CIMAP3

Summary

CIMAP3 (ciliary microtubule associated protein 3, HGNC:27009) is a protein-coding gene on chromosome 1p13.2, encoding Ciliary microtubule-associated protein 3 (Q8TCI5). During primary cilia disassembly, involved in cilia disassembly.

Enables cytoskeletal protein binding activity and enzyme binding activity. Involved in positive regulation of kinase activity. Predicted to be located in ciliary basal body and trans-Golgi network.

Source: NCBI Gene 128344 — RefSeq curated summary.

At a glance

• GWAS associations: 3
• Clinical variants (ClinVar): 31 total
• MANE Select transcript: NM_181643

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27009
Approved symbol	CIMAP3
Name	ciliary microtubule associated protein 3
Location	1p13.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ23853, pitchfork
Ensembl gene	ENSG00000173947
Ensembl biotype	protein_coding
OMIM	614234
Entrez	128344

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 2 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000369737, ENST00000369738, ENST00000468395, ENST00000484512

RefSeq mRNA: 2 — MANE Select: NM_181643 NM_001300831, NM_181643

CCDS: CCDS72836, CCDS833

Canonical transcript exons

ENST00000369738 — 6 exons

Exon	Start	End
ENSE00001189011	111348516	111348646
ENSE00001832812	111346622	111346671
ENSE00003491520	111350106	111350223
ENSE00003578356	111347674	111347772
ENSE00003587786	111346910	111347049
ENSE00003619429	111351259	111353013

Expression profiles

Bgee: expression breadth ubiquitous, 180 present calls, max score 99.60.

FANTOM5 (CAGE): breadth broad, TPM avg 6.8558 / max 340.4910, expressed in 903 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
4629	5.5577	718
4625	1.0155	414
4627	0.1098	52
4628	0.0973	25
4626	0.0384	12
4630	0.0371	18

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
bronchial epithelial cell	CL:0002328	99.60	gold quality
right uterine tube	UBERON:0001302	99.35	gold quality
bronchus	UBERON:0002185	99.03	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.90	gold quality
oviduct epithelium	UBERON:0004804	97.37	gold quality
mucosa of paranasal sinus	UBERON:0005030	96.64	gold quality
sperm	CL:0000019	94.28	gold quality
fallopian tube	UBERON:0003889	92.82	gold quality
nasal cavity epithelium	UBERON:0005384	92.05	gold quality
epithelium of nasopharynx	UBERON:0001951	91.17	gold quality
left testis	UBERON:0004533	91.09	gold quality
right testis	UBERON:0004534	90.87	gold quality
caput epididymis	UBERON:0004358	90.40	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	90.26	gold quality
testis	UBERON:0000473	89.49	gold quality
buccal mucosa cell	CL:0002336	88.04	silver quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	85.78	gold quality
trachea	UBERON:0003126	84.19	gold quality
adenohypophysis	UBERON:0002196	83.59	gold quality
right lung	UBERON:0002167	83.48	gold quality
right atrium auricular region	UBERON:0006631	83.48	gold quality
cardiac atrium	UBERON:0002081	83.26	gold quality
nasal cavity mucosa	UBERON:0001826	83.06	gold quality
apex of heart	UBERON:0002098	82.74	gold quality
pituitary gland	UBERON:0000007	82.55	gold quality
adult organism	UBERON:0007023	82.25	gold quality
hypothalamus	UBERON:0001898	81.01	gold quality
kidney epithelium	UBERON:0004819	80.48	gold quality
caudate nucleus	UBERON:0001873	80.21	gold quality
body of pancreas	UBERON:0001150	80.06	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-HCAD-15	yes	1949.64
E-MTAB-9388	yes	1803.49
E-CURD-114	yes	1341.91
E-MTAB-10283	yes	1311.41
E-MTAB-9154	yes	1139.81
E-MTAB-10287	yes	1000.64
E-MTAB-10485	yes	632.21
E-MTAB-6108	yes	201.97
E-HCAD-1	yes	32.53
E-GEOD-130148	yes	16.03
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

