CYTIP

gene
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Also known as B3-1HECYBRCASPCYTHIP

Summary

CYTIP (cytohesin 1 interacting protein, HGNC:9506) is a protein-coding gene on chromosome 2q24.1, encoding Cytohesin-interacting protein (O60759). By its binding to cytohesin-1 (CYTH1), it modifies activation of ARFs by CYTH1 and its precise function may be to sequester CYTH1 in the cytoplasm.

The protein encoded by this gene contains 2 leucine zipper domains and a putative C-terminal nuclear targeting signal, but does not have any hydrophobic regions. This protein is expressed weakly in resting NK and T cells. The encoded protein modulates the activation of ARF genes by CYTH1. This protein interacts with CYTH1 and SNX27 proteins and may act to sequester CYTH1 protein in the cytoplasm.

Source: NCBI Gene 9595 — RefSeq curated summary.

At a glance

  • GWAS associations: 2
  • Clinical variants (ClinVar): 59 total — 1 pathogenic
  • MANE Select transcript: NM_004288

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:9506
Approved symbolCYTIP
Namecytohesin 1 interacting protein
Location2q24.1
Locus typegene with protein product
StatusApproved
AliasesB3-1, HE, CYBR, CASP, CYTHIP
Ensembl geneENSG00000115165
Ensembl biotypeprotein_coding
OMIM604448
Entrez9595

Gene structure

Transcript identifiers

Ensembl transcripts: 9 — 5 protein_coding, 2 retained_intron, 1 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000264192, ENST00000418920, ENST00000435117, ENST00000439355, ENST00000457793, ENST00000462109, ENST00000483929, ENST00000497432, ENST00000715893

RefSeq mRNA: 1 — MANE Select: NM_004288 NM_004288

CCDS: CCDS2204

Canonical transcript exons

ENST00000264192 — 8 exons

ExonStartEnd
ENSE00003470059157427351157427420
ENSE00003527985157434370157434424
ENSE00003591902157430559157430652
ENSE00003592117157418523157418589
ENSE00003631586157430860157430962
ENSE00003648172157434698157434747
ENSE00004028266157443847157444089
ENSE00004028268157414619157416143

Expression profiles

Bgee: expression breadth ubiquitous, 242 present calls, max score 98.33.

FANTOM5 (CAGE): breadth broad, TPM avg 68.6237 / max 6897.0224, expressed in 540 samples.

FANTOM5 promoters (8 alternative TSS)

Promoter IDTPM avgSamples expressed
3139959.2705496
313987.7354340
313970.8976175
313890.308383
314050.235051
313900.107362
313910.052531
314040.017111

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
bloodUBERON:000017898.33gold quality
bone marrow cellCL:000209296.38gold quality
leukocyteCL:000073896.33gold quality
monocyteCL:000057696.32gold quality
mononuclear cellCL:000084296.31gold quality
vermiform appendixUBERON:000115496.25gold quality
bone marrowUBERON:000237195.45gold quality
lymph nodeUBERON:000002995.40gold quality
granulocyteCL:000009494.39gold quality
colonic epitheliumUBERON:000039793.84gold quality
epithelium of nasopharynxUBERON:000195192.95gold quality
nasopharynxUBERON:000172892.94gold quality
spleenUBERON:000210692.40gold quality
caecumUBERON:000115391.96gold quality
tonsilUBERON:000237291.84gold quality
jejunal mucosaUBERON:000039988.33gold quality
periodontal ligamentUBERON:000826686.92gold quality
right lungUBERON:000216786.78gold quality
pylorusUBERON:000116686.65gold quality
upper lobe of left lungUBERON:000895286.01gold quality
rectumUBERON:000105285.93gold quality
duodenumUBERON:000211485.69gold quality
upper lobe of lungUBERON:000894885.48gold quality
palpebral conjunctivaUBERON:000181285.42gold quality
amniotic fluidUBERON:000017384.20gold quality
parotid glandUBERON:000183184.18gold quality
gall bladderUBERON:000211084.12gold quality
small intestine Peyer’s patchUBERON:000345484.10gold quality
trabecular bone tissueUBERON:000248383.57gold quality
small intestineUBERON:000210883.45gold quality

Single-cell (SCXA)

Detected in 18 experiment(s), a significant marker in 18.

