CCSAP

Summary

CCSAP (centriole, cilia and spindle associated protein, HGNC:29578) is a protein-coding gene on chromosome 1q42.13, encoding Centriole, cilia and spindle-associated protein (Q6IQ19). Plays a role in microtubule (MT) stabilization and this stabilization involves the maintenance of NUMA1 at the spindle poles.

Enables microtubule binding activity. Involved in mitotic spindle microtubule depolymerization and regulation of mitotic spindle assembly. Located in axon; ciliary transition zone; and cytoskeleton.

Source: NCBI Gene 126731 — RefSeq curated summary.

At a glance

• Clinical variants (ClinVar): 38 total
• MANE Select transcript: NM_145257

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:29578
Approved symbol	CCSAP
Name	centriole, cilia and spindle associated protein
Location	1q42.13
Locus type	gene with protein product
Status	Approved
Aliases	FLJ41471, CSAP
Ensembl gene	ENSG00000154429
Ensembl biotype	protein_coding
OMIM	616762
Entrez	126731

Gene structure

Transcript identifiers

Ensembl transcripts: 4 — 3 protein_coding, 1 protein_coding_CDS_not_defined

ENST00000284617, ENST00000366686, ENST00000366687, ENST00000483092

RefSeq mRNA: 2 — MANE Select: NM_145257 NM_001410936, NM_145257

CCDS: CCDS1577, CCDS91172

Canonical transcript exons

ENST00000284617 — 4 exons

Exon	Start	End
ENSE00001069973	229321015	229325411
ENSE00001431026	229342912	229343047
ENSE00003890818	229326738	229327006
ENSE00003892944	229342099	229342513

Expression profiles

Bgee: expression breadth ubiquitous, 252 present calls, max score 97.55.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 11.6557 / max 194.2457, expressed in 1637 samples.

FANTOM5 promoters (6 alternative TSS)

Promoter ID	TPM avg	Samples expressed
17866	7.7147	1533
17869	3.1332	676
17867	0.3888	207
17860	0.2162	73
17871	0.1659	58
17870	0.0371	11

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
Brodmann (1909) area 46	UBERON:0006483	97.55	gold quality
middle temporal gyrus	UBERON:0002771	97.53	gold quality
Brodmann (1909) area 23	UBERON:0013554	97.32	gold quality
cortical plate	UBERON:0005343	97.27	gold quality
secondary oocyte	CL:0000655	96.69	gold quality
postcentral gyrus	UBERON:0002581	96.68	gold quality
entorhinal cortex	UBERON:0002728	96.46	gold quality
parietal lobe	UBERON:0001872	96.40	gold quality
superior frontal gyrus	UBERON:0002661	96.21	gold quality
ganglionic eminence	UBERON:0004023	95.35	gold quality
embryo	UBERON:0000922	95.34	gold quality
pigmented layer of retina	UBERON:0001782	94.77	gold quality
retina	UBERON:0000966	94.75	gold quality
upper arm skin	UBERON:0004263	94.55	gold quality
endothelial cell	CL:0000115	94.46	gold quality
occipital lobe	UBERON:0002021	94.34	gold quality
primary visual cortex	UBERON:0002436	93.91	gold quality
oocyte	CL:0000023	93.89	gold quality
placenta	UBERON:0001987	93.49	gold quality
corpus callosum	UBERON:0002336	93.32	gold quality
upper leg skin	UBERON:0004262	93.29	gold quality
lateral nuclear group of thalamus	UBERON:0002736	93.20	gold quality
dorsal plus ventral thalamus	UBERON:0001897	93.14	gold quality
thymus	UBERON:0002370	93.04	gold quality
subthalamic nucleus	UBERON:0001906	92.11	gold quality
globus pallidus	UBERON:0001875	91.91	gold quality
lateral globus pallidus	UBERON:0002476	91.71	gold quality
medial globus pallidus	UBERON:0002477	91.61	gold quality
pons	UBERON:0000988	91.55	gold quality
cerebellum	UBERON:0002037	90.89	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	4.41

