CSTPP1

Summary

CSTPP1 (centriolar satellite-associated tubulin polyglutamylase complex regulator 1, HGNC:28720) is a protein-coding gene on chromosome 11p11.2, encoding Centriolar satellite-associated tubulin polyglutamylase complex regulator 1 (Q9H6J7). Regulator of the tubulin polyglutamylase complex (TPGC) that controls cytoskeletal organization, nuclear shape, and cilium disassembly by balancing microtubule and actin assembly.

Enables protein-macromolecule adaptor activity. Involved in regulation of protein complex stability. Is active in centriolar satellite.

Source: NCBI Gene 79096 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 29 total
• MANE Select transcript: NM_024113

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:28720
Approved symbol	CSTPP1
Name	centriolar satellite-associated tubulin polyglutamylase complex regulator 1
Location	11p11.2
Locus type	gene with protein product
Status	Approved
Aliases	FLJ22210, MGC4707
Ensembl gene	ENSG00000149179
Ensembl biotype	protein_coding
OMIM	620479
Entrez	79096

Gene structure

Transcript identifiers

Ensembl transcripts: 25 — 8 nonsense_mediated_decay, 7 protein_coding, 6 protein_coding_CDS_not_defined, 3 retained_intron, 1 TEC

ENST00000278460, ENST00000378615, ENST00000378618, ENST00000395460, ENST00000522712, ENST00000525279, ENST00000525895, ENST00000525953, ENST00000526424, ENST00000526827, ENST00000527234, ENST00000527268, ENST00000527667, ENST00000527784, ENST00000528488, ENST00000529980, ENST00000531648, ENST00000532633, ENST00000532840, ENST00000533124, ENST00000534249, ENST00000534581, ENST00000624693, ENST00000940907, ENST00000940908

RefSeq mRNA: 5 — MANE Select: NM_024113 NM_001003676, NM_001003677, NM_001003678, NM_001278222, NM_024113

CCDS: CCDS31479, CCDS31480, CCDS41641, CCDS7925

Canonical transcript exons

ENST00000278460 — 9 exons

Exon	Start	End
ENSE00002154676	47161464	47162247
ENSE00002176256	46936761	46936851
ENSE00003495651	47161127	47161190
ENSE00003497313	46987208	46987310
ENSE00003560153	47137645	47137729
ENSE00003641128	47157023	47157218
ENSE00003647462	47155176	47155261
ENSE00003659364	47052388	47052518
ENSE00003670258	47157813	47157922

Expression profiles

Bgee: expression breadth ubiquitous, 273 present calls, max score 97.73.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 27.7413 / max 312.3113, expressed in 1781 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
114160	26.9666	1781
114161	0.5274	282
114163	0.1206	48
114162	0.1033	9
114159	0.0234	6

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
lateral nuclear group of thalamus	UBERON:0002736	97.73	gold quality
ventricular zone	UBERON:0003053	97.35	gold quality
lateral globus pallidus	UBERON:0002476	96.83	gold quality
substantia nigra pars compacta	UBERON:0001965	96.49	gold quality
right frontal lobe	UBERON:0002810	96.40	gold quality
substantia nigra pars reticulata	UBERON:0001966	96.22	gold quality
anterior cingulate cortex	UBERON:0009835	95.73	gold quality
cingulate cortex	UBERON:0003027	95.72	gold quality
Brodmann (1909) area 9	UBERON:0013540	95.72	gold quality
prefrontal cortex	UBERON:0000451	95.66	gold quality
cortical plate	UBERON:0005343	95.58	gold quality
right uterine tube	UBERON:0001302	95.53	gold quality
frontal cortex	UBERON:0001870	95.52	gold quality
dorsolateral prefrontal cortex	UBERON:0009834	95.51	gold quality
neocortex	UBERON:0001950	95.49	gold quality
nucleus accumbens	UBERON:0001882	95.46	gold quality
ganglionic eminence	UBERON:0004023	95.18	gold quality
hypothalamus	UBERON:0001898	95.13	gold quality
putamen	UBERON:0001874	95.09	gold quality
caudate nucleus	UBERON:0001873	95.06	gold quality
cerebral cortex	UBERON:0000956	95.05	gold quality
telencephalon	UBERON:0001893	94.90	gold quality
pons	UBERON:0000988	94.89	gold quality
adenohypophysis	UBERON:0002196	94.87	gold quality
forebrain	UBERON:0001890	94.85	gold quality
epithelium of bronchus	UBERON:0002031	94.82	gold quality
amygdala	UBERON:0001876	94.72	gold quality
bronchus	UBERON:0002185	94.64	gold quality
parietal lobe	UBERON:0001872	94.58	gold quality
superior frontal gyrus	UBERON:0002661	94.55	gold quality

