CIMIP6

Summary

CIMIP6 (ciliary microtubule inner protein 6, HGNC:26861) is a protein-coding gene on chromosome 2p16.2, encoding Ciliary microtubule inner protein 6 (Q8N5S3).

Predicted to be located in cilium.

Source: NCBI Gene 129852 — RefSeq curated summary.

At a glance

• GWAS associations: 17
• Clinical variants (ClinVar): 5 total
• MANE Select transcript: NM_001100396

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26861
Approved symbol	CIMIP6
Name	ciliary microtubule inner protein 6
Location	2p16.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40298
Ensembl gene	ENSG00000177994
Ensembl biotype	protein_coding
Entrez	129852

Gene structure

Transcript identifiers

Ensembl transcripts: 8 — 5 protein_coding, 2 nonsense_mediated_decay, 1 protein_coding_CDS_not_defined

ENST00000317627, ENST00000398634, ENST00000405749, ENST00000414747, ENST00000447328, ENST00000486488, ENST00000491538, ENST00000615983

RefSeq mRNA: 3 — MANE Select: NM_001100396 NM_001100396, NM_001369401, NM_001369403

CCDS: CCDS46285

Canonical transcript exons

ENST00000398634 — 5 exons

Exon	Start	End
ENSE00001320625	54334817	54335024
ENSE00003461921	54358959	54359074
ENSE00003609448	54343720	54343873
ENSE00003687620	54360203	54361581
ENSE00003849375	54330884	54331001

Expression profiles

Bgee: expression breadth ubiquitous, 147 present calls, max score 91.97.

FANTOM5 (CAGE): breadth broad, TPM avg 0.7485 / max 101.9452, expressed in 206 samples.

FANTOM5 promoters (1 alternative TSS)

Promoter ID	TPM avg	Samples expressed
20252	0.7485	206

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	91.97	gold quality
right testis	UBERON:0004534	91.42	gold quality
right uterine tube	UBERON:0001302	89.83	gold quality
testis	UBERON:0000473	89.64	gold quality
buccal mucosa cell	CL:0002336	89.59	gold quality
sperm	CL:0000019	87.53	gold quality
bronchial epithelial cell	CL:0002328	85.74	gold quality
bronchus	UBERON:0002185	83.94	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	83.84	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	78.15	gold quality
adult organism	UBERON:0007023	74.70	gold quality
oviduct epithelium	UBERON:0004804	74.67	gold quality
mucosa of paranasal sinus	UBERON:0005030	72.40	gold quality
fallopian tube	UBERON:0003889	70.24	gold quality
islet of Langerhans	UBERON:0000006	69.76	gold quality
nucleus accumbens	UBERON:0001882	69.73	gold quality
hypothalamus	UBERON:0001898	69.16	gold quality
kidney epithelium	UBERON:0004819	68.51	gold quality
caudate nucleus	UBERON:0001873	68.29	gold quality
calcaneal tendon	UBERON:0003701	67.28	gold quality
anterior cingulate cortex	UBERON:0009835	66.51	gold quality
amygdala	UBERON:0001876	66.18	gold quality
tendon of biceps brachii	UBERON:0008188	64.80	gold quality
putamen	UBERON:0001874	64.64	gold quality
secondary oocyte	CL:0000655	64.07	gold quality
right frontal lobe	UBERON:0002810	63.77	gold quality
Brodmann (1909) area 9	UBERON:0013540	62.96	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	62.77	gold quality
prefrontal cortex	UBERON:0000451	62.52	gold quality
C1 segment of cervical spinal cord	UBERON:0006469	62.47	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	yes	6.01