ExperimentMarker?Max mean expression
E-MTAB-8142yes1410.42
E-HCAD-36yes863.82
E-CURD-79yes577.40
E-GEOD-135922yes384.61
E-HCAD-8yes88.93
E-HCAD-1yes86.64
E-CURD-122yes48.25
E-CURD-46yes40.53
E-MTAB-8410yes38.72
E-CURD-88yes36.79
E-MTAB-10287yes30.01
E-HCAD-10yes23.22
E-HCAD-11yes21.50
E-MTAB-10553yes13.82
E-MTAB-8498yes8.86

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

82 targeting CYTIP, 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-4795-3P100.0074.624024
HSA-MIR-126-5P100.0072.713180
HSA-MIR-4692100.0067.322066
HSA-MIR-518D-5P100.0067.51979
HSA-MIR-518E-5P100.0067.66954
HSA-MIR-518F-5P100.0067.51979
HSA-MIR-519A-5P100.0067.66954
HSA-MIR-519B-5P100.0067.66954
HSA-MIR-519C-5P100.0067.66954
HSA-MIR-520C-5P100.0067.51979
HSA-MIR-522-5P100.0067.66954
HSA-MIR-523-5P100.0067.66954
HSA-MIR-526A-5P100.0067.51979
HSA-MIR-5692A100.0074.406850
HSA-MIR-223-3P99.9970.141140
HSA-MIR-366299.9973.825684
HSA-MIR-451499.9967.101870
HSA-MIR-365899.9673.874379
HSA-MIR-548AJ-3P99.9673.385345
HSA-MIR-548X-3P99.9673.385345
HSA-MIR-548J-3P99.9472.614881
HSA-MIR-548AE-3P99.9372.664867
HSA-MIR-548AH-3P99.9372.544872
HSA-MIR-548AM-3P99.9372.544872
HSA-MIR-548AQ-3P99.9372.664867
HSA-MIR-6508-5P99.9270.672465
HSA-MIR-450B-5P99.9271.483175
HSA-MIR-10527-5P99.9172.283754
HSA-MIR-589-3P99.9169.622088
HSA-MIR-806799.8669.592260

Literature-anchored findings (GeneRIF, showing 7)

  • observations suggest that CASP is a scaffolding protein that facilitates the function of at least one member of the cytohesin/ARNO family in response to specific cellular stimuli (PMID:12052827)
  • Cybr not only regulates lymphocyte adhesion and cell-cell interaction but also contributes to the regulation of the signaling cascade and of the genetic program downstream of the T cell receptor. (PMID:16702224)
  • These results suggest that endosomal SNX27 may recruit CASP to orchestrate intracellular trafficking and/or signaling complexes. (PMID:17577583)
  • on infection of human monocyte-derived dendritic cells with herpes simplex virus type 1 (HSV-1), CYTIP is rapidly degraded and as a consequence beta-2 integrins, predominantly LFA-1, are activated (PMID:21562043)
  • loss of DNA methylation enables HIF-driven cytohesin 1 interacting protein expression to protect cancer cells from death cytokine signals (PMID:23223005)
  • a newly identified binding partner of CYTIP, SOCS-1, and confirm its function in regulating the degradation of CYTIP by the proteasome (PMID:23469018)
  • CASP has a direct role in the secretion of IFN-gamma, and NK cell motility and ability to kill tumor cells. CASP polarizes to the leading edge of migrating NK cells, and to the immunological synapse when engaged with tumor cells. (PMID:25058460)