Single-cell (SCXA)

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

Experiment	Marker?	Max mean expression
E-ANND-3	no	0.00

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

23 targeting CSTPP1, 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-8068	99.98	73.85	2376
HSA-MIR-185-3P	99.95	67.01	1743
HSA-MIR-9983-3P	99.94	71.48	3631
HSA-MIR-450B-5P	99.92	71.48	3175
HSA-MIR-129-5P	99.88	70.26	3273
HSA-MIR-4492	99.87	68.25	3611
HSA-MIR-6756-5P	99.82	67.97	2466
HSA-MIR-6766-5P	99.68	67.70	2325
HSA-MIR-24-3P	99.59	69.97	1934
HSA-MIR-4505	99.27	67.81	2678
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-5787	99.22	67.86	2628
HSA-MIR-4695-5P	99.06	64.87	1151
HSA-MIR-1227-5P	98.65	65.32	1549
HSA-MIR-4266	98.53	67.29	1035
HSA-MIR-6778-5P	98.19	66.59	1239
HSA-MIR-1972	97.67	67.38	1172
HSA-MIR-3126-5P	96.87	65.83	912
HSA-MIR-6875-5P	96.87	65.49	958
HSA-MIR-6879-3P	93.93	64.00	759

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	cstpp1	ENSDARG00000102060
mus_musculus	Cstpp1	ENSMUSG00000040591
rattus_norvegicus	Cstpp1	ENSRNOG00000014798

Protein

Protein identifiers

Centriolar satellite-associated tubulin polyglutamylase complex regulator 1 — Q9H6J7 (reviewed: Q9H6J7)

All UniProt accessions (7): Q9H6J7, E9PI12, E9PI28, E9PQA0, E9PQS2, H0YDE7, H0YDJ0

UniProt curated annotations — full annotation on UniProt →

Function. Regulator of the tubulin polyglutamylase complex (TPGC) that controls cytoskeletal organization, nuclear shape, and cilium disassembly by balancing microtubule and actin assembly. Regulates the assembly and stability of the TPGC and thereby modulates polyglutamylation of the microtubule, which antagonizes MAP4 binding.

Subunit / interactions. Interacts with PCM1. Interacts with TTLL1, TPGS1, TPGS2 and LRRC49; the interactions link CSTPP1 to the complex TPGC. Binds to alpha-tubulin.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Centriolar satellite.

Similarity. Belongs to the CSTPP1 family.

Isoforms (4)

UniProt ID	Names	Canonical?
Q9H6J7-1	1	yes
Q9H6J7-2	2
Q9H6J7-3	3
Q9H6J7-4	4

RefSeq proteins (5): NP_001003676, NP_001003677, NP_001003678, NP_001265151, NP_077018* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR038968	CSTPP1	Family

UniProt features (11 total): region of interest 4, splice variant 3, chain 1, sequence conflict 1, compositionally biased region 1, modified residue 1

Structure

Experimental structures (PDB)

0 structures.

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q9H6J7-F1	81.05	0.58

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): 319

Function

Pathways and Gene Ontology

Reactome pathways

0 pathways

MSigDB gene sets: 137 (showing top): CAGGTCC_MIR492, GOCC_MICROTUBULE_ORGANIZING_CENTER, GOCC_CENTROSOME, LIAO_METASTASIS, TGANTCA_AP1_C, APPIERTO_RESPONSE_TO_FENRETINIDE_DN, RFX1_02, AML1_01, PARENT_MTOR_SIGNALING_UP, MARSON_BOUND_BY_FOXP3_STIMULATED, MARSON_BOUND_BY_FOXP3_UNSTIMULATED, GOCC_CENTRIOLAR_SATELLITE, MIKKELSEN_ES_ICP_WITH_H3K4ME3, MIKKELSEN_NPC_ICP_WITH_H3K4ME3, BRUINS_UVC_RESPONSE_VIA_TP53_GROUP_A

GO Biological Process (4): regulation of protein complex stability (GO:0061635), microtubule cytoskeleton organization (GO:0000226), microtubule polymerization (GO:0046785), cilium disassembly (GO:0061523)

GO Molecular Function (2): protein-macromolecule adaptor activity (GO:0030674), protein binding (GO:0005515)

