CIMAP1C

Summary

CIMAP1C (ciliary microtubule associated protein 1C, HGNC:28735) is a protein-coding gene on chromosome 15q24.2, encoding Ciliary microtubule associated protein 1C (Q8IXM7).

Predicted to be active in cytoskeleton.

Source: NCBI Gene 161753 — RefSeq curated summary.

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 61 total — 2 pathogenic
• MANE Select transcript: NM_175881

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28735
Approved symbol	CIMAP1C
Name	ciliary microtubule associated protein 1C
Location	15q24.2
Locus type	gene with protein product
Status	Approved
Aliases	MGC48986
Ensembl gene	ENSG00000182950
Ensembl biotype	protein_coding
Entrez	161753

Gene structure

Transcript identifiers

Ensembl transcripts: 1 — 1 protein_coding

ENST00000332145

RefSeq mRNA: 1 — MANE Select: NM_175881 NM_175881

CCDS: CCDS10285

Canonical transcript exons

ENST00000332145 — 4 exons

Exon	Start	End
ENSE00001291640	75726058	75726171
ENSE00001294840	75724041	75724317
ENSE00001310542	75725108	75725218
ENSE00001317124	75727059	75727688

Expression profiles

Bgee: expression breadth ubiquitous, 143 present calls, max score 83.81.

FANTOM5 (CAGE): breadth broad, TPM avg 0.9142 / max 105.5539, expressed in 392 samples.

FANTOM5 promoters (3 alternative TSS)

Promoter ID	TPM avg	Samples expressed
147823	0.8073	391
147821	0.0899	3
147822	0.0170	3

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
left testis	UBERON:0004533	83.81	gold quality
right testis	UBERON:0004534	82.51	gold quality
testis	UBERON:0000473	81.00	gold quality
mucosa of stomach	UBERON:0001199	68.72	gold quality
gall bladder	UBERON:0002110	67.84	gold quality
smooth muscle tissue	UBERON:0001135	62.71	gold quality
cartilage tissue	UBERON:0002418	62.70	gold quality
pancreatic ductal cell	CL:0002079	60.89	silver quality
skin of abdomen	UBERON:0001416	60.53	gold quality
mucosa of transverse colon	UBERON:0004991	60.17	gold quality
stromal cell of endometrium	CL:0002255	59.06	gold quality
right atrium auricular region	UBERON:0006631	58.75	gold quality
cardiac atrium	UBERON:0002081	58.24	gold quality
left uterine tube	UBERON:0001303	58.12	gold quality
muscle layer of sigmoid colon	UBERON:0035805	57.84	gold quality
right uterine tube	UBERON:0001302	57.71	gold quality
omental fat pad	UBERON:0010414	57.47	gold quality
peritoneum	UBERON:0002358	57.42	gold quality
adult organism	UBERON:0007023	56.93	gold quality
adipose tissue of abdominal region	UBERON:0007808	56.54	gold quality
esophagogastric junction muscularis propria	UBERON:0035841	55.92	gold quality
tibialis anterior	UBERON:0001385	55.83	silver quality
popliteal artery	UBERON:0002250	55.75	gold quality
tibial artery	UBERON:0007610	55.74	gold quality
lower esophagus muscularis layer	UBERON:0035833	55.12	gold quality
lower esophagus	UBERON:0013473	55.05	gold quality
body of stomach	UBERON:0001161	54.99	gold quality
epithelial cell of pancreas	CL:0000083	54.76	gold quality
descending thoracic aorta	UBERON:0002345	54.57	gold quality
aorta	UBERON:0000947	54.43	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.17

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

12 targeting CIMAP1C, 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-5692A	100.00	74.40	6850
HSA-MIR-6740-3P	99.48	68.49	1392
HSA-MIR-4688	99.48	64.68	828
HSA-MIR-6743-5P	99.48	63.60	721
HSA-MIR-7158-5P	99.25	67.95	796
HSA-MIR-3675-3P	99.09	67.70	968
HSA-MIR-423-5P	98.69	67.48	1522
HSA-MIR-4700-5P	98.63	67.43	1915
HSA-MIR-3184-5P	98.56	67.13	1491
HSA-MIR-8089	97.74	66.21	1698
HSA-MIR-4667-5P	97.61	66.67	1683
HSA-MIR-5194	96.77	63.91	1021

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cimap1c	ENSMUSG00000045620
rattus_norvegicus	Cimap1c	ENSRNOG00000027109

Paralogs (5): STPG1 (ENSG00000001460), STPG2 (ENSG00000163116), CIMAP1A (ENSG00000177947), CIMAP1B (ENSG00000177989), CIMAP1D (ENSG00000181781)

Protein

Protein identifiers

Ciliary microtubule associated protein 1C — Q8IXM7 (reviewed: Q8IXM7)

Alternative names: Outer dense fiber protein 3-like protein 1, Protein CIMAP1C

All UniProt accessions (1): Q8IXM7

UniProt curated annotations — full annotation on UniProt →

Similarity. Belongs to the CIMAP family.