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

204 targeting CCSAP, 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-29A-3P	100.00	73.11	1835
HSA-MIR-29B-3P	100.00	73.18	1833
HSA-MIR-29C-3P	100.00	73.15	1833
HSA-MIR-3064-3P	100.00	70.09	1254
HSA-MIR-518D-5P	100.00	67.51	979
HSA-MIR-518E-5P	100.00	67.66	954
HSA-MIR-518F-5P	100.00	67.51	979
HSA-MIR-519A-5P	100.00	67.66	954
HSA-MIR-519B-5P	100.00	67.66	954
HSA-MIR-519C-5P	100.00	67.66	954
HSA-MIR-520C-5P	100.00	67.51	979
HSA-MIR-522-5P	100.00	67.66	954
HSA-MIR-523-5P	100.00	67.66	954
HSA-MIR-526A-5P	100.00	67.51	979
HSA-MIR-8485	100.00	77.57	4731
HSA-MIR-5692A	100.00	74.40	6850
HSA-MIR-5692B	100.00	71.32	2622
HSA-MIR-5692C	100.00	71.32	2622
HSA-MIR-200B-3P	100.00	73.31	2693
HSA-MIR-200C-3P	100.00	73.35	2685
HSA-MIR-429	100.00	73.44	2698
HSA-MIR-371B-5P	99.99	75.34	4759
HSA-MIR-548C-3P	99.99	74.01	7587
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-520G-5P	99.99	66.76	658
HSA-MIR-12136	99.98	72.81	5713
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-373-5P	99.98	75.36	4753
HSA-MIR-616-5P	99.98	75.58	4775
HSA-MIR-8068	99.98	73.85	2376

Literature-anchored findings (GeneRIF, showing 2)

• The tubulin binding protein CSAP associates with mitotic microtubules around centrosomes to stabilize mitotic microtubules during mitosis, ensuring proper bipolar spindle formation and maintenance. (PMID:26562023)
• Binding of CSAP to TTLL5 promotes relocalization of TTLL5 toward microtubules. (PMID:30517872)

Cross-species orthologs

4 orthologs

Organism	Symbol	Gene ID
danio_rerio	ccsapa	ENSDARG00000025325
danio_rerio	ccsapb	ENSDARG00000040085
mus_musculus	Ccsap	ENSMUSG00000031971
rattus_norvegicus		ENSRNOG00000074620

Protein

Protein identifiers

Centriole, cilia and spindle-associated protein — Q6IQ19 (reviewed: Q6IQ19)

All UniProt accessions (1): Q6IQ19

UniProt curated annotations — full annotation on UniProt →

Function. Plays a role in microtubule (MT) stabilization and this stabilization involves the maintenance of NUMA1 at the spindle poles. Colocalizes with polyglutamylated MTs to promote MT stabilization and regulate bipolar spindle formation in mitosis. Binding of CCSAP to centrosomes and the spindle around centrosomes during mitosis inhibits MT depolymerization, thereby stabilizing the mitotic spindle. May play a role in embryonic development. May be required for proper cilia beating.

Subunit / interactions. Associates with microtubules; the association occurs on polyglutamylated tubulin.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriole. Spindle. Cilium basal body. Cilium axoneme. Cell projection. Axon. Cilium.

Similarity. Belongs to the CCSAP family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q6IQ19-1	1	yes
Q6IQ19-2	2
Q6IQ19-3	3
Q6IQ19-4	4

RefSeq proteins (2): NP_001397865, NP_660300* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR029774	CSAP	Family

Pfam: PF15748

UniProt features (20 total): compositionally biased region 6, splice variant 6, region of interest 2, short sequence motif 2, chain 1, modified residue 1, sequence variant 1, sequence conflict 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q6IQ19-F1	64.61	0.16

Functional residue map

Curated UniProt residues grouped by drug-discovery relevance — catalytic, ligand-binding, modification, and mutation-validated positions. Source: UniProtKB sequence features.

Post-translational modifications (1): 1

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 196 (showing top): GOBP_CHROMOSOME_ORGANIZATION, GOBP_REGULATION_OF_MICROTUBULE_BASED_PROCESS, RODRIGUES_THYROID_CARCINOMA_POORLY_DIFFERENTIATED_UP, AAGCCAT_MIR135A_MIR135B, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GRAESSMANN_RESPONSE_TO_MC_AND_DOXORUBICIN_DN, GOBP_REGULATION_OF_CELLULAR_COMPONENT_BIOGENESIS, GOCC_MICROTUBULE_ORGANIZING_CENTER, SENESE_HDAC1_AND_HDAC2_TARGETS_DN, GOBP_MITOTIC_SPINDLE_ASSEMBLY, GOBP_ORGANELLE_FISSION, GOBP_MICROTUBULE_DEPOLYMERIZATION, GOBP_REGULATION_OF_SPINDLE_ORGANIZATION, FISCHER_G2_M_CELL_CYCLE, GROSS_HYPOXIA_VIA_HIF1A_DN

GO Biological Process (4): regulation of embryonic development (GO:0045995), cell division (GO:0051301), regulation of mitotic spindle assembly (GO:1901673), mitotic spindle microtubule depolymerization (GO:1990755)

