CIMIP2B

Summary

CIMIP2B (ciliary microtubule inner protein 2B, HGNC:34242) is a protein-coding gene on chromosome 9p13.3, encoding Ciliary microtubule inner protein 2B (A8MTA8). 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 730112 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 62 total — 2 pathogenic
• MANE Select transcript: NM_001164310

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:34242
Approved symbol	CIMIP2B
Name	ciliary microtubule inner protein 2B
Location	9p13.3
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000215187
Ensembl biotype	protein_coding
Entrez	730112

Gene structure

Transcript identifiers

Ensembl transcripts: 5 — 3 protein_coding, 2 protein_coding_CDS_not_defined

ENST00000399742, ENST00000447837, ENST00000478246, ENST00000480287, ENST00000492890

RefSeq mRNA: 4 — MANE Select: NM_001164310 NM_001099951, NM_001164310, NM_001287238, NM_001287239

CCDS: CCDS47963, CCDS56572

Canonical transcript exons

ENST00000399742 — 6 exons

Exon	Start	End
ENSE00001539966	35563166	35563389
ENSE00001787088	35561831	35562095
ENSE00003461385	35562875	35563080
ENSE00003522520	35562380	35562574
ENSE00003630905	35562649	35562700
ENSE00003847210	35563767	35563878

Expression profiles

Bgee: expression breadth ubiquitous, 167 present calls, max score 99.59.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.7873 / max 269.1875, expressed in 155 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
100581	0.7137	129
100582	0.0455	18
100580	0.0282	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
adrenal tissue	UBERON:0018303	99.59	gold quality
right adrenal gland cortex	UBERON:0035827	99.49	gold quality
right adrenal gland	UBERON:0001233	99.34	gold quality
right uterine tube	UBERON:0001302	99.22	gold quality
left adrenal gland cortex	UBERON:0035825	99.13	gold quality
left adrenal gland	UBERON:0001234	99.10	gold quality
adrenal cortex	UBERON:0001235	98.14	gold quality
adrenal gland	UBERON:0002369	97.65	gold quality
hindlimb stylopod muscle	UBERON:0004252	97.03	gold quality
gastrocnemius	UBERON:0001388	95.91	gold quality
muscle of leg	UBERON:0001383	94.68	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	94.23	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.44	gold quality
fallopian tube	UBERON:0003889	84.03	gold quality
skeletal muscle tissue	UBERON:0001134	83.08	gold quality
oviduct epithelium	UBERON:0004804	81.07	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.62	gold quality
quadriceps femoris	UBERON:0001377	80.29	silver quality
vastus lateralis	UBERON:0001379	78.84	silver quality
tibialis anterior	UBERON:0001385	78.59	silver quality
popliteal artery	UBERON:0002250	78.54	gold quality
tibial artery	UBERON:0007610	78.50	gold quality
muscle tissue	UBERON:0002385	78.40	gold quality
aorta	UBERON:0000947	77.94	gold quality
ascending aorta	UBERON:0001496	77.73	gold quality
thoracic aorta	UBERON:0001515	77.65	gold quality
bronchial epithelial cell	CL:0002328	77.25	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	77.07	gold quality
right lung	UBERON:0002167	76.85	gold quality
left coronary artery	UBERON:0001626	76.74	gold quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 3.

Experiment	Marker?	Max mean expression
E-HCAD-1	yes	25.80
E-MTAB-10287	yes	25.70
E-ANND-3	yes	8.14

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

20 targeting CIMIP2B, 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-3924	100.00	72.09	2394
HSA-MIR-6809-3P	99.91	71.45	3814
HSA-MIR-4753-3P	99.90	71.03	3786
HSA-MIR-3202	99.66	67.70	2737
HSA-MIR-2392	99.43	67.50	708
HSA-MIR-103A-1-5P	99.39	67.78	1545
HSA-MIR-103A-2-5P	99.39	67.72	1577
HSA-MIR-18A-5P	99.29	71.05	806
HSA-MIR-18B-5P	99.29	71.05	806
HSA-MIR-4505	99.27	67.81	2678
HSA-MIR-5787	99.22	67.86	2628
HSA-MIR-4735-3P	99.14	69.85	777
HSA-MIR-3926	98.95	69.26	1438
HSA-MIR-548S	98.50	67.17	1213
HSA-MIR-5008-5P	98.42	65.87	1019
HSA-MIR-3144-3P	98.15	67.34	677
HSA-MIR-3652	97.71	65.43	1890
HSA-MIR-4430	97.47	65.61	1813
HSA-MIR-1224-3P	97.24	65.92	851
HSA-MIR-5191	95.22	64.69	354

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	cimip2b	ENSDARG00000100292
mus_musculus	Cimip2b	ENSMUSG00000042788
rattus_norvegicus	Cimip2b	ENSRNOG00000065204
caenorhabditis_elegans		WBGENE00008760

Paralogs (1): TMEM121B (ENSG00000183307)

Protein

Protein identifiers

Ciliary microtubule inner protein 2B — A8MTA8 (reviewed: A8MTA8)

All UniProt accessions (2): A0A8V8TLC2, A8MTA8

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.