48 targeting CIMAP3, top 30 by miRDB confidence (max_score; target_count = how many genes the miRNA targets in total — lower means more specific):

miRNA	Max score	Avg score	miRNA target_count
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4795-3P	100.00	74.62	4024
HSA-MIR-1277-5P	100.00	73.95	5056
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-6748-5P	100.00	65.81	1057
HSA-MIR-3185	99.99	68.12	1959
HSA-MIR-6759-5P	99.99	66.54	785
HSA-MIR-4282	99.99	75.36	6408
HSA-MIR-4666A-3P	99.96	71.71	3434
HSA-MIR-205-3P	99.92	69.92	3165
HSA-MIR-4302	99.89	67.94	1187
HSA-MIR-579-3P	99.86	71.66	3628
HSA-MIR-202-3P	99.84	71.41	1290
HSA-MIR-664B-3P	99.84	71.65	3590
HSA-MIR-6739-5P	99.80	67.87	2806
HSA-MIR-4694-3P	99.79	69.53	2640
HSA-MIR-6733-5P	99.74	67.94	2759
HSA-MIR-4428	99.73	66.41	1733
HSA-MIR-7161-5P	99.68	68.92	1592
HSA-MIR-4743-3P	99.62	68.12	2095
HSA-MIR-3153	99.55	67.59	2337
HSA-MIR-6832-3P	99.52	70.44	1726
HSA-MIR-4489	99.50	65.56	785
HSA-MIR-513C-5P	99.50	68.42	1730
HSA-MIR-6727-3P	99.49	65.92	1333
HSA-MIR-6882-5P	99.35	71.13	1206
HSA-MIR-4477B	99.23	70.49	1733
HSA-MIR-4292	99.16	65.57	1767
HSA-MIR-6791-5P	99.16	65.92	1844
HSA-MIR-323B-3P	99.14	68.89	725

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	si:ch211-66i15.4	ENSDARG00000097071
mus_musculus	Cimap3	ENSMUSG00000010136
rattus_norvegicus	Cimap3	ENSRNOG00000016842

Protein

Protein identifiers

Ciliary microtubule-associated protein 3 — Q8TCI5 (reviewed: Q8TCI5)

Alternative names: Protein pitchfork

All UniProt accessions (1): Q8TCI5

UniProt curated annotations — full annotation on UniProt →

Function. During primary cilia disassembly, involved in cilia disassembly. Required specifically to control cilia retraction as well as the liberation and duplication of the basal body/centrosome. May act by stimulating AURKA activity at the basal body in a cell cycle-dependent manner.

Subunit / interactions. Interacts with proteins involved in ciliary transport, including ARL13B, CETN1, KIF3A, RAB6A, RAB8A, TUBB1 and TUBG1. Interacts with AURKA.

Subcellular location. Cytoplasmic vesicle. Golgi apparatus. trans-Golgi network. Cytoplasm.

Isoforms (3)

UniProt ID	Names	Canonical?
Q8TCI5-1	1	yes
Q8TCI5-2	2
Q8TCI5-3	3

RefSeq proteins (2): NP_001287760, NP_857594* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010736	SHIPPO-rpt	Repeat
IPR033602	CIMAP3	Family

Pfam: PF07004

UniProt features (8 total): sequence variant 3, splice variant 2, sequence conflict 2, chain 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8TCI5-F1	72.99	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 79 (showing top): GOBP_EPITHELIUM_DEVELOPMENT, GOBP_REGULATION_OF_PHOSPHORYLATION, GOBP_REGULATION_OF_TRANSFERASE_ACTIVITY, GOMF_GTPASE_BINDING, CHANDRAN_METASTASIS_DN, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_POSITIVE_REGULATION_OF_CATALYTIC_ACTIVITY, GOBP_REGULATION_OF_CELL_PROJECTION_ORGANIZATION, GOBP_EMBRYONIC_HEART_TUBE_DEVELOPMENT, GOCC_TRANS_GOLGI_NETWORK, GOBP_POSITIVE_REGULATION_OF_MOLECULAR_FUNCTION, SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, GOBP_POSITIVE_REGULATION_OF_PHOSPHORUS_METABOLIC_PROCESS, GOBP_CILIUM_ORGANIZATION, GOBP_EMBRYO_DEVELOPMENT

GO Biological Process (5): regulation of cell projection organization (GO:0031344), positive regulation of kinase activity (GO:0033674), cilium organization (GO:0044782), embryonic heart tube left/right pattern formation (GO:0060971), cell projection organization (GO:0030030)

GO Molecular Function (7): cytoskeletal protein binding (GO:0008092), kinesin binding (GO:0019894), protein kinase binding (GO:0019901), small GTPase binding (GO:0031267), gamma-tubulin binding (GO:0043015), beta-tubulin binding (GO:0048487), protein binding (GO:0005515)

