CIMIP2C

Summary

CIMIP2C (ciliary microtubule inner protein 2C, HGNC:27938) is a protein-coding gene on chromosome 2p23.3, encoding Ciliary microtubule inner protein 2C (A6NJV1). Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating.

Predicted to be involved in flagellated sperm motility. Located in axonemal microtubule.

Source: NCBI Gene 339778 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 11 total
• MANE Select transcript: NM_001105519

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:27938
Approved symbol	CIMIP2C
Name	ciliary microtubule inner protein 2C
Location	2p23.3
Locus type	gene with protein product
Status	Approved
Aliases	LOC339778
Ensembl gene	ENSG00000173557
Ensembl biotype	protein_coding
Entrez	339778

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 retained_intron

ENST00000329615, ENST00000409392, ENST00000453368, ENST00000479453

RefSeq mRNA: 2 — MANE Select: NM_001105519 NM_001105519, NM_001322426

CCDS: CCDS42661, CCDS82429

Canonical transcript exons

ENST00000329615 — 4 exons

Exon	Start	End
ENSE00001293987	26562587	26562686
ENSE00001695953	26579294	26579524
ENSE00003549374	26575902	26576175
ENSE00003599197	26577516	26577628

Expression profiles

Bgee: expression breadth ubiquitous, 143 present calls, max score 96.94.

FANTOM5 (CAGE): breadth broad, TPM avg 0.6386 / max 97.4344, expressed in 189 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
19268	0.6386	189

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	96.94	gold quality
sperm	CL:0000019	89.27	silver quality
left testis	UBERON:0004533	87.05	gold quality
right testis	UBERON:0004534	86.61	gold quality
right uterine tube	UBERON:0001302	83.91	gold quality
testis	UBERON:0000473	83.61	gold quality
tibialis anterior	UBERON:0001385	72.94	silver quality
ventricular zone	UBERON:0003053	72.38	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	71.89	gold quality
bronchial epithelial cell	CL:0002328	67.84	silver quality
bronchus	UBERON:0002185	66.60	silver quality
oviduct epithelium	UBERON:0004804	66.47	silver quality
hypothalamus	UBERON:0001898	65.39	gold quality
ganglionic eminence	UBERON:0004023	64.73	gold quality
fallopian tube	UBERON:0003889	64.66	gold quality
body of stomach	UBERON:0001161	64.60	gold quality
islet of Langerhans	UBERON:0000006	64.39	gold quality
adult organism	UBERON:0007023	63.82	gold quality
ileal mucosa	UBERON:0000331	62.88	gold quality
deltoid	UBERON:0001476	62.06	gold quality
nasal cavity mucosa	UBERON:0001826	61.86	gold quality
stomach	UBERON:0000945	61.79	gold quality
left lobe of thyroid gland	UBERON:0001120	61.62	gold quality
myocardium	UBERON:0002349	60.98	gold quality
thyroid gland	UBERON:0002046	60.33	gold quality
pancreas	UBERON:0001264	60.27	gold quality
body of pancreas	UBERON:0001150	59.35	gold quality
right lobe of thyroid gland	UBERON:0001119	58.70	gold quality
minor salivary gland	UBERON:0001830	58.57	gold quality
saliva-secreting gland	UBERON:0001044	58.00	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 1.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	4.17

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cimip2c	ENSMUSG00000029182
rattus_norvegicus	Cimip2c	ENSRNOG00000009905

Protein

Protein identifiers

Ciliary microtubule inner protein 2C — A6NJV1 (reviewed: A6NJV1)

All UniProt accessions (3): A6NJV1, B8ZZ55, H7C0N2

UniProt curated annotations — full annotation on UniProt →

Function. Microtubule inner protein (MIP) part of the dynein-decorated doublet microtubules (DMTs) in cilia axoneme, which is required for motile cilia beating. Binds to the intra-tubulin interfaces.

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

Subcellular location. Cytoplasm. Cytoskeleton. Cilium axoneme. Flagellum axoneme.

Tissue specificity. Expressed in airway epithelial cells.

Similarity. Belongs to the CIMIP2 family.

RefSeq proteins (2): NP_001098989, NP_001309355 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018902	CMI2A-C-like_dom	Domain
IPR052329	CIMIP2C	Family

Pfam: PF10629

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

Structure

Experimental structures (PDB)

2 structures.

PDB	Method	Resolution (Å)
7UNG	ELECTRON MICROSCOPY	3.6
8J07	ELECTRON MICROSCOPY	4.1

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-A6NJV1-F1	81.55	0.19

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 39 (showing top): GOBP_CILIUM_MOVEMENT, GOBP_CILIUM_OR_FLAGELLUM_DEPENDENT_CELL_MOTILITY, GOCC_CYTOPLASMIC_REGION, GOCC_MOTILE_CILIUM, GOCC_CYTOPLASMIC_MICROTUBULE, GOCC_CILIUM, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MIKKELSEN_MCV6_HCP_WITH_H3K27ME3, MIKKELSEN_MEF_HCP_WITH_H3K27ME3, DELACROIX_RAR_BOUND_ES, GOCC_AXONEMAL_MICROTUBULE, GOCC_9PLUS2_MOTILE_CILIUM, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, GOCC_SUPRAMOLECULAR_POLYMER

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

GO Molecular Function (0):

GO Cellular Component (10): nucleus (GO:0005634), axonemal microtubule (GO:0005879), 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-dependent cell motility	1
cilium movement involved in cell motility	1
sperm motility	1
intracellular membrane-bounded organelle	1
cytoplasmic microtubule	1
axoneme	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
cilium	1