GO Cellular Component (4): microtubule (GO:0005874), centriolar satellite (GO:0034451), cytoplasm (GO:0005737), cytoskeleton (GO:0005856)

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	2
regulation of biological quality	1
cytoskeleton organization	1
microtubule-based process	1
microtubule nucleation	1
microtubule polymerization or depolymerization	1
protein polymerization	1
supramolecular fiber organization	1
cilium organization	1
organelle disassembly	1
protein binding	1
molecular adaptor activity	1
binding	1
microtubule cytoskeleton	1
polymeric cytoskeletal fiber	1
centrosome	1
intracellular anatomical structure	1
intracellular membraneless organelle	1

Protein interactions and networks

STRING

392 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
CSTPP1	ZNF408	Q9H9D4	566
CSTPP1	SLC61A1	Q6N075	562
CSTPP1	ARHGAP1	Q07960	542
CSTPP1	KPRP	Q5T749	527
CSTPP1	PFDN5	Q99471	524
CSTPP1	MYG1	Q9HB07	505
CSTPP1	UQCC3	Q6UW78	488
CSTPP1	LRRC49	Q8IUZ0	448
CSTPP1	TBC1D31	Q96DN5	445
CSTPP1	EIF6	P56537	428
CSTPP1	C19orf47	Q8N9M1	419
CSTPP1	ADRA1D	P25100	409
CSTPP1	TEX9	Q8N6V9	400
CSTPP1	GCSAML	Q5JQS6	400
CSTPP1	C11orf71	Q6IPW1	396
CSTPP1	RARG	P13631	396

IntAct

42 interactions, top by confidence:

A	B	Type	Score
CEP290	CCP110	psi-mi:“MI:2364”(proximity)	0.890
TUBG1	TUBG1	psi-mi:“MI:2364”(proximity)	0.760
EIF3F	EIF3CL	psi-mi:“MI:0914”(association)	0.640
NICN1	TTLL1	psi-mi:“MI:0914”(association)	0.640
TTLL1	CDC27	psi-mi:“MI:0914”(association)	0.640
LRRC49	EIF3F	psi-mi:“MI:0914”(association)	0.640
RAB7L1	CSTPP1	psi-mi:“MI:0915”(physical association)	0.560
RAB17	CSTPP1	psi-mi:“MI:0915”(physical association)	0.560
PNMA5	CSTPP1	psi-mi:“MI:0915”(physical association)	0.560
CSTPP1	RAB17	psi-mi:“MI:0915”(physical association)	0.560
CSTPP1	RAB7L1	psi-mi:“MI:0915”(physical association)	0.560
CSTPP1	PNMA5	psi-mi:“MI:0915”(physical association)	0.560
LRRC49	SNAP29	psi-mi:“MI:0914”(association)	0.530
CSTPP1	TPGS2	psi-mi:“MI:0914”(association)	0.530
RAB29	CSTPP1	psi-mi:“MI:0915”(physical association)	0.370
CSTPP1	GSR	psi-mi:“MI:0915”(physical association)	0.370
CDC16	CSTPP1	psi-mi:“MI:0915”(physical association)	0.370
CSTPP1	ECE1	psi-mi:“MI:0915”(physical association)	0.370
UBE3A	CSTPP1	psi-mi:“MI:0915”(physical association)	0.370
ARHGEF15	CSTPP1	psi-mi:“MI:0915”(physical association)	0.370
TPGS1	PPFIA3	psi-mi:“MI:0914”(association)	0.350
CSTPP1	CRYGS	psi-mi:“MI:0914”(association)	0.350
CSTPP1	PEX5	psi-mi:“MI:0914”(association)	0.350
CSTPP1	KRBA1	psi-mi:“MI:0914”(association)	0.350
CEP290	ARPC3	psi-mi:“MI:2364”(proximity)	0.270
PCM1	CCDC66	psi-mi:“MI:2364”(proximity)	0.270
CANX	PDLIM1	psi-mi:“MI:2364”(proximity)	0.270

BioGRID (106): C11orf49 (Two-hybrid), C11orf49 (Two-hybrid), PNMA5 (Two-hybrid), LRRC49 (Affinity Capture-MS), PRKACB (Affinity Capture-MS), TPGS2 (Affinity Capture-MS), NICN1 (Affinity Capture-MS), C11orf49 (Affinity Capture-MS), C11orf49 (Affinity Capture-MS), C11orf49 (Two-hybrid), C11orf49 (Proximity Label-MS), C11orf49 (Proximity Label-MS), C11orf49 (Proximity Label-MS), C11orf49 (Affinity Capture-MS), LRRC49 (Affinity Capture-MS)

