Evidence Detail for PRKCB

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Basic Information Top

Gene Symbol:	PRKCB ( MGC41878,PKC-beta,PKCB,PRKCB1,PRKCB2 )
Gene Full Name:	protein kinase C, beta
Band:	16p11.2
Quick Links	Entrez ID:5579; OMIM: 176970; Uniprot ID:KPCB_HUMAN; ENSEMBL ID: ENSG00000166501

Sequences Top

nucleotide Sequence
Protein Sequence

>PRKCB|5579|nucleotide
ATGGCTGACCCGGCTGCGGGGCCGCCGCCGAGCGAGGGCGAGGAGAGCACCGTGCGCTTCGCCCGCAAAGGCGCCCTCCGGCAGAAGAACGTGCATGAGGTCAAG
AACCACAAATTCACCGCCCGCTTCTTCAAGCAGCCCACCTTCTGCAGCCACTGCACCGACTTCATCTGGGGCTTCGGGAAGCAGGGATTCCAGTGCCAAGTTTGC
TGCTTTGTGGTGCACAAGCGGTGCCATGAATTTGTCACATTCTCCTGCCCTGGCGCTGACAAGGGTCCAGCCTCCGATGACCCCCGCAGCAAACACAAGTTTAAG
ATCCACACGTACTCCAGCCCCACGTTTTGTGACCACTGTGGGTCACTGCTGTATGGACTCATCCACCAGGGGATGAAATGTGACACCTGCATGATGAATGTGCAC
AAGCGCTGCGTGATGAATGTTCCCAGCCTGTGTGGCACGGACCACACGGAGCGCCGCGGCCGCATCTACATCCAGGCCCACATCGACAGGGACGTCCTCATTGTC
CTCGTAAGAGATGCTAAAAACCTTGTACCTATGGACCCCAATGGCCTGTCAGATCCCTACGTAAAACTGAAACTGATTCCCGATCCCAAAAGTGAGAGCAAACAG
AAGACCAAAACCATCAAATGCTCCCTCAACCCTGAGTGGAATGAGACATTTAGATTTCAGCTGAAAGAATCGGACAAAGACAGAAGACTGTCAGTAGAGATTTGG
GATTGGGATTTGACCAGCAGGAATGACTTCATGGGATCTTTGTCCTTTGGGATTTCTGAACTTCAGAAAGCCAGTGTTGATGGCTGGTTTAAGTTACTGAGCCAG
GAGGAAGGCGAGTACTTCAATGTGCCTGTGCCACCAGAAGGAAGTGAGGCCAATGAAGAACTGCGGCAGAAATTTGAGAGGGCCAAGATCAGTCAGGGAACCAAG
GTCCCGGAAGAAAAGACGACCAACACTGTCTCCAAATTTGACAACAATGGCAACAGAGACCGGATGAAACTGACCGATTTTAACTTCCTAATGGTGCTGGGGAAA
GGCAGCTTTGGCAAGGTCATGCTTTCAGAACGAAAAGGCACAGATGAGCTCTATGCTGTGAAGATCCTGAAGAAGGACGTTGTGATCCAAGATGATGACGTGGAG
TGCACTATGGTGGAGAAGCGGGTGTTGGCCCTGCCTGGGAAGCCGCCCTTCCTGACCCAGCTCCACTCCTGCTTCCAGACCATGGACCGCCTGTACTTTGTGATG
GAGTACGTGAATGGGGGCGACCTCATGTATCACATCCAGCAAGTCGGCCGGTTCAAGGAGCCCCATGCTGTATTTTACGCTGCAGAAATTGCCATCGGTCTGTTC
TTCTTACAGAGTAAGGGCATCATTTACCGTGACCTAAAACTTGACAACGTGATGCTCGATTCTGAGGGACACATCAAGATTGCCGATTTTGGCATGTGTAAGGAA
AACATCTGGGATGGGGTGACAACCAAGACATTCTGTGGCACTCCAGACTACATCGCCCCCGAGATAATTGCTTATCAGCCCTATGGGAAGTCCGTGGATTGGTGG
GCATTTGGAGTCCTGCTGTATGAAATGTTGGCTGGGCAGGCACCCTTTGAAGGGGAGGATGAAGATGAACTCTTCCAATCCATCATGGAACACAACGTAGCCTAT
CCCAAGTCTATGTCCAAGGAAGCTGTGGCCATCTGCAAAGGGCTGATGACCAAACACCCAGGCAAACGTCTGGGTTGTGGACCTGAAGGCGAACGTGATATCAAA
GAGCATGCATTTTTCCGGTATATTGATTGGGAGAAACTTGAACGCAAAGAGATCCAGCCCCCTTATAAGCCAAAAGCTTGTGGGCGAAATGCTGAAAACTTCGAC
CGATTTTTCACCCGCCATCCACCAGTCCTAACACCTCCCGACCAGGAAGTCATCAGGAATATTGACCAATCAGAATTCGAAGGATTTTCCTTTGTTAACTCTGAA
TTTTTAAAACCCGAAGTCAAGAGCTAA
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>PRKCB|5579|nucleotide
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Evidence Statistic Top

