CIMIP2A

Summary

CIMIP2A (ciliary microtubule inner protein 2A, HGNC:33818) is a protein-coding gene on chromosome 9q34.3, encoding Ciliary microtubule inner protein 2A (Q6J272). Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in flagellum axoneme.

Predicted to be involved in flagellated sperm motility. Located in ciliary basal body.

Source: NCBI Gene 401565 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 119 total — 1 pathogenic
• MANE Select transcript: NM_001001710

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:33818
Approved symbol	CIMIP2A
Name	ciliary microtubule inner protein 2A
Location	9q34.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000188163
Ensembl biotype	protein_coding
Entrez	401565

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 retained_intron

ENST00000344774, ENST00000471784, ENST00000484720

RefSeq mRNA: 1 — MANE Select: NM_001001710 NM_001001710

CCDS: CCDS35186

Canonical transcript exons

ENST00000344774 — 7 exons

Exon	Start	End
ENSE00001427633	137243599	137243788
ENSE00001455421	137244171	137244288
ENSE00001455422	137244642	137244736
ENSE00003711528	137247660	137247751
ENSE00003732175	137245639	137245853
ENSE00003746951	137245089	137245218
ENSE00003747150	137245307	137245557

Expression profiles

Bgee: expression breadth ubiquitous, 150 present calls, max score 93.80.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.1302 / max 106.9071, expressed in 3 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
103348	0.1145	3
103350	0.0109	3
103349	0.0048	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	93.80	gold quality
right testis	UBERON:0004534	93.06	gold quality
testis	UBERON:0000473	89.57	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	80.81	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	72.96	gold quality
medial globus pallidus	UBERON:0002477	68.65	silver quality
right lobe of liver	UBERON:0001114	67.60	gold quality
buccal mucosa cell	CL:0002336	65.76	gold quality
granulocyte	CL:0000094	64.68	gold quality
oviduct epithelium	UBERON:0004804	64.26	gold quality
globus pallidus	UBERON:0001875	62.70	silver quality
bone marrow cell	CL:0002092	62.11	silver quality
epithelium of nasopharynx	UBERON:0001951	61.46	gold quality
stromal cell of endometrium	CL:0002255	60.04	gold quality
esophagus squamous epithelium	UBERON:0006920	58.78	silver quality
germinal epithelium of ovary	UBERON:0001304	57.56	gold quality
liver	UBERON:0002107	57.53	gold quality
superficial temporal artery	UBERON:0001614	57.50	gold quality
ventricular zone	UBERON:0003053	57.37	gold quality
sural nerve	UBERON:0015488	57.10	gold quality
parotid gland	UBERON:0001831	56.03	gold quality
tendon of biceps brachii	UBERON:0008188	55.40	silver quality
amniotic fluid	UBERON:0000173	55.31	gold quality
pituitary gland	UBERON:0000007	54.84	gold quality
adenohypophysis	UBERON:0002196	54.51	gold quality
left adrenal gland cortex	UBERON:0035825	54.50	gold quality
subcutaneous adipose tissue	UBERON:0002190	54.26	gold quality
sperm	CL:0000019	54.01	gold quality
tibia	UBERON:0000979	53.79	gold quality
left adrenal gland	UBERON:0001234	53.37	gold quality

Single-cell (SCXA)

Detected in 2 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-GEOD-86618	no	55.91
E-ANND-3	no	1.71

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

8 targeting CIMIP2A, 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-LET-7A-2-3P	99.87	70.53	1921
HSA-LET-7G-3P	99.85	70.43	1929
HSA-MIR-4999-5P	99.35	69.15	926
HSA-MIR-1537-5P	98.70	68.33	999
HSA-MIR-4718	98.55	68.61	814
HSA-MIR-6748-3P	97.20	65.66	836
HSA-MIR-4433A-5P	96.79	65.01	599
HSA-MIR-4680-5P	96.43	67.15	893

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cimip2a	ENSMUSG00000026969
rattus_norvegicus	Cimip2a	ENSRNOG00000010019

Protein

Protein identifiers

Ciliary microtubule inner protein 2A — Q6J272 (reviewed: Q6J272)

All UniProt accessions (2): C9JBW9, Q6J272

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in flagellum axoneme. Binds to the intra-tubulin interfaces.

Subunit / interactions. Microtubule inner protein component of sperm flagellar doublet microtubules.

Subcellular location. Cytoplasm. Cytoskeleton. Flagellum axoneme.

