PCM1

Summary

PCM1 (pericentriolar material 1, HGNC:8727) is a protein-coding gene on chromosome 8p22, encoding Pericentriolar material 1 protein (Q15154). Required for centrosome assembly and function. It is a selective cancer dependency (DepMap: 14.8% of cell lines).

The protein encoded by this gene is a component of centriolar satellites, which are electron dense granules scattered around centrosomes. Inhibition studies show that this protein is essential for the correct localization of several centrosomal proteins, and for anchoring microtubules to the centrosome. Chromosomal aberrations involving this gene are associated with papillary thyroid carcinomas and a variety of hematological malignancies, including atypical chronic myeloid leukemia and T-cell lymphoma. Multiple transcript variants encoding different isoforms have been found for this gene.

Source: NCBI Gene 5108 — RefSeq curated summary.

At a glance

• GWAS associations: 9
• Clinical variants (ClinVar): 513 total
• Cancer dependency (DepMap): dependent in 14.8% of screened cell lines
• MANE Select transcript: NM_006197

Identifiers

Gene identifiers

Field	Value
HGNC ID	HGNC:8727
Approved symbol	PCM1
Name	pericentriolar material 1
Location	8p22
Locus type	gene with protein product
Status	Approved
Aliases	PTC4
Ensembl gene	ENSG00000078674
Ensembl biotype	protein_coding
OMIM	600299
Entrez	5108

Gene structure

Transcript identifiers

Ensembl transcripts: 76 — 61 protein_coding, 10 retained_intron, 5 protein_coding_CDS_not_defined

ENST00000325083, ENST00000517545, ENST00000517730, ENST00000517836, ENST00000518537, ENST00000518762, ENST00000518877, ENST00000518930, ENST00000518936, ENST00000518985, ENST00000519253, ENST00000519802, ENST00000521338, ENST00000522275, ENST00000522777, ENST00000522998, ENST00000523055, ENST00000523540, ENST00000523896, ENST00000524203, ENST00000524226, ENST00000524356, ENST00000857056, ENST00000857057, ENST00000857058, ENST00000857059, ENST00000857060, ENST00000857061, ENST00000857062, ENST00000857063, ENST00000857064, ENST00000937109, ENST00000937110, ENST00000937111, ENST00000937112, ENST00000937113, ENST00000937114, ENST00000937115, ENST00000937116, ENST00000937117, ENST00000937118, ENST00000937119, ENST00000937120, ENST00000937121, ENST00000937122, ENST00000937123, ENST00000937124, ENST00000937125, ENST00000937126, ENST00000937127, ENST00000937128, ENST00000937129, ENST00000937130, ENST00000937131, ENST00000937132, ENST00000969399, ENST00000969400, ENST00000969401, ENST00000969402, ENST00000969403, ENST00000969404, ENST00000969405, ENST00000969406, ENST00000969407, ENST00000969408, ENST00000969409, ENST00000969410, ENST00000969411, ENST00000969412, ENST00000969413, ENST00000969414, ENST00000969415, ENST00000969416, ENST00000969417, ENST00000969418, ENST00000969419

RefSeq mRNA: 32 — MANE Select: NM_006197 NM_001315507, NM_001315508, NM_001352632, NM_001352633, NM_001352634, NM_001352635, NM_001352636, NM_001352637, NM_001352638, NM_001352639, NM_001352640, NM_001352641, NM_001352642, NM_001352643, NM_001352644, NM_001352645, NM_001352646, NM_001352647, NM_001352648, NM_001352649, NM_001352650, NM_001352651, NM_001352652, NM_001352653, NM_001352654, NM_001352655, NM_001352656, NM_001352657, NM_001352658, NM_001352659, NM_001352660, NM_006197

CCDS: CCDS47812, CCDS83255, CCDS83256, CCDS87582

Canonical transcript exons

ENST00000325083 — 39 exons

Exon	Start	End
ENSE00001604755	17985959	17986087
ENSE00001630003	18011237	18011366
ENSE00001686307	18006263	18006397
ENSE00001712594	18009547	18009744
ENSE00001749205	18010609	18010668
ENSE00001762665	18011667	18011827
ENSE00001784449	17993483	17993619
ENSE00001791886	17989859	17989979
ENSE00001804208	17991542	17991700
ENSE00002101939	17922988	17923188
ENSE00002129486	18027637	18029948
ENSE00003243903	18013964	18014036
ENSE00003477503	18025544	18025658
ENSE00003532515	17972329	17972687
ENSE00003572045	17980591	17980755
ENSE00003635792	18025361	18025453
ENSE00003663979	17985447	17985619
ENSE00003665995	18014584	18014840
ENSE00003992579	17963101	17963291
ENSE00003992580	17924713	17924780
ENSE00003992581	17950615	17950724
ENSE00003992582	17960014	17960165
ENSE00003992583	17955470	17955653
ENSE00003992584	17939691	17939861
ENSE00003992585	17952970	17953186
ENSE00003992586	17962034	17962174
ENSE00003992587	17960315	17960444
ENSE00003992588	17964568	17964768
ENSE00003992589	17956604	17956777
ENSE00003992591	17965999	17966218
ENSE00003992592	17947186	17947363
ENSE00003992593	17957540	17957775
ENSE00003992594	17969577	17969748
ENSE00003992595	17957264	17957421
ENSE00003992596	17966328	17966473
ENSE00003992597	17937134	17937379
ENSE00003992598	17935589	17935706
ENSE00003992599	17938740	17939009
ENSE00003992600	17966980	17967170

Expression profiles

Bgee: expression breadth ubiquitous, 292 present calls, max score 99.41.

