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CIMIP1

gene
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Also known as bA196N14.1LLC1

Summary

CIMIP1 (ciliary microtubule inner protein 1, HGNC:16216) is a protein-coding gene on chromosome 20q13.32, encoding Ciliary microtubule inner protein 1 (Q9H1P6).

Located in cilium.

Source: NCBI Gene 128602 — RefSeq curated summary.

At a glance

  • GWAS associations: 3
  • Clinical variants (ClinVar): 7 total
  • MANE Select transcript: NM_178456

Identifiers

Gene identifiers

FieldValue
HGNC IDHGNC:16216
Approved symbolCIMIP1
Nameciliary microtubule inner protein 1
Location20q13.32
Locus typegene with protein product
StatusApproved
AliasesbA196N14.1, LLC1
Ensembl geneENSG00000124237
Ensembl biotypeprotein_coding
OMIM619277
Entrez128602

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000371168

RefSeq mRNA: 1 — MANE Select: NM_178456 NM_178456

CCDS: CCDS13465

Canonical transcript exons

ENST00000371168 — 4 exons

ExonStartEnd
ENSE000008457735815354458153625
ENSE000008457745815546858155569
ENSE000014545295816066158161150
ENSE000014545305815090258151032

Expression profiles

Bgee: expression breadth broad, 85 present calls, max score 99.90.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.8316 / max 285.9782, expressed in 43 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter IDTPM avgSamples expressed
1854900.658936
1854910.172725

Top tissues by expression

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

TissueAnatomy IDExpression scoreQuality
bronchial epithelial cellCL:000232899.90gold quality
bronchusUBERON:000218599.76gold quality
right uterine tubeUBERON:000130299.66gold quality
olfactory segment of nasal mucosaUBERON:000538698.66gold quality
mucosa of paranasal sinusUBERON:000503095.70gold quality
oviduct epitheliumUBERON:000480494.46gold quality
right testisUBERON:000453494.42gold quality
left testisUBERON:000453394.28gold quality
primordial germ cell in gonadCL:0000670 ∩ UBERON:000099194.23gold quality
tracheaUBERON:000312693.63gold quality
nasal cavity epitheliumUBERON:000538493.43gold quality
male germ line stem cell (sensu Vertebrata) in testisCL:0000089 ∩ UBERON:000047392.82gold quality
fallopian tubeUBERON:000388992.18gold quality
testisUBERON:000047391.63gold quality
adult organismUBERON:000702391.04gold quality
epithelium of nasopharynxUBERON:000195189.35gold quality
caput epididymisUBERON:000435885.34gold quality
right lungUBERON:000216784.85gold quality
nasal cavity mucosaUBERON:000182683.07gold quality
left uterine tubeUBERON:000130377.02gold quality
spermCL:000001970.36silver quality
endometriumUBERON:000129569.52gold quality
endocervixUBERON:000045867.31gold quality
lungUBERON:000204867.07gold quality
buccal mucosa cellCL:000233666.01gold quality
upper lobe of left lungUBERON:000895266.01gold quality
upper lobe of lungUBERON:000894865.30gold quality
amniotic fluidUBERON:000017357.26silver quality
pancreatic ductal cellCL:000207957.04silver quality
lower lobe of lungUBERON:000894955.28silver quality

Single-cell (SCXA)

Detected in 11 experiment(s), a significant marker in 11.

ExperimentMarker?Max mean expression
E-HCAD-15yes5058.93
E-MTAB-10283yes2912.17
E-CURD-114yes2599.59
E-MTAB-8221yes2242.04
E-CURD-126yes2057.42
E-GEOD-130148yes1908.01
E-MTAB-10287yes1831.45
E-HCAD-1yes1830.63
E-CURD-122yes1736.51
E-MTAB-9388yes7.50
E-ANND-3no0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

16 targeting CIMIP1, 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-4455100.0065.481587
HSA-MIR-3613-3P100.0076.367965
HSA-MIR-124-3P99.8973.743043
HSA-MIR-506-3P99.8973.553057
HSA-MIR-320299.6667.702737
HSA-MIR-1212399.5271.792990
HSA-MIR-664A-3P99.2271.082696
HSA-MIR-429299.1665.571767
HSA-MIR-6791-5P99.1665.921844
HSA-MIR-6814-5P99.0366.681273
HSA-MIR-331-3P98.7664.91793
HSA-MIR-4662A-5P98.4867.181007
HSA-MIR-3173-5P97.3565.821282
HSA-MIR-6799-3P97.3565.601302
HSA-MIR-129196.2865.891224
HSA-MIR-29C-5P87.3666.9629