Cross-species orthologs

5 orthologs

OrganismSymbolGene ID
danio_reriocytipENSDARG00000061717
mus_musculusCytipENSMUSG00000026832
rattus_norvegicusCytipENSRNOG00000004772
drosophila_melanogasterssp6FBGN0035676
caenorhabditis_elegansgras-1WBGENE00009272

Paralogs (1): TAMALIN (ENSG00000161835)

Protein

Protein identifiers

Cytohesin-interacting proteinO60759 (reviewed: O60759)

Alternative names: Cytohesin binder and regulator, Cytohesin-associated scaffolding protein, Cytohesin-binding protein HE, Pleckstrin homology Sec7 and coiled-coil domains-binding protein

All UniProt accessions (5): C9JNN8, C9JRF8, C9JSM2, O60759, F8WF61

UniProt curated annotations — full annotation on UniProt →

Function. By its binding to cytohesin-1 (CYTH1), it modifies activation of ARFs by CYTH1 and its precise function may be to sequester CYTH1 in the cytoplasm.

Subunit / interactions. Interacts with CYTH1 and SNX27.

Subcellular location. Cytoplasm. Early endosome.

Tissue specificity. Expressed in lymph nodes, thymus, spleen, lung, peripheral blood leukocytes and bone marrow.

Induction. By TNF and bacterial lipopolysaccharides (LPS).

Isoforms (2)

UniProt IDNamesCanonical?
O60759-11yes
O60759-22

RefSeq proteins (1): NP_004279* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR001478PDZDomain
IPR036034PDZ_sfHomologous_superfamily
IPR052122Intracell_Traff_Signaling_RegFamily

Pfam: PF00595

UniProt features (21 total): strand 5, mutagenesis site 3, sequence variant 3, sequence conflict 2, helix 2, chain 1, domain 1, turn 1, region of interest 1, coiled-coil region 1, splice variant 1

Structure

Experimental structures (PDB)

1 structures.

PDBMethodResolution (Å)
2Z17X-RAY DIFFRACTION2.7

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-O60759-F163.240.27

Functional residue map

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

Mutagenesis-validated functional residues (3):

PositionPhenotype
92no membrane-association. no change in the binding to cyth1; when associated with e-82 and a-90.
82no membrane-association. no change in the binding to cyth1; when associated with a-90 and a-92.
90no membrane-association. no change in the binding to cyth1; when associated with e-82 and a-92.

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 300 (showing top): GSE45365_NK_CELL_VS_CD11B_DC_DN, WALLACE_PROSTATE_CANCER_RACE_UP, MCLACHLAN_DENTAL_CARIES_UP, GNF2_CASP8, RACCACAR_AML_Q6, ACEVEDO_LIVER_CANCER_WITH_H3K27ME3_UP, LINDSTEDT_DENDRITIC_CELL_MATURATION_B, RHEIN_ALL_GLUCOCORTICOID_THERAPY_UP, AML_Q6, chr2q24, SU_THYMUS, LEE_EARLY_T_LYMPHOCYTE_DN, ONDER_CDH1_TARGETS_2_UP, GNF2_CD97, COATES_MACROPHAGE_M1_VS_M2_DN

GO Biological Process (1): regulation of cell adhesion (GO:0030155)

GO Molecular Function (1): protein binding (GO:0005515)

GO Cellular Component (6): nucleoplasm (GO:0005654), cytoplasm (GO:0005737), early endosome (GO:0005769), cytosol (GO:0005829), cell cortex (GO:0005938), endosome (GO:0005768)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
cellular anatomical structure3
cytoplasm2
cell adhesion1
regulation of cellular process1
binding1
nuclear lumen1
intracellular anatomical structure1
endosome1
cell periphery1
endomembrane system1
cytoplasmic vesicle1