ESM2 similar proteins: A0A5F9C6I2, A1L3F5, A2BDA5, A3KGS3, A8E4X8, D3ZXK7, F1R7R1, O75129, P21359, P51593, P97526, Q04690, Q1JPG0, Q2PPJ7, Q3SZD5, Q4QQM5, Q4R5A4, Q5RC14, Q5XPI3, Q5XPI4, Q62717, Q66K64, Q6GLR7, Q6NXD8, Q6P4S8, Q6PFH3, Q6VNB8, Q7L4E1, Q7TMY8, Q7Z6Z7, Q80TJ1, Q86UW7, Q8BHR8, Q8BK03, Q8BYR5, Q8CDG3, Q8CF97, Q8CID0, Q8IY22, Q8IZQ1

Diamond homologs: Q32KQ7, Q4R5A4, Q5M9F0, Q5RC14, Q6DGK9, Q8BHR8, Q9H6J7

SIGNOR signaling

1 interactions.

A	Effect	B	Mechanism
C11orf49	“up-regulates quantity by stabilization”	“Tubulin polyglutamylase complex”	binding

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 46 IntAct physical interaction partners (hypergeometric vs the genome-wide background, BH-FDR, gene-set size 15–500, ranked by fold). A functional readout of the neighbourhood — distinct from this gene’s own memberships above, and biased toward well-studied / hub proteins, so read it as themes rather than proof.

Reactome pathways:

Pathway	Partners	Fold	FDR
Carboxyterminal post-translational modifications of tubulin	5	36.0×	6e-05

GO biological processes:

GO term	Partners	Fold	FDR
cilium assembly	5	9.7×	9e-03

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	6
Likely benign	1
Benign	0

Top pathogenic / likely-pathogenic (0)

SpliceAI

2788 predictions. Top by Δscore:

Variant	Effect	Δscore
11:46936805:GATGC:G	donor_gain	1.0000
11:46936849:TGGG:T	donor_loss	1.0000
11:46936850:GG:G	donor_gain	1.0000
11:46936851:GG:G	donor_gain	1.0000
11:46936851:GGT:G	donor_loss	1.0000
11:46936852:G:GG	donor_gain	1.0000
11:46936852:G:T	donor_gain	1.0000
11:46987196:ATTT:A	acceptor_gain	1.0000
11:46987199:T:TA	acceptor_gain	1.0000
11:46987203:TGCA:T	acceptor_loss	1.0000
11:46987204:GCA:G	acceptor_loss	1.0000
11:46987205:CA:C	acceptor_loss	1.0000
11:46987206:A:AG	acceptor_gain	1.0000
11:46987207:G:GG	acceptor_gain	1.0000
11:46987207:GCTC:G	acceptor_gain	1.0000
11:46987207:GCTCA:G	acceptor_gain	1.0000
11:46987306:GAATA:G	donor_gain	1.0000
11:46987308:ATA:A	donor_gain	1.0000
11:46987309:TA:T	donor_gain	1.0000
11:46987311:G:GG	donor_gain	1.0000
11:47052385:CA:C	acceptor_loss	1.0000
11:47052386:A:AG	acceptor_gain	1.0000
11:47052386:A:AT	acceptor_loss	1.0000
11:47052387:G:GT	acceptor_gain	1.0000
11:47052387:GT:G	acceptor_gain	1.0000
11:47052387:GTT:G	acceptor_gain	1.0000
11:47052387:GTTT:G	acceptor_gain	1.0000
11:47052387:GTTTT:G	acceptor_gain	1.0000
11:47052514:TGGCG:T	donor_gain	1.0000
11:47052515:GGCG:G	donor_gain	1.0000