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Evidences	Syndromic Gene	GWAS	Expression	CNV	Linkage	Low Scale Association	Other Studies	Total
Score (No. of Studies)	No	0 (0)	3 (4)	0 (0)	0 (0)	2 (3)	1 (1)	16 (8)

Syndromic Autism Gene Top

Low Scale Association Studies (by Ethnic Group) Top

Family Based Association Studies: 3

Reference	Population	#SNPs/ #VNTRs	#Families	Affecteds						Result
Reference	Population	#SNPs/ #VNTRs	#Families	#Subjects (% Women)	ADI-R	ADOS	Diagnosis	Age (range)	IQ (range)	Result
CAUCASIAN
Philippi, 2005_1	AGRE	92 (detail)	116	- (-)			AD	- -	- -
Yang, 2007_1	Ireland	6 (detail)	171	178 (-)			ASD	- -	>35 -
Lintas, 2008_1	Italy	4 (detail)	234	239 (-)			AD	- -	- -

Case Control Based Association Studies: 0

Reference	Population	#SNPs/ #VNTRs	ASD Cases						Normal Controls		Result
Reference	Population	#SNPs/ #VNTRs	#Subjects (% Women)	ADI-R	ADOS	Diagnosis	Age (range)	IQ	#Subjects (% Women)	Age (range)	Result
No Evidence.

Genome-Wide Association Studies(By Ethnic Group) Top

Reference	Stage	#SNPs/ #VNTRs	#Families	Affecteds	Result
#Subjects (% Women)	ADI-R	ADOS	Diagnosis	Age (range)	IQ (range)
No Evidence.

Reference	Stage	#SNPs/ #VNTRs	ASD Cases	Normal Controls	Result
#Subjects (% Women)	ADI-R	ADOS	Diagnosis	Age (range)	IQ	#Subjects (% Women)	Age (range)
No Evidence.

Other Low Scale Gene Studies Top

Reference	Orangnism	Tissue	ADI-R	ADOS	Diagnosis	Evidence Level
Lintas, 2008_1	human	temporocortical gray matter (BA41/42)	-	-	AD	RNA expression
Subjects: 11 Normal Controls: 11 Methods: real-time PCR Evidence Details: Temporocortical PRKCB1 gene expression was reduced on average by 35 and 31% for the PRKCB1-1 and PRKCB1-2 isoforms (P<0.01 and <0.05, respectively) according to qPCR
Lintas, 2008_1	human	temporocortical gray matter (BA41/42)	-	-	AD	protein expression
Subjects: 11 Normal Controls: 11 Methods: western blotting Evidence Details: Protein amounts measured for the PKCbetaII isoform were similarly decreased by 35% (P=0.05).
Lintas, 2008_1	human	temporocortical gray matter (BA41/42)	-	-	AD	RNA expression
Subjects: 11 Normal Controls: 11 Methods: microarray Evidence Details: Whole genome expression analysis unveiled a partial disruption in the coordinated expression of PKCbeta-driven genes, including several cytokines. These results confirm the association between autism and PRKCB1 gene variants, point toward PKCbeta roles in altered epithelial permeability, demonstrate a significant downregulation of brain PRKCB1 gene expression in autism and suggest that it could represent a compensatory adjustment aimed at limiting an ongoing dysreactive immune process.

