Gene Page: VPS13A

Summary ?
GeneID23230
SymbolVPS13A
SynonymsCHAC|CHOREIN
Descriptionvacuolar protein sorting 13 homolog A (S. cerevisiae)
ReferenceMIM:605978|HGNC:HGNC:1908|Ensembl:ENSG00000197969|HPRD:05814|Vega:OTTHUMG00000020055
Gene typeprotein-coding
Map location9q21
Pascal p-value0.116
Sherlock p-value0.187
Fetal beta-1.811
eGeneCerebellar Hemisphere
Cerebellum
Myers' cis & trans
SupportCompositeSet

Gene in Data Sources
Gene set name Method of gene setDescriptionInfo
CV:PGCnpGenome-wide Association StudyGWAS
DNM:Fromer_2014Whole Exome Sequencing analysisThis study reported a WES study of 623 schizophrenia trios, reporting DNMs using genomic DNA.
PMID:cooccurHigh-throughput literature-searchSystematic search in PubMed for genes co-occurring with SCZ keywords. A total of 3027 genes were included.
LiteratureHigh-throughput literature-searchCo-occurance with Schizophrenia keywords: schizophrenia,schizophreniasClick to show details

Section I. Genetics and epigenetics annotation

@DNM table

GeneChromosomePositionRefAltTranscriptAA changeMutation typeSiftCG46TraitStudy
VPS13Achr979974304GTNM_001018037
NM_001018038
NM_015186
NM_033305		p.2658Q>H
p.2697Q>H
p.2697Q>H
p.2697Q>H		missense
missense
missense
missense		SchizophreniaDNM:Fromer_2014

@eQTL annotation

SNP IDChromosomePositioneGeneGene Entrez IDpvalueqvalueTSS distanceeQTL type
rs823066chr1205771172VPS13A232300.06trans
snp_a-21696230VPS13A232300.03trans
rs16894557chr628999825VPS13A232300.16trans
rs12782979chr104387642VPS13A232300.17trans

Section II. Transcriptome annotation

General gene expression (GTEx)

Not available

Gene expression during devlopment (BrainCloud)

Footnote:
A total of 269 time points ploted, with n=38 fetal samples (x=1:38). Each triangle represents one time point.

Gene expression of temporal and spatial changes (BrainSpan)

Footnote:
SC: sub-cortical regions; SM: sensory-motor regions; FC: frontal cortex; and TP: temporal-parietal cortex
ST1: fetal (13 - 26 postconception weeks), ST2: early infancy to late childhood (4 months to 11 years), and ST3: adolescence to adulthood (13 - 23 years)
The bar shown representes the lower 25% and upper 25% of the expression distribution.

Top co-expressed genes in brain regions

Top 10 positively co-expressed genes
GenePearson's Correlation Spearman's Correlation
IL17RC0.750.82
DNASE20.730.79
LRP100.720.79
ABHD150.720.76
CTDSP10.710.75
HSPB60.700.80
RXRA0.700.71
TTYH10.700.75
OLIG20.700.76
NINJ10.700.76
Top 10 negatively co-expressed genes
GenePearson's Correlation Spearman's Correlation
KLHL1-0.48-0.48
NELL2-0.47-0.47
STMN2-0.46-0.48
NOL4-0.46-0.47
DPP4-0.46-0.45
ATXN7L1-0.46-0.44
PRKAR2B-0.45-0.46
CABYR-0.45-0.45
MPPED1-0.45-0.44
TMC2-0.45-0.41

Section V. Pathway annotation

Pathway namePathway size# SZGR 2.0 genes in pathwayInfo
BASAKI YBX1 TARGETS DN 384230All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER CLUSTER 1 UP 12171All SZGR 2.0 genes in this pathway
LINDGREN BLADDER CANCER WITH LOH IN CHR9Q 11671All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 DN 855609All SZGR 2.0 genes in this pathway
DACOSTA UV RESPONSE VIA ERCC3 COMMON DN 483336All SZGR 2.0 genes in this pathway
PUJANA BRCA2 PCC NETWORK 423265All SZGR 2.0 genes in this pathway
STARK PREFRONTAL CORTEX 22Q11 DELETION DN 517309All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT REJECTED VS OK DN 546351All SZGR 2.0 genes in this pathway
FLECHNER BIOPSY KIDNEY TRANSPLANT OK VS DONOR UP 555346All SZGR 2.0 genes in this pathway
HADDAD B LYMPHOCYTE PROGENITOR 293193All SZGR 2.0 genes in this pathway
YAGI AML FAB MARKERS 191131All SZGR 2.0 genes in this pathway
CUI TCF21 TARGETS 2 DN 830547All SZGR 2.0 genes in this pathway
DAZARD RESPONSE TO UV NHEK DN 318220All SZGR 2.0 genes in this pathway
MITSIADES RESPONSE TO APLIDIN DN 249165All SZGR 2.0 genes in this pathway
MILI PSEUDOPODIA HAPTOTAXIS UP 518299All SZGR 2.0 genes in this pathway
JISON SICKLE CELL DISEASE DN 18197All SZGR 2.0 genes in this pathway
YAGI AML WITH INV 16 TRANSLOCATION 422277All SZGR 2.0 genes in this pathway
GABRIELY MIR21 TARGETS 289187All SZGR 2.0 genes in this pathway
JOHNSTONE PARVB TARGETS 2 DN 336211All SZGR 2.0 genes in this pathway
FORTSCHEGGER PHF8 TARGETS DN 784464All SZGR 2.0 genes in this pathway