Literature-anchored findings (GeneRIF, showing 2)

  • inactivation of LLC1 by means of promoter methylation is a frequent event in nonsmall cell lung cancer and may play a role in lung tumorigenesis. (PMID:17304513)
  • our findings suggest that LLC1 is not a tumor suppressor, and that it is localized in the cilia of the normal lung epithelium but is absent in most non-small cell lung cancer cases (PMID:25786037)

Cross-species orthologs

2 orthologs

OrganismSymbolGene ID
mus_musculusCimip1ENSMUSG00000027518
rattus_norvegicusCimip1ENSRNOG00000028533

Paralogs (1): CIMIP5 (ENSG00000150873)

Protein

Protein identifiers

Ciliary microtubule inner protein 1 — Q9H1P6 (reviewed: Q9H1P6)

All UniProt accessions (1): Q9H1P6

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell projection. Cilium.

Tissue specificity. Expressed in airway epithelial cells, renal tubular cells, pancreatic acinar cells and epithelial cells of the stomach, duodenum, and gallbladder (at protein level).

RefSeq proteins (1): NP_848551* (*=MANE)

Domains & families (InterPro)

IDNameType
IPR020339C20orf85-likeFamily

Pfam: PF14945

UniProt features (4 total): sequence variant 3, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

ModelpLDDTFraction very-high
AF-Q9H1P6-F176.630.20

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 43 (showing top): SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, GOCC_CILIUM, NIKOLSKY_BREAST_CANCER_20Q12_Q13_AMPLICON, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MARTENS_TRETINOIN_RESPONSE_UP, CERIBELLI_GENES_INACTIVE_AND_BOUND_BY_NFY, ZWANG_TRANSIENTLY_UP_BY_2ND_EGF_PULSE_ONLY, GSE13522_CTRL_VS_T_CRUZI_G_STRAIN_INF_SKIN_UP, GSE5503_MLN_DC_VS_SPLEEN_DC_ACTIVATED_ALLOGENIC_TCELL_DN, GSE10239_NAIVE_VS_MEMORY_CD8_TCELL_DN, GSE10239_NAIVE_VS_KLRG1HIGH_EFF_CD8_TCELL_UP, GSE10239_MEMORY_VS_KLRG1INT_EFF_CD8_TCELL_UP, GSE10239_MEMORY_VS_KLRG1HIGH_EFF_CD8_TCELL_UP, MIR6799_3P, MIR3173_5P

GO Biological Process (0):

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

GO Cellular Component (2): cilium (GO:0005929), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

CategoryTerms
binding1
intraciliary transport particle1
membrane-bounded organelle1
plasma membrane bounded cell projection1
cellular anatomical structure1

Protein interactions and networks

STRING

396 interactions, top by confidence (×1000):

Protein AProtein BPartner UniProtScore
CIMIP1CXorf58Q96LI9582
CIMIP1NPEPL1Q8NDH3494
CIMIP1C19orf81C9J6K1475
CIMIP1NCOA5Q9HCD5450
CIMIP1DDX27Q96GQ7449
CIMIP1ACAD10Q6JQN1446
CIMIP1OR7G3Q8NG95419
CIMIP1B3GLCTQ6Y288400
CIMIP1ANKRD60Q9BZ19400
CIMIP1SLC16A8O95907396
CIMIP1WDR49Q8IV35394
CIMIP1AXDND1Q5T1B0392
CIMIP1ZBBXA8MT70391
CIMIP1MTRNR2L3P0CJ70379
CIMIP1PILRBQ9UKJ0379

IntAct

68 interactions, top by confidence:

ABTypeScore
CNOT2CIMIP1psi-mi:“MI:0915”(physical association)0.560
RBPMSCIMIP1psi-mi:“MI:0915”(physical association)0.560
CASKCIMIP1psi-mi:“MI:0915”(physical association)0.560
ASPGCIMIP1psi-mi:“MI:0915”(physical association)0.560
KLHL2CIMIP1psi-mi:“MI:0915”(physical association)0.560
KLHL20CIMIP1psi-mi:“MI:0915”(physical association)0.560
OIP5CIMIP1psi-mi:“MI:0915”(physical association)0.560
KRTAP3-1CIMIP1psi-mi:“MI:0915”(physical association)0.560
KRTAP8-1CIMIP1psi-mi:“MI:0915”(physical association)0.560
KRTAP19-6CIMIP1psi-mi:“MI:0915”(physical association)0.560
KRTAP6-2CIMIP1psi-mi:“MI:0915”(physical association)0.560
PFDN5CIMIP1psi-mi:“MI:0915”(physical association)0.560
LCN2CIMIP1psi-mi:“MI:0915”(physical association)0.560
DTX2CIMIP1psi-mi:“MI:0915”(physical association)0.560
CIMIP1CNOT2psi-mi:“MI:0915”(physical association)0.560
CIMIP1CABP2psi-mi:“MI:0915”(physical association)0.560
ACTN3CIMIP1psi-mi:“MI:0915”(physical association)0.560
FHL2CIMIP1psi-mi:“MI:0915”(physical association)0.560
ALKBH7CIMIP1psi-mi:“MI:0915”(physical association)0.560
CIMIP1MAD2L2psi-mi:“MI:0915”(physical association)0.560
TTC19CIMIP1psi-mi:“MI:0915”(physical association)0.560
EFHC1CIMIP1psi-mi:“MI:0915”(physical association)0.560
CACNB3CIMIP1psi-mi:“MI:0915”(physical association)0.560
CIMIP1VASPpsi-mi:“MI:0915”(physical association)0.400
CIMIP1RBPMSpsi-mi:“MI:0915”(physical association)0.000
CIMIP1KLHL2psi-mi:“MI:0915”(physical association)0.000
CIMIP1CASKpsi-mi:“MI:0915”(physical association)0.000
CIMIP1ASPGpsi-mi:“MI:0915”(physical association)0.000

BioGRID (24): C20orf85 (Two-hybrid), C20orf85 (Two-hybrid), C20orf85 (Two-hybrid), C20orf85 (Two-hybrid), C20orf85 (Two-hybrid), C20orf85 (Two-hybrid), C20orf85 (Two-hybrid), C20orf85 (Two-hybrid), C20orf85 (Two-hybrid), C20orf85 (Two-hybrid), ALKBH7 (Two-hybrid), CASK (Two-hybrid), LCN2 (Two-hybrid), RBPMS (Two-hybrid), ASPG (Two-hybrid)

ESM2 similar proteins: A0A087WRI3, A2BFC9, A2RRW4, A4QMS7, A6NJV1, A6NL82, A6QPC0, A6QQ68, A8E4X8, A8E5W8, A8QW39, A9JS51, D6REC4, F1P3Y5, G3X6E2, P0C875, Q0VB26, Q1MSJ5, Q2IA00, Q2T9Q3, Q2TA11, Q3UY96, Q494V2, Q497Q6, Q4KKZ1, Q4QR77, Q4R5Y0, Q4R8V8, Q5NC57, Q5ZIH9, Q6J272, Q6PII3, Q6ZQR2, Q6ZVS7, Q7Z4T9, Q8CFW7, Q8N1D5, Q8N6G2, Q8WW14, Q95LR0

Diamond homologs: Q9DA42, Q9H1P6

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

ClassificationCount (floor)
Pathogenic0
Likely pathogenic0
Uncertain significance3
Likely benign1
Benign0

Top pathogenic / likely-pathogenic (0)

SpliceAI

584 predictions. Top by Δscore:

VariantEffectΔscore
20:58151022:G:GTdonor_gain1.0000
20:58155553:TGGAG:Tdonor_gain1.0000
20:58151078:G:GTdonor_gain0.9900
20:58151121:G:GTdonor_gain0.9900
20:58151121:G:Tdonor_gain0.9900
20:58153543:GGAA:Gacceptor_gain0.9900
20:58153622:GGAG:Gdonor_gain0.9900
20:58153623:G:GTdonor_gain0.9900
20:58155466:A:AGacceptor_gain0.9900
20:58155467:G:GGacceptor_gain0.9900
20:58155557:G:GTdonor_gain0.9900
20:58153535:CTTTT:Cacceptor_loss0.9800
20:58153536:TTTTT:Tacceptor_loss0.9800
20:58153537:TTTTC:Tacceptor_loss0.9800
20:58153540:TCA:Tacceptor_loss0.9800
20:58153542:AG:Aacceptor_gain0.9800
20:58153543:G:GTacceptor_loss0.9800
20:58153543:GG:Gacceptor_gain0.9800
20:58153621:AGGAG:Adonor_loss0.9800
20:58153622:GGAGG:Gdonor_loss0.9800
20:58153623:GAGGT:Gdonor_loss0.9800
20:58153624:AG:Adonor_loss0.9800
20:58153625:G:GTdonor_loss0.9800
20:58153627:T:TCdonor_loss0.9800
20:58155466:AGTT:Aacceptor_gain0.9800
20:58155467:GTT:Gacceptor_gain0.9800
20:58155467:GTTG:Gacceptor_gain0.9800
20:58155565:TCAAG:Tdonor_loss0.9800
20:58155566:CAAG:Cdonor_loss0.9800
20:58155567:AAG:Adonor_loss0.9800