AlphaMissense

2153 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
11:46987240:G:C	A27P	0.998
11:47052460:T:A	N74K	0.998
11:47052460:T:G	N74K	0.998
11:47137689:T:C	C109R	0.998
11:46987253:T:C	L31P	0.997
11:46987309:T:C	Y50H	0.997
11:47052426:G:C	R63P	0.997
11:47052441:T:A	V68D	0.996
11:47052494:T:C	F86L	0.996
11:47052496:C:A	F86L	0.996
11:47052496:C:G	F86L	0.996
11:47137691:T:G	C109W	0.996
11:47155226:T:C	F139S	0.996
11:46987237:G:C	D26H	0.995
11:46987241:C:A	A27E	0.995
11:47052463:G:C	R75S	0.995
11:47052463:G:T	R75S	0.995
11:47052471:T:C	F78S	0.995
11:47137651:T:C	L96P	0.995
11:47137665:T:C	Y101H	0.995
11:47137665:T:G	Y101D	0.995
11:47137678:T:C	L105P	0.995
11:47137699:T:C	F112S	0.995
11:47137726:C:A	A121D	0.995
11:46987297:T:C	F46L	0.994
11:46987299:C:A	F46L	0.994
11:46987299:C:G	F46L	0.994
11:47052437:T:C	F67L	0.994
11:47052439:C:A	F67L	0.994
11:47052439:C:G	F67L	0.994

dbSNP variants (sampled 300 via entrez): RS1000016350 (11:46969386 T>C), RS1000034755 (11:47020743 A>G), RS1000037381 (11:46956929 A>G), RS1000043893 (11:47139831 G>A,T), RS1000057447 (11:47122716 A>G), RS1000073814 (11:47102853 C>T), RS1000074167 (11:46962494 G>T), RS1000086000 (11:47035775 T>A,C), RS1000086294 (11:46970993 A>G), RS1000092346 (11:46938774 C>T), RS1000095461 (11:46978716 T>C), RS1000126031 (11:47065805 G>A,T), RS1000142078 (11:47136409 T>C), RS1000157047 (11:47066303 T>C,G), RS1000172498 (11:47144925 A>G)

Disease associations

OMIM: gene MIM:620479 | disease phenotypes:

GenCC curated gene-disease

Mondo (0):

Orphanet (0):

HPO phenotypes

0 total (0 of 0 shown, HPO-id order):

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST001049_14	D-dimer levels	9.000000e-06
GCST004521_122	Autism spectrum disorder or schizophrenia	3.000000e-13
GCST004521_165	Autism spectrum disorder or schizophrenia	3.000000e-08
GCST005580_44	Intraocular pressure	1.000000e-12
GCST006940_153	Neurociticism	3.000000e-08
GCST007825_4	Alzheimer’s disease or fasting glucose levels (pleiotropy)	3.000000e-16
GCST010242_377	HDL cholesterol levels	3.000000e-10
GCST012229_140	Hip index	5.000000e-08
GCST90020026_775	Hip index	2.000000e-08

EFO canonical traits (5, from GWAS)

EFO ID	Trait name
EFO:0004507	D dimer measurement
EFO:0004695	intraocular pressure measurement
EFO:0007660	neuroticism measurement
EFO:0004612	high density lipoprotein cholesterol measurement
EFO:0008039	BMI-adjusted hip circumference

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
Benzo(a)pyrene	affects methylation, decreases expression	4
Valproic Acid	affects expression, increases expression	3
Air Pollutants	affects cotreatment, increases abundance, increases oxidation, increases expression	2
Dimethyl Sulfoxide	affects expression, increases expression	2
alpha-pinene	affects cotreatment, increases oxidation, increases abundance	1
uranyl acetate	affects expression	1
bisphenol A	affects cotreatment, increases methylation, decreases methylation	1
sodium arsenite	affects cotreatment, decreases expression, increases abundance	1
manganese chloride	affects cotreatment, decreases expression, increases abundance	1
methacrylaldehyde	affects cotreatment, increases oxidation, increases abundance	1
Grape Seed Proanthocyanidins	affects cotreatment, increases expression	1
Fulvestrant	affects cotreatment, increases methylation	1
Acrolein	affects cotreatment, increases oxidation, increases abundance	1
Arsenic	affects cotreatment, decreases expression, increases abundance	1
Catechin	affects cotreatment, increases expression	1
Doxorubicin	decreases expression	1
Formaldehyde	decreases expression	1
Lead	decreases expression	1
Manganese	decreases expression, increases abundance, affects cotreatment	1
Ozone	increases abundance, affects cotreatment, increases oxidation	1
Smoke	increases abundance, increases expression	1
Tretinoin	decreases expression	1
Uranium	affects expression	1
Urethane	decreases expression	1
7,8-Dihydro-7,8-dihydroxybenzo(a)pyrene 9,10-oxide	decreases expression	1
Aflatoxin B1	decreases expression	1
Copper Sulfate	decreases expression	1
Topotecan	affects response to substance	1
Acrylamide	decreases expression	1
Volatile Organic Compounds	affects cotreatment, increases oxidation	1

Clinical trials (associated diseases)

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