Protein interactions and networks

STRING

1542 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CYTIPSNX27Q96L92957
CYTIPCYTH1Q15438936
CYTIPCYTH3O43739747
CYTIPSERPINB3P29508742
CYTIPDGKZQ13574713
CYTIPRAB11AP24410497
CYTIPTFRCP02786423
CYTIPSERPINE2P07093365
CYTIPTMEM86AQ8N2M4351
CYTIPLHFPL2Q6ZUX7322
CYTIPGPR157Q5UAW9318
CYTIPSNX1Q13596317
CYTIPSLCO6A1Q86UG4314
CYTIPGPA33Q99795293
CYTIPLZTS2Q9BRK4293
CYTIPRPP21Q9H633293

IntAct

184 interactions, top by confidence:

ABTypeScore
CYTIPCYTH1psi-mi:“MI:0915”(physical association)0.810
CYTIPSCNM1psi-mi:“MI:0915”(physical association)0.560
CYTIPMCRS1psi-mi:“MI:0915”(physical association)0.560
CYTIPKIF9psi-mi:“MI:0915”(physical association)0.560
CYTIPFGFR3psi-mi:“MI:0915”(physical association)0.560
CYTIPSPRED1psi-mi:“MI:0915”(physical association)0.560
CYTIPSNX27psi-mi:“MI:0407”(direct interaction)0.440
NHERF2CYTIPpsi-mi:“MI:0407”(direct interaction)0.440
CYTIPSHANK1psi-mi:“MI:0407”(direct interaction)0.440
MAST2CYTIPpsi-mi:“MI:0407”(direct interaction)0.440
CYTIPRHPN1psi-mi:“MI:0407”(direct interaction)0.440
CYTIPPDZK1psi-mi:“MI:0407”(direct interaction)0.440
CYTIPPARD3psi-mi:“MI:0407”(direct interaction)0.440
PARD3BCYTIPpsi-mi:“MI:0407”(direct interaction)0.440
CYTIPMAST1psi-mi:“MI:0407”(direct interaction)0.440
CYTIPPTPN3psi-mi:“MI:0407”(direct interaction)0.440
APBA3CYTIPpsi-mi:“MI:0407”(direct interaction)0.440
CYTIPAHNAKpsi-mi:“MI:0407”(direct interaction)0.440
CYTIPAPBA1psi-mi:“MI:0407”(direct interaction)0.440
CYTIPAPBA2psi-mi:“MI:0407”(direct interaction)0.440
CYTIPARHGAP21psi-mi:“MI:0407”(direct interaction)0.440
CYTIPARHGEF11psi-mi:“MI:0407”(direct interaction)0.440
CYTIPCARD11psi-mi:“MI:0407”(direct interaction)0.440

BioGRID (34): CYTH3 (Affinity Capture-MS), CYTH1 (Affinity Capture-MS), CYTH2 (Affinity Capture-MS), BLK (Affinity Capture-MS), FAM175B (Affinity Capture-MS), EDEM2 (Affinity Capture-MS), HBB (Affinity Capture-MS), CYTH1 (Affinity Capture-MS), CYTH3 (Affinity Capture-MS), CYTH2 (Affinity Capture-MS), FAM175B (Affinity Capture-MS), EDEM2 (Affinity Capture-MS), HBB (Affinity Capture-MS), CYTIP (Affinity Capture-MS), CYTIP (Affinity Capture-MS)

ESM2 similar proteins: A1A5G4, D3YZU1, E9Q9R9, F1MAD2, O15018, O35346, O35867, O60759, P34152, P97306, P97879, Q00944, Q4L1J4, Q5F488, Q5I0L6, Q5JV73, Q5RD32, Q5SGD7, Q5TCQ9, Q68DX3, Q69Z98, Q6DD51, Q6P9H4, Q6RHR9, Q6ZWJ1, Q812E4, Q8BH60, Q8BMA3, Q8IWQ3, Q8TDM6, Q8TDW5, Q8TEW0, Q8TEW8, Q91VY6, Q925T6, Q96QZ7, Q99469, Q99NH2, Q9CSB4, Q9EQJ9

