chr17:44019712:G>A Detail (hg19) (MAPT)

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

Genome

Assembly	Position
hg19	chr17:44,019,712-44,019,712
hg38	chr17:45,942,346-45,942,346 View the variant detail on this assembly version.

HGVS

MAPT

Type	Transcript	Protein
RefSeq	NM_016835.4:c.-17-19975G>A
	NM_001123066.3:c.-17-19975G>A
	NM_001203251.1:c.-17-19975G>A
	NM_001203252.1:c.-17-19975G>A
	NM_005910.5:c.-17-19975G>A
Ensemble	ENST00000446361.7:c.-17-19975G>A
	ENST00000262410.10:c.-17-19975G>A
	ENST00000344290.10:c.-17-19975G>A
	ENST00000535772.6:c.-17-19975G>A
	ENST00000334239.12:c.-17-19975G>A
	ENST00000420682.7:c.-17-19975G>A
	ENST00000680674.1:c.-17-19975G>A
	ENST00000351559.10:c.-17-19975G>A

Summary

MGeND

Clinical significance
Variant entry
GWAS entry
Disease area statistics	Show details

Frequency

JP	HGVD:[No Data.]
	ToMMo:0.447
	NCBN:[No Data.]
	NCBN(Hondo):[No Data.]
	NCBN(Ryukyu):[No Data.]
East asia	ExAC:[No Data.]

Prediction

ClinVar

Clinical Significance
Review star	[No Data.]
Show details

Links

MAPT

Type	Database	ID	Link
Gene	MIM	157140	OMIM
	HGNC	6893	HGNC
	Ensembl	ENSG00000186868	Ensembl
	NCBI		NCBI
	Gene Cards		Gene Cards
	OncoKB		OncoKB

Type	Database	ID	Link
Variant	TogoVar	tgv57935105	TogoVar
	COSMIC
	MONDO

Disease area statistics

[No Data.]

MGeND

[No Data.]

ClinVar

[No Data.]

CIViC

[No Data.]

DisGeNET

Score	Disease name	Description	Source	Pubmed	Links
0.001	Diabetes Mellitus, Insulin-Dependent	We identified novel cisSNP/transcript associations for human disease-associated ...	BeFree	22685416	Detail
<0.001	ulcerative colitis	We identified novel cisSNP/transcript associations for human disease-associated ...	BeFree	22685416	Detail
0.006	Diabetes Mellitus, Insulin-Dependent	We identified novel cisSNP/transcript associations for human disease-associated ...	BeFree	22685416	Detail
<0.001	Diabetes Mellitus, Insulin-Dependent	We identified novel cisSNP/transcript associations for human disease-associated ...	BeFree	22685416	Detail
0.121	ulcerative colitis	We identified novel cisSNP/transcript associations for human disease-associated ...	BeFree	22685416	Detail
<0.001	ulcerative colitis	We identified novel cisSNP/transcript associations for human disease-associated ...	BeFree	22685416	Detail
0.123	progressive supranuclear palsy	We identified novel cisSNP/transcript associations for human disease-associated ...	BeFree	22685416	Detail
<0.001	progressive supranuclear palsy	We identified novel cisSNP/transcript associations for human disease-associated ...	BeFree	22685416	Detail
0.558	progressive supranuclear palsy	[We confirmed two independent variants in MAPT affecting risk for PSP, one of wh...	GAD	21685912	Detail
0.558	progressive supranuclear palsy	We confirmed two independent variants in MAPT affecting risk for PSP, one of whi...	GWASCAT	21685912	Detail
0.342	Parkinson disease	High cerebrospinal tau levels are associated with the rs242557 tau gene variant ...	BeFree	20951764	Detail

Annotation

Annotations

Descrption	Source	Links
We identified novel cisSNP/transcript associations for human disease-associated variants, including ...	DisGeNET	Detail
We identified novel cisSNP/transcript associations for human disease-associated variants, including ...	DisGeNET	Detail
We identified novel cisSNP/transcript associations for human disease-associated variants, including ...	DisGeNET	Detail
We identified novel cisSNP/transcript associations for human disease-associated variants, including ...	DisGeNET	Detail
We identified novel cisSNP/transcript associations for human disease-associated variants, including ...	DisGeNET	Detail
We identified novel cisSNP/transcript associations for human disease-associated variants, including ...	DisGeNET	Detail
We identified novel cisSNP/transcript associations for human disease-associated variants, including ...	DisGeNET	Detail
We identified novel cisSNP/transcript associations for human disease-associated variants, including ...	DisGeNET	Detail
[We confirmed two independent variants in MAPT affecting risk for PSP, one of which influences MAPT ...	DisGeNET	Detail
We confirmed two independent variants in MAPT affecting risk for PSP, one of which influences MAPT b...	DisGeNET	Detail
High cerebrospinal tau levels are associated with the rs242557 tau gene variant and low cerebrospina...	DisGeNET	Detail

Overlapped Transcript

Gene	Transcript ID	Chromosome	Start	Stop	Links

Gene: -
dbSNP: rs242557 dbSNP
Genome: hg19
Position: chr17:44,019,712-44,019,712
Variant Type: snv
Reference Allele: G
Alternative Allele: A
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)): rs242557
Allele frequency, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 0.4473
Allele count in genotypes, for each ALT allele (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 7497
Total number of alleles in called genotypes (ToMMo 8.3KJPN Allele Frequency Panel(v20200831)): 16760

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