rs58598099

rs58598099 is a SNP located in the gene PKD1. The variant allele of this SNP is considered either "definitely pathogenic" or "highly likely pathogenic" for autosomal polycystic kidney disease in the PKD Foundation database. 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.

A;G

see discussion via main rs-page