GO Cellular Component (6): nucleus (GO:0005634), trans-Golgi network (GO:0005802), cytoplasmic vesicle (GO:0031410), ciliary basal body (GO:0036064), cytoplasm (GO:0005737), Golgi apparatus (GO:0005794)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
tubulin binding	2
intracellular membrane-bounded organelle	2
cytoplasm	2
cell projection organization	1
regulation of cellular component organization	1
kinase activity	1
positive regulation of phosphorylation	1
positive regulation of catalytic activity	1
regulation of kinase activity	1
organelle organization	1
plasma membrane bounded cell projection organization	1
embryonic heart tube development	1
left/right pattern formation	1
cellular component organization	1
protein binding	1
cytoskeletal protein binding	1
kinase binding	1
GTPase binding	1
binding	1
Golgi apparatus subcompartment	1
intracellular vesicle	1
microtubule organizing center	1
cilium	1
intracellular anatomical structure	1
cellular anatomical structure	1
endomembrane system	1

Protein interactions and networks

STRING

642 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIMAP3	GPRASP2	Q96D09	805
CIMAP3	RSPH1	Q8WYR4	565
CIMAP3	NEDD9	Q14511	534
CIMAP3	SMO	Q99835	517
CIMAP3	DENND2D	Q9H6A0	517
CIMAP3	TXLNB	Q8N3L3	473
CIMAP3	DYNLT1	P63172	463
CIMAP3	DRC4	O95995	460
CIMAP3	ARMC3	Q5W041	459
CIMAP3	KIF24	Q5T7B8	452
CIMAP3	CDHR3	Q6ZTQ4	448
CIMAP3	STPG3	Q8N7X2	448
CIMAP3	TEKT1	Q969V4	433
CIMAP3	FOXJ1	Q92949	420
CIMAP3	CCP110	O43303	420

IntAct

3 interactions, top by confidence:

A	B	Type	Score
CIMAP3	PSMG3	psi-mi:“MI:0914”(association)	0.530
CIMAP3	EPHA2	psi-mi:“MI:0914”(association)	0.350

BioGRID (23): RAP2A (Affinity Capture-MS), ANAPC1 (Affinity Capture-MS), DAAM1 (Affinity Capture-MS), YES1 (Affinity Capture-MS), GNAQ (Affinity Capture-MS), PSMG3 (Affinity Capture-MS), DUSP28 (Affinity Capture-MS), EPHA2 (Affinity Capture-MS), ANAPC5 (Affinity Capture-MS), CRNN (Affinity Capture-MS), ANAPC1 (Affinity Capture-MS), PSMG3 (Affinity Capture-MS), DUSP28 (Affinity Capture-MS), CSNK1G1 (Affinity Capture-MS), GNAQ (Affinity Capture-MS)

ESM2 similar proteins: A1A5R9, A2AVQ5, A2RRW4, A2RSX4, A5WUY6, A9JS51, B0BM24, B0S4Q5, B1H283, D4A039, F1MMV1, Q08BC4, Q0VB26, Q2T9Q3, Q2TA11, Q2TBS4, Q3KQ80, Q3SX64, Q3TZ65, Q3ZCV2, Q4KKZ1, Q4KLY8, Q4R5Y0, Q5PQN4, Q5RAF2, Q5XI56, Q6ZN84, Q810P2, Q8BUG5, Q8C008, Q8C8J0, Q8IXM7, Q8N412, Q8N6G2, Q8N7U6, Q8N801, Q8TCI5, Q8WW14, Q9D067, Q9D131

Diamond homologs: Q2TBS4, Q8TCI5, Q9D9W1

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	20
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

704 predictions. Top by Δscore:

Variant	Effect	Δscore
1:111347658:A:AG	acceptor_gain	1.0000
1:111350101:TCTA:T	acceptor_loss	1.0000
1:111350102:CTA:C	acceptor_loss	1.0000
1:111350103:TAGCC:T	acceptor_loss	1.0000
1:111350104:A:AG	acceptor_gain	1.0000
1:111350104:AG:A	acceptor_loss	1.0000
1:111350105:G:A	acceptor_loss	1.0000
1:111350105:G:GA	acceptor_gain	1.0000
1:111350105:GC:G	acceptor_gain	1.0000
1:111350105:GCC:G	acceptor_gain	1.0000
1:111350105:GCCC:G	acceptor_gain	1.0000
1:111350105:GCCCT:G	acceptor_gain	1.0000
1:111350189:TTCC:T	donor_gain	1.0000
1:111347637:T:TA	acceptor_gain	0.9900
1:111350098:A:AG	acceptor_gain	0.9900
1:111350099:T:G	acceptor_gain	0.9900
1:111350219:C:G	donor_gain	0.9900
1:111346670:AG:A	donor_loss	0.9800
1:111346671:GG:G	donor_loss	0.9800
1:111346672:G:GC	donor_loss	0.9800
1:111346673:T:G	donor_loss	0.9800
1:111346951:A:T	donor_gain	0.9800
1:111347047:GAT:G	donor_gain	0.9800
1:111347662:T:G	acceptor_gain	0.9800
1:111348507:T:TA	acceptor_gain	0.9800
1:111348511:AACAG:A	acceptor_loss	0.9800
1:111348512:ACAGG:A	acceptor_loss	0.9800
1:111348513:CAGGA:C	acceptor_loss	0.9800
1:111348514:A:AC	acceptor_loss	0.9800
1:111348515:G:GC	acceptor_loss	0.9800

