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rs58598099

From SNPedia

Orientationplus
Stabilizedplus
Make rs58598099(A;A)
Make rs58598099(A;G)
Make rs58598099(G;G)
ReferenceGRCh38.p2 38.2/146
Chromosome16
Position2116917
GenePKD1
is asnp
is mentioned by
dbSNPrs58598099
ebirs58598099
HLIrs58598099
Exacrs58598099
Varsomers58598099
Maprs58598099
PheGenIrs58598099
hapmaprs58598099
1000 genomesrs58598099
hgdprs58598099
ensemblrs58598099
gopubmedrs58598099
geneviewrs58598099
scholarrs58598099
googlers58598099
pharmgkbrs58598099
gwascentralrs58598099
openSNPrs58598099
23andMers58598099
23andMe allrs58598099
SNP Nexus

SNPshotrs58598099
SNPdbers58598099
MSV3drs58598099
GWAS Ctlgrs58598099
Max Magnitude
rs58598099 is a SNP located in the gene PKD1. It is miscalled by 23andMe at least some of the time (see cautionary tale below). Therefore, 23andMe users should not trust their 23andMe data for this SNP. It is exceedingly rare for a person to actually have the A/G genotype at this SNP; the vast majority of people have the normal A/A genotype.

In 2015, a 30-year-old man from Arkansas and his 66-year-old mother took 23andMe's genetic test. The resultant raw data stated that both the man and his mother had the genotype A/G at rs58598099. This was initially concerning, because the G allele of this SNP is strongly associated with autosomal dominant polycystic kidney disease (ADPKD). However, when an ultrasound was done on the man, his kidneys were shown to be completely normal. The man contacted a nephrology researcher at Mayo Clinic about this apparent contradiction and the researcher explained that due to the presence of pseudogenes, it is difficult to accurately sequence the gene PKD1. In other words, the PKD1-resembling pseudogenes may be accidentally sequenced instead of the PKD1 gene itself. A blood sample was taken from the man and, using a more precise genetic test that was able to distinguish between the real PKD1 gene and the PKD1-like pseudogenes, the researcher determined that the man's (and thus, also his mother's) actual genotype was A/A (the normal genotype). This explained the lack of findings on the man's renal ultrasound, as well as the mother's lack of kidney problems. It is worth noting that the man previously had whole-exome sequencing done by the company Gene By Gene, and his genotype was reported as A/G at rs58598099. Therefore, this isn't just a problem with 23andMe; it is a general problem that makes genetic tests prone to giving inaccurate results at this SNP. Do not trust 23andMe or other broad-scope genetic tests to provide an accurate genotype at this SNP.