Gene Report

Basic information

Related studies

Functional annotation

Related other genetic factors

Overlap with SZ and MDD

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Basic Info

Approved Symbol	PCNT
Previous Symbol	PCNT2
Symbol Alias	KEN, KIAA0402, PCN, PCNTB, SCKL4
Approved Name	pericentrin
Previous Name	pericentrin 2 (kendrin)
Name Alias	kendrin, "Seckel syndrome 4"
Location	21q22.3
Position	chr21:46324122-46445769, 1
External Links	HGNC: 16068 Entrez Gene: 5116 Ensembl: ENSG00000160299 UCSC: uc002zji.4
No. of Studies	1 (Positive: 0; Negative: 1; trend: 0)
Overlap with SZ?	YES
Overlap with MDD?	YES

Gene related studies (count: 1)

Reference	Tested Markers	Statistical Values/Author Comments	Result Category	Comment on Study
Anitha, A., 2008	SNP: rs1543756, rs2051190, rs2070426, rs2073376, rs2073378, rs2073380, rs2186350, rs2249057, rs2249060, rs2268522, rs2268524, rs2839212, rs2839215, rs2839222, rs2839223, rs2839224, rs2839227, rs2839251, rs3737438, rs6518289, rs6518291, rs762250, rs9981892	None of the SNPs analyzed in our study showed a significant association with bipolar disorder; a weak tendency toward association was observed for two intronic SNPs. However, significantly higher expression of PCNT2 was observed in the brain samples of bipolar group, compared with the control and schizophrenia groups. In the peripheral blood lymphocytes also, a significantly higher expression of PCNT2 was observed in the bipolar group, compared with the control subjects.	Negative	Comment on Study

Gene functional annotation

Gene related GO terms (count: 29)

GO terms by PBA (count: 2)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0005516	calmodulin binding	molecular function	IEA	20
GO:0016020	membrane	cellular component	IDA[19946888]	137

GO terms by database search (count: 27)

ID	Name	Type	Evidence[PMID]	No. of Genes in BDgene
GO:0001701	in utero embryonic development	biological process	IEA	17
GO:0021772	olfactory bulb development	biological process	IEA	4
GO:0000226	microtubule cytoskeleton organization	biological process	IMP[18955030]	9
GO:0000086	G2/M transition of mitotic cell cycle	biological process	TAS	15
GO:0006996	organelle organization	biological process	TAS	23
GO:0090316	positive regulation of intracellular protein transport	biological process	IMP[22797915]	3
GO:0031514	motile cilium	cellular component	IEA	4
GO:0036064	ciliary basal body	cellular component	IEA	8
GO:0061351	neural precursor cell proliferation	biological process	IEA	1
GO:0005874	microtubule	cellular component	IEA	24
GO:0043066	negative regulation of apoptotic process	biological process	IEA	46
GO:0005829	cytosol	cellular component	TAS	223
GO:0005813	centrosome	cellular component	IDA	34
GO:0000242	pericentriolar material	cellular component	IEA	1
GO:0021696	cerebellar cortex morphogenesis	biological process	IEA	3
GO:0005814	centriole	cellular component	IDA[24421332]	6
GO:0005515	protein binding	molecular function	IPI[12812986]	563
GO:0035108	limb morphogenesis	biological process	IEA	3
GO:0005737	cytoplasm	cellular component	IDA	322
GO:0000278	mitotic cell cycle	biological process	TAS	33
GO:0048854	brain morphogenesis	biological process	IEA	2
GO:0035264	multicellular organism growth	biological process	IEA	9
GO:0045171	intercellular bridge	cellular component	IEA	3
GO:0034451	centriolar satellite	cellular component	IDA[22797915]	1
GO:0007051	spindle organization	biological process	IEA	2
GO:0001764	neuron migration	biological process	IEA	18
GO:0042384	cilium assembly	biological process	IDA[15337773]	7

Gene related KEGG pathways (count: 0)

Gene related BioCarta pathways (count: 1)

BioCarta pathways by PBA (count: 0)

BioCarta pathways by database search (count: 1)

ID	Name	No. of Genes in BDgene	Brief Description
akapCentrosomePathway	Protein Kinase A at the Centrosome	3

Gene related interactors from protein-protein interactions data in HPRD (count: 7)

Gene	Interactor	Interactor in BDgene?	Experiment Type	PMID
PCNT	AKAP9	NO	in vivo	12221128
PCNT	TUBGCP2	NO	in vivo	12221128
PCNT	PCM1	NO	in vitro;in vivo	11171385
PCNT	CALM2	NO	in vivo	12221128 , 10823944
PCNT	CEP55	NO	in vivo	16198290
PCNT	TUBGCP3	NO	in vivo	12221128
PCNT	TUBG1	NO	in vivo	12221128

Related other genetic factors

Gene related SNPs (count: 64)

Literature-origin SNPs (count: 23)

rs_ID	Location	Functional Annotation	No. of Studies (Positive/Negative/Trend)
rs2073376	chr21:46431839 - 46431839(1)	missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs2070426	chr21:46430570 - 46430570(1)	missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs3737438	chr21:46391357 - 46391357(1)	non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant	1(0/1/0)
rs2051190	chr21:46438359 - 46438359(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs2839223	chr21:46357148 - 46357148(1)	downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs6518289	chr21:46367087 - 46367087(1)	missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs2839212	chr21:46331433 - 46331433(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs2268524	chr21:46418786 - 46418786(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1(0/1/0)
rs2073380	chr21:46443844 - 46443844(1)	downstream_gene_variant; intron_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs6518291	chr21:46401674 - 46401674(1)	missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs1543756	chr21:46410020 - 46410020(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs2249057	chr21:46353189 - 46353189(1)	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant	1(0/1/0)
rs2839222	chr21:46356791 - 46356791(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1(0/1/0)
rs2186350	chr21:46397039 - 46397039(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs2839227	chr21:46366609 - 46366609(1)	missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs2249060	chr21:46353263 - 46353263(1)	downstream_gene_variant; missense_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant	1(0/1/0)
rs2839251	chr21:46421778 - 46421778(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs2839215	chr21:46344761 - 46344761(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs2073378	chr21:46385748 - 46385748(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs2839224	chr21:46357307 - 46357307(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant	1(0/1/0)
rs9981892	chr21:46347094 - 46347094(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant	1(0/1/0)
rs762250	chr21:46395124 - 46395124(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)
rs2268522	chr21:46394404 - 46394404(1)	intron_variant; non_coding_transcript_variant	1(0/1/0)