FANTOM5 (CAGE): breadth ubiquitous, TPM avg 57.4128 / max 1710.5511, expressed in 1810 samples.

FANTOM5 promoters (5 alternative TSS)

Promoter ID	TPM avg	Samples expressed
87556	49.1750	1799
87554	3.8150	1300
87553	2.6768	1213
87557	1.2136	508
87555	0.5325	286

Top tissues by expression

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

Tissue	Anatomy ID	Expression score	Quality
calcaneal tendon	UBERON:0003701	99.41	gold quality
left testis	UBERON:0004533	99.11	gold quality
ventricular zone	UBERON:0003053	99.09	gold quality
right testis	UBERON:0004534	99.06	gold quality
sperm	CL:0000019	98.88	gold quality
testis	UBERON:0000473	98.78	gold quality
bronchial epithelial cell	CL:0002328	98.77	gold quality
colonic epithelium	UBERON:0000397	98.72	gold quality
male germ cell	CL:0000015	98.68	gold quality
right uterine tube	UBERON:0001302	98.68	gold quality
sural nerve	UBERON:0015488	98.67	gold quality
male germ line stem cell (sensu Vertebrata) in testis	CL:0000089 ∩ UBERON:0000473	98.36	gold quality
cortical plate	UBERON:0005343	98.26	gold quality
primordial germ cell in gonad	CL:0000670 ∩ UBERON:0000991	98.22	gold quality
ganglionic eminence	UBERON:0004023	98.22	gold quality
epithelium of bronchus	UBERON:0002031	98.15	gold quality
adrenal tissue	UBERON:0018303	98.15	gold quality
tendon	UBERON:0000043	98.13	gold quality
bronchus	UBERON:0002185	98.05	gold quality
gluteal muscle	UBERON:0002000	97.96	gold quality
skeletal muscle tissue of biceps brachii	UBERON:0004502	97.85	gold quality
body of pancreas	UBERON:0001150	97.80	gold quality
olfactory segment of nasal mucosa	UBERON:0005386	97.76	gold quality
epithelium of nasopharynx	UBERON:0001951	97.71	gold quality
gastrocnemius	UBERON:0001388	97.67	gold quality
biceps brachii	UBERON:0001507	97.59	gold quality
left ovary	UBERON:0002119	97.58	gold quality
mucosa of paranasal sinus	UBERON:0005030	97.57	gold quality
muscle of leg	UBERON:0001383	97.53	gold quality
hindlimb stylopod muscle	UBERON:0004252	97.53	gold quality

Single-cell (SCXA)

Detected in 4 experiment(s), a significant marker in 2.

Experiment	Marker?	Max mean expression
E-ANND-3	yes	12.06
E-CURD-114	yes	11.93
E-MTAB-7606	no	652.38
E-GEOD-83139	no	2.95

Regulation

Is transcription factor: no

miRNA regulators (miRDB)

117 targeting PCM1, 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-7110-3P	100.00	73.18	2486
HSA-MIR-6740-5P	100.00	65.64	932
HSA-MIR-6873-3P	100.00	71.42	2626
HSA-MIR-3613-3P	100.00	76.36	7965
HSA-MIR-8485	100.00	77.57	4731
HSA-LET-7A-3P	100.00	74.03	3932
HSA-LET-7B-3P	100.00	74.08	3913
HSA-LET-7F-1-3P	100.00	74.02	3928
HSA-MIR-98-3P	100.00	74.08	3907
HSA-MIR-190A-3P	100.00	80.35	5520
HSA-MIR-574-5P	100.00	66.01	989
HSA-MIR-186-5P	99.99	70.83	3707
HSA-MIR-33A-5P	99.99	68.62	1055
HSA-MIR-33B-5P	99.99	68.58	1062
HSA-MIR-4531	99.99	69.70	3181
HSA-LET-7F-2-3P	99.98	70.98	2588
HSA-MIR-1185-1-3P	99.98	71.04	2593
HSA-MIR-1185-2-3P	99.98	71.04	2593
HSA-MIR-5696	99.98	72.36	4487
HSA-MIR-4789-5P	99.98	70.76	2721
HSA-MIR-3148	99.97	75.06	6478
HSA-MIR-495-3P	99.96	72.81	4197
HSA-MIR-5688	99.96	73.23	4504
HSA-MIR-2110	99.96	66.68	1930
HSA-MIR-548AT-5P	99.96	70.83	2666
HSA-MIR-128-3P	99.95	71.17	2484
HSA-MIR-216A-3P	99.95	71.19	2505
HSA-MIR-335-3P	99.93	73.36	4958
HSA-MIR-6721-5P	99.93	68.92	2981
HSA-MIR-205-3P	99.92	69.92	3165

Functional genomics

DepMap (CRISPR cell-line fitness): dependent in 14.8% of screened cell lines.