AlphaMissense

1254 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:111347713:A:C	S67R	0.991
1:111347715:T:A	S67R	0.991
1:111347715:T:G	S67R	0.991
1:111350164:T:C	F150L	0.989
1:111350166:T:A	F150L	0.989
1:111350166:T:G	F150L	0.989
1:111351290:G:C	R180P	0.989
1:111351296:G:C	R182P	0.980
1:111350152:T:A	W146R	0.979
1:111350152:T:C	W146R	0.979
1:111347742:A:C	R76S	0.974
1:111347742:A:T	R76S	0.974
1:111347722:G:A	G70R	0.973
1:111347722:G:C	G70R	0.973
1:111348591:T:C	F112L	0.970
1:111348593:T:A	F112L	0.970
1:111348593:T:G	F112L	0.970
1:111347754:G:C	R80S	0.968
1:111347754:G:T	R80S	0.968
1:111350154:G:C	W146C	0.961
1:111350154:G:T	W146C	0.961
1:111351301:G:C	A184P	0.960
1:111350181:G:C	W155C	0.959
1:111350181:G:T	W155C	0.959
1:111347723:G:A	G70E	0.958
1:111351304:T:G	Y185D	0.958
1:111351308:T:C	L186P	0.955
1:111350179:T:A	W155R	0.953
1:111350179:T:C	W155R	0.953
1:111347746:G:C	A78P	0.950

dbSNP variants (sampled 300 via entrez): RS1000160193 (1:111331516 T>G), RS1000194599 (1:111331894 G>T), RS1000197153 (1:111329624 G>A), RS1000274730 (1:111350803 G>A), RS1000556042 (1:111333051 A>T), RS1000595753 (1:111340137 A>G), RS1000751132 (1:111346290 T>C), RS1000881634 (1:111352546 T>C), RS1000924660 (1:111339929 G>T), RS1001170983 (1:111349111 G>A), RS1001205474 (1:111349414 C>T), RS1001355254 (1:111352851 G>A), RS1001566901 (1:111328485 G>A), RS1001635892 (1:111328586 C>A,G), RS1001999010 (1:111338990 A>C,G,T)

Disease associations

OMIM: gene MIM:614234 | 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):

Study	Trait	p-value
GCST002666_6	Interferon alpha levels in systemic lupus erythematosus	3.000000e-06
GCST003815_8	Late-onset Alzheimer’s disease	1.000000e-06
GCST007059_13	Response to antidepressants (symptom improvement)	2.000000e-06

EFO canonical traits (2, from GWAS)

EFO ID	Trait name
EFO:0006517	interferon alpha measurement
EFO:1001870	late-onset Alzheimers disease

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

23 total (human), top 23 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, increases expression, affects expression, decreases methylation	8
mercuric bromide	increases expression, affects cotreatment	2
entinostat	increases expression, affects cotreatment	2
belinostat	increases expression, affects cotreatment	2
Benzo(a)pyrene	decreases methylation, increases expression	2
Phenylmercuric Acetate	affects cotreatment, increases expression	2
bisphenol A	increases expression	1
ethyl-p-hydroxybenzoate	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, increases expression	1
dorsomorphin	increases expression, affects cotreatment	1
Sunitinib	decreases expression	1
Vorinostat	increases expression, affects cotreatment	1
Panobinostat	affects cotreatment, increases expression	1
Air Pollutants	increases expression, increases abundance	1
Amiodarone	increases expression	1
Diethylhexyl Phthalate	increases expression	1
Doxorubicin	decreases expression	1
Methyl Methanesulfonate	increases expression	1
Smoke	increases expression, increases abundance	1
Tobacco Smoke Pollution	decreases expression	1
Urethane	increases expression	1
Cyclosporine	decreases expression	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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