Diamond homologs: O15021, O60307, O60759, Q3T0X8, Q3U214, Q4ACU6, Q4L1J4, Q5I0L6, Q5RCF7, Q5T2W1, Q69ZH9, Q6AX33, Q6AYQ0, Q6RHR9, Q7Z6J2, Q811L6, Q865P3, Q8R4T5, Q91VY6, Q96QZ7, Q9BYB0, Q9JIL4, Q9JJ40, Q9JJA9, Q9JLU4, Q9P227, A1ZA47, A2RUV4, A4D2P6, A5PKA5, A8MUH7, B9EJ80, D3YZU1, D3ZFD0, G5EDM4, O14745, O14907, O14910, O15085, O88951

SIGNOR signaling

0 interactions.

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 115 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

PathwayPartnersFoldFDR
Ras activation upon Ca2+ influx through NMDA receptor538.6×9e-06
Unblocking of NMDA receptors, glutamate binding and activation536.7×9e-06
Negative regulation of NMDA receptor-mediated neuronal transmission536.7×9e-06
Assembly and cell surface presentation of NMDA receptors1034.3×3e-11
Dopamine Neurotransmitter Release Cycle533.5×1e-05
Long-term potentiation532.1×1e-05
Neurexins and neuroligins1129.3×2e-11
Protein-protein interactions at synapses725.1×1e-06

GO biological processes:

GO termPartnersFoldFDR
establishment or maintenance of epithelial cell apical/basal polarity1159.7×9e-15
protein localization to synapse643.0×7e-07
receptor clustering740.8×9e-08
regulation of postsynaptic membrane neurotransmitter receptor levels732.4×4e-07
protein-containing complex assembly99.6×3e-05
cell-cell adhesion109.5×1e-05
regulation of small GTPase mediated signal transduction68.1×3e-03
chemical synaptic transmission75.1×9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic1
Likely pathogenic0
Uncertain significance44
Likely benign2
Benign0

Top pathogenic / likely-pathogenic (1)

Variant IDHGVSClassification
2684808GRCh37/hg19 2q24.1(chr2:156828817-158377885)x1Pathogenic

SpliceAI

978 predictions. Top by Δscore:

VariantEffectΔscore
2:157418598:T:TCacceptor_gain1.0000
2:157427426:T:Cacceptor_gain1.0000
2:157430557:A:ACdonor_gain1.0000
2:157430558:C:CCdonor_gain1.0000
2:157434743:GCAAG:Gacceptor_gain1.0000
2:157434744:CAAG:Cacceptor_gain1.0000
2:157434744:CAAGC:Cacceptor_gain1.0000
2:157434748:C:CCacceptor_gain1.0000
2:157443843:ATAC:Adonor_loss1.0000
2:157443844:TACCT:Tdonor_loss1.0000
2:157443846:C:CTdonor_loss1.0000
2:157443846:CCTG:Cdonor_gain1.0000
2:157418585:GTTTG:Gacceptor_gain0.9900
2:157418586:TTTG:Tacceptor_gain0.9900
2:157418590:C:CCacceptor_gain0.9900
2:157418598:T:Cacceptor_gain0.9900
2:157427346:ATTAC:Adonor_loss0.9900
2:157427347:TTAC:Tdonor_loss0.9900
2:157427348:TA:Tdonor_loss0.9900
2:157427349:A:Cdonor_loss0.9900
2:157427350:C:Adonor_loss0.9900
2:157427353:TTAAA:Tdonor_gain0.9900
2:157427416:CTATC:Cacceptor_gain0.9900
2:157427419:TC:Tacceptor_gain0.9900
2:157427420:CC:Cacceptor_gain0.9900
2:157427421:C:CAacceptor_loss0.9900
2:157427421:C:CCacceptor_gain0.9900
2:157427422:T:Aacceptor_loss0.9900
2:157427426:T:TCacceptor_gain0.9900
2:157430563:G:Cdonor_gain0.9900