Large Scale Expression Studies Top

Microarray Studies: 4

Reference	Population	Tissue	#Subjects (% Women)	Endo- pheno	Diagnosis	Normal Controls (% Women)	Fold Change	Up/ Down	P/Q value
Nishimura, 2007_1	America	lymphoblastoid cell lines	8 (-)	autism with FMR1-FM	autism	15 (-)	1.21	Up	0.0000063
Platform: Whole Human Genome Array G4112A (Agilent) ProbeSet: - RefSeq_ID/ EST: NM_212535 GEO_ID: GSE7329 Statistic Method: ANOVA by MeV3.1, PCA by GeneSpring GX7.3(Aligent), SAM and RankProd by Bioconductor packages
Nishimura, 2007_2	America	lymphoblastoid cell lines	7 (-)	autism with dup(15q)	autism	15 (-)	1.21	Up	0.0000063
Platform: Whole Human Genome Array G4112A (Agilent) ProbeSet: - RefSeq_ID/ EST: NM_212535 GEO_ID: GSE7329 Statistic Method: ANOVA by MeV3.1, PCA by GeneSpring GX7.3(Aligent), SAM and RankProd by Bioconductor packages
Voineagu, 2011_1	Unknown	16 frontal cortex(BA9) and 13 temporal cortex(BA41	16 (25.00%)	-	autism	16 (6.25%)	0.658273	Down	0.305455
Platform: Illumina Ref8 v3 microarrays ProbeSet: ILMN_1713603 RefSeq_ID/ EST: - GEO_ID: GSE28521 Statistic Method: SAM package and unless otherwise specified the significance threshold was FDR,0.05 and fold changes.1.3.
Voineagu, 2011_1	Unknown	16 frontal cortex(BA9) and 13 temporal cortex(BA41	16 (25.00%)	-	autism	16 (6.25%)	0.714466	Down	1.1752
Platform: Illumina Ref8 v3 microarrays ProbeSet: ILMN_1716563 RefSeq_ID/ EST: - GEO_ID: GSE28521 Statistic Method: SAM package and unless otherwise specified the significance threshold was FDR,0.05 and fold changes.1.3.
Voineagu, 2011_2	Unknown	frontal, BA44/45	10 (0.00%)	-	autism	6 (0.00%)	0.860797	Down	0.525872
Platform: Illumina Ref8 v4 microarrays ProbeSet: ILMN_1713603 RefSeq_ID/ EST: - GEO_ID: GSE28521 Statistic Method: SAM package and unless otherwise specified the significance threshold was FDR,0.05 and fold changes.1.3.

Proteomics Studies:0

Reference	Population	Tissue	Platform	#Subjects (% Women)	ADI-R	ADOS	Diagnosis	Normal Controls(% Women)
No Evidence.

CNV Studies Top

CNV Name	Chr	Band	Gain/Loss	Number of CNVs	Evidence Type	Reference
Case	Control
No matched CNVs !

Linkage Studies Top

Linkage Name	Band	Chr	Marker	LOD	NPL	P_Value	Reference
No Matched Linkage Regions !

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Syndromic Genes

Non-syndromic Genes

AutismKB Statistics

Studies: 616
Genes: 3,075
SNPs/VNTRs: 3,386
CNVs: 4,617
Linkage Regions: 158
Last Update: 05/25/2012
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