CIMIP4

Summary

CIMIP4 (ciliary microtubule inner protein 4, HGNC:28568) is a protein-coding gene on chromosome 22q12.3, encoding Ciliary microtubule inner protein 4 (O43247). Seems to be associated with spermiogenesis but is not essential for sperm development and male fertility.

Predicted to be located in sperm flagellum.

Source: NCBI Gene 339669 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 63 total
• MANE Select transcript: NM_001163857

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28568
Approved symbol	CIMIP4
Name	ciliary microtubule inner protein 4
Location	22q12.3
Locus type	gene with protein product
Status	Approved
Aliases	MGC35206, EAN57
Ensembl gene	ENSG00000185264
Ensembl biotype	protein_coding
OMIM	620945
Entrez	339669

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 4 protein_coding

ENST00000381821, ENST00000402860, ENST00000405091, ENST00000442538

RefSeq mRNA: 2 — MANE Select: NM_001163857 NM_001163857, NM_178552

CCDS: CCDS13937, CCDS54524

Canonical transcript exons

ENST00000381821 — 6 exons

Exon	Start	End
ENSE00001293324	36999840	36999984
ENSE00001306821	36991481	36991591
ENSE00001489958	37007729	37007851
ENSE00001557225	36991125	36991276
ENSE00001792594	37001837	37002303
ENSE00003603544	37003966	37004025

Expression profiles

Bgee: expression breadth broad, 50 present calls, max score 94.75.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.0868 / max 98.3365, expressed in 3 samples.

FANTOM5 promoters (2 alternative TSS)

Promoter ID	TPM avg	Samples expressed
193986	0.0726	3
193985	0.0142	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
right testis	UBERON:0004534	94.75	gold quality
left testis	UBERON:0004533	94.73	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	92.96	gold quality
testis	UBERON:0000473	91.65	gold quality
sperm	CL:0000019	91.55	gold quality
adult organism	UBERON:0007023	72.46	gold quality
pancreatic ductal cell	CL:0002079	68.32	silver quality
epithelial cell of pancreas	CL:0000083	55.66	gold quality
cardiac muscle of right atrium	UBERON:0003379	54.34	gold quality
left ventricle myocardium	UBERON:0006566	54.23	gold quality
kidney epithelium	UBERON:0004819	53.93	gold quality
upper arm skin	UBERON:0004263	53.52	gold quality
tibialis anterior	UBERON:0001385	52.73	silver quality
myocardium	UBERON:0002349	50.25	gold quality
deltoid	UBERON:0001476	49.23	gold quality
mucosa of stomach	UBERON:0001199	47.98	gold quality
nasal cavity epithelium	UBERON:0005384	47.03	gold quality
right coronary artery	UBERON:0001625	46.50	gold quality
quadriceps femoris	UBERON:0001377	46.34	gold quality
ileal mucosa	UBERON:0000331	45.95	silver quality
vastus lateralis	UBERON:0001379	45.40	gold quality
sural nerve	UBERON:0015488	45.01	gold quality
skin of hip	UBERON:0001554	44.12	silver quality
lower lobe of lung	UBERON:0008949	43.97	silver quality
colonic epithelium	UBERON:0000397	43.69	gold quality
layer of synovial tissue	UBERON:0007616	43.55	gold quality
skeletal muscle tissue of rectus abdominis	UBERON:0004511	43.37	gold quality
secondary oocyte	CL:0000655	42.57	gold quality
granulocyte	CL:0000094	42.19	silver quality
superficial temporal artery	UBERON:0001614	41.33	gold quality

Single-cell (SCXA)

Detected in 1 experiment(s), a significant marker in 0.

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.64

Regulation

Is transcription factor: no

Literature-anchored findings (GeneRIF, showing 1)

• Testis-expressed protein 33 is not essential for spermiogenesis and fertility in mice. (PMID:33760102)

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cimip4	ENSMUSG00000062154
rattus_norvegicus	Cimip4	ENSRNOG00000063601

Protein

Protein identifiers

Ciliary microtubule inner protein 4 — O43247 (reviewed: O43247)

Alternative names: Testis-expressed protein 33

All UniProt accessions (2): H0Y6N4, O43247

UniProt curated annotations — full annotation on UniProt →

Function. Seems to be associated with spermiogenesis but is not essential for sperm development and male fertility.