GO Molecular Function (1): microtubule binding (GO:0008017)

GO Cellular Component (14): centrosome (GO:0005813), centriole (GO:0005814), spindle (GO:0005819), cilium (GO:0005929), axoneme (GO:0005930), axon (GO:0030424), ciliary transition zone (GO:0035869), ciliary basal body (GO:0036064), mitotic spindle astral microtubule (GO:0061673), mitotic spindle (GO:0072686), cytoplasm (GO:0005737), cytoskeleton (GO:0005856), microtubule (GO:0005874), cell projection (GO:0042995)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	4
microtubule organizing center	3
intracellular membraneless organelle	3
microtubule cytoskeleton	2
cilium	2
embryo development	1
regulation of multicellular organismal development	1
cellular process	1
regulation of mitotic spindle organization	1
regulation of spindle assembly	1
mitotic spindle assembly	1
microtubule depolymerization	1
tubulin binding	1
centriole	1
intraciliary transport particle	1
membrane-bounded organelle	1
plasma membrane bounded cell projection	1
cytoskeleton	1
microtubule	1
ciliary plasm	1
neuron projection	1
astral microtubule	1
mitotic spindle	1
spindle	1
intracellular anatomical structure	1
polymeric cytoskeletal fiber	1

Protein interactions and networks

STRING

360 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CCSAP	CEP72	Q9P209	437
CCSAP	EOLA2	Q96DE9	432
CCSAP	CEP120	Q8N960	431
CCSAP	CEP85L	Q5SZL2	410
CCSAP	SPICE1	Q8N0Z3	409
CCSAP	FER1L6	Q2WGJ9	352
CCSAP	CEP85	Q6P2H3	339
CCSAP	HDHD5	Q9BXW7	336
CCSAP	RASL11B	Q9BPW5	334
CCSAP	CEP170B	Q9Y4F5	332
CCSAP	HOOK1	Q9UJC3	331
CCSAP	ZSWIM3	Q96MP5	324
CCSAP	SESN3	P58005	312
CCSAP	C9orf40	Q8IXQ3	311
CCSAP	ZSCAN5A	Q9BUG6	311

IntAct

5 interactions, top by confidence:

A	B	Type	Score
HDAC1	ZBTB43	psi-mi:“MI:0914”(association)	0.350
CEP63	CIBAR1	psi-mi:“MI:0914”(association)	0.350
DISC1	CCSAP	psi-mi:“MI:0915”(physical association)	0.000
CCSAP		psi-mi:“MI:0915”(physical association)	0.000

BioGRID (5): CCSAP (Affinity Capture-RNA), CCSAP (Affinity Capture-RNA), CCSAP (Affinity Capture-MS), CCSAP (Proximity Label-MS), CCSAP (Affinity Capture-RNA)

ESM2 similar proteins: A0A1L8HTT5, A0A8I5ZM56, A2AJI0, B0KYV5, B0S4Q5, C0SPG1, D3ZUI5, E1C2Q8, F1LR10, K7SGN7, O70240, O73737, O75128, O88566, P34926, P51826, Q0P591, Q13625, Q14BB9, Q15554, Q3KQU3, Q5PQN4, Q5PR69, Q5RC32, Q5ZJJ1, Q5ZMW6, Q63560, Q69Z61, Q6IQ19, Q6NV74, Q6ZU35, Q7T3T9, Q7T3U0, Q7TSJ2, Q80XA6, Q86XL3, Q8CG79, Q8N7J2, Q8N9B5, Q8NFH8

Diamond homologs: Q6IQ19, Q6P3G4, Q8QZT2

SIGNOR signaling

0 interactions.

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	33
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

800 predictions. Top by Δscore:

Variant	Effect	Δscore
1:229325199:CA:C	donor_gain	1.0000
1:229326783:T:TA	donor_gain	1.0000
1:229326870:TTTG:T	donor_gain	1.0000
1:229327010:T:TC	acceptor_gain	1.0000
1:229325245:G:A	donor_gain	0.9900
1:229326881:T:A	donor_gain	0.9900
1:229327007:C:CC	acceptor_gain	0.9900
1:229327008:T:C	acceptor_gain	0.9900
1:229327010:T:C	acceptor_gain	0.9900
1:229327432:TC:T	donor_gain	0.9900
1:229327433:CC:C	donor_gain	0.9900
1:229328848:A:AC	donor_gain	0.9900
1:229328856:G:C	donor_gain	0.9900
1:229328877:T:TA	donor_gain	0.9900
1:229326732:GCGCA:G	donor_loss	0.9800
1:229326733:CGCAC:C	donor_loss	0.9800
1:229326734:GCA:G	donor_loss	0.9800
1:229326735:CACCT:C	donor_loss	0.9800
1:229326736:ACCT:A	donor_loss	0.9800
1:229326737:CCTC:C	donor_loss	0.9800
1:229327002:CAGTG:C	acceptor_gain	0.9800
1:229327395:T:TA	donor_gain	0.9800
1:229328926:TTAA:T	donor_gain	0.9800
1:229342093:GGGTA:G	donor_loss	0.9800
1:229342094:GGTAC:G	donor_loss	0.9800
1:229342095:GTAC:G	donor_loss	0.9800
1:229342096:TA:T	donor_loss	0.9800
1:229342098:C:CT	donor_loss	0.9800
1:229325141:TAA:T	donor_gain	0.9700
1:229325142:AAA:A	donor_gain	0.9700