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

88 targeting CIMIP6, 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-6856-5P	100.00	65.47	1298
HSA-MIR-6758-5P	100.00	66.21	1470
HSA-MIR-5011-5P	100.00	83.46	5820
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-4531	99.99	69.70	3181
HSA-MIR-548N	99.98	71.94	4170
HSA-MIR-19A-3P	99.98	75.33	2762
HSA-MIR-19B-3P	99.98	75.44	2754
HSA-MIR-3688-3P	99.97	72.02	2834
HSA-MIR-570-3P	99.96	72.41	4910
HSA-MIR-1468-3P	99.96	72.74	3797
HSA-MIR-548AB	99.95	71.31	3488
HSA-MIR-559	99.95	72.28	3609
HSA-MIR-96-5P	99.95	72.80	2140
HSA-MIR-548A-5P	99.94	71.27	3482
HSA-MIR-548AD-5P	99.94	71.23	3502
HSA-MIR-548AE-5P	99.94	71.23	3502
HSA-MIR-548AK	99.94	71.24	3488
HSA-MIR-548AM-5P	99.94	71.24	3488
HSA-MIR-548AP-5P	99.94	71.14	3489
HSA-MIR-548AQ-5P	99.94	71.34	3426
HSA-MIR-548AR-5P	99.94	71.28	3515
HSA-MIR-548AS-5P	99.94	71.22	3482
HSA-MIR-548AU-5P	99.94	71.24	3488
HSA-MIR-548AY-5P	99.94	71.23	3502
HSA-MIR-548B-5P	99.94	71.23	3502
HSA-MIR-548BB-5P	99.94	71.27	3509
HSA-MIR-548C-5P	99.94	71.24	3488
HSA-MIR-548D-5P	99.94	71.23	3502
HSA-MIR-548H-5P	99.94	71.24	3488

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cimip6	ENSMUSG00000040919
rattus_norvegicus	C14h2orf73	ENSRNOG00000006356

Protein

Protein identifiers

Ciliary microtubule inner protein 6 — Q8N5S3 (reviewed: Q8N5S3)

All UniProt accessions (7): B5MBY8, B7ZM11, C9J598, Q8N5S3, E7ENW1, F8WD05, H7C1Z5

UniProt curated annotations — full annotation on UniProt →

Subcellular location. Cell projection. Cilium.

Isoforms (2)

UniProt ID	Names	Canonical?
Q8N5S3-1	1	yes
Q8N5S3-2	2

RefSeq proteins (3): NP_001093866, NP_001356330, NP_001356332 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR031365	CMIP6	Family

Pfam: PF15667

UniProt features (13 total): region of interest 4, compositionally biased region 4, sequence variant 3, chain 1, splice variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8N5S3-F1	54.11	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 59 (showing top): OCT1_03, HFH3_01, CYTAGCAAY_UNKNOWN, TGGAAA_NFAT_Q4_01, RFX1_01, WGTTNNNNNAAA_UNKNOWN, GOCC_CILIUM, DODD_NASOPHARYNGEAL_CARCINOMA_DN, SRC_UP.V1_UP, CREB3L4_TARGET_GENES, FOXJ2_TARGET_GENES, FOXN3_TARGET_GENES, RYBP_TARGET_GENES, SUPT16H_TARGET_GENES, ZNF30_TARGET_GENES

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (2): cilium (GO:0005929), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cellular anatomical structure	1

Protein interactions and networks

STRING

286 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIMIP6	LRRC66	Q68CR7	506
CIMIP6	TSPYL6	Q8N831	506
CIMIP6	OSER1	Q9NX31	474
CIMIP6	DCUN1D4	Q92564	400
CIMIP6	CPA5	Q8WXQ8	398
CIMIP6	KLHL29	Q96CT2	398
CIMIP6	RABGGTB	P53611	394
CIMIP6	MINDY4	Q4G0A6	379
CIMIP6	CWH43	Q9H720	370
CIMIP6	SPAG16	Q8N0X2	349
CIMIP6	SHISA6	Q6ZSJ9	349
CIMIP6	CNTNAP5	Q8WYK1	348
CIMIP6	Q6NXN5	Q6NXN5	341
CIMIP6	ABLIM3	O94929	340
CIMIP6	NAALADL2	Q58DX5	325

