CIMAP2

Summary

CIMAP2 (ciliary microtubule associated protein 2, HGNC:26854) is a protein-coding gene on chromosome 1p32.3, encoding Ciliary microtubule-associated protein 2 (Q3ZCV2).

At a glance

• GWAS associations: 1
• Clinical variants (ClinVar): 66 total
• MANE Select transcript: NM_001110533

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:26854
Approved symbol	CIMAP2
Name	ciliary microtubule associated protein 2
Location	1p32.3
Locus type	gene with protein product
Status	Approved
Aliases	FLJ40201, LEM
Ensembl gene	ENSG00000162398
Ensembl biotype	protein_coding
OMIM	616446
Entrez	163747

Gene structure

Transcript identifiers

Ensembl transcripts: 2 — 2 protein_coding

ENST00000358193, ENST00000371273

RefSeq mRNA: 2 — MANE Select: NM_001110533 NM_001110533, NM_152607

CCDS: CCDS44153, CCDS599

Canonical transcript exons

ENST00000371273 — 10 exons

Exon	Start	End
ENSE00001064762	54806996	54807083
ENSE00001064764	54806063	54806220
ENSE00001064766	54807526	54807690
ENSE00001139699	54807889	54808011
ENSE00001156721	54811794	54811931
ENSE00001214475	54816989	54817122
ENSE00001214485	54814914	54815039
ENSE00001214492	54813814	54813975
ENSE00001214503	54812046	54812189
ENSE00003509785	54841801	54842252

Expression profiles

Bgee: expression breadth broad, 85 present calls, max score 90.52.

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
esophagus squamous epithelium	UBERON:0006920	90.52	gold quality
lower esophagus mucosa	UBERON:0035834	83.40	gold quality
esophagus mucosa	UBERON:0002469	79.87	gold quality
buccal mucosa cell	CL:0002336	79.41	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	75.66	gold quality
sperm	CL:0000019	70.25	gold quality
granulocyte	CL:0000094	69.00	gold quality
oral cavity	UBERON:0000167	68.69	gold quality
left testis	UBERON:0004533	64.25	gold quality
vagina	UBERON:0000996	62.78	gold quality
testis	UBERON:0000473	62.27	gold quality
right testis	UBERON:0004534	61.77	gold quality
jejunal mucosa	UBERON:0000399	61.24	silver quality
duodenum	UBERON:0002114	61.08	gold quality
mucosa of transverse colon	UBERON:0004991	59.53	gold quality
gingiva	UBERON:0001828	56.44	gold quality
esophagus	UBERON:0001043	55.98	gold quality
gingival epithelium	UBERON:0001949	55.36	gold quality
right lobe of liver	UBERON:0001114	53.88	gold quality
tonsil	UBERON:0002372	53.50	gold quality
skin of abdomen	UBERON:0001416	53.49	gold quality
rectum	UBERON:0001052	52.79	gold quality
islet of Langerhans	UBERON:0000006	52.02	gold quality
upper leg skin	UBERON:0004262	51.76	silver quality
jejunum	UBERON:0002115	51.73	silver quality
small intestine	UBERON:0002108	51.18	gold quality
nucleus accumbens	UBERON:0001882	51.16	gold quality
skin of leg	UBERON:0001511	51.09	gold quality
zone of skin	UBERON:0000014	50.96	gold quality
bone marrow cell	CL:0002092	50.39	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	1.94

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

30 targeting CIMAP2, 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-150-5P	99.99	66.69	1976
HSA-MIR-4650-5P	99.98	64.69	999
HSA-MIR-3119	99.92	71.34	2390
HSA-MIR-4713-5P	99.78	67.80	1794
HSA-MIR-2116-3P	99.74	64.32	889
HSA-MIR-1976	99.74	65.48	1127
HSA-MIR-4446-5P	99.72	69.19	2544
HSA-MIR-4755-5P	99.71	70.34	2716
HSA-MIR-5006-3P	99.71	70.26	2728
HSA-MIR-3128	99.50	67.85	1258
HSA-MIR-532-3P	99.34	65.76	1195
HSA-MIR-12113	99.32	67.54	1072
HSA-MIR-3064-5P	99.26	66.13	1497
HSA-MIR-3085-3P	99.26	66.16	1490
HSA-MIR-6504-5P	99.26	65.95	1487
HSA-MIR-149-5P	99.25	67.16	1315
HSA-MIR-4477B	99.23	70.49	1733
HSA-MIR-361-3P	99.19	66.45	1381
HSA-MIR-522-3P	98.91	68.56	1817
HSA-MIR-4539	98.78	67.18	888
HSA-MIR-4680-3P	98.64	68.60	2093
HSA-MIR-3664-3P	97.85	67.62	1452
HSA-MIR-4660	97.79	67.44	1328
HSA-MIR-10400-3P	97.29	64.66	597
HSA-MIR-4674	97.29	64.62	597
HSA-MIR-4474-3P	96.97	65.87	870
HSA-MIR-4433A-5P	96.79	65.01	599
HSA-MIR-4794	96.47	65.53	1063
HSA-MIR-664A-5P	95.84	64.93	949
HSA-MIR-6879-3P	93.93	64.00	759

