chr5:67588148:G>A Detail (hg19) (PIK3R1)

Information

Genome

Assembly Position
hg19 chr5:67,588,148-67,588,148
hg38 chr5:68,292,320-68,292,320 View the variant detail on this assembly version.

HGVS

Type Transcript Protein
RefSeq NM_181504.3:c.168G>A NP_852556.2:p.Met56Ile
NM_181523.2:c.978G>A NP_852664.1:p.Met326Ile
NM_181524.1:c.78G>A NP_852665.1:p.Met26Ile
Summary

MGeND

Clinical significance Benign
Variant entry 1,839
GWAS entry
Disease area statistics Show details

Frequency

JP HGVD:0.155
ToMMo:0.150
NCBN:[No Data.]
NCBN(Hondo):[No Data.]
NCBN(Ryukyu):[No Data.]
East asia ExAC:0.170

Prediction

ClinVar

Clinical Significance Benign Likely benign
Review star
Show details
Links
Type Database ID Link
Gene MIM 171833 OMIM
HGNC 8979 HGNC
Ensembl ENSG00000145675 Ensembl
NCBI NCBI
Gene Cards Gene Cards
OncoKB OncoKB
Type Database ID Link
Variant TogoVar tgv21422733 TogoVar
COSMIC COSM3727824 COSMIC
MONDO
Disease area statistics
MGeND
Clinical significance Last evaluated Condition Origin Submission ID Submitter Institute Citation Comment Image
Benign 2020/04/20 bronchus or lung, unspecified not provided MGS000041
(TMGS000094)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 abdominal part of oesophagus not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 upper third of oesophagus not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 middle third of oesophagus not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 lower third of oesophagus not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 oesophagus, unspecified not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 fundus of stomach not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 body of stomach not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 pyloric antrum not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 stomach, unspecified not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 duodenum not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 jejunum not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ileum not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 small intestine, unspecified not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 caecum not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 appendix not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ascending colon not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 transverse colon not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 descending colon not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 sigmoid colon not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 colon, unspecified not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of rectosigmoid junction not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of rectum not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 anal canal not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 intrahepatic bile duct carcinoma not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 malignant neoplasm of gallbladder not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 extrahepatic bile duct not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ampulla of vater not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 head of pancreas not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 body of pancreas not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 tail of pancreas not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 ill-defined sites within the digestive system not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 bronchus or lung, unspecified not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 retroperitoneum not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
Benign 2020/04/20 other not provided MGS000042
(TMGS000093)
Hitoshi Nakagama National Cancer Center Japan
ClinVar
Clinical significance Last evaluated Review status Condition Origin Links
Benign Likely benign 2023-11-12 criteria provided, multiple submitters, no conflicts not specified germline Detail
Benign 2023-11-28 criteria provided, multiple submitters, no conflicts not provided germline Detail
Benign 2024-02-01 criteria provided, single submitter Agammaglobulinemia 7, autosomal recessive,immunodeficiency 36,SHORT syndrome germline Detail
Benign 2024-02-01 criteria provided, single submitter Agammaglobulinemia 7, autosomal recessive,immunodeficiency 36,SHORT syndrome germline Detail
Benign 2024-02-01 criteria provided, single submitter Agammaglobulinemia 7, autosomal recessive,immunodeficiency 36,SHORT syndrome germline Detail
CIViC
[No Data.]
DisGeNET
Score Disease name Description Source Pubmed Links
0.089 Diabetes Mellitus, Non-Insulin-Dependent In addition, we screened other reported T2D-associated polymorphisms: PIK3R1 rs3... BeFree 23133645 Detail
0.004 Diabetes Mellitus, Non-Insulin-Dependent The aim of our study was to investigate whether common polymorphisms in the gene... BeFree 15127203 Detail
0.374 Diabetes Mellitus, Non-Insulin-Dependent The aim of our study was to investigate whether common polymorphisms in the gene... BeFree 15127203 Detail
0.005 Diabetes The aim of our study was to investigate whether common polymorphisms in the gene... BeFree 15127203 Detail
<0.001 Diabetes The aim of our study was to investigate whether common polymorphisms in the gene... BeFree 15127203 Detail
0.088 Diabetes Mellitus, Non-Insulin-Dependent The aim of our study was to investigate whether common polymorphisms in the gene... BeFree 15127203 Detail
0.002 Diabetes Mellitus, Non-Insulin-Dependent The aim of our study was to investigate whether common polymorphisms in the gene... BeFree 15127203 Detail
0.002 Diabetes Mellitus, Non-Insulin-Dependent The aim of our study was to investigate whether common polymorphisms in the gene... BeFree 15127203 Detail
0.089 Diabetes Mellitus, Non-Insulin-Dependent The aim of our study was to investigate whether common polymorphisms in the gene... BeFree 15127203 Detail
<0.001 diabetes mellitus The aim of our study was to investigate whether common polymorphisms in the gene... BeFree 15127203 Detail
0.330 Diabetes Mellitus, Non-Insulin-Dependent The aim of our study was to investigate whether common polymorphisms in the gene... BeFree 15127203 Detail
0.010 Diabetes Mellitus, Non-Insulin-Dependent The aim of our study was to investigate whether common polymorphisms in the gene... BeFree 15127203 Detail
0.005 diabetes mellitus The aim of our study was to investigate whether common polymorphisms in the gene... BeFree 15127203 Detail
0.089 Diabetes Mellitus, Non-Insulin-Dependent Met326Ile aminoacid polymorphism in the human p85 alpha gene has no major impact... BeFree 15523593 Detail
Annotation