Literature-anchored findings (GeneRIF, showing 28)

• multiple processes involved in regulating the abundance of NIMA (never in mitosis gene a)-related kinase 2 kinase at the centrosome including microtubule binding, the centriolar satellite component PCM-1, and localized protein degradation (PMID:15659651)
• To study the rearrangement created by the t(8;9)(p22;p24)used dual-colour FISH on metaphases from patient cells using labelled-BAC clones centred on PCM1. (PMID:16034466)
• A genetic translocation in atypical chronic myeloid leukemia yields a new PCM1-JAK2 fusion gene. (PMID:16091753)
• The PCM1 gene is implicated in susceptibility to schizophrenia and is associated with orbitofrontal gray matter volumetric deficits. (PMID:16894060)
• cytogenetic change of t(8;9)(p22;p24) may induce HLA-DR immunophenotypic switch and a coordination of the two evolutional changes may play a role in leukemic cell progression (PMID:18594780)
• PCM1 gene is implicated in schizophrenia. (PMID:18762586)
• CEP290 binds to PCM-1 and localizes to centriolar satellites in a PCM-1- and microtubule-dependent manner. (PMID:18772192)
• decreased colocalization of DISC1 and its binding partner PCM1 after Phe607 DISC1 transfection (PMID:19455170)
• Hook3- and PCM1-mediated dynamic assembly of pericentriolar material is essential for interkinetic nuclear migration. (PMID:20152126)
• DISC1 coding variants modulate centrosomal PCM1 localization, highlight a role for DISC1 in glial function and provide a possible cellular mechanism contributing to the association of these DISC1 variants with psychiatric phenotypes. (PMID:20360304)
• These data provide further evidence that PCM1-though certainly not a major risk factor in the Northern Swedish population-cannot be ruled out as a contributor to schizophrenia risk and/or protection. (PMID:20468070)
• The data failed to find a significant association between SNPs or haplotypes of the PCM1 gene and schizophrenia in the Japanese population (P>0.28). (PMID:21481569)
• WT HTT regulates ciliogenesis by interacting through huntingtin-associated protein 1 (HAP1) with pericentriolar material 1 protein (PCM1). (PMID:21985783)
• PCM1 interacts with Hook2 in a complex that regulates a limiting step required for further initiation of ciliogenesis after centriole maturation. (PMID:21998199)
• NEK7 is essential for PCM accumulation in a cell cycle stage-specific manner. (PMID:22100915)
• CEP90 physically interacts with PCM-1 at centriolar satellites, and this interaction is essential for centrosomal accumulation of the centriolar satellites and eventually for primary cilia formation. (PMID:23110211)
• these data suggest a mechanism whereby the recruitment of Plk1 to pericentriolar matrix by PCM1 plays a pivotal role in the regulation of primary cilia disassembly before mitotic entry. (PMID:23345402)
• Chromosomal translocation [t(8;9)(p22;p24)]/PCM1-JAK2 fusion protein activates SOCS2 and SOCS3 via STAT5 in a cutaneous T-cell lymphoma cell line. (PMID:23372669)
• no association between the PCM1 gene and schizophrenia in a Japanese population (PMID:24576429)
• a novel variant in the PCM1 3’UTR is significantly associated with ovarian cancer (PMID:24909162)
• Haematological neoplasms associated with t(8;9)(p22;p24); PCM1-JAK2 have features in common and we suggest that they should be recognized as a specific entity in the WHO classification (PMID:24913195)
• In the absence of PCM1, Mib1 destabilizes Talpid3 through poly-ubiquitylation and suppresses cilium assembly. (PMID:27146717)
• Data suggest that USP9X as an integral component of centrosome where it functions to stabilize PCM1 and CEP55 and to promote centrosome biogenesis; N-terminal domain of USP9X appears to be responsible for physical association of USP9X with PCM1 and CEP55. (USP9X = ubiquitin-specific protease 9X; PCM1 = pericentriolar material 1 protein; CEP55 = 55kDa centrosomal protein) (PMID:28620049)
• detecting PDGFRA, PDGFRB, FGFR1 and PCM1-JAK2 rearrangements is a prerequisite for up-to-date WHO classification, and an essential step in the differential diagnosis of neoplasms with eosinophilia. (PMID:29567772)
• study reveals that USP9X is a constituent of centriolar satellites and functions to maintain centriolar satellite integrity by stabilizing PCM1. (PMID:30584065)
• SNX17 Recruits USP9X to Antagonize MIB1-Mediated Ubiquitination and Degradation of PCM1 during Serum-Starvation-Induced Ciliogenesis. (PMID:31671755)
• PCM1 is necessary for focal ciliary integrity and is a candidate for severe schizophrenia. (PMID:33214552)
• LncRNA-ENST00000421645 promotes T cells to secrete IFN-gamma by sponging PCM1 in neurosyphilis. (PMID:34382410)

Cross-species orthologs

3 orthologs

Organism	Symbol	Gene ID
danio_rerio	pcm1	ENSDARG00000062198
mus_musculus	Pcm1	ENSMUSG00000031592
rattus_norvegicus	Pcm1	ENSRNOG00000010155

Protein

Protein identifiers

Pericentriolar material 1 protein — Q15154 (reviewed: Q15154)

All UniProt accessions (7): Q15154, A0A4W8VX11, A0A5H1ZRS1, E5RGQ4, E7EV93, E9PGW9, H0YBA1

UniProt curated annotations — full annotation on UniProt →

Function. Required for centrosome assembly and function. Essential for the correct localization of several centrosomal proteins including CEP250, CETN3, PCNT and NEK2. Required to anchor microtubules to the centrosome. Also involved in cilium biogenesis by recruiting the BBSome, a ciliary protein complex involved in cilium biogenesis, to the centriolar satellites. Recruits the tubulin polyglutamylase complex (TPGC) to centriolar satellites.