Cross-species orthologs

2 orthologs

Organism	Symbol	Gene ID
mus_musculus	Cimap2	ENSMUSG00000054362
rattus_norvegicus	Cimap2	ENSRNOG00000030914

Protein

Protein identifiers

Ciliary microtubule-associated protein 2 — Q3ZCV2 (reviewed: Q3ZCV2)

Alternative names: Lymphocyte expansion molecule

All UniProt accessions (1): Q3ZCV2

UniProt curated annotations — full annotation on UniProt →

Tissue specificity. Sperm.

Isoforms (2)

UniProt ID	Names	Canonical?
Q3ZCV2-1	1	yes
Q3ZCV2-2	2

RefSeq proteins (2): NP_001104003, NP_689820 (=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR033557	CIMAP2	Family

UniProt features (5 total): sequence variant 2, chain 1, splice variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q3ZCV2-F1	64.45	0.00

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 26 (showing top): GSE45365_NK_CELL_VS_CD8A_DC_MCMV_INFECTION_UP, BACH2_01, TGANTCA_AP1_C, KMT2D_TARGET_GENES, MIR4755_5P, MIR5006_3P, MIR4680_3P, MIR3085_3P, MIR3064_5P, MIR6504_5P, MIR12113, MIR4539, DESCARTES_FETAL_INTESTINE_INTESTINAL_EPITHELIAL_CELLS, PATEL_SKIN_OF_BODY_ZOSTAVAX_AGE_70_93YO_VZV_CHALLENGE_6HR_DN, PATEL_SKIN_OF_BODY_ZOSTAVAX_AGE_70_93YO_VZV_CHALLENGE_6HR_UP

GO Biological Process (0):

GO Molecular Function (0):

GO Cellular Component (0):

Protein interactions and networks

STRING

208 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CIMAP2	BANF2	Q9H503	615
CIMAP2	ANKLE1	Q8NAG6	567
CIMAP2	TLDC2	A0PJX2	530
CIMAP2	LEMD3	Q9Y2U8	529
CIMAP2	SPEM2	Q0P670	510
CIMAP2	LEMD2	Q8NC56	484
CIMAP2	ZNF385C	Q66K41	450
CIMAP2	EMD	P50402	447
CIMAP2	LEMD1	Q68G75	399
CIMAP2	ANKLE2	Q86XL3	394
CIMAP2	NCAM1	P13591	392
CIMAP2	FTMT	Q8N4E7	374
CIMAP2	CCER1	Q8TC90	366
CIMAP2	SEL1L3	Q68CR1	355
CIMAP2	DENND1B	Q6P3S1	352

IntAct

2 interactions, top by confidence:

A	B	Type	Score
CIMAP2	HERC1	psi-mi:“MI:0914”(association)	0.350

BioGRID (5): HERC1 (Affinity Capture-MS), MMADHC (Affinity Capture-MS), C1orf177 (Cross-Linking-MS (XL-MS)), C1orf177 (Proximity Label-MS), C1orf177 (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: A2AVQ5, B1H283, Q3ZCV2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	61
Likely benign	2
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

1400 predictions. Top by Δscore:

Variant	Effect	Δscore
1:54806327:GGC:G	donor_gain	1.0000
1:54807081:GTG:G	donor_gain	1.0000
1:54807688:AAGG:A	donor_loss	1.0000
1:54807689:AGGTG:A	donor_loss	1.0000
1:54807692:T:A	donor_loss	1.0000
1:54807881:T:A	acceptor_gain	1.0000
1:54808009:GGG:G	donor_gain	1.0000
1:54808009:GGGGT:G	donor_loss	1.0000
1:54808010:GG:G	donor_gain	1.0000
1:54808010:GGG:G	donor_gain	1.0000
1:54808010:GGGT:G	donor_loss	1.0000
1:54808011:GG:G	donor_gain	1.0000
1:54808011:GGTAG:G	donor_loss	1.0000
1:54808012:G:GG	donor_gain	1.0000
1:54808012:G:T	donor_loss	1.0000
1:54808013:TAGG:T	donor_loss	1.0000
1:54813811:TA:T	acceptor_loss	1.0000
1:54813812:A:AG	acceptor_gain	1.0000
1:54813812:A:T	acceptor_loss	1.0000
1:54813813:G:GG	acceptor_gain	1.0000
1:54813813:GA:G	acceptor_gain	1.0000
1:54813813:GAA:G	acceptor_gain	1.0000
1:54813813:GAAA:G	acceptor_gain	1.0000
1:54813813:GAAAA:G	acceptor_gain	1.0000
1:54813973:CTGGT:C	donor_loss	1.0000
1:54813974:TGGTG:T	donor_loss	1.0000
1:54813975:GGT:G	donor_loss	1.0000
1:54813976:G:A	donor_loss	1.0000
1:54813976:G:GG	donor_gain	1.0000
1:54813977:TGAG:T	donor_loss	1.0000

AlphaMissense

2740 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:54807994:T:C	F155L	0.976
1:54807996:C:A	F155L	0.976
1:54807996:C:G	F155L	0.976
1:54806997:T:C	F36L	0.962
1:54806999:T:A	F36L	0.962
1:54806999:T:G	F36L	0.962
1:54806186:T:C	F24L	0.958
1:54806188:C:A	F24L	0.958
1:54806188:C:G	F24L	0.958
1:54806201:T:C	F29L	0.952
1:54806203:C:A	F29L	0.952
1:54806203:C:G	F29L	0.952
1:54812139:T:C	F238L	0.951
1:54812141:C:A	F238L	0.951
1:54812141:C:G	F238L	0.951
1:54813895:T:C	F282L	0.940
1:54813897:T:A	F282L	0.940
1:54813897:T:G	F282L	0.940
1:54807928:T:C	F133L	0.939
1:54807930:C:A	F133L	0.939
1:54807930:C:G	F133L	0.939
1:54807958:A:C	S143R	0.931
1:54807960:C:A	S143R	0.931
1:54807960:C:G	S143R	0.931
1:54812049:A:C	S208R	0.928
1:54812051:T:A	S208R	0.928
1:54812051:T:G	S208R	0.928
1:54814980:T:C	F331L	0.922
1:54814982:C:A	F331L	0.922
1:54814982:C:G	F331L	0.922

dbSNP variants (sampled 300 via entrez): RS1000033737 (1:54833806 C>T), RS1000085227 (1:54835395 G>A), RS1000210699 (1:54804810 G>A), RS1000253456 (1:54840087 T>C), RS1000318065 (1:54810234 G>A), RS1000476063 (1:54828317 A>G), RS1000499838 (1:54833731 G>A), RS1000601239 (1:54822535 T>G), RS1000608412 (1:54809137 C>T), RS1000641810 (1:54839286 G>A), RS1000672892 (1:54839147 G>C), RS1000673429 (1:54822908 A>G), RS1000907364 (1:54826791 T>A), RS1000973240 (1:54841459 G>T), RS1001019457 (1:54835685 G>A,T)

Disease associations

OMIM: gene MIM:616446 | 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
GCST010652_1	Early-onset ischemic stroke	4.000000e-07

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

10 total (human), top 10 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
GSK-J4	decreases expression	1
bisphenol A	affects cotreatment, increases methylation	1
terbufos	increases methylation	1
Fulvestrant	affects cotreatment, increases methylation	1
Acetaminophen	decreases expression	1
Fonofos	increases methylation	1
N-Nitrosopyrrolidine	increases expression	1
Parathion	increases methylation	1
Valproic Acid	increases methylation	1
Okadaic Acid	increases expression	1

Clinical trials (associated diseases)

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