chr7:82824392:A>C Detail (hg38) (PCLO)

Information

Genome

Assembly Position
hg19 chr7:82,453,708-82,453,708 View the variant detail on this assembly version.
hg38 chr7:82,824,392-82,824,392

HGVS

Type Transcript Protein
RefSeq NM_033026.5:c.14440T>G NP_149015.2:p.Ser4814Ala
NM_014510.2:c.14440T>G NP_055325.2:p.Ser4814Ala
Ensemble ENST00000333891.14:c.14440T>G ENST00000333891.14:p.Ser4814Ala
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.602
ToMMo:0.601
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.699

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 604918 OMIM
HGNC 13406 HGNC
Ensembl ENSG00000186472 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv29908424 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign no assertion criteria provided not specified germline Detail
Benign 2021-09-05 criteria provided, single submitter pontocerebellar hypoplasia type 3 germline Detail
Benign 2024-02-01 criteria provided, single submitter not provided germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.130 major depressive disorder Recent genome-wide association studies have pointed to single-nucleotide polymor... BeFree 24643163 Detail
0.003 major depressive disorder Recent genome-wide association studies have pointed to single-nucleotide polymor... BeFree 24643163 Detail
0.003 Unipolar Depression Recent genome-wide association studies have pointed to single-nucleotide polymor... BeFree 24643163 Detail
0.002 Mood Disorders Recent genome-wide association studies have pointed to single-nucleotide polymor... BeFree 24643163 Detail
<0.001 Mood Disorders Recent genome-wide association studies have pointed to single-nucleotide polymor... BeFree 24643163 Detail
0.002 Unipolar Depression Recent genome-wide association studies have pointed to single-nucleotide polymor... BeFree 24643163 Detail
0.130 major depressive disorder NA GAD Detail
0.002 Unipolar Depression Although we did not take into account rare variants, we conclude that our result... BeFree 24278217 Detail
0.002 Unipolar Depression Recent genetic studies showed evidence for a role of the single-nucleotide polym... BeFree 22832399 Detail
0.002 Unipolar Depression PCLO rs2522833 modulates HPA system response to antidepressant treatment in majo... BeFree 20701824 Detail
0.002 Mental Depression We aimed to validate the association of single-nucleotide polymorphism (SNP) rs2... BeFree 19942622 Detail
0.130 major depressive disorder Although we did not take into account rare variants, we conclude that our result... BeFree 24278217 Detail
0.130 major depressive disorder PCLO rs2522833 modulates HPA system response to antidepressant treatment in majo... BeFree 20701824 Detail
0.130 major depressive disorder Recent genetic studies showed evidence for a role of the single-nucleotide polym... BeFree 22832399 Detail
0.002 Unipolar Depression A genome-wide association study implicated the polymorphism rs2522833 in the pic... BeFree 22832909 Detail
0.130 major depressive disorder A genome-wide association study implicated the polymorphism rs2522833 in the pic... BeFree 22832909 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_033026.6(PCLO):c.14440T>G (p.Ser4814Ala) AND not specified ClinVar Detail
NM_033026.6(PCLO):c.14440T>G (p.Ser4814Ala) AND Pontocerebellar hypoplasia type 3 ClinVar Detail
NM_033026.6(PCLO):c.14440T>G (p.Ser4814Ala) AND not provided ClinVar Detail
Recent genome-wide association studies have pointed to single-nucleotide polymorphisms (SNPs) in gen... DisGeNET Detail
Recent genome-wide association studies have pointed to single-nucleotide polymorphisms (SNPs) in gen... DisGeNET Detail
Recent genome-wide association studies have pointed to single-nucleotide polymorphisms (SNPs) in gen... DisGeNET Detail
Recent genome-wide association studies have pointed to single-nucleotide polymorphisms (SNPs) in gen... DisGeNET Detail
Recent genome-wide association studies have pointed to single-nucleotide polymorphisms (SNPs) in gen... DisGeNET Detail
Recent genome-wide association studies have pointed to single-nucleotide polymorphisms (SNPs) in gen... DisGeNET Detail
NA DisGeNET Detail
Although we did not take into account rare variants, we conclude that our results provide further su... DisGeNET Detail
Recent genetic studies showed evidence for a role of the single-nucleotide polymorphism rs2522833 wi... DisGeNET Detail
PCLO rs2522833 modulates HPA system response to antidepressant treatment in major depressive disorde... DisGeNET Detail
We aimed to validate the association of single-nucleotide polymorphism (SNP) rs2522833 in the PCLO g... DisGeNET Detail
Although we did not take into account rare variants, we conclude that our results provide further su... DisGeNET Detail
PCLO rs2522833 modulates HPA system response to antidepressant treatment in major depressive disorde... DisGeNET Detail
Recent genetic studies showed evidence for a role of the single-nucleotide polymorphism rs2522833 wi... DisGeNET Detail
A genome-wide association study implicated the polymorphism rs2522833 in the piccolo (PCLO) gene--in... DisGeNET Detail
A genome-wide association study implicated the polymorphism rs2522833 in the piccolo (PCLO) gene--in... DisGeNET Detail

Overlapped Transcript Coordinates

Gene Transcript ID Exon Number Chromosome Start Stop Type Amino Mutation Transcript Position Links

Overlapped Transcript

Gene Transcript ID Chromosome Start Stop Links
Gene
-
dbSNP
rs2522833 dbSNP
Genome
hg38
Position
chr7:82,824,392-82,824,392
Variant Type
snv
Reference Allele
A
Alternative Allele
C
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1202
Mean of sample read depth (HGVD)
37.21
Standard deviation of sample read depth (HGVD)
21.81
Number of reference allele (HGVD)
957
Number of alternative allele (HGVD)
1447
Allele Frequency (HGVD)
0.6019134775374376
Gene Symbol (HGVD)
PCLO
ToMMo VCF FILTER column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
PASS
Total VCF ID column value (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
rs2522833
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.6013
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
10077
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
8594
East Asian Allele Counts (ExAC)
6009
East Asian Heterozygous Counts (ExAC)
1775
East Asian Homozygous Counts (ExAC)
2117
East Asian Allele Frequency (ExAC)
0.6992087502909007
Chromosome Counts in All Race (ExAC)
120346
Allele Counts in All Race (ExAC)
53331
Heterozygous Counts in All Race (ExAC)
27333
Homozygous Counts in All Race (ExAC)
12999
Allele Frequency in All Race (ExAC)
0.4431472587373074
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