CIMIP3

Summary

CIMIP3 (ciliary microtubule inner protein 3, HGNC:55126) is a protein-coding gene on chromosome 6p21.1, encoding Ciliary microtubule inner protein 3 (X6R8D5).

Predicted to enable calcium ion binding activity. Predicted to be involved in visual perception.

Source: NCBI Gene 114841037 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 5 total
• MANE Select transcript: NM_001384994

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:55126
Approved symbol	CIMIP3
Name	ciliary microtubule inner protein 3
Location	6p21.1
Locus type	gene with protein product
Status	Approved
Ensembl gene	ENSG00000287363
Ensembl biotype	protein_coding
Entrez	114841037

Gene structure

Transcript identifiers

Ensembl transcripts: 3 — 2 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000372963, ENST00000623004, ENST00000850906

RefSeq mRNA: 2 — MANE Select: NM_001384994 NM_001370581, NM_001384994

CCDS: CCDS93921, CCDS93922

Canonical transcript exons

ENST00000623004 — 2 exons

Exon	Start	End
ENSE00001792492	42155406	42155485
ENSE00004282682	42162920	42163418

Expression profiles

Bgee: expression breadth broad, 20 present calls, max score 82.89.

FANTOM5 (CAGE): breadth tissue_specific, TPM avg 0.2695 / max 255.7652, expressed in 3 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
67785	0.2695	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	82.89	gold quality
right testis	UBERON:0004534	82.74	gold quality
testis	UBERON:0000473	82.49	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	80.49	gold quality
bone marrow cell	CL:0002092	38.10	gold quality
colonic epithelium	UBERON:0000397	37.20	gold quality
ventricular zone	UBERON:0003053	36.48	gold quality
cortical plate	UBERON:0005343	36.47	gold quality
ganglionic eminence	UBERON:0004023	35.49	gold quality
skeletal muscle tissue	UBERON:0001134	33.38	gold quality
bone marrow	UBERON:0002371	32.74	gold quality
hindlimb stylopod muscle	UBERON:0004252	32.15	gold quality
muscle tissue	UBERON:0002385	31.06	gold quality
sural nerve	UBERON:0015488	30.93	gold quality
prefrontal cortex	UBERON:0000451	30.32	silver quality
stromal cell of endometrium	CL:0002255	29.87	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	29.57	gold quality
tonsil	UBERON:0002372	28.67	gold quality
liver	UBERON:0002107	28.28	gold quality
duodenum	UBERON:0002114	28.14	gold quality
lymph node	UBERON:0000029	27.57	gold quality
superior frontal gyrus	UBERON:0002661	27.44	gold quality
blood	UBERON:0000178	27.38	gold quality
islet of Langerhans	UBERON:0000006	26.91	gold quality
urinary bladder	UBERON:0001255	26.67	gold quality
vermiform appendix	UBERON:0001154	26.42	gold quality
gall bladder	UBERON:0002110	25.98	gold quality
muscle of leg	UBERON:0001383	25.89	gold quality
placenta	UBERON:0001987	25.81	gold quality
frontal cortex	UBERON:0001870	25.43	silver quality

Single-cell (SCXA)

Detected in 3 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-MTAB-7316	yes	56.80
E-GEOD-134144	yes	32.26
E-GEOD-137537	no	945.09

Regulation

Is transcription factor: no

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cimip3	ENSMUSG00000047150
rattus_norvegicus	Cimip3	ENSRNOG00000015386

Protein

Protein identifiers

Ciliary microtubule inner protein 3 — X6R8D5 (reviewed: X6R8D5)

Alternative names: GUCA1A neighbor

All UniProt accessions (2): X6R8D5, A0A096LNT9

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cytoplasm. Cytoskeleton. Flagellum axoneme.

Similarity. Belongs to the CIMIP3-like family.

Isoforms (2)

UniProt ID	Names	Canonical?
X6R8D5-1	1	yes
X6R8D5-2	2

RefSeq proteins (2): NP_001357510, NP_001371923* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR054446	CIMIP3-like	Family

Pfam: PF22581

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

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-X6R8D5-F1	58.15	0.01

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 6 (showing top): GRAESSMANN_APOPTOSIS_BY_SERUM_DEPRIVATION_UP, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_UP, MEISSNER_BRAIN_HCP_WITH_H3K4ME3_AND_H3K27ME3, MEISSNER_NPC_HCP_WITH_H3K4ME2_AND_H3K27ME3, MIKKELSEN_NPC_HCP_WITH_H3K27ME3, chr6p21

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (5): cytoplasm (GO:0005737), cytoskeleton (GO:0005856), cilium (GO:0005929), 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
intracellular anatomical structure	1
intracellular membraneless organelle	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cilium	1

Protein interactions and networks

STRING

18 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIMIP3	ARHGEF40	Q8TER5	0
CIMIP3	TMEM132B	Q14DG7	0
CIMIP3	SRRM2	Q9UQ35	0
CIMIP3	TACC2	O95359	0
CIMIP3	POU2AF3	A8K830	0
CIMIP3	C4orf54	D6RIA3	0
CIMIP3	NCKAP5	O14513	0
CIMIP3	NPS	P0C0P6	0
CIMIP3	CD44	P16070	0