AlphaMissense

1731 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
1:229325264:A:G	Y262H	0.998
1:229342435:A:G	Y11H	0.998
1:229325263:T:C	Y262C	0.997
1:229326763:A:T	V204D	0.997
1:229342357:G:T	R37S	0.997
1:229325276:A:G	W258R	0.996
1:229325276:A:T	W258R	0.996
1:229326822:A:C	F184L	0.996
1:229326822:A:T	F184L	0.996
1:229326824:A:G	F184L	0.996
1:229342343:C:A	E41D	0.996
1:229342343:C:G	E41D	0.996
1:229342366:G:T	R34S	0.996
1:229325252:A:C	Y266D	0.995
1:229325269:G:A	T260I	0.995
1:229325379:T:A	R223S	0.995
1:229325379:T:G	R223S	0.995
1:229342434:T:C	Y11C	0.995
1:229325376:T:A	R224S	0.994
1:229325376:T:G	R224S	0.994
1:229325410:A:G	I213T	0.994
1:229326820:G:T	A185D	0.994
1:229342336:G:C	H44D	0.994
1:229342344:T:A	E41V	0.994
1:229325274:C:A	W258C	0.993
1:229325274:C:G	W258C	0.993
1:229325410:A:C	I213S	0.993
1:229326765:G:C	N203K	0.993
1:229326765:G:T	N203K	0.993
1:229342387:A:C	Y27D	0.993

dbSNP variants (sampled 300 via entrez): RS1000013783 (1:229338162 G>A), RS1000035290 (1:229340594 C>A), RS1000254981 (1:229343847 A>T), RS1000292018 (1:229332238 G>A), RS1000400820 (1:229327977 T>C), RS1000410920 (1:229327666 G>A), RS1000598935 (1:229333198 C>T), RS1000769006 (1:229327286 T>C), RS1000803239 (1:229327561 G>A), RS1001033082 (1:229333237 C>T), RS1001497247 (1:229340045 T>C), RS1001714263 (1:229331904 C>G), RS1001828770 (1:229333234 C>A,T), RS1001947606 (1:229327634 C>A), RS1001957758 (1:229327324 G>A)

Disease associations

OMIM: gene MIM:616762 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

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

36 total (human), top 30 by PubMed support.

Chemical	Actions (top 5)	PubMed papers
bisphenol A	decreases methylation, increases expression	2
sodium arsenite	increases expression, affects cotreatment, increases abundance	2
Acetaminophen	increases expression	2
aristolochic acid I	decreases expression	1
GSK-J4	increases expression	1
FR900359	increases phosphorylation	1
triphenyl phosphate	affects expression	1
tris(2-butoxyethyl) phosphate	affects expression	1
arsenite	affects binding, decreases reaction	1
manganese chloride	increases abundance, increases expression, affects cotreatment	1
hydroquinone	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
2-palmitoylglycerol	increases expression	1
torcetrapib	increases expression	1
abrine	decreases expression	1
bisphenol S	affects cotreatment, decreases methylation	1
Sunitinib	decreases expression	1
Fulvestrant	affects cotreatment, decreases methylation	1
Arsenic	affects cotreatment, increases abundance, increases expression	1
Benzo(a)pyrene	decreases methylation	1
Calcitriol	decreases expression, affects cotreatment	1
Cisplatin	decreases expression	1
Formaldehyde	decreases expression	1
Gallic Acid	decreases expression	1
Hydrogen Peroxide	increases expression	1
Iron	increases expression	1
Manganese	increases abundance, increases expression, affects cotreatment	1
Smoke	decreases expression	1
Dihydrotestosterone	increases expression	1
Testosterone	affects cotreatment, decreases expression	1

Clinical trials (associated diseases)

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