Subcellular location. Cytoplasmic vesicle. Secretory vesicle. Acrosome. Cell projection. Cilium. Flagellum.

Isoforms (2)

UniProt ID	Names	Canonical?
O43247-1	1	yes
O43247-2	2

RefSeq proteins (2): NP_001157329, NP_848647 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029234	CIMIP4	Family

Pfam: PF15400

UniProt features (6 total): compositionally biased region 3, chain 1, region of interest 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-O43247-F1	60.78	0.12

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 20 (showing top): GOCC_SECRETORY_GRANULE, LFA1_Q6, RFX1_02, GOCC_SECRETORY_VESICLE, GOCC_MOTILE_CILIUM, GOCC_ACROSOMAL_VESICLE, GOCC_CILIUM, GOCC_9PLUS2_MOTILE_CILIUM, ZWANG_CLASS_1_TRANSIENTLY_INDUCED_BY_EGF, ZNF184_TARGET_GENES, chr22q12, GSE32423_MEMORY_VS_NAIVE_CD8_TCELL_UP, GSE3720_VD1_VS_VD2_GAMMADELTA_TCELL_WITH_LPS_STIM_DN, GSE5589_UNSTIM_VS_45MIN_LPS_AND_IL10_STIM_MACROPHAGE_DN, ODONNELL_TFRC_TARGETS_UP

GO Biological Process (0):

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

GO Cellular Component (6): acrosomal vesicle (GO:0001669), sperm flagellum (GO:0036126), cilium (GO:0005929), cytoplasmic vesicle (GO:0031410), motile cilium (GO:0031514), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
secretory granule	1
9+2 motile cilium	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cytoplasm	1
intracellular vesicle	1
cilium	1
cellular anatomical structure	1

Protein interactions and networks

STRING

336 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIMIP4	CCER1	Q8TC90	642
CIMIP4	MORN5	Q5VZ52	591
CIMIP4	TMCO5A	Q8N6Q1	576
CIMIP4	GARIN1B	Q96KD3	570
CIMIP4	CXorf65	A6NEN9	507
CIMIP4	SCP2D1	Q9UJQ7	507
CIMIP4	CCDC187	A0A096LP49	506
CIMIP4	GARIN5A	Q6IPT2	506
CIMIP4	C20orf173	Q96LM9	506
CIMIP4	TMCO2	Q7Z6W1	505
CIMIP4	ZC3H11D	Q8NA57	479
CIMIP4	FAM209A	Q5JX71	479
CIMIP4	CCDC54	Q8NEL0	476
CIMIP4	PEBP4	Q96S96	452
CIMIP4	C22orf23	Q9BZE7	445

IntAct

4 interactions, top by confidence:

A	B	Type	Score
LRRK1	CIMIP4	psi-mi:“MI:0407”(direct interaction)	0.440
CIMIP4	LRRK2	psi-mi:“MI:0407”(direct interaction)	0.440
CIMIP4	ATE1	psi-mi:“MI:0914”(association)	0.350

BioGRID (28): YWHAE (Affinity Capture-MS), CARM1 (Affinity Capture-MS), ATE1 (Affinity Capture-MS), UBR2 (Affinity Capture-MS), MAN2C1 (Affinity Capture-MS), MAN2C1 (Affinity Capture-MS), CARM1 (Affinity Capture-MS), YWHAG (Affinity Capture-MS), UBR2 (Affinity Capture-MS), ATE1 (Affinity Capture-MS), RGAG1 (Affinity Capture-MS), YWHAZ (Affinity Capture-MS), TEX33 (Reconstituted Complex), TEX33 (Two-hybrid), TEX33 (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: O43247, Q9D9J2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	53
Likely benign	9
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

947 predictions. Top by Δscore:

Variant	Effect	Δscore
22:36991603:C:CT	acceptor_gain	0.9800
22:36991272:CCGCC:C	acceptor_gain	0.9700
22:36991273:CGCCC:C	acceptor_gain	0.9700
22:37002191:AC:A	donor_gain	0.9700
22:37002192:CC:C	donor_gain	0.9700
22:37002202:TGA:T	donor_gain	0.9700
22:36999825:G:A	donor_gain	0.9600
22:36991275:CC:C	acceptor_gain	0.9400
22:36991276:CC:C	acceptor_gain	0.9400
22:36991287:C:CT	acceptor_gain	0.9200
22:36999778:C:A	donor_gain	0.9200
22:37002134:C:A	donor_gain	0.9200
22:37007500:C:A	donor_gain	0.9200
22:37007557:A:AC	donor_gain	0.9200
22:37007558:C:CC	donor_gain	0.9200
22:36991277:C:CA	acceptor_loss	0.9100
22:37007560:T:TA	donor_gain	0.9100
22:36991589:CCC:C	acceptor_gain	0.8900
22:36991590:CCC:C	acceptor_gain	0.8900
22:37001786:ATGT:A	donor_gain	0.8900
22:37007499:T:TA	donor_gain	0.8900
22:36991479:AC:A	donor_gain	0.8800
22:36991480:CC:C	donor_gain	0.8800
22:36991690:T:TC	acceptor_gain	0.8700
22:37002117:T:TA	donor_gain	0.8700
22:37005765:A:AC	donor_gain	0.8700
22:37005766:C:CC	donor_gain	0.8700
22:36991277:C:CC	acceptor_gain	0.8600
22:37001829:TATGA:T	donor_gain	0.8600
22:36999854:G:T	donor_gain	0.8500

AlphaMissense

1844 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
22:36991269:C:A	W251C	0.996
22:36991269:C:G	W251C	0.996
22:36991271:A:G	W251R	0.996
22:36991271:A:T	W251R	0.996
22:36991569:G:C	S219R	0.993
22:36991569:G:T	S219R	0.993
22:36991571:T:G	S219R	0.993
22:37001876:A:C	F150L	0.992
22:37001876:A:T	F150L	0.992
22:37001878:A:G	F150L	0.992
22:36991497:C:A	R243S	0.991
22:36991497:C:G	R243S	0.991
22:36991506:C:A	W240C	0.988
22:36991506:C:G	W240C	0.988
22:36991508:A:G	W240R	0.987
22:36991508:A:T	W240R	0.987
22:36991240:A:G	L261S	0.986
22:36991270:C:G	W251S	0.986
22:36991268:G:C	H252D	0.985
22:36991483:A:G	L248P	0.983
22:36999844:A:C	F210L	0.982
22:36999844:A:T	F210L	0.982
22:36999846:A:G	F210L	0.982
22:36991232:C:G	A264P	0.980
22:36991273:C:G	R250P	0.980
22:36991256:C:G	A256P	0.977
22:36991498:C:G	R243T	0.976
22:36991556:A:G	S224P	0.976
22:36991267:T:G	H252P	0.975
22:36991553:A:C	Y225D	0.975

dbSNP variants (sampled 300 via entrez): RS1000008858 (22:36999015 T>C), RS1000145244 (22:37002498 T>C), RS1000468931 (22:37000525 T>C), RS1000636296 (22:37004490 T>C), RS1000920715 (22:36994713 C>T), RS1001289152 (22:36994902 T>C), RS1001298805 (22:37002906 A>C,T), RS1001388215 (22:36994109 A>C,G), RS1001528789 (22:37000000 G>A,C,T), RS1001531948 (22:37006066 T>C,G), RS1001907662 (22:36993654 A>G), RS1002022350 (22:36993101 T>C), RS1002360542 (22:37009501 C>A,T), RS1002372095 (22:36995560 G>A,C), RS1002560562 (22:36990881 G>A)

Disease associations

OMIM: gene MIM:620945 | disease phenotypes: MIM:613960

GenCC curated gene-disease

Mondo (1): granulomatous disease, chronic, autosomal recessive, cytochrome b-positive, type 3 (MONDO:0013507)

Orphanet (1): Chronic granulomatous disease (Orphanet:379)

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

1 total (human), top 1 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, increases methylation	1

Clinical trials (associated diseases)

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