Annotations

DescrptionSourceLinks
NM_181523.3(PIK3R1):c.978G>A (p.Met326Ile) AND not specified ClinVar Detail
NM_181523.3(PIK3R1):c.978G>A (p.Met326Ile) AND not provided ClinVar Detail
NM_181523.3(PIK3R1):c.978G>A (p.Met326Ile) AND multiple conditions ClinVar Detail
NM_181523.3(PIK3R1):c.978G>A (p.Met326Ile) AND multiple conditions ClinVar Detail
NM_181523.3(PIK3R1):c.978G>A (p.Met326Ile) AND multiple conditions ClinVar Detail
In addition, we screened other reported T2D-associated polymorphisms: PIK3R1 rs3730089, IRS1 rs18012... DisGeNET Detail
The aim of our study was to investigate whether common polymorphisms in the genes regulating the ear... DisGeNET Detail
The aim of our study was to investigate whether common polymorphisms in the genes regulating the ear... DisGeNET Detail
The aim of our study was to investigate whether common polymorphisms in the genes regulating the ear... DisGeNET Detail
The aim of our study was to investigate whether common polymorphisms in the genes regulating the ear... DisGeNET Detail
The aim of our study was to investigate whether common polymorphisms in the genes regulating the ear... DisGeNET Detail
The aim of our study was to investigate whether common polymorphisms in the genes regulating the ear... DisGeNET Detail
The aim of our study was to investigate whether common polymorphisms in the genes regulating the ear... DisGeNET Detail
The aim of our study was to investigate whether common polymorphisms in the genes regulating the ear... DisGeNET Detail
The aim of our study was to investigate whether common polymorphisms in the genes regulating the ear... DisGeNET Detail
The aim of our study was to investigate whether common polymorphisms in the genes regulating the ear... DisGeNET Detail
The aim of our study was to investigate whether common polymorphisms in the genes regulating the ear... DisGeNET Detail
The aim of our study was to investigate whether common polymorphisms in the genes regulating the ear... DisGeNET Detail
Met326Ile aminoacid polymorphism in the human p85 alpha gene has no major impact on early insulin si... 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
rs3730089 dbSNP
Genome
hg19
Position
chr5:67,588,148-67,588,148
Variant Type
snv
Reference Allele
G
Alternative Allele
A
Filtering Status (HGVD)
PASS
# of samples (HGVD)
1210
Mean of sample read depth (HGVD)
71.04
Standard deviation of sample read depth (HGVD)
35.47
Number of reference allele (HGVD)
2045
Number of alternative allele (HGVD)
375
Allele Frequency (HGVD)
0.15495867768595042
Gene Symbol (HGVD)
PIK3R1
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))
rs3730089
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
0.1497
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
2509
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831))
16760
East Asian Chromosome Counts (ExAC)
8652
East Asian Allele Counts (ExAC)
1470
East Asian Heterozygous Counts (ExAC)
1226
East Asian Homozygous Counts (ExAC)
122
East Asian Allele Frequency (ExAC)
0.16990291262135923
Chromosome Counts in All Race (ExAC)
121388
Allele Counts in All Race (ExAC)
21145
Heterozygous Counts in All Race (ExAC)
16583
Homozygous Counts in All Race (ExAC)
2281
Allele Frequency in All Race (ExAC)
0.17419349523840907
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