chr2:240868897:C>G Detail (hg38) (AGXT)

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

Genome

Assembly	Position
hg19	chr2:241,808,314-241,808,314 View the variant detail on this assembly version.
hg38	chr2:240,868,897-240,868,897

HGVS

AGXT

Type	Transcript	Protein
RefSeq	NM_000030.2:c.32C>G	NP_000021.1:p.Pro11Arg
Ensemble	ENST00000307503.4:c.32C>G	ENST00000307503.4:p.Pro11Arg

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:[No Data.]
	ToMMo:[No Data.]
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:0.002

Prediction

ClinVar

Clinical Significance	Conflicting classifications of pathogenicity
Review star
Show details

Links

AGXT

Type	Database	ID	Link
Gene	MIM	604285	OMIM
	HGNC	341	HGNC
	Ensembl	ENSG00000172482	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv315827077	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

Clinical significance	Last evaluated	Review status	Condition	Origin	Links
Conflicting interpretations of pathogenicity	2024-03-25	criteria provided, conflicting interpretations	Primary hyperoxaluria, type I	germline unknown	Detail
Likely pathogenic	2023-12-15	criteria provided, single submitter	primary hyperoxaluria	germline	Detail
Pathogenic Likely pathogenic	2024-01-28	criteria provided, multiple submitters, no conflicts	not provided	germline	Detail

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.579	Primary hyperoxaluria, type I	The G170R variant of the alanine:glyoxylate aminotransferase (AGT) is the most c...	BeFree	21103899	Detail
<0.001	NEPHROLITHIASIS, CALCIUM OXALATE	The AGT Pro11Leu polymorphism in the alanine:glyoxylate aminotransferase (AGT) e...	BeFree	24344980	Detail
0.002	Kidney Calculi	The AGT Pro11Leu polymorphism in the alanine:glyoxylate aminotransferase (AGT) e...	BeFree	24344980	Detail
0.579	Primary hyperoxaluria, type I	NA	CLINVAR		Detail

Annotation

Annotations

Descrption	Source	Links
NM_000030.3(AGXT):c.32C>G (p.Pro11Arg) AND Primary hyperoxaluria, type I	ClinVar	Detail
NM_000030.3(AGXT):c.32C>G (p.Pro11Arg) AND Primary hyperoxaluria	ClinVar	Detail
NM_000030.3(AGXT):c.32C>G (p.Pro11Arg) AND not provided	ClinVar	Detail
The G170R variant of the alanine:glyoxylate aminotransferase (AGT) is the most common pathogenic all...	DisGeNET	Detail
The AGT Pro11Leu polymorphism in the alanine:glyoxylate aminotransferase (AGT) enzyme has been sugge...	DisGeNET	Detail
The AGT Pro11Leu polymorphism in the alanine:glyoxylate aminotransferase (AGT) enzyme has been sugge...	DisGeNET	Detail
NA	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: rs34116584 dbSNP
Genome: hg38
Position: chr2:240,868,897-240,868,897
Variant Type: snv
Reference Allele: C
Alternative Allele: G
East Asian Chromosome Counts (ExAC): 8330
East Asian Allele Counts (ExAC): 13
East Asian Heterozygous Counts (ExAC): 11
East Asian Homozygous Counts (ExAC): 1
East Asian Allele Frequency (ExAC): 0.00156062424969988
Chromosome Counts in All Race (ExAC): 114234
Allele Counts in All Race (ExAC): 18
Heterozygous Counts in All Race (ExAC): 16
Homozygous Counts in All Race (ExAC): 1
Allele Frequency in All Race (ExAC): 1.575713010137087E-4

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