IntAct

0 interactions, top by confidence:

ESM2 similar proteins: A0A023PZL7, A7RHB3, A8MQ11, O13913, O29755, O83374, P11301, P14588, P16802, P16805, P25352, P25603, P27982, P38178, P40895, P47003, P47839, P53175, P55248, P58513, P92537, P92552, P93294, Q03831, Q04655, Q05898, Q06695, Q12240, Q14236, Q16048, Q32M92, Q3E806, Q3SY05, Q4ZGE2, Q6B0X1, Q6UXP9, Q6ZS49, Q7LIF2, Q86U37, Q8N326

Diamond homologs: A0A3Q1LFG5, X6R8D5

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	3
Likely benign	0
Benign	2

Top pathogenic / likely-pathogenic (0)

SpliceAI

393 predictions. Top by Δscore:

Variant	Effect	Δscore
6:42163264:G:GT	donor_gain	0.9900
6:42155549:A:T	donor_gain	0.9800
6:42162915:CCCA:C	acceptor_loss	0.9800
6:42162917:CA:C	acceptor_loss	0.9800
6:42162919:G:GA	acceptor_loss	0.9800
6:42162919:GGACT:G	acceptor_gain	0.9800
6:42163250:GCC:G	donor_gain	0.9800
6:42163304:TCCCC:T	donor_gain	0.9800
6:42160764:G:GT	donor_gain	0.9700
6:42162919:GGAC:G	acceptor_gain	0.9700
6:42163264:G:T	donor_gain	0.9700
6:42163397:G:T	donor_gain	0.9700
6:42162918:A:AG	acceptor_gain	0.9600
6:42162919:G:GG	acceptor_gain	0.9600
6:42162919:GGA:G	acceptor_gain	0.9600
6:42155476:G:GT	donor_gain	0.9500
6:42162918:AG:A	acceptor_gain	0.9500
6:42162919:GG:G	acceptor_gain	0.9500
6:42163116:A:AG	donor_gain	0.9500
6:42163117:G:GG	donor_gain	0.9500
6:42162917:CAGGA:C	acceptor_gain	0.9400
6:42163056:T:TA	donor_gain	0.9400
6:42160732:TTTC:T	donor_gain	0.9300
6:42162916:CCAGG:C	acceptor_gain	0.9300
6:42162918:AGGAC:A	acceptor_gain	0.9300
6:42155592:AGGT:A	donor_loss	0.9200
6:42155594:G:GA	donor_loss	0.9200
6:42155595:T:A	donor_loss	0.9200
6:42155592:AGG:A	donor_loss	0.9100
6:42162915:CCCAG:C	acceptor_gain	0.9100

AlphaMissense

718 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
6:42163139:T:C	F77L	0.979
6:42163141:C:A	F77L	0.979
6:42163141:C:G	F77L	0.979
6:42163238:T:A	W110R	0.968
6:42163238:T:C	W110R	0.968
6:42163156:G:C	K82N	0.966
6:42163156:G:T	K82N	0.966
6:42163167:G:A	G86D	0.962
6:42163195:C:A	H95Q	0.959
6:42163195:C:G	H95Q	0.959
6:42163126:C:A	N72K	0.954
6:42163126:C:G	N72K	0.954
6:42163163:T:C	C85R	0.953
6:42163204:G:C	K98N	0.953
6:42163204:G:T	K98N	0.953
6:42163153:G:C	Q81H	0.947
6:42163153:G:T	Q81H	0.947
6:42163103:T:C	F65L	0.945
6:42163105:C:A	F65L	0.945
6:42163105:C:G	F65L	0.945
6:42163175:T:G	Y89D	0.943
6:42163164:G:A	C85Y	0.941
6:42163240:G:C	W110C	0.940
6:42163240:G:T	W110C	0.940
6:42163167:G:T	G86V	0.938
6:42163140:T:C	F77S	0.935
6:42163166:G:C	G86R	0.935
6:42163165:T:G	C85W	0.933
6:42163154:A:G	K82E	0.930
6:42163199:C:A	R97S	0.916

dbSNP variants (sampled 300 via entrez): RS1000424098 (6:42162614 G>A,C), RS1000536993 (6:42163311 G>A), RS1000756018 (6:42163551 C>A,T), RS1000923922 (6:42158139 T>A), RS1001119308 (6:42158951 G>T), RS1001147487 (6:42162320 CAGA>C), RS1001601933 (6:42163090 G>A,C), RS1001793569 (6:42156259 G>C), RS1002547749 (6:42158980 G>A), RS1002585884 (6:42153924 G>A,T), RS1002763719 (6:42157563 T>C,G), RS1002874902 (6:42161378 G>A,C,T), RS1003699649 (6:42153629 G>A), RS1004553017 (6:42159852 C>T), RS1004705690 (6:42153486 A>C)

Disease associations

OMIM: gene `` | disease phenotypes: MIM:602093

GenCC curated gene-disease

Mondo (1): cone dystrophy 3 (MONDO:0011193)

Orphanet (1): Cone rod dystrophy (Orphanet:1872)

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)

Clinical trials (associated diseases)

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