Similarity. Belongs to the CIMIP2 family.

Isoforms (2)

UniProt ID	Names	Canonical?
Q6J272-1	1	yes
Q6J272-2	2

RefSeq proteins (1): NP_001001710* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018902	CMI2A-C-like_dom	Domain
IPR052683	CIMIP2A	Family

Pfam: PF10629

UniProt features (4 total): splice variant 2, chain 1, region of interest 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6J272-F1	61.88	0.04

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 48 (showing top): SP3_Q3, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOCC_CYTOPLASMIC_REGION, GOCC_MOTILE_CILIUM, RFX1_01, GOCC_CYTOPLASMIC_MICROTUBULE, GOCC_CILIUM, GOCC_CILIARY_BASAL_BODY, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MARTENS_TRETINOIN_RESPONSE_DN, WAKABAYASHI_ADIPOGENESIS_PPARG_RXRA_BOUND_8D, GOCC_AXONEMAL_MICROTUBULE, GOCC_9PLUS2_MOTILE_CILIUM

GO Biological Process (1): flagellated sperm motility (GO:0030317)

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

GO Cellular Component (10): nucleus (GO:0005634), ciliary basal body (GO:0036064), sperm flagellum (GO:0036126), axonemal A tubule inner sheath (GO:0160111), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), microtubule cytoskeleton (GO:0015630), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	3
cilium	2
cilium-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
binding	1
intracellular membrane-bounded organelle	1
microtubule organizing center	1
9+2 motile cilium	1
A axonemal microtubule	1
axonemal microtubule doublet inner sheath	1
intracellular anatomical structure	1
intracellular membraneless organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cytoskeleton	1

Protein interactions and networks

STRING

216 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIMIP2A	STPG3	Q8N7X2	620
CIMIP2A	OR6C70	A6NIJ9	574
CIMIP2A	H0YIS7	H0YIS7	506
CIMIP2A	TEX38	Q6PEX7	497
CIMIP2A	PRR30	Q53SZ7	474
CIMIP2A	SPATA31F1	Q6ZU69	472
CIMIP2A	CKS2	P33552	468
CIMIP2A	LYZL6	O75951	422
CIMIP2A	MYO15B	Q96JP2	418
CIMIP2A	GARIN1B	Q96KD3	409
CIMIP2A	DYNLT4	Q5JR98	404
CIMIP2A	SETSIP	P0DME0	398
CIMIP2A	NICOL1	Q5BLP8	394
CIMIP2A	FRG2	Q64ET8	387
CIMIP2A	ARMC12	Q5T9G4	383

IntAct

15 interactions, top by confidence:

A	B	Type	Score
HGS	CIMIP2A	psi-mi:“MI:0915”(physical association)	0.560
CIMIP2A	RHOXF2	psi-mi:“MI:0915”(physical association)	0.560
PROP1	CIMIP2A	psi-mi:“MI:0915”(physical association)	0.560
CIMIP2A	SMYD1	psi-mi:“MI:0915”(physical association)	0.560
CIMIP2A	ACY3	psi-mi:“MI:0915”(physical association)	0.400
NEK4	E2F8	psi-mi:“MI:0914”(association)	0.350
PROP1	CIMIP2A	psi-mi:“MI:0915”(physical association)	0.000
RHOXF2	CIMIP2A	psi-mi:“MI:0915”(physical association)	0.000
SMYD1	CIMIP2A	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (7): FAM166A (Affinity Capture-MS), FAM166A (Two-hybrid), FAM166A (Two-hybrid), FAM166A (Two-hybrid), FAM166A (Two-hybrid), FAM166A (Affinity Capture-MS), ACY3 (Affinity Capture-MS)

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: A2AIP0, A2RRW4, A8E5W8, A8MTA8, A9JS51, Q2TBR5, Q6J272, G3X6E2, Q4QR77, Q9D4K5, Q28YX9, Q7JRP4

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	1
Likely pathogenic	0
Uncertain significance	98
Likely benign	10
Benign	3

Top pathogenic / likely-pathogenic (1)

Variant ID	HGVS	Classification
3245386	NC_000009.11:g.(?140127344)(140164869_?)del	Pathogenic

SpliceAI

1248 predictions. Top by Δscore:

Variant	Effect	Δscore
9:137244289:C:CC	acceptor_gain	1.0000
9:137244705:CCAGG:C	acceptor_gain	1.0000
9:137245637:A:AC	donor_gain	1.0000
9:137245638:C:CC	donor_gain	1.0000
9:137245849:CATAG:C	acceptor_gain	1.0000
9:137245854:C:CC	acceptor_gain	1.0000
9:137244284:AGGAA:A	acceptor_gain	0.9900
9:137244285:GGAA:G	acceptor_gain	0.9900
9:137244697:CCCAT:C	acceptor_gain	0.9900
9:137244706:C:T	acceptor_gain	0.9900
9:137244706:CAGG:C	acceptor_gain	0.9900
9:137245084:CCCA:C	donor_loss	0.9900
9:137245086:CACC:C	donor_loss	0.9900
9:137245087:A:AG	donor_loss	0.9900
9:137245088:C:A	donor_loss	0.9900
9:137245216:CAG:C	acceptor_gain	0.9900
9:137245399:T:TA	donor_gain	0.9900
9:137245850:ATAGC:A	acceptor_loss	0.9900
9:137245851:TAG:T	acceptor_gain	0.9900
9:137245852:AG:A	acceptor_gain	0.9900
9:137245853:GCTG:G	acceptor_loss	0.9900
9:137245854:C:CG	acceptor_loss	0.9900
9:137247658:A:AC	donor_gain	0.9900
9:137247658:AC:A	donor_gain	0.9900
9:137247659:C:CC	donor_gain	0.9900
9:137247659:CC:C	donor_gain	0.9900
9:137244286:GAA:G	acceptor_gain	0.9800
9:137244287:AA:A	acceptor_gain	0.9800
9:137244707:A:T	acceptor_gain	0.9800
9:137245360:C:A	donor_gain	0.9800

AlphaMissense

2092 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:137244654:G:C	F245L	0.987
9:137244654:G:T	F245L	0.987
9:137244656:A:G	F245L	0.987
9:137244723:G:C	F222L	0.985
9:137244723:G:T	F222L	0.985
9:137244725:A:G	F222L	0.985
9:137245841:G:C	F23L	0.981
9:137245841:G:T	F23L	0.981
9:137245843:A:G	F23L	0.981
9:137244668:C:G	A241P	0.976
9:137244178:G:C	F286L	0.964
9:137244178:G:T	F286L	0.964
9:137244180:A:G	F286L	0.964
9:137243760:G:C	F298L	0.949
9:137243760:G:T	F298L	0.949
9:137243762:A:G	F298L	0.949
9:137244183:C:A	G285W	0.949
9:137245757:G:C	S51R	0.949
9:137245757:G:T	S51R	0.949
9:137245759:T:G	S51R	0.949
9:137244655:A:G	F245S	0.934
9:137245807:A:C	Y35D	0.934
9:137245852:A:G	Y20H	0.933
9:137244190:G:C	F282L	0.932
9:137244190:G:T	F282L	0.932
9:137244192:A:G	F282L	0.932
9:137243751:G:C	S301R	0.931
9:137243751:G:T	S301R	0.931
9:137243753:T:G	S301R	0.931
9:137244655:A:C	F245C	0.930

dbSNP variants (sampled 300 via entrez): RS1000357207 (9:137250582 A>G), RS1000801398 (9:137249230 A>G), RS1000942528 (9:137253731 C>G), RS1000952112 (9:137253537 G>A,C,T), RS1001148781 (9:137249393 T>C), RS1001153927 (9:137243959 G>C), RS1001431152 (9:137247210 G>C), RS1001531715 (9:137253719 A>G,T), RS1001945062 (9:137244930 T>C), RS1002017162 (9:137248759 T>C), RS1002106086 (9:137254781 C>A), RS1002143217 (9:137244594 G>A), RS1002636924 (9:137252437 A>C,G), RS1002770411 (9:137248064 C>T), RS1002831519 (9:137256753 C>A,T)

Disease associations

OMIM: gene `` | 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

12 total (human), top 12 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
sodium arsenite	increases expression, decreases expression	2
Benzo(a)pyrene	decreases expression, decreases methylation	2
aristolochic acid I	increases expression	1
sotorasib	increases expression, affects cotreatment	1
licochalcone B	increases expression	1
trametinib	affects cotreatment, increases expression	1
NVP-BKM120	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Leflunomide	decreases expression	1
N-Nitrosopyrrolidine	decreases expression	1
Plant Extracts	affects cotreatment, decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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