Subunit / interactions. Self-associates. Interacts with C2CD3. Interacts with BBS4, BBS8, CETN3, HAP1, NDE1, NDEL1, MAP1LC3B, GABARAPAL2, and GABARAP. Interacts with CEP131; the interaction increases in response to ultraviolet light (UV) radiation. Associates with microtubule; association to microtubule is reduced in response to cellular stress, such as ultraviolet light (UV) radiation or heat shock, in a process that requires p38 MAP kinase signaling. Interacts with CFAP263. Interacts with SSX2IP. Interacts with CCDC13. Interacts with CEP290. Interacts with PARD6A. Interacts with KIAA0753/OFIP, CEP20/FOR20 and OFD1; the interaction with CEP20/FOR20 and OFD1 may be mediated by KIAA0753/OFIP. Interacts with CCDC66. Interacts with CCDC61. Interacts with DZIP1; localizes DZIP1 and the associated BBSome to centriolar satellite. Interacts with CSTPP1, TTLL1, TPGS1 and LRRC49. Interacts with CFAP53.

Subcellular location. Cytoplasm. Cytoskeleton. Microtubule organizing center. Centrosome. Cytoplasmic granule. Centriolar satellite. Cilium basal body.

Tissue specificity. Expressed in blood, bone marrow, breast, lymph node, ovary and thyroid.

Post-translational modifications. Ubiquitinated. Undergoes monoubiquitination catalyzed by the E3 ubiquitin-protein ligase MIB1 in proliferating cells, preventing cilia formation. Monoubiquitination by MIB1 is inhibited in response to cellular stress, such as ultraviolet light (UV) radiation or heat shock, resulting in cilia formation initiation. Variant Ser-159 is phosphorylated. Phosphorylated on multiple serine and threonine residues by DYRK3 during the G2-to-M transition, after the nuclear-envelope breakdown. Phosphorylation by DYRK3 promotes disassembly of pericentriolar material. Phosphorylation at Ser-372 mediated by PLK4 is required to maintain the integrity of centriolar satellites.

Disease relevance. A chromosomal aberration involving PCM1 is found in papillary thyroid carcinomas (PTCs). Translocation t(8;10)(p21.3;q11.2) with RET links the protein kinase domain of RET to the major portion of PCM1. A chromosomal aberration involving PCM1 is found in a variety of hematological malignancies including atypical chronic myeloid leukemia (atypical CML) and T-cell lymphoma. Translocation t(8;9)(p22;p24) with JAK2 links the protein kinase domain of JAK2 to the major portion of PCM1.

Induction. Expression is reduced in breast and ovarian cancer.

Similarity. Belongs to the PCM1 family.

Isoforms (5)

UniProt ID	Names	Canonical?
Q15154-1	1	yes
Q15154-2	2
Q15154-3	3
Q15154-4	4
Q15154-5	5

RefSeq proteins (32): NP_001302436, NP_001302437, NP_001339561, NP_001339562, NP_001339563, NP_001339564, NP_001339565, NP_001339566, NP_001339567, NP_001339568, NP_001339569, NP_001339570, NP_001339571, NP_001339572, NP_001339573, NP_001339574, NP_001339575, NP_001339576, NP_001339577, NP_001339578, NP_001339579, NP_001339580, NP_001339581, NP_001339582, NP_001339583, NP_001339584, NP_001339585, NP_001339586, NP_001339587, NP_001339588, NP_001339589, NP_006188* (*=MANE)

Domains & families (InterPro)

ID	Name	Type
IPR024138	Pericentriolar_Pcm1	Family
IPR031446	PCM1_C	Domain

Pfam: PF15717

UniProt features (138 total): modified residue 45, compositionally biased region 22, sequence conflict 21, region of interest 17, sequence variant 11, coiled-coil region 8, splice variant 6, site 5, initiator methionine 1, chain 1, mutagenesis site 1

Structure

Experimental structures (PDB)

3 structures.

PDB	Method	Resolution (Å)
6HYL	X-RAY DIFFRACTION	1.56
6HYM	X-RAY DIFFRACTION	1.86
7Q46	X-RAY DIFFRACTION	2.46

Predicted structure (AlphaFold)

Model	pLDDT	Fraction very-high
AF-Q15154-F1	48.98	0.10

Functional residue map

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

Catalytic / active sites (5): 1314–1315 (breakpoint for translocation to form pcm1-jak2 fusion protein); 1369–1370 (breakpoint for translocation to form pcm1-jak2 fusion protein); 1470–1471 (breakpoint for translocation to form pcm1-jak2 fusion protein); 1609–1610 (breakpoint for translocation to form pcm1-ret fusion protein); 1947–1948 (breakpoint for translocation to form pcm1-jak2 fusion protein)

Post-translational modifications (45): 2, 65, 68, 69, 93, 110, 116, 119, 159, 370, 372, 384, 399, 588, 643, 859, 861, 866, 869, 872 …

Mutagenesis-validated functional residues (1):

Position	Phenotype
372	phosphomimetic mutant.