AlphaMissense

890 scored. Top likely-pathogenic:

VariantProtein changeam_pathogenicity
20:58160709:T:AW101R0.984
20:58160709:T:CW101R0.984
20:58160711:G:CW101C0.975
20:58160711:G:TW101C0.975
20:58153602:T:CF43L0.972
20:58153604:T:AF43L0.972
20:58153604:T:GF43L0.972
20:58160714:A:CR102S0.963
20:58160714:A:TR102S0.963
20:58153586:G:CW37C0.954
20:58153586:G:TW37C0.954
20:58153584:T:AW37R0.950
20:58153584:T:CW37R0.950
20:58153596:T:AW41R0.948
20:58153596:T:CW41R0.948
20:58160710:G:CW101S0.946
20:58160799:T:AW131R0.937
20:58160799:T:CW131R0.937
20:58153598:G:CW41C0.936
20:58153598:G:TW41C0.936
20:58160713:G:CR102T0.936
20:58160707:G:AG100D0.934
20:58153552:G:CR26P0.923
20:58160710:G:TW101L0.923
20:58153572:G:CA33P0.921
20:58160801:G:CW131C0.919
20:58160801:G:TW131C0.919
20:58160704:T:AI99N0.913
20:58153555:T:CL27P0.908
20:58160683:C:AP92Q0.906

dbSNP variants (sampled 300 via entrez): RS1000266879 (20:58149428 C>T), RS1000298080 (20:58149719 T>C), RS1000815480 (20:58159766 C>A), RS1000866497 (20:58159441 G>A,C), RS1001103212 (20:58149355 G>A), RS1001274182 (20:58150893 C>G,T), RS1001527106 (20:58153985 C>T), RS1001655700 (20:58151621 G>T), RS1001754098 (20:58151874 G>A), RS1001769750 (20:58156255 C>T), RS1002132945 (20:58155304 T>C), RS1002506696 (20:58155112 G>A), RS1002756660 (20:58153301 G>T), RS1002768881 (20:58157628 T>C), RS1002801158 (20:58157957 T>C,G)

Disease associations

OMIM: gene MIM:619277 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

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

GWAS associations

3 associations (top):

StudyTraitp-value
GCST001762_241Obesity-related traits7.000000e-06
GCST003219_45Advanced age-related macular degeneration3.000000e-16
GCST90011900_11Serum alkaline phosphatase levels1.000000e-09

EFO canonical traits (3, from GWAS)

EFO IDTrait name
EFO:0003939energy intake
EFO:1001492atrophic macular degeneration
EFO:0004533alkaline phosphatase measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

5 total (human), top 5 by PubMed support.

ChemicalActions (top 5)PubMed papers
Air Pollutantsincreases abundance, increases expression1
Benzo(a)pyreneincreases methylation1
Methotrexateincreases expression1
Smokeincreases expression, increases abundance1
Tobacco Smoke Pollutiondecreases expression1

Clinical trials (associated diseases)

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

About this page

Generated deterministically by Sugi Atlas from primary biomedical databases via BioBTree. Every record on this page traces to a primary source.

Generated
Atlas version
v1.1.2
BioBTree
v2.0.2

Sources 74

This page pulls from 74 datasets indexed by BioBTree:

alphafoldalphamissenseantibodybgeebgee_evidencebindingdbbiogrid_interactionbrendabrenda_kineticsccdscellosauruschembl_activitychembl_targetciviccivic_evidenceclingen_dosageclingen_gene_validityclinical_trialsclinvarcollectrictd_gene_interactiondbsnpdepmapdiamond_similarityefoensemblentrezesm2_similarityexonfantom5_genefantom5_promotergenccgenerifgogoparentgtopdbgwasgwas_studyhgnchpointactinterprointogenjasparmeshmimmirdbmondomsigdborphanetorthologparalogpdbpfampharmgkb_clinicalpharmgkb_genepharmgkb_guidelinepharmgkb_variantpubchempubchem_activitypubchem_assaypubmedreactomerefseqrhearnacentralscxa_expressionscxa_gene_experimentsignorspliceaistring_interactiontranscriptufeatureuniprot