LD-proxies (count: 41)

rs_ID	Location	Functional Annotation
rs2073379	chr21:46443112 - 46443112(1)	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs2236616	chr21:46436193 - 46436193(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs11702704	chr21:46448408 - 46448408(1)	downstream_gene_variant
rs11909560	chr21:46449965 - 46449965(1)	downstream_gene_variant
rs8129460	chr21:46402630 - 46402630(1)	intron_variant; non_coding_transcript_variant
rs2839265	chr21:46447405 - 46447405(1)	downstream_gene_variant
rs2839241	chr21:46401812 - 46401812(1)	intron_variant; non_coding_transcript_variant
rs2839261	chr21:46442307 - 46442307(1)	intron_variant; non_coding_transcript_variant
rs2839258	chr21:46434316 - 46434316(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2073377	chr21:46440304 - 46440304(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2839250	chr21:46421640 - 46421640(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2839257	chr21:46430491 - 46430491(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2073374	chr21:46427938 - 46427938(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2839243	chr21:46410929 - 46410929(1)	intron_variant; non_coding_transcript_variant
rs2073382	chr21:46398384 - 46398384(1)	intron_variant; non_coding_transcript_variant
rs2839231	chr21:46370521 - 46370521(1)	intron_variant; non_coding_transcript_variant
rs2839217	chr21:46346736 - 46346736(1)	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; splice_region_variant; upstream_gene_variant
rs10854482	chr21:46442275 - 46442275(1)	intron_variant; non_coding_transcript_variant
rs3788265	chr21:46413875 - 46413875(1)	intron_variant; non_coding_transcript_variant
rs2839262	chr21:46442711 - 46442711(1)	intron_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant
rs2839218	chr21:46351142 - 46351142(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs7279193	chr21:46337878 - 46337878(1)	intron_variant; non_coding_transcript_variant
rs4819239	chr21:46340485 - 46340485(1)	intron_variant; non_coding_transcript_variant
rs9979185	chr21:46345594 - 46345594(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs9983528	chr21:46352525 - 46352525(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs11701058	chr21:46356467 - 46356467(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs2839220	chr21:46354415 - 46354415(1)	downstream_gene_variant; intron_variant; non_coding_transcript_variant
rs9980536	chr21:46342460 - 46342460(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs17371795	chr21:46435963 - 46435963(1)	downstream_gene_variant; non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant; upstream_gene_variant
rs8134832	chr21:46425328 - 46425328(1)	intron_variant; non_coding_transcript_variant; upstream_gene_variant
rs2839240	chr21:46400072 - 46400072(1)	intron_variant; non_coding_transcript_variant
rs4818837	chr21:46393779 - 46393779(1)	intron_variant; non_coding_transcript_variant
rs7279052	chr21:46388702 - 46388702(1)	intron_variant; non_coding_transcript_variant
rs9306152	chr21:46387871 - 46387871(1)	intron_variant; non_coding_transcript_variant
rs2839235	chr21:46380677 - 46380677(1)	intron_variant; non_coding_transcript_variant
rs2839234	chr21:46376959 - 46376959(1)	intron_variant; non_coding_transcript_variant
rs2839232	chr21:46372959 - 46372959(1)	intron_variant; non_coding_transcript_variant
rs3788261	chr21:46370320 - 46370320(1)	intron_variant; non_coding_transcript_variant
rs2839228	chr21:46366902 - 46366902(1)	non_coding_transcript_exon_variant; non_coding_transcript_variant; synonymous_variant
rs2839226	chr21:46366579 - 46366579(1)	intron_variant; non_coding_transcript_variant; splice_region_variant
rs4819241	chr21:46362149 - 46362149(1)	intron_variant; non_coding_transcript_variant

Gene related CNVs (count: 0)

Gene related other variants (count: 0)

Gene related regions (count: 3)

Region Name	Position	No. of Studies (Positive/Negative/Trend)
Chr 21	chr21:0-46709983	1 (0/1/0)
21q22	chr21:30200000-46709983	2 (0/0/2)
21q21.3-qter	chr21:25500000-46709983	1 (0/1/0)

Overlap with schizophrenia (SZ) and major depressive disorder (MDD)

Gene relationship with SZ

Overlap with SZ from cross-disorder studies (count: 0)

Overlap with SZ from candidate gene intersection analysis (count: 3)

Reference	ID in SZGene	Result Category
19937158	763	Trend
19191256	763	Positive
19251251	763	Negative

Gene relationship with MDD

Overlap with MDD from cross-disorder studies (count: 0)

Overlap with MDD from candidate gene intersection analysis (count: 1)

Reference	Description	Category in MDD	Link in MK4MDD
19448849	We found a significant allelic association between 3 SNPs (rs3788265, rs2073376 and rs2073380) of the PCNT gene and MDD (p = 0.006, 0.005 and 0.021, respectively)	Pos	PCNT

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Region: chr21:46324122..46445769 View in gBrowse