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rs17580

From SNPedia

Pi-S allele
Orientationminus
Stabilizedminus
Geno Mag Summary
(A;A) 0 common in complete genomics
(A;T) 2.5 carrier of a variant in Alpha-1 Antitrypsin Deficiency
(T;T) 2.5 a slightly reduced functionality form of Alpha-1 Antitrypsin Deficiency
ReferenceGRCh38 38.1/141
Chromosome14
Position94380925
GeneSERPINA1
is asnp
is mentioned by
dbSNPrs17580
ebirs17580
HLIrs17580
Exacrs17580
Varsomers17580
Maprs17580
PheGenIrs17580
hapmaprs17580
1000 genomesrs17580
hgdprs17580
ensemblrs17580
gopubmedrs17580
geneviewrs17580
scholarrs17580
googlers17580
pharmgkbrs17580
gwascentralrs17580
openSNPrs17580
23andMers17580
23andMe allrs17580
SNP Nexus

SNPshotrs17580
SNPdbers17580
MSV3drs17580
GWAS Ctlgrs17580
GMAF0.03122
Max Magnitude2.5
OMIM107400
DescPI S
Variant0013
Relatedalso
Neighborrs28929472
Distance24
rs17580, also known as the S or PiS allele, is a SNP in the SERPINA1 gene.

Levels of alpha-1 antitrypsin (encoded by the SERPINA1 gene) may be reduced in carriers of the rs17580(T) allele, but there is no known association with liver disease or cystic fibrosis. The rs17580 PiS variant is most associated with risk of developing COPD, especially in smokers, but it's association with emphysema is variable. See rs28929474 for the most common pathologic SNP (PiZ) in the SERPINA1 gene.

Due to orientation, be careful when interpreting results for this SNP which is an ambiguous flip.

[PMID 21138453] a relatively small study of 182 patients found no association between rs17580 and risk for cholangiocarcinoma

? (A;A) (A;T)


ClinVar
Risk rs17580(T;T)
Alt rs17580(T;T)
Reference rs17580(A;A)
Significance Other
Disease PI S Alpha-1-antitrypsin deficiency not provided
Variation info
Gene SERPINA1
CLNDBN PI S Alpha-1-antitrypsin deficiency not provided
Reversed 1
HGVS NC_000014.8:g.94847262T>A
CLNSRC OMIM Allelic Variant
CLNACC RCV000019569.2, RCV000148878.2, RCV000177031.1,



[PMID 16608528OA-icon.png] Genetic polymorphisms and susceptibility to lung disease.


[PMID 20170533OA-icon.png] Prevalence of genetic polymorphisms in the promoter region of the alpha-1 antitrypsin (SERPINA1) gene in chronic liver disease: a case control study.


[PMID 22426792] Serum levels and genotype distribution of alpha1-antitrypsin in the general population.


[PMID 301355OA-icon.png] Molecular abnormality of PI S variant of human alpha1-antitrypsin.


[PMID 2539391OA-icon.png] Alpha 1-antitrypsin deficiency caused by the alpha 1-antitrypsin Nullmattawa gene. An insertion mutation rendering the alpha 1-antitrypsin gene incapable of producing alpha 1-antitrypsin.


[PMID 22912729OA-icon.png] SERPINA1 PiZ and PiS Heterozygotes and Lung Function Decline in the SAPALDIA Cohort


GET Evidence
SERPINA1-E288V
aa_change Glu288Val
aa_change_short E288V
impact pathogenic
qualified_impact Low clinical importance, pathogenic
overall_frequency 0.0304889
summary This variant represents the PiS variant in alpha-1-antitrypsin deficiency where a homozygous individual has 60% enzymatic activity. This variant alone is unlikely to much effect, but 3-4% of heterozygotes are compound heterozygous with the more severe PiZ variant, which is associated with an increased risk of emphysema and COPD.



Alpha-1 Antitrypsin Deficiency


[PMID 25454901] Prevalence of alpha-1 antitrypsin high-risk variants in Mexican mestizo population and their association with lung function values