IntAct

6 interactions, top by confidence:

A	B	Type	Score
CIMIP6	HSPB1	psi-mi:“MI:0915”(physical association)	0.370
CIMIP6	ABRAXAS2	psi-mi:“MI:0914”(association)	0.350
CIMIP6	DHX16	psi-mi:“MI:0914”(association)	0.350
CIMIP6	SH3BP4	psi-mi:“MI:0915”(physical association)	0.000
FCHSD2	CIMIP6	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (20): C2orf73 (Two-hybrid), BRE (Affinity Capture-MS), BABAM1 (Affinity Capture-MS), ATG3 (Affinity Capture-MS), MGME1 (Affinity Capture-MS), FAM175B (Affinity Capture-MS), BRCC3 (Affinity Capture-MS), SLTM (Affinity Capture-MS), NEK9 (Affinity Capture-MS), NDRG1 (Affinity Capture-MS), TXN2 (Affinity Capture-MS), MCTS1 (Affinity Capture-MS), HABP4 (Affinity Capture-MS), DHX16 (Affinity Capture-MS), MTHFD2 (Affinity Capture-MS)

ESM2 similar proteins: A0A1B0GTD5, A0A1B0GUX0, A0A3Q1MT14, A4D263, A6NL82, A6QQL5, A8QW39, B0UXH9, B5X5D0, B9EJX3, E1B9R1, F1MMV1, Q148A4, Q1JPL0, Q2T9T0, Q32KQ1, Q32L72, Q32L77, Q32P67, Q3V0J4, Q5BN46, Q5NC57, Q5NC83, Q5SPV6, Q5SS90, Q5SVJ3, Q5VTT2, Q5VZQ5, Q66HC0, Q66HR9, Q6AYM0, Q6NXP0, Q6P3G4, Q6ZVS7, Q80X60, Q8CDT5, Q8CDU5, Q8N5S3, Q8N7U6, Q8N865

Diamond homologs: A6QQL5, Q5SPV6, Q8N5S3

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	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

648 predictions. Top by Δscore:

Variant	Effect	Δscore
2:54330988:GAAGA:G	donor_gain	1.0000
2:54331002:G:GG	donor_gain	1.0000
2:54334930:G:GT	donor_gain	1.0000
2:54334930:G:T	donor_gain	1.0000
2:54343716:AAAG:A	acceptor_gain	1.0000
2:54358957:A:AG	acceptor_gain	1.0000
2:54358958:G:GA	acceptor_gain	1.0000
2:54330992:A:G	donor_gain	0.9900
2:54330997:CATCA:C	donor_gain	0.9900
2:54330998:ATCA:A	donor_gain	0.9900
2:54330999:TCA:T	donor_gain	0.9900
2:54331000:CA:C	donor_gain	0.9900
2:54331000:CAGT:C	donor_loss	0.9900
2:54331001:AGTA:A	donor_loss	0.9900
2:54331002:GTAA:G	donor_loss	0.9900
2:54331003:T:A	donor_loss	0.9900
2:54334924:G:GT	donor_gain	0.9900
2:54334929:GGAC:G	donor_gain	0.9900
2:54358958:GT:G	acceptor_gain	0.9900
2:54358958:GTACC:G	acceptor_gain	0.9900
2:54359071:AAAG:A	donor_loss	0.9900
2:54359072:AAG:A	donor_loss	0.9900
2:54359073:AGG:A	donor_loss	0.9900
2:54359074:GGT:G	donor_loss	0.9900
2:54359075:G:GT	donor_loss	0.9900
2:54359076:T:A	donor_loss	0.9900
2:54331004:AAGT:A	donor_loss	0.9800
2:54334815:A:AG	acceptor_gain	0.9800
2:54334816:G:GG	acceptor_gain	0.9800
2:54334816:GACA:G	acceptor_gain	0.9800

