19:36029582 G>A), RS1002375382 (19:36016740 G>A), RS1002443314 (19:36018384 G>T), RS1002615392 (19:36024792 T>G)

Disease associations

OMIM: gene MIM:607382 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

0 associations (top):

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

PharmGKB: 1 entry (VIP=true, CPIC=false)

CTD chemical–gene interactions

39 total (human), top 30 by PubMed support.

ChemicalActions (top 5)PubMed papers
Valproic Acidaffects cotreatment, decreases expression, affects expression, increases expression, increases methylation5
trichostatin Aaffects cotreatment, decreases expression3
sodium arseniteincreases abundance, affects cotreatment, increases expression, decreases expression3
afuresertibincreases expression1
6,7-dimethoxy-2-(pyrrolidin-1-yl)-N-(5-(pyrrolidin-1-yl)pentyl)quinazolin-4-aminedecreases expression1
FR900359increases phosphorylation1
moringindecreases expression1
bisphenol Aincreases expression1
lead acetateaffects cotreatment, increases expression1
cobaltous chlorideincreases expression1
butyraldehydedecreases expression1
cyfluthrinincreases expression1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamideaffects cotreatment, decreases expression1
dorsomorphinaffects cotreatment, decreases expression1
jinfukangincreases expression1
(+)-JQ1 compoundincreases expression1
Resveratrolaffects cotreatment, decreases expression1
Temozolomidedecreases expression1
Decitabineaffects expression1
Acetaminophendecreases expression1
Air Pollutantsdecreases expression, increases abundance1
Arsenicincreases abundance, increases expression1
Aspirinincreases expression1
Cadmiumdecreases expression, increases abundance1
Cannabidioldecreases expression1
Carbamazepineaffects expression1
Cisplatinaffects expression1
Diethylhexyl Phthalatedecreases expression1
Chlorpyrifosincreases expression1
Mustard Gasincreases expression1

Clinical trials (associated diseases)

0 trials via MONDO — disease-level, not drug-specific.

No linked Atlas pages yet — the cross-entity mesh grows as the corpus expands.