Function

Pathways and Gene Ontology

Reactome pathways

7 pathways

ID	Pathway
R-HSA-2565942	Regulation of PLK1 Activity at G2/M Transition
R-HSA-380259	Loss of Nlp from mitotic centrosomes
R-HSA-380270	Recruitment of mitotic centrosome proteins and complexes
R-HSA-380284	Loss of proteins required for interphase microtubule organization from the centrosome
R-HSA-380320	Recruitment of NuMA to mitotic centrosomes
R-HSA-5620912	Anchoring of the basal body to the plasma membrane
R-HSA-8854518	AURKA Activation by TPX2

MSigDB gene sets: 302 (showing top): GSE45365_CD8A_DC_VS_CD11B_DC_IFNAR_KO_DN, GSE45365_CTRL_VS_MCMV_INFECTION_NK_CELL_DN, GOBP_PROTEIN_LOCALIZATION_TO_CYTOSKELETON, GOBP_NEGATIVE_REGULATION_OF_CELL_DEVELOPMENT, GOBP_CYTOPLASMIC_MICROTUBULE_ORGANIZATION, GOBP_BEHAVIOR, GOBP_INTRACELLULAR_PROTEIN_TRANSPORT, GOBP_MICROTUBULE_ANCHORING, GCANCTGNY_MYOD_Q6, GOBP_POSITIVE_REGULATION_OF_INTRACELLULAR_PROTEIN_TRANSPORT, GRAESSMANN_APOPTOSIS_BY_DOXORUBICIN_DN, GOBP_POSITIVE_REGULATION_OF_PROTEIN_LOCALIZATION, GOBP_NEUROGENESIS, GOBP_REGULATION_OF_NERVOUS_SYSTEM_DEVELOPMENT, GOBP_CELL_PROLIFERATION_IN_FOREBRAIN

GO Biological Process (17): neuron migration (GO:0001764), centrosome cycle (GO:0007098), interkinetic nuclear migration (GO:0022027), cytoplasmic microtubule organization (GO:0031122), microtubule anchoring (GO:0034453), microtubule anchoring at centrosome (GO:0034454), social behavior (GO:0035176), intraciliary transport involved in cilium assembly (GO:0035735), negative regulation of neurogenesis (GO:0050768), cilium assembly (GO:0060271), regulation of protein complex stability (GO:0061635), protein localization to centrosome (GO:0071539), positive regulation of intracellular protein transport (GO:0090316), neuronal stem cell population maintenance (GO:0097150), protein-containing complex localization to centriolar satellite (GO:0140706), non-motile cilium assembly (GO:1905515), cell projection organization (GO:0030030)

GO Molecular Function (3): identical protein binding (GO:0042802), molecular adaptor activity (GO:0060090), protein binding (GO:0005515)

GO Cellular Component (17): pericentriolar material (GO:0000242), nucleoplasm (GO:0005654), cytoplasm (GO:0005737), centrosome (GO:0005813), centriole (GO:0005814), cytosol (GO:0005829), cilium (GO:0005929), microtubule cytoskeleton (GO:0015630), membrane (GO:0016020), nuclear membrane (GO:0031965), protein-containing complex (GO:0032991), centriolar satellite (GO:0034451), ciliary transition zone (GO:0035869), ciliary basal body (GO:0036064), apical part of cell (GO:0045177), cytoskeleton (GO:0005856), cell projection (GO:0042995)

Reactome top-level categories

Rollup of top-5 pathways:

Category	Pathways
G2/M Transition	2
Centrosome maturation	2
Loss of proteins required for interphase microtubule organization from the centrosome	1
Mitotic Prometaphase	1
Assembly of the 9+0 primary cilium	1

GO top-level categories

Rollup of top GO terms by namespace:

Category	Terms
cellular anatomical structure	9
microtubule organizing center	3
microtubule cytoskeleton organization	2
cilium assembly	2
binding	2
centrosome	2
intracellular membraneless organelle	2
cilium	2
cell migration	1
generation of neurons	1
cell cycle process	1
microtubule organizing center organization	1
nuclear migration	1
cell proliferation in forebrain	1
supramolecular fiber organization	1
microtubule anchoring at microtubule organizing center	1
behavior	1
biological process involved in intraspecies interaction between organisms	1
intraciliary transport	1
negative regulation of cell development	1
neurogenesis	1
regulation of neurogenesis	1
negative regulation of nervous system development	1
axoneme assembly	1
intraciliary transport involved in cilium assembly	1
cilium organization	1
protein localization to cilium	1
organelle assembly	1
trans-Golgi to periciliary membrane compartment transport	1
plasma membrane bounded cell projection assembly	1
ciliary transition zone assembly	1
regulation of biological quality	1
protein localization to microtubule organizing center	1
intracellular protein transport	1
positive regulation of intracellular transport	1
regulation of intracellular protein transport	1
positive regulation of protein transport	1
stem cell population maintenance	1
protein-containing complex localization	1
cellular component organization	1

Protein interactions and networks

STRING

1508 interactions, top by confidence (×1000):

Protein A	Protein B	Partner UniProt	Score
PCM1	BBS4	Q96RK4	928
PCM1	NIN	Q8N4C6	854
PCM1	PCNT	O95613	851
PCM1	CEP290	O15078	833
PCM1	HAP1	P54257	811
PCM1	DISC1	Q9NRI5	809
PCM1	OFD1	O75665	746
PCM1	CETN1	Q12798	740
PCM1	DCTN1	Q14203	739
PCM1	BBS1	Q8NFJ9	695
PCM1	HOOK3	Q86VS8	694
PCM1	BBS7	Q8IWZ6	679
PCM1	BBS2	Q9BXC9	673
PCM1	RAB8A	P24407	668
PCM1	BBS5	Q8N3I7	663

IntAct

399 interactions, top by confidence:

A	B	Type	Score
MAP1LC3B	SQSTM1	psi-mi:“MI:0914”(association)	0.980
GABARAPL2	SQSTM1	psi-mi:“MI:0914”(association)	0.970
GABARAP	SQSTM1	psi-mi:“MI:0914”(association)	0.950
BBS4	PCM1	psi-mi:“MI:0915”(physical association)	0.910
PCM1	BBS4	psi-mi:“MI:0915”(physical association)	0.910
PCM1	BBS4	psi-mi:“MI:0403”(colocalization)	0.910
BBS4	PCM1	psi-mi:“MI:0403”(colocalization)	0.910
MED4	MED19	psi-mi:“MI:2364”(proximity)	0.900
MED4	MED19	psi-mi:“MI:0914”(association)	0.900
CEP290	CCP110	psi-mi:“MI:2364”(proximity)	0.890
PCM1	CEP72	psi-mi:“MI:0915”(physical association)	0.850
CEP72	PCM1	psi-mi:“MI:0915”(physical association)	0.850
CSNK1E	PER1	psi-mi:“MI:0914”(association)	0.840
BBS4	BBIP1	psi-mi:“MI:0914”(association)	0.810
TUBG1	TUBG1	psi-mi:“MI:2364”(proximity)	0.760
WASHC3	PCM1	psi-mi:“MI:0915”(physical association)	0.740
PCM1	CEP131	psi-mi:“MI:0915”(physical association)	0.740
PCM1	WASHC3	psi-mi:“MI:0915”(physical association)	0.740
DYNLL1	BLTP3B	psi-mi:“MI:0914”(association)	0.730
GABARAP	PCM1	psi-mi:“MI:0915”(physical association)	0.730

BioGRID (821): CCDC53 (Two-hybrid), PCM1 (Affinity Capture-MS), PCM1 (Affinity Capture-MS), PCM1 (Affinity Capture-MS), PCM1 (Affinity Capture-MS), PCM1 (Affinity Capture-MS), PCM1 (Affinity Capture-MS), PCM1 (Affinity Capture-MS), PCM1 (Affinity Capture-MS), PCM1 (Affinity Capture-MS), PCM1 (Two-hybrid), ING5 (Two-hybrid), KIAA0368 (Two-hybrid), PCM1 (Two-hybrid), CCDC53 (Two-hybrid)

ESM2 similar proteins: A6ZMG4, A6ZR60, B3LLZ8, B6LI37, C5DBV2, C5E1C7, C7GWA2, C8ZEW0, O48767, P34399, P34402, P34518, P35198, P38306, P40063, P40214, P43598, P48437, Q00682, Q02831, Q03564, Q04438, Q06616, Q09599, Q12365, Q15154, Q1T763, Q4R309, Q60JJ0, Q6C3T0, Q6CL13, Q6CQB7, Q6CRT5, Q6CWB2, Q6FWU4, Q6GQM0, Q7Z5L4, Q8AV28, Q8C729, Q8WWF3

Diamond homologs: Q15154, Q8AV28, Q9PVV4, Q9R0L6

SIGNOR signaling

9 interactions.

A	Effect	B	Mechanism
PCM1	up-regulates	CEP250	relocalization
PCM1	up-regulates	NEK2	relocalization
MIB1	down-regulates	PCM1	ubiquitination
PLK4	“up-regulates activity”	PCM1	phosphorylation
PCM1	up-regulates	CETN1	relocalization
PCM1	up-regulates	CETN2	relocalization
PCM1	up-regulates	CETN3	relocalization
PCM1	up-regulates	NIN	relocalization
PCM1	up-regulates	PCNT	relocalization

Enriched among interaction partners

Reactome pathways and GO biological processes over-represented among this gene’s 173 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
Loss of Nlp from mitotic centrosomes	25	45.1×	8e-34
Loss of proteins required for interphase microtubule organization from the centrosome	25	45.1×	8e-34
AURKA Activation by TPX2	25	43.3×	2e-33
Anchoring of the basal body to the plasma membrane	31	39.8×	3e-40
Recruitment of mitotic centrosome proteins and complexes	25	38.6×	4e-32
Regulation of PLK1 Activity at G2/M Transition	25	36.0×	2e-31
Centrosome maturation	12	34.6×	2e-14
Recruitment of NuMA to mitotic centrosomes	26	34.4×	5e-32

GO biological processes:

GO term	Partners	Fold	FDR
centriole replication	9	51.9×	2e-11
microtubule nucleation	9	44.2×	6e-11
protein localization to centrosome	8	42.5×	2e-09
non-motile cilium assembly	13	29.7×	3e-13
motile cilium assembly	5	22.9×	1e-04
centrosome cycle	8	21.2×	4e-07
mitophagy	8	20.0×	6e-07
spindle assembly	5	17.5×	4e-04

Disease & clinical

Clinical variants and AI predictions

ClinVar

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

Classification	Count (floor)
Pathogenic	0
Likely pathogenic	0
Uncertain significance	400
Likely benign	38
Benign	8

Top pathogenic / likely-pathogenic (0)

SpliceAI

0 predictions. Top by Δscore:

AlphaMissense

13527 scored. Top likely-pathogenic:

Variant	Protein change	am_pathogenicity
8:17939794:T:C	L239P	1.000
8:17939815:T:C	L246P	1.000
8:17956639:T:C	L503P	1.000
8:17985555:T:C	L1406P	1.000
8:17985567:T:C	L1410P	1.000
8:18009599:T:C	L1672P	1.000
8:18009625:T:C	F1681L	1.000
8:18009627:C:A	F1681L	1.000
8:18009627:C:G	F1681L	1.000
8:18009640:T:C	F1686L	1.000
8:18009642:C:A	F1686L	1.000
8:18009642:C:G	F1686L	1.000
8:18009650:T:C	L1689P	1.000
8:17939704:T:C	L209P	0.999
8:17939733:G:C	A219P	0.999
8:17939734:C:A	A219D	0.999
8:17939746:G:C	R223P	0.999
8:17939755:T:C	L226P	0.999
8:17939803:T:C	L242P	0.999
8:17953148:T:C	L417P	0.999
8:17956630:T:C	L500S	0.999
8:17960389:T:C	L756P	0.999
8:17966446:T:C	L1065P	0.999
8:17985483:G:C	R1382P	0.999
8:17985506:G:C	A1390P	0.999
8:17985507:C:A	A1390D	0.999
8:17985516:T:A	I1393N	0.999
8:17985546:T:C	L1403P	0.999
8:17985557:T:C	F1407L	0.999
8:17985559:C:A	F1407L	0.999

dbSNP variants (sampled 300 via entrez): RS1000014797 (8:18025310 A>G,T), RS1000023189 (8:17955912 A>C), RS1000031521 (8:17994173 C>T), RS1000058874 (8:17951922 T>TA), RS1000068578 (8:17946130 C>G,T), RS1000095346 (8:17936257 G>A), RS1000131534 (8:17926932 T>A,G), RS1000135200 (8:17980496 A>G), RS1000167771 (8:18006864 T>C), RS1000170741 (8:17975663 T>C,G), RS1000179826 (8:17956778 G>A), RS1000180994 (8:17947141 G>A), RS1000196058 (8:18018578 C>T), RS1000216049 (8:17922734 C>G), RS1000229705 (8:17976290 G>A)

Disease associations

OMIM: gene MIM:600299 | disease phenotypes: MIM:188550

GenCC curated gene-disease

Mondo (2): thyroid cancer, nonmedullary, 1 (MONDO:0008567), congenital heart disease (MONDO:0005453)

Orphanet (0):

HPO phenotypes

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

GWAS associations

9 associations (top):

Study	Trait	p-value
GCST001519_14	Economic and political preferences	9.000000e-07
GCST003830_30	Response to bronchodilator in chronic obstructive pulmonary disease (change in FEV1)	6.000000e-07
GCST004297_6	Atrial fibrillation	6.000000e-10
GCST007056_1	Waist-hip ratio	9.000000e-08
GCST008152_63	Weight	2.000000e-06
GCST010244_414	Triglyceride levels	5.000000e-10
GCST012489_91	Heel bone mineral density x serum urate levels interaction	8.000000e-09
GCST90002396_362	Mean reticulocyte volume	3.000000e-09
GCST90002397_318	Mean spheric corpuscular volume	4.000000e-09

EFO canonical traits (8, from GWAS)

EFO ID	Trait name
EFO:0004827	economic and social preference
EFO:0005921	FEV change measurement
EFO:0004343	waist-hip ratio
EFO:0004338	body weight
EFO:0004530	triglyceride measurement
EFO:0004531	urate measurement
EFO:0009270	heel bone mineral density
EFO:0010701	mean reticulocyte volume

MeSH disease descriptors (1)

Descriptor	Name	Tree numbers
D006330	Heart Defects, Congenital	C14.240.400; C14.280.400; C16.131.240.400

Drugs & pharmacology

Drug and pharmacology data

Is drug target: no

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

CTD chemical–gene interactions

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

Chemical	Actions (top 5)	PubMed papers
trichostatin A	affects cotreatment, decreases expression	3
Valproic Acid	affects cotreatment, decreases expression	3
entinostat	decreases expression, affects cotreatment	2
Arsenic Trioxide	decreases expression, increases response to substance	2
Hydrogen Peroxide	affects expression, increases expression	2
Phenylmercuric Acetate	affects cotreatment, decreases expression	2
Tobacco Smoke Pollution	decreases expression	2
aristolochic acid I	decreases expression	1
FR900359	affects phosphorylation	1
ginger extract	decreases expression, increases abundance	1
geldanamycin	increases expression	1
methylmercuric chloride	decreases expression	1
triphenyl phosphate	affects expression	1
sodium arsenate	decreases expression	1
arsenite	affects binding, decreases reaction	1
tris(1,3-dichloro-2-propyl)phosphate	decreases expression	1
butyraldehyde	decreases expression	1
cupric chloride	decreases expression	1
coumarin	decreases phosphorylation	1
S-(1,2-dichlorovinyl)cysteine	affects response to substance, increases expression, affects cotreatment, decreases expression	1
pentanal	decreases expression	1
perfluorooctane sulfonic acid	decreases expression	1
4-(5-benzo(1,3)dioxol-5-yl-4-pyridin-2-yl-1H-imidazol-2-yl)benzamide	affects cotreatment, decreases expression	1
torcetrapib	increases expression	1
abrine	decreases expression	1
dorsomorphin	affects cotreatment, decreases expression	1
jinfukang	decreases expression	1
Vorinostat	decreases expression	1
Panobinostat	affects cotreatment, decreases expression	1
Acetaminophen	decreases expression	1

Cellosaurus cell lines

1 cell lines: 1 cancer cell line

First 10 cell lines (id-ordered, not curated):

Cellosaurus	Name	Category	Sex
CVCL_D7WN	Ubigene A-549 PCM1 KO	Cancer cell line	Male

Clinical trials (associated diseases)