RefSeq proteins (1): NP_787077* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR010736	SHIPPO-rpt	Repeat
IPR051291	CIMAP	Family

Pfam: PF07004

UniProt features (6 total): repeat 2, chain 1, region of interest 1, compositionally biased region 1, sequence variant 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q8IXM7-F1	69.94	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 24 (showing top): FOXO1_01, ATF3_Q6, HFH1_01, PAX2_02, NFE2L2.V2, FOXJ2_TARGET_GENES, MIR423_5P, MIR3184_5P, MIR7158_5P, STAT4_01, GSE7568_IL4_TGFB_DEXAMETHASONE_VS_IL4_TGFB_TREATED_MACROPHAGE_UP, RTAAACA_FREAC2_01, HARALAMBIEVA_PBMC_FLUARIX_AGE_50_74YO_CORR_WITH_28D_MEM_B_CELL_RESPONSE_AT_28DY_POSITIVE, PEREZ_TP53_TARGETS, HE_LIM_SUN_FETAL_LUNG_C1_SMG_CELL

GO Biological Process (0):

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

GO Cellular Component (1): cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
binding	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

192 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIMAP1C	KRTAP10-6	P60371	582
CIMAP1C	ATXN7L3B	Q96GX2	578
CIMAP1C	TEDDM1	Q5T9Z0	489
CIMAP1C	BICD2	Q8TD16	487
CIMAP1C	ENY2	Q9NPA8	475
CIMAP1C	CISD3	P0C7P0	453
CIMAP1C	DEFB130A	P0DP74	447
CIMAP1C	DEFB125	Q8N687	447
CIMAP1C	DNAJC30	Q96LL9	440
CIMAP1C	LY6G5B	Q8NDX9	415
CIMAP1C	KLHL29	Q96CT2	382
CIMAP1C	CDC42BPG	Q6DT37	371
CIMAP1C	MILR1	Q7Z6M3	371
CIMAP1C	DENND5B	Q6ZUT9	366
CIMAP1C	D6RI10	D6RI10	343

IntAct

10 interactions, top by confidence:

A	B	Type	Score
CIMAP1C	CYSRT1	psi-mi:“MI:0915”(physical association)	0.560
CYSRT1	CIMAP1C	psi-mi:“MI:0915”(physical association)	0.560
BAG4	CIMAP1C	psi-mi:“MI:0915”(physical association)	0.560
CIMAP1C	STAMBP	psi-mi:“MI:0914”(association)	0.530
CIMAP1C	GGPS1	psi-mi:“MI:0914”(association)	0.350
BAG4	CIMAP1C	psi-mi:“MI:0915”(physical association)	0.000

BioGRID (17): C9orf41 (Affinity Capture-MS), STAMBP (Affinity Capture-MS), STAMBP (Affinity Capture-MS), C9orf41 (Affinity Capture-MS), ODF3L1 (Two-hybrid), STAMBP (Affinity Capture-MS), C9orf41 (Affinity Capture-MS), CLPB (Affinity Capture-MS), HSPA8 (Affinity Capture-MS), HSPA6 (Affinity Capture-MS), GGPS1 (Affinity Capture-MS), HSPD1 (Affinity Capture-MS), LONP1 (Affinity Capture-MS), PNN (Cross-Linking-MS (XL-MS)), ODF3L1 (Proximity Label-MS)

ESM2 similar proteins: A1A5R9, A2AVQ5, A2RRW4, A2RSX4, A5WUY6, A9JS51, B0BM24, B0S4Q5, B1H283, D4A039, F1MMV1, Q08BC4, Q0VB26, Q2T9Q3, Q2TA11, Q2TBS4, Q3KQ80, Q3SX64, Q3TZ65, Q3ZCV2, Q4KKZ1, Q4KLY8, Q4R5Y0, Q5PQN4, Q5RAF2, Q5XI56, Q6ZN84, Q810P2, Q8BUG5, Q8C008, Q8C8J0, Q8IXM7, Q8N412, Q8N6G2, Q8N7U6, Q8N801, Q8TCI5, Q8WW14, Q9D067, Q9D131

Diamond homologs: A3KQA5, A8MYP8, Q2TBH0, Q3SX64, Q3TZ65, Q5EB30, Q5M8M2, Q8AVY1, Q8IXM7, Q920N1, Q96PU9, Q2KIH8, Q810P2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	2
Likely pathogenic	0
Uncertain significance	54
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (2)

Variant ID	HGVS	Classification
2685524	GRCh37/hg19 15q24.2(chr15:75601120-76081362)x1	Pathogenic
59384	GRCh38/hg38 15q24.2(chr15:75596961-76049787)x1	Pathogenic

SpliceAI

497 predictions. Top by Δscore:

Variant	Effect	Δscore
15:75725214:GAAGC:G	donor_gain	1.0000
15:75725217:GC:G	donor_gain	1.0000
15:75725277:G:T	donor_gain	1.0000
15:75726168:CTGC:C	donor_gain	1.0000
15:75726170:GC:G	donor_gain	1.0000
15:75726172:G:GG	donor_gain	1.0000
15:75727055:TCAG:T	acceptor_loss	1.0000
15:75727056:CAG:C	acceptor_loss	1.0000
15:75727057:A:AG	acceptor_gain	1.0000
15:75727057:AGG:A	acceptor_loss	1.0000
15:75727058:G:GG	acceptor_gain	1.0000
15:75727058:GGCCT:G	acceptor_gain	1.0000
15:75724315:AAGGT:A	donor_loss	0.9900
15:75724316:AGG:A	donor_loss	0.9900
15:75724317:GGT:G	donor_loss	0.9900
15:75724318:G:GC	donor_loss	0.9900
15:75724319:T:G	donor_loss	0.9900
15:75725214:G:GT	donor_gain	0.9900
15:75725219:G:GG	donor_gain	0.9900
15:75725267:G:GT	donor_gain	0.9900
15:75726055:CA:C	acceptor_loss	0.9900
15:75726056:A:AC	acceptor_loss	0.9900
15:75726056:A:AG	acceptor_gain	0.9900
15:75726056:AG:A	acceptor_gain	0.9900
15:75726056:AGG:A	acceptor_gain	0.9900
15:75726057:G:GC	acceptor_gain	0.9900
15:75726057:GG:G	acceptor_gain	0.9900
15:75726057:GGG:G	acceptor_gain	0.9900
15:75726167:CCTGC:C	donor_gain	0.9900
15:75726168:CTGCG:C	donor_loss	0.9900

AlphaMissense

1787 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
15:75727478:T:C	F255L	0.913
15:75727480:C:A	F255L	0.913
15:75727480:C:G	F255L	0.913
15:75724317:G:C	G40R	0.806
15:75726117:T:C	F97L	0.803
15:75726119:T:A	F97L	0.803
15:75726119:T:G	F97L	0.803
15:75727283:T:C	F190L	0.785
15:75727285:C:A	F190L	0.785
15:75727285:C:G	F190L	0.785
15:75727462:G:C	K249N	0.773
15:75727462:G:T	K249N	0.773
15:75725125:T:C	Y46H	0.771
15:75727373:A:C	S220R	0.761
15:75727375:C:A	S220R	0.761
15:75727375:C:G	S220R	0.761
15:75725126:A:C	Y46S	0.759
15:75725125:T:G	Y46D	0.756
15:75727388:T:C	F225L	0.751
15:75727390:C:A	F225L	0.751
15:75727390:C:G	F225L	0.751
15:75725173:T:C	F62L	0.730
15:75725175:C:A	F62L	0.730
15:75725175:C:G	F62L	0.730
15:75725163:C:A	D58E	0.720
15:75725163:C:G	D58E	0.720
15:75727142:T:C	F143L	0.718
15:75727144:T:A	F143L	0.718
15:75727144:T:G	F143L	0.718
15:75725142:C:G	C51W	0.706

dbSNP variants (sampled 300 via entrez): RS1000691984 (15:75726905 C>A,T), RS1001124188 (15:75726516 G>C), RS1001687671 (15:75725422 G>A), RS1001718807 (15:75725196 G>C,T), RS1002669849 (15:75723829 C>G), RS1002721700 (15:75723690 G>C), RS1002904545 (15:75723455 T>C,G), RS1003235669 (15:75728150 G>A), RS1003694401 (15:75722591 C>T), RS1004930669 (15:75722807 G>A), RS1005641472 (15:75724626 G>A,T), RS1005727293 (15:75722834 T>C), RS1005749605 (15:75725135 C>T), RS1006080043 (15:75723777 G>A), RS1006526478 (15:75727842 G>A)

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
GCST005580_170	Intraocular pressure	1.000000e-08

EFO canonical traits (1, from GWAS)

EFO ID	Trait name
EFO:0004695	intraocular pressure measurement

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

20 total (human), top 20 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
Aflatoxin B1	decreases methylation, increases expression, increases methylation	4
Benzo(a)pyrene	decreases expression, increases methylation	2
dimethylselenide	increases expression, increases oxidation	1
butyraldehyde	decreases expression	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression	1
CGP 52608	affects binding, increases reaction	1
jinfukang	affects cotreatment, increases expression	1
Resveratrol	affects cotreatment, decreases expression	1
Cisplatin	affects cotreatment, increases expression	1
Demecolcine	increases expression	1
Ethyl Methanesulfonate	increases expression	1
Lead	decreases expression	1
Lipopolysaccharides	affects response to substance, increases expression	1
Methyl Methanesulfonate	increases expression	1
Ozone	increases expression, increases oxidation	1
Plant Extracts	decreases expression, affects cotreatment	1
Valproic Acid	increases methylation	1
Hydroxyl Radical	increases expression, increases oxidation	1
Okadaic Acid	increases expression	1
Magnetite Nanoparticles	increases expression	1

Clinical trials (associated diseases)

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