AlphaMissense

2376 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
2:157434380:A:GF90S0.997
2:157430586:A:GL150P0.994
2:157430883:G:TA120D0.992
2:157434379:A:CF90L0.992
2:157434379:A:TF90L0.992
2:157434381:A:GF90L0.992
2:157430562:A:GL158P0.991
2:157430868:A:GL125P0.991
2:157434383:C:TG89E0.991
2:157434385:A:CF88L0.990
2:157434385:A:TF88L0.990
2:157434387:A:GF88L0.990
2:157415723:A:GI345T0.989
2:157418552:A:GL195P0.987
2:157430631:T:AN135I0.986
2:157430643:A:TL131H0.986
2:157430888:G:CS118R0.986
2:157430888:G:TS118R0.986
2:157430890:T:GS118R0.986
2:157434380:A:CF90C0.984
2:157415723:A:TI345N0.983
2:157430583:A:TI151N0.983
2:157430634:A:TI134N0.982
2:157430643:A:CL131R0.982
2:157434384:C:GG89R0.982
2:157434384:C:TG89R0.982
2:157430634:A:CI134S0.981
2:157430630:A:CN135K0.980
2:157430630:A:TN135K0.980
2:157415725:A:CF344L0.979

dbSNP variants (sampled 300 via entrez): RS1000233226 (2:157414589 G>GAC), RS1000238425 (2:157443719 A>T), RS1000464971 (2:157420854 G>A,C), RS1000670294 (2:157414861 G>A), RS1000696968 (2:157426249 G>A), RS1000752363 (2:157432236 C>G), RS1000764716 (2:157427711 T>C), RS1000973584 (2:157438871 A>C,G), RS1001117582 (2:157431733 C>A), RS1001183565 (2:157422871 A>G), RS1001218448 (2:157440202 A>G), RS1001358530 (2:157425863 T>C), RS1001435889 (2:157429044 T>C), RS1001460042 (2:157439768 A>G), RS1001504299 (2:157415505 A>G)

Disease associations

OMIM: gene MIM:604448 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

2 associations (top):

StudyTraitp-value
GCST008972_202Urate levels1.000000e-11
GCST009379_238Type 2 diabetes7.000000e-10

EFO canonical traits (1, from GWAS)

EFO IDTrait name
EFO:0004531urate measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

ChemicalActions (top 5)PubMed papers
bisphenol Adecreases methylation, decreases expression, affects cotreatment2
Benzo(a)pyrenedecreases methylation, affects methylation, decreases expression2
Dinitrochlorobenzeneincreases expression2
3-((6-(2-methoxyphenyl)pyrimidin-4-yl)amino)phenyl)methane sulfonamidedecreases expression1
GSK-J4increases expression1
testosterone enanthateaffects expression1
triphenyl phosphateaffects expression1
propionaldehydedecreases expression1
kojic acidincreases expression1
sodium arseniteaffects methylation1
ammonium hexachloroplatinateincreases expression1
butyraldehydedecreases expression1
4-phenylenediamineincreases expression1
nickel sulfateincreases expression1
pentanaldecreases expression1
di-n-butylphosphoric acidaffects expression1
CGP 52608affects binding, increases reaction1
ON 01910increases expression1
(+)-JQ1 compounddecreases expression1
Bortezomibincreases expression1
Zoledronic Acidincreases expression1
Fulvestrantaffects cotreatment, decreases methylation1
Air Pollutantsincreases abundance, increases expression1
Air Pollutants, Occupationalaffects expression1
Aldehydesdecreases expression1
Cisplatinincreases expression1
Dinitrofluorobenzeneincreases expression1
Diurondecreases expression1
Drugs, Chinese Herbalincreases expression1
Dustincreases 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.