chr10:89621863:G>C Detail (hg19) (PTEN, KLLN)

Information

Genome

Assembly Position
hg19 chr10:89,621,863-89,621,863
hg38 chr10:87,862,106-87,862,106 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_001126049.1:c.382C>G NP_001119521.1:p.Arg128Gly
Ensemble ENST00000445946.5:c.382C>G ENST00000445946.5:p.Arg128Gly
Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:<0.001
ToMMo:<0.001
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.021

Prediction

ClinVar

Clinical Significance Benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 612105 OMIM
HGNC 37212 HGNC
Ensembl ENSG00000227268 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv40099601 TogoVar
COSMIC
MONDO
Disease area statistics
[No Data.]
MGeND
[No Data.]
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign 2020-08-25 criteria provided, single submitter not specified germline Detail
Benign 2023-11-01 criteria provided, single submitter not provided germline Detail
Benign 2019-05-15 criteria provided, single submitter KLLN-related disorder germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.001 Adenocarcinoma of lung (disorder) Therefore, we created a tetracycline inducible expression system of wild-type PT... BeFree 21333374 Detail
0.182 Glioma In contrast, ectopic expression of wild type PTEN, but not the PTEN(G129R) mutan... BeFree 10435616 Detail
0.007 Glioma In contrast, ectopic expression of wild type PTEN, but not the PTEN(G129R) mutan... BeFree 10435616 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_001126049.2(KLLN):c.382C>G (p.Arg128Gly) AND not specified ClinVar Detail
NM_001126049.2(KLLN):c.382C>G (p.Arg128Gly) AND not provided ClinVar Detail
NM_001126049.2(KLLN):c.382C>G (p.Arg128Gly) AND KLLN-related disorder ClinVar Detail
Therefore, we created a tetracycline inducible expression system of wild-type PTEN (PTEN-WT) as well... DisGeNET Detail
In contrast, ectopic expression of wild type PTEN, but not the PTEN(G129R) mutant, in PTEN-mutant gl... DisGeNET Detail
In contrast, ectopic expression of wild type PTEN, but not the PTEN(G129R) mutant, in PTEN-mutant gl... 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
rs201652303 dbSNP
Genome
hg19
Position
chr10:89,621,863-89,621,863
Variant Type
snv
Reference Allele
G
Alternative Allele
C
Filtering Status (HGVD)
LowQual
# of samples (HGVD)
1187
Mean of sample read depth (HGVD)
72.10
Standard deviation of sample read depth (HGVD)
35.63
Number of reference allele (HGVD)
2373
Number of alternative allele (HGVD)
1
Allele Frequency (HGVD)
4.2122999157540015E-4
Gene Symbol (HGVD)
KLLN
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))
rs201652303
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.0001
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16758
East Asian Chromosome Counts (ExAC)
536
East Asian Allele Counts (ExAC)
11
East Asian Heterozygous Counts (ExAC)
11
East Asian Homozygous Counts (ExAC)
0
East Asian Allele Frequency (ExAC)
0.020522388059701493
Chromosome Counts in All Race (ExAC)
12550
Allele Counts in All Race (ExAC)
200
Heterozygous Counts in All Race (ExAC)
196
Homozygous Counts in All Race (ExAC)
2
Allele Frequency in All Race (ExAC)
0.01593625498007968
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