Rs601338

From SNPedia
Jump to: navigation, search

Orientationplus
Geno Mag Summary
(A;A) 2.5 resistance to Norovirus infection
(A;G) 0.1 susceptible to Norovirus infections
(G;G) 0.1 susceptible to Norovirus infections
ReferenceGRCh38 38.1/141
Chromosome19
Position48703417
GeneFUT2
is asnp
is mentioned by
dbSNPrs601338
Exacrs601338
PheGenIrs601338
nextbiors601338
hapmaprs601338
1000 genomesrs601338
hgdprs601338
ensemblrs601338
gopubmedrs601338
geneviewrs601338
scholarrs601338
googlers601338
pharmgkbrs601338
gwascentralrs601338
openSNPrs601338
23andMers601338
23andMe allrs601338
SNP Nexus

SNPshotrs601338
SNPdbers601338
MSV3drs601338
GMAF0.3242
? (A;A) (A;G) (G;G) 28
rs601338 is found on chromosome 19 in the alpha(1,2)-fucosyltransferase FUT2 gene. The wild-type rs601338(G) encodes the "secretor" (Se) allele, while rs601338(A) encodes the "non-secretor" (se) allele.

A study of 115 Swedish adults concluded that rs601338(A;A) homozygotes have genetic immunity to infection by the Norwalk norovirus, a major (and contagious) cause of acute gastroenteritis worldwide among adults. [PMID 12692541] [PMID 16306606OA-icon.png] This illness is also known as "cruise ship gastroenteritis."

Being a non-secretor may have other consequences, such as greater susceptibility to infection by influenza viruses and by some types of bacteria. 23andMe discusses these topics.

In some non-Caucasian populations, a different SNP is responsible for non-secretor phenotypes. For example, although the Se allele is absent in Japanese, 15% are non-secretors based on being homozygous for the non-secretor "sej" allele of SNP rs1047781. [PMID 8621666]

http://blog.personalgenomes.org/2012/02/29/invulnerability-to-stomach-flu-is-my-secret-superpower/

http://evidence.personalgenomes.org/FUT2-W154X

Neighborrs492602
Distance257
OMIM612542
DescVITAMIN B12 PLASMA LEVEL QUANTITATIVE TRAIT LOCUS 1; B12QTL1
Variant
Relatedalso
OMIM182100
DescFUCOSYLTRANSFERASE 2; FUT2
Variant
Relatedalso
[PMID 19744961OA-icon.png] Genome-wide significant predictors of metabolites in the one-carbon metabolism pathway



[PMID 22521342OA-icon.png] Extended Analysis of a Genome-Wide Association Study in Primary Sclerosing Cholangitis Detects Multiple Novel Risk Loci.


ClinVar
Risk rs601338(A;A)
Alt rs601338(A;A)
Reference rs601338(G;G)
Significance Other
Disease SECRETOR/NONSECRETOR POLYMORPHISM Norwalk virus infection Vitamin b12 plasma level quantitative trait locus 1
Variation info
Gene FUT2
CLNDBN SECRETOR/NONSECRETOR POLYMORPHISM Norwalk virus infection, resistance to Vitamin b12 plasma level quantitative trait locus 1
Reversed 0
HGVS NC_000019.9:g.49206674G>A
CLNSRC OMIM Allelic Variant
CLNACC RCV000013808.2, RCV000013809.22, RCV000013810.2,



[PMID 18604267OA-icon.png] Novel association of ABO histo-blood group antigen with soluble ICAM-1: results of a genome-wide association study of 6,578 women.

[PMID 18776911OA-icon.png] Common variants of FUT2 are associated with plasma vitamin B12 levels.

[PMID 19169360OA-icon.png] Histo-blood group gene polymorphisms as potential genetic modifiers of infection and cystic fibrosis lung disease severity.

[PMID 19379518OA-icon.png] Development of a fingerprinting panel using medically relevant polymorphisms.

[PMID 19474294OA-icon.png] Potential etiologic and functional implications of genome-wide association loci for human diseases and traits.

[PMID 20041166OA-icon.png] Common genetic variation and the control of HIV-1 in humans.

[PMID 20565774OA-icon.png] Population based allele frequencies of disease associated polymorphisms in the Personalized Medicine Research Project.

[PMID 22025780OA-icon.png] FUT2 nonsecretor status links type 1 diabetes susceptibility and resistance to infection.


GET Evidence
FUT2-W154X
aa_change Trp154Stop
aa_change_short W154X
impact protective
qualified_impact Moderate clinical importance, protective
overall_frequency 0.490519
summary This recessive protective variant confers resistance to norovirus (which causes stomach flu). 20% of Caucasians and Africans are homozygous for this variant and are "non-secretors": they do not express ABO blood type antigens in their saliva or mucosal surfaces. Most strains of norovirus bind to these antigens in the gut, and so this non-secretor status confers almost total resistantance to most types of norovirus. There are notable exceptions, some strains of norovirus bind a different target and are equally infectious for secretors and non-secretors.



Norovirus Resistance


[PMID 23402911] Gastric intrinsic factor deficiency with combined GIF heterozygous mutations and FUT2 secretor variant


[PMID 23075394] Association study of FUT2 (rs601338) with celiac disease and inflammatory bowel disease in the Finnish population.

GWAS snp
PMID [PMID 24816252]
Trait Blood metabolite levels
Title An atlas of genetic influences on human blood metabolites.
Risk Allele A
P-val 3E-11
Odds Ratio .04 [0.029-0.053] unit increase