AlphaMissense

1872 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
2:54334950:T:C	F54L	0.975
2:54334952:C:A	F54L	0.975
2:54334952:C:G	F54L	0.975
2:54359021:T:C	F151L	0.974
2:54359023:T:A	F151L	0.974
2:54359023:T:G	F151L	0.974
2:54343783:A:C	S100R	0.970
2:54343785:C:A	S100R	0.970
2:54343785:C:G	S100R	0.970
2:54343801:T:C	F106L	0.969
2:54343803:C:A	F106L	0.969
2:54343803:C:G	F106L	0.969
2:54334945:C:A	A52D	0.960
2:54360215:T:C	F173L	0.948
2:54360217:T:A	F173L	0.948
2:54360217:T:G	F173L	0.948
2:54343794:G:C	R103S	0.945
2:54343794:G:T	R103S	0.945
2:54343726:T:A	W81R	0.918
2:54343726:T:C	W81R	0.918
2:54360210:G:A	G171E	0.908
2:54334951:T:C	F54S	0.907
2:54358959:T:A	V130E	0.899
2:54334944:G:C	A52P	0.898
2:54359044:A:C	R158S	0.897
2:54359044:A:T	R158S	0.897
2:54334964:T:A	N58K	0.896
2:54334964:T:G	N58K	0.896
2:54343868:G:A	G128E	0.895
2:54343802:T:C	F106S	0.890

dbSNP variants (sampled 300 via entrez): RS1000072481 (2:54332999 G>T), RS1000162787 (2:54366115 C>G), RS1000165354 (2:54359208 G>A), RS1000339090 (2:54363441 G>A), RS1000385974 (2:54340839 C>A,T), RS1000442522 (2:54353522 C>T), RS1000491527 (2:54364235 C>G), RS1000501890 (2:54358086 C>G), RS1000532960 (2:54375451 A>G,T), RS1000667687 (2:54332163 A>G), RS1000691260 (2:54331884 G>A), RS1000853887 (2:54375673 T>A), RS1000876580 (2:54337704 A>G), RS1000922485 (2:54346303 T>C), RS1000952138 (2:54370455 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

17 associations (top):

Study	Trait	p-value
GCST005580_162	Intraocular pressure	1.000000e-09
GCST006979_880	Heel bone mineral density	3.000000e-15
GCST007344_123	Estimated glomerular filtration rate	2.000000e-15
GCST007344_131	Estimated glomerular filtration rate	2.000000e-09
GCST007344_24	Estimated glomerular filtration rate	7.000000e-08
GCST007344_59	Estimated glomerular filtration rate	1.000000e-12
GCST007876_44	Estimated glomerular filtration rate	5.000000e-10
GCST008745_96	Estimated glomerular filtration rate in non-diabetics	1.000000e-09
GCST008747_20	Estimated glomerular filtration rate	4.000000e-06
GCST008747_43	Estimated glomerular filtration rate	3.000000e-11
GCST010697_43	Cortical surface area (min-P)	3.000000e-17
GCST010698_83	Subcortical volume (min-P)	5.000000e-20
GCST010699_9	Brain morphology (min-P)	1.000000e-10
GCST010700_58	Cortical thickness (MOSTest)	7.000000e-10
GCST010701_110	Cortical surface area (MOSTest)	5.000000e-12
GCST010702_66	Subcortical volume (MOSTest)	2.000000e-11
GCST010703_178	Brain morphology (MOSTest)	5.000000e-11

EFO canonical traits (4, from GWAS)

EFO ID	Trait name
EFO:0004695	intraocular pressure measurement
EFO:0009270	heel bone mineral density
EFO:0004346	neuroimaging measurement
EFO:0004840	cortical thickness

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

8 total (human), top 8 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
propionaldehyde	increases expression	1
Air Pollutants	increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Silicon Dioxide	decreases expression	1
Smoke	increases abundance, increases expression	1
Tobacco Smoke Pollution	decreases expression	1
Cadmium Chloride	decreases expression	1
Okadaic Acid	decreases expression	1

Clinical trials (associated diseases)

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