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

Trial	Phase	Status	Title
NCT00668824	PHASE4	UNKNOWN	Improved Diagnosis of Congenital Heart Disease by Magnetic Resonance Imaging Using Vasovist
NCT01368705	PHASE4	COMPLETED	Nitrogen Balance in Infants After Post Cardiothoracic Surgery
NCT01619982	PHASE4	COMPLETED	Pre-operative Prophylaxis With Vancomycin and Cefazolin in Pediatric Cardiovascular Surgery Patients
NCT02122679	PHASE4	WITHDRAWN	Tranexamic Acid Effect on Platelet Aggregation Following Infant Cardiopulmonary Bypass
NCT02527811	PHASE4	UNKNOWN	Ulinastatin Injection in in Pediatric Patients Undergoing Open Heart Surgery
NCT03014700	PHASE4	COMPLETED	Fibrinogen Concentrate vs Cryoprecipitate
NCT03408340	PHASE4	TERMINATED	Paravertebral Nerve Blocks in Neonates
NCT03630796	PHASE4	UNKNOWN	Effect of Sevoflurane in Postoperative Troponin I Levels in Children Undergoing Congenital Heart Defects Surgery
NCT03667703	PHASE4	COMPLETED	Stress Ulcer Prophylaxis Versus Placebo in Critically Ill Infants With Congenital Heart Disease
NCT04453761	PHASE4	UNKNOWN	Thiamine Influenced on Substrate Energy Effectiveness in Indonesian Children Undergoing Cardiopulmonary Bypass
NCT06668389	PHASE4	RECRUITING	Sodium-Glucose Cotransporter 2 Inhibitors for Repaired Tetralogy of Fallot Patients for Enhancement of Cardio-Pulmonary Status Trial
NCT07499154	PHASE4	NOT_YET_RECRUITING	Perioperative Lidocaine for Lung Protection in Infants Undergoing Cardiac Surgery
NCT00000470	PHASE3	COMPLETED	Infant Heart Surgery: Central Nervous System Sequelae of Circulatory Arrest
NCT00000494	PHASE3	COMPLETED	Management of Patent Ductus in Premature Infants
NCT01134302	PHASE3	UNKNOWN	Hybrid Versus Norwood Management Strategies in Infants Undergoing Single Ventricle Palliation
NCT01607983	PHASE3	WITHDRAWN	Effects of Pulmonary Vasodilation Upon VA Coupling in Fontan Patients
NCT01662011	PHASE3	UNKNOWN	Application of Neurally Adjusted Ventilatory Assist to Children After Congenital Cardiac Surgery
NCT02320669	PHASE3	COMPLETED	Phase 3 Triiodothyronine Supplementation for Infants After Cardiopulmonary Bypass
NCT02615262	PHASE3	COMPLETED	Intraoperative Dexamethasone in Pediatric Cardiac Surgery
NCT03153137	PHASE3	COMPLETED	Clinical Study Assessing the Efficacy and Safety of Macitentan in Fontan-palliated Subjects
NCT03154476	PHASE3	COMPLETED	Role of Sildenafil for Fontan Associated Liver Disease (SiFALD) Study
NCT04536194	PHASE3	COMPLETED	Dopamine Versus Norepinephrine Under General Anesthesia
NCT04702373	PHASE3	ACTIVE_NOT_RECRUITING	Training in Exercise Activities and Motion for Growth (TEAM 4 Growth) RCT
NCT05049590	PHASE3	COMPLETED	Acute Normovolemic Hemodilution in Complex Cardiac Surgery
NCT06406517	PHASE3	UNKNOWN	Comparative Effectiveness of Gadopiclenol for Evaluation of Adult Congenital Heart Anatomy and Hemodynamics
NCT06693674	PHASE3	RECRUITING	Effect of Sacubitril-Valsartan on Cardiac Structure and Function
NCT06955260	PHASE3	NOT_YET_RECRUITING	SGLT2 Inhibition With Empagliflozin in Fontan Circulatory Failure
NCT00115375	PHASE2	COMPLETED	Platelet Aggregation Inhibition in Children on Clopidogrel (PICOLO)
NCT00350220	PHASE2	COMPLETED	Transfusion Strategies in Pediatric Cardiothoracic Surgery
NCT00374088	PHASE2	COMPLETED	N-Acetylcysteine in Neonatal Congenital Heart Surgery (INACT Study)
NCT00538785	PHASE2	COMPLETED	A Study to Evaluate MEDI-524 In Children With Hemodynamically Significant Congenital Heart Disease
NCT00770705	PHASE2	WITHDRAWN	Parenteral Phenoxybenzamine During Congenital Heart Disease Surgery
NCT00919945	PHASE2	TERMINATED	Impact of Early Enteral Feeding on Splanchnic Blood Flow After Surgery for Critical Heart Disease in the Newborn
NCT01063712	PHASE2	COMPLETED	Safety and Effectiveness of the Device Nit-Occlud® PDA-R
NCT01069510	PHASE2	COMPLETED	Spironolactone in Adult Congenital Heart Disease
NCT01189981	PHASE2	COMPLETED	Effect of eHealth Encouragements to Intensive Exercise in Adolescents With Congenital Heart Disease
NCT01330433	PHASE2	COMPLETED	Effects of CoSeal on Bleeding & Adhesions in Pediatric Heart Surgery
NCT01662037	PHASE2	COMPLETED	Bosentan Therapy in Children With Functional Single Ventricle
NCT01668264	PHASE2	UNKNOWN	Imaging Assessment of Diastolic Function
NCT01827059	PHASE2	UNKNOWN	Bosentan In Exercise Induced Pulmonary Arterial Hypertension in CongenitaL Heart diseasE