Protein interactions and networks

STRING

258 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIMIP2C	ZNF441	Q8N8Z8	528
CIMIP2C	LHFPL7	Q6ICI0	506
CIMIP2C	APOL5	Q9BWW9	447
CIMIP2C	TAF6L	Q9Y6J9	398
CIMIP2C	BTBD3	Q9Y2F9	371
CIMIP2C	MRPS33	Q9Y291	370
CIMIP2C	RCBTB1	Q8NDN9	369
CIMIP2C	RBKS	Q9H477	337
CIMIP2C	NIFK	Q9BYG3	326
CIMIP2C	PCBP4	P57723	325
CIMIP2C	PACSIN3	Q9UKS6	324
CIMIP2C	GJB5	O95377	307
CIMIP2C	PHOSPHO1	Q8TCT1	303
CIMIP2C	LZTS1	Q9Y250	294
CIMIP2C	DGKB	Q9Y6T7	275

IntAct

0 interactions, top by confidence:

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: A4II40, A6NJV1, Q3SZR5, Q5M7D8, Q5M7F8, Q9DAS2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	0
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

827 predictions. Top by Δscore:

Variant	Effect	Δscore
2:26576173:CAGG:C	donor_loss	1.0000
2:26576176:G:GG	donor_gain	1.0000
2:26576176:GTA:G	donor_loss	1.0000
2:26576177:T:A	donor_loss	1.0000
2:26577502:T:TA	acceptor_gain	1.0000
2:26577506:T:A	acceptor_gain	1.0000
2:26577509:A:AG	acceptor_gain	1.0000
2:26577512:ATAGA:A	acceptor_loss	1.0000
2:26577513:T:G	acceptor_gain	1.0000
2:26577513:TA:T	acceptor_loss	1.0000
2:26577514:A:AG	acceptor_gain	1.0000
2:26577514:A:C	acceptor_loss	1.0000
2:26577514:AGAT:A	acceptor_gain	1.0000
2:26577515:G:GA	acceptor_gain	1.0000
2:26577515:GA:G	acceptor_gain	1.0000
2:26577515:GAT:G	acceptor_gain	1.0000
2:26577515:GATG:G	acceptor_gain	1.0000
2:26577624:GTCCT:G	donor_gain	1.0000
2:26577629:G:GG	donor_gain	1.0000
2:26562683:CCGGG:C	donor_loss	0.9900
2:26562685:GG:G	donor_gain	0.9900
2:26562686:GG:G	donor_gain	0.9900
2:26562687:G:GC	donor_loss	0.9900
2:26562688:T:A	donor_loss	0.9900
2:26575938:T:TA	acceptor_gain	0.9900
2:26575941:C:CA	acceptor_gain	0.9900
2:26575949:AC:A	acceptor_gain	0.9900
2:26575950:C:CA	acceptor_gain	0.9900
2:26575950:C:G	acceptor_gain	0.9900
2:26576172:CCAG:C	donor_gain	0.9900

AlphaMissense

1310 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:26577532:G:C	R122P	0.975
2:26579421:T:C	F197L	0.959
2:26579423:T:A	F197L	0.959
2:26579423:T:G	F197L	0.959
2:26579411:A:C	R193S	0.958
2:26579411:A:T	R193S	0.958
2:26579401:G:C	R190P	0.957
2:26577579:T:C	F138L	0.952
2:26577581:T:A	F138L	0.952
2:26577581:T:G	F138L	0.952
2:26575985:G:C	R53P	0.951
2:26579367:T:C	F179L	0.951
2:26579369:C:A	F179L	0.951
2:26579369:C:G	F179L	0.951
2:26562649:T:C	F13L	0.949
2:26562651:C:A	F13L	0.949
2:26562651:C:G	F13L	0.949
2:26562644:C:T	T11I	0.929
2:26579432:A:C	R200S	0.928
2:26579432:A:T	R200S	0.928
2:26575984:C:A	R53S	0.927
2:26577546:G:C	D127H	0.922
2:26577580:T:C	F138S	0.912
2:26579427:T:C	F199L	0.910
2:26579429:C:A	F199L	0.910
2:26579429:C:G	F199L	0.910
2:26575909:G:C	G28R	0.897
2:26575903:T:C	Y26H	0.893
2:26575903:T:G	Y26D	0.880
2:26575916:T:A	V30D	0.879

dbSNP variants (sampled 300 via entrez): RS1000015832 (2:26572467 G>A,C), RS1000284351 (2:26576912 C>G), RS1000766464 (2:26571281 C>T), RS1001294165 (2:26566865 G>A), RS1001407118 (2:26560667 G>A), RS1001828129 (2:26566223 T>G), RS1001880733 (2:26570430 T>C), RS1001912004 (2:26570630 G>A), RS1002019848 (2:26569879 C>T), RS1002093586 (2:26569564 T>A), RS1002300863 (2:26574883 G>A), RS1002427022 (2:26565119 T>C), RS1002569172 (2:26575264 C>T), RS1002605983 (2:26579605 T>C,G), RS1002889155 (2:26569192 A>C,G)

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

1 associations (top):

Study	Trait	p-value
GCST001588_13	Periodontal microbiota	2.000000e-06

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

16 total (human), top 16 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol S	affects cotreatment, increases methylation, decreases expression	2
Air Pollutants	increases abundance, increases methylation, increases expression	2
Benzo(a)pyrene	affects methylation, increases methylation	2
benzo(e)pyrene	decreases methylation	1
aflatoxin B2	increases methylation	1
abrine	decreases expression	1
(+)-JQ1 compound	decreases expression	1
Temozolomide	increases expression	1
Zoledronic Acid	decreases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Methapyrilene	decreases methylation	1
Silicon Dioxide	decreases expression	1
Smoke	increases expression, increases abundance	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	decreases methylation	1
Soot	increases methylation, increases abundance	1

Clinical trials (associated diseases)

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