chr5:68292320:G>A Detail (hg38) (PIK3R1)

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Summary
Information
Links
Disease area statistics
MGeND
ClinVar
CIViC
DisGeNET
Annotation
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Information

Genome

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

HGVS

PIK3R1

Type	Transcript	Protein
RefSeq	NM_181524.1:c.78G>A	NP_852665.1:p.Met26Ile
	NM_181504.3:c.168G>A	NP_852556.2:p.Met56Ile
	NM_181523.2:c.978G>A	NP_852664.1:p.Met326Ile
Ensemble	ENST00000697460.1:c.453G>A	ENST00000697460.1:p.Met151Ile
	ENST00000697461.1:c.978G>A	ENST00000697461.1:p.Met326Ile
	ENST00000697462.1:c.168G>A	ENST00000697462.1:p.Met56Ile
	ENST00000320694.13:c.78G>A	ENST00000320694.13:p.Met26Ile
	ENST00000336483.10:c.168G>A	ENST00000336483.10:p.Met56Ile
	ENST00000517643.2:c.978G>A	ENST00000517643.2:p.Met326Ile
	ENST00000521381.6:c.978G>A	ENST00000521381.6:p.Met326Ile
	ENST00000521657.6:c.978G>A	ENST00000521657.6:p.Met326Ile
	ENST00000522084.6:c.168G>A	ENST00000522084.6:p.Met56Ile
	ENST00000697457.1:c.903G>A	ENST00000697457.1:p.Met301Ile
	ENST00000697458.1:c.978G>A	ENST00000697458.1:p.Met326Ile
	ENST00000697465.1:c.15G>A	ENST00000697465.1:p.Met5Ile
	ENST00000697466.1:c.-11G>A

Summary

MGeND

Clinical significance
Variant entry
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

PIK3R1

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

[No Data.]

MGeND

[No Data.]

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

Descrption	Source	Links
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: hg38
Position: chr5:68,292,320-68,292,320
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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