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.

Isoforms (2)

UniProt ID	Names	Canonical?
A8MTA8-1	1	yes
A8MTA8-2	2

RefSeq proteins (4): NP_001093421, NP_001157782, NP_001274167, NP_001274168 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR018902	CMI2A-C-like_dom	Domain

Pfam: PF10629

UniProt features (7 total): region of interest 2, compositionally biased region 2, splice 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-A8MTA8-F1	68.93	0.12

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 35 (showing top): SENGUPTA_NASOPHARYNGEAL_CARCINOMA_DN, chr9p13, GOCC_CYTOPLASMIC_REGION, GOCC_CYTOPLASMIC_MICROTUBULE, GOCC_CILIUM, DODD_NASOPHARYNGEAL_CARCINOMA_DN, MIKKELSEN_IPS_ICP_WITH_H3K4ME3_AND_H327ME3, MARTENS_TRETINOIN_RESPONSE_UP, GOCC_AXONEMAL_MICROTUBULE, GOCC_SUPRAMOLECULAR_COMPLEX, GOCC_POLYMERIC_CYTOSKELETAL_FIBER, GOCC_SUPRAMOLECULAR_POLYMER, MIR3924, MIR4505, MIR5787

GO Biological Process (0):

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

GO Cellular Component (7): axonemal microtubule (GO:0005879), 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	2
binding	1
cytoplasmic microtubule	1
axoneme	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

316 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIMIP2B	TMEM235	A6NFC5	577
CIMIP2B	TEKTIP1	A6NCJ1	576
CIMIP2B	CCDC172	P0C7W6	520
CIMIP2B	ZNF780B	Q9Y6R6	511
CIMIP2B	ZNF445	P59923	443
CIMIP2B	CFAP184	Q2M329	434
CIMIP2B	TMEM254	Q8TBM7	431
CIMIP2B	DCAF10	Q5QP82	376
CIMIP2B	B3GNT9	Q6UX72	371
CIMIP2B	EXD1	Q8NHP7	367
CIMIP2B	SBK2	P0C263	351
CIMIP2B	CFAP161	Q6P656	350
CIMIP2B	TTC23	Q5W5X9	348
CIMIP2B	PIERCE1	Q5BN46	348
CIMIP2B	TTC9	Q92623	338
CIMIP2B	EFHC2	Q5JST6	338

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CIMIP2B	LACRT	psi-mi:“MI:0915”(physical association)	0.400

BioGRID (24): FAM166B (Affinity Capture-RNA), FAM166B (Two-hybrid), FAM166B (Two-hybrid), FAM166B (Two-hybrid), FAM166B (Two-hybrid), FAM166B (Two-hybrid), FAM166B (Two-hybrid), FAM166B (Two-hybrid), FAM166B (Two-hybrid), FAM166B (Two-hybrid), FAM166B (Two-hybrid), FAM166B (Two-hybrid), FAM166B (Two-hybrid), FAM166B (Two-hybrid), FAM166B (Two-hybrid)

ESM2 similar proteins: A0A087WRI3, A2AIP0, A2RRW4, A4D2P6, A6QPC0, A8E5W8, A8MTA8, A9JS51, E9PGG2, G3X6E2, H3BNL1, O08856, O43247, O43566, O70373, P54098, P54099, Q0VB26, Q12770, Q2TA11, Q2TBR5, Q3ZBN4, Q400G9, Q4QR77, Q5MNU5, Q5RDC3, Q6J272, Q6ZQR2, Q70EL4, Q8BL74, Q8BUM9, Q8BX43, Q8C0R7, Q8C4S8, Q8N1D5, Q8N6G2, Q8WUA4, Q8WW14, Q969Z4, Q96MK2

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

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	51
Likely benign	5
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
394346	GRCh37/hg19 9p24.3-13.1(chr9:32396-39140211)	Pathogenic
583851	NC_000009.11:g.(?34458984)(35809462_?)del	Pathogenic

SpliceAI

765 predictions. Top by Δscore:

Variant	Effect	Δscore
9:35562853:C:A	donor_gain	1.0000
9:35562873:A:AC	donor_gain	1.0000
9:35562874:C:CC	donor_gain	1.0000
9:35562888:T:TA	donor_gain	1.0000
9:35563081:C:CC	acceptor_gain	1.0000
9:35563082:T:A	acceptor_loss	1.0000
9:35563090:C:CT	acceptor_gain	1.0000
9:35563091:A:T	acceptor_gain	1.0000
9:35563765:AC:A	donor_gain	1.0000
9:35563766:CC:C	donor_gain	1.0000
9:35562852:C:CA	donor_gain	0.9900
9:35562863:T:TA	donor_gain	0.9900
9:35563077:AAAC:A	acceptor_gain	0.9900
9:35563078:AAC:A	acceptor_gain	0.9900
9:35563079:AC:A	acceptor_gain	0.9900
9:35563080:CC:C	acceptor_gain	0.9900
9:35563087:A:T	acceptor_gain	0.9900
9:35563761:TCTTA:T	donor_loss	0.9900
9:35563762:CTTA:C	donor_loss	0.9900
9:35563763:TTACC:T	donor_loss	0.9900
9:35563764:TA:T	donor_loss	0.9900
9:35563765:A:AC	donor_gain	0.9900
9:35563766:C:CC	donor_gain	0.9900
9:35563076:AAAAC:A	acceptor_gain	0.9800
9:35563078:AACCT:A	acceptor_gain	0.9800
9:35563079:ACCT:A	acceptor_gain	0.9800
9:35563080:CCT:C	acceptor_gain	0.9800
9:35563081:C:G	acceptor_gain	0.9800
9:35563086:C:CT	acceptor_gain	0.9800
9:35563760:GTCTT:G	donor_loss	0.9800

AlphaMissense

1792 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
9:35562570:G:C	F183L	0.985
9:35562570:G:T	F183L	0.985
9:35562572:A:G	F183L	0.985
9:35563076:A:C	F97L	0.977
9:35563076:A:T	F97L	0.977
9:35563078:A:G	F97L	0.977
9:35563359:G:C	F31L	0.963
9:35563359:G:T	F31L	0.963
9:35563361:A:G	F31L	0.963
9:35562085:G:C	F250L	0.957
9:35562085:G:T	F250L	0.957
9:35562087:A:G	F250L	0.957
9:35562659:G:C	F178L	0.955
9:35562659:G:T	F178L	0.955
9:35562661:A:G	F178L	0.955
9:35563052:A:C	F105L	0.948
9:35563052:A:T	F105L	0.948
9:35563054:A:G	F105L	0.948
9:35562079:A:C	F252L	0.947
9:35562079:A:T	F252L	0.947
9:35562081:A:G	F252L	0.947
9:35562525:A:C	F198L	0.943
9:35562525:A:T	F198L	0.943
9:35562527:A:G	F198L	0.943
9:35562514:G:A	T202I	0.937
9:35562492:A:C	F209L	0.935
9:35562492:A:T	F209L	0.935
9:35562494:A:G	F209L	0.935
9:35562543:G:C	F192L	0.934
9:35562543:G:T	F192L	0.934

dbSNP variants (sampled 300 via entrez): RS1000305348 (9:35562549 G>A), RS1000624189 (9:35562475 G>A,C), RS1000636325 (9:35563021 C>A,T), RS1001237657 (9:35561354 G>A), RS1001507875 (9:35562137 G>GTA), RS1002103144 (9:35561877 AAG>A), RS1002715356 (9:35565231 G>C), RS1003445397 (9:35564316 G>C), RS1004448558 (9:35563081 C>G), RS1004823684 (9:35563287 A>G), RS1004932896 (9:35562764 C>T), RS1005416548 (9:35561822 G>A), RS1006812309 (9:35565188 C>G,T), RS1006945572 (9:35565299 A>G), RS1007812179 (9:35563892 C>A,T)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:619751, MIM:614749, MIM:249000

GenCC curated gene-disease

Mondo (3): Stuve-Wiedemann syndrome 2 (MONDO:0030756), hyperphosphatasia with intellectual disability syndrome 2 (MONDO:0013882), Meckel syndrome (MONDO:0018921)

Orphanet (2): Hyperphosphatasia-intellectual disability syndrome (Orphanet:247262), Meckel syndrome (Orphanet:564)

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

15 total (human), top 15 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Valproic Acid	affects cotreatment, decreases expression, increases methylation	4
tris(1,3-dichloro-2-propyl)phosphate	affects expression	1
butyraldehyde	increases expression	1
pentanal	increases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
torcetrapib	increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	affects methylation, increases methylation	1
Diethylhexyl Phthalate	decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Aflatoxin B1	decreases methylation	1
Lactic Acid	decreases expression	1

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT01401998	Not specified	RECRUITING	ARPKD Database Study