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rs7527939

From SNPedia

Orientationplus
Stabilizedplus
Make rs7527939(C;C)
Make rs7527939(C;T)
Make rs7527939(T;T)
ReferenceGRCh38 38.1/141
Chromosome1
Position210362681
GeneHHAT
is asnp
is mentioned by
dbSNPrs7527939
ebirs7527939
HLIrs7527939
Exacrs7527939
Varsomers7527939
Maprs7527939
PheGenIrs7527939
hapmaprs7527939
1000 genomesrs7527939
hgdprs7527939
ensemblrs7527939
gopubmedrs7527939
geneviewrs7527939
scholarrs7527939
googlers7527939
pharmgkbrs7527939
gwascentralrs7527939
openSNPrs7527939
23andMers7527939
23andMe allrs7527939
SNP Nexus

SNPshotrs7527939
SNPdbers7527939
MSV3drs7527939
GWAS Ctlgrs7527939
GMAF0.2668
Max Magnitude
? (C;C) (C;T) (T;T) 28
GWAS snp
PMID [PMID 23142968]
Trait Schizophrenia
Title Whole-genome-wide association study in the Bulgarian population reveals HHAT as schizophrenia susceptibility gene.
Risk Allele C
P-val 6E-9
Odds Ratio 2.63 [1.89-3.66]

rs7527939 is a C/T polymorphism located in the second intronic region of the hedgehog acyltransferase gene (HHAT), located on human chromosome 1 1 [PMID 32142968]. HHAT, also known as SKI1, is responsible for an enzyme that catalyzes amino-terminal palmitoylation 2 of hedgehog (SHH) through the secretory pathway 3, [PMID 32142968]. According to dbSNP, the ancestral allele is C, and the minor allele frequency from the 1000 Genomes Project is 26.6% 1. Population-specific allele frequencies from the International HapMap Project are given below in graphic form.

A GWAS found a significant association between rs7527939 and a diagnosis of schizophrenia or schizoaffective disorder in a Bulgarian population. Using 188 affected and 376 unaffected individuals, the study tested 554, 496 SNPs for association with schizophrenia. After this initial test, the 100 SNPs with the lowest p-values were re-genotyped and re-tested for significance in a validation set of 99 cases and 328 controls. None of the SNPs were significant in this validation study, but combined with the initial analysis, rs7527939 showed a significant association, with a p-value of 6.49E-9. The odds ratio for the major allele was found be 2.63 with a 95% confidence interval of 1.89-3.66 [PMID 23142968].

The results of this study have not been validated by any other studies, as this is the only paper that has been published on this SNP.

While the understanding of the cause of schizophrenia is still not very well understood, it is hypothesized that the disease may stem from compromised neuronal network development during development, which leads to increased vulnerability to environmental stresses. The authors state that disruption of the SHH gene, which interacts with HHAT, may cause errors in neuronal cell migration and interaction during development, possibly leading to schizophrenia or schizoaffective disorder [PMID 32142968].

Overall, this study may shed some light on the cause of schizophrenia, and provides preliminary evidence that rs7527939 might be added to the growing list of SNPs associated with schizophrenia.